# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 11:40:11 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: (~{E})-3-[3-nitro-4,5-bis(oxidanyl)phenyl]-2-(1,3-oxazinan-3-ylcarbonyl)prop-2-enenitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cc(\C=C(/C#N)C(=O)N2CCCOC2)cc(c1O)[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
 7YC  7YC  (~{E})-3-[3-nitro-4,5-bis(oxidanyl)phenyl]-2-(1,3-oxazinan-3-ylcarbonyl)prop-2-enenitrile  ligand  36  23  .  2022-07-23  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_7YC
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
 7YC  C10  C  CSP    0   0.040   1.5123  -1.1437  -1.6340
 7YC  N12  N  NT     0  -0.475   3.8556   0.1754  -0.6123
 7YC  C21  C  CH2    0  -0.199   5.5676  -0.0480   1.5961
 7YC  C22  C  CH2    0  -0.457   5.5893   1.2205   0.7577
 7YC  O15  O  O      0  -0.418  -5.3421   0.7385   1.4644
 7YC  O16  O  O     -1  -0.351  -3.7737   2.1044   1.9241
 7YC  C03  C  CR6    0   0.222  -3.2727   0.3238   0.5896
 7YC  C04  C  CR16   0  -0.398  -1.9508   0.7435   0.4890
 7YC  C02  C  CR6    0   0.267  -3.7245  -0.8323  -0.0588
 7YC  O17  O  OH1    0  -0.595  -4.9510  -1.3209  -0.0326
 7YC  C01  C  CR6    0   0.348  -2.7906  -1.5639  -0.8280
 7YC  O18  O  OH1    0  -0.617  -3.1683  -2.6733  -1.4758
 7YC  C06  C  CR16   0  -0.402  -1.4863  -1.1457  -0.9210
 7YC  C05  C  CR6    0   0.166  -1.0417   0.0148  -0.2609
 7YC  C07  C  C1     0  -0.220   0.3115   0.5312  -0.3033
 7YC  C08  C  C      0  -0.163   1.4386   0.0458  -0.8616
 7YC  N11  N  NS     0  -0.237   1.6210  -2.0882  -2.2882
 7YC  C09  C  C      0   0.574   2.6991   0.8653  -0.7754
 7YC  O13  O  O      0  -0.447   2.6438   2.0715  -0.9190
 7YC  C23  C  CH2    0  -0.343   5.1253   0.8964  -0.6565
 7YC  O20  O  O2     0  -0.474   4.2984  -0.6789   1.5278
 7YC  C19  C  CH2    0  -0.061   3.9494  -1.0115   0.2166
 7YC  H1   H  HCH2   0   0.211   6.3466  -0.7388   1.2443
 7YC  H2   H  HCH2   0   0.243   4.9359   1.9780   1.1971
 7YC  H3   H  HCR6   0   0.311  -1.6329   1.6418   0.9984
 7YC  H4   H  HOH1   0   0.497  -5.5171  -0.7531   0.5253
 7YC  H5   H  HOH1   0   0.485  -4.1059  -2.8603  -1.3421
 7YC  H6   H  HCR6   0   0.289  -0.8204  -1.7411  -1.5279
 7YC  H7   H  H      0   0.298   0.4377   1.4694   0.2262
 7YC  H8   H  HCH2   0   0.261   5.8498   0.2420  -1.1493
 7YC  H9   H  HCH2   0   0.263   3.0012  -1.5403   0.2671
 7YC  H10  H  HCH2   0   0.249   5.7605   0.1646   2.6476
 7YC  H11  H  HCH2   0   0.251   6.6006   1.6305   0.7362
 7YC  H12  H  HCH2   0   0.274   5.0235   1.7896  -1.2669
 7YC  H13  H  HCH2   0   0.242   4.6961  -1.6774  -0.2327
 7YC  N14  N  N      1   0.365  -4.1821   1.1133   1.3803

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
 7YC  C10  C08  single    1.420  0.020  1.420
 7YC  C10  N11  triple    1.154  0.020  1.154
 7YC  N12  C09  single    1.356  0.020  1.356
 7YC  N12  C23  single    1.461  0.020  1.461
 7YC  N12  C19  single    1.451  0.020  1.451
 7YC  C21  C22  single    1.521  0.020  1.521
 7YC  C21  O20  single    1.419  0.020  1.419
 7YC  C22  C23  single    1.523  0.020  1.523
 7YC  N14  C03  single    1.441  0.020  1.441
 7YC  C03  C04  aromatic  1.391  0.020  1.391
 7YC  C03  C02  aromatic  1.400  0.020  1.400
 7YC  C04  C05  aromatic  1.386  0.020  1.386
 7YC  C02  O17  single    1.321  0.020  1.321
 7YC  C02  C01  aromatic  1.414  0.020  1.414
 7YC  C01  O18  single    1.339  0.020  1.339
 7YC  C01  C06  aromatic  1.373  0.020  1.373
 7YC  C06  C05  aromatic  1.407  0.020  1.407
 7YC  C05  C07  single    1.449  0.020  1.449
 7YC  C07  C08  double    1.348  0.020  1.348
 7YC  C08  C09  single    1.506  0.020  1.506
 7YC  C09  O13  double    1.216  0.020  1.216
 7YC  O20  C19  single    1.397  0.020  1.397
 7YC  N14  O16  single    1.202  0.020  1.202
 7YC  N14  O15  double    1.222  0.020  1.222
 7YC  C21  H1   single    0.970  0.020  1.090
 7YC  C22  H2   single    0.970  0.020  1.090
 7YC  C04  H3   single    0.930  0.020  1.080
 7YC  O17  H4   single    0.850  0.020  0.980
 7YC  O18  H5   single    0.850  0.020  0.980
 7YC  C06  H6   single    0.930  0.020  1.080
 7YC  C07  H7   single    0.930  0.020  1.080
 7YC  C23  H8   single    0.970  0.020  1.090
 7YC  C19  H9   single    0.970  0.020  1.090
 7YC  C21  H10  single    0.970  0.020  1.090
 7YC  C22  H11  single    0.970  0.020  1.090
 7YC  C23  H12  single    0.970  0.020  1.090
 7YC  C19  H13  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
 7YC  N11  C10  C08  180.00  3.000
 7YC  C19  N12  C23  111.40  3.000
 7YC  C19  N12  C09  122.68  3.000
 7YC  C23  N12  C09  119.10  3.000
 7YC  H10  C21  H1   107.82  3.000
 7YC  H10  C21  O20  106.94  3.000
 7YC  H1   C21  O20  109.82  3.000
 7YC  H10  C21  C22  111.51  3.000
 7YC  H1   C21  C22  109.74  3.000
 7YC  O20  C21  C22  110.92  3.000
 7YC  H11  C22  H2   107.55  3.000
 7YC  H11  C22  C23  110.12  3.000
 7YC  H2   C22  C23  109.80  3.000
 7YC  H11  C22  C21  109.72  3.000
 7YC  H2   C22  C21  110.37  3.000
 7YC  C23  C22  C21  109.27  3.000
 7YC  C02  C03  C04  121.49  3.000
 7YC  C02  C03  N14  120.19  3.000
 7YC  C04  C03  N14  118.32  3.000
 7YC  H3   C04  C05  119.96  3.000
 7YC  H3   C04  C03  119.77  3.000
 7YC  C05  C04  C03  120.27  3.000
 7YC  C01  C02  O17  115.65  3.000
 7YC  C01  C02  C03  117.77  3.000
 7YC  O17  C02  C03  126.58  3.000
 7YC  H4   O17  C02  109.55  3.000
 7YC  C06  C01  O18  119.18  3.000
 7YC  C06  C01  C02  120.45  3.000
 7YC  O18  C01  C02  120.37  3.000
 7YC  H5   O18  C01  111.55  3.000
 7YC  H6   C06  C05  121.57  3.000
 7YC  H6   C06  C01  117.13  3.000
 7YC  C05  C06  C01  121.30  3.000
 7YC  C07  C05  C06  125.11  3.000
 7YC  C07  C05  C04  116.18  3.000
 7YC  C06  C05  C04  118.71  3.000
 7YC  H7   C07  C08  114.60  3.000
 7YC  H7   C07  C05  113.74  3.000
 7YC  C08  C07  C05  131.65  3.000
 7YC  C09  C08  C07  118.70  3.000
 7YC  C09  C08  C10  116.32  3.000
 7YC  C07  C08  C10  124.76  3.000
 7YC  O13  C09  C08  119.67  3.000
 7YC  O13  C09  N12  123.88  3.000
 7YC  C08  C09  N12  116.34  3.000
 7YC  H12  C23  H8   107.51  3.000
 7YC  H12  C23  C22  112.03  3.000
 7YC  H8   C23  C22  110.11  3.000
 7YC  H12  C23  N12  109.95  3.000
 7YC  H8   C23  N12  107.11  3.000
 7YC  C22  C23  N12  109.98  3.000
 7YC  C19  O20  C21  111.99  3.000
 7YC  H13  C19  H9   108.51  3.000
 7YC  H13  C19  O20  111.04  3.000
 7YC  H9   C19  O20  106.87  3.000
 7YC  H13  C19  N12  107.86  3.000
 7YC  H9   C19  N12  111.61  3.000
 7YC  O20  C19  N12  110.96  3.000
 7YC  C03  N14  O16  119.06  3.000
 7YC  O16  N14  O15  122.98  3.000
 7YC  C03  N14  O15  117.97  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
 7YC  CONST_01  C06  C05  C04  C03    0.00   0.0  0
 7YC  CONST_02  C06  C01  C02  C03    0.00   0.0  0
 7YC  CONST_03  C01  C02  C03  C04    0.00   0.0  0
 7YC  CONST_04  C01  C06  C05  C04    0.00   0.0  0
 7YC  CONST_05  C05  C04  C03  C02    0.00   0.0  0
 7YC  CONST_06  C05  C06  C01  C02    0.00   0.0  0
 7YC  CONST_07  C05  C04  C03  N14  180.00   0.0  0
 7YC  CONST_08  C01  C02  C03  N14  180.00   0.0  0
 7YC  CONST_09  C07  C05  C04  C03  180.00   0.0  0
 7YC  CONST_10  O18  C01  C02  C03  180.00   0.0  0
 7YC  CONST_11  O17  C02  C03  C04  180.00   0.0  0
 7YC  CONST_12  C06  C01  C02  O17  180.00   0.0  0
 7YC  CONST_13  C07  C05  C06  C01  180.00   0.0  0
 7YC  CONST_14  C05  C06  C01  O18  180.00   0.0  0
 7YC  CONST_15  H6   C06  C05  C04  180.00   0.0  0
 7YC  CONST_16  H3   C04  C03  C02  180.00   0.0  0
 7YC  CONST_17  C23  N12  C09  C08  180.00   0.0  0
 7YC  CONST_19  C23  N12  C09  O13    0.00   0.0  0
 7YC  CONST_21  C04  C03  N14  O15  180.00   0.0  0
 7YC  CONST_22  C02  C03  N14  O15    0.00   0.0  0
 7YC  CONST_23  C04  C03  N14  O16    0.00   0.0  0
 7YC  CONST_24  C02  C03  N14  O16  180.00   0.0  0
 7YC  Var_01    C21  C22  C23  N12   51.39  30.0  1
 7YC  Var_02    C19  N12  C23  C22  -55.09  30.0  1
 7YC  Var_03    O20  C19  N12  C23   59.84  30.0  1
 7YC  Var_04    O20  C21  C22  C23  -53.08  30.0  1
 7YC  Var_05    H9   C19  O20  C21  176.55  30.0  1
 7YC  Var_06    C08  C07  C05  C04  175.81  30.0  2
 7YC  Var_07    C05  C07  C08  C10    3.11   0.0  2
 7YC  Var_08    N12  C09  C08  C10  -41.50  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
 7YC  plan-1  C03  0.020
 7YC  plan-1  C04  0.020
 7YC  plan-1  C02  0.020
 7YC  plan-1  O17  0.020
 7YC  plan-1  C01  0.020
 7YC  plan-1  O18  0.020
 7YC  plan-1  C06  0.020
 7YC  plan-1  C05  0.020
 7YC  plan-1  C07  0.020
 7YC  plan-1  H3   0.020
 7YC  plan-1  H6   0.020
 7YC  plan-1  N14  0.020
 7YC  plan-2  O15  0.020
 7YC  plan-2  O16  0.020
 7YC  plan-2  C03  0.020
 7YC  plan-2  N14  0.020
 7YC  plan-3  N12  0.020
 7YC  plan-3  C08  0.020
 7YC  plan-3  C09  0.020
 7YC  plan-3  O13  0.020
 7YC  plan-3  C23  0.020
 7YC  plan-3  C19  0.020
 7YC  plan-4  C10  0.020
 7YC  plan-4  C05  0.020
 7YC  plan-4  C07  0.020
 7YC  plan-4  C08  0.020
 7YC  plan-4  C09  0.020
 7YC  plan-4  H7   0.020

