# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 07:33:48 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: 2-(5-methylsulfonylpyridin-3-yl)-1,1-bis(oxidanylidene)-4-[[2,4,6-tris(fluoranyl)phenyl]methyl]pyrido[2,3-e][1,2,4]thiadiazin-3-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S](=O)(=O)c1cncc(c1)N2C(=O)N(Cc3c(F)cc(F)cc3F)c4ncccc4[S]2(=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
 NVH  NVH  2-(5-methylsulfonylpyridin-3-yl)-1,1-bis(oxidanylidene)-4-[[2,4,6-tris(fluoranyl)phenyl]methyl]pyrido[2,3-e][1,2,4]thiadiazin-3-one  ligand  46  33  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_NVH
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
 NVH  C1   C  CR16  0  -0.120  -2.6096  -3.5770   0.9156
 NVH  C10  C  CR6   0   0.219   1.6819  -1.3453  -0.2832
 NVH  C11  C  CR16  0  -0.022   2.3547  -2.4159  -0.8550
 NVH  C13  C  CR6   0   0.557  -2.1245   4.1569   0.4221
 NVH  C14  C  CR16  0  -0.576  -1.6341   4.1082  -0.8668
 NVH  C15  C  CR6   0   0.577  -1.7816   2.9189  -1.5557
 NVH  C16  C  CR6   0  -0.302  -2.3905   1.7940  -1.0199
 NVH  C17  C  CR6   0   0.584  -2.8640   1.9298   0.2783
 NVH  C18  C  CR16  0  -0.567  -2.7491   3.0827   1.0263
 NVH  C19  C  CH3   0  -0.790   4.9816   2.0453  -0.4471
 NVH  C2   C  CR16  0  -0.340  -3.8466  -3.8584   0.3650
 NVH  C3   C  CR16  0  -0.021  -4.3408  -2.9931  -0.6002
 NVH  C4   C  CR66  0   0.625  -2.4935  -1.6641  -0.5468
 NVH  C5   C  CR6   0   0.780  -0.4324  -0.4531  -1.0617
 NVH  C6   C  CR66  0  -0.319  -1.9430  -2.4528   0.4623
 NVH  C7   C  CR16  0  -0.012   4.3823  -1.5012  -0.3820
 NVH  C8   C  CR6   0  -0.301   3.7861  -0.3922   0.2035
 NVH  C9   C  CR16  0  -0.100   2.4066  -0.3037   0.2678
 NVH  F2   F  F     0  -0.295  -1.3213   2.8659  -2.8063
 NVH  F3   F  F     0  -0.296  -3.4672   0.8738   0.8330
 NVH  N1   N  N     0  -0.439  -3.6790  -1.9371  -1.0533
 NVH  N2   N  N     0  -0.391   3.6754  -2.4941  -0.9015
 NVH  N3   N  NR6   0  -0.613  -1.8014  -0.5722  -1.0665
 NVH  N4   N  NR6   0  -0.801   0.2620  -1.3608  -0.2565
 NVH  O1   O  O     0  -0.423   0.1525   0.3660  -1.7243
 NVH  S1   S  S     0   1.376  -0.4530  -1.9147   1.1767
 NVH  S2   S  S     0   1.222   4.7878   0.9025   0.8980
 NVH  H1   H  HCR6  0   0.309  -2.1808  -4.2057   1.6845
 NVH  H2   H  HCR6  0   0.304   1.7921  -3.2353  -1.2874
 NVH  H3   H  HCH2  0   0.318  -3.5739   0.1891  -1.8103
 NVH  H4   H  HCH2  0   0.302  -2.1805   0.5788  -2.7841
 NVH  H5   H  HCR6  0   0.311  -1.1522   4.9626  -1.3223
 NVH  H6   H  HCR6  0   0.311  -3.1325   3.1402   2.0361
 NVH  H7   H  HCH3  0   0.300   4.0047   2.4060  -0.7605
 NVH  H8   H  HCH3  0   0.319   5.5863   2.8747  -0.0805
 NVH  H9   H  HCH3  0   0.302   5.4882   1.5495  -1.2716
 NVH  H10  H  HCR6  0   0.296  -4.4190  -4.7174   0.6817
 NVH  H11  H  HCR6  0   0.294  -5.3157  -3.1658  -1.0387
 NVH  H12  H  HCR6  0   0.303   5.4606  -1.5932  -0.4319
 NVH  H13  H  HCR6  0   0.314   1.9125   0.5414   0.7292
 NVH  C12  C  CH2   0  -0.385  -2.5328   0.4949  -1.7597
 NVH  O2   O  OS    0  -0.605   0.3446  -3.0203   1.6540
 NVH  O3   O  OS    0  -0.595  -0.6962  -0.7764   2.0364
 NVH  F1   F  F     0  -0.300  -1.9916   5.2898   1.1147
 NVH  O4   O  OS    0  -0.656   6.0901   0.3309   1.2219
 NVH  O5   O  OS    0  -0.655   4.0087   1.5438   1.9517

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
 NVH  O2   S1   double    1.444  0.020  1.444
 NVH  C1   C2   aromatic  1.383  0.020  1.383
 NVH  C1   C6   aromatic  1.383  0.020  1.383
 NVH  C2   C3   aromatic  1.387  0.020  1.387
 NVH  O3   S1   double    1.447  0.020  1.447
 NVH  S1   C6   single    1.738  0.020  1.738
 NVH  S1   N4   single    1.695  0.020  1.695
 NVH  C6   C4   aromatic  1.394  0.020  1.394
 NVH  C3   N1   aromatic  1.326  0.020  1.326
 NVH  C11  N2   aromatic  1.324  0.020  1.324
 NVH  C11  C10  aromatic  1.388  0.020  1.388
 NVH  N2   C7   aromatic  1.325  0.020  1.325
 NVH  O4   S2   double    1.459  0.020  1.459
 NVH  C4   N1   aromatic  1.318  0.020  1.318
 NVH  C4   N3   single    1.393  0.020  1.393
 NVH  N4   C10  single    1.420  0.020  1.420
 NVH  N4   C5   single    1.398  0.020  1.398
 NVH  C10  C9   aromatic  1.383  0.020  1.383
 NVH  C7   C8   aromatic  1.389  0.020  1.389
 NVH  C9   C8   aromatic  1.384  0.020  1.384
 NVH  C8   S2   single    1.778  0.020  1.778
 NVH  C19  S2   single    1.776  0.020  1.776
 NVH  S2   O5   double    1.459  0.020  1.459
 NVH  N3   C5   single    1.374  0.020  1.374
 NVH  N3   C12  single    1.468  0.020  1.468
 NVH  C5   O1   double    1.205  0.020  1.205
 NVH  F3   C17  single    1.337  0.020  1.337
 NVH  C12  C16  single    1.502  0.020  1.502
 NVH  C17  C16  aromatic  1.388  0.020  1.388
 NVH  C17  C18  aromatic  1.379  0.020  1.379
 NVH  C16  C15  aromatic  1.387  0.020  1.387
 NVH  C18  C13  aromatic  1.382  0.020  1.382
 NVH  C15  F2   single    1.334  0.020  1.334
 NVH  C15  C14  aromatic  1.382  0.020  1.382
 NVH  C13  C14  aromatic  1.380  0.020  1.380
 NVH  C13  F1   single    1.334  0.020  1.334
 NVH  C1   H1   single    0.930  0.020  1.080
 NVH  C11  H2   single    0.930  0.020  1.080
 NVH  C12  H3   single    0.970  0.020  1.090
 NVH  C12  H4   single    0.970  0.020  1.090
 NVH  C14  H5   single    0.930  0.020  1.080
 NVH  C18  H6   single    0.930  0.020  1.080
 NVH  C19  H7   single    0.970  0.020  1.090
 NVH  C19  H8   single    0.970  0.020  1.090
 NVH  C19  H9   single    0.970  0.020  1.090
 NVH  C2   H10  single    0.930  0.020  1.080
 NVH  C3   H11  single    0.930  0.020  1.080
 NVH  C7   H12  single    0.930  0.020  1.080
 NVH  C9   H13  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
 NVH  H1   C1   C6   120.94  3.000
 NVH  H1   C1   C2   121.28  3.000
 NVH  C6   C1   C2   117.78  3.000
 NVH  N4   C10  C9   121.63  3.000
 NVH  C9   C10  C11  119.41  3.000
 NVH  N4   C10  C11  118.95  3.000
 NVH  H2   C11  N2   117.33  3.000
 NVH  H2   C11  C10  119.73  3.000
 NVH  N2   C11  C10  122.94  3.000
 NVH  F1   C13  C18  118.56  3.000
 NVH  F1   C13  C14  118.64  3.000
 NVH  C18  C13  C14  122.80  3.000
 NVH  H5   C14  C15  121.16  3.000
 NVH  H5   C14  C13  121.59  3.000
 NVH  C15  C14  C13  117.26  3.000
 NVH  F2   C15  C16  118.79  3.000
 NVH  F2   C15  C14  117.69  3.000
 NVH  C16  C15  C14  123.52  3.000
 NVH  C17  C16  C15  115.57  3.000
 NVH  C15  C16  C12  123.57  3.000
 NVH  C17  C16  C12  120.86  3.000
 NVH  F3   C17  C18  118.22  3.000
 NVH  C18  C17  C16  124.09  3.000
 NVH  F3   C17  C16  117.69  3.000
 NVH  H6   C18  C17  121.42  3.000
 NVH  H6   C18  C13  121.81  3.000
 NVH  C17  C18  C13  116.77  3.000
 NVH  H9   C19  H8   110.09  3.000
 NVH  H9   C19  H7   110.56  3.000
 NVH  H8   C19  H7   110.06  3.000
 NVH  H9   C19  S2   109.38  3.000
 NVH  H8   C19  S2   107.19  3.000
 NVH  H7   C19  S2   109.50  3.000
 NVH  H10  C2   C3   120.76  3.000
 NVH  H10  C2   C1   121.29  3.000
 NVH  C3   C2   C1   117.95  3.000
 NVH  H11  C3   N1   115.98  3.000
 NVH  H11  C3   C2   120.19  3.000
 NVH  N1   C3   C2   123.82  3.000
 NVH  N3   C4   N1   117.77  3.000
 NVH  N3   C4   C6   121.14  3.000
 NVH  N1   C4   C6   121.09  3.000
 NVH  O1   C5   N4   121.13  3.000
 NVH  O1   C5   N3   122.72  3.000
 NVH  N4   C5   N3   116.14  3.000
 NVH  S1   C6   C4   117.45  3.000
 NVH  C4   C6   C1   120.44  3.000
 NVH  S1   C6   C1   122.02  3.000
 NVH  H12  C7   N2   116.70  3.000
 NVH  H12  C7   C8   120.98  3.000
 NVH  N2   C7   C8   122.32  3.000
 NVH  S2   C8   C9   119.79  3.000
 NVH  S2   C8   C7   120.28  3.000
 NVH  C9   C8   C7   119.91  3.000
 NVH  H13  C9   C8   121.66  3.000
 NVH  H13  C9   C10  121.24  3.000
 NVH  C8   C9   C10  117.10  3.000
 NVH  C4   N1   C3   118.86  3.000
 NVH  C7   N2   C11  118.31  3.000
 NVH  C5   N3   C4   124.16  3.000
 NVH  C5   N3   C12  115.79  3.000
 NVH  C4   N3   C12  119.89  3.000
 NVH  S1   N4   C5   119.32  3.000
 NVH  C5   N4   C10  118.60  3.000
 NVH  S1   N4   C10  116.19  3.000
 NVH  O3   S1   O2   119.90  3.000
 NVH  O3   S1   N4   108.44  3.000
 NVH  O2   S1   N4   107.26  3.000
 NVH  N4   S1   C6    96.62  3.000
 NVH  O3   S1   C6   110.10  3.000
 NVH  O2   S1   C6   111.86  3.000
 NVH  O5   S2   O4   119.25  3.000
 NVH  O5   S2   C8   107.54  3.000
 NVH  O4   S2   C8   107.72  3.000
 NVH  O5   S2   C19  108.81  3.000
 NVH  C8   S2   C19  103.55  3.000
 NVH  O4   S2   C19  108.84  3.000
 NVH  H4   C12  H3   106.77  3.000
 NVH  H4   C12  N3   109.87  3.000
 NVH  H3   C12  N3   107.16  3.000
 NVH  H4   C12  C16  111.52  3.000
 NVH  H3   C12  C16  110.93  3.000
 NVH  N3   C12  C16  110.43  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
 NVH  CONST_01  N1   C3   C2   C1     0.00   0.0  0
 NVH  CONST_02  N1   C4   C6   C1     0.00   0.0  0
 NVH  CONST_03  C7   N2   C11  C10    0.00   0.0  0
 NVH  CONST_04  C7   C8   C9   C10    0.00   0.0  0
 NVH  CONST_05  C8   C7   N2   C11    0.00   0.0  0
 NVH  CONST_06  C8   C9   C10  C11    0.00   0.0  0
 NVH  CONST_07  C16  C17  C18  C13    0.00   0.0  0
 NVH  CONST_08  C16  C15  C14  C13    0.00   0.0  0
 NVH  CONST_09  C17  C16  C15  C14    0.00   0.0  0
 NVH  CONST_10  C17  C18  C13  C14    0.00   0.0  0
 NVH  CONST_11  C18  C17  C16  C15    0.00   0.0  0
 NVH  CONST_12  C18  C13  C14  C15    0.00   0.0  0
 NVH  CONST_13  C4   C6   C1   C2     0.00   0.0  0
 NVH  CONST_14  C4   N1   C3   C2     0.00   0.0  0
 NVH  CONST_15  C6   C1   C2   C3     0.00   0.0  0
 NVH  CONST_16  C6   C4   N1   C3     0.00   0.0  0
 NVH  CONST_17  N2   C11  C10  C9     0.00   0.0  0
 NVH  CONST_18  N2   C7   C8   C9     0.00   0.0  0
 NVH  CONST_19  N4   C10  C9   C8   180.00   0.0  0
 NVH  CONST_20  N4   C10  C11  N2   180.00   0.0  0
 NVH  CONST_21  N3   C5   N4   C10  180.00   0.0  0
 NVH  CONST_22  N4   C5   N3   C4     0.00   0.0  0
 NVH  CONST_24  S2   C8   C9   C10  180.00   0.0  0
 NVH  CONST_25  C18  C17  C16  C12  180.00   0.0  0
 NVH  CONST_26  C14  C15  C16  C12  180.00   0.0  0
 NVH  CONST_27  F3   C17  C18  C13  180.00   0.0  0
 NVH  CONST_28  F2   C15  C14  C13  180.00   0.0  0
 NVH  CONST_29  F3   C17  C16  C15  180.00   0.0  0
 NVH  CONST_30  F1   C13  C14  C15  180.00   0.0  0
 NVH  CONST_31  F2   C15  C16  C17  180.00   0.0  0
 NVH  CONST_32  F1   C13  C18  C17  180.00   0.0  0
 NVH  CONST_33  S2   C8   C7   N2   180.00   0.0  0
 NVH  CONST_34  O1   C5   N4   C10    0.00   0.0  0
 NVH  CONST_35  N4   C5   N3   C12  180.00   0.0  0
 NVH  CONST_36  O1   C5   N3   C4   180.00   0.0  0
 NVH  CONST_38  H11  C3   C2   C1   180.00   0.0  0
 NVH  CONST_39  H12  C7   N2   C11  180.00   0.0  0
 NVH  CONST_40  H13  C9   C10  C11  180.00   0.0  0
 NVH  CONST_41  H6   C18  C13  C14  180.00   0.0  0
 NVH  CONST_42  H5   C14  C15  C16  180.00   0.0  0
 NVH  CONST_43  H1   C1   C2   C3   180.00   0.0  0
 NVH  CONST_44  H10  C2   C1   C6   180.00   0.0  0
 NVH  CONST_45  H2   C11  N2   C7   180.00   0.0  0
 NVH  CONST_46  O1   C5   N3   C12    0.00   0.0  0
 NVH  Var_01    S1   N4   C10  C11   96.38  30.0  2
 NVH  Var_02    O2   S1   C6   C1    32.79  30.0  1
 NVH  Var_03    N3   C12  C16  C15  117.49  30.0  2
 NVH  Var_04    C4   N3   C12  C16  116.87  30.0  2
 NVH  Var_05    C7   C8   S2   C19   92.02  30.0  3
 NVH  Var_06    H7   C19  S2   C8    60.21  30.0  3

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
 NVH  plan-1  C10  0.020
 NVH  plan-1  C11  0.020
 NVH  plan-1  C7   0.020
 NVH  plan-1  C8   0.020
 NVH  plan-1  C9   0.020
 NVH  plan-1  N2   0.020
 NVH  plan-1  N4   0.020
 NVH  plan-1  S2   0.020
 NVH  plan-1  H2   0.020
 NVH  plan-1  H12  0.020
 NVH  plan-1  H13  0.020
 NVH  plan-2  C13  0.020
 NVH  plan-2  C14  0.020
 NVH  plan-2  C15  0.020
 NVH  plan-2  C16  0.020
 NVH  plan-2  C17  0.020
 NVH  plan-2  C18  0.020
 NVH  plan-2  F2   0.020
 NVH  plan-2  F3   0.020
 NVH  plan-2  H5   0.020
 NVH  plan-2  H6   0.020
 NVH  plan-2  C12  0.020
 NVH  plan-2  F1   0.020
 NVH  plan-3  C1   0.020
 NVH  plan-3  C10  0.020
 NVH  plan-3  C2   0.020
 NVH  plan-3  C3   0.020
 NVH  plan-3  C4   0.020
 NVH  plan-3  C5   0.020
 NVH  plan-3  C6   0.020
 NVH  plan-3  N1   0.020
 NVH  plan-3  N3   0.020
 NVH  plan-3  N4   0.020
 NVH  plan-3  O1   0.020
 NVH  plan-3  S1   0.020
 NVH  plan-3  H1   0.020
 NVH  plan-3  H10  0.020
 NVH  plan-3  H11  0.020
 NVH  plan-3  C12  0.020

