# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 05:33:31 2020
#   Inital geometry file: a 141 line input string
#   Ligand name: 1-[(3-carbamimidoylphenyl)methyl]-N-[(3,5-dichlorophenyl)methyl]-4-methyl-indole-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc2n(Cc3cccc(c3)C(N)=N)c(cc12)C(=O)NCc4cc(Cl)cc(Cl)c4
#
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
 CMB  CMB  1-[(3-carbamimidoylphenyl)methyl]-N-[(3,5-dichlorophenyl)methyl]-4-methyl-indole-2-carboxamide  ligand  54  32  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_CMB
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
 CMB  C1    C   CR16  0  -0.261  -4.0539   3.2829  -1.1845
 CMB  C2    C   CR16  0  -0.321  -3.6935   2.2358  -0.3638
 CMB  C3    C   CR56  0   0.379  -2.3262   2.0501  -0.1418
 CMB  C4    C   CR56  0   0.053  -1.3558   2.8965  -0.7132
 CMB  C5    C   CR6   0   0.032  -1.7407   3.9577  -1.5525
 CMB  C6    C   CR16  0  -0.335  -3.0940   4.1280  -1.7709
 CMB  N7    N   NR5   0  -0.580  -1.6868   1.1127   0.6206
 CMB  C8    C   CR5   0   0.251  -0.3327   1.3508   0.5543
 CMB  C9    C   CR15  0  -0.451  -0.0935   2.4335  -0.2514
 CMB  C10   C   CH3   0  -0.739  -0.7120   4.8569  -2.1646
 CMB  C11   C   C     0   0.518   0.6779   0.4798   1.1907
 CMB  N12   N   NH1   0  -0.647   1.8047   1.1131   1.5608
 CMB  C13   C   CH2   0  -0.351   2.9212   0.3938   2.1204
 CMB  C14   C   CR6   0   0.097   3.6112  -0.5079   1.1263
 CMB  C17   C   CH2   0  -0.399  -2.3958   0.1362   1.4218
 CMB  C18   C   CR6   0   0.127  -3.0434  -0.9437   0.5918
 CMB  C21   C   CR16  0  -0.281  -2.3301  -1.6130  -0.4006
 CMB  C22   C   CR16  0  -0.227  -2.9402  -2.6139  -1.1378
 CMB  C23   C   CR16  0  -0.308  -4.2645  -2.9584  -0.8985
 CMB  C24   C   CR6   0   0.065  -4.9897  -2.2966   0.0880
 CMB  C25   C   CR16  0  -0.347  -4.3635  -1.2946   0.8277
 CMB  C26   C   CR16  0  -0.261   4.0235  -1.7748   1.5163
 CMB  C27   C   CR6   0  -0.028   4.6960  -2.5820   0.6126
 CMB  C28   C   CR16  0  -0.190   4.9646  -2.1647  -0.6799
 CMB  C29   C   CR6   0  -0.029   4.5390  -0.8970  -1.0471
 CMB  C30   C   CR16  0  -0.237   3.8707  -0.0650  -0.1660
 CMB  C31   C   C     0   0.337  -6.4124  -2.6305   0.3796
 CMB  N32   N   N     0  -0.652  -6.8691  -2.3865   1.5476
 CMB  CL1   CL  CL    0  -0.114   5.2051  -4.1615   1.1039
 CMB  CL2   CL  CL    0  -0.115   4.8597  -0.3444  -2.6558
 CMB  O45   O   O     0  -0.471   0.5196  -0.7243   1.3416
 CMB  N53   N   NH2   0  -0.823  -7.0939  -3.2245  -0.6435
 CMB  HC1   H   HCR6  0   0.253  -5.1022   3.4608  -1.3866
 CMB  HC6   H   HCR6  0   0.243  -3.4303   4.9386  -2.4066
 CMB  HC9   H   HCR5  0   0.262   0.8773   2.8238  -0.5157
 CMB  H101  H   HCH3  0   0.244  -0.0113   4.2953  -2.7859
 CMB  H102  H   HCH3  0   0.249  -1.1740   5.6213  -2.7876
 CMB  H103  H   HCH3  0   0.244  -0.1205   5.3631  -1.3992
 CMB  H12   H   HNH1  0   0.417   1.8473   2.1179   1.5246
 CMB  H131  H   HCH2  0   0.290   3.6286   1.1387   2.4853
 CMB  H132  H   HCH2  0   0.268   2.6052  -0.1901   2.9874
 CMB  H171  H   HCH2  0   0.296  -1.7031  -0.3049   2.1334
 CMB  H172  H   HCH2  0   0.280  -3.1548   0.6556   2.0112
 CMB  H21   H   HCR6  0   0.257  -1.2975  -1.3544  -0.5951
 CMB  H22   H   HCR6  0   0.260  -2.3798  -3.1373  -1.9012
 CMB  H23   H   HCR6  0   0.259  -4.7129  -3.7569  -1.4758
 CMB  H251  H   HCR6  0   0.254  -4.9320  -0.7770   1.5907
 CMB  H26   H   HCR6  0   0.281   3.8187  -2.1316   2.5175
 CMB  H28   H   HCR6  0   0.301   5.4862  -2.8041  -1.3780
 CMB  H30   H   HCR6  0   0.277   3.5523   0.9192  -0.4835
 CMB  H32   H   H     0   0.324  -7.8548  -2.6259   1.6164
 CMB  H531  H   HNH2  0   0.395  -6.8080  -3.0279  -1.5884
 CMB  H532  H   HNH2  0   0.391  -8.0909  -3.3251  -0.5378
 CMB  HC2   H   HCR6  0   0.264  -4.4422   1.5906   0.0759

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
 CMB  C1   C2    aromatic  1.378  0.020  1.378
 CMB  C1   C6    aromatic  1.407  0.020  1.407
 CMB  C1   HC1   single    0.930  0.020  1.080
 CMB  C2   C3    aromatic  1.398  0.020  1.398
 CMB  C3   C4    aromatic  1.409  0.020  1.409
 CMB  C3   N7    aromatic  1.367  0.020  1.367
 CMB  C4   C5    aromatic  1.407  0.020  1.407
 CMB  C4   C9    aromatic  1.422  0.020  1.422
 CMB  C5   C6    aromatic  1.381  0.020  1.381
 CMB  C5   C10   single    1.497  0.020  1.497
 CMB  C6   HC6   single    0.930  0.020  1.080
 CMB  N7   C8    aromatic  1.377  0.020  1.377
 CMB  N7   C17   single    1.449  0.020  1.449
 CMB  C8   C9    aromatic  1.371  0.020  1.371
 CMB  C8   C11   single    1.478  0.020  1.478
 CMB  C9   HC9   single    0.930  0.020  1.080
 CMB  C10  H101  single    0.970  0.020  1.090
 CMB  C10  H102  single    0.970  0.020  1.090
 CMB  C10  H103  single    0.970  0.020  1.090
 CMB  C11  N12   single    1.344  0.020  1.344
 CMB  C11  O45   double    1.224  0.020  1.224
 CMB  N12  C13   single    1.441  0.020  1.441
 CMB  N12  H12   single    0.860  0.020  1.020
 CMB  C13  C14   single    1.509  0.020  1.509
 CMB  C13  H131  single    0.970  0.020  1.090
 CMB  C13  H132  single    0.970  0.020  1.090
 CMB  C14  C26   aromatic  1.388  0.020  1.388
 CMB  C14  C30   aromatic  1.391  0.020  1.391
 CMB  C17  C18   single    1.508  0.020  1.508
 CMB  C17  H171  single    0.970  0.020  1.090
 CMB  C17  H172  single    0.970  0.020  1.090
 CMB  C18  C21   aromatic  1.393  0.020  1.393
 CMB  C18  C25   aromatic  1.386  0.020  1.386
 CMB  C21  C22   aromatic  1.385  0.020  1.385
 CMB  C21  H21   single    0.930  0.020  1.080
 CMB  C22  C23   aromatic  1.389  0.020  1.389
 CMB  C22  H22   single    0.930  0.020  1.080
 CMB  C23  C24   aromatic  1.392  0.020  1.392
 CMB  C23  H23   single    0.930  0.020  1.080
 CMB  C24  C25   aromatic  1.394  0.020  1.394
 CMB  C24  C31   single    1.490  0.020  1.490
 CMB  C25  H251  single    0.930  0.020  1.080
 CMB  C26  C27   aromatic  1.386  0.020  1.386
 CMB  C26  H26   single    0.930  0.020  1.080
 CMB  C27  C28   aromatic  1.384  0.020  1.384
 CMB  C27  CL1   single    1.731  0.020  1.731
 CMB  C28  C29   aromatic  1.387  0.020  1.387
 CMB  C28  H28   single    0.930  0.020  1.080
 CMB  C29  C30   aromatic  1.384  0.020  1.384
 CMB  C29  CL2   single    1.731  0.020  1.731
 CMB  C30  H30   single    0.930  0.020  1.080
 CMB  C31  N32   double    1.278  0.020  1.278
 CMB  C31  N53   single    1.365  0.020  1.365
 CMB  N32  H32   single    0.890  0.020  1.040
 CMB  N53  H531  single    0.890  0.020  1.040
 CMB  N53  H532  single    0.890  0.020  1.040
 CMB  C2   HC2   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
 CMB  HC1   C1   C6    118.96  3.000
 CMB  HC1   C1   C2    119.29  3.000
 CMB  C6    C1   C2    121.74  3.000
 CMB  HC2   C2   C3    122.23  3.000
 CMB  HC2   C2   C1    120.94  3.000
 CMB  C3    C2   C1    116.83  3.000
 CMB  N7    C3   C4    108.42  3.000
 CMB  N7    C3   C2    129.59  3.000
 CMB  C4    C3   C2    121.98  3.000
 CMB  C9    C4   C5    133.04  3.000
 CMB  C9    C4   C3    106.51  3.000
 CMB  C5    C4   C3    120.45  3.000
 CMB  C10   C5   C6    122.31  3.000
 CMB  C10   C5   C4    120.60  3.000
 CMB  C6    C5   C4    117.09  3.000
 CMB  HC6   C6   C5    119.28  3.000
 CMB  HC6   C6   C1    118.82  3.000
 CMB  C5    C6   C1    121.90  3.000
 CMB  C17   N7   C8    128.67  3.000
 CMB  C17   N7   C3    122.80  3.000
 CMB  C8    N7   C3    108.34  3.000
 CMB  C11   C8   C9    126.82  3.000
 CMB  C11   C8   N7    123.36  3.000
 CMB  C9    C8   N7    109.67  3.000
 CMB  HC9   C9   C8    125.92  3.000
 CMB  HC9   C9   C4    126.97  3.000
 CMB  C8    C9   C4    107.05  3.000
 CMB  H103  C10  H102  107.79  3.000
 CMB  H103  C10  H101  106.84  3.000
 CMB  H102  C10  H101  107.92  3.000
 CMB  H103  C10  C5    111.35  3.000
 CMB  H102  C10  C5    111.34  3.000
 CMB  H101  C10  C5    111.39  3.000
 CMB  O45   C11  N12   122.54  3.000
 CMB  O45   C11  C8    122.98  3.000
 CMB  N12   C11  C8    114.45  3.000
 CMB  H12   N12  C13   118.65  3.000
 CMB  H12   N12  C11   119.73  3.000
 CMB  C13   N12  C11   121.40  3.000
 CMB  H132  C13  H131  106.70  3.000
 CMB  H132  C13  C14   109.62  3.000
 CMB  H131  C13  C14   109.40  3.000
 CMB  H132  C13  N12   110.55  3.000
 CMB  H131  C13  N12   106.95  3.000
 CMB  C14   C13  N12   113.36  3.000
 CMB  C30   C14  C26   119.75  3.000
 CMB  C30   C14  C13   120.48  3.000
 CMB  C26   C14  C13   119.74  3.000
 CMB  H172  C17  H171  106.42  3.000
 CMB  H172  C17  C18   109.82  3.000
 CMB  H171  C17  C18   110.09  3.000
 CMB  H172  C17  N7    108.54  3.000
 CMB  H171  C17  N7    108.89  3.000
 CMB  C18   C17  N7    112.86  3.000
 CMB  C25   C18  C21   119.15  3.000
 CMB  C25   C18  C17   119.77  3.000
 CMB  C21   C18  C17   121.07  3.000
 CMB  H21   C21  C22   119.83  3.000
 CMB  H21   C21  C18   120.11  3.000
 CMB  C22   C21  C18   120.05  3.000
 CMB  H22   C22  C23   119.69  3.000
 CMB  H22   C22  C21   119.81  3.000
 CMB  C23   C22  C21   120.50  3.000
 CMB  H23   C23  C24   120.86  3.000
 CMB  H23   C23  C22   119.07  3.000
 CMB  C24   C23  C22   120.06  3.000
 CMB  C31   C24  C25   119.09  3.000
 CMB  C31   C24  C23   121.98  3.000
 CMB  C25   C24  C23   118.94  3.000
 CMB  H251  C25  C24   118.78  3.000
 CMB  H251  C25  C18   119.91  3.000
 CMB  C24   C25  C18   121.30  3.000
 CMB  H26   C26  C27   120.20  3.000
 CMB  H26   C26  C14   120.29  3.000
 CMB  C27   C26  C14   119.51  3.000
 CMB  CL1   C27  C28   118.88  3.000
 CMB  CL1   C27  C26   119.29  3.000
 CMB  C28   C27  C26   121.83  3.000
 CMB  H28   C28  C29   121.19  3.000
 CMB  H28   C28  C27   121.22  3.000
 CMB  C29   C28  C27   117.59  3.000
 CMB  CL2   C29  C30   119.29  3.000
 CMB  CL2   C29  C28   118.76  3.000
 CMB  C30   C29  C28   121.95  3.000
 CMB  H30   C30  C29   120.14  3.000
 CMB  H30   C30  C14   120.49  3.000
 CMB  C29   C30  C14   119.36  3.000
 CMB  N53   C31  N32   126.13  3.000
 CMB  N53   C31  C24   115.31  3.000
 CMB  N32   C31  C24   118.51  3.000
 CMB  H32   N32  C31   111.32  3.000
 CMB  H532  N53  H531  113.51  3.000
 CMB  H532  N53  C31   117.30  3.000
 CMB  H531  N53  C31   118.47  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
 CMB  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 CMB  CONST_02  N7    C3   C2   C1    180.00   0.0  0
 CMB  CONST_03  C4    C5   C6   C1      0.00   0.0  0
 CMB  CONST_04  C5    C6   C1   C2      0.00   0.0  0
 CMB  CONST_05  C5    C4   C3   C2      0.00   0.0  0
 CMB  CONST_06  C9    C4   C3   C2    180.00   0.0  0
 CMB  CONST_07  C8    N7   C3   C2    180.00   0.0  0
 CMB  CONST_08  C6    C1   C2   C3      0.00   0.0  0
 CMB  CONST_09  C6    C5   C4   C3      0.00   0.0  0
 CMB  CONST_10  C8    C9   C4   C3      0.00   0.0  0
 CMB  CONST_11  C9    C8   N7   C3      0.00   0.0  0
 CMB  CONST_12  C8    N7   C3   C4      0.00   0.0  0
 CMB  CONST_13  N7    C8   C9   C4      0.00   0.0  0
 CMB  CONST_14  N7    C3   C4   C5    180.00   0.0  0
 CMB  CONST_15  C8    C9   C4   C5    180.00   0.0  0
 CMB  CONST_16  C9    C4   C5   C6    180.00   0.0  0
 CMB  CONST_17  C9    C4   C3   N7      0.00   0.0  0
 CMB  CONST_18  C28   C27  C26  C14     0.00   0.0  0
 CMB  CONST_19  C28   C29  C30  C14     0.00   0.0  0
 CMB  CONST_20  C23   C22  C21  C18     0.00   0.0  0
 CMB  CONST_21  C23   C24  C25  C18     0.00   0.0  0
 CMB  CONST_22  C24   C25  C18  C21     0.00   0.0  0
 CMB  CONST_23  C24   C23  C22  C21     0.00   0.0  0
 CMB  CONST_24  C25   C18  C21  C22     0.00   0.0  0
 CMB  CONST_25  C25   C24  C23  C22     0.00   0.0  0
 CMB  CONST_26  C29   C30  C14  C26     0.00   0.0  0
 CMB  CONST_27  C29   C28  C27  C26     0.00   0.0  0
 CMB  CONST_28  C30   C14  C26  C27     0.00   0.0  0
 CMB  CONST_29  C30   C29  C28  C27     0.00   0.0  0
 CMB  CONST_30  C10   C5   C6   C1    180.00   0.0  0
 CMB  CONST_31  C17   N7   C3   C2      0.00   0.0  0
 CMB  CONST_32  C10   C5   C4   C3    180.00   0.0  0
 CMB  CONST_33  C11   C8   N7   C3    180.00   0.0  0
 CMB  CONST_34  C17   N7   C3   C4    180.00   0.0  0
 CMB  CONST_35  C11   C8   C9   C4    180.00   0.0  0
 CMB  CONST_36  C10   C5   C4   C9      0.00   0.0  0
 CMB  CONST_37  C17   N7   C8   C9    180.00   0.0  0
 CMB  CONST_38  C27   C26  C14  C13   180.00   0.0  0
 CMB  CONST_39  C29   C30  C14  C13   180.00   0.0  0
 CMB  CONST_40  CL1   C27  C26  C14   180.00   0.0  0
 CMB  CONST_41  CL2   C29  C30  C14   180.00   0.0  0
 CMB  CONST_42  C22   C21  C18  C17   180.00   0.0  0
 CMB  CONST_43  C24   C25  C18  C17   180.00   0.0  0
 CMB  CONST_44  C31   C24  C25  C18   180.00   0.0  0
 CMB  CONST_45  C31   C24  C23  C22   180.00   0.0  0
 CMB  CONST_46  CL2   C29  C28  C27   180.00   0.0  0
 CMB  CONST_47  CL1   C27  C28  C29   180.00   0.0  0
 CMB  CONST_48  HC6   C6   C1   C2    180.00   0.0  0
 CMB  CONST_49  HC1   C1   C2   C3    180.00   0.0  0
 CMB  CONST_50  HC9   C9   C4   C3    180.00   0.0  0
 CMB  CONST_51  HC2   C2   C3   C4    180.00   0.0  0
 CMB  CONST_52  H22   C22  C21  C18   180.00   0.0  0
 CMB  CONST_53  H251  C25  C18  C21   180.00   0.0  0
 CMB  CONST_54  H23   C23  C22  C21   180.00   0.0  0
 CMB  CONST_55  H21   C21  C22  C23   180.00   0.0  0
 CMB  CONST_56  H30   C30  C14  C26   180.00   0.0  0
 CMB  CONST_57  H28   C28  C27  C26   180.00   0.0  0
 CMB  CONST_58  H26   C26  C27  C28   180.00   0.0  0
 CMB  CONST_59  C13   N12  C11  C8    180.00   0.0  0
 CMB  CONST_60  H12   N12  C11  C8      0.00   0.0  0
 CMB  CONST_61  H32   N32  C31  C24   180.00   0.0  0
 CMB  CONST_63  H532  N53  C31  C24   180.00   0.0  0
 CMB  CONST_64  O45   C11  N12  C13     0.00   0.0  0
 CMB  Var_01    C18   C17  N7   C3     72.94  30.0  2
 CMB  Var_02    C21   C18  C17  N7     48.67  30.0  2
 CMB  Var_03    N12   C11  C8   N7   -151.01  30.0  2
 CMB  Var_04    C26   C14  C13  N12  -138.60  30.0  2
 CMB  Var_05    N32   C31  C24  C23   154.40  30.0  2
 CMB  Var_06    H101  C10  C5   C4     59.26  30.0  2
 CMB  Var_07    C14   C13  N12  C11    68.57  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
 CMB  plan-1  C13   0.020
 CMB  plan-1  C14   0.020
 CMB  plan-1  C26   0.020
 CMB  plan-1  C27   0.020
 CMB  plan-1  C28   0.020
 CMB  plan-1  C29   0.020
 CMB  plan-1  C30   0.020
 CMB  plan-1  CL1   0.020
 CMB  plan-1  CL2   0.020
 CMB  plan-1  H26   0.020
 CMB  plan-1  H28   0.020
 CMB  plan-1  H30   0.020
 CMB  plan-2  C17   0.020
 CMB  plan-2  C18   0.020
 CMB  plan-2  C21   0.020
 CMB  plan-2  C22   0.020
 CMB  plan-2  C23   0.020
 CMB  plan-2  C24   0.020
 CMB  plan-2  C25   0.020
 CMB  plan-2  C31   0.020
 CMB  plan-2  H21   0.020
 CMB  plan-2  H22   0.020
 CMB  plan-2  H23   0.020
 CMB  plan-2  H251  0.020
 CMB  plan-3  C1    0.020
 CMB  plan-3  C2    0.020
 CMB  plan-3  C3    0.020
 CMB  plan-3  C4    0.020
 CMB  plan-3  C5    0.020
 CMB  plan-3  C6    0.020
 CMB  plan-3  N7    0.020
 CMB  plan-3  C8    0.020
 CMB  plan-3  C9    0.020
 CMB  plan-3  C10   0.020
 CMB  plan-3  C11   0.020
 CMB  plan-3  C17   0.020
 CMB  plan-3  HC1   0.020
 CMB  plan-3  HC6   0.020
 CMB  plan-3  HC9   0.020
 CMB  plan-3  HC2   0.020
 CMB  plan-4  C8    0.020
 CMB  plan-4  C11   0.020
 CMB  plan-4  N12   0.020
 CMB  plan-4  C13   0.020
 CMB  plan-4  O45   0.020
 CMB  plan-4  H12   0.020
 CMB  plan-5  C24   0.020
 CMB  plan-5  C31   0.020
 CMB  plan-5  N32   0.020
 CMB  plan-5  N53   0.020
 CMB  plan-5  H32   0.020
 CMB  plan-5  H531  0.020
 CMB  plan-5  H532  0.020

