# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 15:55:40 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: 3-(aminomethyl)-4-(2,4-dichlorophenyl)-6-(2-methoxyethyl)-2-methyl-5,6-dihydro-7H-pyrrolo[3,4-b]pyridin-7-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCCN1Cc2c(nc(C)c(CN)c2c3ccc(Cl)cc3Cl)C1=O
#
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
 KXB  KXB  3-(aminomethyl)-4-(2,4-dichlorophenyl)-6-(2-methoxyethyl)-2-methyl-5,6-dihydro-7H-pyrrolo[3,4-b]pyridin-7-one  ligand  44  25  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_KXB
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
 KXB  C01   C   CR16  0  -0.315  -2.3231  -0.0290  -1.2737
 KXB  C02   C   CR16  0  -0.182  -3.4008   0.8397  -1.3187
 KXB  C03   C   CR16  0  -0.144  -2.8036   1.6603   0.8740
 KXB  C04   C   CR6   0   0.099  -1.4730  -0.0790  -0.1728
 KXB  C05   C   CR6   0   0.182  -0.3106  -0.9968  -0.1717
 KXB  C06   C   CR56  0   0.034   0.9486  -0.5214  -0.5046
 KXB  C07   C   CR6   0  -0.002  -0.4220  -2.3526   0.1233
 KXB  C08   C   CR6   0  -0.059  -3.6289   1.6769  -0.2386
 KXB  C09   C   CR6   0  -0.115  -1.7325   0.7815   0.8891
 KXB  C10   C   CR56  0  -0.005   2.0023  -1.4015  -0.5390
 KXB  C11   C   CR6   0   0.205   0.7289  -3.1702   0.0416
 KXB  C12   C   CR5   0   0.562   3.2353  -0.6617  -0.9203
 KXB  C13   C   CH2   0  -0.303   1.4270   0.8411  -0.8723
 KXB  C14   C   CH3   0  -0.750   0.6387  -4.6365   0.3343
 KXB  C15   C   CH3   0  -0.394   4.8566   2.6857   1.8698
 KXB  C16   C   CH2   0  -0.416  -1.7497  -2.9531   0.5037
 KXB  C18   C   CH2   0  -0.147   3.9988   2.6309  -0.3012
 KXB  N19   N   N     0  -0.439   1.9258  -2.6960  -0.2823
 KXB  N20   N   NR5   0  -0.500   2.8378   0.6169  -1.1197
 KXB  N21   N   NH2   0  -0.782  -2.3454  -3.6364  -0.6360
 KXB  O22   O   O     0  -0.478   4.3597  -1.1118  -1.0439
 KXB  O23   O   O2    0  -0.477   4.6236   1.9081   0.7234
 KXB  CL1   CL  CL    0  -0.107  -4.9675   2.7688  -0.2732
 KXB  CL2   CL  CL    0  -0.103  -0.7059   0.7518   2.2790
 KXB  H01   H   HCR6  0   0.279  -2.1300  -0.6768  -2.1193
 KXB  H02   H   HCR6  0   0.292  -4.0480   0.8623  -2.1841
 KXB  H03   H   HCR6  0   0.306  -2.9903   2.3158   1.7133
 KXB  H13   H   HCH2  0   0.279   0.9271   1.2328  -1.7633
 KXB  H13A  H   HCH2  0   0.267   1.2736   1.5624  -0.0638
 KXB  H14   H   HCH3  0   0.256  -0.1535  -5.1012  -0.2524
 KXB  H14A  H   HCH3  0   0.256   1.5837  -5.1251   0.1088
 KXB  H14B  H   HCH3  0   0.255   0.4050  -4.8143   1.3863
 KXB  H15   H   HCH3  0   0.234   5.3330   2.0512   2.6164
 KXB  H15A  H   HCH3  0   0.205   5.5182   3.5359   1.6654
 KXB  H15B  H   HCH3  0   0.204   3.9258   3.0811   2.2941
 KXB  H16   H   HCH2  0   0.256  -1.5946  -3.6890   1.2946
 KXB  H16A  H   HCH2  0   0.233  -2.3876  -2.1748   0.9383
 KXB  H17   H   HCH2  0   0.262   3.2736   2.2831  -2.2775
 KXB  H17A  H   HCH2  0   0.266   4.6511   1.2802  -1.8436
 KXB  H18   H   HCH2  0   0.217   4.6312   3.4559  -0.6587
 KXB  H18A  H   HCH2  0   0.205   3.0634   3.0882   0.0549
 KXB  HN21  H   HNH2  0   0.357  -3.1607  -4.1500  -0.3260
 KXB  HN2A  H   HNH2  0   0.345  -2.6859  -2.9549  -1.3030
 KXB  C17   C   CH2   0  -0.338   3.7196   1.7021  -1.4667

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
 KXB  C02  C01   aromatic  1.385  0.020  1.385
 KXB  C01  C04   aromatic  1.392  0.020  1.392
 KXB  C01  H01   single    0.930  0.020  1.080
 KXB  C08  C02   aromatic  1.385  0.020  1.385
 KXB  C02  H02   single    0.930  0.020  1.080
 KXB  C08  C03   aromatic  1.385  0.020  1.385
 KXB  C03  C09   aromatic  1.386  0.020  1.386
 KXB  C03  H03   single    0.930  0.020  1.080
 KXB  C09  C04   aromatic  1.391  0.020  1.391
 KXB  C04  C05   single    1.481  0.020  1.481
 KXB  C05  C06   aromatic  1.386  0.020  1.386
 KXB  C05  C07   aromatic  1.392  0.020  1.392
 KXB  C13  C06   single    1.490  0.020  1.490
 KXB  C06  C10   aromatic  1.373  0.020  1.373
 KXB  C16  C07   single    1.506  0.020  1.506
 KXB  C07  C11   aromatic  1.414  0.020  1.414
 KXB  CL1  C08   single    1.728  0.020  1.728
 KXB  C09  CL2   single    1.728  0.020  1.728
 KXB  C10  C12   single    1.488  0.020  1.488
 KXB  C10  N19   aromatic  1.322  0.020  1.322
 KXB  C11  N19   aromatic  1.328  0.020  1.328
 KXB  C11  C14   single    1.498  0.020  1.498
 KXB  N20  C12   single    1.354  0.020  1.354
 KXB  C12  O22   double    1.217  0.020  1.217
 KXB  C13  N20   single    1.450  0.020  1.450
 KXB  C13  H13   single    0.970  0.020  1.090
 KXB  C13  H13A  single    0.970  0.020  1.090
 KXB  C14  H14   single    0.970  0.020  1.090
 KXB  C14  H14A  single    0.970  0.020  1.090
 KXB  C14  H14B  single    0.970  0.020  1.090
 KXB  C15  O23   single    1.405  0.020  1.405
 KXB  C15  H15   single    0.970  0.020  1.090
 KXB  C15  H15A  single    0.970  0.020  1.090
 KXB  C15  H15B  single    0.970  0.020  1.090
 KXB  N21  C16   single    1.456  0.020  1.456
 KXB  C16  H16   single    0.970  0.020  1.090
 KXB  C16  H16A  single    0.970  0.020  1.090
 KXB  C18  C17   single    1.516  0.020  1.516
 KXB  N20  C17   single    1.441  0.020  1.441
 KXB  C17  H17   single    0.970  0.020  1.090
 KXB  C17  H17A  single    0.970  0.020  1.090
 KXB  O23  C18   single    1.401  0.020  1.401
 KXB  C18  H18   single    0.970  0.020  1.090
 KXB  C18  H18A  single    0.970  0.020  1.090
 KXB  N21  HN21  single    0.890  0.020  1.040
 KXB  N21  HN2A  single    0.890  0.020  1.040

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
 KXB  H01   C01  C04   119.17  3.000
 KXB  H01   C01  C02   119.26  3.000
 KXB  C04   C01  C02   121.57  3.000
 KXB  H02   C02  C08   120.86  3.000
 KXB  H02   C02  C01   120.33  3.000
 KXB  C08   C02  C01   118.80  3.000
 KXB  H03   C03  C09   120.64  3.000
 KXB  H03   C03  C08   120.89  3.000
 KXB  C09   C03  C08   118.48  3.000
 KXB  C09   C04  C05   121.95  3.000
 KXB  C05   C04  C01   120.15  3.000
 KXB  C09   C04  C01   117.88  3.000
 KXB  C07   C05  C06   117.23  3.000
 KXB  C07   C05  C04   122.75  3.000
 KXB  C06   C05  C04   120.01  3.000
 KXB  C13   C06  C10   109.48  3.000
 KXB  C10   C06  C05   118.89  3.000
 KXB  C13   C06  C05   131.63  3.000
 KXB  C16   C07  C11   120.10  3.000
 KXB  C11   C07  C05   119.06  3.000
 KXB  C16   C07  C05   120.83  3.000
 KXB  CL1   C08  C03   119.02  3.000
 KXB  CL1   C08  C02   119.59  3.000
 KXB  C03   C08  C02   121.39  3.000
 KXB  CL2   C09  C04   119.50  3.000
 KXB  CL2   C09  C03   118.61  3.000
 KXB  C04   C09  C03   121.88  3.000
 KXB  N19   C10  C12   125.78  3.000
 KXB  N19   C10  C06   125.33  3.000
 KXB  C12   C10  C06   108.89  3.000
 KXB  N19   C11  C14   116.85  3.000
 KXB  C14   C11  C07   120.38  3.000
 KXB  N19   C11  C07   122.77  3.000
 KXB  O22   C12  N20   127.26  3.000
 KXB  O22   C12  C10   127.43  3.000
 KXB  N20   C12  C10   105.31  3.000
 KXB  H13A  C13  H13   107.55  3.000
 KXB  H13A  C13  N20   111.37  3.000
 KXB  H13   C13  N20   111.16  3.000
 KXB  H13A  C13  C06   112.04  3.000
 KXB  H13   C13  C06   112.44  3.000
 KXB  N20   C13  C06   102.31  3.000
 KXB  H14B  C14  H14A  108.21  3.000
 KXB  H14B  C14  H14   107.07  3.000
 KXB  H14A  C14  H14   109.18  3.000
 KXB  H14B  C14  C11   111.13  3.000
 KXB  H14A  C14  C11   110.30  3.000
 KXB  H14   C14  C11   110.86  3.000
 KXB  H15B  C15  H15A  107.74  3.000
 KXB  H15B  C15  H15   108.42  3.000
 KXB  H15A  C15  H15   108.39  3.000
 KXB  H15B  C15  O23   111.99  3.000
 KXB  H15A  C15  O23   112.16  3.000
 KXB  H15   C15  O23   108.03  3.000
 KXB  H16A  C16  H16   105.91  3.000
 KXB  H16A  C16  N21   113.91  3.000
 KXB  H16   C16  N21   107.99  3.000
 KXB  H16A  C16  C07   109.28  3.000
 KXB  H16   C16  C07   109.07  3.000
 KXB  N21   C16  C07   110.48  3.000
 KXB  H18A  C18  H18   106.40  3.000
 KXB  H18A  C18  O23   110.91  3.000
 KXB  H18   C18  O23   111.62  3.000
 KXB  H18A  C18  C17   110.29  3.000
 KXB  H18   C18  C17   108.40  3.000
 KXB  O23   C18  C17   109.17  3.000
 KXB  C11   N19  C10   116.71  3.000
 KXB  C17   N20  C13   121.35  3.000
 KXB  C17   N20  C12   124.56  3.000
 KXB  C13   N20  C12   114.00  3.000
 KXB  HN2A  N21  HN21  105.80  3.000
 KXB  HN2A  N21  C16   109.71  3.000
 KXB  HN21  N21  C16   109.14  3.000
 KXB  C18   O23  C15   112.66  3.000
 KXB  H17A  C17  H17   107.34  3.000
 KXB  H17A  C17  N20   108.35  3.000
 KXB  H17   C17  N20   109.23  3.000
 KXB  H17A  C17  C18   110.22  3.000
 KXB  H17   C17  C18   108.66  3.000
 KXB  N20   C17  C18   112.89  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
 KXB  CONST_01  C03   C08  C02  C01     0.00   0.0  0
 KXB  CONST_02  C03   C09  C04  C01     0.00   0.0  0
 KXB  CONST_05  C09   C04  C01  C02     0.00   0.0  0
 KXB  CONST_06  C05   C04  C01  C02   180.00   0.0  0
 KXB  CONST_07  C09   C03  C08  C02     0.00   0.0  0
 KXB  CONST_08  C05   C04  C09  C03   180.00   0.0  0
 KXB  CONST_09  C08   C02  C01  C04     0.00   0.0  0
 KXB  CONST_10  C08   C03  C09  C04     0.00   0.0  0
 KXB  CONST_11  C10   C06  C05  C04   180.00   0.0  0
 KXB  CONST_12  C11   C07  C05  C04   180.00   0.0  0
 KXB  CONST_13  N19   C10  C06  C05     0.00   0.0  0
 KXB  CONST_14  N19   C11  C07  C05     0.00   0.0  0
 KXB  CONST_16  C11   C07  C05  C06     0.00   0.0  0
 KXB  CONST_17  C11   N19  C10  C06     0.00   0.0  0
 KXB  CONST_19  C10   C06  C05  C07     0.00   0.0  0
 KXB  CONST_20  C10   N19  C11  C07     0.00   0.0  0
 KXB  CONST_21  C13   C06  C05  C04     0.00   0.0  0
 KXB  CONST_22  C13   N20  C12  C10     0.00   0.0  0
 KXB  CONST_23  CL1   C08  C02  C01   180.00   0.0  0
 KXB  CONST_24  CL2   C09  C04  C01   180.00   0.0  0
 KXB  CONST_25  C16   C07  C05  C04     0.00   0.0  0
 KXB  CONST_26  CL2   C09  C04  C05     0.00   0.0  0
 KXB  CONST_27  C14   C11  C07  C05   180.00   0.0  0
 KXB  CONST_28  C16   C07  C05  C06   180.00   0.0  0
 KXB  CONST_29  CL2   C09  C03  C08   180.00   0.0  0
 KXB  CONST_30  CL1   C08  C03  C09   180.00   0.0  0
 KXB  CONST_31  C14   C11  N19  C10   180.00   0.0  0
 KXB  CONST_32  N19   C11  C07  C16   180.00   0.0  0
 KXB  CONST_33  C17   N20  C12  C10   180.00   0.0  0
 KXB  CONST_34  O22   C12  N20  C13   180.00   0.0  0
 KXB  CONST_35  H03   C03  C08  C02   180.00   0.0  0
 KXB  CONST_36  H02   C02  C08  C03   180.00   0.0  0
 KXB  CONST_37  H01   C01  C04  C05     0.00   0.0  0
 KXB  CONST_38  O22   C12  N20  C17     0.00   0.0  0
 KXB  Var_01    H13   C13  C06  C05   -59.55  30.0  1
 KXB  Var_02    N21   C16  C07  C05   100.35  30.0  1
 KXB  Var_03    C18   C17  N20  C12  -104.55  30.0  3
 KXB  Var_04    H14   C14  C11  C07    52.21  30.0  2
 KXB  Var_05    O23   C18  C17  N20    61.18  30.0  1
 KXB  Var_06    HN21  N21  C16  C07   171.40  30.0  3
 KXB  Var_07    C17   C18  O23  C15  -177.03  30.0  3
 KXB  Var_08    H15   C15  O23  C18   179.48  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
 KXB  plan-1  C01  0.020
 KXB  plan-1  C02  0.020
 KXB  plan-1  C03  0.020
 KXB  plan-1  C04  0.020
 KXB  plan-1  C05  0.020
 KXB  plan-1  C08  0.020
 KXB  plan-1  C09  0.020
 KXB  plan-1  CL1  0.020
 KXB  plan-1  CL2  0.020
 KXB  plan-1  H01  0.020
 KXB  plan-1  H02  0.020
 KXB  plan-1  H03  0.020
 KXB  plan-2  C04  0.020
 KXB  plan-2  C05  0.020
 KXB  plan-2  C06  0.020
 KXB  plan-2  C07  0.020
 KXB  plan-2  C10  0.020
 KXB  plan-2  C11  0.020
 KXB  plan-2  C12  0.020
 KXB  plan-2  C13  0.020
 KXB  plan-2  C14  0.020
 KXB  plan-2  C16  0.020
 KXB  plan-2  N19  0.020
 KXB  plan-2  N20  0.020
 KXB  plan-2  O22  0.020
 KXB  plan-2  C17  0.020

