# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 13:08:45 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: 4-[(3S)-1-azabicyclo[2.2.2]oct-3-ylamino]-3-(1H-benzimidazol-2-yl)-6-chloroquinolin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc2NC(=O)C(=C(N[C@@H]3CN4CCC3CC4)c2c1)c5[nH]c6ccccc6n5
#
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
 12C  12C  4-[(3S)-1-azabicyclo[2.2.2]oct-3-ylamino]-3-(1H-benzimidazol-2-yl)-6-chloroquinolin-2(1H)-one  ligand  52  30  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_12C
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
 12C  C1    C   CR66  0  -0.011  -1.9128   1.0159   0.0214
 12C  C2    C   CR16  0  -0.262  -2.9411   0.1316  -0.3381
 12C  C3    C   CR6   0  -0.052  -4.2545   0.5334  -0.3021
 12C  CL    CL  CL    0  -0.123  -5.5009  -0.5805  -0.7552
 12C  C4    C   CR16  0  -0.213  -4.5985   1.8300   0.0784
 12C  C5    C   CR16  0  -0.322  -3.6013   2.7312   0.3640
 12C  C6    C   CR66  0   0.381  -2.2582   2.3442   0.3020
 12C  N1    N   NR16  0  -0.761  -1.2762   3.2719   0.4807
 12C  C7    C   CR6   0   0.525   0.0587   3.0499   0.2817
 12C  O1    O   OC    0  -0.515   0.8327   4.0084   0.3571
 12C  C8    C   CR6   0  -0.403   0.4540   1.6809   0.0503
 12C  C9    C   CR5   0   0.586   1.8731   1.3902  -0.0522
 12C  C10   C   CR6   0   0.469  -0.5028   0.6475   0.0259
 12C  N2    N   NH1   0  -0.706  -0.1173  -0.6305  -0.0306
 12C  C11   C   CH1   0  -0.132  -0.7575  -1.8181   0.5176
 12C  N3    N   NR15  0  -0.725   2.8477   2.3364   0.0109
 12C  C12   C   CR56  0   0.307   4.0555   1.7119  -0.1276
 12C  C13   C   CR56  0   0.203   3.7449   0.3501  -0.2744
 12C  N4    N   N     0  -0.599   2.3870   0.1846  -0.2262
 12C  C14   C   CR16  0  -0.318   5.3629   2.1825  -0.1400
 12C  C15   C   CR16  0  -0.281   6.3638   1.2390  -0.3057
 12C  C16   C   CR16  0  -0.271   6.0687  -0.1247  -0.4526
 12C  C17   C   CR16  0  -0.338   4.7639  -0.5865  -0.4383
 12C  C18   C   CH2   0  -0.338   0.1512  -2.4583   1.6114
 12C  N5    N   NT    0  -0.388   0.6009  -3.7873   1.2422
 12C  C19   C   CH2   0  -0.340   1.2995  -3.7285  -0.0371
 12C  C20   C   CH2   0  -0.470   0.3504  -3.2876  -1.1773
 12C  C21   C   CH2   0  -0.329  -0.5513  -4.6756   1.1312
 12C  C22   C   CH2   0  -0.459  -1.5943  -4.1198   0.1321
 12C  C23   C   CH1   0  -0.276  -0.9891  -2.8935  -0.5524
 12C  H2    H   HCR6  0   0.301  -2.7099  -0.8605  -0.6912
 12C  H4    H   HCR6  0   0.293  -5.6347   2.1355   0.1222
 12C  H5    H   HCR6  0   0.292  -3.8535   3.7526   0.6178
 12C  HN1   H   HNR6  0   0.417  -1.5454   4.2283   0.6665
 12C  HN2   H   HNH1  0   0.440   0.9000  -0.7203  -0.1397
 12C  H11   H   HCH1  0   0.283  -1.7038  -1.5363   0.9779
 12C  HN3   H   HNR5  0   0.423   2.6522   3.3200   0.1351
 12C  H14   H   HCR6  0   0.264   5.5906   3.2342  -0.0256
 12C  H15   H   HCR6  0   0.254   7.3972   1.5600  -0.3213
 12C  H16   H   HCR6  0   0.252   6.8810  -0.8284  -0.5788
 12C  H17   H   HCR6  0   0.254   4.5395  -1.6398  -0.5502
 12C  H181  H   HCH2  0   0.249   1.0217  -1.8240   1.8018
 12C  H182  H   HCH2  0   0.257  -0.3981  -2.5228   2.5531
 12C  H191  H   HCH2  0   0.239   2.1358  -3.0311   0.0654
 12C  H192  H   HCH2  0   0.245   1.7314  -4.7097  -0.2447
 12C  H201  H   HCH2  0   0.239   0.7739  -2.4587  -1.7484
 12C  H202  H   HCH2  0   0.246   0.1875  -4.0993  -1.8892
 12C  H211  H   HCH2  0   0.240  -0.1934  -5.6588   0.8176
 12C  H212  H   HCH2  0   0.241  -0.9899  -4.8014   2.1233
 12C  H221  H   HCH2  0   0.237  -2.5213  -3.8464   0.6429
 12C  H222  H   HCH2  0   0.243  -1.8549  -4.8674  -0.6195
 12C  H23   H   HCH1  0   0.253  -1.6643  -2.5207  -1.3272

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
 12C  C1   C2    aromatic  1.403  0.020  1.403
 12C  C1   C6    aromatic  1.401  0.020  1.401
 12C  C1   C10   aromatic  1.457  0.020  1.457
 12C  C2   C3    aromatic  1.374  0.020  1.374
 12C  C2   H2    single    0.930  0.020  1.080
 12C  C3   CL    single    1.732  0.020  1.732
 12C  C3   C4    aromatic  1.394  0.020  1.394
 12C  C4   C5    aromatic  1.374  0.020  1.374
 12C  C4   H4    single    0.930  0.020  1.080
 12C  C5   C6    aromatic  1.399  0.020  1.399
 12C  C5   H5    single    0.930  0.020  1.080
 12C  C6   N1    aromatic  1.363  0.020  1.363
 12C  N1   C7    aromatic  1.368  0.020  1.368
 12C  N1   HN1   single    0.860  0.020  1.020
 12C  C7   O1    double    1.234  0.020  1.234
 12C  C7   C8    aromatic  1.444  0.020  1.444
 12C  C8   C9    single    1.452  0.020  1.452
 12C  C8   C10   aromatic  1.409  0.020  1.409
 12C  C9   N3    aromatic  1.360  0.020  1.360
 12C  C9   N4    aromatic  1.322  0.020  1.322
 12C  C10  N2    single    1.336  0.020  1.336
 12C  N2   C11   single    1.456  0.020  1.456
 12C  N2   HN2   single    0.890  0.020  1.040
 12C  C11  C18   single    1.559  0.020  1.559
 12C  C11  C23   single    1.535  0.020  1.535
 12C  C11  H11   single    0.970  0.020  1.090
 12C  N3   C12   aromatic  1.367  0.020  1.367
 12C  N3   HN3   single    0.860  0.020  1.020
 12C  C12  C13   aromatic  1.404  0.020  1.404
 12C  C12  C14   aromatic  1.390  0.020  1.390
 12C  C13  N4    aromatic  1.369  0.020  1.369
 12C  C13  C17   aromatic  1.394  0.020  1.394
 12C  C14  C15   aromatic  1.385  0.020  1.385
 12C  C14  H14   single    0.930  0.020  1.080
 12C  C15  C16   aromatic  1.403  0.020  1.403
 12C  C15  H15   single    0.930  0.020  1.080
 12C  C16  C17   aromatic  1.384  0.020  1.384
 12C  C16  H16   single    0.930  0.020  1.080
 12C  C17  H17   single    0.930  0.020  1.080
 12C  C18  N5    single    1.451  0.020  1.451
 12C  C18  H181  single    0.970  0.020  1.090
 12C  C18  H182  single    0.970  0.020  1.090
 12C  N5   C19   single    1.459  0.020  1.459
 12C  N5   C21   single    1.459  0.020  1.459
 12C  C19  C20   single    1.548  0.020  1.548
 12C  C19  H191  single    0.970  0.020  1.090
 12C  C19  H192  single    0.970  0.020  1.090
 12C  C20  C23   single    1.530  0.020  1.530
 12C  C20  H201  single    0.970  0.020  1.090
 12C  C20  H202  single    0.970  0.020  1.090
 12C  C21  C22   single    1.548  0.020  1.548
 12C  C21  H211  single    0.970  0.020  1.090
 12C  C21  H212  single    0.970  0.020  1.090
 12C  C22  C23   single    1.529  0.020  1.529
 12C  C22  H221  single    0.970  0.020  1.090
 12C  C22  H222  single    0.970  0.020  1.090
 12C  C23  H23   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
 12C  C10   C1   C6    118.53  3.000
 12C  C10   C1   C2    123.41  3.000
 12C  C6    C1   C2    117.92  3.000
 12C  H2    C2   C3    118.86  3.000
 12C  H2    C2   C1    120.44  3.000
 12C  C3    C2   C1    120.64  3.000
 12C  C4    C3   CL    119.47  3.000
 12C  C4    C3   C2    120.99  3.000
 12C  CL    C3   C2    119.54  3.000
 12C  H4    C4   C5    120.12  3.000
 12C  H4    C4   C3    120.68  3.000
 12C  C5    C4   C3    119.18  3.000
 12C  H5    C5   C6    119.67  3.000
 12C  H5    C5   C4    119.91  3.000
 12C  C6    C5   C4    120.40  3.000
 12C  N1    C6   C5    119.85  3.000
 12C  N1    C6   C1    119.61  3.000
 12C  C5    C6   C1    120.52  3.000
 12C  HN1   N1   C7    116.12  3.000
 12C  HN1   N1   C6    118.45  3.000
 12C  C7    N1   C6    125.01  3.000
 12C  C8    C7   O1    125.06  3.000
 12C  C8    C7   N1    116.39  3.000
 12C  O1    C7   N1    118.50  3.000
 12C  C10   C8   C9    121.04  3.000
 12C  C10   C8   C7    120.83  3.000
 12C  C9    C8   C7    117.96  3.000
 12C  N4    C9   N3    111.23  3.000
 12C  N4    C9   C8    124.87  3.000
 12C  N3    C9   C8    123.90  3.000
 12C  N2    C10  C8    120.43  3.000
 12C  N2    C10  C1    121.39  3.000
 12C  C8    C10  C1    118.15  3.000
 12C  HN2   N2   C11   113.83  3.000
 12C  HN2   N2   C10   111.96  3.000
 12C  C11   N2   C10   129.59  3.000
 12C  H11   C11  C23   110.17  3.000
 12C  H11   C11  C18   108.42  3.000
 12C  C23   C11  C18   106.82  3.000
 12C  H11   C11  N2    109.27  3.000
 12C  C23   C11  N2    112.04  3.000
 12C  C18   C11  N2    110.04  3.000
 12C  HN3   N3   C12   128.91  3.000
 12C  HN3   N3   C9    122.99  3.000
 12C  C12   N3   C9    108.10  3.000
 12C  C14   C12  C13   122.38  3.000
 12C  C14   C12  N3    132.66  3.000
 12C  C13   C12  N3    104.96  3.000
 12C  C17   C13  N4    130.40  3.000
 12C  C17   C13  C12   120.15  3.000
 12C  N4    C13  C12   109.45  3.000
 12C  C13   N4   C9    106.25  3.000
 12C  H14   C14  C15   121.50  3.000
 12C  H14   C14  C12   121.74  3.000
 12C  C15   C14  C12   116.75  3.000
 12C  H15   C15  C16   119.19  3.000
 12C  H15   C15  C14   119.31  3.000
 12C  C16   C15  C14   121.50  3.000
 12C  H16   C16  C17   119.46  3.000
 12C  H16   C16  C15   119.10  3.000
 12C  C17   C16  C15   121.44  3.000
 12C  H17   C17  C16   121.25  3.000
 12C  H17   C17  C13   120.96  3.000
 12C  C16   C17  C13   117.79  3.000
 12C  H182  C18  H181  106.53  3.000
 12C  H182  C18  N5    108.74  3.000
 12C  H181  C18  N5    109.20  3.000
 12C  H182  C18  C11   109.63  3.000
 12C  H181  C18  C11   110.35  3.000
 12C  N5    C18  C11   112.22  3.000
 12C  C21   N5   C19   109.63  3.000
 12C  C21   N5   C18   109.41  3.000
 12C  C19   N5   C18   109.55  3.000
 12C  H192  C19  H191  106.76  3.000
 12C  H192  C19  C20   111.00  3.000
 12C  H191  C19  C20   110.88  3.000
 12C  H192  C19  N5    108.66  3.000
 12C  H191  C19  N5    108.04  3.000
 12C  C20   C19  N5    111.34  3.000
 12C  H202  C20  H201  106.34  3.000
 12C  H202  C20  C23   109.10  3.000
 12C  H201  C20  C23   110.95  3.000
 12C  H202  C20  C19   111.10  3.000
 12C  H201  C20  C19   111.33  3.000
 12C  C23   C20  C19   108.02  3.000
 12C  H212  C21  H211  106.79  3.000
 12C  H212  C21  C22   110.93  3.000
 12C  H211  C21  C22   111.02  3.000
 12C  H212  C21  N5    108.55  3.000
 12C  H211  C21  N5    108.12  3.000
 12C  C22   C21  N5    111.26  3.000
 12C  H222  C22  H221  106.89  3.000
 12C  H222  C22  C23   109.60  3.000
 12C  H221  C22  C23   110.13  3.000
 12C  H222  C22  C21   111.07  3.000
 12C  H221  C22  C21   111.08  3.000
 12C  C23   C22  C21   108.08  3.000
 12C  H23   C23  C22   110.26  3.000
 12C  H23   C23  C20   109.82  3.000
 12C  C22   C23  C20   108.83  3.000
 12C  H23   C23  C11   110.39  3.000
 12C  C22   C23  C11   108.03  3.000
 12C  C20   C23  C11   109.46  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
 12C  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 12C  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 12C  CONST_03  C7   N1   C6   C1     0.00   0.0  0
 12C  CONST_04  C7   C8   C10  C1     0.00   0.0  0
 12C  CONST_05  C9   C8   C10  C1   180.00   0.0  0
 12C  CONST_06  C5   C6   C1   C2     0.00   0.0  0
 12C  CONST_07  N1   C6   C1   C2   180.00   0.0  0
 12C  CONST_09  C5   C4   C3   C2     0.00   0.0  0
 12C  CONST_10  C6   C1   C2   C3     0.00   0.0  0
 12C  CONST_11  C10  C1   C2   C3   180.00   0.0  0
 12C  CONST_12  C6   C5   C4   C3     0.00   0.0  0
 12C  CONST_13  N1   C6   C5   C4   180.00   0.0  0
 12C  CONST_14  C10  C1   C6   C5   180.00   0.0  0
 12C  CONST_15  C7   N1   C6   C5   180.00   0.0  0
 12C  CONST_16  C8   C10  C1   C6     0.00   0.0  0
 12C  CONST_17  C8   C7   N1   C6     0.00   0.0  0
 12C  CONST_18  C10  C1   C6   N1     0.00   0.0  0
 12C  CONST_19  C9   C8   C7   N1   180.00   0.0  0
 12C  CONST_20  C10  C8   C7   N1     0.00   0.0  0
 12C  CONST_21  N3   C9   C8   C7     0.00   0.0  0
 12C  CONST_22  N4   C9   C8   C7   180.00   0.0  0
 12C  CONST_23  C12  N3   C9   C8   180.00   0.0  0
 12C  CONST_24  C13  N4   C9   C8   180.00   0.0  0
 12C  CONST_25  C13  C12  N3   C9     0.00   0.0  0
 12C  CONST_26  C14  C12  N3   C9   180.00   0.0  0
 12C  CONST_27  C12  C13  N4   C9     0.00   0.0  0
 12C  CONST_28  C17  C13  N4   C9   180.00   0.0  0
 12C  CONST_29  N3   C9   C8   C10  180.00   0.0  0
 12C  CONST_30  N4   C9   C8   C10    0.00   0.0  0
 12C  CONST_31  C13  N4   C9   N3     0.00   0.0  0
 12C  CONST_32  N4   C13  C12  N3     0.00   0.0  0
 12C  CONST_33  C17  C13  C12  N3   180.00   0.0  0
 12C  CONST_34  C15  C14  C12  N3   180.00   0.0  0
 12C  CONST_35  N4   C9   N3   C12    0.00   0.0  0
 12C  CONST_36  C16  C17  C13  C12    0.00   0.0  0
 12C  CONST_37  C16  C15  C14  C12    0.00   0.0  0
 12C  CONST_38  C15  C14  C12  C13    0.00   0.0  0
 12C  CONST_39  C15  C16  C17  C13    0.00   0.0  0
 12C  CONST_40  C14  C12  C13  N4   180.00   0.0  0
 12C  CONST_41  C16  C17  C13  N4   180.00   0.0  0
 12C  CONST_42  C17  C13  C12  C14    0.00   0.0  0
 12C  CONST_43  C17  C16  C15  C14    0.00   0.0  0
 12C  CONST_44  CL   C3   C2   C1   180.00   0.0  0
 12C  CONST_45  N2   C10  C1   C2     0.00   0.0  0
 12C  CONST_46  C5   C4   C3   CL   180.00   0.0  0
 12C  CONST_47  N2   C10  C1   C6   180.00   0.0  0
 12C  CONST_48  O1   C7   N1   C6   180.00   0.0  0
 12C  CONST_49  N2   C10  C8   C7   180.00   0.0  0
 12C  CONST_50  C9   C8   C7   O1     0.00   0.0  0
 12C  CONST_51  C10  C8   C7   O1   180.00   0.0  0
 12C  CONST_52  N2   C10  C8   C9     0.00   0.0  0
 12C  CONST_55  H5   C5   C6   C1   180.00   0.0  0
 12C  CONST_56  HN1  N1   C6   C1   180.00   0.0  0
 12C  CONST_57  H4   C4   C3   C2   180.00   0.0  0
 12C  CONST_58  H2   C2   C3   C4   180.00   0.0  0
 12C  CONST_59  HN3  N3   C9   C8     0.00   0.0  0
 12C  CONST_60  H14  C14  C12  N3     0.00   0.0  0
 12C  CONST_61  H17  C17  C13  C12  180.00   0.0  0
 12C  CONST_62  H15  C15  C14  C12  180.00   0.0  0
 12C  CONST_63  H16  C16  C17  C13  180.00   0.0  0
 12C  CONST_64  HN2  N2   C10  C1   180.00   0.0  0
 12C  Var_01    C19  N5   C18  C11   56.69  30.0  1
 12C  Var_02    C20  C19  N5   C18  -63.96  30.0  1
 12C  Var_03    C22  C21  N5   C18   55.79  30.0  3
 12C  Var_04    C23  C20  C19  N5     6.65  30.0  1
 12C  Var_05    C23  C22  C21  N5     7.09  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 12C  chir_01  C11  N2   C18  C23  positiv
 12C  chir_02  C23  C22  C20  C11  positiv

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
 12C  plan-1  C8   0.020
 12C  plan-1  C9   0.020
 12C  plan-1  N3   0.020
 12C  plan-1  C12  0.020
 12C  plan-1  C13  0.020
 12C  plan-1  N4   0.020
 12C  plan-1  C14  0.020
 12C  plan-1  C15  0.020
 12C  plan-1  C16  0.020
 12C  plan-1  C17  0.020
 12C  plan-1  HN3  0.020
 12C  plan-1  H14  0.020
 12C  plan-1  H15  0.020
 12C  plan-1  H16  0.020
 12C  plan-1  H17  0.020
 12C  plan-2  C1   0.020
 12C  plan-2  C2   0.020
 12C  plan-2  C3   0.020
 12C  plan-2  CL   0.020
 12C  plan-2  C4   0.020
 12C  plan-2  C5   0.020
 12C  plan-2  C6   0.020
 12C  plan-2  N1   0.020
 12C  plan-2  C7   0.020
 12C  plan-2  O1   0.020
 12C  plan-2  C8   0.020
 12C  plan-2  C9   0.020
 12C  plan-2  C10  0.020
 12C  plan-2  N2   0.020
 12C  plan-2  H2   0.020
 12C  plan-2  H4   0.020
 12C  plan-2  H5   0.020
 12C  plan-2  HN1  0.020
 12C  plan-3  C10  0.020
 12C  plan-3  N2   0.020
 12C  plan-3  C11  0.020
 12C  plan-3  HN2  0.020

