# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 13:18:00 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: 4-methyl-2-(2-naphthalen-1-yl-2-oxidanylidene-ethyl)sulfanyl-1~{H}-pyrimidin-6-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CC(=O)NC(=N1)SCC(=O)c2cccc3ccccc23
#
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
 7NC  7NC  4-methyl-2-(2-naphthalen-1-yl-2-oxidanylidene-ethyl)sulfanyl-1~{H}-pyrimidin-6-one  ligand  36  22  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_7NC
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
 7NC  O1   O  O     0  -0.390  -1.0609  -1.8424  -0.1514
 7NC  C2   C  C     0   0.383  -0.9909  -0.6321  -0.1022
 7NC  C3   C  CH2   0  -0.709   0.3854   0.0054  -0.0740
 7NC  S    S  S2    0   0.106   1.5930  -1.3401  -0.1008
 7NC  C4   C  CR6   0   0.364   3.0702  -0.4037  -0.0567
 7NC  N1   N  NR16  0  -0.689   4.2014  -1.1425  -0.0644
 7NC  C7   C  CR6   0   0.551   5.4781  -0.5857  -0.0318
 7NC  O    O  O     0  -0.482   6.4629  -1.3069  -0.0420
 7NC  C6   C  CR16  0  -0.490   5.4562   0.8475   0.0126
 7NC  N    N  N     0  -0.456   3.0642   0.8868  -0.0201
 7NC  C5   C  CR6   0   0.289   4.2739   1.5203   0.0160
 7NC  C8   C  CH3   0  -0.712   4.2082   3.0100   0.0572
 7NC  C1   C  CR6   0  -0.018  -2.1680   0.2689  -0.0684
 7NC  C11  C  CR16  0  -0.315  -1.9319   1.6291  -0.0658
 7NC  C12  C  CR16  0  -0.242  -2.9697   2.5708  -0.0434
 7NC  C10  C  CR16  0  -0.299  -4.2646   2.1409  -0.0209
 7NC  C9   C  CR66  0   0.096  -4.5701   0.7611  -0.0179
 7NC  C16  C  CR16  0  -0.302  -5.9228   0.3508   0.0109
 7NC  C15  C  CR16  0  -0.258  -6.2540  -0.9745   0.0176
 7NC  C14  C  CR16  0  -0.231  -5.2302  -1.9375  -0.0037
 7NC  C13  C  CR16  0  -0.344  -3.9091  -1.5716  -0.0334
 7NC  C    C  CR66  0   0.131  -3.5248  -0.2074  -0.0426
 7NC  H1   H  HCH2  0   0.328   0.5399   0.6537  -0.9368
 7NC  H2   H  HCH2  0   0.328   0.5243   0.6098   0.8228
 7NC  H3   H  HCR6  0   0.275   6.3985   1.3764   0.0441
 7NC  H5   H  HCH3  0   0.260   3.7098   3.3883  -0.8366
 7NC  H6   H  HCH3  0   0.259   3.6204   3.3385   0.9154
 7NC  H7   H  HCH3  0   0.251   5.1975   3.4570   0.1200
 7NC  H8   H  HCR6  0   0.283  -0.9204   2.0097  -0.0831
 7NC  H9   H  HCR6  0   0.272  -2.7357   3.6263  -0.0455
 7NC  H10  H  HCR6  0   0.271  -5.0785   2.8552  -0.0041
 7NC  H11  H  HCR6  0   0.263  -6.6937   1.1112   0.0281
 7NC  H12  H  HCR6  0   0.263  -7.2910  -1.2822   0.0398
 7NC  H13  H  HCR6  0   0.263  -5.4850  -2.9894   0.0036
 7NC  H14  H  HCR6  0   0.272  -3.1611  -2.3443  -0.0503
 7NC  H16  H  HNR6  0   0.430   4.1468  -2.1542  -0.0907

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
 7NC  C10  C12  aromatic  1.365  0.020  1.365
 7NC  C10  C9   aromatic  1.413  0.020  1.413
 7NC  C16  C9   aromatic  1.414  0.020  1.414
 7NC  C16  C15  aromatic  1.366  0.020  1.366
 7NC  C12  C11  aromatic  1.402  0.020  1.402
 7NC  C9   C    aromatic  1.425  0.020  1.425
 7NC  C15  C14  aromatic  1.406  0.020  1.406
 7NC  C11  C1   aromatic  1.381  0.020  1.381
 7NC  C8   C5   single    1.492  0.020  1.492
 7NC  C    C1   aromatic  1.438  0.020  1.438
 7NC  C    C13  aromatic  1.417  0.020  1.417
 7NC  C14  C13  aromatic  1.371  0.020  1.371
 7NC  C1   C2   single    1.483  0.020  1.483
 7NC  C5   C6   double    1.360  0.020  1.360
 7NC  C5   N    single    1.366  0.020  1.366
 7NC  C6   C7   single    1.434  0.020  1.434
 7NC  C2   O1   double    1.213  0.020  1.213
 7NC  C2   C3   single    1.517  0.020  1.517
 7NC  N    C4   double    1.291  0.020  1.291
 7NC  C3   S    single    1.808  0.020  1.808
 7NC  C7   O    double    1.221  0.020  1.221
 7NC  C7   N1   single    1.393  0.020  1.393
 7NC  C4   N1   single    1.351  0.020  1.351
 7NC  C4   S    single    1.750  0.020  1.750
 7NC  C3   H1   single    0.970  0.020  1.090
 7NC  C3   H2   single    0.970  0.020  1.090
 7NC  C6   H3   single    0.930  0.020  1.080
 7NC  C8   H5   single    0.970  0.020  1.090
 7NC  C8   H6   single    0.970  0.020  1.090
 7NC  C8   H7   single    0.970  0.020  1.090
 7NC  C11  H8   single    0.930  0.020  1.080
 7NC  C12  H9   single    0.930  0.020  1.080
 7NC  C10  H10  single    0.930  0.020  1.080
 7NC  C16  H11  single    0.930  0.020  1.080
 7NC  C15  H12  single    0.930  0.020  1.080
 7NC  C14  H13  single    0.930  0.020  1.080
 7NC  C13  H14  single    0.930  0.020  1.080
 7NC  N1   H16  single    0.860  0.020  1.020

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
 7NC  C1   C2   C3   117.67  3.000
 7NC  C3   C2   O1   118.18  3.000
 7NC  C1   C2   O1   124.15  3.000
 7NC  H2   C3   H1   107.66  3.000
 7NC  H2   C3   S    109.86  3.000
 7NC  H1   C3   S    109.64  3.000
 7NC  H2   C3   C2   111.33  3.000
 7NC  H1   C3   C2   111.33  3.000
 7NC  S    C3   C2   107.03  3.000
 7NC  C4   S    C3    99.51  3.000
 7NC  N    C4   N1   123.41  3.000
 7NC  N1   C4   S    114.46  3.000
 7NC  N    C4   S    122.12  3.000
 7NC  H16  N1   C7   116.67  3.000
 7NC  H16  N1   C4   120.06  3.000
 7NC  C7   N1   C4   123.27  3.000
 7NC  C6   C7   O    127.09  3.000
 7NC  O    C7   N1   120.20  3.000
 7NC  C6   C7   N1   112.71  3.000
 7NC  H3   C6   C5   121.03  3.000
 7NC  H3   C6   C7   118.46  3.000
 7NC  C5   C6   C7   120.51  3.000
 7NC  C5   N    C4   117.40  3.000
 7NC  C8   C5   N    115.14  3.000
 7NC  N    C5   C6   122.70  3.000
 7NC  C8   C5   C6   122.16  3.000
 7NC  H7   C8   H6   108.72  3.000
 7NC  H7   C8   H5   108.68  3.000
 7NC  H6   C8   H5   107.10  3.000
 7NC  H7   C8   C5   111.84  3.000
 7NC  H6   C8   C5   110.26  3.000
 7NC  H5   C8   C5   110.11  3.000
 7NC  C    C1   C11  119.18  3.000
 7NC  C    C1   C2   123.24  3.000
 7NC  C11  C1   C2   117.58  3.000
 7NC  H8   C11  C12  117.17  3.000
 7NC  H8   C11  C1   120.46  3.000
 7NC  C12  C11  C1   122.37  3.000
 7NC  H9   C12  C10  120.87  3.000
 7NC  H9   C12  C11  119.71  3.000
 7NC  C10  C12  C11  119.42  3.000
 7NC  H10  C10  C9   118.78  3.000
 7NC  H10  C10  C12  120.37  3.000
 7NC  C9   C10  C12  120.85  3.000
 7NC  C    C9   C16  120.32  3.000
 7NC  C    C9   C10  120.32  3.000
 7NC  C16  C9   C10  119.36  3.000
 7NC  H11  C16  C15  120.56  3.000
 7NC  H11  C16  C9   118.53  3.000
 7NC  C15  C16  C9   120.91  3.000
 7NC  H12  C15  C14  120.23  3.000
 7NC  H12  C15  C16  120.56  3.000
 7NC  C14  C15  C16  119.20  3.000
 7NC  H13  C14  C13  119.09  3.000
 7NC  H13  C14  C15  119.62  3.000
 7NC  C13  C14  C15  121.29  3.000
 7NC  H14  C13  C    120.19  3.000
 7NC  H14  C13  C14  118.60  3.000
 7NC  C    C13  C14  121.21  3.000
 7NC  C13  C    C9   117.07  3.000
 7NC  C13  C    C1   125.08  3.000
 7NC  C9   C    C1   117.85  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
 7NC  CONST_01  C10  C12  C11  C1      0.00   0.0  0
 7NC  CONST_02  C10  C9   C    C1      0.00   0.0  0
 7NC  CONST_03  C16  C9   C    C1    180.00   0.0  0
 7NC  CONST_04  C14  C13  C    C1    180.00   0.0  0
 7NC  CONST_05  C9   C10  C12  C11     0.00   0.0  0
 7NC  CONST_06  C9   C    C1   C11     0.00   0.0  0
 7NC  CONST_07  C13  C    C1   C11   180.00   0.0  0
 7NC  CONST_08  C16  C9   C10  C12   180.00   0.0  0
 7NC  CONST_09  C    C9   C10  C12     0.00   0.0  0
 7NC  CONST_10  C    C1   C11  C12     0.00   0.0  0
 7NC  CONST_11  C15  C16  C9   C10   180.00   0.0  0
 7NC  CONST_12  C13  C    C9   C10   180.00   0.0  0
 7NC  CONST_13  C14  C15  C16  C9      0.00   0.0  0
 7NC  CONST_14  C14  C13  C    C9      0.00   0.0  0
 7NC  CONST_15  C13  C    C9   C16     0.00   0.0  0
 7NC  CONST_16  C13  C14  C15  C16     0.00   0.0  0
 7NC  CONST_17  C    C9   C16  C15     0.00   0.0  0
 7NC  CONST_18  C    C13  C14  C15     0.00   0.0  0
 7NC  CONST_19  C6   C7   N1   C4      0.00   0.0  0
 7NC  CONST_20  C5   N    C4   N1      0.00   0.0  0
 7NC  CONST_21  N    C4   N1   C7      0.00   0.0  0
 7NC  CONST_22  C12  C11  C1   C2    180.00   0.0  0
 7NC  CONST_23  C9   C    C1   C2    180.00   0.0  0
 7NC  CONST_24  C13  C    C1   C2      0.00   0.0  0
 7NC  CONST_25  C5   N    C4   S     180.00   0.0  0
 7NC  CONST_26  C7   N1   C4   S     180.00   0.0  0
 7NC  CONST_27  O    C7   N1   C4    180.00   0.0  0
 7NC  CONST_28  H9   C12  C11  C1    180.00   0.0  0
 7NC  CONST_29  H14  C13  C    C1      0.00   0.0  0
 7NC  CONST_30  H10  C10  C12  C11   180.00   0.0  0
 7NC  CONST_31  H8   C11  C12  C10   180.00   0.0  0
 7NC  CONST_32  H11  C16  C9   C10     0.00   0.0  0
 7NC  CONST_33  H12  C15  C16  C9    180.00   0.0  0
 7NC  CONST_34  H13  C14  C15  C16   180.00   0.0  0
 7NC  CONST_35  H16  N1   C7   C6    180.00   0.0  0
 7NC  Var_01    C11  C1   C2   O1   -177.52  30.0  2
 7NC  Var_02    N    C4   S    C3     -0.10  30.0  3
 7NC  Var_03    H5   C8   C5   C6    118.84  30.0  3
 7NC  Var_04    C1   C2   C3   S     179.18  30.0  1
 7NC  Var_05    H1   C3   S    C4     59.36  30.0  1

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
 7NC  plan-1  S    0.020
 7NC  plan-1  C4   0.020
 7NC  plan-1  N1   0.020
 7NC  plan-1  C7   0.020
 7NC  plan-1  O    0.020
 7NC  plan-1  C6   0.020
 7NC  plan-1  N    0.020
 7NC  plan-1  C5   0.020
 7NC  plan-1  C8   0.020
 7NC  plan-1  H3   0.020
 7NC  plan-1  H16  0.020
 7NC  plan-2  C2   0.020
 7NC  plan-2  C1   0.020
 7NC  plan-2  C11  0.020
 7NC  plan-2  C12  0.020
 7NC  plan-2  C10  0.020
 7NC  plan-2  C9   0.020
 7NC  plan-2  C16  0.020
 7NC  plan-2  C15  0.020
 7NC  plan-2  C14  0.020
 7NC  plan-2  C13  0.020
 7NC  plan-2  C    0.020
 7NC  plan-2  H8   0.020
 7NC  plan-2  H9   0.020
 7NC  plan-2  H10  0.020
 7NC  plan-2  H11  0.020
 7NC  plan-2  H12  0.020
 7NC  plan-2  H13  0.020
 7NC  plan-2  H14  0.020
 7NC  plan-3  O1   0.020
 7NC  plan-3  C2   0.020
 7NC  plan-3  C3   0.020
 7NC  plan-3  C1   0.020

