# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 04:11:37 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: N-{1-[6-(phenylamino)pyrazin-2-yl]-1H-benzimidazol-6-yl}prop-2-enamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C=CC(=O)Nc1ccc2ncn(c3cncc(Nc4ccccc4)n3)c2c1
#
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
 37Q  37Q  N-{1-[6-(phenylamino)pyrazin-2-yl]-1H-benzimidazol-6-yl}prop-2-enamide  ligand  43  27  .  2021-08-04  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_37Q
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
 37Q  C4   C  CR16  0  -0.247  -0.4462  -4.3784   0.5464
 37Q  C5   C  CR16  0  -0.304  -0.7737  -2.0266  -0.8950
 37Q  C6   C  CR16  0  -0.327  -1.6171  -3.6474   0.6708
 37Q  C7   C  CR16  0  -0.312   2.8427   2.1049  -0.0168
 37Q  C8   C  CR16  0  -0.316   2.1827   3.3059  -0.1973
 37Q  C10  C  CR16  0  -0.166  -4.4800   0.0912   0.4025
 37Q  C13  C  C1    0  -0.337   4.2106  -2.1791   0.2312
 37Q  C15  C  CR6   0   0.378   2.1214   0.9183   0.2055
 37Q  C17  C  CR56  0   0.346   0.0878   2.1345   0.0707
 37Q  C20  C  C     0   0.529   3.9199  -0.7630  -0.1104
 37Q  C1   C  C2    0  -0.467   5.3028  -2.7906  -0.2123
 37Q  C2   C  CR16  0  -0.269   0.5781  -3.9315  -0.2784
 37Q  C3   C  CR16  0  -0.262   0.4025  -2.7566  -0.9971
 37Q  C9   C  CR16  0  -0.390   0.7322   0.9221   0.2611
 37Q  C11  C  CR16  0  -0.169  -3.6332   2.2076   0.4292
 37Q  C12  C  CR15  0   0.116  -1.2588   3.8622  -0.1945
 37Q  C14  C  CR6   0   0.346  -1.7884  -2.4589  -0.0406
 37Q  C16  C  CR56  0   0.113   0.7929   3.3236  -0.1566
 37Q  C18  C  CR6   0   0.484  -3.1868  -0.4289   0.1843
 37Q  C19  C  CR6   0   0.482  -2.3698   1.6867   0.1837
 37Q  N21  N  N     0  -0.340  -4.6716   1.3827   0.5243
 37Q  N22  N  N     0  -0.446  -0.0816   4.3780  -0.3173
 37Q  N23  N  N     0  -0.463  -2.1551   0.3901   0.0688
 37Q  N24  N  NH1   0  -0.775  -3.0005  -1.7730   0.1028
 37Q  N25  N  NH1   0  -0.760   2.7458  -0.3208   0.4108
 37Q  N26  N  NR5   0  -0.639  -1.2468   2.5076   0.0463
 37Q  O27  O  O     0  -0.468   4.6623  -0.0780  -0.7931
 37Q  H1   H  HCR6  0   0.261  -0.3324  -5.2967   1.1075
 37Q  H2   H  HCR6  0   0.278  -0.8912  -1.1283  -1.4820
 37Q  H3   H  HCR6  0   0.269  -2.4037  -3.9968   1.3289
 37Q  H4   H  HCR6  0   0.273   3.9205   2.0904  -0.0384
 37Q  H5   H  HCR6  0   0.265   2.7416   4.2172  -0.3641
 37Q  H6   H  HCR6  0   0.283  -5.3394  -0.5652   0.4850
 37Q  H7   H  H     0   0.271   3.5022  -2.7136   0.8547
 37Q  H9   H  H     0   0.266   5.5036  -3.8230   0.0371
 37Q  H10  H  H     0   0.262   6.0282  -2.2836  -0.8349
 37Q  H12  H  HCR6  0   0.257   1.4956  -4.4981  -0.3672
 37Q  H13  H  HCR6  0   0.262   1.1812  -2.4053  -1.6624
 37Q  H14  H  HCR6  0   0.303   0.1824   0.0078   0.4231
 37Q  H15  H  HCR6  0   0.285  -3.8223   3.2650   0.5552
 37Q  H16  H  HCR5  0   0.304  -2.1836   4.4110  -0.2862
 37Q  H17  H  HNH1  0   0.415  -3.7903  -2.3363   0.3780
 37Q  H18  H  HNH1  0   0.412   2.1835  -1.0063   0.8921

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
 37Q  N21  C10  aromatic  1.311  0.020  1.311
 37Q  N21  C11  aromatic  1.330  0.020  1.330
 37Q  C10  C18  aromatic  1.411  0.020  1.411
 37Q  N24  C18  single    1.359  0.020  1.359
 37Q  N24  C14  single    1.400  0.020  1.400
 37Q  C11  C19  aromatic  1.388  0.020  1.388
 37Q  C18  N23  aromatic  1.322  0.020  1.322
 37Q  C5   C14  aromatic  1.395  0.020  1.395
 37Q  C5   C3   aromatic  1.388  0.020  1.388
 37Q  C14  C6   aromatic  1.396  0.020  1.396
 37Q  C19  N23  aromatic  1.319  0.020  1.319
 37Q  C19  N26  single    1.398  0.020  1.398
 37Q  C3   C2   aromatic  1.388  0.020  1.388
 37Q  C6   C4   aromatic  1.386  0.020  1.386
 37Q  N26  C12  aromatic  1.376  0.020  1.376
 37Q  N26  C17  aromatic  1.386  0.020  1.386
 37Q  C12  N22  aromatic  1.291  0.020  1.291
 37Q  C2   C4   aromatic  1.389  0.020  1.389
 37Q  C17  C9   aromatic  1.386  0.020  1.386
 37Q  C17  C16  aromatic  1.401  0.020  1.401
 37Q  N22  C16  aromatic  1.379  0.020  1.379
 37Q  C9   C15  aromatic  1.390  0.020  1.390
 37Q  C16  C8   aromatic  1.390  0.020  1.390
 37Q  C15  N25  single    1.403  0.020  1.403
 37Q  C15  C7   aromatic  1.406  0.020  1.406
 37Q  N25  C20  single    1.359  0.020  1.359
 37Q  C8   C7   aromatic  1.382  0.020  1.382
 37Q  C20  C13  single    1.485  0.020  1.485
 37Q  C20  O27  double    1.219  0.020  1.219
 37Q  C13  C1   double    1.328  0.020  1.328
 37Q  C4   H1   single    0.930  0.020  1.080
 37Q  C5   H2   single    0.930  0.020  1.080
 37Q  C6   H3   single    0.930  0.020  1.080
 37Q  C7   H4   single    0.930  0.020  1.080
 37Q  C8   H5   single    0.930  0.020  1.080
 37Q  C10  H6   single    0.930  0.020  1.080
 37Q  C13  H7   single    0.930  0.020  1.080
 37Q  C1   H9   single    0.930  0.020  1.080
 37Q  C1   H10  single    0.930  0.020  1.080
 37Q  C2   H12  single    0.930  0.020  1.080
 37Q  C3   H13  single    0.930  0.020  1.080
 37Q  C9   H14  single    0.930  0.020  1.080
 37Q  C11  H15  single    0.930  0.020  1.080
 37Q  C12  H16  single    0.930  0.020  1.080
 37Q  N24  H17  single    0.860  0.020  1.020
 37Q  N25  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
 37Q  H1   C4   C2   120.22  3.000
 37Q  H1   C4   C6   119.33  3.000
 37Q  C2   C4   C6   120.44  3.000
 37Q  H2   C5   C14  120.78  3.000
 37Q  H2   C5   C3   119.33  3.000
 37Q  C14  C5   C3   119.89  3.000
 37Q  H3   C6   C14  119.68  3.000
 37Q  H3   C6   C4   119.85  3.000
 37Q  C14  C6   C4   120.47  3.000
 37Q  H4   C7   C15  120.30  3.000
 37Q  H4   C7   C8   119.11  3.000
 37Q  C15  C7   C8   120.59  3.000
 37Q  H5   C8   C16  120.67  3.000
 37Q  H5   C8   C7   120.35  3.000
 37Q  C16  C8   C7   118.98  3.000
 37Q  H6   C10  N21  118.24  3.000
 37Q  H6   C10  C18  120.99  3.000
 37Q  N21  C10  C18  120.76  3.000
 37Q  H7   C13  C1   120.15  3.000
 37Q  H7   C13  C20  118.31  3.000
 37Q  C1   C13  C20  121.54  3.000
 37Q  N25  C15  C9   116.19  3.000
 37Q  N25  C15  C7   122.70  3.000
 37Q  C9   C15  C7   121.09  3.000
 37Q  N26  C17  C16  104.67  3.000
 37Q  C16  C17  C9   122.05  3.000
 37Q  N26  C17  C9   133.28  3.000
 37Q  O27  C20  N25  123.93  3.000
 37Q  O27  C20  C13  123.04  3.000
 37Q  N25  C20  C13  113.03  3.000
 37Q  H10  C1   H9   117.11  3.000
 37Q  H10  C1   C13  121.85  3.000
 37Q  H9   C1   C13  121.04  3.000
 37Q  H12  C2   C3   120.52  3.000
 37Q  H12  C2   C4   120.37  3.000
 37Q  C3   C2   C4   119.10  3.000
 37Q  H13  C3   C2   120.11  3.000
 37Q  H13  C3   C5   118.94  3.000
 37Q  C2   C3   C5   120.94  3.000
 37Q  H14  C9   C17  121.66  3.000
 37Q  H14  C9   C15  120.85  3.000
 37Q  C17  C9   C15  117.48  3.000
 37Q  H15  C11  N21  117.50  3.000
 37Q  H15  C11  C19  123.13  3.000
 37Q  N21  C11  C19  119.37  3.000
 37Q  H16  C12  N26  121.53  3.000
 37Q  H16  C12  N22  124.76  3.000
 37Q  N26  C12  N22  113.70  3.000
 37Q  N24  C14  C6   118.11  3.000
 37Q  C6   C14  C5   119.13  3.000
 37Q  N24  C14  C5   122.72  3.000
 37Q  N22  C16  C17  110.41  3.000
 37Q  N22  C16  C8   129.80  3.000
 37Q  C17  C16  C8   119.80  3.000
 37Q  N24  C18  N23  120.01  3.000
 37Q  N23  C18  C10  120.02  3.000
 37Q  N24  C18  C10  119.96  3.000
 37Q  N26  C19  N23  115.97  3.000
 37Q  N26  C19  C11  121.87  3.000
 37Q  N23  C19  C11  122.16  3.000
 37Q  C11  N21  C10  119.36  3.000
 37Q  C16  N22  C12  105.17  3.000
 37Q  C19  N23  C18  118.30  3.000
 37Q  H17  N24  C18  115.38  3.000
 37Q  H17  N24  C14  115.61  3.000
 37Q  C18  N24  C14  127.53  3.000
 37Q  H18  N25  C20  116.33  3.000
 37Q  H18  N25  C15  114.96  3.000
 37Q  C20  N25  C15  128.03  3.000
 37Q  C19  N26  C12  126.05  3.000
 37Q  C12  N26  C17  106.05  3.000
 37Q  C19  N26  C17  127.86  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
 37Q  CONST_01  C5   C14  C6   C4      0.00   0.0  0
 37Q  CONST_02  C5   C3   C2   C4      0.00   0.0  0
 37Q  CONST_03  C3   C5   C14  C6      0.00   0.0  0
 37Q  CONST_04  C3   C2   C4   C6      0.00   0.0  0
 37Q  CONST_05  C17  C9   C15  C7      0.00   0.0  0
 37Q  CONST_06  C17  C16  C8   C7      0.00   0.0  0
 37Q  CONST_07  N22  C16  C8   C7    180.00   0.0  0
 37Q  CONST_08  N26  C17  C16  C8    180.00   0.0  0
 37Q  CONST_09  C9   C17  C16  C8      0.00   0.0  0
 37Q  CONST_10  C12  N22  C16  C8    180.00   0.0  0
 37Q  CONST_11  C9   C15  C7   C8      0.00   0.0  0
 37Q  CONST_12  C19  C11  N21  C10     0.00   0.0  0
 37Q  CONST_13  C19  N23  C18  C10     0.00   0.0  0
 37Q  CONST_14  N26  C17  C9   C15   180.00   0.0  0
 37Q  CONST_15  C16  C17  C9   C15     0.00   0.0  0
 37Q  CONST_16  C16  C8   C7   C15     0.00   0.0  0
 37Q  CONST_17  C11  C19  N26  C17   180.00   0.0  0
 37Q  CONST_18  N23  C19  N26  C17     0.00   0.0  0
 37Q  CONST_19  N22  C12  N26  C17     0.00   0.0  0
 37Q  CONST_20  C12  N22  C16  C17     0.00   0.0  0
 37Q  CONST_21  C14  C5   C3   C2      0.00   0.0  0
 37Q  CONST_22  C14  C6   C4   C2      0.00   0.0  0
 37Q  CONST_23  C19  N26  C17  C9      0.00   0.0  0
 37Q  CONST_24  C12  N26  C17  C9    180.00   0.0  0
 37Q  CONST_25  N22  C16  C17  C9    180.00   0.0  0
 37Q  CONST_26  C18  C10  N21  C11     0.00   0.0  0
 37Q  CONST_27  C18  N23  C19  C11     0.00   0.0  0
 37Q  CONST_30  C16  C17  N26  C12     0.00   0.0  0
 37Q  CONST_31  C19  N26  C17  C16   180.00   0.0  0
 37Q  CONST_32  N26  C12  N22  C16     0.00   0.0  0
 37Q  CONST_33  N26  C19  N23  C18   180.00   0.0  0
 37Q  CONST_34  N22  C12  N26  C19   180.00   0.0  0
 37Q  CONST_35  N23  C18  C10  N21     0.00   0.0  0
 37Q  CONST_36  N23  C19  C11  N21     0.00   0.0  0
 37Q  CONST_37  N26  C19  C11  N21   180.00   0.0  0
 37Q  CONST_38  N26  C17  C16  N22     0.00   0.0  0
 37Q  CONST_39  N24  C14  C6   C4    180.00   0.0  0
 37Q  CONST_40  N25  C15  C7   C8    180.00   0.0  0
 37Q  CONST_41  N25  C15  C9   C17   180.00   0.0  0
 37Q  CONST_42  N24  C14  C5   C3    180.00   0.0  0
 37Q  CONST_43  N24  C18  N23  C19   180.00   0.0  0
 37Q  CONST_44  N24  C18  C10  N21   180.00   0.0  0
 37Q  CONST_45  H13  C3   C2   C4    180.00   0.0  0
 37Q  CONST_46  H3   C6   C14  C5    180.00   0.0  0
 37Q  CONST_47  H12  C2   C3   C5    180.00   0.0  0
 37Q  CONST_48  H2   C5   C14  C6    180.00   0.0  0
 37Q  CONST_49  H14  C9   C15  C7    180.00   0.0  0
 37Q  CONST_50  H15  C11  N21  C10   180.00   0.0  0
 37Q  CONST_51  H5   C8   C7   C15   180.00   0.0  0
 37Q  CONST_52  H16  C12  N26  C17   180.00   0.0  0
 37Q  CONST_53  H1   C4   C2   C3    180.00   0.0  0
 37Q  CONST_54  H4   C7   C15  C9    180.00   0.0  0
 37Q  CONST_55  H6   C10  N21  C11   180.00   0.0  0
 37Q  CONST_59  C15  N25  C20  C13   180.00   0.0  0
 37Q  CONST_60  O27  C20  N25  C15     0.00   0.0  0
 37Q  Var_01    C18  N24  C14  C5    -41.54  30.0  2
 37Q  Var_02    C14  N24  C18  C10  -176.49  30.0  2
 37Q  Var_03    N25  C20  C13  C1    178.72  30.0  1
 37Q  Var_04    H9   C1   C13  C20  -179.67   0.0  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
 37Q  plan-1  C4   0.020
 37Q  plan-1  C5   0.020
 37Q  plan-1  C6   0.020
 37Q  plan-1  C2   0.020
 37Q  plan-1  C3   0.020
 37Q  plan-1  C14  0.020
 37Q  plan-1  N24  0.020
 37Q  plan-1  H1   0.020
 37Q  plan-1  H2   0.020
 37Q  plan-1  H3   0.020
 37Q  plan-1  H12  0.020
 37Q  plan-1  H13  0.020
 37Q  plan-2  C10  0.020
 37Q  plan-2  C11  0.020
 37Q  plan-2  C18  0.020
 37Q  plan-2  C19  0.020
 37Q  plan-2  N21  0.020
 37Q  plan-2  N23  0.020
 37Q  plan-2  N24  0.020
 37Q  plan-2  N26  0.020
 37Q  plan-2  H6   0.020
 37Q  plan-2  H15  0.020
 37Q  plan-3  C7   0.020
 37Q  plan-3  C8   0.020
 37Q  plan-3  C15  0.020
 37Q  plan-3  C17  0.020
 37Q  plan-3  C9   0.020
 37Q  plan-3  C12  0.020
 37Q  plan-3  C16  0.020
 37Q  plan-3  C19  0.020
 37Q  plan-3  N22  0.020
 37Q  plan-3  N25  0.020
 37Q  plan-3  N26  0.020
 37Q  plan-3  H4   0.020
 37Q  plan-3  H5   0.020
 37Q  plan-3  H14  0.020
 37Q  plan-3  H16  0.020
 37Q  plan-4  C13  0.020
 37Q  plan-4  C15  0.020
 37Q  plan-4  C20  0.020
 37Q  plan-4  N25  0.020
 37Q  plan-4  O27  0.020
 37Q  plan-4  H18  0.020
 37Q  plan-5  C13  0.020
 37Q  plan-5  C20  0.020
 37Q  plan-5  C1   0.020
 37Q  plan-5  H7   0.020
 37Q  plan-5  H9   0.020
 37Q  plan-5  H10  0.020

