# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 23 09:45:58 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: 2-[3-(aminomethyl)-4-(2,4-dichlorophenyl)-2-methyl-5-oxo-5,7-dihydro-6H-pyrrolo[3,4-b]pyridin-6-yl]-N,N-dimethylacetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)C(=O)CN1Cc2nc(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
 1MD  1MD  2-[3-(aminomethyl)-4-(2,4-dichlorophenyl)-2-methyl-5-oxo-5,7-dihydro-6H-pyrrolo[3,4-b]pyridin-6-yl]-N,N-dimethylacetamide  ligand  47  27  .  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_1MD
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
 1MD  C1   C   CR6   0   0.227   1.0169   1.0981   0.4418
 1MD  C2   C   CR6   0  -0.037   1.5648   2.3724   0.3023
 1MD  C3   C   CR6   0   0.207   0.7040   3.4875   0.3221
 1MD  N4   N   N     0  -0.451  -0.6141   3.3885   0.5069
 1MD  C4   C   CR56  0  -0.146  -0.3537   1.0183   0.6282
 1MD  C6   C   CR56  0   0.179  -1.1033   2.1753   0.6582
 1MD  C5   C   CH2   0  -0.282  -2.5429   1.8339   0.8771
 1MD  N1   N   NR5   0  -0.492  -2.4913   0.3948   1.0117
 1MD  C9   C   CR5   0   0.514  -1.2572  -0.1356   0.8049
 1MD  C10  C   CH2   0  -0.450  -3.6709  -0.4063   1.0825
 1MD  C7   C   C     0   0.546  -4.2435  -0.6727  -0.3139
 1MD  C13  C   CH3   0  -0.753   1.2316   4.8783   0.1279
 1MD  C14  C   CR6   0   0.137   1.8534  -0.1220   0.4150
 1MD  C15  C   CH2   0  -0.404   3.0418   2.5390   0.0604
 1MD  N16  N   NH2   0  -0.766   3.3615   2.1822  -1.3142
 1MD  C17  C   CR16  0  -0.316   2.5686  -0.5081   1.5418
 1MD  C18  C   CR16  0  -0.193   3.3515  -1.6517   1.5475
 1MD  C19  C   CR6   0  -0.060   3.4134  -2.4212   0.3980
 1MD  C20  C   CR16  0  -0.159   2.7122  -2.0697  -0.7442
 1MD  C21  C   CR6   0  -0.078   1.9382  -0.9216  -0.7177
 1MD  CL1  CL  CL    0  -0.117   1.0489  -0.4954  -2.1333
 1MD  CL2  CL  CL    0  -0.117   4.3826  -3.8545   0.3784
 1MD  N2   N   NT    0  -0.448  -5.3881  -1.3768  -0.3725
 1MD  C25  C   CH3   0  -0.529  -6.1060  -1.8683   0.7844
 1MD  O2   O   O     0  -0.488  -3.6609  -0.2469  -1.2997
 1MD  O1   O   O     0  -0.467  -0.9824  -1.3209   0.7929
 1MD  C8   C   CH3   0  -0.523  -6.0593  -1.5985  -1.6361
 1MD  H1   H   HCH2  0   0.278  -2.9445   2.3091   1.7763
 1MD  H2   H   HCH2  0   0.276  -3.1602   2.1412   0.0284
 1MD  H3   H   HCH2  0   0.299  -3.4304  -1.3477   1.5802
 1MD  H4   H   HCH2  0   0.299  -4.4093   0.1005   1.7078
 1MD  H5   H   HCH3  0   0.251   1.8612   4.9507  -0.7595
 1MD  H6   H   HCH3  0   0.262   0.4051   5.5765   0.0210
 1MD  H7   H   HCH3  0   0.261   1.8379   5.1980   0.9776
 1MD  H8   H   HCH2  0   0.233   3.3514   3.5500   0.3459
 1MD  H9   H   HCH2  0   0.248   3.5920   1.8657   0.7202
 1MD  H10  H   HNH2  0   0.340   2.8879   2.8125  -1.9497
 1MD  H11  H   HNH2  0   0.351   4.3521   2.3246  -1.4688
 1MD  H13  H   HCR6  0   0.275   2.5131   0.0985   2.4366
 1MD  H14  H   HCR6  0   0.286   3.9007  -1.9347   2.4347
 1MD  H15  H   HCR6  0   0.300   2.7648  -2.6775  -1.6367
 1MD  H16  H   HCH3  0   0.246  -6.9596  -1.2302   1.0248
 1MD  H17  H   HCH3  0   0.253  -6.4819  -2.8698   0.5741
 1MD  H18  H   HCH3  0   0.266  -5.4733  -1.9420   1.6628
 1MD  H19  H   HCH3  0   0.243  -6.1567  -2.6679  -1.8307
 1MD  H20  H   HCH3  0   0.241  -7.0615  -1.1660  -1.6103
 1MD  H21  H   HCH3  0   0.259  -5.5049  -1.1438  -2.4496

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
 1MD  C25  N2   single    1.448  0.020  1.448
 1MD  C13  C3   single    1.500  0.020  1.500
 1MD  N4   C6   aromatic  1.317  0.020  1.317
 1MD  N4   C3   aromatic  1.335  0.020  1.335
 1MD  O2   C7   double    1.222  0.020  1.222
 1MD  N2   C7   single    1.345  0.020  1.345
 1MD  N2   C8   single    1.448  0.020  1.448
 1MD  C5   C6   single    1.496  0.020  1.496
 1MD  C5   N1   single    1.446  0.020  1.446
 1MD  C7   C10  single    1.533  0.020  1.533
 1MD  C6   C4   aromatic  1.379  0.020  1.379
 1MD  C3   C2   aromatic  1.409  0.020  1.409
 1MD  C10  N1   single    1.428  0.020  1.428
 1MD  N1   C9   single    1.359  0.020  1.359
 1MD  C4   C9   single    1.476  0.020  1.476
 1MD  C4   C1   aromatic  1.385  0.020  1.385
 1MD  C2   C15  single    1.506  0.020  1.506
 1MD  C2   C1   aromatic  1.394  0.020  1.394
 1MD  C9   O1   double    1.217  0.020  1.217
 1MD  C15  N16  single    1.456  0.020  1.456
 1MD  C1   C14  single    1.480  0.020  1.480
 1MD  C14  C17  aromatic  1.389  0.020  1.389
 1MD  C14  C21  aromatic  1.389  0.020  1.389
 1MD  C17  C18  aromatic  1.386  0.020  1.386
 1MD  CL1  C21  single    1.725  0.020  1.725
 1MD  C21  C20  aromatic  1.385  0.020  1.385
 1MD  C18  C19  aromatic  1.385  0.020  1.385
 1MD  C20  C19  aromatic  1.386  0.020  1.386
 1MD  C19  CL2  single    1.730  0.020  1.730
 1MD  C5   H1   single    0.970  0.020  1.090
 1MD  C5   H2   single    0.970  0.020  1.090
 1MD  C10  H3   single    0.970  0.020  1.090
 1MD  C10  H4   single    0.970  0.020  1.090
 1MD  C13  H5   single    0.970  0.020  1.090
 1MD  C13  H6   single    0.970  0.020  1.090
 1MD  C13  H7   single    0.970  0.020  1.090
 1MD  C15  H8   single    0.970  0.020  1.090
 1MD  C15  H9   single    0.970  0.020  1.090
 1MD  N16  H10  single    0.890  0.020  1.040
 1MD  N16  H11  single    0.890  0.020  1.040
 1MD  C17  H13  single    0.930  0.020  1.080
 1MD  C18  H14  single    0.930  0.020  1.080
 1MD  C20  H15  single    0.930  0.020  1.080
 1MD  C25  H16  single    0.970  0.020  1.090
 1MD  C25  H17  single    0.970  0.020  1.090
 1MD  C25  H18  single    0.970  0.020  1.090
 1MD  C8   H19  single    0.970  0.020  1.090
 1MD  C8   H20  single    0.970  0.020  1.090
 1MD  C8   H21  single    0.970  0.020  1.090

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
 1MD  C14  C1   C4   120.95  3.000
 1MD  C14  C1   C2   121.99  3.000
 1MD  C4   C1   C2   117.06  3.000
 1MD  C15  C2   C3   120.93  3.000
 1MD  C15  C2   C1   120.18  3.000
 1MD  C3   C2   C1   118.81  3.000
 1MD  C13  C3   N4   115.72  3.000
 1MD  N4   C3   C2   123.14  3.000
 1MD  C13  C3   C2   121.14  3.000
 1MD  C6   N4   C3   116.82  3.000
 1MD  C9   C4   C6   108.69  3.000
 1MD  C9   C4   C1   131.80  3.000
 1MD  C6   C4   C1   119.50  3.000
 1MD  C5   C6   C4   109.57  3.000
 1MD  C4   C6   N4   124.65  3.000
 1MD  C5   C6   N4   125.78  3.000
 1MD  H2   C5   H1   107.99  3.000
 1MD  H2   C5   N1   111.84  3.000
 1MD  H1   C5   N1   111.65  3.000
 1MD  H2   C5   C6   111.44  3.000
 1MD  H1   C5   C6   112.01  3.000
 1MD  N1   C5   C6   101.91  3.000
 1MD  C10  N1   C9   122.61  3.000
 1MD  C9   N1   C5   113.98  3.000
 1MD  C10  N1   C5   122.24  3.000
 1MD  O1   C9   N1   125.92  3.000
 1MD  O1   C9   C4   128.47  3.000
 1MD  N1   C9   C4   105.60  3.000
 1MD  H4   C10  H3   106.74  3.000
 1MD  H4   C10  C7   110.47  3.000
 1MD  H3   C10  C7   110.35  3.000
 1MD  H4   C10  N1   109.06  3.000
 1MD  H3   C10  N1   108.93  3.000
 1MD  C7   C10  N1   111.17  3.000
 1MD  O2   C7   N2   123.57  3.000
 1MD  N2   C7   C10  116.66  3.000
 1MD  O2   C7   C10  119.77  3.000
 1MD  H7   C13  H6   108.10  3.000
 1MD  H7   C13  H5   107.06  3.000
 1MD  H6   C13  H5   108.44  3.000
 1MD  H7   C13  C3   111.47  3.000
 1MD  H6   C13  C3   109.93  3.000
 1MD  H5   C13  C3   111.71  3.000
 1MD  C21  C14  C17  118.03  3.000
 1MD  C21  C14  C1   121.60  3.000
 1MD  C17  C14  C1   120.36  3.000
 1MD  H9   C15  H8   105.62  3.000
 1MD  H9   C15  N16  108.00  3.000
 1MD  H8   C15  N16  114.22  3.000
 1MD  H9   C15  C2   109.21  3.000
 1MD  H8   C15  C2   109.73  3.000
 1MD  N16  C15  C2   109.88  3.000
 1MD  H11  N16  H10  105.91  3.000
 1MD  H11  N16  C15  108.94  3.000
 1MD  H10  N16  C15  109.72  3.000
 1MD  H13  C17  C18  119.21  3.000
 1MD  H13  C17  C14  119.23  3.000
 1MD  C18  C17  C14  121.57  3.000
 1MD  H14  C18  C19  120.87  3.000
 1MD  H14  C18  C17  120.42  3.000
 1MD  C19  C18  C17  118.71  3.000
 1MD  CL2  C19  C20  118.96  3.000
 1MD  CL2  C19  C18  119.66  3.000
 1MD  C20  C19  C18  121.38  3.000
 1MD  H15  C20  C21  120.60  3.000
 1MD  H15  C20  C19  120.88  3.000
 1MD  C21  C20  C19  118.51  3.000
 1MD  CL1  C21  C20  118.50  3.000
 1MD  C20  C21  C14  121.80  3.000
 1MD  CL1  C21  C14  119.70  3.000
 1MD  C8   N2   C25  114.55  3.000
 1MD  C8   N2   C7   120.85  3.000
 1MD  C25  N2   C7   124.39  3.000
 1MD  H18  C25  H17  107.15  3.000
 1MD  H18  C25  H16  108.49  3.000
 1MD  H17  C25  H16  108.04  3.000
 1MD  H18  C25  N2   112.39  3.000
 1MD  H17  C25  N2   109.19  3.000
 1MD  H16  C25  N2   111.41  3.000
 1MD  H21  C8   H20  108.71  3.000
 1MD  H21  C8   H19  108.83  3.000
 1MD  H20  C8   H19  108.09  3.000
 1MD  H21  C8   N2   110.70  3.000
 1MD  H20  C8   N2   110.14  3.000
 1MD  H19  C8   N2   110.31  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
 1MD  CONST_01  N4   C6   C4   C1     0.00   0.0  0
 1MD  CONST_02  N4   C3   C2   C1     0.00   0.0  0
 1MD  CONST_03  C18  C17  C14  C1   180.00   0.0  0
 1MD  CONST_04  C20  C21  C14  C1   180.00   0.0  0
 1MD  CONST_05  C6   N4   C3   C2     0.00   0.0  0
 1MD  CONST_06  C6   C4   C1   C2     0.00   0.0  0
 1MD  CONST_09  C4   C6   N4   C3     0.00   0.0  0
 1MD  CONST_10  C4   C1   C2   C3     0.00   0.0  0
 1MD  CONST_11  C14  C1   C2   C3   180.00   0.0  0
 1MD  CONST_14  C14  C1   C4   C6   180.00   0.0  0
 1MD  CONST_15  C19  C18  C17  C14    0.00   0.0  0
 1MD  CONST_16  C19  C20  C21  C14    0.00   0.0  0
 1MD  CONST_17  C20  C21  C14  C17    0.00   0.0  0
 1MD  CONST_18  C20  C19  C18  C17    0.00   0.0  0
 1MD  CONST_19  C21  C14  C17  C18    0.00   0.0  0
 1MD  CONST_20  C21  C20  C19  C18    0.00   0.0  0
 1MD  CONST_21  C14  C1   C4   C9     0.00   0.0  0
 1MD  CONST_22  C5   N1   C9   C4     0.00   0.0  0
 1MD  CONST_23  C13  C3   C2   C1   180.00   0.0  0
 1MD  CONST_24  CL1  C21  C14  C1     0.00   0.0  0
 1MD  CONST_25  C15  C2   C3   N4   180.00   0.0  0
 1MD  CONST_26  C15  C2   C1   C4   180.00   0.0  0
 1MD  CONST_27  C13  C3   N4   C6   180.00   0.0  0
 1MD  CONST_28  C15  C2   C1   C14    0.00   0.0  0
 1MD  CONST_29  CL1  C21  C14  C17  180.00   0.0  0
 1MD  CONST_30  CL2  C19  C18  C17  180.00   0.0  0
 1MD  CONST_31  CL1  C21  C20  C19  180.00   0.0  0
 1MD  CONST_32  CL2  C19  C20  C21  180.00   0.0  0
 1MD  CONST_33  C10  N1   C9   C4   180.00   0.0  0
 1MD  CONST_34  O1   C9   N1   C5   180.00   0.0  0
 1MD  CONST_35  H13  C17  C14  C1     0.00   0.0  0
 1MD  CONST_36  H14  C18  C17  C14  180.00   0.0  0
 1MD  CONST_37  H15  C20  C21  C14  180.00   0.0  0
 1MD  CONST_38  O1   C9   N1   C10    0.00   0.0  0
 1MD  CONST_39  C25  N2   C7   C10    0.00   0.0  0
 1MD  CONST_40  C8   N2   C7   C10  180.00   0.0  0
 1MD  CONST_41  O2   C7   N2   C25  180.00   0.0  0
 1MD  CONST_42  C8   N2   C7   O2     0.00   0.0  0
 1MD  Var_01    H1   C5   C6   N4   -58.90  30.0  1
 1MD  Var_02    N16  C15  C2   C1    74.73  30.0  2
 1MD  Var_03    C7   C10  N1   C5    81.41  30.0  2
 1MD  Var_04    H5   C13  C3   C2    50.76  30.0  2
 1MD  Var_05    O2   C7   C10  N1     2.29  30.0  1
 1MD  Var_06    H10  N16  C15  C2    62.87  30.0  3
 1MD  Var_07    H16  C25  N2   C7   100.75  30.0  3
 1MD  Var_08    H19  C8   N2   C7   121.33  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
 1MD  plan-1  C1   0.020
 1MD  plan-1  C14  0.020
 1MD  plan-1  C17  0.020
 1MD  plan-1  C18  0.020
 1MD  plan-1  C19  0.020
 1MD  plan-1  C20  0.020
 1MD  plan-1  C21  0.020
 1MD  plan-1  CL1  0.020
 1MD  plan-1  CL2  0.020
 1MD  plan-1  H13  0.020
 1MD  plan-1  H14  0.020
 1MD  plan-1  H15  0.020
 1MD  plan-2  C10  0.020
 1MD  plan-2  C7   0.020
 1MD  plan-2  N2   0.020
 1MD  plan-2  C25  0.020
 1MD  plan-2  O2   0.020
 1MD  plan-2  C8   0.020
 1MD  plan-3  C1   0.020
 1MD  plan-3  C2   0.020
 1MD  plan-3  C3   0.020
 1MD  plan-3  N4   0.020
 1MD  plan-3  C4   0.020
 1MD  plan-3  C6   0.020
 1MD  plan-3  C5   0.020
 1MD  plan-3  N1   0.020
 1MD  plan-3  C9   0.020
 1MD  plan-3  C10  0.020
 1MD  plan-3  C13  0.020
 1MD  plan-3  C14  0.020
 1MD  plan-3  C15  0.020
 1MD  plan-3  O1   0.020

