# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 04:57:10 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: 5-methyl-1-(4-nitrophenyl)-2-oxo-2,5-dihydro-1H-pyrido[3,2-b]indole-3-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1c2ccccc2c3N(C(=O)C(=Cc13)C#N)c4ccc(cc4)[N+]([O-])=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
 IY1  IY1  5-methyl-1-(4-nitrophenyl)-2-oxo-2,5-dihydro-1H-pyrido[3,2-b]indole-3-carbonitrile  ligand  38  26  .  2022-03-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_IY1
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
 IY1  N3   N  NS     0  -0.254   3.2869   4.7354   0.0108
 IY1  C18  C  CSP    0   0.066   2.8753   3.6582   0.0081
 IY1  C10  C  CR6    0  -0.224   2.3780   2.3303   0.0047
 IY1  C9   C  CR16   0  -0.156   3.2365   1.2577  -0.0064
 IY1  C8   C  CR56   0   0.311   2.6826  -0.0195  -0.0097
 IY1  N    N  NR5    0  -0.622   3.2939  -1.2500  -0.0285
 IY1  C    C  CH3    0  -0.542   4.7160  -1.4858   0.0320
 IY1  C11  C  CR6    0   0.552   0.9332   2.1948   0.0124
 IY1  O    O  O      0  -0.465   0.1544   3.1355   0.0193
 IY1  N1   N  NR6    0  -0.700   0.4698   0.8872   0.0109
 IY1  C12  C  CR6    0   0.243  -0.9426   0.6905   0.0112
 IY1  C17  C  CR16   0  -0.238  -1.6182   0.6176   1.2186
 IY1  C16  C  CR16   0  -0.273  -2.9815   0.3798   1.2238
 IY1  C15  C  CR6    0   0.271  -3.6354   0.2236   0.0110
 IY1  N2   N  N      1   0.331  -5.0713  -0.0367   0.0119
 IY1  O2   O  O     -1  -0.370  -5.6211  -0.1733  -1.0539
 IY1  O1   O  O      0  -0.370  -5.6322  -0.1028   1.0786
 IY1  C14  C  CR16   0  -0.272  -2.9690   0.3062  -1.2020
 IY1  C13  C  CR16   0  -0.239  -1.6059   0.5458  -1.1966
 IY1  C7   C  CR56   0   0.270   1.3023  -0.1950   0.0056
 IY1  C6   C  CR56   0   0.076   1.0439  -1.5923   0.0124
 IY1  C1   C  CR56   0   0.350   2.3250  -2.2038  -0.0002
 IY1  C5   C  CR16   0  -0.295  -0.1066  -2.3986   0.0325
 IY1  C4   C  CR16   0  -0.267   0.0438  -3.7649   0.0440
 IY1  C3   C  CR16   0  -0.256   1.3220  -4.3542   0.0374
 IY1  C2   C  CR16   0  -0.316   2.4695  -3.5939   0.0178
 IY1  H1   H  HCR6   0   0.317   4.3077   1.4136  -0.0104
 IY1  H2   H  HCH3   0   0.262   5.0575  -1.6130   1.0595
 IY1  H3   H  HCH3   0   0.270   4.9665  -2.3773  -0.5379
 IY1  H4   H  HCH3   0   0.270   5.2479  -0.6501  -0.4154
 IY1  H5   H  HCR6   0   0.294  -1.0833   0.7352   2.1512
 IY1  H6   H  HCR6   0   0.310  -3.5128   0.3164   2.1618
 IY1  H7   H  HCR6   0   0.310  -3.4894   0.1855  -2.1404
 IY1  H8   H  HCR6   0   0.295  -1.0614   0.6094  -2.1289
 IY1  H9   H  HCR6   0   0.250  -1.0973  -1.9675   0.0421
 IY1  H10  H  HCR6   0   0.263  -0.8311  -4.4001   0.0603
 IY1  H11  H  HCR6   0   0.268   1.4041  -5.4329   0.0507
 IY1  H12  H  HCR6   0   0.278   3.4456  -4.0597   0.0197

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
 IY1  C3   C2   aromatic  1.377  0.020  1.377
 IY1  C3   C4   aromatic  1.408  0.020  1.408
 IY1  C2   C1   aromatic  1.398  0.020  1.398
 IY1  C4   C5   aromatic  1.375  0.020  1.375
 IY1  C    N    single    1.443  0.020  1.443
 IY1  C1   N    aromatic  1.360  0.020  1.360
 IY1  C1   C6   aromatic  1.420  0.020  1.420
 IY1  C5   C6   aromatic  1.405  0.020  1.405
 IY1  N    C8   aromatic  1.374  0.020  1.374
 IY1  C6   C7   aromatic  1.421  0.020  1.421
 IY1  C8   C7   aromatic  1.391  0.020  1.391
 IY1  C8   C9   single    1.392  0.020  1.392
 IY1  C7   N1   single    1.365  0.020  1.365
 IY1  C17  C16  aromatic  1.384  0.020  1.384
 IY1  C17  C12  aromatic  1.386  0.020  1.386
 IY1  C16  C15  aromatic  1.387  0.020  1.387
 IY1  C9   C10  double    1.374  0.020  1.374
 IY1  O2   N2   single    1.207  0.020  1.207
 IY1  N1   C12  single    1.426  0.020  1.426
 IY1  N1   C11  single    1.387  0.020  1.387
 IY1  C12  C13  aromatic  1.386  0.020  1.386
 IY1  C10  C11  single    1.451  0.020  1.451
 IY1  C10  C18  single    1.418  0.020  1.418
 IY1  C15  N2   single    1.459  0.020  1.459
 IY1  C15  C14  aromatic  1.387  0.020  1.387
 IY1  N2   O1   double    1.207  0.020  1.207
 IY1  C11  O    double    1.221  0.020  1.221
 IY1  C18  N3   triple    1.153  0.020  1.153
 IY1  C13  C14  aromatic  1.384  0.020  1.384
 IY1  C9   H1   single    0.930  0.020  1.080
 IY1  C    H2   single    0.970  0.020  1.090
 IY1  C    H3   single    0.970  0.020  1.090
 IY1  C    H4   single    0.970  0.020  1.090
 IY1  C17  H5   single    0.930  0.020  1.080
 IY1  C16  H6   single    0.930  0.020  1.080
 IY1  C14  H7   single    0.930  0.020  1.080
 IY1  C13  H8   single    0.930  0.020  1.080
 IY1  C5   H9   single    0.930  0.020  1.080
 IY1  C4   H10  single    0.930  0.020  1.080
 IY1  C3   H11  single    0.930  0.020  1.080
 IY1  C2   H12  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
 IY1  C10  C18  N3   180.00  3.000
 IY1  C11  C10  C9   123.32  3.000
 IY1  C11  C10  C18  115.89  3.000
 IY1  C9   C10  C18  120.80  3.000
 IY1  H1   C9   C8   121.73  3.000
 IY1  H1   C9   C10  120.39  3.000
 IY1  C8   C9   C10  117.88  3.000
 IY1  C7   C8   N    109.18  3.000
 IY1  C7   C8   C9   120.69  3.000
 IY1  N    C8   C9   130.13  3.000
 IY1  C1   N    C    125.93  3.000
 IY1  C1   N    C8   108.11  3.000
 IY1  C    N    C8   125.75  3.000
 IY1  H4   C    H3   107.57  3.000
 IY1  H4   C    H2   108.93  3.000
 IY1  H3   C    H2   109.03  3.000
 IY1  H4   C    N    109.84  3.000
 IY1  H3   C    N    109.82  3.000
 IY1  H2   C    N    111.55  3.000
 IY1  N1   C11  O    120.87  3.000
 IY1  O    C11  C10  124.27  3.000
 IY1  N1   C11  C10  114.87  3.000
 IY1  C7   N1   C12  119.64  3.000
 IY1  C12  N1   C11  117.44  3.000
 IY1  C7   N1   C11  122.92  3.000
 IY1  C13  C12  C17  121.38  3.000
 IY1  C13  C12  N1   119.24  3.000
 IY1  C17  C12  N1   119.37  3.000
 IY1  H5   C17  C16  120.18  3.000
 IY1  H5   C17  C12  120.30  3.000
 IY1  C16  C17  C12  119.51  3.000
 IY1  H6   C16  C15  121.41  3.000
 IY1  H6   C16  C17  119.87  3.000
 IY1  C15  C16  C17  118.73  3.000
 IY1  C14  C15  N2   118.95  3.000
 IY1  C14  C15  C16  122.13  3.000
 IY1  N2   C15  C16  118.92  3.000
 IY1  O1   N2   O2   124.23  3.000
 IY1  O1   N2   C15  117.88  3.000
 IY1  O2   N2   C15  117.90  3.000
 IY1  H7   C14  C13  119.83  3.000
 IY1  H7   C14  C15  121.47  3.000
 IY1  C13  C14  C15  118.70  3.000
 IY1  H8   C13  C14  120.18  3.000
 IY1  H8   C13  C12  120.28  3.000
 IY1  C14  C13  C12  119.54  3.000
 IY1  C6   C7   N1   131.95  3.000
 IY1  N1   C7   C8   120.32  3.000
 IY1  C6   C7   C8   107.73  3.000
 IY1  C5   C6   C1   119.46  3.000
 IY1  C5   C6   C7   135.50  3.000
 IY1  C1   C6   C7   105.04  3.000
 IY1  C2   C1   C6   121.44  3.000
 IY1  C6   C1   N    109.94  3.000
 IY1  C2   C1   N    128.62  3.000
 IY1  H9   C5   C4   119.79  3.000
 IY1  H9   C5   C6   121.46  3.000
 IY1  C4   C5   C6   118.75  3.000
 IY1  H10  C4   C3   119.27  3.000
 IY1  H10  C4   C5   119.70  3.000
 IY1  C3   C4   C5   121.03  3.000
 IY1  H11  C3   C2   119.18  3.000
 IY1  H11  C3   C4   119.10  3.000
 IY1  C2   C3   C4   121.72  3.000
 IY1  H12  C2   C3   120.95  3.000
 IY1  H12  C2   C1   121.45  3.000
 IY1  C3   C2   C1   117.60  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
 IY1  CONST_01  C2   C1   N    C8   180.00   0.0  0
 IY1  CONST_02  C6   C1   N    C8     0.00   0.0  0
 IY1  CONST_03  C1   C6   C7   C8     0.00   0.0  0
 IY1  CONST_04  C5   C6   C7   C8   180.00   0.0  0
 IY1  CONST_05  C3   C2   C1   N    180.00   0.0  0
 IY1  CONST_06  C5   C6   C1   N    180.00   0.0  0
 IY1  CONST_07  C7   C6   C1   N      0.00   0.0  0
 IY1  CONST_08  C6   C7   C8   N      0.00   0.0  0
 IY1  CONST_09  C15  C16  C17  C12    0.00   0.0  0
 IY1  CONST_10  C15  C14  C13  C12    0.00   0.0  0
 IY1  CONST_11  C14  C15  C16  C17    0.00   0.0  0
 IY1  CONST_12  C14  C13  C12  C17    0.00   0.0  0
 IY1  CONST_13  C13  C12  C17  C16    0.00   0.0  0
 IY1  CONST_14  C13  C14  C15  C16    0.00   0.0  0
 IY1  CONST_15  C2   C1   C6   C7   180.00   0.0  0
 IY1  CONST_16  C4   C5   C6   C7   180.00   0.0  0
 IY1  CONST_17  C1   N    C8   C7     0.00   0.0  0
 IY1  CONST_18  C3   C2   C1   C6     0.00   0.0  0
 IY1  CONST_19  C3   C4   C5   C6     0.00   0.0  0
 IY1  CONST_20  C4   C3   C2   C1     0.00   0.0  0
 IY1  CONST_21  C4   C5   C6   C1     0.00   0.0  0
 IY1  CONST_22  C2   C3   C4   C5     0.00   0.0  0
 IY1  CONST_23  C2   C1   C6   C5     0.00   0.0  0
 IY1  CONST_24  C16  C17  C12  N1   180.00   0.0  0
 IY1  CONST_25  C14  C13  C12  N1   180.00   0.0  0
 IY1  CONST_26  C7   N1   C11  C10    0.00   0.0  0
 IY1  CONST_27  C12  N1   C11  C10  180.00   0.0  0
 IY1  CONST_28  C    N    C8   C9     0.00   0.0  0
 IY1  CONST_29  C2   C1   N    C      0.00   0.0  0
 IY1  CONST_30  C6   C1   N    C    180.00   0.0  0
 IY1  CONST_31  C7   C8   N    C    180.00   0.0  0
 IY1  CONST_32  N2   C15  C16  C17  180.00   0.0  0
 IY1  CONST_33  C13  C14  C15  N2   180.00   0.0  0
 IY1  CONST_34  C7   N1   C11  O    180.00   0.0  0
 IY1  CONST_35  C12  N1   C11  O      0.00   0.0  0
 IY1  CONST_36  H12  C2   C1   N      0.00   0.0  0
 IY1  CONST_37  H5   C17  C12  N1     0.00   0.0  0
 IY1  CONST_38  H8   C13  C12  N1     0.00   0.0  0
 IY1  CONST_39  H6   C16  C17  C12  180.00   0.0  0
 IY1  CONST_40  H7   C14  C13  C12  180.00   0.0  0
 IY1  CONST_41  H9   C5   C6   C7     0.00   0.0  0
 IY1  CONST_42  H10  C4   C5   C6   180.00   0.0  0
 IY1  CONST_43  H11  C3   C2   C1   180.00   0.0  0
 IY1  CONST_44  O2   N2   C15  C16  180.00   0.0  0
 IY1  CONST_45  O1   N2   C15  C16    0.00   0.0  0
 IY1  CONST_46  C14  C15  N2   O2     0.00   0.0  0
 IY1  CONST_47  C14  C15  N2   O1   180.00   0.0  0
 IY1  Var_01    C17  C12  N1   C11  -88.93  30.0  2
 IY1  Var_02    H2   C    N    C8    91.24  30.0  2

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
 IY1  plan-1  N1   0.020
 IY1  plan-1  C12  0.020
 IY1  plan-1  C17  0.020
 IY1  plan-1  C16  0.020
 IY1  plan-1  C15  0.020
 IY1  plan-1  N2   0.020
 IY1  plan-1  C14  0.020
 IY1  plan-1  C13  0.020
 IY1  plan-1  H5   0.020
 IY1  plan-1  H6   0.020
 IY1  plan-1  H7   0.020
 IY1  plan-1  H8   0.020
 IY1  plan-2  N3   0.020
 IY1  plan-2  C18  0.020
 IY1  plan-2  C10  0.020
 IY1  plan-2  C9   0.020
 IY1  plan-2  C8   0.020
 IY1  plan-2  N    0.020
 IY1  plan-2  C    0.020
 IY1  plan-2  C11  0.020
 IY1  plan-2  O    0.020
 IY1  plan-2  N1   0.020
 IY1  plan-2  C12  0.020
 IY1  plan-2  C7   0.020
 IY1  plan-2  C6   0.020
 IY1  plan-2  C1   0.020
 IY1  plan-2  C5   0.020
 IY1  plan-2  C4   0.020
 IY1  plan-2  C3   0.020
 IY1  plan-2  C2   0.020
 IY1  plan-2  H1   0.020
 IY1  plan-2  H9   0.020
 IY1  plan-2  H10  0.020
 IY1  plan-2  H11  0.020
 IY1  plan-2  H12  0.020
 IY1  plan-3  C15  0.020
 IY1  plan-3  N2   0.020
 IY1  plan-3  O2   0.020
 IY1  plan-3  O1   0.020

