# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 13:58:54 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: methyl [3-(aminomethyl)-4-(2,4-dichlorophenyl)-2-methyl-7-oxo-5,7-dihydro-6H-pyrrolo[3,4-b]pyridin-6-yl]acetate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)CN1Cc2c(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
 LGE  LGE  'methyl [3-(aminomethyl)-4-(2,4-dichlorophenyl)-2-methyl-7-oxo-5,7-dihydro-6H-pyrrolo[3,4-b]pyridin-6-yl]acetate'  ligand  43  26  .  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_LGE
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
 LGE  C01   C   CR16  0  -0.275  -2.1207  -0.6054   1.4244
 LGE  C02   C   CR16  0  -0.190  -3.0249  -1.6521   1.4895
 LGE  C03   C   CR16  0  -0.147  -3.1120  -1.7071  -0.9238
 LGE  C04   C   CR6   0   0.087  -1.6874  -0.0951   0.2040
 LGE  C05   C   CR6   0   0.198  -0.6817   0.9906   0.1585
 LGE  C06   C   CR56  0   0.024   0.6361   0.7102  -0.1680
 LGE  C07   C   CR6   0  -0.009  -0.9972   2.3175   0.4445
 LGE  C08   C   CR6   0  -0.058  -3.5110  -2.1929   0.3099
 LGE  C09   C   CR6   0  -0.122  -2.2017  -0.6624  -0.9581
 LGE  C10   C   CR56  0  -0.000   1.5473   1.7399  -0.1856
 LGE  C11   C   CR6   0   0.202   0.0227   3.2939   0.3989
 LGE  C12   C   CR5   0   0.568   2.8805   1.1947  -0.5480
 LGE  C13   C   C     0   0.593   4.3572  -1.5782   0.2282
 LGE  C14   C   CH2   0  -0.297   1.3194  -0.5690  -0.5162
 LGE  C15   C   CH3   0  -0.752  -0.2739   4.7348   0.6953
 LGE  C16   C   CH3   0  -0.425   5.9899  -3.0598   1.0529
 LGE  C17   C   CH2   0  -0.407  -2.4008   2.7021   0.8292
 LGE  N19   N   N     0  -0.437   1.2809   3.0041   0.0869
 LGE  N20   N   NR5   0  -0.501   2.6754  -0.1263  -0.7762
 LGE  N21   N   NH2   0  -0.780  -2.5905   2.5476   2.2666
 LGE  O22   O   O     0  -0.469   3.9379   1.7884  -0.6373
 LGE  O23   O   O     0  -0.438   4.0288  -1.2452   1.3362
 LGE  O24   O   O2    0  -0.449   5.3047  -2.4555  -0.0471
 LGE  CL25  CL  CL    0  -0.110  -4.6419  -3.4985   0.3705
 LGE  CL26  CL  CL    0  -0.104  -1.7187  -0.0469  -2.5010
 LGE  H01   H   HCR6  0   0.271  -1.7452  -0.1685   2.3384
 LGE  H02   H   HCR6  0   0.289  -3.3435  -2.0386   2.4473
 LGE  H03   H   HCR6  0   0.306  -3.5003  -2.1288  -1.8402
 LGE  H14   H   HCH2  0   0.280   1.2810  -1.2882   0.3073
 LGE  H14A  H   HCH2  0   0.274   0.8886  -1.0487  -1.3993
 LGE  H15   H   HCH3  0   0.248  -0.7496   4.8643   1.6683
 LGE  H15A  H   HCH3  0   0.263   0.6478   5.3117   0.6913
 LGE  H15B  H   HCH3  0   0.261  -0.9463   5.1649  -0.0493
 LGE  H16   H   HCH3  0   0.243   6.5094  -2.3143   1.6537
 LGE  H16A  H   HCH3  0   0.243   5.3030  -3.6199   1.6861
 LGE  H16B  H   HCH3  0   0.255   6.7143  -3.7395   0.6148
 LGE  H17   H   HCH2  0   0.235  -2.6167   3.7103   0.4581
 LGE  H17A  H   HCH2  0   0.251  -3.1049   2.0387   0.3247
 LGE  H18   H   HCH2  0   0.312   4.5106  -0.5487  -1.6396
 LGE  H18A  H   HCH2  0   0.311   3.3659  -1.8731  -1.6500
 LGE  HN21  H   HNH2  0   0.346  -2.0318   3.2323   2.7618
 LGE  HN2A  H   HNH2  0   0.357  -3.5531   2.7661   2.4928
 LGE  C18   C   CH2   0  -0.446   3.7361  -1.0407  -1.0474

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
 LGE  C04   C01   aromatic  1.392  0.020  1.392
 LGE  C01   C02   aromatic  1.385  0.020  1.385
 LGE  C01   H01   single    0.930  0.020  1.080
 LGE  C02   C08   aromatic  1.386  0.020  1.386
 LGE  C02   H02   single    0.930  0.020  1.080
 LGE  C09   C03   aromatic  1.386  0.020  1.386
 LGE  C03   C08   aromatic  1.385  0.020  1.385
 LGE  C03   H03   single    0.930  0.020  1.080
 LGE  C05   C04   single    1.481  0.020  1.481
 LGE  C04   C09   aromatic  1.392  0.020  1.392
 LGE  C07   C05   aromatic  1.394  0.020  1.394
 LGE  C06   C05   aromatic  1.386  0.020  1.386
 LGE  C10   C06   aromatic  1.375  0.020  1.375
 LGE  C06   C14   single    1.491  0.020  1.491
 LGE  C11   C07   aromatic  1.413  0.020  1.413
 LGE  C07   C17   single    1.505  0.020  1.505
 LGE  C08   CL25  single    1.728  0.020  1.728
 LGE  CL26  C09   single    1.730  0.020  1.730
 LGE  N19   C10   aromatic  1.320  0.020  1.320
 LGE  C12   C10   single    1.485  0.020  1.485
 LGE  C15   C11   single    1.501  0.020  1.501
 LGE  N19   C11   aromatic  1.328  0.020  1.328
 LGE  O22   C12   double    1.216  0.020  1.216
 LGE  C12   N20   single    1.356  0.020  1.356
 LGE  O23   C13   double    1.203  0.020  1.203
 LGE  O24   C13   single    1.320  0.020  1.320
 LGE  C13   C18   single    1.517  0.020  1.517
 LGE  N20   C14   single    1.450  0.020  1.450
 LGE  C14   H14   single    0.970  0.020  1.090
 LGE  C14   H14A  single    0.970  0.020  1.090
 LGE  C15   H15   single    0.970  0.020  1.090
 LGE  C15   H15A  single    0.970  0.020  1.090
 LGE  C15   H15B  single    0.970  0.020  1.090
 LGE  C16   O24   single    1.430  0.020  1.430
 LGE  C16   H16   single    0.970  0.020  1.090
 LGE  C16   H16A  single    0.970  0.020  1.090
 LGE  C16   H16B  single    0.970  0.020  1.090
 LGE  C17   N21   single    1.458  0.020  1.458
 LGE  C17   H17   single    0.970  0.020  1.090
 LGE  C17   H17A  single    0.970  0.020  1.090
 LGE  C18   N20   single    1.427  0.020  1.427
 LGE  C18   H18   single    0.970  0.020  1.090
 LGE  C18   H18A  single    0.970  0.020  1.090
 LGE  N21   HN21  single    0.890  0.020  1.040
 LGE  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
 LGE  H01   C01  C04   119.03  3.000
 LGE  H01   C01  C02   119.53  3.000
 LGE  C04   C01  C02   121.44  3.000
 LGE  H02   C02  C08   120.76  3.000
 LGE  H02   C02  C01   120.30  3.000
 LGE  C08   C02  C01   118.95  3.000
 LGE  H03   C03  C09   120.60  3.000
 LGE  H03   C03  C08   121.00  3.000
 LGE  C09   C03  C08   118.40  3.000
 LGE  C09   C04  C05   121.62  3.000
 LGE  C09   C04  C01   117.87  3.000
 LGE  C05   C04  C01   120.48  3.000
 LGE  C07   C05  C06   117.14  3.000
 LGE  C06   C05  C04   120.31  3.000
 LGE  C07   C05  C04   122.55  3.000
 LGE  C14   C06  C10   109.62  3.000
 LGE  C14   C06  C05   131.60  3.000
 LGE  C10   C06  C05   118.78  3.000
 LGE  C17   C07  C11   120.32  3.000
 LGE  C17   C07  C05   120.45  3.000
 LGE  C11   C07  C05   119.21  3.000
 LGE  CL25  C08  C03   119.00  3.000
 LGE  CL25  C08  C02   119.63  3.000
 LGE  C03   C08  C02   121.37  3.000
 LGE  CL26  C09  C04   119.77  3.000
 LGE  CL26  C09  C03   118.27  3.000
 LGE  C04   C09  C03   121.96  3.000
 LGE  N19   C10  C12   125.66  3.000
 LGE  C12   C10  C06   108.84  3.000
 LGE  N19   C10  C06   125.50  3.000
 LGE  N19   C11  C15   116.30  3.000
 LGE  N19   C11  C07   122.73  3.000
 LGE  C15   C11  C07   120.97  3.000
 LGE  O22   C12  N20   126.49  3.000
 LGE  N20   C12  C10   105.24  3.000
 LGE  O22   C12  C10   128.26  3.000
 LGE  O24   C13  O23   124.89  3.000
 LGE  O24   C13  C18   110.72  3.000
 LGE  O23   C13  C18   124.39  3.000
 LGE  H14A  C14  H14   107.80  3.000
 LGE  H14A  C14  N20   110.95  3.000
 LGE  H14   C14  N20   111.62  3.000
 LGE  H14A  C14  C06   112.60  3.000
 LGE  H14   C14  C06   111.85  3.000
 LGE  N20   C14  C06   102.03  3.000
 LGE  H15B  C15  H15A  108.10  3.000
 LGE  H15B  C15  H15   107.04  3.000
 LGE  H15A  C15  H15   108.06  3.000
 LGE  H15B  C15  C11   111.43  3.000
 LGE  H15A  C15  C11   109.94  3.000
 LGE  H15   C15  C11   112.11  3.000
 LGE  H16B  C16  H16A  109.48  3.000
 LGE  H16B  C16  H16   109.44  3.000
 LGE  H16A  C16  H16   109.40  3.000
 LGE  H16B  C16  O24   105.89  3.000
 LGE  H16A  C16  O24   111.24  3.000
 LGE  H16   C16  O24   111.32  3.000
 LGE  H17A  C17  H17   106.00  3.000
 LGE  H17A  C17  N21   107.91  3.000
 LGE  H17   C17  N21   113.94  3.000
 LGE  H17A  C17  C07   109.16  3.000
 LGE  H17   C17  C07   109.40  3.000
 LGE  N21   C17  C07   110.26  3.000
 LGE  C11   N19  C10   116.65  3.000
 LGE  C18   N20  C14   122.26  3.000
 LGE  C18   N20  C12   122.95  3.000
 LGE  C14   N20  C12   114.12  3.000
 LGE  HN2A  N21  HN21  105.62  3.000
 LGE  HN2A  N21  C17   108.73  3.000
 LGE  HN21  N21  C17   109.79  3.000
 LGE  C16   O24  C13   117.67  3.000
 LGE  H18A  C18  H18   106.54  3.000
 LGE  H18A  C18  N20   109.96  3.000
 LGE  H18   C18  N20   109.98  3.000
 LGE  H18A  C18  C13   109.43  3.000
 LGE  H18   C18  C13   108.98  3.000
 LGE  N20   C18  C13   111.81  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
 LGE  CONST_03  C03   C09  C04  C01    0.00   0.0  0
 LGE  CONST_04  C03   C08  C02  C01    0.00   0.0  0
 LGE  CONST_05  C05   C04  C01  C02  180.00   0.0  0
 LGE  CONST_06  C09   C04  C01  C02    0.00   0.0  0
 LGE  CONST_07  C09   C03  C08  C02    0.00   0.0  0
 LGE  CONST_08  C05   C04  C09  C03  180.00   0.0  0
 LGE  CONST_09  C08   C02  C01  C04    0.00   0.0  0
 LGE  CONST_10  C11   C07  C05  C04  180.00   0.0  0
 LGE  CONST_11  C10   C06  C05  C04  180.00   0.0  0
 LGE  CONST_12  C08   C03  C09  C04    0.00   0.0  0
 LGE  CONST_13  N19   C11  C07  C05    0.00   0.0  0
 LGE  CONST_14  N19   C10  C06  C05    0.00   0.0  0
 LGE  CONST_16  C11   C07  C05  C06    0.00   0.0  0
 LGE  CONST_17  C11   N19  C10  C06    0.00   0.0  0
 LGE  CONST_19  C10   C06  C05  C07    0.00   0.0  0
 LGE  CONST_20  C10   N19  C11  C07    0.00   0.0  0
 LGE  CONST_21  C14   C06  C05  C04    0.00   0.0  0
 LGE  CONST_22  C14   N20  C12  C10    0.00   0.0  0
 LGE  CONST_23  CL26  C09  C04  C01  180.00   0.0  0
 LGE  CONST_24  CL25  C08  C02  C01  180.00   0.0  0
 LGE  CONST_25  C17   C07  C05  C04    0.00   0.0  0
 LGE  CONST_26  CL26  C09  C04  C05    0.00   0.0  0
 LGE  CONST_27  C15   C11  C07  C05  180.00   0.0  0
 LGE  CONST_28  C17   C07  C05  C06  180.00   0.0  0
 LGE  CONST_29  CL26  C09  C03  C08  180.00   0.0  0
 LGE  CONST_30  CL25  C08  C03  C09  180.00   0.0  0
 LGE  CONST_31  C15   C11  N19  C10  180.00   0.0  0
 LGE  CONST_32  N19   C11  C07  C17  180.00   0.0  0
 LGE  CONST_33  C18   N20  C12  C10  180.00   0.0  0
 LGE  CONST_34  O22   C12  N20  C14  180.00   0.0  0
 LGE  CONST_35  H03   C03  C08  C02  180.00   0.0  0
 LGE  CONST_36  H02   C02  C08  C03  180.00   0.0  0
 LGE  CONST_37  H01   C01  C04  C05    0.00   0.0  0
 LGE  CONST_38  O22   C12  N20  C18    0.00   0.0  0
 LGE  Var_01    H14   C14  C06  C05  -62.11  30.0  1
 LGE  Var_02    N21   C17  C07  C05   86.83  30.0  2
 LGE  Var_03    C13   C18  N20  C12   85.55  30.0  2
 LGE  Var_04    H15   C15  C11  C07   55.03  30.0  2
 LGE  Var_05    O23   C13  C18  N20   -2.25  30.0  1
 LGE  Var_06    HN21  N21  C17  C07   67.78  30.0  3
 LGE  Var_07    H16   C16  O24  C13  -61.29  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
 LGE  plan-1  C01   0.020
 LGE  plan-1  C02   0.020
 LGE  plan-1  C03   0.020
 LGE  plan-1  C04   0.020
 LGE  plan-1  C05   0.020
 LGE  plan-1  C08   0.020
 LGE  plan-1  C09   0.020
 LGE  plan-1  CL25  0.020
 LGE  plan-1  CL26  0.020
 LGE  plan-1  H01   0.020
 LGE  plan-1  H02   0.020
 LGE  plan-1  H03   0.020
 LGE  plan-2  C04   0.020
 LGE  plan-2  C05   0.020
 LGE  plan-2  C06   0.020
 LGE  plan-2  C07   0.020
 LGE  plan-2  C10   0.020
 LGE  plan-2  C11   0.020
 LGE  plan-2  C12   0.020
 LGE  plan-2  C14   0.020
 LGE  plan-2  C15   0.020
 LGE  plan-2  C17   0.020
 LGE  plan-2  N19   0.020
 LGE  plan-2  N20   0.020
 LGE  plan-2  O22   0.020
 LGE  plan-2  C18   0.020
 LGE  plan-3  C13   0.020
 LGE  plan-3  O23   0.020
 LGE  plan-3  O24   0.020
 LGE  plan-3  C18   0.020

