# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 07:41:17 2022
#   Inital geometry file: a 113 line input string
#   Ligand name: 1-[5-(5-azanyl-1~{H}-benzimidazol-2-yl)-2-methyl-4-phenyl-1~{H}-pyrrol-3-yl]ethanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)c1c(C)[nH]c(c2[nH]c3ccc(N)cc3n2)c1c4ccccc4
#
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
 N03  N03  "1-[5-(5-azanyl-1H-benzimidazol-2-yl)-2-methyl-4-phenyl-1H-pyrrol-3-yl]ethanone"  ligand  43  25  .  2022-08-10  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_N03
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
 N03  C1   C  CR16  0  -0.433  18.6008  28.2898  40.9519
 N03  C10  C  CR5   0   0.297  20.4269  30.9387  37.3171
 N03  C11  C  CR5   0   0.034  21.4887  31.5719  36.7155
 N03  C12  C  CR5   0  -0.136  20.9817  32.1894  35.5285
 N03  C13  C  CR5   0   0.364  19.6162  31.8939  35.4648
 N03  C15  C  CH3   0  -0.727  18.5710  32.2545  34.4720
 N03  C16  C  C     0   0.294  21.6757  33.0000  34.5286
 N03  C17  C  CH3   0  -0.798  23.1483  33.2681  34.6954
 N03  C19  C  CR6   0  -0.118  22.8631  31.5731  37.2536
 N03  C2   C  CR56  0   0.167  19.4459  28.9980  40.0974
 N03  C20  C  CR16  0  -0.268  23.7734  30.5885  36.8723
 N03  C21  C  CR16  0  -0.243  25.0588  30.5768  37.3959
 N03  C22  C  CR16  0  -0.254  25.4481  31.5467  38.3102
 N03  C23  C  CR16  0  -0.243  24.5454  32.5268  38.7011
 N03  C24  C  CR16  0  -0.267  23.2603  32.5395  38.1765
 N03  C3   C  CR56  0   0.302  20.8167  29.1008  40.3775
 N03  C4   C  CR16  0  -0.312  21.3783  28.5113  41.5008
 N03  C5   C  CR16  0  -0.338  20.5325  27.8094  42.3392
 N03  C6   C  CR6   0   0.294  19.1482  27.6877  42.0807
 N03  C8   C  CR5   0   0.407  20.3026  30.1593  38.5237
 N03  N14  N  NR15  0  -0.686  19.3196  31.1527  36.5405
 N03  N25  N  NH2   0  -0.863  18.3632  26.9182  42.9299
 N03  N7   N  NR15  0  -0.737  21.3341  29.8503  39.3484
 N03  N9   N  N     0  -0.501  19.1560  29.6690  38.9375
 N03  O18  O  O     0  -0.419  21.0745  33.4578  33.5704
 N03  H1   H  HCR6  0   0.248  17.5414  28.2098  40.7380
 N03  H2   H  HCH3  0   0.258  18.8222  31.8825  33.4797
 N03  H3   H  HCH3  0   0.249  17.6089  31.8327  34.7598
 N03  H4   H  HCH3  0   0.258  18.4571  33.3345  34.3911
 N03  H5   H  HCH3  0   0.260  23.5055  33.8966  33.8821
 N03  H6   H  HCH3  0   0.263  23.3550  33.7648  35.6439
 N03  H7   H  HCH3  0   0.264  23.7186  32.3384  34.6989
 N03  H8   H  HCR6  0   0.254  23.4710  29.8282  36.1626
 N03  H9   H  HCR6  0   0.259  25.7556  29.8067  37.0914
 N03  H10  H  HCR6  0   0.258  26.4498  31.5368  38.7199
 N03  H11  H  HCR6  0   0.259  24.8405  33.2834  39.4166
 N03  H12  H  HCR6  0   0.254  22.5575  33.3043  38.4834
 N03  H13  H  HCR6  0   0.260  22.4345  28.5919  41.7230
 N03  H14  H  HCR6  0   0.254  20.9411  27.3350  43.2235
 N03  H15  H  HNR5  0   0.416  18.4048  30.7850  36.7613
 N03  H16  H  HNH2  0   0.371  18.6985  26.8670  43.8793
 N03  H17  H  HNH2  0   0.372  17.3812  27.1459  42.9145
 N03  H18  H  HNR5  0   0.426  22.2993  30.1145  39.2283

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
 N03  C17  C16  single    1.506  0.020  1.506
 N03  O18  C16  double    1.220  0.020  1.220
 N03  C15  C13  single    1.486  0.020  1.486
 N03  C16  C12  single    1.462  0.020  1.462
 N03  C13  C12  aromatic  1.399  0.020  1.399
 N03  C13  N14  aromatic  1.340  0.020  1.340
 N03  C12  C11  aromatic  1.431  0.020  1.431
 N03  N14  C10  aromatic  1.369  0.020  1.369
 N03  C11  C19  single    1.476  0.020  1.476
 N03  C11  C10  aromatic  1.375  0.020  1.375
 N03  C20  C19  aromatic  1.394  0.020  1.394
 N03  C20  C21  aromatic  1.388  0.020  1.388
 N03  C19  C24  aromatic  1.394  0.020  1.394
 N03  C10  C8   single    1.442  0.020  1.442
 N03  C21  C22  aromatic  1.389  0.020  1.389
 N03  C24  C23  aromatic  1.388  0.020  1.388
 N03  C22  C23  aromatic  1.389  0.020  1.389
 N03  C8   N9   aromatic  1.314  0.020  1.314
 N03  C8   N7   aromatic  1.356  0.020  1.356
 N03  N9   C2   aromatic  1.371  0.020  1.371
 N03  N7   C3   aromatic  1.374  0.020  1.374
 N03  C2   C3   aromatic  1.403  0.020  1.403
 N03  C2   C1   aromatic  1.395  0.020  1.395
 N03  C3   C4   aromatic  1.387  0.020  1.387
 N03  C1   C6   aromatic  1.392  0.020  1.392
 N03  C4   C5   aromatic  1.382  0.020  1.382
 N03  C6   C5   aromatic  1.413  0.020  1.413
 N03  C6   N25  single    1.389  0.020  1.389
 N03  C1   H1   single    0.930  0.020  1.080
 N03  C15  H2   single    0.970  0.020  1.090
 N03  C15  H3   single    0.970  0.020  1.090
 N03  C15  H4   single    0.970  0.020  1.090
 N03  C17  H5   single    0.970  0.020  1.090
 N03  C17  H6   single    0.970  0.020  1.090
 N03  C17  H7   single    0.970  0.020  1.090
 N03  C20  H8   single    0.930  0.020  1.080
 N03  C21  H9   single    0.930  0.020  1.080
 N03  C22  H10  single    0.930  0.020  1.080
 N03  C23  H11  single    0.930  0.020  1.080
 N03  C24  H12  single    0.930  0.020  1.080
 N03  C4   H13  single    0.930  0.020  1.080
 N03  C5   H14  single    0.930  0.020  1.080
 N03  N14  H15  single    0.860  0.020  1.020
 N03  N25  H16  single    0.890  0.020  1.040
 N03  N25  H17  single    0.890  0.020  1.040
 N03  N7   H18  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
 N03  H1   C1   C6   120.84  3.000
 N03  H1   C1   C2   120.58  3.000
 N03  C6   C1   C2   118.57  3.000
 N03  N14  C10  C8   119.30  3.000
 N03  C8   C10  C11  132.98  3.000
 N03  N14  C10  C11  107.72  3.000
 N03  C19  C11  C12  129.20  3.000
 N03  C19  C11  C10  124.06  3.000
 N03  C12  C11  C10  106.75  3.000
 N03  C16  C12  C13  123.32  3.000
 N03  C13  C12  C11  107.01  3.000
 N03  C16  C12  C11  129.67  3.000
 N03  N14  C13  C15  121.00  3.000
 N03  N14  C13  C12  107.25  3.000
 N03  C15  C13  C12  131.75  3.000
 N03  H4   C15  H3   108.13  3.000
 N03  H4   C15  H2   107.17  3.000
 N03  H3   C15  H2   108.19  3.000
 N03  H4   C15  C13  111.34  3.000
 N03  H3   C15  C13  110.53  3.000
 N03  H2   C15  C13  111.32  3.000
 N03  O18  C16  C17  120.13  3.000
 N03  O18  C16  C12  120.73  3.000
 N03  C17  C16  C12  119.14  3.000
 N03  H7   C17  H6   106.64  3.000
 N03  H7   C17  H5   108.85  3.000
 N03  H6   C17  H5   108.95  3.000
 N03  H7   C17  C16  111.09  3.000
 N03  H6   C17  C16  111.27  3.000
 N03  H5   C17  C16  109.94  3.000
 N03  C24  C19  C20  118.99  3.000
 N03  C24  C19  C11  120.48  3.000
 N03  C20  C19  C11  120.51  3.000
 N03  N9   C2   C3   109.85  3.000
 N03  C3   C2   C1   120.46  3.000
 N03  N9   C2   C1   129.69  3.000
 N03  H8   C20  C21  119.98  3.000
 N03  H8   C20  C19  119.52  3.000
 N03  C21  C20  C19  120.49  3.000
 N03  H9   C21  C22  120.11  3.000
 N03  H9   C21  C20  119.74  3.000
 N03  C22  C21  C20  120.14  3.000
 N03  H10  C22  C23  120.11  3.000
 N03  H10  C22  C21  120.16  3.000
 N03  C23  C22  C21  119.73  3.000
 N03  H11  C23  C24  119.73  3.000
 N03  H11  C23  C22  120.14  3.000
 N03  C24  C23  C22  120.13  3.000
 N03  H12  C24  C23  120.01  3.000
 N03  H12  C24  C19  119.49  3.000
 N03  C23  C24  C19  120.50  3.000
 N03  N7   C3   C4   133.29  3.000
 N03  C4   C3   C2   121.74  3.000
 N03  N7   C3   C2   104.97  3.000
 N03  H13  C4   C5   120.69  3.000
 N03  H13  C4   C3   121.98  3.000
 N03  C5   C4   C3   117.33  3.000
 N03  H14  C5   C6   118.74  3.000
 N03  H14  C5   C4   119.11  3.000
 N03  C6   C5   C4   122.14  3.000
 N03  N25  C6   C5   119.30  3.000
 N03  N25  C6   C1   120.89  3.000
 N03  C5   C6   C1   119.76  3.000
 N03  N9   C8   N7   112.78  3.000
 N03  N7   C8   C10  124.50  3.000
 N03  N9   C8   C10  122.71  3.000
 N03  H15  N14  C13  125.26  3.000
 N03  H15  N14  C10  123.46  3.000
 N03  C13  N14  C10  111.28  3.000
 N03  H17  N25  H16  110.48  3.000
 N03  H17  N25  C6   114.58  3.000
 N03  H16  N25  C6   114.57  3.000
 N03  H18  N7   C8   126.59  3.000
 N03  H18  N7   C3   126.35  3.000
 N03  C8   N7   C3   107.05  3.000
 N03  C8   N9   C2   105.34  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
 N03  CONST_01  C8   N9   C2   C1    180.00   0.0  0
 N03  CONST_02  N7   C3   C2   C1    180.00   0.0  0
 N03  CONST_03  C4   C3   C2   C1      0.00   0.0  0
 N03  CONST_04  C4   C5   C6   C1      0.00   0.0  0
 N03  CONST_05  C12  C13  N14  C10     0.00   0.0  0
 N03  CONST_06  C13  C12  C11  C10     0.00   0.0  0
 N03  CONST_09  C2   N9   C8   C10   180.00   0.0  0
 N03  CONST_10  C3   N7   C8   C10   180.00   0.0  0
 N03  CONST_11  N14  C13  C12  C11     0.00   0.0  0
 N03  CONST_12  C21  C20  C19  C11   180.00   0.0  0
 N03  CONST_13  C23  C24  C19  C11   180.00   0.0  0
 N03  CONST_14  C13  N14  C10  C11     0.00   0.0  0
 N03  CONST_15  N9   C8   C10  C11   180.00   0.0  0
 N03  CONST_16  N7   C8   C10  C11     0.00   0.0  0
 N03  CONST_19  N14  C10  C11  C12     0.00   0.0  0
 N03  CONST_20  C8   C10  C11  C12   180.00   0.0  0
 N03  CONST_21  C19  C11  C12  C13   180.00   0.0  0
 N03  CONST_22  C8   C10  N14  C13   180.00   0.0  0
 N03  CONST_23  N14  C10  C11  C19   180.00   0.0  0
 N03  CONST_24  C8   C10  C11  C19     0.00   0.0  0
 N03  CONST_25  C22  C21  C20  C19     0.00   0.0  0
 N03  CONST_26  C22  C23  C24  C19     0.00   0.0  0
 N03  CONST_27  N7   C8   N9   C2      0.00   0.0  0
 N03  CONST_28  C8   N7   C3   C2      0.00   0.0  0
 N03  CONST_29  C5   C4   C3   C2      0.00   0.0  0
 N03  CONST_30  C5   C6   C1   C2      0.00   0.0  0
 N03  CONST_31  C23  C24  C19  C20     0.00   0.0  0
 N03  CONST_32  C23  C22  C21  C20     0.00   0.0  0
 N03  CONST_33  C24  C19  C20  C21     0.00   0.0  0
 N03  CONST_34  C24  C23  C22  C21     0.00   0.0  0
 N03  CONST_35  N9   C8   N7   C3      0.00   0.0  0
 N03  CONST_36  C8   N9   C2   C3      0.00   0.0  0
 N03  CONST_37  C6   C1   C2   C3      0.00   0.0  0
 N03  CONST_38  C6   C5   C4   C3      0.00   0.0  0
 N03  CONST_39  C8   N7   C3   C4    180.00   0.0  0
 N03  CONST_40  N9   C2   C3   C4    180.00   0.0  0
 N03  CONST_41  N7   C3   C4   C5    180.00   0.0  0
 N03  CONST_42  N9   C2   C1   C6    180.00   0.0  0
 N03  CONST_43  N9   C8   C10  N14     0.00   0.0  0
 N03  CONST_44  N7   C8   C10  N14   180.00   0.0  0
 N03  CONST_45  N9   C2   C3   N7      0.00   0.0  0
 N03  CONST_46  C15  C13  N14  C10   180.00   0.0  0
 N03  CONST_47  C16  C12  C11  C10   180.00   0.0  0
 N03  CONST_48  C15  C13  C12  C11   180.00   0.0  0
 N03  CONST_49  N14  C13  C12  C16   180.00   0.0  0
 N03  CONST_50  C19  C11  C12  C16     0.00   0.0  0
 N03  CONST_51  N25  C6   C1   C2    180.00   0.0  0
 N03  CONST_52  N25  C6   C5   C4    180.00   0.0  0
 N03  CONST_53  H14  C5   C6   C1    180.00   0.0  0
 N03  CONST_54  H18  N7   C8   C10     0.00   0.0  0
 N03  CONST_55  H8   C20  C19  C11     0.00   0.0  0
 N03  CONST_56  H12  C24  C19  C11     0.00   0.0  0
 N03  CONST_57  H15  N14  C10  C11   180.00   0.0  0
 N03  CONST_58  H15  N14  C13  C12   180.00   0.0  0
 N03  CONST_59  H9   C21  C20  C19   180.00   0.0  0
 N03  CONST_60  H11  C23  C24  C19   180.00   0.0  0
 N03  CONST_61  H18  N7   C3   C2    180.00   0.0  0
 N03  CONST_62  H13  C4   C3   C2    180.00   0.0  0
 N03  CONST_63  H12  C24  C19  C20   180.00   0.0  0
 N03  CONST_64  H10  C22  C21  C20   180.00   0.0  0
 N03  CONST_65  H11  C23  C22  C21   180.00   0.0  0
 N03  CONST_66  H8   C20  C21  C22   180.00   0.0  0
 N03  CONST_67  H12  C24  C23  C22   180.00   0.0  0
 N03  CONST_68  H9   C21  C22  C23   180.00   0.0  0
 N03  CONST_69  H8   C20  C19  C24   180.00   0.0  0
 N03  CONST_70  H10  C22  C23  C24   180.00   0.0  0
 N03  CONST_71  H1   C1   C2   C3    180.00   0.0  0
 N03  CONST_72  H14  C5   C4   C3    180.00   0.0  0
 N03  CONST_73  H18  N7   C3   C4      0.00   0.0  0
 N03  CONST_74  H1   C1   C6   C5    180.00   0.0  0
 N03  CONST_75  H13  C4   C5   C6    180.00   0.0  0
 N03  CONST_76  H15  N14  C10  C8      0.00   0.0  0
 N03  CONST_77  H13  C4   C3   N7      0.00   0.0  0
 N03  CONST_78  H18  N7   C8   N9    180.00   0.0  0
 N03  CONST_79  H1   C1   C2   N9      0.00   0.0  0
 N03  Var_01    C17  C16  C12  C11     0.29  30.0  2
 N03  Var_02    O18  C16  C12  C11  -179.59  30.0  2
 N03  Var_03    C17  C16  C12  C13   179.56  30.0  2
 N03  Var_04    O18  C16  C12  C13    -0.32  30.0  2
 N03  Var_05    H2   C15  C13  C12    59.42  30.0  2
 N03  Var_06    H3   C15  C13  C12   179.69  30.0  2
 N03  Var_07    H4   C15  C13  C12   -60.10  30.0  2
 N03  Var_08    H2   C15  C13  N14  -120.60  30.0  2
 N03  Var_09    H3   C15  C13  N14    -0.33  30.0  2
 N03  Var_10    H4   C15  C13  N14   119.88  30.0  2
 N03  Var_11    H5   C17  C16  C12  -178.99  30.0  3
 N03  Var_12    H6   C17  C16  C12   -58.19  30.0  3
 N03  Var_13    H7   C17  C16  C12    60.46  30.0  3
 N03  Var_14    H5   C17  C16  O18     0.89  30.0  3
 N03  Var_15    H6   C17  C16  O18   121.69  30.0  3
 N03  Var_16    H7   C17  C16  O18  -119.66  30.0  3

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
 N03  plan-1  C10  0.020
 N03  plan-1  C11  0.020
 N03  plan-1  C12  0.020
 N03  plan-1  C13  0.020
 N03  plan-1  C15  0.020
 N03  plan-1  C16  0.020
 N03  plan-1  C19  0.020
 N03  plan-1  C8   0.020
 N03  plan-1  N14  0.020
 N03  plan-1  H15  0.020
 N03  plan-2  C11  0.020
 N03  plan-2  C19  0.020
 N03  plan-2  C20  0.020
 N03  plan-2  C21  0.020
 N03  plan-2  C22  0.020
 N03  plan-2  C23  0.020
 N03  plan-2  C24  0.020
 N03  plan-2  H8   0.020
 N03  plan-2  H9   0.020
 N03  plan-2  H10  0.020
 N03  plan-2  H11  0.020
 N03  plan-2  H12  0.020
 N03  plan-3  C1   0.020
 N03  plan-3  C10  0.020
 N03  plan-3  C2   0.020
 N03  plan-3  C3   0.020
 N03  plan-3  C4   0.020
 N03  plan-3  C5   0.020
 N03  plan-3  C6   0.020
 N03  plan-3  C8   0.020
 N03  plan-3  N25  0.020
 N03  plan-3  N7   0.020
 N03  plan-3  N9   0.020
 N03  plan-3  H1   0.020
 N03  plan-3  H13  0.020
 N03  plan-3  H14  0.020
 N03  plan-3  H18  0.020
 N03  plan-4  C6   0.020
 N03  plan-4  N25  0.020
 N03  plan-4  H16  0.020
 N03  plan-4  H17  0.020
 N03  plan-5  C12  0.020
 N03  plan-5  C16  0.020
 N03  plan-5  C17  0.020
 N03  plan-5  O18  0.020

