# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 03:37:52 2020
#   Inital geometry file: a 146 line input string
#   Ligand name: 6-(but-3-en-1-yl)-4-[1-methyl-6-(morpholine-4-carbonyl)-1H-benzimidazol-4-yl]-1,6-dihydro-7H-pyrrolo[2,3-c]pyridin-7-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cnc2c1cc(cc2C3=CN(CCC=C)C(=O)c4[nH]ccc34)C(=O)N5CCOCC5
#
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
 G9V  G9V  6-(but-3-en-1-yl)-4-[1-methyl-6-(morpholine-4-carbonyl)-1H-benzimidazol-4-yl]-1,6-dihydro-7H-pyrrolo[2,3-c]pyridin-7-one  ligand  57  32  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_G9V
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
 G9V  C7   C  CR16  0  -0.326   2.3606   1.7233   0.3281
 G9V  C9   C  CR16  0  -0.388   1.0663  -0.3079   0.6536
 G9V  N2   N  NR5   0  -0.504   0.8897   3.5985  -0.4690
 G9V  C10  C  CR6   0   0.032  -0.1223   0.2837   0.2478
 G9V  C6   C  CR56  0   0.379   1.1714   2.3230  -0.0596
 G9V  C29  C  CH2   0  -0.336   4.7899   0.1176  -0.8414
 G9V  N20  N  NR15  0  -0.645  -2.5449  -3.7080  -0.7591
 G9V  C18  C  CR15  0  -0.460  -0.5431  -2.7371  -0.8366
 G9V  C11  C  CR6   0  -0.092  -1.3805  -0.4734   0.2145
 G9V  C1   C  CH3   0  -0.532   1.8282   4.6891  -0.5836
 G9V  C8   C  CR6   0  -0.074   2.2874   0.3841   0.6803
 G9V  C16  C  CR56  0   0.137  -2.6959  -2.4622  -0.2324
 G9V  C5   C  CR56  0   0.057  -0.0547   1.6389  -0.1140
 G9V  N13  N  NR6   0  -0.532  -3.7424  -0.5823   0.6757
 G9V  C24  C  C1    0  -0.162  -6.8461   1.5846   0.4682
 G9V  C25  C  C2    0  -0.530  -6.9937   2.9040   0.4550
 G9V  C32  C  CH2   0  -0.184   6.3934  -1.9086   0.3071
 G9V  C17  C  CR56  0   0.166  -1.4613  -1.8216  -0.2612
 G9V  C22  C  CH2   0  -0.321  -4.9181   0.1537   1.1298
 G9V  O31  O  O2    0  -0.481   6.5635  -1.5353  -1.0428
 G9V  C12  C  CR16  0  -0.012  -2.5412   0.0773   0.6538
 G9V  C19  C  CR15  0  -0.011  -1.2538  -3.8792  -1.1241
 G9V  C14  C  CR6   0   0.530  -3.9154  -1.8783   0.2240
 G9V  N28  N  NT    0  -0.464   4.6467  -0.2251   0.5650
 G9V  C33  C  CH2   0  -0.333   5.8779  -0.7460   1.1364
 G9V  C3   C  CR15  0   0.101  -0.4349   3.6258  -0.7458
 G9V  C23  C  CH2   0  -0.495  -5.6336   0.8593  -0.0214
 G9V  C26  C  C     0   0.518   3.4805  -0.3241   1.2386
 G9V  C30  C  CH2   0  -0.174   5.3566  -1.0729  -1.6026
 G9V  O27  O  O     0  -0.488   3.3763  -0.9271   2.2997
 G9V  N4   N  N     0  -0.456  -1.0396   2.4868  -0.5520
 G9V  H1   H  HCR6  0   0.285   3.2918   2.2749   0.3685
 G9V  H2   H  HCR6  0   0.257   1.0531  -1.3406   0.9774
 G9V  H4   H  HCH2  0   0.252   5.4570   0.9795  -0.9377
 G9V  H5   H  HNR5  0   0.415  -3.2796  -4.3883  -0.8663
 G9V  H6   H  HCR5  0   0.254   0.5060  -2.5858  -1.0309
 G9V  H7   H  HCH3  0   0.262   2.6742   4.3955  -1.2024
 G9V  H8   H  HCH3  0   0.272   1.3339   5.5359  -1.0512
 G9V  H9   H  HCH3  0   0.263   2.1930   4.9914   0.3968
 G9V  H10  H  H     0   0.247  -7.6432   0.9661   0.8737
 G9V  H11  H  H     0   0.239  -7.8903   3.3781   0.8321
 G9V  H12  H  H     0   0.235  -6.2233   3.5589   0.0640
 G9V  H13  H  HCH2  0   0.210   5.6977  -2.7553   0.3910
 G9V  H14  H  HCH2  0   0.245   7.3655  -2.2310   0.6823
 G9V  H15  H  HCH2  0   0.269  -5.5903  -0.5369   1.6357
 G9V  H16  H  HCH2  0   0.268  -4.5895   0.8839   1.8687
 G9V  H17  H  HCR6  0   0.289  -2.5775   1.0893   1.0287
 G9V  H18  H  HCR5  0   0.288  -0.9215  -4.8034  -1.5677
 G9V  H19  H  HCH2  0   0.269   5.7113  -1.0604   2.1632
 G9V  H20  H  HCH2  0   0.253   6.6197   0.0589   1.1472
 G9V  H21  H  HCR5  0   0.291  -0.9110   4.5300  -1.0976
 G9V  H22  H  HCH2  0   0.253  -5.9244   0.1133  -0.7662
 G9V  H23  H  HCH2  0   0.243  -4.9460   1.5557  -0.5083
 G9V  H24  H  HCH2  0   0.207   4.6062  -1.8762  -1.6225
 G9V  H25  H  HCH2  0   0.247   5.5633  -0.7806  -2.6330
 G9V  O15  O  O     0  -0.515  -5.0119  -2.4349   0.2254
 G9V  H3   H  HCH2  0   0.278   3.8313   0.3856  -1.2774

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
 G9V  C19  N20  aromatic  1.353  0.020  1.353
 G9V  C19  C18  aromatic  1.376  0.020  1.376
 G9V  N20  C16  aromatic  1.361  0.020  1.361
 G9V  C18  C17  aromatic  1.419  0.020  1.419
 G9V  C16  C17  aromatic  1.391  0.020  1.391
 G9V  C16  C14  single    1.427  0.020  1.427
 G9V  C17  C11  single    1.432  0.020  1.432
 G9V  C3   N4   aromatic  1.304  0.020  1.304
 G9V  C3   N2   aromatic  1.353  0.020  1.353
 G9V  N4   C5   aromatic  1.371  0.020  1.371
 G9V  O15  C14  double    1.230  0.020  1.230
 G9V  C14  N13  single    1.383  0.020  1.383
 G9V  N2   C1   single    1.443  0.020  1.443
 G9V  N2   C6   aromatic  1.369  0.020  1.369
 G9V  C5   C6   aromatic  1.405  0.020  1.405
 G9V  C5   C10  aromatic  1.404  0.020  1.404
 G9V  C11  C10  single    1.469  0.020  1.469
 G9V  C11  C12  double    1.358  0.020  1.358
 G9V  C6   C7   aromatic  1.387  0.020  1.387
 G9V  C10  C9   aromatic  1.388  0.020  1.388
 G9V  N13  C12  single    1.371  0.020  1.371
 G9V  N13  C22  single    1.460  0.020  1.460
 G9V  C7   C8   aromatic  1.387  0.020  1.387
 G9V  C9   C8   aromatic  1.404  0.020  1.404
 G9V  C8   C26  single    1.496  0.020  1.496
 G9V  C22  C23  single    1.528  0.020  1.528
 G9V  C23  C24  single    1.495  0.020  1.495
 G9V  O27  C26  double    1.225  0.020  1.225
 G9V  C26  N28  single    1.350  0.020  1.350
 G9V  C24  C25  double    1.328  0.020  1.328
 G9V  N28  C29  single    1.455  0.020  1.455
 G9V  N28  C33  single    1.454  0.020  1.454
 G9V  C29  C30  single    1.522  0.020  1.522
 G9V  C33  C32  single    1.518  0.020  1.518
 G9V  C30  O31  single    1.408  0.020  1.408
 G9V  C32  O31  single    1.411  0.020  1.411
 G9V  C7   H1   single    0.930  0.020  1.080
 G9V  C9   H2   single    0.930  0.020  1.080
 G9V  C29  H3   single    0.970  0.020  1.090
 G9V  C29  H4   single    0.970  0.020  1.090
 G9V  N20  H5   single    0.860  0.020  1.020
 G9V  C18  H6   single    0.930  0.020  1.080
 G9V  C1   H7   single    0.970  0.020  1.090
 G9V  C1   H8   single    0.970  0.020  1.090
 G9V  C1   H9   single    0.970  0.020  1.090
 G9V  C24  H10  single    0.930  0.020  1.080
 G9V  C25  H11  single    0.930  0.020  1.080
 G9V  C25  H12  single    0.930  0.020  1.080
 G9V  C32  H13  single    0.970  0.020  1.090
 G9V  C32  H14  single    0.970  0.020  1.090
 G9V  C22  H15  single    0.970  0.020  1.090
 G9V  C22  H16  single    0.970  0.020  1.090
 G9V  C12  H17  single    0.930  0.020  1.080
 G9V  C19  H18  single    0.930  0.020  1.080
 G9V  C33  H19  single    0.970  0.020  1.090
 G9V  C33  H20  single    0.970  0.020  1.090
 G9V  C3   H21  single    0.930  0.020  1.080
 G9V  C23  H22  single    0.970  0.020  1.090
 G9V  C23  H23  single    0.970  0.020  1.090
 G9V  C30  H24  single    0.970  0.020  1.090
 G9V  C30  H25  single    0.970  0.020  1.090

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
 G9V  H1   C7   C8   121.86  3.000
 G9V  H1   C7   C6   121.82  3.000
 G9V  C8   C7   C6   116.31  3.000
 G9V  H2   C9   C8   118.37  3.000
 G9V  H2   C9   C10  118.93  3.000
 G9V  C8   C9   C10  122.70  3.000
 G9V  C3   N2   C1   127.22  3.000
 G9V  C1   N2   C6   126.44  3.000
 G9V  C3   N2   C6   106.34  3.000
 G9V  C5   C10  C11  122.20  3.000
 G9V  C11  C10  C9   121.35  3.000
 G9V  C5   C10  C9   116.45  3.000
 G9V  C5   C6   N2   105.22  3.000
 G9V  C5   C6   C7   123.26  3.000
 G9V  N2   C6   C7   131.52  3.000
 G9V  H4   C29  H3   107.95  3.000
 G9V  H4   C29  C30  110.19  3.000
 G9V  H3   C29  C30  108.70  3.000
 G9V  H4   C29  N28  109.31  3.000
 G9V  H3   C29  N28  111.05  3.000
 G9V  C30  C29  N28  109.63  3.000
 G9V  H5   N20  C19  125.60  3.000
 G9V  H5   N20  C16  125.36  3.000
 G9V  C19  N20  C16  109.04  3.000
 G9V  H6   C18  C19  125.58  3.000
 G9V  H6   C18  C17  127.78  3.000
 G9V  C19  C18  C17  106.63  3.000
 G9V  C12  C11  C17  116.18  3.000
 G9V  C12  C11  C10  121.06  3.000
 G9V  C17  C11  C10  122.76  3.000
 G9V  H9   C1   H8   108.88  3.000
 G9V  H9   C1   H7   109.05  3.000
 G9V  H8   C1   H7   108.62  3.000
 G9V  H9   C1   N2   110.86  3.000
 G9V  H8   C1   N2   109.10  3.000
 G9V  H7   C1   N2   110.28  3.000
 G9V  C26  C8   C9   117.88  3.000
 G9V  C26  C8   C7   120.66  3.000
 G9V  C9   C8   C7   121.14  3.000
 G9V  C14  C16  C17  125.21  3.000
 G9V  C14  C16  N20  126.38  3.000
 G9V  C17  C16  N20  108.36  3.000
 G9V  N4   C5   C6   109.76  3.000
 G9V  C6   C5   C10  120.12  3.000
 G9V  N4   C5   C10  130.12  3.000
 G9V  C14  N13  C12  123.73  3.000
 G9V  C12  N13  C22  117.92  3.000
 G9V  C14  N13  C22  118.25  3.000
 G9V  H10  C24  C23  116.15  3.000
 G9V  H10  C24  C25  119.18  3.000
 G9V  C23  C24  C25  124.67  3.000
 G9V  H12  C25  H11  116.73  3.000
 G9V  H12  C25  C24  121.67  3.000
 G9V  H11  C25  C24  121.60  3.000
 G9V  H14  C32  H13  108.07  3.000
 G9V  H14  C32  C33  109.94  3.000
 G9V  H13  C32  C33  109.47  3.000
 G9V  H14  C32  O31  107.45  3.000
 G9V  H13  C32  O31  110.69  3.000
 G9V  C33  C32  O31  111.15  3.000
 G9V  C16  C17  C11  118.47  3.000
 G9V  C11  C17  C18  134.90  3.000
 G9V  C16  C17  C18  106.60  3.000
 G9V  H16  C22  H15  107.23  3.000
 G9V  H16  C22  C23  110.04  3.000
 G9V  H15  C22  C23  110.73  3.000
 G9V  H16  C22  N13  107.82  3.000
 G9V  H15  C22  N13  108.79  3.000
 G9V  C23  C22  N13  112.07  3.000
 G9V  C30  O31  C32  111.33  3.000
 G9V  H17  C12  N13  114.58  3.000
 G9V  H17  C12  C11  121.42  3.000
 G9V  N13  C12  C11  124.00  3.000
 G9V  H18  C19  C18  129.70  3.000
 G9V  H18  C19  N20  120.93  3.000
 G9V  C18  C19  N20  109.37  3.000
 G9V  N13  C14  O15  122.36  3.000
 G9V  N13  C14  C16  112.39  3.000
 G9V  O15  C14  C16  125.25  3.000
 G9V  C26  N28  C33  120.60  3.000
 G9V  C33  N28  C29  112.40  3.000
 G9V  C26  N28  C29  125.77  3.000
 G9V  H20  C33  H19  107.89  3.000
 G9V  H20  C33  N28  108.32  3.000
 G9V  H19  C33  N28  110.19  3.000
 G9V  H20  C33  C32  109.78  3.000
 G9V  H19  C33  C32  110.28  3.000
 G9V  N28  C33  C32  110.32  3.000
 G9V  H21  C3   N4   125.09  3.000
 G9V  H21  C3   N2   120.97  3.000
 G9V  N4   C3   N2   113.94  3.000
 G9V  H23  C23  H22  107.38  3.000
 G9V  H23  C23  C22  109.58  3.000
 G9V  H22  C23  C22  108.82  3.000
 G9V  H23  C23  C24  110.30  3.000
 G9V  H22  C23  C24  109.77  3.000
 G9V  C22  C23  C24  110.91  3.000
 G9V  O27  C26  N28  122.80  3.000
 G9V  N28  C26  C8   117.91  3.000
 G9V  O27  C26  C8   119.25  3.000
 G9V  H25  C30  H24  107.94  3.000
 G9V  H25  C30  O31  107.51  3.000
 G9V  H24  C30  O31  110.62  3.000
 G9V  H25  C30  C29  109.47  3.000
 G9V  H24  C30  C29  109.05  3.000
 G9V  O31  C30  C29  112.14  3.000
 G9V  C3   N4   C5   104.74  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
 G9V  CONST_01  C3   N2   C6   C7    180.00   0.0  0
 G9V  CONST_02  N4   C5   C6   C7    180.00   0.0  0
 G9V  CONST_03  C10  C5   C6   C7      0.00   0.0  0
 G9V  CONST_04  C10  C9   C8   C7      0.00   0.0  0
 G9V  CONST_05  N4   C5   C10  C9    180.00   0.0  0
 G9V  CONST_06  C6   C5   C10  C9      0.00   0.0  0
 G9V  CONST_07  C6   C7   C8   C9      0.00   0.0  0
 G9V  CONST_08  C5   N4   C3   N2      0.00   0.0  0
 G9V  CONST_09  N4   C5   C6   N2      0.00   0.0  0
 G9V  CONST_10  C10  C5   C6   N2    180.00   0.0  0
 G9V  CONST_11  C8   C7   C6   N2    180.00   0.0  0
 G9V  CONST_12  C3   N4   C5   C10   180.00   0.0  0
 G9V  CONST_13  N4   C3   N2   C6      0.00   0.0  0
 G9V  CONST_14  C3   N4   C5   C6      0.00   0.0  0
 G9V  CONST_15  C17  C18  C19  N20     0.00   0.0  0
 G9V  CONST_16  C18  C17  C16  N20     0.00   0.0  0
 G9V  CONST_17  C16  N20  C19  C18     0.00   0.0  0
 G9V  CONST_18  C5   C6   C7   C8      0.00   0.0  0
 G9V  CONST_19  C5   C10  C9   C8      0.00   0.0  0
 G9V  CONST_20  C19  C18  C17  C16     0.00   0.0  0
 G9V  CONST_21  C3   N2   C6   C5      0.00   0.0  0
 G9V  CONST_22  C19  N20  C16  C17     0.00   0.0  0
 G9V  CONST_23  C11  C10  C5   C6    180.00   0.0  0
 G9V  CONST_24  N4   C5   C10  C11     0.00   0.0  0
 G9V  CONST_25  C8   C9   C10  C11   180.00   0.0  0
 G9V  CONST_26  C12  N13  C14  C16     0.00   0.0  0
 G9V  CONST_27  C1   N2   C6   C7      0.00   0.0  0
 G9V  CONST_28  C26  C8   C9   C10   180.00   0.0  0
 G9V  CONST_29  C26  C8   C7   C6    180.00   0.0  0
 G9V  CONST_30  N4   C3   N2   C1    180.00   0.0  0
 G9V  CONST_31  C5   C6   N2   C1    180.00   0.0  0
 G9V  CONST_33  C33  N28  C26  C8    180.00   0.0  0
 G9V  CONST_34  C22  N13  C14  C16   180.00   0.0  0
 G9V  CONST_35  C12  N13  C14  O15   180.00   0.0  0
 G9V  CONST_36  H2   C9   C8   C7    180.00   0.0  0
 G9V  CONST_37  H1   C7   C8   C9    180.00   0.0  0
 G9V  CONST_38  H21  C3   N2   C6    180.00   0.0  0
 G9V  CONST_39  H6   C18  C19  N20   180.00   0.0  0
 G9V  CONST_40  H5   N20  C19  C18   180.00   0.0  0
 G9V  CONST_41  H18  C19  N20  C16   180.00   0.0  0
 G9V  CONST_43  O27  C26  N28  C33     0.00   0.0  0
 G9V  CONST_44  C22  N13  C14  O15     0.00   0.0  0
 G9V  Var_01    C17  C11  C10  C9    -41.56  30.0  2
 G9V  Var_02    C32  C33  N28  C29   -53.69  30.0  1
 G9V  Var_03    N28  C29  C30  O31   -54.73  30.0  1
 G9V  Var_04    N28  C33  C32  O31    55.61  30.0  1
 G9V  Var_05    C30  C29  N28  C33    52.77  30.0  1
 G9V  Var_06    N28  C26  C8   C7    -50.67  30.0  2
 G9V  Var_07    H24  C30  O31  C32   -63.69  30.0  1
 G9V  Var_08    C23  C22  N13  C12    90.01  30.0  3
 G9V  Var_09    H7   C1   N2   C6     53.66  30.0  2
 G9V  Var_10    C24  C23  C22  N13   179.00  30.0  3
 G9V  Var_11    C22  C23  C24  C25   114.23  30.0  2
 G9V  Var_12    H11  C25  C24  C23  -179.36   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
 G9V  plan-1  C10  0.020
 G9V  plan-1  N20  0.020
 G9V  plan-1  C18  0.020
 G9V  plan-1  C11  0.020
 G9V  plan-1  C16  0.020
 G9V  plan-1  N13  0.020
 G9V  plan-1  C17  0.020
 G9V  plan-1  C22  0.020
 G9V  plan-1  C12  0.020
 G9V  plan-1  C19  0.020
 G9V  plan-1  C14  0.020
 G9V  plan-1  H5   0.020
 G9V  plan-1  H6   0.020
 G9V  plan-1  H17  0.020
 G9V  plan-1  H18  0.020
 G9V  plan-1  O15  0.020
 G9V  plan-2  C7   0.020
 G9V  plan-2  C9   0.020
 G9V  plan-2  N2   0.020
 G9V  plan-2  C10  0.020
 G9V  plan-2  C6   0.020
 G9V  plan-2  C11  0.020
 G9V  plan-2  C1   0.020
 G9V  plan-2  C8   0.020
 G9V  plan-2  C5   0.020
 G9V  plan-2  C3   0.020
 G9V  plan-2  C26  0.020
 G9V  plan-2  N4   0.020
 G9V  plan-2  H1   0.020
 G9V  plan-2  H2   0.020
 G9V  plan-2  H21  0.020
 G9V  plan-3  C29  0.020
 G9V  plan-3  C8   0.020
 G9V  plan-3  N28  0.020
 G9V  plan-3  C33  0.020
 G9V  plan-3  C26  0.020
 G9V  plan-3  O27  0.020
 G9V  plan-4  C24  0.020
 G9V  plan-4  C25  0.020
 G9V  plan-4  C23  0.020
 G9V  plan-4  H10  0.020
 G9V  plan-4  H11  0.020
 G9V  plan-4  H12  0.020

