# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 09:12:09 2022
#   Inital geometry file: a 130 line input string
#   Ligand name: [(1~{S})-2-[(2,3-dimethoxyphenyl)methylamino]-1-(4-nitrophenyl)-2-oxidanylidene-ethyl] prop-2-enoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(CNC(=O)[C@@H](OC(=O)C=C)c2ccc(cc2)[N+]([O-])=O)c1OC
#
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
 URK  URK  '[(1~{S})-2-[(2,3-dimethoxyphenyl)methylamino]-1-(4-nitrophenyl)-2-oxidanylidene-ethyl] prop-2-enoate'  ligand  49  29  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_URK
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
 URK  C1   C  C2     0  -0.454  20.0315   2.0062  -25.4490
 URK  C2   C  C1     0  -0.328  20.3717   3.1133  -24.7967
 URK  C3   C  C      0   0.590  20.8509   4.3506  -25.4371
 URK  O1   O  O2     0  -0.463  20.9465   4.2561  -26.7652
 URK  C4   C  CH1    0  -0.129  21.3540   5.4133  -27.4637
 URK  C5   C  CR6    0   0.099  21.4344   5.0613  -28.9255
 URK  C6   C  CR16   0  -0.297  22.5457   5.4445  -29.6665
 URK  C7   C  CR16   0  -0.250  22.6160   5.1830  -31.0243
 URK  C8   C  CR6    0   0.246  21.5559   4.5290  -31.6306
 URK  N1   N  N      1   0.328  21.6236   4.2398  -33.0572
 URK  O2   O  O      0  -0.372  22.6227   4.5637  -33.6539
 URK  O3   O  O     -1  -0.371  20.6776   3.6906  -33.5694
 URK  C9   C  CR16   0  -0.250  20.4346   4.1378  -30.9125
 URK  C10  C  CR16   0  -0.264  20.3787   4.4087  -29.5577
 URK  C11  C  C      0   0.534  20.3104   6.5283  -27.3036
 URK  N2   N  NH1    0  -0.636  20.7842   7.7587  -27.5272
 URK  C12  C  CH2    0  -0.331  19.9107   8.9068  -27.5878
 URK  C13  C  CR6    0  -0.001  19.0198   8.9167  -28.8105
 URK  C14  C  CR6    0   0.229  17.7980   9.5741  -28.7645
 URK  O4   O  O2     0  -0.485  17.3961  10.1906  -27.6167
 URK  C15  C  CH3    0  -0.414  16.5399   9.3977  -26.8028
 URK  C16  C  CR6    0   0.335  16.9683   9.6298  -29.8974
 URK  O5   O  O2     0  -0.462  15.8113  10.2959  -29.7409
 URK  C17  C  CH3    0  -0.435  14.9127  10.3491  -30.8294
 URK  C18  C  CR16   0  -0.397  17.3799   9.0204  -31.0767
 URK  C19  C  CR16   0  -0.243  18.6065   8.3667  -31.1176
 URK  C20  C  CR16   0  -0.312  19.4241   8.3183  -30.0040
 URK  O6   O  O      0  -0.458  19.1451   6.2730  -27.0653
 URK  O7   O  O      0  -0.442  21.1421   5.3485  -24.8263
 URK  H1   H  H      0   0.272  20.0807   1.9166  -26.5257
 URK  H2   H  H      0   0.269  19.6848   1.1374  -24.9065
 URK  H4   H  H      0   0.285  20.3064   3.1627  -23.7171
 URK  H6   H  HCH1   0   0.307  22.3333   5.7537  -27.1120
 URK  H7   H  HCR6   0   0.280  23.3732   5.9471  -29.1824
 URK  H8   H  HCR6   0   0.301  23.4884   5.4833  -31.5858
 URK  H9   H  HCR6   0   0.300  19.6108   3.6309  -31.3931
 URK  H10  H  HCR6   0   0.278  19.5012   4.1093  -29.0008
 URK  H11  H  HNH1   0   0.414  21.7675   7.8952  -27.7003
 URK  H12  H  HCH2   0   0.285  20.5470   9.7926  -27.5929
 URK  H13  H  HCH2   0   0.268  19.3213   8.9591  -26.6734
 URK  H14  H  HCH3   0   0.238  16.3457   9.9633  -25.8934
 URK  H15  H  HCH3   0   0.228  15.5883   9.1874  -27.2958
 URK  H16  H  HCH3   0   0.216  17.0110   8.4483  -26.5333
 URK  H17  H  HCH3   0   0.258  14.0427  10.9022  -30.4841
 URK  H18  H  HCH3   0   0.228  15.3413  10.8709  -31.6892
 URK  H19  H  HCH3   0   0.228  14.5933   9.3527  -31.1459
 URK  H20  H  HCR6   0   0.279  16.7629   9.0453  -31.9646
 URK  H21  H  HCR6   0   0.254  18.9221   7.8949  -32.0390
 URK  H22  H  HCR6   0   0.246  20.3757   7.8050  -30.0581

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
 URK  O3   N1   single    1.208  0.020  1.208
 URK  O2   N1   double    1.208  0.020  1.208
 URK  N1   C8   single    1.457  0.020  1.457
 URK  C9   C8   aromatic  1.388  0.020  1.388
 URK  C9   C10  aromatic  1.383  0.020  1.383
 URK  C8   C7   aromatic  1.385  0.020  1.385
 URK  C19  C18  aromatic  1.390  0.020  1.390
 URK  C19  C20  aromatic  1.382  0.020  1.382
 URK  C18  C16  aromatic  1.390  0.020  1.390
 URK  C10  C5   aromatic  1.393  0.020  1.393
 URK  C20  C13  aromatic  1.395  0.020  1.395
 URK  C7   C6   aromatic  1.384  0.020  1.384
 URK  C16  O5   single    1.344  0.020  1.344
 URK  C16  C14  aromatic  1.405  0.020  1.405
 URK  C5   C6   aromatic  1.390  0.020  1.390
 URK  C5   C4   single    1.506  0.020  1.506
 URK  C13  C14  aromatic  1.388  0.020  1.388
 URK  C13  C12  single    1.513  0.020  1.513
 URK  C17  O5   single    1.412  0.020  1.412
 URK  N2   C11  single    1.337  0.020  1.337
 URK  N2   C12  single    1.444  0.020  1.444
 URK  O6   C11  double    1.216  0.020  1.216
 URK  C14  O4   single    1.363  0.020  1.363
 URK  C11  C4   single    1.536  0.020  1.536
 URK  C4   O1   single    1.412  0.020  1.412
 URK  O4   C15  single    1.423  0.020  1.423
 URK  O1   C3   single    1.335  0.020  1.335
 URK  C3   O7   double    1.206  0.020  1.206
 URK  C3   C2   single    1.473  0.020  1.473
 URK  C2   C1   double    1.329  0.020  1.329
 URK  C1   H1   single    0.930  0.020  1.080
 URK  C1   H2   single    0.930  0.020  1.080
 URK  C2   H4   single    0.930  0.020  1.080
 URK  C4   H6   single    0.970  0.020  1.090
 URK  C6   H7   single    0.930  0.020  1.080
 URK  C7   H8   single    0.930  0.020  1.080
 URK  C9   H9   single    0.930  0.020  1.080
 URK  C10  H10  single    0.930  0.020  1.080
 URK  N2   H11  single    0.860  0.020  1.020
 URK  C12  H12  single    0.970  0.020  1.090
 URK  C12  H13  single    0.970  0.020  1.090
 URK  C15  H14  single    0.970  0.020  1.090
 URK  C15  H15  single    0.970  0.020  1.090
 URK  C15  H16  single    0.970  0.020  1.090
 URK  C17  H17  single    0.970  0.020  1.090
 URK  C17  H18  single    0.970  0.020  1.090
 URK  C17  H19  single    0.970  0.020  1.090
 URK  C18  H20  single    0.930  0.020  1.080
 URK  C19  H21  single    0.930  0.020  1.080
 URK  C20  H22  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
 URK  H2   C1   H1   116.58  3.000
 URK  H2   C1   C2   120.33  3.000
 URK  H1   C1   C2   123.08  3.000
 URK  H4   C2   C3   114.50  3.000
 URK  H4   C2   C1   120.79  3.000
 URK  C3   C2   C1   124.71  3.000
 URK  O7   C3   O1   123.04  3.000
 URK  O7   C3   C2   123.60  3.000
 URK  O1   C3   C2   113.35  3.000
 URK  C4   O1   C3   117.06  3.000
 URK  H6   C4   C11  110.41  3.000
 URK  H6   C4   C5   109.68  3.000
 URK  C11  C4   C5   107.89  3.000
 URK  H6   C4   O1   110.74  3.000
 URK  C11  C4   O1   110.33  3.000
 URK  C5   C4   O1   107.71  3.000
 URK  C10  C5   C6   119.56  3.000
 URK  C6   C5   C4   119.73  3.000
 URK  C10  C5   C4   120.64  3.000
 URK  H7   C6   C7   119.18  3.000
 URK  H7   C6   C5   120.06  3.000
 URK  C7   C6   C5   120.77  3.000
 URK  H8   C7   C8   121.46  3.000
 URK  H8   C7   C6   119.89  3.000
 URK  C8   C7   C6   118.65  3.000
 URK  C9   C8   N1   119.22  3.000
 URK  C9   C8   C7   121.66  3.000
 URK  N1   C8   C7   119.12  3.000
 URK  O3   N1   O2   124.07  3.000
 URK  O2   N1   C8   117.96  3.000
 URK  O3   N1   C8   117.97  3.000
 URK  H9   C9   C10  119.81  3.000
 URK  H9   C9   C8   121.22  3.000
 URK  C10  C9   C8   118.97  3.000
 URK  H10  C10  C9   118.89  3.000
 URK  H10  C10  C5   120.72  3.000
 URK  C9   C10  C5   120.39  3.000
 URK  O6   C11  N2   124.41  3.000
 URK  O6   C11  C4   121.27  3.000
 URK  N2   C11  C4   114.19  3.000
 URK  H11  N2   C12  118.39  3.000
 URK  H11  N2   C11  119.94  3.000
 URK  C12  N2   C11  121.62  3.000
 URK  H13  C12  H12  106.30  3.000
 URK  H13  C12  C13  111.08  3.000
 URK  H12  C12  C13  109.54  3.000
 URK  H13  C12  N2   109.29  3.000
 URK  H12  C12  N2   107.04  3.000
 URK  C13  C12  N2   113.29  3.000
 URK  C20  C13  C14  119.12  3.000
 URK  C14  C13  C12  119.64  3.000
 URK  C20  C13  C12  121.20  3.000
 URK  C16  C14  O4   119.13  3.000
 URK  O4   C14  C13  120.10  3.000
 URK  C16  C14  C13  120.77  3.000
 URK  C15  O4   C14  114.02  3.000
 URK  H16  C15  H15  108.63  3.000
 URK  H16  C15  H14  108.79  3.000
 URK  H15  C15  H14  108.77  3.000
 URK  H16  C15  O4   111.45  3.000
 URK  H15  C15  O4   111.92  3.000
 URK  H14  C15  O4   107.20  3.000
 URK  C18  C16  O5   124.82  3.000
 URK  O5   C16  C14  115.71  3.000
 URK  C18  C16  C14  119.47  3.000
 URK  C17  O5   C16  118.46  3.000
 URK  H19  C17  H18  108.77  3.000
 URK  H19  C17  H17  108.78  3.000
 URK  H18  C17  H17  108.71  3.000
 URK  H19  C17  O5   112.00  3.000
 URK  H18  C17  O5   112.01  3.000
 URK  H17  C17  O5   106.47  3.000
 URK  H20  C18  C19  119.34  3.000
 URK  H20  C18  C16  121.17  3.000
 URK  C19  C18  C16  119.49  3.000
 URK  H21  C19  C20  119.87  3.000
 URK  H21  C19  C18  119.16  3.000
 URK  C20  C19  C18  120.97  3.000
 URK  H22  C20  C19  119.76  3.000
 URK  H22  C20  C13  120.05  3.000
 URK  C19  C20  C13  120.18  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
 URK  CONST_01  C8   C9   C10  C5     0.00   0.0  0
 URK  CONST_02  C8   C7   C6   C5     0.00   0.0  0
 URK  CONST_03  C9   C8   C7   C6     0.00   0.0  0
 URK  CONST_04  C9   C10  C5   C6     0.00   0.0  0
 URK  CONST_05  C10  C9   C8   C7     0.00   0.0  0
 URK  CONST_06  C10  C5   C6   C7     0.00   0.0  0
 URK  CONST_07  C18  C19  C20  C13    0.00   0.0  0
 URK  CONST_08  C18  C16  C14  C13    0.00   0.0  0
 URK  CONST_09  C19  C18  C16  C14    0.00   0.0  0
 URK  CONST_10  C19  C20  C13  C14    0.00   0.0  0
 URK  CONST_11  C20  C19  C18  C16    0.00   0.0  0
 URK  CONST_12  C20  C13  C14  C16    0.00   0.0  0
 URK  CONST_13  C9   C10  C5   C4   180.00   0.0  0
 URK  CONST_14  C7   C6   C5   C4   180.00   0.0  0
 URK  CONST_15  N1   C8   C7   C6   180.00   0.0  0
 URK  CONST_16  C10  C9   C8   N1   180.00   0.0  0
 URK  CONST_17  C19  C20  C13  C12  180.00   0.0  0
 URK  CONST_18  C16  C14  C13  C12  180.00   0.0  0
 URK  CONST_19  O5   C16  C14  C13  180.00   0.0  0
 URK  CONST_20  C18  C16  C14  O4   180.00   0.0  0
 URK  CONST_21  C20  C13  C14  O4   180.00   0.0  0
 URK  CONST_22  C19  C18  C16  O5   180.00   0.0  0
 URK  CONST_23  H9   C9   C10  C5   180.00   0.0  0
 URK  CONST_24  H8   C7   C6   C5   180.00   0.0  0
 URK  CONST_25  H10  C10  C5   C6   180.00   0.0  0
 URK  CONST_26  H7   C6   C7   C8   180.00   0.0  0
 URK  CONST_27  H21  C19  C20  C13  180.00   0.0  0
 URK  CONST_28  H20  C18  C16  C14  180.00   0.0  0
 URK  CONST_29  H22  C20  C13  C14  180.00   0.0  0
 URK  CONST_30  O3   N1   C8   C7   180.00   0.0  0
 URK  CONST_31  O2   N1   C8   C7     0.00   0.0  0
 URK  CONST_32  C9   C8   N1   O2   180.00   0.0  0
 URK  CONST_33  C9   C8   N1   O3     0.00   0.0  0
 URK  CONST_34  C12  N2   C11  C4   180.00   0.0  0
 URK  CONST_35  O6   C11  N2   C12    0.00   0.0  0
 URK  CONST_36  H11  N2   C11  C4     0.00   0.0  0
 URK  Var_01    C20  C13  C12  N2   -29.28  30.0  2
 URK  Var_02    C16  C14  O4   C15   84.96  30.0  2
 URK  Var_03    C18  C16  O5   C17    2.46  30.0  3
 URK  Var_04    C13  C12  N2   C11  -69.43  30.0  3
 URK  Var_05    H14  C15  O4   C14  176.12  30.0  3
 URK  Var_06    H17  C17  O5   C16  178.38  30.0  3
 URK  Var_07    O1   C3   C2   C1    -1.44  30.0  2
 URK  Var_08    H1   C1   C2   C3     0.16   0.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 URK  chir_01  C4  C5  C11  O1  negativ

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
 URK  plan-1  C4   0.020
 URK  plan-1  C5   0.020
 URK  plan-1  C6   0.020
 URK  plan-1  C7   0.020
 URK  plan-1  C8   0.020
 URK  plan-1  N1   0.020
 URK  plan-1  C9   0.020
 URK  plan-1  C10  0.020
 URK  plan-1  H7   0.020
 URK  plan-1  H8   0.020
 URK  plan-1  H9   0.020
 URK  plan-1  H10  0.020
 URK  plan-2  C12  0.020
 URK  plan-2  C13  0.020
 URK  plan-2  C14  0.020
 URK  plan-2  O4   0.020
 URK  plan-2  C16  0.020
 URK  plan-2  O5   0.020
 URK  plan-2  C18  0.020
 URK  plan-2  C19  0.020
 URK  plan-2  C20  0.020
 URK  plan-2  H20  0.020
 URK  plan-2  H21  0.020
 URK  plan-2  H22  0.020
 URK  plan-3  C4   0.020
 URK  plan-3  C11  0.020
 URK  plan-3  N2   0.020
 URK  plan-3  C12  0.020
 URK  plan-3  O6   0.020
 URK  plan-3  H11  0.020
 URK  plan-4  C8   0.020
 URK  plan-4  N1   0.020
 URK  plan-4  O2   0.020
 URK  plan-4  O3   0.020
 URK  plan-5  C2   0.020
 URK  plan-5  C3   0.020
 URK  plan-5  O1   0.020
 URK  plan-5  O7   0.020
 URK  plan-6  C1   0.020
 URK  plan-6  C2   0.020
 URK  plan-6  C3   0.020
 URK  plan-6  H1   0.020
 URK  plan-6  H2   0.020
 URK  plan-6  H4   0.020

