# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 05:04:27 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: (2S)-N-(4-nitrophenyl)-2-phenyl-thiomorpholine-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [O-][N+](=O)c1ccc(NC(=O)N2CCS[C@H](C2)c3ccccc3)cc1
#
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
 QYD  QYD  (2S)-N-(4-nitrophenyl)-2-phenyl-thiomorpholine-4-carboxamide  ligand  41  24  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QYD
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
 QYD  C1    C  CR16   0  -0.264   5.0832  -3.2005  -0.1367
 QYD  C2    C  CR16   0  -0.238   3.9638  -3.1728  -0.9568
 QYD  C3    C  CR16   0  -0.315   3.1826  -2.0268  -1.0293
 QYD  C4    C  CR6    0   0.167   3.5094  -0.8967  -0.2854
 QYD  C5    C  CR16   0  -0.288   4.6381  -0.9311   0.5328
 QYD  C6    C  CR16   0  -0.240   5.4186  -2.0757   0.6070
 QYD  C7    C  CH1    0  -0.475   2.6311   0.3215  -0.3432
 QYD  C8    C  CH2    0  -0.303   1.9834   0.6100   1.0136
 QYD  N9    N  NT     0  -0.491   1.1017   1.7631   0.9587
 QYD  C10   C  CH2    0  -0.309   1.8032   3.0193   0.7418
 QYD  C11   C  CH2    0  -0.565   2.4334   3.0785  -0.6391
 QYD  S12   S  S2     0   0.007   3.6428   1.7451  -0.8832
 QYD  C13   C  C      0   0.745  -0.2126   1.7066   0.5907
 QYD  O14   O  O      0  -0.497  -0.8161   2.6708   0.1533
 QYD  N15   N  NH1    0  -0.792  -0.8256   0.4850   0.7890
 QYD  C16   C  CR6    0   0.421  -2.0969   0.1102   0.4034
 QYD  C17   C  CR16   0  -0.357  -2.6059  -1.0662   0.9737
 QYD  C18   C  CR16   0  -0.254  -3.8480  -1.5478   0.6294
 QYD  C19   C  CR6    0   0.230  -4.6104  -0.8525  -0.3021
 QYD  C20   C  CR16   0  -0.259  -4.1234   0.3104  -0.8839
 QYD  C21   C  CR16   0  -0.306  -2.8771   0.7928  -0.5388
 QYD  N22   N  N      1   0.326  -5.9153  -1.3449  -0.6704
 QYD  O23   O  O     -1  -0.391  -6.3068  -2.3701  -0.1578
 QYD  O24   O  O      0  -0.391  -6.5614  -0.7121  -1.4761
 QYD  H1    H  HCR6   0   0.258   5.6930  -4.0926  -0.0776
 QYD  H2    H  HCR6   0   0.258   3.6975  -4.0425  -1.5435
 QYD  H6    H  HCR6   0   0.259   6.2923  -2.0888   1.2456
 QYD  H3    H  HCR6   0   0.257   2.3104  -2.0102  -1.6721
 QYD  H5    H  HCR6   0   0.255   4.9165  -0.0575   1.1101
 QYD  H7    H  HCH1   0   0.297   1.8412   0.1599  -1.0824
 QYD  H81C  H  HCH2   0   0.277   1.4685  -0.2857   1.3574
 QYD  H82C  H  HCH2   0   0.273   2.7561   0.8099   1.7584
 QYD  H101  H  HCH2   0   0.279   1.1131   3.8501   0.8703
 QYD  H102  H  HCH2   0   0.263   2.5744   3.1120   1.5089
 QYD  H111  H  HCH2   0   0.275   1.6675   3.0342  -1.4151
 QYD  H112  H  HCH2   0   0.291   2.9842   4.0115  -0.7626
 QYD  H15   H  HNH1   0   0.424  -0.3751  -0.1677   1.4098
 QYD  H17   H  HCR6   0   0.288  -2.0139  -1.6093   1.6999
 QYD  H21   H  HCR6   0   0.293  -2.5231   1.6928  -1.0116
 QYD  H18   H  HCR6   0   0.298  -4.2099  -2.4549   1.0906
 QYD  H20   H  HCR6   0   0.297  -4.7066   0.8511  -1.6148

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
 QYD  C1   C2    aromatic  1.388  0.020  1.388
 QYD  C1   C6    aromatic  1.390  0.020  1.390
 QYD  C2   C3    aromatic  1.389  0.020  1.389
 QYD  C3   C4    aromatic  1.392  0.020  1.392
 QYD  C4   C5    aromatic  1.394  0.020  1.394
 QYD  C4   C7    single    1.503  0.020  1.503
 QYD  C5   C6    aromatic  1.387  0.020  1.387
 QYD  C7   C8    single    1.531  0.020  1.531
 QYD  C7   S12   single    1.828  0.020  1.828
 QYD  C8   N9    single    1.453  0.020  1.453
 QYD  N9   C10   single    1.455  0.020  1.455
 QYD  N9   C13   single    1.366  0.020  1.366
 QYD  C10  C11   single    1.519  0.020  1.519
 QYD  C11  S12   single    1.817  0.020  1.817
 QYD  C13  O14   double    1.219  0.020  1.219
 QYD  C13  N15   single    1.381  0.020  1.381
 QYD  N15  C16   single    1.380  0.020  1.380
 QYD  C16  C17   aromatic  1.403  0.020  1.403
 QYD  C16  C21   aromatic  1.401  0.020  1.401
 QYD  C17  C18   aromatic  1.376  0.020  1.376
 QYD  C18  C19   aromatic  1.390  0.020  1.390
 QYD  C19  C20   aromatic  1.389  0.020  1.389
 QYD  C19  N22   single    1.442  0.020  1.442
 QYD  C20  C21   aromatic  1.380  0.020  1.380
 QYD  N22  O23   single    1.211  0.020  1.211
 QYD  N22  O24   double    1.211  0.020  1.211
 QYD  C1   H1    single    0.930  0.020  1.080
 QYD  C2   H2    single    0.930  0.020  1.080
 QYD  C6   H6    single    0.930  0.020  1.080
 QYD  C3   H3    single    0.930  0.020  1.080
 QYD  C5   H5    single    0.930  0.020  1.080
 QYD  C7   H7    single    0.970  0.020  1.090
 QYD  C8   H81C  single    0.970  0.020  1.090
 QYD  C8   H82C  single    0.970  0.020  1.090
 QYD  C10  H101  single    0.970  0.020  1.090
 QYD  C10  H102  single    0.970  0.020  1.090
 QYD  C11  H111  single    0.970  0.020  1.090
 QYD  C11  H112  single    0.970  0.020  1.090
 QYD  N15  H15   single    0.860  0.020  1.020
 QYD  C17  H17   single    0.930  0.020  1.080
 QYD  C21  H21   single    0.930  0.020  1.080
 QYD  C18  H18   single    0.930  0.020  1.080
 QYD  C20  H20   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
 QYD  H1    C1   C6    120.13  3.000
 QYD  H1    C1   C2    120.21  3.000
 QYD  C6    C1   C2    119.65  3.000
 QYD  H2    C2   C3    119.75  3.000
 QYD  H2    C2   C1    120.18  3.000
 QYD  C3    C2   C1    120.07  3.000
 QYD  H3    C3   C4    119.58  3.000
 QYD  H3    C3   C2    119.76  3.000
 QYD  C4    C3   C2    120.66  3.000
 QYD  C7    C4   C5    121.03  3.000
 QYD  C7    C4   C3    120.02  3.000
 QYD  C5    C4   C3    118.92  3.000
 QYD  H5    C5   C6    119.48  3.000
 QYD  H5    C5   C4    120.05  3.000
 QYD  C6    C5   C4    120.47  3.000
 QYD  H6    C6   C5    119.72  3.000
 QYD  H6    C6   C1    120.06  3.000
 QYD  C5    C6   C1    120.22  3.000
 QYD  H7    C7   S12   108.36  3.000
 QYD  H7    C7   C8    108.74  3.000
 QYD  S12   C7   C8    110.44  3.000
 QYD  H7    C7   C4    109.16  3.000
 QYD  S12   C7   C4    108.61  3.000
 QYD  C8    C7   C4    111.47  3.000
 QYD  H82C  C8   H81C  105.66  3.000
 QYD  H82C  C8   N9    108.06  3.000
 QYD  H81C  C8   N9    112.20  3.000
 QYD  H82C  C8   C7    109.86  3.000
 QYD  H81C  C8   C7    108.96  3.000
 QYD  N9    C8   C7    111.90  3.000
 QYD  C13   N9   C10   117.35  3.000
 QYD  C13   N9   C8    124.15  3.000
 QYD  C10   N9   C8    113.47  3.000
 QYD  H102  C10  H101  107.48  3.000
 QYD  H102  C10  C11   110.02  3.000
 QYD  H101  C10  C11   109.93  3.000
 QYD  H102  C10  N9    108.01  3.000
 QYD  H101  C10  N9    109.63  3.000
 QYD  C11   C10  N9    111.66  3.000
 QYD  H112  C11  H111  107.98  3.000
 QYD  H112  C11  S12   106.05  3.000
 QYD  H111  C11  S12   109.99  3.000
 QYD  H112  C11  C10   110.23  3.000
 QYD  H111  C11  C10   110.71  3.000
 QYD  S12   C11  C10   111.70  3.000
 QYD  C11   S12  C7     99.41  3.000
 QYD  N15   C13  O14   122.11  3.000
 QYD  N15   C13  N9    115.15  3.000
 QYD  O14   C13  N9    122.72  3.000
 QYD  H15   N15  C16   114.09  3.000
 QYD  H15   N15  C13   117.59  3.000
 QYD  C16   N15  C13   127.51  3.000
 QYD  C21   C16  C17   118.68  3.000
 QYD  C21   C16  N15   124.65  3.000
 QYD  C17   C16  N15   116.63  3.000
 QYD  H17   C17  C18   119.06  3.000
 QYD  H17   C17  C16   119.66  3.000
 QYD  C18   C17  C16   121.28  3.000
 QYD  H18   C18  C19   121.50  3.000
 QYD  H18   C18  C17   119.31  3.000
 QYD  C19   C18  C17   119.19  3.000
 QYD  N22   C19  C20   119.75  3.000
 QYD  N22   C19  C18   119.77  3.000
 QYD  C20   C19  C18   120.48  3.000
 QYD  H20   C20  C21   118.80  3.000
 QYD  H20   C20  C19   120.89  3.000
 QYD  C21   C20  C19   120.31  3.000
 QYD  H21   C21  C20   118.65  3.000
 QYD  H21   C21  C16   121.30  3.000
 QYD  C20   C21  C16   120.05  3.000
 QYD  O24   N22  O23   123.45  3.000
 QYD  O24   N22  C19   118.30  3.000
 QYD  O23   N22  C19   118.25  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
 QYD  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 QYD  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 QYD  CONST_03  C5   C6   C1   C2     0.00   0.0  0
 QYD  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 QYD  CONST_05  C6   C1   C2   C3     0.00   0.0  0
 QYD  CONST_06  C6   C5   C4   C3     0.00   0.0  0
 QYD  CONST_07  C19  C18  C17  C16    0.00   0.0  0
 QYD  CONST_08  C19  C20  C21  C16    0.00   0.0  0
 QYD  CONST_09  C20  C21  C16  C17    0.00   0.0  0
 QYD  CONST_10  C20  C19  C18  C17    0.00   0.0  0
 QYD  CONST_11  C21  C16  C17  C18    0.00   0.0  0
 QYD  CONST_12  C21  C20  C19  C18    0.00   0.0  0
 QYD  CONST_13  C7   C4   C3   C2   180.00   0.0  0
 QYD  CONST_14  C7   C4   C5   C6   180.00   0.0  0
 QYD  CONST_15  C18  C17  C16  N15  180.00   0.0  0
 QYD  CONST_16  C20  C21  C16  N15  180.00   0.0  0
 QYD  CONST_17  N22  C19  C18  C17  180.00   0.0  0
 QYD  CONST_18  N22  C19  C20  C21  180.00   0.0  0
 QYD  CONST_19  H3   C3   C2   C1   180.00   0.0  0
 QYD  CONST_20  H5   C5   C6   C1   180.00   0.0  0
 QYD  CONST_21  H6   C6   C1   C2   180.00   0.0  0
 QYD  CONST_22  H1   C1   C2   C3   180.00   0.0  0
 QYD  CONST_23  H2   C2   C3   C4   180.00   0.0  0
 QYD  CONST_24  H18  C18  C17  C16  180.00   0.0  0
 QYD  CONST_25  H20  C20  C21  C16  180.00   0.0  0
 QYD  CONST_26  H21  C21  C16  C17  180.00   0.0  0
 QYD  CONST_27  H17  C17  C18  C19  180.00   0.0  0
 QYD  CONST_29  O14  C13  N9   C10    0.00   0.0  0
 QYD  CONST_30  C16  N15  C13  N9   180.00   0.0  0
 QYD  CONST_31  C17  C16  N15  C13  180.00   0.0  0
 QYD  CONST_33  O23  N22  C19  C18    0.00   0.0  0
 QYD  CONST_34  O24  N22  C19  C18  180.00   0.0  0
 QYD  CONST_35  O23  N22  C19  C20  180.00   0.0  0
 QYD  CONST_36  O24  N22  C19  C20    0.00   0.0  0
 QYD  CONST_38  N15  C13  N9   C10  180.00   0.0  0
 QYD  CONST_39  H15  N15  C16  C17    0.00   0.0  0
 QYD  CONST_40  C16  N15  C13  O14    0.00   0.0  0
 QYD  Var_01    C10  N9   C8   C7   -67.78  30.0  1
 QYD  Var_02    C10  C11  S12  C7    50.02  30.0  1
 QYD  Var_03    C11  C10  N9   C8    66.97  30.0  1
 QYD  Var_04    S12  C11  C10  N9   -60.20  30.0  1

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
 QYD  chir_01  C7  C4  C8  S12  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
 QYD  plan-1  C1   0.020
 QYD  plan-1  C2   0.020
 QYD  plan-1  C3   0.020
 QYD  plan-1  C4   0.020
 QYD  plan-1  C5   0.020
 QYD  plan-1  C6   0.020
 QYD  plan-1  C7   0.020
 QYD  plan-1  H1   0.020
 QYD  plan-1  H2   0.020
 QYD  plan-1  H6   0.020
 QYD  plan-1  H3   0.020
 QYD  plan-1  H5   0.020
 QYD  plan-2  N15  0.020
 QYD  plan-2  C16  0.020
 QYD  plan-2  C17  0.020
 QYD  plan-2  C18  0.020
 QYD  plan-2  C19  0.020
 QYD  plan-2  C20  0.020
 QYD  plan-2  C21  0.020
 QYD  plan-2  N22  0.020
 QYD  plan-2  H17  0.020
 QYD  plan-2  H21  0.020
 QYD  plan-2  H18  0.020
 QYD  plan-2  H20  0.020
 QYD  plan-3  C8   0.020
 QYD  plan-3  N9   0.020
 QYD  plan-3  C10  0.020
 QYD  plan-3  C13  0.020
 QYD  plan-3  O14  0.020
 QYD  plan-3  N15  0.020
 QYD  plan-3  C16  0.020
 QYD  plan-3  H15  0.020
 QYD  plan-4  C19  0.020
 QYD  plan-4  N22  0.020
 QYD  plan-4  O23  0.020
 QYD  plan-4  O24  0.020

