# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 09:19:33 2022
#   Inital geometry file: a 95 line input string
#   Ligand name: methyl ~{N}-[6-(phenylcarbonyl)-1~{H}-benzimidazol-2-yl]carbamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)Nc1[nH]c2cc(ccc2n1)C(=O)c3ccccc3
#
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
 V95  V95  "methyl N-(6-benzoyl-1H-benzimidazol-2-yl)carbamate"  ligand  35  22  .  2022-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_V95
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
 V95  C11   C  CR16  0  -0.331  16.6246  10.7575  27.0389
 V95  C12   C  CR6   0  -0.063  16.3174  11.4568  25.8699
 V95  C01   C  CH3   0  -0.420  17.3661  10.5782  34.6854
 V95  C03   C  C     0   0.759  16.9358  11.1576  32.4546
 V95  C06   C  CR5   0   0.685  16.3925  12.1440  30.2957
 V95  C08   C  CR56  0   0.167  16.0186  12.7625  28.3060
 V95  C09   C  CR56  0   0.375  16.4811  11.4348  28.2307
 V95  C13   C  CR16  0  -0.288  15.8507  12.7826  25.9335
 V95  C14   C  CR16  0  -0.322  15.6881  13.4426  27.1368
 V95  C15   C  C     0   0.353  16.4295  10.7429  24.5763
 V95  C17   C  CR6   0  -0.038  16.6853  11.5264  23.3344
 V95  C18   C  CR16  0  -0.273  16.0996  11.1122  22.1381
 V95  C19   C  CR16  0  -0.243  16.3592  11.7940  20.9603
 V95  C20   C  CR16  0  -0.248  17.2334  12.8745  20.9595
 V95  C21   C  CR16  0  -0.239  17.8394  13.2770  22.1416
 V95  C22   C  CR16  0  -0.277  17.5595  12.6123  23.3268
 V95  N05   N  NH1   0  -0.755  16.4880  12.1775  31.6601
 V95  N07   N  N     0  -0.506  15.9745  13.1761  29.6094
 V95  N10   N  NR15  0  -0.719  16.7111  11.0709  29.5369
 V95  O02   O  O2    0  -0.461  16.9118  11.5291  33.7207
 V95  O04   O  O     0  -0.482  17.2979  10.0792  32.0460
 V95  O16   O  O     0  -0.394  16.3217   9.5324  24.5167
 V95  H111  H  HCR6  0   0.272  16.9784   9.7354  27.0052
 V95  H012  H  HCH3  0   0.257  17.2662  11.0678  35.6490
 V95  H011  H  HCH3  0   0.245  16.7558   9.6761  34.6722
 V95  H013  H  HCH3  0   0.245  18.4099  10.3141  34.5199
 V95  H131  H  HCR6  0   0.265  15.5854  13.2971  25.0199
 V95  H141  H  HCR6  0   0.260  15.3149  14.4575  27.1691
 V95  H181  H  HCR6  0   0.261  15.4245  10.2659  22.1331
 V95  H191  H  HCR6  0   0.261  15.8846  11.4798  20.0400
 V95  H201  H  HCR6  0   0.263  17.4422  13.4007  20.0370
 V95  H211  H  HCR6  0   0.262  18.5304  14.1096  22.1426
 V95  H221  H  HCR6  0   0.268  18.0404  12.9310  24.2427
 V95  H051  H  HNH1  0   0.433  16.2122  13.0502  32.0900
 V95  H101  H  HNR5  0   0.430  17.0532  10.1856  29.8796

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
 V95  C20  C19   aromatic  1.390  0.020  1.390
 V95  C20  C21   aromatic  1.388  0.020  1.388
 V95  C19  C18   aromatic  1.385  0.020  1.385
 V95  C21  C22   aromatic  1.387  0.020  1.387
 V95  C18  C17   aromatic  1.395  0.020  1.395
 V95  C22  C17   aromatic  1.394  0.020  1.394
 V95  C17  C15   single    1.491  0.020  1.491
 V95  C15  O16   double    1.217  0.020  1.217
 V95  C15  C12   single    1.482  0.020  1.482
 V95  C13  C12   aromatic  1.407  0.020  1.407
 V95  C13  C14   aromatic  1.382  0.020  1.382
 V95  C12  C11   aromatic  1.396  0.020  1.396
 V95  C14  C08   aromatic  1.392  0.020  1.392
 V95  C11  C09   aromatic  1.378  0.020  1.378
 V95  C08  C09   aromatic  1.408  0.020  1.408
 V95  C08  N07   aromatic  1.368  0.020  1.368
 V95  C09  N10   aromatic  1.375  0.020  1.375
 V95  N07  C06   aromatic  1.308  0.020  1.308
 V95  N10  C06   aromatic  1.352  0.020  1.352
 V95  C06  N05   single    1.368  0.020  1.368
 V95  N05  C03   single    1.368  0.020  1.368
 V95  O04  C03   double    1.209  0.020  1.209
 V95  C03  O02   single    1.320  0.020  1.320
 V95  O02  C01   single    1.429  0.020  1.429
 V95  C11  H111  single    0.930  0.020  1.080
 V95  C01  H012  single    0.970  0.020  1.090
 V95  C01  H011  single    0.970  0.020  1.090
 V95  C01  H013  single    0.970  0.020  1.090
 V95  C13  H131  single    0.930  0.020  1.080
 V95  C14  H141  single    0.930  0.020  1.080
 V95  C18  H181  single    0.930  0.020  1.080
 V95  C19  H191  single    0.930  0.020  1.080
 V95  C20  H201  single    0.930  0.020  1.080
 V95  C21  H211  single    0.930  0.020  1.080
 V95  C22  H221  single    0.930  0.020  1.080
 V95  N05  H051  single    0.860  0.020  1.020
 V95  N10  H101  single    0.860  0.020  1.020

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
 V95  H111  C11  C09   121.68  3.000
 V95  H111  C11  C12   121.26  3.000
 V95  C09   C11  C12   117.06  3.000
 V95  C15   C12  C13   121.23  3.000
 V95  C13   C12  C11   120.47  3.000
 V95  C15   C12  C11   118.22  3.000
 V95  H013  C01  H011  109.53  3.000
 V95  H013  C01  H012  109.42  3.000
 V95  H011  C01  H012  109.44  3.000
 V95  H013  C01  O02   111.31  3.000
 V95  H011  C01  O02   111.40  3.000
 V95  H012  C01  O02   105.66  3.000
 V95  O04   C03  O02   125.52  3.000
 V95  O02   C03  N05   109.95  3.000
 V95  O04   C03  N05   124.52  3.000
 V95  N10   C06  N07   114.02  3.000
 V95  N10   C06  N05   124.23  3.000
 V95  N07   C06  N05   121.75  3.000
 V95  N07   C08  C14   130.14  3.000
 V95  N07   C08  C09   110.27  3.000
 V95  C14   C08  C09   119.58  3.000
 V95  N10   C09  C08   104.69  3.000
 V95  N10   C09  C11   132.36  3.000
 V95  C08   C09  C11   122.94  3.000
 V95  H131  C13  C14   118.65  3.000
 V95  H131  C13  C12   119.44  3.000
 V95  C14   C13  C12   121.90  3.000
 V95  H141  C14  C13   120.97  3.000
 V95  H141  C14  C08   121.00  3.000
 V95  C13   C14  C08   118.03  3.000
 V95  O16   C15  C17   119.82  3.000
 V95  O16   C15  C12   121.02  3.000
 V95  C17   C15  C12   119.15  3.000
 V95  C22   C17  C18   119.34  3.000
 V95  C22   C17  C15   121.44  3.000
 V95  C18   C17  C15   119.10  3.000
 V95  H181  C18  C19   119.85  3.000
 V95  H181  C18  C17   119.86  3.000
 V95  C19   C18  C17   120.28  3.000
 V95  H191  C19  C20   120.07  3.000
 V95  H191  C19  C18   119.86  3.000
 V95  C20   C19  C18   120.06  3.000
 V95  H201  C20  C21   120.05  3.000
 V95  H201  C20  C19   119.99  3.000
 V95  C21   C20  C19   119.97  3.000
 V95  H211  C21  C22   119.78  3.000
 V95  H211  C21  C20   120.18  3.000
 V95  C22   C21  C20   120.04  3.000
 V95  H221  C22  C21   119.48  3.000
 V95  H221  C22  C17   120.22  3.000
 V95  C21   C22  C17   120.29  3.000
 V95  H051  N05  C06   115.22  3.000
 V95  H051  N05  C03   119.06  3.000
 V95  C06   N05  C03   125.71  3.000
 V95  C08   N07  C06   104.54  3.000
 V95  H101  N10  C09   127.69  3.000
 V95  H101  N10  C06   125.84  3.000
 V95  C09   N10  C06   106.47  3.000
 V95  C03   O02  C01   117.04  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
 V95  CONST_01  C14   C13  C12  C11     0.00   0.0  0
 V95  CONST_02  C14   C08  C09  C11     0.00   0.0  0
 V95  CONST_03  N07   C08  C09  C11   180.00   0.0  0
 V95  CONST_04  C06   N10  C09  C11   180.00   0.0  0
 V95  CONST_05  C08   C14  C13  C12     0.00   0.0  0
 V95  CONST_06  C08   C09  C11  C12     0.00   0.0  0
 V95  CONST_07  N10   C09  C11  C12   180.00   0.0  0
 V95  CONST_08  C14   C08  N07  C06   180.00   0.0  0
 V95  CONST_09  C09   C08  N07  C06     0.00   0.0  0
 V95  CONST_10  C08   C09  N10  C06     0.00   0.0  0
 V95  CONST_11  N10   C06  N07  C08     0.00   0.0  0
 V95  CONST_12  C13   C12  C11  C09     0.00   0.0  0
 V95  CONST_13  C13   C14  C08  C09     0.00   0.0  0
 V95  CONST_14  N07   C06  N10  C09     0.00   0.0  0
 V95  CONST_15  N07   C08  C14  C13   180.00   0.0  0
 V95  CONST_16  N10   C09  C08  C14   180.00   0.0  0
 V95  CONST_17  C20   C19  C18  C17     0.00   0.0  0
 V95  CONST_18  C20   C21  C22  C17     0.00   0.0  0
 V95  CONST_19  C21   C20  C19  C18     0.00   0.0  0
 V95  CONST_20  C21   C22  C17  C18     0.00   0.0  0
 V95  CONST_21  C22   C21  C20  C19     0.00   0.0  0
 V95  CONST_22  C22   C17  C18  C19     0.00   0.0  0
 V95  CONST_23  N10   C09  C08  N07     0.00   0.0  0
 V95  CONST_24  N05   C06  N07  C08   180.00   0.0  0
 V95  CONST_25  C15   C12  C11  C09   180.00   0.0  0
 V95  CONST_26  N05   C06  N10  C09   180.00   0.0  0
 V95  CONST_27  C15   C12  C13  C14   180.00   0.0  0
 V95  CONST_28  C19   C18  C17  C15   180.00   0.0  0
 V95  CONST_29  C21   C22  C17  C15   180.00   0.0  0
 V95  CONST_30  H131  C13  C12  C11   180.00   0.0  0
 V95  CONST_31  H101  N10  C09  C11     0.00   0.0  0
 V95  CONST_32  H141  C14  C13  C12   180.00   0.0  0
 V95  CONST_33  H131  C13  C14  C08   180.00   0.0  0
 V95  CONST_34  H111  C11  C09  C08   180.00   0.0  0
 V95  CONST_35  H101  N10  C09  C08   180.00   0.0  0
 V95  CONST_36  H141  C14  C08  C09   180.00   0.0  0
 V95  CONST_37  H111  C11  C12  C13   180.00   0.0  0
 V95  CONST_38  H191  C19  C18  C17   180.00   0.0  0
 V95  CONST_39  H211  C21  C22  C17   180.00   0.0  0
 V95  CONST_40  H201  C20  C19  C18   180.00   0.0  0
 V95  CONST_41  H221  C22  C17  C18   180.00   0.0  0
 V95  CONST_42  H211  C21  C20  C19   180.00   0.0  0
 V95  CONST_43  H181  C18  C19  C20   180.00   0.0  0
 V95  CONST_44  H221  C22  C21  C20   180.00   0.0  0
 V95  CONST_45  H191  C19  C20  C21   180.00   0.0  0
 V95  CONST_46  H201  C20  C21  C22   180.00   0.0  0
 V95  CONST_47  H181  C18  C17  C22   180.00   0.0  0
 V95  CONST_48  H141  C14  C08  N07     0.00   0.0  0
 V95  CONST_49  H101  N10  C06  N07   180.00   0.0  0
 V95  CONST_50  H111  C11  C09  N10     0.00   0.0  0
 V95  CONST_51  N07   C06  N05  C03   180.00   0.0  0
 V95  CONST_52  N10   C06  N05  C03     0.00   0.0  0
 V95  CONST_53  H051  N05  C06  N07     0.00   0.0  0
 V95  CONST_54  H051  N05  C06  N10   180.00   0.0  0
 V95  CONST_55  O04   C03  N05  C06     0.00   0.0  0
 V95  CONST_56  O02   C03  N05  C06   180.00   0.0  0
 V95  Var_01    C17   C15  C12  C11  -154.17  30.0  2
 V95  Var_02    C18   C17  C15  C12  -144.74  30.0  3
 V95  Var_03    C22   C17  C15  C12    39.23  30.0  3
 V95  Var_04    C17   C15  C12  C13    28.96  30.0  2
 V95  Var_05    O16   C15  C12  C11    25.51  30.0  2
 V95  Var_06    O16   C15  C12  C13  -151.35  30.0  2
 V95  Var_07    O16   C15  C17  C18    35.57  30.0  2
 V95  Var_08    O16   C15  C17  C22  -140.46  30.0  2
 V95  Var_09    N05   C03  O02  C01  -179.29  30.0  1
 V95  Var_10    O04   C03  O02  C01     0.69  30.0  1
 V95  Var_11    H012  C01  O02  C03  -179.88  30.0  3
 V95  Var_12    H011  C01  O02  C03   -61.12  30.0  3
 V95  Var_13    H013  C01  O02  C03    61.44  30.0  3
 V95  Var_14    H051  N05  C03  O02     0.49  30.0  2
 V95  Var_15    H051  N05  C03  O04  -179.49  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
 V95  plan-1  C15   0.020
 V95  plan-1  C17   0.020
 V95  plan-1  C18   0.020
 V95  plan-1  C19   0.020
 V95  plan-1  C20   0.020
 V95  plan-1  C21   0.020
 V95  plan-1  C22   0.020
 V95  plan-1  H181  0.020
 V95  plan-1  H191  0.020
 V95  plan-1  H201  0.020
 V95  plan-1  H211  0.020
 V95  plan-1  H221  0.020
 V95  plan-2  C11   0.020
 V95  plan-2  C12   0.020
 V95  plan-2  C06   0.020
 V95  plan-2  C08   0.020
 V95  plan-2  C09   0.020
 V95  plan-2  C13   0.020
 V95  plan-2  C14   0.020
 V95  plan-2  C15   0.020
 V95  plan-2  N05   0.020
 V95  plan-2  N07   0.020
 V95  plan-2  N10   0.020
 V95  plan-2  H111  0.020
 V95  plan-2  H131  0.020
 V95  plan-2  H141  0.020
 V95  plan-2  H101  0.020
 V95  plan-3  C03   0.020
 V95  plan-3  C06   0.020
 V95  plan-3  N05   0.020
 V95  plan-3  H051  0.020
 V95  plan-4  C12   0.020
 V95  plan-4  C15   0.020
 V95  plan-4  C17   0.020
 V95  plan-4  O16   0.020
 V95  plan-5  C03   0.020
 V95  plan-5  N05   0.020
 V95  plan-5  O02   0.020
 V95  plan-5  O04   0.020

