# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 12:18:13 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: 8-[[(3R,4R)-3-[[1,1-bis(oxidanylidene)thian-4-yl]methoxy]piperidin-4-yl]amino]-3-methyl-1H-1,7-naphthyridin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=Cc2ccnc(N[C@@H]3CCNC[C@H]3OCC4CC[S](=O)(=O)CC4)c2NC1=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
 YEJ  YEJ  8-[[(3R,4R)-3-[[1,1-bis(oxidanylidene)thian-4-yl]methoxy]piperidin-4-yl]amino]-3-methyl-1H-1,7-naphthyridin-2-one  ligand  57  29  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_YEJ
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
 YEJ  O3    O  O     0  -0.475   0.8088  -3.1825   1.6935
 YEJ  C19   C  CR6   0   0.520   1.6203  -2.6962   0.9165
 YEJ  C1    C  CR6   0  -0.110   2.5999  -3.4837   0.1654
 YEJ  C     C  CH3   0  -0.711   2.6160  -4.9544   0.4157
 YEJ  N3    N  NR16  0  -0.755   1.6547  -1.3469   0.6910
 YEJ  C18   C  CR66  0   0.215   2.4815  -0.7072  -0.1977
 YEJ  C3    C  CR66  0   0.131   3.3739  -1.4576  -0.9489
 YEJ  C2    C  CR16  0  -0.193   3.4153  -2.8726  -0.7201
 YEJ  C6    C  CR6   0   0.504   2.4201   0.7000  -0.3958
 YEJ  N     N  N     0  -0.460   3.1416   1.2816  -1.3305
 YEJ  C5    C  CR16  0  -0.081   3.9769   0.5471  -2.0793
 YEJ  C4    C  CR16  0  -0.425   4.1551  -0.8007  -1.9165
 YEJ  N1    N  NH1   0  -0.696   1.5496   1.4436   0.3490
 YEJ  C7    C  CH1   0  -0.104   1.2880   2.8376   0.0678
 YEJ  C11   C  CH1   0   0.088  -0.1315   3.1897   0.5093
 YEJ  C10   C  CH2   0  -0.318  -0.4077   4.6684   0.2382
 YEJ  N2    N  NH1   0  -0.600   0.5652   5.4857   0.9346
 YEJ  C9    C  CH2   0  -0.297   1.9127   5.2365   0.4555
 YEJ  C8    C  CH2   0  -0.438   2.2881   3.7880   0.7261
 YEJ  O     O  O2    0  -0.497  -1.0294   2.3633  -0.1871
 YEJ  C12   C  CH2   0  -0.115  -2.2212   2.0318   0.4823
 YEJ  C13   C  CH1   0  -0.282  -2.7702   0.7320  -0.0878
 YEJ  C17   C  CH2   0  -0.454  -4.1181   0.4209   0.5657
 YEJ  C16   C  CH2   0  -0.614  -4.7857  -0.8184  -0.0144
 YEJ  S     S  S     0   1.215  -3.7625  -2.2632   0.2269
 YEJ  O1    O  OS    0  -0.685  -4.3144  -3.3902  -0.5271
 YEJ  O2    O  OS    0  -0.689  -3.5470  -2.4423   1.6658
 YEJ  C15   C  CH2   0  -0.613  -2.2259  -1.7286  -0.5108
 YEJ  C14   C  CH2   0  -0.464  -1.7654  -0.4080   0.0916
 YEJ  H3    H  HNR6  0   0.406   0.9553  -0.8101   1.1847
 YEJ  HC1   H  HCH3  0   0.252   2.8171  -5.1720   1.4656
 YEJ  HC2   H  HCH3  0   0.252   1.6525  -5.4072   0.1763
 YEJ  HC3   H  HCH3  0   0.248   3.3801  -5.4432  -0.1853
 YEJ  H2    H  HCR6  0   0.271   4.1266  -3.4599  -1.2900
 YEJ  H4    H  HCR6  0   0.263   4.8588  -1.3535  -2.5239
 YEJ  H1    H  HNH1  0   0.384   1.4351   1.1805   1.3167
 YEJ  H5    H  HCR6  0   0.257   4.5333   1.0895  -2.8344
 YEJ  H7    H  HCH1  0   0.244   1.3504   2.9644  -1.0170
 YEJ  H11   H  HCH1  0   0.205  -0.2135   3.0188   1.5948
 YEJ  H81C  H  HCH2  0   0.220   2.3042   3.6112   1.8063
 YEJ  H82C  H  HCH2  0   0.245   3.2894   3.5796   0.3455
 YEJ  H101  H  HCH2  0   0.194  -0.4014   4.8250  -0.8537
 YEJ  H102  H  HCH2  0   0.240  -1.4078   4.9270   0.5946
 YEJ  HA    H  HNH1  0   0.357   0.3323   6.4628   0.8180
 YEJ  H91C  H  HCH2  0   0.193   2.0218   5.4379  -0.6231
 YEJ  H92C  H  HCH2  0   0.238   2.6033   5.9040   0.9740
 YEJ  H121  H  HCH2  0   0.201  -2.0383   1.9063   1.5591
 YEJ  H122  H  HCH2  0   0.216  -2.9732   2.8254   0.3762
 YEJ  H13   H  HCH1  0   0.244  -2.9427   0.8761  -1.1617
 YEJ  H171  H  HCH2  0   0.250  -3.9988   0.3009   1.6457
 YEJ  H172  H  HCH2  0   0.271  -4.8027   1.2595   0.4214
 YEJ  H141  H  HCH2  0   0.274  -0.8236  -0.1400  -0.3878
 YEJ  H142  H  HCH2  0   0.241  -1.5560  -0.5495   1.1564
 YEJ  H161  H  HCH2  0   0.321  -5.7413  -1.0383   0.4658
 YEJ  H162  H  HCH2  0   0.299  -4.9525  -0.7251  -1.0891
 YEJ  H151  H  HCH2  0   0.315  -1.5081  -2.5334  -0.3363
 YEJ  H152  H  HCH2  0   0.300  -2.3996  -1.6483  -1.5854

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
 YEJ  O3   C19   double    1.224  0.020  1.224
 YEJ  C19  C1    single    1.464  0.020  1.464
 YEJ  C19  N3    single    1.368  0.020  1.368
 YEJ  C1   C     single    1.492  0.020  1.492
 YEJ  C1   C2    double    1.350  0.020  1.350
 YEJ  N3   C18   single    1.372  0.020  1.372
 YEJ  C18  C3    aromatic  1.387  0.020  1.387
 YEJ  C18  C6    aromatic  1.422  0.020  1.422
 YEJ  C3   C2    single    1.434  0.020  1.434
 YEJ  C3   C4    aromatic  1.406  0.020  1.406
 YEJ  C6   N     aromatic  1.316  0.020  1.316
 YEJ  C6   N1    single    1.366  0.020  1.366
 YEJ  N    C5    aromatic  1.341  0.020  1.341
 YEJ  C5   C4    aromatic  1.369  0.020  1.369
 YEJ  N1   C7    single    1.446  0.020  1.446
 YEJ  C7   C11   single    1.528  0.020  1.528
 YEJ  C7   C8    single    1.529  0.020  1.529
 YEJ  C11  C10   single    1.529  0.020  1.529
 YEJ  C11  O     single    1.405  0.020  1.405
 YEJ  C10  N2    single    1.449  0.020  1.449
 YEJ  N2   C9    single    1.452  0.020  1.452
 YEJ  C9   C8    single    1.521  0.020  1.521
 YEJ  O    C12   single    1.406  0.020  1.406
 YEJ  C12  C13   single    1.522  0.020  1.522
 YEJ  C13  C17   single    1.530  0.020  1.530
 YEJ  C13  C14   single    1.530  0.020  1.530
 YEJ  C17  C16   single    1.522  0.020  1.522
 YEJ  C16  S     single    1.787  0.020  1.787
 YEJ  S    O1    double    1.464  0.020  1.464
 YEJ  S    O2    double    1.466  0.020  1.466
 YEJ  S    C15   single    1.786  0.020  1.786
 YEJ  C15  C14   single    1.523  0.020  1.523
 YEJ  N3   H3    single    0.860  0.020  1.020
 YEJ  C    HC1   single    0.970  0.020  1.090
 YEJ  C    HC2   single    0.970  0.020  1.090
 YEJ  C    HC3   single    0.970  0.020  1.090
 YEJ  C2   H2    single    0.930  0.020  1.080
 YEJ  C4   H4    single    0.930  0.020  1.080
 YEJ  N1   H1    single    0.890  0.020  1.040
 YEJ  C5   H5    single    0.930  0.020  1.080
 YEJ  C7   H7    single    0.970  0.020  1.090
 YEJ  C11  H11   single    0.970  0.020  1.090
 YEJ  C8   H81C  single    0.970  0.020  1.090
 YEJ  C8   H82C  single    0.970  0.020  1.090
 YEJ  C10  H101  single    0.970  0.020  1.090
 YEJ  C10  H102  single    0.970  0.020  1.090
 YEJ  N2   HA    single    0.890  0.020  1.040
 YEJ  C9   H91C  single    0.970  0.020  1.090
 YEJ  C9   H92C  single    0.970  0.020  1.090
 YEJ  C12  H121  single    0.970  0.020  1.090
 YEJ  C12  H122  single    0.970  0.020  1.090
 YEJ  C13  H13   single    0.970  0.020  1.090
 YEJ  C17  H171  single    0.970  0.020  1.090
 YEJ  C17  H172  single    0.970  0.020  1.090
 YEJ  C14  H141  single    0.970  0.020  1.090
 YEJ  C14  H142  single    0.970  0.020  1.090
 YEJ  C16  H161  single    0.970  0.020  1.090
 YEJ  C16  H162  single    0.970  0.020  1.090
 YEJ  C15  H151  single    0.970  0.020  1.090
 YEJ  C15  H152  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
 YEJ  N3    C19  C1    115.40  3.000
 YEJ  N3    C19  O3    120.86  3.000
 YEJ  C1    C19  O3    123.73  3.000
 YEJ  C2    C1   C     123.35  3.000
 YEJ  C2    C1   C19   119.81  3.000
 YEJ  C     C1   C19   116.83  3.000
 YEJ  HC3   C    HC2   108.21  3.000
 YEJ  HC3   C    HC1   108.21  3.000
 YEJ  HC2   C    HC1   106.93  3.000
 YEJ  HC3   C    C1    110.96  3.000
 YEJ  HC2   C    C1    111.26  3.000
 YEJ  HC1   C    C1    111.10  3.000
 YEJ  H3    N3   C18   119.07  3.000
 YEJ  H3    N3   C19   115.21  3.000
 YEJ  C18   N3   C19   125.57  3.000
 YEJ  C6    C18  C3    119.18  3.000
 YEJ  C6    C18  N3    121.70  3.000
 YEJ  C3    C18  N3    119.09  3.000
 YEJ  C4    C3   C2    123.68  3.000
 YEJ  C4    C3   C18   118.51  3.000
 YEJ  C2    C3   C18   117.78  3.000
 YEJ  H2    C2   C3    118.01  3.000
 YEJ  H2    C2   C1    119.72  3.000
 YEJ  C3    C2   C1    122.27  3.000
 YEJ  N1    C6   N     119.73  3.000
 YEJ  N1    C6   C18   119.35  3.000
 YEJ  N     C6   C18   120.83  3.000
 YEJ  C5    N    C6    119.73  3.000
 YEJ  H5    C5   C4    120.58  3.000
 YEJ  H5    C5   N     115.78  3.000
 YEJ  C4    C5   N     123.64  3.000
 YEJ  H4    C4   C5    121.41  3.000
 YEJ  H4    C4   C3    120.60  3.000
 YEJ  C5    C4   C3    117.99  3.000
 YEJ  H1    N1   C7    114.66  3.000
 YEJ  H1    N1   C6    116.95  3.000
 YEJ  C7    N1   C6    122.29  3.000
 YEJ  H7    C7   C8    108.52  3.000
 YEJ  H7    C7   C11   108.23  3.000
 YEJ  C8    C7   C11   109.88  3.000
 YEJ  H7    C7   N1    107.12  3.000
 YEJ  C8    C7   N1    113.41  3.000
 YEJ  C11   C7   N1    109.52  3.000
 YEJ  H11   C11  O     110.45  3.000
 YEJ  H11   C11  C10   108.14  3.000
 YEJ  O     C11  C10   111.45  3.000
 YEJ  H11   C11  C7    108.55  3.000
 YEJ  O     C11  C7    108.36  3.000
 YEJ  C10   C11  C7    109.85  3.000
 YEJ  H102  C10  H101  107.13  3.000
 YEJ  H102  C10  N2    108.92  3.000
 YEJ  H101  C10  N2    113.07  3.000
 YEJ  H102  C10  C11   109.66  3.000
 YEJ  H101  C10  C11   108.17  3.000
 YEJ  N2    C10  C11   109.82  3.000
 YEJ  HA    N2   C9    109.98  3.000
 YEJ  HA    N2   C10   109.57  3.000
 YEJ  C9    N2   C10   111.58  3.000
 YEJ  H92C  C9   H91C  106.88  3.000
 YEJ  H92C  C9   C8    109.99  3.000
 YEJ  H91C  C9   C8    108.88  3.000
 YEJ  H92C  C9   N2    109.00  3.000
 YEJ  H91C  C9   N2    112.54  3.000
 YEJ  C8    C9   N2    109.51  3.000
 YEJ  H82C  C8   H81C  107.44  3.000
 YEJ  H82C  C8   C9    110.26  3.000
 YEJ  H81C  C8   C9    109.46  3.000
 YEJ  H82C  C8   C7    109.35  3.000
 YEJ  H81C  C8   C7    109.52  3.000
 YEJ  C9    C8   C7    110.74  3.000
 YEJ  C12   O    C11   116.37  3.000
 YEJ  H122  C12  H121  106.91  3.000
 YEJ  H122  C12  C13   109.50  3.000
 YEJ  H121  C12  C13   109.23  3.000
 YEJ  H122  C12  O     111.34  3.000
 YEJ  H121  C12  O     110.62  3.000
 YEJ  C13   C12  O     109.19  3.000
 YEJ  H13   C13  C14   108.41  3.000
 YEJ  H13   C13  C17   107.84  3.000
 YEJ  C14   C13  C17   112.15  3.000
 YEJ  H13   C13  C12   108.13  3.000
 YEJ  C14   C13  C12   110.82  3.000
 YEJ  C17   C13  C12   109.36  3.000
 YEJ  H172  C17  H171  106.45  3.000
 YEJ  H172  C17  C16   107.45  3.000
 YEJ  H171  C17  C16   109.56  3.000
 YEJ  H172  C17  C13   109.86  3.000
 YEJ  H171  C17  C13   110.38  3.000
 YEJ  C16   C17  C13   112.90  3.000
 YEJ  H162  C16  H161  108.45  3.000
 YEJ  H162  C16  S     106.83  3.000
 YEJ  H161  C16  S     106.19  3.000
 YEJ  H162  C16  C17   111.88  3.000
 YEJ  H161  C16  C17   112.35  3.000
 YEJ  S     C16  C17   110.83  3.000
 YEJ  C15   S    O2    108.39  3.000
 YEJ  C15   S    O1    109.99  3.000
 YEJ  O2    S    O1    117.83  3.000
 YEJ  C15   S    C16   101.23  3.000
 YEJ  O2    S    C16   108.40  3.000
 YEJ  O1    S    C16   109.70  3.000
 YEJ  H152  C15  H151  108.43  3.000
 YEJ  H152  C15  C14   111.95  3.000
 YEJ  H151  C15  C14   112.15  3.000
 YEJ  H152  C15  S     106.96  3.000
 YEJ  H151  C15  S     106.19  3.000
 YEJ  C14   C15  S     110.87  3.000
 YEJ  H142  C14  H141  107.12  3.000
 YEJ  H142  C14  C15   109.31  3.000
 YEJ  H141  C14  C15   107.48  3.000
 YEJ  H142  C14  C13   109.64  3.000
 YEJ  H141  C14  C13   109.43  3.000
 YEJ  C15   C14  C13   113.65  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
 YEJ  CONST_01  C5   C4   C3   C18     0.00   0.0  0
 YEJ  CONST_02  C5   N    C6   C18     0.00   0.0  0
 YEJ  CONST_03  N    C6   C18  C3      0.00   0.0  0
 YEJ  CONST_04  N    C5   C4   C3      0.00   0.0  0
 YEJ  CONST_05  C4   C3   C18  C6      0.00   0.0  0
 YEJ  CONST_06  C4   C5   N    C6      0.00   0.0  0
 YEJ  CONST_07  C18  N3   C19  C1      0.00   0.0  0
 YEJ  CONST_08  N1   C6   C18  N3      0.00   0.0  0
 YEJ  CONST_09  N1   C6   C18  C3    180.00   0.0  0
 YEJ  CONST_10  N1   C6   N    C5    180.00   0.0  0
 YEJ  CONST_11  C7   N1   C6   C18   180.00   0.0  0
 YEJ  CONST_12  C7   N1   C6   N       0.00   0.0  0
 YEJ  CONST_13  C18  N3   C19  O3    180.00   0.0  0
 YEJ  CONST_14  H4   C4   C3   C18   180.00   0.0  0
 YEJ  CONST_15  H5   C5   C4   C3    180.00   0.0  0
 YEJ  CONST_16  H3   N3   C19  C1    180.00   0.0  0
 YEJ  Var_01    N2   C9   C8   C7     57.26  30.0  1
 YEJ  Var_02    C9   N2   C10  C11    62.79  30.0  1
 YEJ  Var_03    C8   C9   N2   C10   -62.19  30.0  1
 YEJ  Var_04    S    C16  C17  C13    60.74  30.0  1
 YEJ  Var_05    S    C15  C14  C13   -59.35  30.0  1
 YEJ  Var_06    C15  S    C16  C17   -54.47  30.0  1
 YEJ  Var_07    C14  C15  S    C16    53.59  30.0  1
 YEJ  Var_08    C13  C12  O    C11  -155.93  30.0  3
 YEJ  Var_09    HC1  C    C1   C19   -59.25  30.0  3

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
 YEJ  chir_01  C7   N1   C11  C8   negativ
 YEJ  chir_02  C11  O    C7   C10  negativ
 YEJ  chir_03  C13  C14  C17  C12  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
 YEJ  plan-1  C6   0.020
 YEJ  plan-1  N1   0.020
 YEJ  plan-1  C7   0.020
 YEJ  plan-1  H1   0.020
 YEJ  plan-2  O3   0.020
 YEJ  plan-2  C19  0.020
 YEJ  plan-2  C1   0.020
 YEJ  plan-2  C    0.020
 YEJ  plan-2  N3   0.020
 YEJ  plan-2  C18  0.020
 YEJ  plan-2  C3   0.020
 YEJ  plan-2  C2   0.020
 YEJ  plan-2  C6   0.020
 YEJ  plan-2  N    0.020
 YEJ  plan-2  C5   0.020
 YEJ  plan-2  C4   0.020
 YEJ  plan-2  N1   0.020
 YEJ  plan-2  H3   0.020
 YEJ  plan-2  H2   0.020
 YEJ  plan-2  H4   0.020
 YEJ  plan-2  H5   0.020

