# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 12:02:15 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 3-(aminomethyl)-4-(2,4-dichlorophenyl)-6-(2-methoxyphenyl)-2-methyl-5,6-dihydro-7H-pyrrolo[3,4-b]pyridin-7-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccccc1N2Cc3c(nc(C)c(CN)c3c4ccc(Cl)cc4Cl)C2=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
 KXA  KXA  3-(aminomethyl)-4-(2,4-dichlorophenyl)-6-(2-methoxyphenyl)-2-methyl-5,6-dihydro-7H-pyrrolo[3,4-b]pyridin-7-one  ligand  48  29  .  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_KXA
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
 KXA  C01   C   CR16  0  -0.287   5.1018  -1.8728   2.0425
 KXA  C02   C   CR16  0  -0.238   5.7350  -2.2380   0.8655
 KXA  C03   C   CR16  0  -0.275  -2.8532  -0.3276   1.4692
 KXA  C04   C   CR16  0  -0.271   3.9811  -1.0540   1.9815
 KXA  C05   C   CR16  0  -0.391   5.2639  -1.8026  -0.3678
 KXA  C06   C   CR16  0  -0.190  -3.6877  -1.4234   1.6121
 KXA  C07   C   CR16  0  -0.147  -3.0393  -2.1840  -0.5878
 KXA  C08   C   CR6   0   0.084  -2.0948  -0.1380   0.3176
 KXA  C09   C   CR6   0   0.196  -1.1835   1.0227   0.2018
 KXA  C10   C   CR56  0   0.024   0.1852   0.8572   0.3468
 KXA  C11   C   CR6   0  -0.005  -1.6467   2.3128  -0.0497
 KXA  C12   C   CR6   0   0.231   3.4993  -0.6122   0.7621
 KXA  C13   C   CR6   0   0.375   4.1374  -0.9868  -0.4299
 KXA  C14   C   CR6   0  -0.058  -3.7696  -2.3423   0.5780
 KXA  C15   C   CR6   0  -0.120  -2.2084  -1.0804  -0.7002
 KXA  C16   C   CR56  0  -0.002   0.9982   1.9622   0.2520
 KXA  C17   C   CR6   0   0.201  -0.7180   3.3746  -0.1305
 KXA  C18   C   CR5   0   0.554   2.4105   1.5416   0.4421
 KXA  C19   C   CH2   0  -0.308   1.0130  -0.3537   0.6173
 KXA  C20   C   CH3   0  -0.751  -1.1658   4.7787  -0.4145
 KXA  C21   C   CH3   0  -0.437   4.1808  -0.8735  -2.7961
 KXA  C22   C   CH2   0  -0.408  -3.1214   2.5770  -0.1957
 KXA  N23   N   N     0  -0.436   0.5896   3.1963   0.0206
 KXA  N24   N   NR5   0  -0.611   2.3534   0.2065   0.6926
 KXA  N25   N   NH2   0  -0.780  -3.7150   2.8428   1.1091
 KXA  O27   O   O2    0  -0.456   3.5910  -0.5176  -1.5600
 KXA  CL1   CL  CL    0  -0.110  -4.8057  -3.7167   0.7366
 KXA  CL2   CL  CL    0  -0.104  -1.3145  -0.8712  -2.1664
 KXA  H01   H   HCR6  0   0.259   5.4750  -2.2135   2.9984
 KXA  H02   H   HCR6  0   0.264   6.6110  -2.8727   0.8956
 KXA  H03   H   HCR6  0   0.271  -2.7948   0.4061   2.2603
 KXA  H04   H   HCR6  0   0.266   3.4698  -0.7520   2.8868
 KXA  H05   H   HCR6  0   0.285   5.7828  -2.1077  -1.2664
 KXA  H06   H   HCR6  0   0.289  -4.2667  -1.5546   2.5156
 KXA  H07   H   HCR6  0   0.305  -3.1156  -2.9002  -1.3939
 KXA  H19   H   HCH2  0   0.282   0.7355  -0.8454   1.5532
 KXA  H19A  H   HCH2  0   0.273   0.9430  -1.0933  -0.1848
 KXA  H20   H   HCH3  0   0.247  -1.9555   5.1072   0.2614
 KXA  H20A  H   HCH3  0   0.263  -0.3264   5.4618  -0.3097
 KXA  H20B  H   HCH3  0   0.261  -1.5548   4.8744  -1.4299
 KXA  H21   H   HCH3  0   0.232   5.2068  -0.5064  -2.8780
 KXA  H21A  H   HCH3  0   0.231   4.1780  -1.9552  -2.9507
 KXA  H21B  H   HCH3  0   0.262   3.5779  -0.4058  -3.5699
 KXA  H22   H   HCH2  0   0.236  -3.2792   3.3769  -0.9278
 KXA  H22A  H   HCH2  0   0.251  -3.6061   1.6914  -0.6097
 KXA  HN25  H   HNH2  0   0.346  -3.3641   3.7202   1.4746
 KXA  HN2A  H   HNH2  0   0.357  -4.7123   2.9753   0.9938
 KXA  O26   O   O     0  -0.461   3.4108   2.2273   0.3919

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
 KXA  C02  C01   aromatic  1.385  0.020  1.385
 KXA  C04  C01   aromatic  1.389  0.020  1.389
 KXA  C01  H01   single    0.930  0.020  1.080
 KXA  C05  C02   aromatic  1.390  0.020  1.390
 KXA  C02  H02   single    0.930  0.020  1.080
 KXA  C08  C03   aromatic  1.392  0.020  1.392
 KXA  C03  C06   aromatic  1.385  0.020  1.385
 KXA  C03  H03   single    0.930  0.020  1.080
 KXA  C12  C04   aromatic  1.384  0.020  1.384
 KXA  C04  H04   single    0.930  0.020  1.080
 KXA  C13  C05   aromatic  1.392  0.020  1.392
 KXA  C05  H05   single    0.930  0.020  1.080
 KXA  C06  C14   aromatic  1.386  0.020  1.386
 KXA  C06  H06   single    0.930  0.020  1.080
 KXA  C15  C07   aromatic  1.386  0.020  1.386
 KXA  C07  C14   aromatic  1.385  0.020  1.385
 KXA  C07  H07   single    0.930  0.020  1.080
 KXA  C09  C08   single    1.480  0.020  1.480
 KXA  C08  C15   aromatic  1.392  0.020  1.392
 KXA  C11  C09   aromatic  1.394  0.020  1.394
 KXA  C10  C09   aromatic  1.386  0.020  1.386
 KXA  C16  C10   aromatic  1.375  0.020  1.375
 KXA  C10  C19   single    1.492  0.020  1.492
 KXA  C17  C11   aromatic  1.413  0.020  1.413
 KXA  C11  C22   single    1.505  0.020  1.505
 KXA  C13  C12   aromatic  1.403  0.020  1.403
 KXA  N24  C12   single    1.410  0.020  1.410
 KXA  O27  C13   single    1.340  0.020  1.340
 KXA  C14  CL1   single    1.728  0.020  1.728
 KXA  CL2  C15   single    1.730  0.020  1.730
 KXA  N23  C16   aromatic  1.320  0.020  1.320
 KXA  C18  C16   single    1.486  0.020  1.486
 KXA  C20  C17   single    1.501  0.020  1.501
 KXA  N23  C17   aromatic  1.328  0.020  1.328
 KXA  O26  C18   double    1.214  0.020  1.214
 KXA  C18  N24   single    1.360  0.020  1.360
 KXA  N24  C19   single    1.455  0.020  1.455
 KXA  C19  H19   single    0.970  0.020  1.090
 KXA  C19  H19A  single    0.970  0.020  1.090
 KXA  C20  H20   single    0.970  0.020  1.090
 KXA  C20  H20A  single    0.970  0.020  1.090
 KXA  C20  H20B  single    0.970  0.020  1.090
 KXA  C21  O27   single    1.415  0.020  1.415
 KXA  C21  H21   single    0.970  0.020  1.090
 KXA  C21  H21A  single    0.970  0.020  1.090
 KXA  C21  H21B  single    0.970  0.020  1.090
 KXA  C22  N25   single    1.458  0.020  1.458
 KXA  C22  H22   single    0.970  0.020  1.090
 KXA  C22  H22A  single    0.970  0.020  1.090
 KXA  N25  HN25  single    0.890  0.020  1.040
 KXA  N25  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
 KXA  H01   C01  C04   120.20  3.000
 KXA  H01   C01  C02   120.68  3.000
 KXA  C04   C01  C02   119.13  3.000
 KXA  H02   C02  C05   118.86  3.000
 KXA  H02   C02  C01   120.07  3.000
 KXA  C05   C02  C01   121.07  3.000
 KXA  H03   C03  C08   118.94  3.000
 KXA  H03   C03  C06   119.62  3.000
 KXA  C08   C03  C06   121.44  3.000
 KXA  H04   C04  C12   118.91  3.000
 KXA  H04   C04  C01   120.57  3.000
 KXA  C12   C04  C01   120.52  3.000
 KXA  H05   C05  C13   121.09  3.000
 KXA  H05   C05  C02   119.09  3.000
 KXA  C13   C05  C02   119.82  3.000
 KXA  H06   C06  C14   120.76  3.000
 KXA  H06   C06  C03   120.33  3.000
 KXA  C14   C06  C03   118.91  3.000
 KXA  H07   C07  C15   120.63  3.000
 KXA  H07   C07  C14   120.98  3.000
 KXA  C15   C07  C14   118.39  3.000
 KXA  C15   C08  C09   121.60  3.000
 KXA  C15   C08  C03   117.93  3.000
 KXA  C09   C08  C03   120.46  3.000
 KXA  C11   C09  C10   117.23  3.000
 KXA  C10   C09  C08   120.40  3.000
 KXA  C11   C09  C08   122.37  3.000
 KXA  C19   C10  C16   109.68  3.000
 KXA  C19   C10  C09   131.59  3.000
 KXA  C16   C10  C09   118.72  3.000
 KXA  C22   C11  C17   120.43  3.000
 KXA  C22   C11  C09   120.37  3.000
 KXA  C17   C11  C09   119.18  3.000
 KXA  N24   C12  C13   118.87  3.000
 KXA  N24   C12  C04   120.79  3.000
 KXA  C13   C12  C04   120.34  3.000
 KXA  O27   C13  C12   115.94  3.000
 KXA  O27   C13  C05   124.94  3.000
 KXA  C12   C13  C05   119.12  3.000
 KXA  CL1   C14  C07   118.97  3.000
 KXA  CL1   C14  C06   119.62  3.000
 KXA  C07   C14  C06   121.41  3.000
 KXA  CL2   C15  C08   119.72  3.000
 KXA  CL2   C15  C07   118.34  3.000
 KXA  C08   C15  C07   121.93  3.000
 KXA  N23   C16  C18   125.53  3.000
 KXA  C18   C16  C10   109.01  3.000
 KXA  N23   C16  C10   125.46  3.000
 KXA  N23   C17  C20   116.15  3.000
 KXA  N23   C17  C11   122.66  3.000
 KXA  C20   C17  C11   121.18  3.000
 KXA  O26   C18  N24   126.65  3.000
 KXA  N24   C18  C16   105.16  3.000
 KXA  O26   C18  C16   128.18  3.000
 KXA  H19A  C19  H19   107.92  3.000
 KXA  H19A  C19  N24   110.94  3.000
 KXA  H19   C19  N24   111.28  3.000
 KXA  H19A  C19  C10   112.37  3.000
 KXA  H19   C19  C10   112.31  3.000
 KXA  N24   C19  C10   102.01  3.000
 KXA  H20B  C20  H20A  108.04  3.000
 KXA  H20B  C20  H20   106.99  3.000
 KXA  H20A  C20  H20   108.07  3.000
 KXA  H20B  C20  C17   111.36  3.000
 KXA  H20A  C20  C17   109.83  3.000
 KXA  H20   C20  C17   112.38  3.000
 KXA  H21B  C21  H21A  108.90  3.000
 KXA  H21B  C21  H21   108.84  3.000
 KXA  H21A  C21  H21   108.93  3.000
 KXA  H21B  C21  O27   106.41  3.000
 KXA  H21A  C21  O27   111.81  3.000
 KXA  H21   C21  O27   111.86  3.000
 KXA  H22A  C22  H22   105.96  3.000
 KXA  H22A  C22  N25   107.86  3.000
 KXA  H22   C22  N25   113.97  3.000
 KXA  H22A  C22  C11   109.24  3.000
 KXA  H22   C22  C11   109.51  3.000
 KXA  N25   C22  C11   110.13  3.000
 KXA  C17   N23  C16   116.74  3.000
 KXA  C19   N24  C18   114.04  3.000
 KXA  C19   N24  C12   121.86  3.000
 KXA  C18   N24  C12   123.03  3.000
 KXA  HN2A  N25  HN25  105.60  3.000
 KXA  HN2A  N25  C22   108.84  3.000
 KXA  HN25  N25  C22   109.86  3.000
 KXA  C21   O27  C13   118.59  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
 KXA  CONST_01  C13   C05  C02  C01    0.00   0.0  0
 KXA  CONST_02  C13   C12  C04  C01    0.00   0.0  0
 KXA  CONST_03  C12   C04  C01  C02    0.00   0.0  0
 KXA  CONST_04  C12   C13  C05  C02    0.00   0.0  0
 KXA  CONST_07  C07   C15  C08  C03    0.00   0.0  0
 KXA  CONST_08  C07   C14  C06  C03    0.00   0.0  0
 KXA  CONST_09  C05   C02  C01  C04    0.00   0.0  0
 KXA  CONST_10  C05   C13  C12  C04    0.00   0.0  0
 KXA  CONST_11  C09   C08  C03  C06  180.00   0.0  0
 KXA  CONST_12  C15   C08  C03  C06    0.00   0.0  0
 KXA  CONST_13  C15   C07  C14  C06    0.00   0.0  0
 KXA  CONST_14  C09   C08  C15  C07  180.00   0.0  0
 KXA  CONST_15  C14   C06  C03  C08    0.00   0.0  0
 KXA  CONST_16  C17   C11  C09  C08  180.00   0.0  0
 KXA  CONST_17  C16   C10  C09  C08  180.00   0.0  0
 KXA  CONST_18  C14   C07  C15  C08    0.00   0.0  0
 KXA  CONST_19  N23   C17  C11  C09    0.00   0.0  0
 KXA  CONST_20  N23   C16  C10  C09    0.00   0.0  0
 KXA  CONST_22  C17   C11  C09  C10    0.00   0.0  0
 KXA  CONST_23  C17   N23  C16  C10    0.00   0.0  0
 KXA  CONST_25  C16   C10  C09  C11    0.00   0.0  0
 KXA  CONST_26  C16   N23  C17  C11    0.00   0.0  0
 KXA  CONST_27  N24   C12  C04  C01  180.00   0.0  0
 KXA  CONST_28  N24   C12  C13  C05  180.00   0.0  0
 KXA  CONST_29  C19   C10  C09  C08    0.00   0.0  0
 KXA  CONST_30  C16   C18  N24  C12  180.00   0.0  0
 KXA  CONST_31  C19   N24  C18  C16    0.00   0.0  0
 KXA  CONST_32  O27   C13  C05  C02  180.00   0.0  0
 KXA  CONST_33  CL2   C15  C08  C03  180.00   0.0  0
 KXA  CONST_34  CL1   C14  C06  C03  180.00   0.0  0
 KXA  CONST_35  O27   C13  C12  C04  180.00   0.0  0
 KXA  CONST_36  C22   C11  C09  C08    0.00   0.0  0
 KXA  CONST_37  CL2   C15  C08  C09    0.00   0.0  0
 KXA  CONST_38  C20   C17  C11  C09  180.00   0.0  0
 KXA  CONST_39  C22   C11  C09  C10  180.00   0.0  0
 KXA  CONST_40  CL2   C15  C07  C14  180.00   0.0  0
 KXA  CONST_41  CL1   C14  C07  C15  180.00   0.0  0
 KXA  CONST_42  C20   C17  N23  C16  180.00   0.0  0
 KXA  CONST_43  N23   C17  C11  C22  180.00   0.0  0
 KXA  CONST_44  O27   C13  C12  N24    0.00   0.0  0
 KXA  CONST_45  O26   C18  N24  C12    0.00   0.0  0
 KXA  CONST_46  O26   C18  N24  C19  180.00   0.0  0
 KXA  CONST_47  H05   C05  C02  C01  180.00   0.0  0
 KXA  CONST_48  H04   C04  C01  C02  180.00   0.0  0
 KXA  CONST_49  H02   C02  C01  C04  180.00   0.0  0
 KXA  CONST_50  H01   C01  C02  C05  180.00   0.0  0
 KXA  CONST_51  H07   C07  C14  C06  180.00   0.0  0
 KXA  CONST_52  H06   C06  C14  C07  180.00   0.0  0
 KXA  CONST_53  H03   C03  C08  C09    0.00   0.0  0
 KXA  Var_01    C18   N24  C12  C04  104.67  30.0  2
 KXA  Var_02    H19   C19  C10  C09  -58.71  30.0  1
 KXA  Var_03    N25   C22  C11  C09   87.78  30.0  2
 KXA  Var_04    H20   C20  C17  C11   52.44  30.0  2
 KXA  Var_05    HN25  N25  C22  C11   67.41  30.0  3
 KXA  Var_06    H21   C21  O27  C13  -62.18  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
 KXA  plan-1  C01  0.020
 KXA  plan-1  C02  0.020
 KXA  plan-1  C04  0.020
 KXA  plan-1  C05  0.020
 KXA  plan-1  C12  0.020
 KXA  plan-1  C13  0.020
 KXA  plan-1  N24  0.020
 KXA  plan-1  O27  0.020
 KXA  plan-1  H01  0.020
 KXA  plan-1  H02  0.020
 KXA  plan-1  H04  0.020
 KXA  plan-1  H05  0.020
 KXA  plan-2  C03  0.020
 KXA  plan-2  C06  0.020
 KXA  plan-2  C07  0.020
 KXA  plan-2  C08  0.020
 KXA  plan-2  C09  0.020
 KXA  plan-2  C14  0.020
 KXA  plan-2  C15  0.020
 KXA  plan-2  CL1  0.020
 KXA  plan-2  CL2  0.020
 KXA  plan-2  H03  0.020
 KXA  plan-2  H06  0.020
 KXA  plan-2  H07  0.020
 KXA  plan-3  C08  0.020
 KXA  plan-3  C09  0.020
 KXA  plan-3  C10  0.020
 KXA  plan-3  C11  0.020
 KXA  plan-3  C12  0.020
 KXA  plan-3  C16  0.020
 KXA  plan-3  C17  0.020
 KXA  plan-3  C18  0.020
 KXA  plan-3  C19  0.020
 KXA  plan-3  C20  0.020
 KXA  plan-3  C22  0.020
 KXA  plan-3  N23  0.020
 KXA  plan-3  N24  0.020
 KXA  plan-3  O26  0.020

