# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 00:38:07 2020
#   Inital geometry file: a 51 line input string
#   Ligand name: 1H-benzimidazol-2-ylmethanethiol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: SCc1[nH]c2ccccc2n1
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 2XO  2XO  1H-benzimidazol-2-ylmethanethiol  ligand  19  11  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_2XO
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 2XO  SAH  S  S2    0  -0.231   3.3687   0.4202  -0.6813
 2XO  CAI  C  CH2   0  -0.660   2.4655  -0.1959   0.7871
 2XO  CAJ  C  CR56  0   0.134  -1.0273  -0.7247   0.2211
 2XO  NAK  N  N     0  -0.463   0.2274  -1.2132   0.5024
 2XO  CAL  C  CR5   0   0.450   1.0061  -0.1671   0.5142
 2XO  NAM  N  NR15  0  -0.681   0.3433   0.9891   0.2490
 2XO  CAN  C  CR56  0   0.342  -0.9730   0.6696   0.0555
 2XO  CAO  C  CR16  0  -0.307  -2.0962   1.4330  -0.2413
 2XO  CAP  C  CR16  0  -0.277  -3.2936   0.7506  -0.3696
 2XO  CAQ  C  CR16  0  -0.271  -3.3669  -0.6417  -0.2076
 2XO  CAR  C  CR16  0  -0.332  -2.2440  -1.3935   0.0877
 2XO  H1   H  HSH1  0   0.237   4.5534   0.5798  -0.0820
 2XO  H2   H  HCH2  0   0.302   2.7596  -1.2166   1.0186
 2XO  H3   H  HCH2  0   0.308   2.7066   0.4421   1.6377
 2XO  H5   H  HNR5  0   0.420   0.7505   1.9110   0.2133
 2XO  H6   H  HCR6  0   0.267  -2.0411   2.5064  -0.3654
 2XO  H7   H  HCR6  0   0.256  -4.1949   1.3030  -0.6005
 2XO  H8   H  HCR6  0   0.253  -4.3244  -1.1340  -0.3177
 2XO  H9   H  HCR6  0   0.255  -2.3042  -2.4672   0.2108

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 2XO  CAO  CAP  aromatic  1.384  0.020  1.384
 2XO  CAO  CAN  aromatic  1.390  0.020  1.390
 2XO  CAP  CAQ  aromatic  1.404  0.020  1.404
 2XO  CAN  NAM  aromatic  1.368  0.020  1.368
 2XO  CAN  CAJ  aromatic  1.405  0.020  1.405
 2XO  NAM  CAL  aromatic  1.359  0.020  1.359
 2XO  CAQ  CAR  aromatic  1.383  0.020  1.383
 2XO  SAH  CAI  single    1.831  0.020  1.831
 2XO  CAJ  CAR  aromatic  1.395  0.020  1.395
 2XO  CAJ  NAK  aromatic  1.376  0.020  1.376
 2XO  CAL  CAI  single    1.485  0.020  1.485
 2XO  CAL  NAK  aromatic  1.304  0.020  1.304
 2XO  SAH  H1   single    1.200  0.020  1.300
 2XO  CAI  H2   single    0.970  0.020  1.090
 2XO  CAI  H3   single    0.970  0.020  1.090
 2XO  NAM  H5   single    0.860  0.020  1.020
 2XO  CAO  H6   single    0.930  0.020  1.080
 2XO  CAP  H7   single    0.930  0.020  1.080
 2XO  CAQ  H8   single    0.930  0.020  1.080
 2XO  CAR  H9   single    0.930  0.020  1.080

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 2XO  H1   SAH  CAI   96.76  3.000
 2XO  H3   CAI  H2   108.87  3.000
 2XO  H3   CAI  CAL  110.45  3.000
 2XO  H2   CAI  CAL  108.86  3.000
 2XO  H3   CAI  SAH  108.65  3.000
 2XO  H2   CAI  SAH  110.69  3.000
 2XO  CAL  CAI  SAH  109.32  3.000
 2XO  CAR  CAJ  CAN  119.89  3.000
 2XO  CAR  CAJ  NAK  130.16  3.000
 2XO  CAN  CAJ  NAK  109.95  3.000
 2XO  CAL  NAK  CAJ  105.17  3.000
 2XO  NAM  CAL  NAK  112.92  3.000
 2XO  NAK  CAL  CAI  124.95  3.000
 2XO  NAM  CAL  CAI  122.13  3.000
 2XO  H5   NAM  CAN  126.65  3.000
 2XO  H5   NAM  CAL  126.00  3.000
 2XO  CAN  NAM  CAL  107.35  3.000
 2XO  CAO  CAN  NAM  132.79  3.000
 2XO  NAM  CAN  CAJ  104.61  3.000
 2XO  CAO  CAN  CAJ  122.60  3.000
 2XO  H6   CAO  CAP  121.51  3.000
 2XO  H6   CAO  CAN  121.88  3.000
 2XO  CAP  CAO  CAN  116.62  3.000
 2XO  H7   CAP  CAQ  119.18  3.000
 2XO  H7   CAP  CAO  119.25  3.000
 2XO  CAQ  CAP  CAO  121.57  3.000
 2XO  H8   CAQ  CAR  119.52  3.000
 2XO  H8   CAQ  CAP  119.06  3.000
 2XO  CAR  CAQ  CAP  121.42  3.000
 2XO  H9   CAR  CAQ  121.22  3.000
 2XO  H9   CAR  CAJ  120.88  3.000
 2XO  CAQ  CAR  CAJ  117.90  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 2XO  CONST_01  CAP  CAO  CAN  CAJ    0.00   0.0  0
 2XO  CONST_02  CAL  NAM  CAN  CAJ    0.00   0.0  0
 2XO  CONST_03  CAP  CAQ  CAR  CAJ    0.00   0.0  0
 2XO  CONST_04  NAM  CAL  NAK  CAJ    0.00   0.0  0
 2XO  CONST_05  CAO  CAN  CAJ  NAK  180.00   0.0  0
 2XO  CONST_06  NAM  CAN  CAJ  NAK    0.00   0.0  0
 2XO  CONST_07  CAQ  CAR  CAJ  NAK  180.00   0.0  0
 2XO  CONST_08  CAN  NAM  CAL  NAK    0.00   0.0  0
 2XO  CONST_09  CAO  CAN  NAM  CAL  180.00   0.0  0
 2XO  CONST_10  CAN  CAJ  NAK  CAL    0.00   0.0  0
 2XO  CONST_11  CAR  CAJ  NAK  CAL  180.00   0.0  0
 2XO  CONST_12  CAP  CAO  CAN  NAM  180.00   0.0  0
 2XO  CONST_13  CAR  CAJ  CAN  NAM  180.00   0.0  0
 2XO  CONST_14  CAQ  CAP  CAO  CAN    0.00   0.0  0
 2XO  CONST_15  CAQ  CAR  CAJ  CAN    0.00   0.0  0
 2XO  CONST_16  CAR  CAQ  CAP  CAO    0.00   0.0  0
 2XO  CONST_17  CAR  CAJ  CAN  CAO    0.00   0.0  0
 2XO  CONST_18  CAN  NAM  CAL  CAI  180.00   0.0  0
 2XO  CONST_19  CAJ  NAK  CAL  CAI  180.00   0.0  0
 2XO  CONST_20  H6   CAO  CAN  CAJ  180.00   0.0  0
 2XO  CONST_21  H5   NAM  CAN  CAJ  180.00   0.0  0
 2XO  CONST_22  H8   CAQ  CAR  CAJ  180.00   0.0  0
 2XO  CONST_23  H9   CAR  CAJ  NAK    0.00   0.0  0
 2XO  CONST_24  H7   CAP  CAO  CAN  180.00   0.0  0
 2XO  Var_01    NAM  CAL  CAI  SAH  -61.75  30.0  2

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 2XO  plan-1  CAI  0.020
 2XO  plan-1  CAJ  0.020
 2XO  plan-1  NAK  0.020
 2XO  plan-1  CAL  0.020
 2XO  plan-1  NAM  0.020
 2XO  plan-1  CAN  0.020
 2XO  plan-1  CAO  0.020
 2XO  plan-1  CAP  0.020
 2XO  plan-1  CAQ  0.020
 2XO  plan-1  CAR  0.020
 2XO  plan-1  H5   0.020
 2XO  plan-1  H6   0.020
 2XO  plan-1  H7   0.020
 2XO  plan-1  H8   0.020
 2XO  plan-1  H9   0.020

