ReactionMechanismGenerator / ReactionMechanismGenerator/ARC
Force field conformer generated by ARC has atoms too close to each other
@alongd is already working on this.
Since Apr 18, 2020.
- Dominant language
- Python
- Stars
- 51
- Forks
- 25
- Avg merge
- 4d 5h
- Merged PRs (30d)
- 15
Description
Describe the bug
Force field conformer generated by ARC has atoms too close to each other

How to reproduce
Species smile: [O]OCN(C(CCN1C2C=CC=CC=2CCC2=C1C=CC=C2)OO)C
Species xyz:
0 2
O 5.98370000 0.37132000 0.46074000
O 5.70019000 -0.58273000 -0.54099000
C 4.89638000 0.08236000 -1.53025000
N 3.47911000 -0.32753000 -1.58480000
C 2.75429000 0.12718000 -0.38202000
C 1.23215000 -0.04819000 -0.51236000
C 0.50213000 0.59642000 0.67840000
N 0.63095199 -0.22176957 1.91046465
C 1.91775900 -0.44150718 2.46475683
C 2.93204116 0.53225871 2.28433134
C 4.21492887 0.40509149 2.82465662
C 4.52931847 -0.70313101 3.58772941
C 3.55910549 -1.67610048 3.79821252
C 2.26000874 -1.57330963 3.23938139
C 1.34230800 -2.73703090 3.55623530
C 0.17198268 -2.97584869 2.61259074
C -0.88117179 -1.92739539 2.82622894
C -0.60860500 -0.59605047 2.48293610
C -1.60503399 0.36726902 2.72838932
C -2.83907055 0.01721923 3.28052924
C -3.10010228 -1.30875490 3.60302411
C -2.12492120 -2.27788511 3.38009565
O 3.18162000 -0.57639000 0.79475000
O 3.61429000 0.43375000 1.75761000
C 3.36444000 -1.76545000 -1.82144000
H 5.35957000 -0.14014000 -2.49930000
H 4.97056000 1.17379000 -1.42745000
H 2.94372000 1.20385000 -0.26734000
H 0.87508000 0.40834000 -1.44429000
H 0.98694000 -1.11327000 -0.55965000
H -0.54952307 0.69051069 0.37359323
H 0.83474295 1.62168646 0.87168515
H 2.73463317 1.44500815 1.72908443
H 4.95321941 1.18400765 2.65664949
H 5.51805753 -0.81002778 4.02364674
H 3.81837557 -2.54017643 4.40836142
H 0.98296633 -2.61552897 4.58698686
H 1.94613530 -3.65503546 3.53781130
H -0.24918518 -3.96835316 2.81672544
H 0.48954951 -2.98882076 1.56263967
H -1.41153777 1.41478581 2.51035066
H -3.58756991 0.78273301 3.46496066
H -4.05633257 -1.58710101 4.03728002
H -2.33487495 -3.31048390 3.64871419
H 4.57563000 0.38668000 1.54970000
H 3.83868749 -2.33937731 -1.01950162
H 2.31118150 -2.06982729 -1.81935035
H 3.80130490 -2.07692004 -2.77652275
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