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gaff.py
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from textwrap import dedent
#AMBER General Force Field for organic molecules (Version 1.4, March 2010) add. info. at the end
gaff_atom_types = dedent("""
c 12.01 0.616 Sp2 C carbonyl group
c1 12.01 0.360 Sp C
c2 12.01 0.360 Sp2 C
c3 12.01 0.878 Sp3 C
ca 12.01 0.360 Sp2 C in pure aromatic systems
cp 12.01 0.360 Head Sp2 C that connect two rings in biphenyl sys.
cq 12.01 0.360 Head Sp2 C that connect two rings in biphenyl sys. identical to cp
cc 12.01 0.360 Sp2 carbons in non-pure aromatic systems
cd 12.01 0.360 Sp2 carbons in non-pure aromatic systems, identical to cc
ce 12.01 0.360 Inner Sp2 carbons in conjugated systems
cf 12.01 0.360 Inner Sp2 carbons in conjugated systems, identical to ce
cg 12.01 0.360 Inner Sp carbons in conjugated systems
ch 12.01 0.360 Inner Sp carbons in conjugated systems, identical to cg
cx 12.01 0.360 Sp3 carbons in triangle systems
cy 12.01 0.360 Sp3 carbons in square systems
cu 12.01 0.360 Sp2 carbons in triangle systems
cv 12.01 0.360 Sp2 carbons in square systems
cz 12.01 0.360 Sp2 carbon in guanidine group
h1 1.008 0.135 H bonded to aliphatic carbon with 1 electrwd. group
h2 1.008 0.135 H bonded to aliphatic carbon with 2 electrwd. group
h3 1.008 0.135 H bonded to aliphatic carbon with 3 electrwd. group
h4 1.008 0.135 H bonded to non-sp3 carbon with 1 electrwd. group
h5 1.008 0.135 H bonded to non-sp3 carbon with 2 electrwd. group
ha 1.008 0.135 H bonded to aromatic carbon
hc 1.008 0.135 H bonded to aliphatic carbon without electrwd. group
hn 1.008 0.161 H bonded to nitrogen atoms
ho 1.008 0.135 Hydroxyl group
hp 1.008 0.135 H bonded to phosphate
hs 1.008 0.135 Hydrogen bonded to sulphur
hw 1.008 0.135 Hydrogen in water
hx 1.008 0.135 H bonded to C next to positively charged group
f 19.00 0.320 Fluorine
cl 35.45 1.910 Chlorine
br 79.90 2.880 Bromine
i 126.9 4.690 Iodine
n 14.01 0.530 Sp2 nitrogen in amide groups
n1 14.01 0.530 Sp N
n2 14.01 0.530 aliphatic Sp2 N with two connected atoms
n3 14.01 0.530 Sp3 N with three connected atoms
n4 14.01 0.530 Sp3 N with four connected atoms
na 14.01 0.530 Sp2 N with three connected atoms
nb 14.01 0.530 Sp2 N in pure aromatic systems
nc 14.01 0.530 Sp2 N in non-pure aromatic systems
nd 14.01 0.530 Sp2 N in non-pure aromatic systems, identical to nc
ne 14.01 0.530 Inner Sp2 N in conjugated systems
nf 14.01 0.530 Inner Sp2 N in conjugated systems, identical to ne
nh 14.01 0.530 Amine N connected one or more aromatic rings
no 14.01 0.530 Nitro N
o 16.00 0.434 Oxygen with one connected atom
oh 16.00 0.465 Oxygen in hydroxyl group
os 16.00 0.465 Ether and ester oxygen
ow 16.00 0.465 Oxygen in water
p2 30.97 1.538 Phosphate with two connected atoms
p3 30.97 1.538 Phosphate with three connected atoms, such as PH3
p4 30.97 1.538 Phosphate with three connected atoms, such as O=P(CH3)2
p5 30.97 1.538 Phosphate with four connected atoms, such as O=P(OH)3
pb 30.97 1.538 Sp2 P in pure aromatic systems
pc 30.97 1.538 Sp2 P in non-pure aromatic systems
pd 30.97 1.538 Sp2 P in non-pure aromatic systems, identical to pc
pe 30.97 1.538 Inner Sp2 P in conjugated systems
pf 30.97 1.538 Inner Sp2 P in conjugated systems, identical to pe
px 30.97 1.538 Special p4 in conjugated systems
py 30.97 1.538 Special p5 in conjugated systems
s 32.06 2.900 S with one connected atom
s2 32.06 2.900 S with two connected atom, involved at least one double bond
s4 32.06 2.900 S with three connected atoms
s6 32.06 2.900 S with four connected atoms
sh 32.06 2.900 Sp3 S connected with hydrogen
ss 32.06 2.900 Sp3 S in thio-ester and thio-ether
sx 32.06 2.900 Special s4 in conjugated systems
sy 32.06 2.900 Special s6 in conjugated systems
""")
gaff_bonds = dedent("""
ow-hw 553.0 0.9572 TIP3P_Water 1
br-br 123.2 2.5420 SOURCE1 4 0.0000
br-c1 352.7 1.7870 SOURCE2 4 0.0024
br-c2 278.7 1.8830 SOURCE1 31 0.0000
br-c 240.3 1.9460 SOURCE2 2 0.0285
br-c3 229.5 1.9660 SOURCE1 100 0.0000
br-ca 269.6 1.8970 SOURCE1 127 0.0058
br-cc 277.6 1.8847 SOURCE4 39 0.0068
br-cx 261.4 1.9100 SOURCE1 8 0.0000
br-i 142.4 2.6710 SOURCE1 2 0.0245
br-n1 330.4 1.8600 SOUECE3 1
br-n2 219.0 2.0380 SOURCE3 5 0.1082
br-n 320.2 1.8730 SOURCE3 4 0.0046
br-n3 265.9 1.9520 SOURCE3 2 0.0000
br-n4 282.4 1.9260 SOURCE3 3 0.0013
br-na 237.3 2.0020 SOURCE3 7 0.2156
br-nh 270.9 1.9440 SOURCE3 1 0.0000
br-no 191.0 2.1010 SOURCE3 1 0.0000
br-o 278.9 1.8000 SOUECE3 1
br-oh 237.2 1.8660 SOURCE3 1 0.0000
br-os 225.6 1.8870 SOURCE3 2 0.0000
br-p2 174.3 2.2100 SOURCE3 9 0.0510
br-p3 167.0 2.2310 SOURCE3 3 0.0101
br-p4 188.8 2.1710 SOUECE3 1
br-p5 179.3 2.1960 SOURCE3 3 0.0099
br-s 170.6 2.2200 SOUECE3 1
br-s4 134.3 2.3410 SOURCE3 1 0.0000
br-s6 172.7 2.2140 SOURCE3 3 0.0443
br-sh 174.4 2.2090 SOURCE3 1 0.0000
br-ss 176.6 2.2030 SOURCE3 3 0.0035
c1-c1 986.2 1.1810 SOURCE1 265 0.0031
c1-c2 625.0 1.3070 SOURCE1 18 0.0000
c1-c3 368.3 1.4700 SOURCE1 215 0.0017
c1-ca 404.1 1.4400 SOUECE3 1
c1-ce 607.4 1.3153 SOURCE4 6 0.0086
c1-cg 845.8 1.2220 SOURCE3 22 0.0101
c1-ch 845.8 1.2220 SOURCE3 22 same_as_c1-cg
c1-cl 419.7 1.6310 SOURCE2 6 0.0050
c1-cx 399.1 1.4440 SOURCE1 38 0.0000
c1-f 469.4 1.2700 SOURCE2 2 0.0085
c1-ha 375.9 1.0660 SOURCE3 63 0.0035
c1-hc 385.6 1.0600 SOUECE3 1
c1-i 318.8 1.9890 SOURCE2 4 0.0032
c1-n1 1014.5 1.1380 SOURCE1 170 0.0055
c1-n2 769.8 1.2100 SOURCE3 5 0.0115
c1-n3 409.8 1.3920 SOURCE2 1 0.0000
c1-n4 378.2 1.4170 SOURCE3 3 0.0032
c1-n 503.0 1.3300 SOUECE3 1
c1-na 452.0 1.3620 SOURCE3 8 0.0034
c1-ne 803.3 1.1986 SOURCE4 10 0.0088
c1-nf 803.3 1.1986 SOURCE4 10 same_as_c1-ne
c1-nh 485.0 1.3408 SOURCE4 11 0.0037
c1-no 393.0 1.4050 SOURCE3 3 0.0005
c1-o 777.0 1.1660 SOURCE2 9 0.0052
c1-oh 435.6 1.3260 SOURCE3 1 0.0000
c1-os 437.1 1.3250 SOURCE3 3 0.0148
c1-p2 289.3 1.7700 SOUECE3 1
c1-p3 275.1 1.7900 SOUECE3 1
c1-p4 275.1 1.7900 SOUECE3 1
c1-p5 302.2 1.7530 SOURCE3 2 0.0000
c1-s2 410.0 1.5950 SOURCE3 1 0.0000
c1-s 371.8 1.6300 SOURCE1 14 0.0000
c1-s4 272.9 1.7460 SOURCE3 2 0.0000
c1-s6 290.4 1.7220 SOURCE3 2 0.0000
c1-sh 324.5 1.6800 SOUECE3 1
c1-ss 325.4 1.6790 SOURCE1 10 0.0000
c2-c2 589.7 1.3240 SOURCE1 974 0.0096
c2-c3 328.3 1.5080 SOURCE1 2536 0.0021
c2-ca 357.2 1.4800 SOUECE3 1
c2-cc 522.6 1.3600 SOURCE1 771 0.0185
c2-cd 522.6 1.3600 SOURCE1 771 0.0185
c2-ce 560.5 1.3390 SOURCE3 62 0.0128
c2-cf 560.5 1.3390 SOURCE3 62 same_as_c2-ce
c2-cl 328.8 1.7220 SOURCE1 163 0.0098
c2-cu 573.9 1.3320 SOURCE2 1 0.0000
c2-cx 353.3 1.4836 SOURCE4 26 0.0064
c2-cy 331.7 1.5046 SOURCE4 9 0.0053
c2-f 368.7 1.3400 SOURCE1 34 0.0000
c2-h4 348.6 1.0840 SOURCE3 40 0.0058
c2-h5 338.0 1.0915 SOURCE4 42 0.0017
c2-ha 344.3 1.0870 SOURCE3 797 0.0046
c2-hc 344.3 1.0870 SOURCE3 789 0.0046
c2-hx 350.1 1.0830 SOURCE3 3 0.0008
c2-i 223.2 2.1530 SOURCE3 2 0.0000
c2-n1 546.0 1.3060 SOURCE3 4 0.0161
c2-n2 581.1 1.2880 SOURCE1 103 0.0100
c2-n3 486.3 1.3400 SOUECE3 1
c2-n 390.5 1.4070 SOURCE3 9 0.0124
c2-n4 309.1 1.4820 SOURCE3 5 0.0064
c2-na 411.1 1.3910 SOURCE3 31 0.0289
c2-nc 533.0 1.3130 SOURCE1 99 0.0095
c2-nd 533.0 1.3130 SOURCE1 99 same_as_c2-nc
c2-ne 597.7 1.2800 SOURCE3 37 0.0110
c2-nf 597.7 1.2800 SOURCE3 37 same_as_c2-ne
c2-nh 462.6 1.3550 SOURCE3 38 0.0413
c2-no 345.6 1.4457 SOURCE4 7 0.0087
c2-o 623.6 1.2244 SOURCE4 15 0.0036
c2-oh 425.4 1.3330 SOURCE1 53 0.0000
c2-os 392.6 1.3570 SOURCE1 315 0.0097
c2-p2 375.9 1.6700 SOURCE3 62 0.0147
c2-p3 246.6 1.8340 SOURCE3 5 0.0042
c2-p4 254.0 1.8220 SOUECE3 1
c2-p5 228.2 1.8658 SOURCE4 5 0.0025
c2-pe 355.3 1.6910 SOURCE3 52 0.0542
c2-pf 355.3 1.6910 SOURCE3 52 same_as_c2-pe
c2-s2 393.1 1.6100 SOURCE2 1 0.0000
c2-s 281.5 1.7340 SOURCE3 4 0.0034
c2-s4 263.2 1.7600 SOUECE3 1
c2-s6 263.2 1.7600 SOUECE3 1
c2-sh 252.0 1.7771 SOURCE4 5 0.0037
c2-ss 280.0 1.7360 SOURCE1 209 0.0155
c3-c3 303.1 1.5350 SOURCE1 14664 0.0048
c3-ca 323.5 1.5130 SOURCE1 1813 0.0000
c3-cc 337.3 1.4990 SOURCE3 50 0.0096
c3-cd 337.3 1.4990 SOURCE3 50 0.0096
c3-ce 331.3 1.5050 SOURCE3 9 0.0024
c3-cf 331.3 1.5050 SOURCE3 9 same_as_c3-ce
c3-cl 279.0 1.7860 SOURCE1 267 0.0194
c3-cu 359.4 1.4780 SOURCE1 7 0.0000
c3-cv 347.6 1.4890 SOURCE1 11 0.0000
c3-cx 322.5 1.5140 SOURCE1 712 0.0045
c3-cy 308.5 1.5290 SOURCE1 376 0.0000
c3-f 363.8 1.3440 SOURCE1 617 0.0281
c3-h1 335.9 1.0930 SOURCE3 2175 0.0082
c3-h2 326.4 1.1000 SOURCE3 66 0.0280
c3-h3 333.4 1.0948 SOURCE4 25 0.0026
c3-hc 337.3 1.0920 SOURCE3 2815 0.0059
c3-hx 338.7 1.0910 SOURCE3 146 0.0066
c3-i 219.1 2.1620 SOURCE1 15 0.0000
c3-n1 325.1 1.4700 SOURCE3 0
c3-n2 313.8 1.4770 SOURCE1 129 0.0138
c3-n 330.6 1.4600 SOURCE1 187 0.0079
c3-n3 320.6 1.4700 SOURCE1 1678 0.0017
c3-n4 293.6 1.4990 SOURCE1 1370 0.0000
c3-na 334.7 1.4560 SOURCE3 23 0.0119
c3-nc 334.7 1.4560 SOURCE3 9 0.0109
c3-nd 334.7 1.4560 SOURCE3 9 same_as_c3-nc
c3-nh 332.7 1.4580 SOURCE3 27 0.0085
c3-no 265.4 1.5330 SOURCE1 83 0.0212
c3-o 449.9 1.3165 SOURCE4 8 0.0193
c3-oh 314.1 1.4260 SOURCE1 914 0.0129
c3-os 301.5 1.4390 SOURCE1 3123 0.0126
c3-p2 234.3 1.8550 SOURCE3 9 0.0125
c3-p3 240.6 1.8440 SOURCE3 109 0.0107
c3-p4 247.2 1.8330 SOURCE3 29 0.0138
c3-p5 259.7 1.8130 SOURCE1 84 0.0000
c3-px 252.7 1.8240 SOURCE3 28 0.0098
c3-py 259.7 1.8130 SOURCE3 13 0.0163
c3-s 212.9 1.8450 SOURCE3 4 0.0185
c3-s4 233.8 1.8070 SOURCE1 139 0.0023
c3-s6 254.0 1.7740 SOURCE1 118 0.0103
c3-sh 225.3 1.8220 SOURCE3 12 0.0051
c3-ss 225.8 1.8210 SOURCE1 358 0.0075
c3-sx 232.6 1.8090 SOURCE3 30 0.0067
c3-sy 248.9 1.7820 SOURCE3 31 0.0039
ca-ca 478.4 1.3870 SOURCE1 6228 0.0147
ca-cc 411.7 1.4340 SOURCE1 80 0.0000
ca-cd 411.7 1.4340 SOURCE1 80 0.0000
ca-ce 366.0 1.4720 SOURCE1 71 0.0030
ca-cf 366.0 1.4720 SOURCE1 71 0.0030
ca-cg 406.6 1.4380 SOURCE1 71 0.0045
ca-ch 406.6 1.4380 SOURCE1 71 0.0045
ca-cl 322.8 1.7290 SOURCE1 704 0.0095
ca-cp 466.1 1.3950 SOURCE3 14 0.0110
ca-cq 457.4 1.4009 SOURCE4 14 0.0058
ca-cx 350.8 1.4860 SOURCE1 98 0.0118
ca-cy 323.0 1.5135 SOURCE4 8 0.0043
ca-f 363.8 1.3440 SOURCE1 205 0.0089
ca-h4 342.9 1.0880 SOURCE3 57 0.0026
ca-h5 347.2 1.0850 SOURCE3 15 0.0048
ca-ha 344.3 1.0870 SOURCE3 1496 0.0045
ca-i 252.4 2.0950 SOURCE1 51 0.0000
ca-n1 398.1 1.4000 SOURCE3 0
ca-n2 551.6 1.3030 SOURCE4 7 0.0058
ca-n 372.3 1.4220 SOURCE3 9 0.0098
ca-n4 325.6 1.4650 SOURCE1 23 0.0000
ca-na 470.3 1.3500 SOURCE1 150 0.0103
ca-nb 483.1 1.3420 SOURCE3 104 0.0076
ca-nc 492.9 1.3360 SOURCE1 1826 0.0020
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na-p3 288.0 1.7620 SOURCE3 8 0.0113
na-p4 492.4 1.5640 SOURCE3 5 0.2161
na-p5 325.3 1.7150 SOURCE3 11 0.0238
na-pc 311.1 1.7320 SOURCE3 81 0.0207
na-pd 311.1 1.7320 SOURCE3 81 same_as_na-pc
na-py 327.8 1.7120 SOURCE3 2 0.0000
na-s 248.7 1.7650 SOURCE3 8 0.0095
na-s4 231.7 1.7930 SOURCE3 10 0.0421
na-s6 274.3 1.7270 SOURCE3 10 0.0201
na-sh 278.6 1.7210 SOURCE3 9 0.0113
na-ss 270.1 1.7330 SOURCE3 38 0.0412
na-sy 274.3 1.7270 SOURCE3 1
nb-nb 550.2 1.3420 SOURCE1 15 0.0314
nb-pb 461.1 1.5870 SOURCE1 162 0.0091
nc-nc 486.8 1.3790 SOURCE3 9 0.0164
nc-nd 602.9 1.3150 SOURCE3 9 0.0221
nc-os 414.9 1.3950 SOURCE1 46 0.0188
nc-ss 433.5 1.5600 SOURCE1 74 0.0000
nc-sy 439.8 1.5550 SOURCE3 2
nd-nd 486.8 1.3790 SOURCE3 9 0.0164
nd-os 414.9 1.3950 SOURCE1 46 0.0188
nd-ss 433.5 1.5600 SOURCE1 74 0.0000
nd-sy 439.8 1.5550 SOURCE3 2
ne-ne 355.3 1.4790 SOURCE3 19 0.1705
ne-nf 721.6 1.2635 SOURCE4 25 0.0034
ne-o 736.4 1.2280 SOURCE3 40 0.0255
ne-p2 493.9 1.5630 SOURCE3 14 0.1325
ne-pe 327.8 1.7120 SOURCE3 28 0.1076
ne-px 336.6 1.7020 SOURCE3 11 0.0883
ne-py 425.4 1.6157 SOURCE4 10 0.0094
ne-s 463.5 1.5370 SOURCE3 22 0.1708
ne-sx 207.3 1.8380 SOURCE3 7 0.1060
ne-sy 257.1 1.7520 SOURCE3 7 0.0814
nf-nf 355.3 1.4790 SOURCE3 19 same_as_ne-ne
nf-o 736.4 1.2280 SOURCE3 40 same_as_ne-o
nf-p2 493.9 1.5630 SOURCE3 14 same_as_ne-p2
nf-pf 327.8 1.7120 SOURCE3 28 same_as_ne-pe
nf-px 336.6 1.7020 SOURCE3 11 same_as_ne-px
nf-py 425.4 1.6157 SOURCE4 10 same_as_ne-py
nf-s 463.5 1.5370 SOURCE3 22 same_as_ne-s
nf-sx 207.3 1.8380 SOURCE3 7 same_as_ne-sx
nf-sy 257.1 1.7520 SOURCE3 7 same_as_ne-sy
nh-nh 453.3 1.4010 SOURCE1 40 0.0000
nh-no 477.4 1.3850 SOURCE4 7 0.0036
nh-o 596.2 1.2870 SOURCE3 3 0.0450
nh-oh 389.9 1.4144 SOURCE4 19 0.0064
nh-os 387.8 1.4161 SOURCE4 6 0.0039
nh-p2 357.8 1.6790 SOURCE3 17 0.0872
nh-p3 312.8 1.7300 SOURCE3 3 0.0016
nh-p4 333.1 1.7060 SOURCE3 3 0.0008
nh-p5 365.6 1.6710 SOURCE3 3 0.0007
nh-s 237.0 1.7840 SOURCE3 3 0.0076
nh-s4 259.1 1.7490 SOURCE3 3 0.0203
nh-s6 297.2 1.6965 SOURCE4 33 0.0062
nh-sh 288.3 1.7080 SOURCE3 1 0.0000
nh-ss 288.3 1.7080 SOURCE1 52 0.0015
nh-sy 283.5 1.7144 SOURCE4 80 0.0066
n -n1 553.9 1.3400 SOUECE3 1
n -n2 499.7 1.3710 SOURCE3 9 0.0200
n -n3 443.3 1.4080 SOURCE3 5 0.0087
n -n4 410.8 1.4320 SOURCE3 5 0.0098
n -n 469.7 1.3900 SOURCE3 5 0.0038
n -na 486.8 1.3790 SOURCE3 11 0.0071
n -nc 524.9 1.3561 SOURCE4 63 0.0104
n -nd 517.7 1.3603 SOURCE4 13 0.0122
n -nh 451.2 1.4025 SOURCE4 20 0.0074
n -no 381.2 1.4560 SOURCE3 4 0.0327
n -o 646.6 1.2640 SOURCE3 9 0.0381
n -oh 395.4 1.4100 SOURCE3 6 0.0106
no-no 138.3 1.8240 SOURCE3 1 0.0000
no-o 761.2 1.2190 SOURCE1 1838 0.0049
no-oh 400.5 1.4060 SOURCE2 1 0.0000
no-os 379.5 1.4229 SOURCE4 53 0.0076
no-os 379.5 1.4229 SOURCE4 53 0.0076
no-p2 306.3 1.7380 SOURCE3 10 0.2231
no-p3 234.7 1.8440 SOURCE3 3 0.0005
no-p4 220.4 1.8700 SOURCE3 3 0.0006
no-p5 240.5 1.8340 SOURCE3 4 0.0020
no-s 263.8 1.7420 SOURCE3 2 0.0000
n -os 395.0 1.4103 SOURCE4 30 0.0112
no-s4 143.0 1.9960 SOURCE3 3 0.0313
no-s6 149.6 1.9760 SOURCE3 3 0.0520
no-sh 225.4 1.8040 SOURCE3 1 0.0000
no-ss 212.4 1.8280 SOURCE3 3 0.0244
n -p2 310.3 1.7330 SOURCE3 8 0.0217
n -p3 282.2 1.7700 SOURCE3 9 0.0118
n -p4 309.5 1.7340 SOURCE3 1 0.0000
n -p5 331.3 1.7080 SOURCE4 6 0.0022
n -pc 304.8 1.7400 SOURCE3 3 0.0010
n -pd 304.8 1.7400 SOURCE3 3 same_as_n-pc
n -s 247.5 1.7670 SOURCE3 3 0.0011
n -s4 238.2 1.7820 SOURCE3 4 0.0214
n -s6 283.0 1.7151 SOURCE4 13 0.0138
n -sh 273.6 1.7280 SOURCE3 4 0.0128
n -ss 281.6 1.7170 SOURCE3 7 0.0133
n -sy 282.9 1.7152 SOURCE4 51 0.0079
oh-oh 340.5 1.4690 SOURCE3 1 0.0000
oh-os 355.8 1.4547 SOURCE4 19 0.0050
oh-p2 316.8 1.6300 SOURCE3 8 0.0916
oh-p3 278.8 1.6770 SOURCE3 3 0.0148
oh-p4 307.4 1.6410 SOURCE3 4 0.0092
oh-p5 321.2 1.6250 SOURCE3 92 0.0451
oh-py 332.1 1.6130 SOURCE3 79 0.0138
oh-s 190.0 1.8120 SOURCE3 2 0.0000
oh-s4 256.3 1.6954 SOURCE4 10 0.0091
oh-s6 344.1 1.5880 SOURCE3 13 0.0091
oh-sh 258.6 1.6920 SOURCE3 2 0.0003
oh-ss 265.6 1.6820 SOURCE3 4 0.0131
oh-sy 290.4 1.6490 SOURCE4 33 0.0044
o -o 384.3 1.4300 SOURCE3 2 0.0500
o -oh 294.6 1.5170 SOURCE3 2 0.0000
o -os 306.3 1.5040 SOURCE3 3 0.0117
o -p2 449.7 1.5080 SOURCE3 17 0.0306
o -p3 440.4 1.5150 SOURCE3 35 0.0297
o -p4 456.4 1.5030 SOURCE3 42 0.0749
o -p5 487.7 1.4810 SOURCE1 263 0.0205
o -pe 432.6 1.5210 SOURCE3 20 0.0171
o -pf 432.6 1.5210 SOURCE3 20 same_as_o-pe
o -px 459.2 1.5010 SOURCE3 37 0.0160
o -py 477.5 1.4880 SOURCE3 63 0.0091
o -s 194.8 1.8020 SOURCE3 2 0.0000
o -s2 333.6 1.5990 SOURCE3 3 0.0707
o -s4 448.7 1.4970 SOURCE1 90 0.0000
o -s6 541.1 1.4360 SOURCE1 1038 0.0128
o -sh 328.0 1.6050 SOURCE3 2 0.0000
os-os 343.6 1.4660 SOURCE1 20 0.0067
os-p2 371.9 1.5730 SOURCE1 16 0.0000
os-p3 272.2 1.6860 SOURCE3 6 0.0201
os-p4 311.6 1.6360 SOURCE3 4 0.0057
os-p5 342.5 1.6020 SOURCE1 248 0.0400
os-py 328.5 1.6170 SOURCE3 17 0.0139
os-s 195.8 1.8000 SOURCE3 3 0.0052
o -ss 398.5 1.5370 SOURCE3 3 0.0501
os-s4 253.9 1.6990 SOURCE3 8 0.0223
os-s6 355.0 1.5770 SOURCE1 75 0.0030
os-sh 273.6 1.6710 SOURCE3 3 0.0106
os-ss 250.5 1.7040 SOURCE3 9 0.0277
os-sy 253.9 1.6990 SOURCE3 1 0.0000
o -sx 434.2 1.5080 SOURCE3 40 0.0130
o -sy 493.0 1.4660 SOURCE3 92 0.0114
p2-p2 490.3 1.7860 SOURCE3 25 0.3488
p2-p3 211.9 2.1520 SOURCE3 9 0.1777
p2-p4 200.4 2.1790 SOUECE3 1
p2-p5 199.9 2.1800 SOUECE3 1
p2-pe 401.6 1.8670 SOURCE3 16 0.3571
p2-pf 401.6 1.8670 SOURCE3 16 same_as_p2-pe
p2-s 361.6 1.7720 SOURCE3 26 0.3014
p2-s4 139.4 2.1900 SOUECE3 1
p2-s6 142.3 2.1800 SOUECE3 1
p2-sh 224.0 1.9710 SOURCE3 10 0.2829
p2-ss 226.6 1.9660 SOURCE3 10 0.2739
p3-p3 186.5 2.2140 SOURCE1 41 0.0000
p3-p4 185.7 2.2160 SOURCE3 3 0.0011
p3-p5 186.9 2.2130 SOURCE3 9 0.0265
p3-s 179.7 2.0700 SOUECE3 1
p3-s4 173.2 2.0870 SOURCE3 8 0.2235
p3-s6 176.9 2.0770 SOURCE3 11 0.1420
p3-sh 157.3 2.1320 SOURCE3 3 0.0078
p3-ss 161.0 2.1210 SOURCE3 3 0.0059
p4-p4 273.1 2.0340 SOURCE1 1 0.0000
p4-p5 178.0 2.2370 SOUECE3 1
p4-s 152.7 2.1460 SOURCE3 5 0.0601
p4-s4 123.2 2.2510 SOUECE3 1
p4-s6 118.9 2.2690 SOUECE3 1
p4-sh 163.1 2.1150 SOURCE3 4 0.0008
p4-ss 167.0 2.1040 SOURCE3 4 0.0044
p5-p5 261.4 2.0540 SOURCE1 1 0.0000
p5-s 250.8 1.9220 SOURCE1 89 0.0140
p5-s4 191.9 2.0400 SOUECE3 1
p5-s6 191.9 2.0400 SOUECE3 1
p5-sh 175.0 2.0820 SOURCE3 3 0.0035
p5-ss 163.1 2.1149 SOURCE4 24 0.0106
pe-pe 240.7 2.0920 SOURCE3 7 0.1369
pe-pf 260.8 2.0550 SOURCE3 1 0.0000
pe-px 291.4 2.0050 SOURCE3 12 0.2609
pe-py 278.6 2.0250 SOURCE3 12 0.2617
pe-s 374.7 1.7580 SOURCE3 31 0.3197
pe-sx 145.9 2.1680 SOURCE3 9 0.1743
pe-sy 133.0 2.2130 SOURCE3 6 0.0127
pf-pf 240.7 2.0920 SOURCE3 7 same_as_pe-pe
pf-px 291.4 2.0050 SOURCE3 12 same_as_pe-px
pf-py 278.6 2.0250 SOURCE3 12 same_as_pe-py
pf-s 374.7 1.7580 SOURCE3 31 same_as_pe-s
pf-sx 145.9 2.1680 SOURCE3 9 same_as_pe-sx
pf-sy 133.0 2.2130 SOURCE3 6 same_as_pe-sy
px-py 192.3 2.1990 SOURCE3 5 0.0238
px-sx 125.4 2.2420 SOURCE3 3 0.0119
px-sy 123.7 2.2490 SOURCE3 3 0.0272
py-py 197.5 2.1860 SOURCE3 8 0.0132
py-sx 121.2 2.2590 SOURCE3 7 0.0603
py-sy 141.7 2.1820 SOURCE3 5 0.0047
s4-s4 151.5 2.0800 SOUECE3 1
s4-s6 151.5 2.0800 SOUECE3 1
s4-sh 125.7 2.1680 SOURCE3 3 0.0227
s4-ss 126.2 2.1660 SOURCE3 5 0.0247
s6-s6 151.5 2.0800 SOUECE3 1
s6-sh 142.6 2.1080 SOURCE3 3 0.0144
s6-ss 139.6 2.1180 SOURCE3 5 0.0209
sh-sh 158.9 2.0580 SOURCE2 1 0.0000
sh-ss 155.8 2.0670 SOURCE3 3 0.0029
s -s 169.0 2.0300 SOURCE3 1 0.0000
s -s2 229.2 1.8970 SOURCE1 5 0.0000
s -s4 152.8 2.0760 SOURCE3 4 0.0345
s -s6 166.0 2.0380 SOURCE3 3 0.0311
s -sh 142.0 2.1100 SOURCE3 2 0.0000
s -ss 148.5 2.0890 SOURCE3 1 0.0000
ss-ss 161.7 2.0500 SOURCE1 225 0.0015
sx-sx 80.9 2.3910 SOURCE3 3 0.0185
sx-sy 105.3 2.2550 SOURCE3 5 0.0737
sy-sy 106.4 2.2500 SOURCE3 3 0.0289
""")
gaff_angles = dedent("""
hw-ow-hw 42.730 104.520 AMBER 1 TIP3P_water
hw-hw-ow 0.000 127.740 AMBER 1 (found_in_crystallographic_water_with_3_bonds)
br-c1-br 57.760 180.000 Guess 0
br-c1-c1 54.930 180.000 SOURCE3 1 0.0000
c1-c1-c1 64.410 180.000 SOURCE3 1 0.0000
c1-c1-c2 60.840 180.000 SOURCE3 2 0.0000
c1-c1-c3 56.280 178.460 SOURCE4 188 0.6631
c1-c1-ca 56.920 180.000 SOURCE3 1
c1-c1-cl 55.270 180.000 SOURCE3 1
c1-c1-f 61.020 180.000 SOURCE3 1
c1-c1-ha 44.840 178.380 SOURCE3 41 2.0683
c1-c1-hc 44.730 180.000 SOURCE3 1
c1-c1-i 49.800 180.000 SOURCE3 1 0.0000
c1-c1-n1 67.170 180.000 SOURCE3 1
c1-c1-n2 65.170 180.000 SOURCE3 1
c1-c1-n3 59.770 180.000 SOURCE3 1
c1-c1-n4 59.090 179.560 SOURCE3 3 0.3096
c1-c1-n 62.130 177.180 SOURCE3 1 0.0000
c1-c1-na 61.230 176.750 SOURCE3 8 2.9328
c1-c1-nh 61.440 179.270 SOURCE3 3 0.2357
c1-c1-no 59.380 180.000 SOURCE3 3 0.0000
c1-c1-o 66.790 180.000 SOURCE3 1 0.0000
c1-c1-oh 62.700 176.650 SOURCE3 1 0.0000
c1-c1-os 62.770 176.420 SOURCE3 2 0.0000
c1-c1-p2 51.510 180.000 SOURCE3 1
c1-c1-p3 52.470 169.630 SOURCE3 2 0.0000
c1-c1-p4 50.940 180.000 SOURCE3 1
c1-c1-p5 52.560 176.170 SOURCE3 2 0.0000
c1-c1-s4 68.490 167.470 SOURCE3 2 0.0000
c1-c1-s6 68.020 174.380 SOURCE3 2 0.0000
c1-c1-s 70.430 179.970 SOURCE3 1 0.0000
c1-c1-sh 68.520 180.000 SOURCE3 1
c1-c1-ss 69.890 173.220 SOURCE3 2 0.0000
c2-c1-c2 58.200 180.000 SOURCE3 1 0.0000
c2-c1-ce 58.180 179.010 SOURCE4 6 0.4656
c2-c1-n1 63.140 180.000 HF/6-31G* 1
c2-c1-o 63.070 179.500 SOURCE2 1 0.0000
c2-c1-s2 71.800 172.980 SOURCE3 1 0.0000
c3-c1-c3 51.750 180.000 Guess 0
c3-c1-cg 55.790 178.520 SOURCE4 39 0.5063
c3-c1-n1 58.100 178.500 SOURCE4 77 0.5443
ca-c1-ca 52.830 180.000 Guess 0
c -c1-c1 56.330 180.000 SOURCE3 1
cg-c1-ha 43.980 177.410 SOURCE3 22 2.4947
ch-c1-ha 43.980 177.410 SOURCE3 22 same_as_cg-c1-ha
cl-c1-cl 53.920 180.000 Guess 0
f -c1-f 58.190 180.000 Guess 0
i -c1-i 53.410 180.000 Guess 0
n1-c1-n1 93.200 102.010 SOURCE3 1
n1-c1-n3 63.710 169.700 SOURCE2 1 0.0000
n1-c1-nh 64.020 177.430 SOURCE4 7 0.7877
n1-c1-os 64.720 178.590 SOURCE3 1 0.0000
n1-c1-p3 53.480 171.200 SOURCE2 1 0.0000
n1-c1-ss 70.640 178.680 SOURCE3 1 0.0000
n2-c1-n2 65.990 180.000 Guess 0
n2-c1-o 69.150 171.790 SOURCE3 2 0.3594
n2-c1-s 72.750 176.010 SOURCE4 9 0.1123
n3-c1-n3 57.360 180.000 Guess 0
n4-c1-n4 56.350 180.000 Guess 0
na-c1-na 58.620 180.000 Guess 0
ne-c1-o 69.390 172.330 SOURCE3 1 0.0000
ne-c1-s 72.880 175.810 SOURCE4 8 0.2356
nf-c1-o 69.390 172.330 SOURCE3 1 same_as_ne-c1-o
nh-c1-nh 59.550 180.000 Guess 0
n -c1-n 60.030 180.000 Guess 0
no-c1-no 56.830 180.000 Guess 0
oh-c1-oh 60.910 180.000 Guess 0
o -c1-o 69.270 180.000 Guess 0
os-c1-os 60.960 180.000 Guess 0
p2-c1-p2 50.310 180.000 Guess 0
p3-c1-p3 49.750 180.000 Guess 0
p4-c1-p4 49.750 180.000 Guess 0
p5-c1-p5 50.800 180.000 Guess 0
s2-c1-s2 89.430 180.000 Guess 0
s4-c1-s4 81.700 180.000 Guess 0
s6-c1-s6 82.840 180.000 Guess 0
sh-c1-sh 84.910 180.000 Guess 0
s -c1-s 87.510 180.000 Guess 0
ss-c1-ss 84.960 180.000 Guess 0
br-c2-br 68.560 115.060 SOURCE3 1 0.0000
br-c2-c2 63.970 118.960 SOURCE4 6 0.4902
br-c2-c3 63.710 115.330 SOURCE4 6 0.5872
br-c2-ce 63.210 121.590 SOURCE4 7 0.7078
br-c2-h4 43.040 113.940 SOURCE4 6 0.4017
br-c2-ha 43.180 113.280 SOURCE3 1 0.0000
c1-c2-c1 72.260 116.770 SOURCE3 1
c1-c2-c2 70.340 121.620 SOURCE3 1
c1-c2-c3 64.220 124.920 SOURCE4 17 0.7576
c1-c2-f 67.990 124.900 SOURCE2 1 0.0000
c1-c2-ha 50.430 121.370 SOURCE3 8 0.0055
c2-c2-c2 69.840 121.810 SOURCE3 10 0.3843
c2-c2-c3 64.330 123.420 SOURCE3 41 2.6057
c2-c2-ca 66.880 117.000 SOURCE3 1
c2-c2-cc 70.220 117.210 SOURCE3 2 0.3418
c2-c2-cd 70.220 117.210 SOURCE3 2 same_as_c2-c2-cc
c2-c2-cl 62.820 122.850 SOURCE4 23 0.6711
c2-c2-cx 64.500 125.400 SOURCE4 12 1.8494
c2-c2-cy 70.420 103.300 SOURCE2 1 0.0000
c2-c2-f 68.110 122.920 SOURCE4 12 0.5301
c2-c2-h4 49.750 122.540 SOURCE4 69 1.1900
c2-c2-ha 50.040 120.940 SOURCE3 254 1.3150
c2-c2-hc 50.300 119.700 SOURCE3 1
c2-c2-hx 48.980 126.450 SOURCE3 3 0.0219
c2-c2-i 56.280 121.030 SOURCE3 2 0.0000
c2-c2-n1 71.690 122.980 HF/6-31G* 1
c2-c2-n2 71.290 126.010 SOURCE3 1 0.0000
c2-c2-n3 70.330 124.550 SOURCE3 1
c2-c2-n4 67.180 121.520 SOURCE3 5 1.2656
c2-c2-n 68.860 123.200 SOURCE4 15 1.8657
c2-c2-na 69.830 121.380 SOURCE3 26 6.9463
c2-c2-nh 69.800 124.990 SOURCE3 7 0.9929
c2-c2-no 67.520 124.090 SOURCE4 6 1.2772
c2-c2-o 71.920 130.890 SOURCE3 2 0.0201
c2-c2-oh 71.640 122.070 SOURCE4 6 1.0883
c2-c2-os 71.040 121.890 SOURCE4 33 1.3457
c2-c2-p2 66.940 115.100 SOURCE3 1
c2-c2-p3 59.410 124.830 SOURCE3 5 2.1222
c2-c2-p4 61.010 119.760 SOURCE3 1
c2-c2-p5 58.230 125.970 SOURCE3 1
c2-c2-s4 79.550 119.840 SOURCE3 1
c2-c2-s6 79.490 120.010 SOURCE3 1
c2-c2-s 77.520 129.370 SOURCE3 2 0.0000
c2-c2-sh 77.030 125.700 SOURCE3 3 1.3390
c2-c2-ss 79.470 122.860 SOURCE4 13 1.7467
c3-c2-c3 62.700 116.520 SOURCE3 15 3.1001
c3-c2-cc 63.220 125.380 SOURCE4 26 1.8978
c3-c2-cd 63.160 125.640 SOURCE3 1 same_as_c3-c2-cc
c3-c2-ce 64.190 123.020 SOURCE4 1189 1.9006