# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 22:19:34 2022
#   Inital geometry file: a 96 line input string
#   Ligand name: 11-ethyl-6-methyl-9-nitro-6,11-dihydro-5H-pyrido[2,3-b][1,5]benzodiazepin-5-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN1c2cc(ccc2N(C)C(=O)c3cccnc13)[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
 U05  U05  11-ethyl-6-methyl-9-nitro-6,11-dihydro-5H-pyrido[2,3-b][1,5]benzodiazepin-5-one  ligand  36  22  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_U05
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
 U05  N1    N  N      0  -0.430  -2.0995  -0.0193   2.2208
 U05  C2    C  CR16   0  -0.045  -2.4615   0.9144   3.0902
 U05  C3    C  CR16   0  -0.341  -1.5898   1.8655   3.5930
 U05  C4    C  CR16   0  -0.151  -0.2591   1.7742   3.2246
 U05  C4A   C  CR6    0  -0.195   0.1459   0.7906   2.3303
 U05  C5    C  C      0   0.556   1.6057   0.5635   2.1652
 U05  O13   O  O      0  -0.453   2.3573   0.8043   3.0931
 U05  N6    N  NT     0  -0.569   2.0880   0.0747   0.9863
 U05  C12   C  CH3    0  -0.558   3.5219  -0.1809   0.9082
 U05  C6A   C  CR6    0   0.333   1.3636   0.0959  -0.2141
 U05  C7    C  CR16   0  -0.298   1.9484   0.6401  -1.3567
 U05  C8    C  CR16   0  -0.279   1.3048   0.6039  -2.5764
 U05  C9    C  CR6    0   0.265   0.0464   0.0265  -2.6395
 U05  N     N  N      1   0.326  -0.6543  -0.0203  -3.9106
 U05  O1    O  O     -1  -0.377  -0.1123   0.4676  -4.8745
 U05  O2    O  O      0  -0.378  -1.7442  -0.5423  -3.9425
 U05  C10   C  CR16   0  -0.330  -0.5688  -0.4980  -1.5159
 U05  C11   C  CR6    0   0.294   0.0924  -0.4799  -0.2957
 U05  N11   N  NT     0  -0.572  -0.5016  -1.0206   0.8607
 U05  C14   C  CH2    0  -0.318  -1.3809  -2.1782   0.7092
 U05  C15   C  CH3    0  -0.679  -0.6600  -3.3469   0.0622
 U05  C1A   C  CR6    0   0.456  -0.8399  -0.0662   1.8186
 U05  H2    H  HCR6   0   0.274  -3.5022   0.9075   3.3935
 U05  H3    H  HCR6   0   0.276  -1.9355   2.6269   4.2770
 U05  H4    H  HCR6   0   0.280   0.4707   2.4519   3.6470
 U05  H121  H  HCH3   0   0.273   3.8503  -0.6944   1.8073
 U05  H122  H  HCH3   0   0.264   3.7182  -0.8262   0.0562
 U05  H123  H  HCH3   0   0.255   4.1014   0.7368   0.8017
 U05  H7    H  HCR6   0   0.298   2.9274   1.0951  -1.2963
 U05  H8    H  HCR6   0   0.302   1.7827   1.0220  -3.4494
 U05  H10   H  HCR6   0   0.306  -1.5555  -0.9327  -1.5869
 U05  H141  H  HCH2   0   0.235  -2.2970  -1.9322   0.1632
 U05  H142  H  HCH2   0   0.264  -1.6961  -2.4652   1.7106
 U05  H151  H  HCH3   0   0.246  -1.3241  -4.2106   0.0428
 U05  H152  H  HCH3   0   0.234  -0.3585  -3.1476  -0.9663
 U05  H153  H  HCH3   0   0.236   0.2305  -3.6164   0.6300

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
 U05  N1   C2    aromatic  1.326  0.020  1.326
 U05  N1   C1A   aromatic  1.323  0.020  1.323
 U05  C2   C3    aromatic  1.385  0.020  1.385
 U05  C2   H2    single    0.930  0.020  1.080
 U05  C3   C4    aromatic  1.384  0.020  1.384
 U05  C3   H3    single    0.930  0.020  1.080
 U05  C4   C4A   aromatic  1.390  0.020  1.390
 U05  C4   H4    single    0.930  0.020  1.080
 U05  C4A  C5    single    1.487  0.020  1.487
 U05  C4A  C1A   aromatic  1.403  0.020  1.403
 U05  C5   O13   double    1.218  0.020  1.218
 U05  C5   N6    single    1.364  0.020  1.364
 U05  N6   C12   single    1.459  0.020  1.459
 U05  N6   C6A   single    1.402  0.020  1.402
 U05  C12  H121  single    0.970  0.020  1.090
 U05  C12  H122  single    0.970  0.020  1.090
 U05  C12  H123  single    0.970  0.020  1.090
 U05  C6A  C7    aromatic  1.394  0.020  1.394
 U05  C6A  C11   aromatic  1.398  0.020  1.398
 U05  C7   C8    aromatic  1.380  0.020  1.380
 U05  C7   H7    single    0.930  0.020  1.080
 U05  C8   C9    aromatic  1.386  0.020  1.386
 U05  C8   H8    single    0.930  0.020  1.080
 U05  C9   N     single    1.452  0.020  1.452
 U05  C9   C10   aromatic  1.384  0.020  1.384
 U05  N    O1    single    1.209  0.020  1.209
 U05  N    O2    double    1.209  0.020  1.209
 U05  C10  C11   aromatic  1.388  0.020  1.388
 U05  C10  H10   single    0.930  0.020  1.080
 U05  C11  N11   single    1.408  0.020  1.408
 U05  N11  C14   single    1.462  0.020  1.462
 U05  N11  C1A   single    1.394  0.020  1.394
 U05  C14  C15   single    1.518  0.020  1.518
 U05  C14  H141  single    0.970  0.020  1.090
 U05  C14  H142  single    0.970  0.020  1.090
 U05  C15  H151  single    0.970  0.020  1.090
 U05  C15  H152  single    0.970  0.020  1.090
 U05  C15  H153  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
 U05  C1A   N1   C2    118.95  3.000
 U05  H2    C2   C3    120.48  3.000
 U05  H2    C2   N1    116.17  3.000
 U05  C3    C2   N1    123.35  3.000
 U05  H3    C3   C4    121.53  3.000
 U05  H3    C3   C2    120.83  3.000
 U05  C4    C3   C2    117.61  3.000
 U05  H4    C4   C4A   119.87  3.000
 U05  H4    C4   C3    120.23  3.000
 U05  C4A   C4   C3    119.89  3.000
 U05  C1A   C4A  C5    123.80  3.000
 U05  C1A   C4A  C4    117.53  3.000
 U05  C5    C4A  C4    117.76  3.000
 U05  N6    C5   O13   120.72  3.000
 U05  N6    C5   C4A   119.86  3.000
 U05  O13   C5   C4A   119.42  3.000
 U05  C6A   N6   C12   117.69  3.000
 U05  C6A   N6   C5    123.48  3.000
 U05  C12   N6   C5    117.17  3.000
 U05  H123  C12  H122  109.10  3.000
 U05  H123  C12  H121  108.54  3.000
 U05  H122  C12  H121  108.28  3.000
 U05  H123  C12  N6    112.34  3.000
 U05  H122  C12  N6    108.88  3.000
 U05  H121  C12  N6    109.62  3.000
 U05  C11   C6A  C7    119.63  3.000
 U05  C11   C6A  N6    120.90  3.000
 U05  C7    C6A  N6    119.39  3.000
 U05  H7    C7   C8    118.87  3.000
 U05  H7    C7   C6A   119.89  3.000
 U05  C8    C7   C6A   121.24  3.000
 U05  H8    C8   C9    121.76  3.000
 U05  H8    C8   C7    119.89  3.000
 U05  C9    C8   C7    118.35  3.000
 U05  C10   C9   N     118.94  3.000
 U05  C10   C9   C8    121.63  3.000
 U05  N     C9   C8    119.43  3.000
 U05  O2    N    O1    123.88  3.000
 U05  O2    N    C9    118.17  3.000
 U05  O1    N    C9    117.95  3.000
 U05  H10   C10  C11   119.87  3.000
 U05  H10   C10  C9    120.33  3.000
 U05  C11   C10  C9    119.80  3.000
 U05  N11   C11  C10   121.07  3.000
 U05  N11   C11  C6A   119.60  3.000
 U05  C10   C11  C6A   119.34  3.000
 U05  C1A   N11  C14   117.88  3.000
 U05  C1A   N11  C11   113.82  3.000
 U05  C14   N11  C11   118.22  3.000
 U05  H142  C14  H141  106.01  3.000
 U05  H142  C14  C15   109.07  3.000
 U05  H141  C14  C15   110.97  3.000
 U05  H142  C14  N11   106.72  3.000
 U05  H141  C14  N11   112.17  3.000
 U05  C15   C14  N11   111.61  3.000
 U05  H153  C15  H152  108.10  3.000
 U05  H153  C15  H151  108.13  3.000
 U05  H152  C15  H151  107.26  3.000
 U05  H153  C15  C14   110.87  3.000
 U05  H152  C15  C14   113.12  3.000
 U05  H151  C15  C14   109.17  3.000
 U05  N11   C1A  C4A   119.89  3.000
 U05  N11   C1A  N1    117.66  3.000
 U05  C4A   C1A  N1    122.44  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
 U05  CONST_01  C4    C3   C2   N1      0.00   0.0  0
 U05  CONST_02  C4    C4A  C1A  N1      0.00   0.0  0
 U05  CONST_03  C4A   C1A  N1   C2      0.00   0.0  0
 U05  CONST_04  C4A   C4   C3   C2      0.00   0.0  0
 U05  CONST_05  C1A   N1   C2   C3      0.00   0.0  0
 U05  CONST_06  C1A   C4A  C4   C3      0.00   0.0  0
 U05  CONST_07  C9    C8   C7   C6A     0.00   0.0  0
 U05  CONST_08  C9    C10  C11  C6A     0.00   0.0  0
 U05  CONST_09  C10   C11  C6A  C7      0.00   0.0  0
 U05  CONST_10  C10   C9   C8   C7      0.00   0.0  0
 U05  CONST_11  C11   C6A  C7   C8      0.00   0.0  0
 U05  CONST_12  C11   C10  C9   C8      0.00   0.0  0
 U05  CONST_14  N     C9   C8   C7    180.00   0.0  0
 U05  CONST_15  C11   C10  C9   N     180.00   0.0  0
 U05  CONST_16  C12   N6   C5   C4A   180.00   0.0  0
 U05  CONST_18  H3    C3   C2   N1    180.00   0.0  0
 U05  CONST_19  H4    C4   C3   C2    180.00   0.0  0
 U05  CONST_20  H2    C2   C3   C4    180.00   0.0  0
 U05  CONST_21  H7    C7   C6A  N6      0.00   0.0  0
 U05  CONST_22  H8    C8   C7   C6A   180.00   0.0  0
 U05  CONST_23  H10   C10  C11  C6A   180.00   0.0  0
 U05  CONST_24  C12   N6   C5   O13     0.00   0.0  0
 U05  CONST_25  O1    N    C9   C8      0.00   0.0  0
 U05  CONST_26  O2    N    C9   C8    180.00   0.0  0
 U05  CONST_27  C10   C9   N    O1    180.00   0.0  0
 U05  CONST_28  C10   C9   N    O2      0.00   0.0  0
 U05  Var_01    C11   N11  C1A  N1    123.75  30.0  1
 U05  Var_02    N6    C5   C4A  C4   -152.51  30.0  1
 U05  Var_03    C7    C6A  N6   C5    127.85  30.0  1
 U05  Var_04    C1A   N11  C11  C6A    67.78  30.0  1
 U05  Var_05    C15   C14  N11  C11    58.43  30.0  3
 U05  Var_06    H121  C12  N6   C5     45.02  30.0  3
 U05  Var_07    H151  C15  C14  N11   175.41  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
 U05  plan-1  C4A  0.020
 U05  plan-1  C5   0.020
 U05  plan-1  O13  0.020
 U05  plan-1  N6   0.020
 U05  plan-1  C12  0.020
 U05  plan-1  C6A  0.020
 U05  plan-2  N1   0.020
 U05  plan-2  C2   0.020
 U05  plan-2  C3   0.020
 U05  plan-2  C4   0.020
 U05  plan-2  C4A  0.020
 U05  plan-2  C5   0.020
 U05  plan-2  N11  0.020
 U05  plan-2  C1A  0.020
 U05  plan-2  H2   0.020
 U05  plan-2  H3   0.020
 U05  plan-2  H4   0.020
 U05  plan-3  N6   0.020
 U05  plan-3  C6A  0.020
 U05  plan-3  C7   0.020
 U05  plan-3  C8   0.020
 U05  plan-3  C9   0.020
 U05  plan-3  N    0.020
 U05  plan-3  C10  0.020
 U05  plan-3  C11  0.020
 U05  plan-3  N11  0.020
 U05  plan-3  H7   0.020
 U05  plan-3  H8   0.020
 U05  plan-3  H10  0.020
 U05  plan-4  C9   0.020
 U05  plan-4  N    0.020
 U05  plan-4  O1   0.020
 U05  plan-4  O2   0.020

