# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 03:32:02 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: (1S)-1-(5-{[1-(2,6-difluorobenzyl)-1H-pyrazol-3-yl]amino}-1,3,4-thiadiazol-2-yl)-1-(4-methyl-1,3-thiazol-2-yl)ethanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1csc(n1)[C@](C)(O)c2sc(Nc3ccn(Cc4c(F)cccc4F)n3)nn2
#
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
 VMY  VMY  (1S)-1-(5-{[1-(2,6-difluorobenzyl)-1H-pyrazol-3-yl]amino}-1,3,4-thiadiazol-2-yl)-1-(4-methyl-1,3-thiazol-2-yl)ethanol  ligand  45  29  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_VMY
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
 VMY  F1    F  F     0  -0.303  -5.5486  -1.7070  -1.5709
 VMY  C13   C  CR6   0   0.550  -5.7061  -0.3899  -1.3905
 VMY  C14   C  CR16  0  -0.419  -6.0560   0.3877  -2.4777
 VMY  C15   C  CR16  0  -0.232  -6.2144   1.7523  -2.2890
 VMY  C16   C  CR16  0  -0.416  -6.0263   2.3251  -1.0390
 VMY  C17   C  CR6   0   0.559  -5.6811   1.4988   0.0106
 VMY  F     F  F     0  -0.304  -5.4919   2.0386   1.2227
 VMY  C12   C  CR6   0  -0.267  -5.5159   0.1264  -0.1171
 VMY  C11   C  CH2   0  -0.372  -5.1193  -0.7290   1.0535
 VMY  N4    N  NR5   0  -0.264  -3.7027  -0.6341   1.3257
 VMY  C10   C  CR15  0   0.066  -3.1005  -0.0475   2.3697
 VMY  C9    C  CR15  0  -0.543  -1.7423  -0.1518   2.1718
 VMY  N5    N  N     0  -0.329  -2.8300  -1.1122   0.4383
 VMY  C8    C  CR5   0   0.499  -1.6431  -0.8286   0.9411
 VMY  N3    N  NH1   0  -0.747  -0.5286  -1.2197   0.2160
 VMY  C7    C  CR5   0   0.325   0.7592  -1.0678   0.5873
 VMY  N2    N  N     0  -0.324   1.1621  -0.5061   1.6899
 VMY  N1    N  N     0  -0.230   2.5102  -0.5037   1.7965
 VMY  S1    S  S2    0   0.204   2.0508  -1.6506  -0.4206
 VMY  C6    C  CR5   0   0.059   3.1121  -1.0437   0.8050
 VMY  C4    C  CT    0   0.122   4.6065  -1.1449   0.6273
 VMY  C5    C  CH3   0  -0.647   5.2614  -1.6395   1.9163
 VMY  O     O  OH1   0  -0.665   4.8426  -2.0303  -0.4296
 VMY  C3    C  CR5   0   0.052   5.1440   0.2205   0.2500
 VMY  S     S  S2    0   0.261   4.9909   1.6234   1.2270
 VMY  C2    C  CR15  0  -0.556   5.8781   2.5012   0.0470
 VMY  N     N  N     0  -0.428   5.7888   0.3997  -0.8525
 VMY  C1    C  CR5   0   0.348   6.2183   1.6957  -0.9932
 VMY  C     C  CH3   0  -0.722   6.9775   2.0985  -2.2099
 VMY  H14   H  HCR6  0   0.286  -6.1987  -0.0646  -3.4498
 VMY  H15   H  HCR6  0   0.283  -6.4862   2.3784  -3.1276
 VMY  H16   H  HCR6  0   0.287  -6.1458   3.3885  -0.8823
 VMY  H111  H  HCH2  0   0.294  -5.6474  -0.4242   1.9551
 VMY  H112  H  HCH2  0   0.296  -5.3721  -1.7725   0.8767
 VMY  H10   H  HCR5  0   0.296  -3.6603   0.3939   3.1780
 VMY  H9    H  HCR5  0   0.279  -0.9532   0.1981   2.8107
 VMY  H3    H  HNH1  0   0.422  -0.7236  -1.6820  -0.6585
 VMY  H51C  H  HCH3  0   0.258   4.9098  -2.6444   2.1486
 VMY  H52C  H  HCH3  0   0.255   6.3446  -1.6624   1.7988
 VMY  H53C  H  HCH3  0   0.240   5.0169  -0.9895   2.7554
 VMY  H     H  HOH1  0   0.462   5.3528  -1.5552  -1.1054
 VMY  H2    H  HCR5  0   0.308   6.0936   3.5503   0.1757
 VMY  HC1   H  HCH3  0   0.253   7.8673   1.4806  -2.3359
 VMY  HC2   H  HCH3  0   0.253   6.3681   1.9786  -3.1067
 VMY  HC3   H  HCH3  0   0.250   7.2912   3.1385  -2.1493

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
 VMY  F1   C13   single    1.339  0.020  1.339
 VMY  C13  C14   aromatic  1.382  0.020  1.382
 VMY  C13  C12   aromatic  1.387  0.020  1.387
 VMY  C14  C15   aromatic  1.387  0.020  1.387
 VMY  C15  C16   aromatic  1.388  0.020  1.388
 VMY  C16  C17   aromatic  1.380  0.020  1.380
 VMY  C17  F     single    1.340  0.020  1.340
 VMY  C17  C12   aromatic  1.388  0.020  1.388
 VMY  C12  C11   single    1.503  0.020  1.503
 VMY  C11  N4    single    1.446  0.020  1.446
 VMY  N4   C10   aromatic  1.340  0.020  1.340
 VMY  N4   N5    aromatic  1.333  0.020  1.333
 VMY  C10  C9    aromatic  1.376  0.020  1.376
 VMY  C9   C8    aromatic  1.408  0.020  1.408
 VMY  N5   C8    aromatic  1.320  0.020  1.320
 VMY  C8   N3    single    1.386  0.020  1.386
 VMY  N3   C7    single    1.349  0.020  1.349
 VMY  C7   N2    aromatic  1.301  0.020  1.301
 VMY  C7   S1    aromatic  1.739  0.020  1.739
 VMY  N2   N1    aromatic  1.352  0.020  1.352
 VMY  N1   C6    aromatic  1.279  0.020  1.279
 VMY  S1   C6    aromatic  1.731  0.020  1.731
 VMY  C6   C4    single    1.508  0.020  1.508
 VMY  C4   C5    single    1.528  0.020  1.528
 VMY  C4   O     single    1.399  0.020  1.399
 VMY  C4   C3    single    1.515  0.020  1.515
 VMY  C3   S     aromatic  1.716  0.020  1.716
 VMY  C3   N     aromatic  1.290  0.020  1.290
 VMY  S    C2    aromatic  1.717  0.020  1.717
 VMY  C2   C1    aromatic  1.359  0.020  1.359
 VMY  N    C1    aromatic  1.373  0.020  1.373
 VMY  C1   C     single    1.490  0.020  1.490
 VMY  C14  H14   single    0.930  0.020  1.080
 VMY  C15  H15   single    0.930  0.020  1.080
 VMY  C16  H16   single    0.930  0.020  1.080
 VMY  C11  H111  single    0.970  0.020  1.090
 VMY  C11  H112  single    0.970  0.020  1.090
 VMY  C10  H10   single    0.930  0.020  1.080
 VMY  C9   H9    single    0.930  0.020  1.080
 VMY  N3   H3    single    0.860  0.020  1.020
 VMY  C5   H51C  single    0.970  0.020  1.090
 VMY  C5   H52C  single    0.970  0.020  1.090
 VMY  C5   H53C  single    0.970  0.020  1.090
 VMY  O    H     single    0.850  0.020  0.980
 VMY  C2   H2    single    0.930  0.020  1.080
 VMY  C    HC1   single    0.970  0.020  1.090
 VMY  C    HC2   single    0.970  0.020  1.090
 VMY  C    HC3   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
 VMY  C12   C13  C14   123.20  3.000
 VMY  C12   C13  F1    118.28  3.000
 VMY  C14   C13  F1    118.52  3.000
 VMY  H14   C14  C15   121.25  3.000
 VMY  H14   C14  C13   120.35  3.000
 VMY  C15   C14  C13   118.41  3.000
 VMY  H15   C15  C16   119.58  3.000
 VMY  H15   C15  C14   119.54  3.000
 VMY  C16   C15  C14   120.88  3.000
 VMY  H16   C16  C17   120.42  3.000
 VMY  H16   C16  C15   121.42  3.000
 VMY  C17   C16  C15   118.16  3.000
 VMY  C12   C17  F     117.68  3.000
 VMY  C12   C17  C16   123.50  3.000
 VMY  F     C17  C16   118.82  3.000
 VMY  C11   C12  C17   121.49  3.000
 VMY  C11   C12  C13   122.64  3.000
 VMY  C17   C12  C13   115.86  3.000
 VMY  H112  C11  H111  106.88  3.000
 VMY  H112  C11  N4    108.73  3.000
 VMY  H111  C11  N4    107.52  3.000
 VMY  H112  C11  C12   110.97  3.000
 VMY  H111  C11  C12   110.97  3.000
 VMY  N4    C11  C12   111.58  3.000
 VMY  N5    N4   C10   112.41  3.000
 VMY  N5    N4   C11   119.51  3.000
 VMY  C10   N4   C11   128.00  3.000
 VMY  H10   C10  C9    130.65  3.000
 VMY  H10   C10  N4    122.01  3.000
 VMY  C9    C10  N4    107.35  3.000
 VMY  H9    C9   C8    128.67  3.000
 VMY  H9    C9   C10   127.94  3.000
 VMY  C8    C9   C10   103.40  3.000
 VMY  C8    N5   N4    104.95  3.000
 VMY  N3    C8   N5    117.59  3.000
 VMY  N3    C8   C9    130.52  3.000
 VMY  N5    C8   C9    111.89  3.000
 VMY  H3    N3   C7    118.36  3.000
 VMY  H3    N3   C8    115.32  3.000
 VMY  C7    N3   C8    126.30  3.000
 VMY  S1    C7   N2    113.94  3.000
 VMY  S1    C7   N3    120.79  3.000
 VMY  N2    C7   N3    125.27  3.000
 VMY  N1    N2   C7    112.10  3.000
 VMY  C6    N1   N2    114.03  3.000
 VMY  C6    S1   C7     85.85  3.000
 VMY  C4    C6   S1    120.03  3.000
 VMY  C4    C6   N1    125.86  3.000
 VMY  S1    C6   N1    114.09  3.000
 VMY  C3    C4   O     108.81  3.000
 VMY  C3    C4   C5    110.46  3.000
 VMY  O     C4   C5    111.11  3.000
 VMY  C3    C4   C6    108.68  3.000
 VMY  O     C4   C6    107.38  3.000
 VMY  C5    C4   C6    110.30  3.000
 VMY  H53C  C5   H52C  108.58  3.000
 VMY  H53C  C5   H51C  108.28  3.000
 VMY  H52C  C5   H51C  108.92  3.000
 VMY  H53C  C5   C4    111.13  3.000
 VMY  H52C  C5   C4    110.00  3.000
 VMY  H51C  C5   C4    109.87  3.000
 VMY  H     O    C4    107.75  3.000
 VMY  N     C3   S     114.68  3.000
 VMY  N     C3   C4    121.03  3.000
 VMY  S     C3   C4    124.28  3.000
 VMY  C2    S    C3     88.89  3.000
 VMY  H2    C2   C1    128.15  3.000
 VMY  H2    C2   S     121.22  3.000
 VMY  C1    C2   S     110.63  3.000
 VMY  C1    N    C3    112.04  3.000
 VMY  C     C1   N     119.90  3.000
 VMY  C     C1   C2    126.34  3.000
 VMY  N     C1   C2    113.76  3.000
 VMY  HC3   C    HC2   108.17  3.000
 VMY  HC3   C    HC1   108.23  3.000
 VMY  HC2   C    HC1   107.37  3.000
 VMY  HC3   C    C1    111.09  3.000
 VMY  HC2   C    C1    110.92  3.000
 VMY  HC1   C    C1    110.92  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
 VMY  CONST_01  C16  C15  C14  C13    0.00   0.0  0
 VMY  CONST_02  C16  C17  C12  C13    0.00   0.0  0
 VMY  CONST_03  C17  C12  C13  C14    0.00   0.0  0
 VMY  CONST_04  C17  C16  C15  C14    0.00   0.0  0
 VMY  CONST_05  C12  C13  C14  C15    0.00   0.0  0
 VMY  CONST_06  C12  C17  C16  C15    0.00   0.0  0
 VMY  CONST_07  C8   C9   C10  N4     0.00   0.0  0
 VMY  CONST_08  C9   C8   N5   N4     0.00   0.0  0
 VMY  CONST_09  C8   N5   N4   C10    0.00   0.0  0
 VMY  CONST_10  N5   C8   C9   C10    0.00   0.0  0
 VMY  CONST_11  N5   N4   C10  C9     0.00   0.0  0
 VMY  CONST_12  C6   N1   N2   C7     0.00   0.0  0
 VMY  CONST_13  N1   C6   S1   C7     0.00   0.0  0
 VMY  CONST_14  C6   S1   C7   N2     0.00   0.0  0
 VMY  CONST_15  S1   C6   N1   N2     0.00   0.0  0
 VMY  CONST_16  S1   C7   N2   N1     0.00   0.0  0
 VMY  CONST_17  C1   C2   S    C3     0.00   0.0  0
 VMY  CONST_18  C2   C1   N    C3     0.00   0.0  0
 VMY  CONST_19  C1   N    C3   S      0.00   0.0  0
 VMY  CONST_20  N    C1   C2   S      0.00   0.0  0
 VMY  CONST_21  N    C3   S    C2     0.00   0.0  0
 VMY  CONST_22  C15  C14  C13  F1   180.00   0.0  0
 VMY  CONST_23  C17  C12  C13  F1   180.00   0.0  0
 VMY  CONST_24  F    C17  C12  C13  180.00   0.0  0
 VMY  CONST_25  C11  C12  C13  C14  180.00   0.0  0
 VMY  CONST_26  F    C17  C16  C15  180.00   0.0  0
 VMY  CONST_27  C11  C12  C17  C16  180.00   0.0  0
 VMY  CONST_28  C9   C10  N4   C11  180.00   0.0  0
 VMY  CONST_29  C8   N5   N4   C11  180.00   0.0  0
 VMY  CONST_30  N3   C8   N5   N4   180.00   0.0  0
 VMY  CONST_31  N3   C8   C9   C10  180.00   0.0  0
 VMY  CONST_32  N1   N2   C7   N3   180.00   0.0  0
 VMY  CONST_33  C6   S1   C7   N3   180.00   0.0  0
 VMY  CONST_34  C4   C6   S1   C7   180.00   0.0  0
 VMY  CONST_35  C4   C6   N1   N2   180.00   0.0  0
 VMY  CONST_36  C2   S    C3   C4   180.00   0.0  0
 VMY  CONST_37  C1   N    C3   C4   180.00   0.0  0
 VMY  CONST_38  C    C1   N    C3   180.00   0.0  0
 VMY  CONST_39  C    C1   C2   S    180.00   0.0  0
 VMY  CONST_40  H15  C15  C14  C13  180.00   0.0  0
 VMY  CONST_41  H16  C16  C15  C14  180.00   0.0  0
 VMY  CONST_42  H14  C14  C15  C16  180.00   0.0  0
 VMY  CONST_43  H9   C9   C10  N4   180.00   0.0  0
 VMY  CONST_44  H10  C10  N4   N5   180.00   0.0  0
 VMY  CONST_45  H2   C2   S    C3   180.00   0.0  0
 VMY  Var_01    N4   C11  C12  C13   99.80  30.0  2
 VMY  Var_02    C10  N4   C11  C12  109.92  30.0  2
 VMY  Var_03    C7   N3   C8   C9     2.86  30.0  2
 VMY  Var_04    N2   C7   N3   C8    -1.04  30.0  2
 VMY  Var_05    HC1  C    C1   C2   123.65  30.0  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
 VMY  chir_01  C4  C6  O  C3  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
 VMY  plan-1  C11  0.020
 VMY  plan-1  N4   0.020
 VMY  plan-1  C10  0.020
 VMY  plan-1  C9   0.020
 VMY  plan-1  N5   0.020
 VMY  plan-1  C8   0.020
 VMY  plan-1  N3   0.020
 VMY  plan-1  H10  0.020
 VMY  plan-1  H9   0.020
 VMY  plan-2  N3   0.020
 VMY  plan-2  C7   0.020
 VMY  plan-2  N2   0.020
 VMY  plan-2  N1   0.020
 VMY  plan-2  S1   0.020
 VMY  plan-2  C6   0.020
 VMY  plan-2  C4   0.020
 VMY  plan-3  C4   0.020
 VMY  plan-3  C3   0.020
 VMY  plan-3  S    0.020
 VMY  plan-3  C2   0.020
 VMY  plan-3  N    0.020
 VMY  plan-3  C1   0.020
 VMY  plan-3  C    0.020
 VMY  plan-3  H2   0.020
 VMY  plan-4  F1   0.020
 VMY  plan-4  C13  0.020
 VMY  plan-4  C14  0.020
 VMY  plan-4  C15  0.020
 VMY  plan-4  C16  0.020
 VMY  plan-4  C17  0.020
 VMY  plan-4  F    0.020
 VMY  plan-4  C12  0.020
 VMY  plan-4  C11  0.020
 VMY  plan-4  H14  0.020
 VMY  plan-4  H15  0.020
 VMY  plan-4  H16  0.020

