# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 12:40:20 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: 3-(aminomethyl)-4-(2,4-dichlorophenyl)-6-(2-methoxyethyl)-2-methyl-6,7-dihydro-5H-pyrrolo[3,4-b]pyridin-5-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCCN1Cc2nc(C)c(CN)c(c3ccc(Cl)cc3Cl)c2C1=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
 1WH  1WH  3-(aminomethyl)-4-(2,4-dichlorophenyl)-6-(2-methoxyethyl)-2-methyl-6,7-dihydro-5H-pyrrolo[3,4-b]pyridin-5-one  ligand  44  25  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_1WH
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
 1WH  C    C   CR5   0   0.511  -1.6035  -0.6951   0.6341
 1WH  C7A  C   CR56  0  -0.141  -1.0874   0.6163   0.1886
 1WH  N    N   NH2   0  -0.783   1.8539   3.0541  -2.2984
 1WH  C1   C   CH2   0  -0.413   1.6936   2.9419  -0.8551
 1WH  C2   C   CR6   0   0.207   0.1914   1.0422  -0.1420
 1WH  C3   C   CR6   0  -0.014   0.3408   2.3778  -0.5079
 1WH  C4   C   CH3   0  -0.751  -0.6915   4.6404  -0.9552
 1WH  C5   C   CR6   0   0.216  -0.8051   3.2006  -0.5608
 1WH  N1   N   N     0  -0.451  -2.0276   2.7665  -0.2548
 1WH  C3A  C   CR56  0   0.179  -2.1360   1.5047   0.1130
 1WH  C6   C   CH2   0  -0.285  -3.4033   0.8138   0.5026
 1WH  N2   N   NR5   0  -0.497  -2.9368  -0.5175   0.8243
 1WH  C7   C   CH2   0  -0.339  -3.8421  -1.5661   1.2187
 1WH  C8   C   CH2   0  -0.141  -4.6216  -2.1489   0.0554
 1WH  O1   O   O2    0  -0.477  -3.7232  -2.6897  -0.8737
 1WH  C10  C   CH3   0  -0.393  -4.3634  -3.2194  -2.0058
 1WH  C14  C   CR6   0   0.121   1.3319   0.0973  -0.1395
 1WH  C15  C   CR6   0  -0.098   1.9622  -0.2983   1.0343
 1WH  CL   CL  CL    0  -0.113   1.4155   0.3307   2.5471
 1WH  C16  C   CR16  0  -0.151   3.0313  -1.1785   1.0295
 1WH  C17  C   CR6   0  -0.061   3.4689  -1.6810  -0.1855
 1WH  CL1  CL  CL    0  -0.113   4.7997  -2.7845  -0.2059
 1WH  C18  C   CR16  0  -0.185   2.8617  -1.3179  -1.3758
 1WH  C19  C   CR16  0  -0.322   1.7982  -0.4306  -1.3381
 1WH  O2   O   O     0  -0.469  -0.9739  -1.7203   0.8188
 1WH  H1   H   HNH2  0   0.356   2.7204   3.5378  -2.4986
 1WH  H2   H   HNH2  0   0.344   1.9530   2.1317  -2.7042
 1WH  H4   H   HCH2  0   0.232   2.4706   2.3402  -0.3700
 1WH  H5   H   HCH2  0   0.254   1.7849   3.9432  -0.4296
 1WH  H6   H   HCH3  0   0.257  -0.0678   4.7583  -1.8401
 1WH  H7   H   HCH3  0   0.257  -1.6768   5.0572  -1.1517
 1WH  H8   H   HCH3  0   0.258  -0.2331   5.2265  -0.1548
 1WH  H9   H   HCH2  0   0.278  -3.8818   1.2896   1.3637
 1WH  H10  H   HCH2  0   0.275  -4.1261   0.8101  -0.3192
 1WH  H11  H   HCH2  0   0.262  -3.2673  -2.3482   1.7141
 1WH  H12  H   HCH2  0   0.262  -4.5497  -1.1717   1.9513
 1WH  H13  H   HCH2  0   0.214  -5.3073  -2.9132   0.4481
 1WH  H14  H   HCH2  0   0.202  -5.2488  -1.3744  -0.4103
 1WH  H15  H   HCH3  0   0.233  -3.5969  -3.6192  -2.6687
 1WH  H16  H   HCH3  0   0.204  -5.0546  -4.0309  -1.7486
 1WH  H17  H   HCH3  0   0.204  -4.9298  -2.4566  -2.5535
 1WH  H18  H   HCR6  0   0.303   3.5117  -1.4664   1.9542
 1WH  H19  H   HCR6  0   0.289   3.2059  -1.7179  -2.3190
 1WH  H20  H   HCR6  0   0.275   1.3103  -0.1550  -2.2645

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
 1WH  C10  O1   single    1.404  0.020  1.404
 1WH  C6   C3A  single    1.495  0.020  1.495
 1WH  C6   N2   single    1.447  0.020  1.447
 1WH  N1   C3A  aromatic  1.319  0.020  1.319
 1WH  N1   C5   aromatic  1.333  0.020  1.333
 1WH  C8   O1   single    1.401  0.020  1.401
 1WH  C8   C7   single    1.517  0.020  1.517
 1WH  C4   C5   single    1.497  0.020  1.497
 1WH  C3A  C7A  aromatic  1.376  0.020  1.376
 1WH  C7   N2   single    1.440  0.020  1.440
 1WH  C5   C3   aromatic  1.412  0.020  1.412
 1WH  N2   C    single    1.359  0.020  1.359
 1WH  C7A  C    single    1.478  0.020  1.478
 1WH  C7A  C2   aromatic  1.388  0.020  1.388
 1WH  C    O2   double    1.217  0.020  1.217
 1WH  C3   C2   aromatic  1.393  0.020  1.393
 1WH  C3   C1   single    1.506  0.020  1.506
 1WH  C2   C14  single    1.481  0.020  1.481
 1WH  C1   N    single    1.457  0.020  1.457
 1WH  C14  C19  aromatic  1.390  0.020  1.390
 1WH  C14  C15  aromatic  1.390  0.020  1.390
 1WH  C19  C18  aromatic  1.386  0.020  1.386
 1WH  CL   C15  single    1.727  0.020  1.727
 1WH  C15  C16  aromatic  1.385  0.020  1.385
 1WH  C18  C17  aromatic  1.385  0.020  1.385
 1WH  C16  C17  aromatic  1.386  0.020  1.386
 1WH  C17  CL1  single    1.729  0.020  1.729
 1WH  N    H1   single    0.890  0.020  1.040
 1WH  N    H2   single    0.890  0.020  1.040
 1WH  C1   H4   single    0.970  0.020  1.090
 1WH  C1   H5   single    0.970  0.020  1.090
 1WH  C4   H6   single    0.970  0.020  1.090
 1WH  C4   H7   single    0.970  0.020  1.090
 1WH  C4   H8   single    0.970  0.020  1.090
 1WH  C6   H9   single    0.970  0.020  1.090
 1WH  C6   H10  single    0.970  0.020  1.090
 1WH  C7   H11  single    0.970  0.020  1.090
 1WH  C7   H12  single    0.970  0.020  1.090
 1WH  C8   H13  single    0.970  0.020  1.090
 1WH  C8   H14  single    0.970  0.020  1.090
 1WH  C10  H15  single    0.970  0.020  1.090
 1WH  C10  H16  single    0.970  0.020  1.090
 1WH  C10  H17  single    0.970  0.020  1.090
 1WH  C16  H18  single    0.930  0.020  1.080
 1WH  C18  H19  single    0.930  0.020  1.080
 1WH  C19  H20  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
 1WH  O2   C    N2   126.62  3.000
 1WH  O2   C    C7A  127.77  3.000
 1WH  N2   C    C7A  105.60  3.000
 1WH  C3A  C7A  C2   119.40  3.000
 1WH  C2   C7A  C    131.74  3.000
 1WH  C3A  C7A  C    108.86  3.000
 1WH  H2   N    H1   105.79  3.000
 1WH  H2   N    C1   109.74  3.000
 1WH  H1   N    C1   109.09  3.000
 1WH  H5   C1   H4   105.77  3.000
 1WH  H5   C1   C3   109.20  3.000
 1WH  H4   C1   C3   109.22  3.000
 1WH  H5   C1   N    107.84  3.000
 1WH  H4   C1   N    113.76  3.000
 1WH  C3   C1   N    110.86  3.000
 1WH  C14  C2   C3   121.98  3.000
 1WH  C14  C2   C7A  120.89  3.000
 1WH  C3   C2   C7A  117.11  3.000
 1WH  C5   C3   C2   118.80  3.000
 1WH  C2   C3   C1   121.06  3.000
 1WH  C5   C3   C1   120.14  3.000
 1WH  H8   C4   H7   107.86  3.000
 1WH  H8   C4   H6   107.27  3.000
 1WH  H7   C4   H6   109.30  3.000
 1WH  H8   C4   C5   110.77  3.000
 1WH  H7   C4   C5   110.32  3.000
 1WH  H6   C4   C5   111.20  3.000
 1WH  N1   C5   C4   116.31  3.000
 1WH  C4   C5   C3   120.59  3.000
 1WH  N1   C5   C3   123.09  3.000
 1WH  C3A  N1   C5   116.81  3.000
 1WH  C6   C3A  N1   125.77  3.000
 1WH  N1   C3A  C7A  124.77  3.000
 1WH  C6   C3A  C7A  109.46  3.000
 1WH  H10  C6   H9   107.68  3.000
 1WH  H10  C6   N2   112.13  3.000
 1WH  H9   C6   N2   111.48  3.000
 1WH  H10  C6   C3A  111.45  3.000
 1WH  H9   C6   C3A  112.02  3.000
 1WH  N2   C6   C3A  102.11  3.000
 1WH  C7   N2   C6   121.88  3.000
 1WH  C7   N2   C    124.06  3.000
 1WH  C6   N2   C    113.93  3.000
 1WH  H12  C7   H11  107.21  3.000
 1WH  H12  C7   C8   108.67  3.000
 1WH  H11  C7   C8   110.12  3.000
 1WH  H12  C7   N2   109.15  3.000
 1WH  H11  C7   N2   108.40  3.000
 1WH  C8   C7   N2   113.12  3.000
 1WH  H14  C8   H13  106.57  3.000
 1WH  H14  C8   O1   110.89  3.000
 1WH  H13  C8   O1   111.62  3.000
 1WH  H14  C8   C7   110.31  3.000
 1WH  H13  C8   C7   108.29  3.000
 1WH  O1   C8   C7   109.11  3.000
 1WH  C10  O1   C8   112.82  3.000
 1WH  H17  C10  H16  107.84  3.000
 1WH  H17  C10  H15  108.35  3.000
 1WH  H16  C10  H15  108.34  3.000
 1WH  H17  C10  O1   112.07  3.000
 1WH  H16  C10  O1   112.17  3.000
 1WH  H15  C10  O1   107.95  3.000
 1WH  C19  C14  C15  117.90  3.000
 1WH  C15  C14  C2   122.16  3.000
 1WH  C19  C14  C2   119.94  3.000
 1WH  C16  C15  CL   118.61  3.000
 1WH  C16  C15  C14  121.88  3.000
 1WH  CL   C15  C14  119.51  3.000
 1WH  H18  C16  C17  120.87  3.000
 1WH  H18  C16  C15  120.62  3.000
 1WH  C17  C16  C15  118.51  3.000
 1WH  C18  C17  CL1  119.65  3.000
 1WH  CL1  C17  C16  119.01  3.000
 1WH  C18  C17  C16  121.34  3.000
 1WH  H19  C18  C19  120.34  3.000
 1WH  H19  C18  C17  120.90  3.000
 1WH  C19  C18  C17  118.76  3.000
 1WH  H20  C19  C18  119.06  3.000
 1WH  H20  C19  C14  119.33  3.000
 1WH  C18  C19  C14  121.60  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
 1WH  CONST_01  C5   N1   C3A  C7A     0.00   0.0  0
 1WH  CONST_02  C5   C3   C2   C7A     0.00   0.0  0
 1WH  CONST_05  N1   C3A  C7A  C2      0.00   0.0  0
 1WH  CONST_06  N1   C5   C3   C2      0.00   0.0  0
 1WH  CONST_07  C18  C19  C14  C2    180.00   0.0  0
 1WH  CONST_08  C16  C15  C14  C2    180.00   0.0  0
 1WH  CONST_09  C3A  N1   C5   C3      0.00   0.0  0
 1WH  CONST_10  C3A  C7A  C2   C3      0.00   0.0  0
 1WH  CONST_13  C14  C2   C3   C5    180.00   0.0  0
 1WH  CONST_14  C14  C2   C7A  C3A   180.00   0.0  0
 1WH  CONST_15  C17  C18  C19  C14     0.00   0.0  0
 1WH  CONST_16  C17  C16  C15  C14     0.00   0.0  0
 1WH  CONST_17  C18  C19  C14  C15     0.00   0.0  0
 1WH  CONST_18  C18  C17  C16  C15     0.00   0.0  0
 1WH  CONST_19  C19  C14  C15  C16     0.00   0.0  0
 1WH  CONST_20  C19  C18  C17  C16     0.00   0.0  0
 1WH  CONST_21  C14  C2   C7A  C       0.00   0.0  0
 1WH  CONST_22  C6   N2   C    C7A     0.00   0.0  0
 1WH  CONST_23  C1   C3   C2   C7A   180.00   0.0  0
 1WH  CONST_24  N1   C5   C3   C1    180.00   0.0  0
 1WH  CONST_25  C14  C2   C3   C1      0.00   0.0  0
 1WH  CONST_26  C4   C5   C3   C2    180.00   0.0  0
 1WH  CONST_27  CL   C15  C14  C2      0.00   0.0  0
 1WH  CONST_28  C3A  N1   C5   C4    180.00   0.0  0
 1WH  CONST_29  CL1  C17  C16  C15   180.00   0.0  0
 1WH  CONST_30  C19  C14  C15  CL    180.00   0.0  0
 1WH  CONST_31  C17  C16  C15  CL    180.00   0.0  0
 1WH  CONST_32  C19  C18  C17  CL1   180.00   0.0  0
 1WH  CONST_33  C7   N2   C    C7A   180.00   0.0  0
 1WH  CONST_34  O2   C    N2   C6    180.00   0.0  0
 1WH  CONST_35  H20  C19  C14  C2      0.00   0.0  0
 1WH  CONST_36  H19  C18  C19  C14   180.00   0.0  0
 1WH  CONST_37  H18  C16  C15  C14   180.00   0.0  0
 1WH  CONST_38  O2   C    N2   C7      0.00   0.0  0
 1WH  Var_01    H9   C6   N2   C    -121.76  30.0  1
 1WH  Var_02    C8   C7   N2   C     -99.59  30.0  1
 1WH  Var_03    C5   C3   C1   N     -77.75  30.0  2
 1WH  Var_04    H6   C4   C5   C3     46.22  30.0  2
 1WH  Var_05    O1   C8   C7   N2     60.17  30.0  1
 1WH  Var_06    H1   N    C1   C3    173.17  30.0  3
 1WH  Var_07    H15  C10  O1   C8   -179.77  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
 1WH  plan-1  C2   0.020
 1WH  plan-1  C14  0.020
 1WH  plan-1  C15  0.020
 1WH  plan-1  CL   0.020
 1WH  plan-1  C16  0.020
 1WH  plan-1  C17  0.020
 1WH  plan-1  CL1  0.020
 1WH  plan-1  C18  0.020
 1WH  plan-1  C19  0.020
 1WH  plan-1  H18  0.020
 1WH  plan-1  H19  0.020
 1WH  plan-1  H20  0.020
 1WH  plan-2  C    0.020
 1WH  plan-2  C7A  0.020
 1WH  plan-2  C1   0.020
 1WH  plan-2  C2   0.020
 1WH  plan-2  C3   0.020
 1WH  plan-2  C4   0.020
 1WH  plan-2  C5   0.020
 1WH  plan-2  N1   0.020
 1WH  plan-2  C3A  0.020
 1WH  plan-2  C6   0.020
 1WH  plan-2  N2   0.020
 1WH  plan-2  C7   0.020
 1WH  plan-2  C14  0.020
 1WH  plan-2  O2   0.020

