# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 04:27:14 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: 1-ethyl-3-[5-(5-fluoropyridin-3-yl)-7-(pyrimidin-2-yl)-1H-benzimidazol-2-yl]urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCNC(=O)Nc1[nH]c2c(cc(cc2c3ncccn3)c4cncc(F)c4)n1
#
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
 883  883  1-ethyl-3-[5-(5-fluoropyridin-3-yl)-7-(pyrimidin-2-yl)-1H-benzimidazol-2-yl]urea  ligand  44  28  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_883
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
 883  C1   C  CH3   0  -0.705   7.9549   2.4932   0.0253
 883  C2   C  CH2   0  -0.256   6.9124   1.3924   0.0173
 883  N3   N  NH1   0  -0.677   5.5795   1.9658   0.0430
 883  C4   C  C     0   0.761   4.4793   1.2011   0.0229
 883  O5   O  O     0  -0.523   4.5041  -0.0220  -0.0129
 883  N6   N  NH1   0  -0.780   3.2919   1.9135   0.0465
 883  C7   C  CR5   0   0.673   2.0387   1.3732   0.0412
 883  N8   N  N     0  -0.520   0.9577   2.1060   0.0865
 883  C9   C  CR56  0   0.184  -0.0743   1.1995   0.0574
 883  C10  C  CR16  0  -0.400  -1.4430   1.4150   0.0880
 883  C11  C  CR6   0   0.094  -2.2927   0.3084   0.0576
 883  C12  C  CR16  0  -0.410  -1.7640  -0.9856  -0.0064
 883  C13  C  CR6   0  -0.011  -0.3930  -1.2328  -0.0386
 883  C14  C  CR6   0   0.432   0.1441  -2.5990  -0.1166
 883  N15  N  N     0  -0.424  -0.7219  -3.6073  -0.1561
 883  C16  C  CR16  0  -0.010  -0.2240  -4.8314  -0.2282
 883  C17  C  CR16  0  -0.359   1.1396  -5.0762  -0.2615
 883  C18  C  CR16  0  -0.002   1.9581  -3.9620  -0.2149
 883  N19  N  N     0  -0.461   1.4694  -2.7315  -0.1430
 883  C20  C  CR56  0   0.332   0.4337  -0.1114  -0.0037
 883  N21  N  NR15  0  -0.713   1.7913   0.0410  -0.0146
 883  C23  C  CR6   0   0.012  -3.7541   0.4996   0.0884
 883  C24  C  CR16  0  -0.106  -4.5874  -0.3716   0.7940
 883  N25  N  N     0  -0.382  -5.9047  -0.2487   0.8502
 883  C26  C  CR16  0  -0.211  -6.4833   0.7589   0.2121
 883  C27  C  CR6   0   0.451  -5.7322   1.6751  -0.5005
 883  F28  F  F     0  -0.302  -6.3509   2.6799  -1.1312
 883  C29  C  CR16  0  -0.355  -4.3618   1.5608  -0.5784
 883  H1   H  HCH3  0   0.237   7.8585   3.1402  -0.8473
 883  H2   H  HCH3  0   0.237   7.8766   3.1103   0.9213
 883  H3   H  HCH3  0   0.249   8.9521   2.0565   0.0082
 883  H4   H  HCH2  0   0.238   7.0317   0.7717  -0.8734
 883  H5   H  HCH2  0   0.237   7.0524   0.7396   0.8817
 883  H6   H  HNH1  0   0.407   5.4965   2.9691   0.0676
 883  H7   H  HNH1  0   0.424   3.3121   2.9227   0.0801
 883  H9   H  HCR6  0   0.262  -1.8349   2.4227   0.1547
 883  H10  H  HCR6  0   0.257  -2.4354  -1.8318  -0.0562
 883  H11  H  HCR6  0   0.281  -0.9374  -5.6467  -0.2608
 883  H12  H  HCR6  0   0.289   1.5393  -6.0774  -0.3213
 883  H13  H  HCR6  0   0.282   3.0372  -4.0579  -0.2358
 883  H14  H  HNR5  0   0.426   2.4715  -0.7039  -0.0497
 883  H15  H  HCR6  0   0.266  -4.1602  -1.1972   1.3522
 883  H16  H  HCR6  0   0.285  -7.5628   0.8464   0.2667
 883  H17  H  HCR6  0   0.293  -3.7844   2.2700  -1.1581

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
 883  C17  C16  aromatic  1.386  0.020  1.386
 883  C17  C18  aromatic  1.383  0.020  1.383
 883  C16  N15  aromatic  1.323  0.020  1.323
 883  C18  N19  aromatic  1.326  0.020  1.326
 883  N15  C14  aromatic  1.330  0.020  1.330
 883  N19  C14  aromatic  1.332  0.020  1.332
 883  C14  C13  single    1.470  0.020  1.470
 883  O5   C4   double    1.224  0.020  1.224
 883  C2   C1   single    1.516  0.020  1.516
 883  C2   N3   single    1.451  0.020  1.451
 883  C13  C12  aromatic  1.394  0.020  1.394
 883  C13  C20  aromatic  1.394  0.020  1.394
 883  C4   N3   single    1.340  0.020  1.340
 883  C4   N6   single    1.385  0.020  1.385
 883  N21  C20  aromatic  1.366  0.020  1.366
 883  N21  C7   aromatic  1.356  0.020  1.356
 883  C12  C11  aromatic  1.399  0.020  1.399
 883  C20  C9   aromatic  1.407  0.020  1.407
 883  C7   N6   single    1.365  0.020  1.365
 883  C7   N8   aromatic  1.307  0.020  1.307
 883  C11  C23  single    1.474  0.020  1.474
 883  C11  C10  aromatic  1.396  0.020  1.396
 883  C9   N8   aromatic  1.374  0.020  1.374
 883  C9   C10  aromatic  1.386  0.020  1.386
 883  C24  C23  aromatic  1.397  0.020  1.397
 883  C24  N25  aromatic  1.324  0.020  1.324
 883  C23  C29  aromatic  1.393  0.020  1.393
 883  N25  C26  aromatic  1.326  0.020  1.326
 883  C29  C27  aromatic  1.377  0.020  1.377
 883  C26  C27  aromatic  1.383  0.020  1.383
 883  C27  F28  single    1.338  0.020  1.338
 883  C1   H1   single    0.970  0.020  1.090
 883  C1   H2   single    0.970  0.020  1.090
 883  C1   H3   single    0.970  0.020  1.090
 883  C2   H4   single    0.970  0.020  1.090
 883  C2   H5   single    0.970  0.020  1.090
 883  N3   H6   single    0.860  0.020  1.020
 883  N6   H7   single    0.860  0.020  1.020
 883  C10  H9   single    0.930  0.020  1.080
 883  C12  H10  single    0.930  0.020  1.080
 883  C16  H11  single    0.930  0.020  1.080
 883  C17  H12  single    0.930  0.020  1.080
 883  C18  H13  single    0.930  0.020  1.080
 883  N21  H14  single    0.860  0.020  1.020
 883  C24  H15  single    0.930  0.020  1.080
 883  C26  H16  single    0.930  0.020  1.080
 883  C29  H17  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
 883  H3   C1   H2   107.79  3.000
 883  H3   C1   H1   107.84  3.000
 883  H2   C1   H1   108.37  3.000
 883  H3   C1   C2   109.78  3.000
 883  H2   C1   C2   111.45  3.000
 883  H1   C1   C2   111.45  3.000
 883  H5   C2   H4   106.96  3.000
 883  H5   C2   N3   109.87  3.000
 883  H4   C2   N3   109.84  3.000
 883  H5   C2   C1   109.97  3.000
 883  H4   C2   C1   109.99  3.000
 883  N3   C2   C1   110.16  3.000
 883  H6   N3   C4   120.08  3.000
 883  H6   N3   C2   118.02  3.000
 883  C4   N3   C2   121.89  3.000
 883  N6   C4   O5   122.14  3.000
 883  N6   C4   N3   114.21  3.000
 883  O5   C4   N3   123.65  3.000
 883  H7   N6   C7   114.46  3.000
 883  H7   N6   C4   119.83  3.000
 883  C7   N6   C4   125.70  3.000
 883  N21  C7   N8   113.66  3.000
 883  N8   C7   N6   122.52  3.000
 883  N21  C7   N6   123.82  3.000
 883  C9   N8   C7   104.52  3.000
 883  C20  C9   C10  120.16  3.000
 883  C10  C9   N8   129.70  3.000
 883  C20  C9   N8   110.14  3.000
 883  H9   C10  C11  121.24  3.000
 883  H9   C10  C9   120.22  3.000
 883  C11  C10  C9   118.52  3.000
 883  C23  C11  C12  119.70  3.000
 883  C23  C11  C10  120.02  3.000
 883  C12  C11  C10  120.28  3.000
 883  H10  C12  C13  118.10  3.000
 883  H10  C12  C11  119.42  3.000
 883  C13  C12  C11  122.47  3.000
 883  C20  C13  C14  122.17  3.000
 883  C20  C13  C12  116.12  3.000
 883  C14  C13  C12  121.71  3.000
 883  N19  C14  N15  124.88  3.000
 883  N19  C14  C13  117.19  3.000
 883  N15  C14  C13  117.93  3.000
 883  C16  N15  C14  117.26  3.000
 883  H11  C16  C17  120.93  3.000
 883  H11  C16  N15  116.73  3.000
 883  C17  C16  N15  122.34  3.000
 883  H12  C17  C18  121.99  3.000
 883  H12  C17  C16  121.96  3.000
 883  C18  C17  C16  116.05  3.000
 883  H13  C18  N19  116.76  3.000
 883  H13  C18  C17  121.15  3.000
 883  N19  C18  C17  122.09  3.000
 883  C18  N19  C14  117.39  3.000
 883  N21  C20  C13  132.77  3.000
 883  N21  C20  C9   104.78  3.000
 883  C13  C20  C9   122.45  3.000
 883  H14  N21  C20  125.99  3.000
 883  H14  N21  C7   127.12  3.000
 883  C20  N21  C7   106.89  3.000
 883  C29  C23  C24  117.17  3.000
 883  C29  C23  C11  121.42  3.000
 883  C24  C23  C11  121.40  3.000
 883  H15  C24  N25  116.15  3.000
 883  H15  C24  C23  119.99  3.000
 883  N25  C24  C23  123.85  3.000
 883  C26  N25  C24  118.96  3.000
 883  H16  C26  C27  120.88  3.000
 883  H16  C26  N25  118.14  3.000
 883  C27  C26  N25  120.98  3.000
 883  C29  C27  F28  119.72  3.000
 883  F28  C27  C26  119.30  3.000
 883  C29  C27  C26  120.97  3.000
 883  H17  C29  C27  120.43  3.000
 883  H17  C29  C23  121.51  3.000
 883  C27  C29  C23  118.05  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
 883  CONST_01  C13  C20  N21  C7   180.00   0.0  0
 883  CONST_02  C9   C20  N21  C7     0.00   0.0  0
 883  CONST_03  C20  C9   N8   C7     0.00   0.0  0
 883  CONST_04  C10  C9   N8   C7   180.00   0.0  0
 883  CONST_05  C20  N21  C7   N8     0.00   0.0  0
 883  CONST_06  C13  C20  C9   N8   180.00   0.0  0
 883  CONST_07  N21  C20  C9   N8     0.00   0.0  0
 883  CONST_08  C11  C10  C9   N8   180.00   0.0  0
 883  CONST_09  C14  C13  C20  C9   180.00   0.0  0
 883  CONST_10  C12  C13  C20  C9     0.00   0.0  0
 883  CONST_11  N21  C7   N8   C9     0.00   0.0  0
 883  CONST_12  C12  C11  C10  C9     0.00   0.0  0
 883  CONST_13  C23  C11  C10  C9   180.00   0.0  0
 883  CONST_14  C13  C12  C11  C10    0.00   0.0  0
 883  CONST_17  C13  C20  C9   C10    0.00   0.0  0
 883  CONST_18  N21  C20  C9   C10  180.00   0.0  0
 883  CONST_19  C14  C13  C12  C11  180.00   0.0  0
 883  CONST_20  C20  C13  C12  C11    0.00   0.0  0
 883  CONST_21  N25  C24  C23  C11  180.00   0.0  0
 883  CONST_22  C27  C29  C23  C11  180.00   0.0  0
 883  CONST_23  C20  C9   C10  C11    0.00   0.0  0
 883  CONST_24  N15  C14  C13  C12    0.00   0.0  0
 883  CONST_25  N19  C14  C13  C12  180.00   0.0  0
 883  CONST_26  N21  C20  C13  C12  180.00   0.0  0
 883  CONST_29  C16  N15  C14  C13  180.00   0.0  0
 883  CONST_30  C18  N19  C14  C13  180.00   0.0  0
 883  CONST_31  C23  C11  C12  C13  180.00   0.0  0
 883  CONST_32  C17  C16  N15  C14    0.00   0.0  0
 883  CONST_33  C17  C18  N19  C14    0.00   0.0  0
 883  CONST_34  N21  C20  C13  C14    0.00   0.0  0
 883  CONST_35  C18  C17  C16  N15    0.00   0.0  0
 883  CONST_36  C18  N19  C14  N15    0.00   0.0  0
 883  CONST_37  C20  C13  C14  N15  180.00   0.0  0
 883  CONST_38  N19  C18  C17  C16    0.00   0.0  0
 883  CONST_39  N19  C14  N15  C16    0.00   0.0  0
 883  CONST_40  C20  C13  C14  N19    0.00   0.0  0
 883  CONST_41  C26  N25  C24  C23    0.00   0.0  0
 883  CONST_42  C26  C27  C29  C23    0.00   0.0  0
 883  CONST_43  C27  C29  C23  C24    0.00   0.0  0
 883  CONST_44  C27  C26  N25  C24    0.00   0.0  0
 883  CONST_45  C29  C23  C24  N25    0.00   0.0  0
 883  CONST_46  C29  C27  C26  N25    0.00   0.0  0
 883  CONST_47  C20  N21  C7   N6   180.00   0.0  0
 883  CONST_48  C9   N8   C7   N6   180.00   0.0  0
 883  CONST_49  F28  C27  C29  C23  180.00   0.0  0
 883  CONST_50  F28  C27  C26  N25  180.00   0.0  0
 883  CONST_51  H14  N21  C7   N8   180.00   0.0  0
 883  CONST_52  H9   C10  C9   N8     0.00   0.0  0
 883  CONST_53  H10  C12  C11  C10  180.00   0.0  0
 883  CONST_54  H15  C24  C23  C11    0.00   0.0  0
 883  CONST_55  H17  C29  C23  C11    0.00   0.0  0
 883  CONST_56  H11  C16  N15  C14  180.00   0.0  0
 883  CONST_57  H13  C18  N19  C14  180.00   0.0  0
 883  CONST_58  H12  C17  C16  N15  180.00   0.0  0
 883  CONST_59  H16  C26  N25  C24  180.00   0.0  0
 883  CONST_60  N21  C7   N6   C4     0.00   0.0  0
 883  CONST_61  N8   C7   N6   C4   180.00   0.0  0
 883  CONST_62  H7   N6   C7   N8     0.00   0.0  0
 883  CONST_63  C7   N6   C4   O5     0.00   0.0  0
 883  CONST_64  C7   N6   C4   N3   180.00   0.0  0
 883  CONST_65  O5   C4   N3   C2     0.00   0.0  0
 883  CONST_66  N6   C4   N3   C2   180.00   0.0  0
 883  CONST_67  H6   N3   C4   O5   180.00   0.0  0
 883  Var_01    C4   N3   C2   C1   179.05  30.0  3
 883  Var_02    H1   C1   C2   N3   -60.71  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
 883  plan-1  C13  0.020
 883  plan-1  C14  0.020
 883  plan-1  N15  0.020
 883  plan-1  C16  0.020
 883  plan-1  C17  0.020
 883  plan-1  C18  0.020
 883  plan-1  N19  0.020
 883  plan-1  H11  0.020
 883  plan-1  H12  0.020
 883  plan-1  H13  0.020
 883  plan-2  C11  0.020
 883  plan-2  C23  0.020
 883  plan-2  C24  0.020
 883  plan-2  N25  0.020
 883  plan-2  C26  0.020
 883  plan-2  C27  0.020
 883  plan-2  F28  0.020
 883  plan-2  C29  0.020
 883  plan-2  H15  0.020
 883  plan-2  H16  0.020
 883  plan-2  H17  0.020
 883  plan-3  N6   0.020
 883  plan-3  C7   0.020
 883  plan-3  N8   0.020
 883  plan-3  C9   0.020
 883  plan-3  C10  0.020
 883  plan-3  C11  0.020
 883  plan-3  C12  0.020
 883  plan-3  C13  0.020
 883  plan-3  C14  0.020
 883  plan-3  C20  0.020
 883  plan-3  N21  0.020
 883  plan-3  C23  0.020
 883  plan-3  H9   0.020
 883  plan-3  H10  0.020
 883  plan-3  H14  0.020
 883  plan-4  C2   0.020
 883  plan-4  N3   0.020
 883  plan-4  C4   0.020
 883  plan-4  O5   0.020
 883  plan-4  N6   0.020
 883  plan-4  C7   0.020
 883  plan-4  H6   0.020
 883  plan-4  H7   0.020

