# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jun  9 20:11:12 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 2,6-difluoro-N-[(1S)-1-(5-{[2-(4-fluorophenoxy)ethyl]sulfanyl}-4-methyl-4H-1,2,4-triazol-3-yl)ethyl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](NC(=O)c1c(F)cccc1F)c2nnc(SCCOc3ccc(F)cc3)n2C
#
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
 ZVX  ZVX  2,6-difluoro-N-[(1S)-1-(5-{[2-(4-fluorophenoxy)ethyl]sulfanyl}-4-methyl-4H-1,2,4-triazol-3-yl)ethyl]benzamide  ligand  49  30  .  2021-08-25  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ZVX
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
 ZVX  F9    F  F     0  -0.321  -10.6106   1.2001  -0.1562
 ZVX  C6    C  CR6   0   0.500   -9.2752   1.0613  -0.0607
 ZVX  C7    C  CR16  0  -0.393   -8.5269   2.0975   0.4688
 ZVX  C8    C  CR16  0  -0.327   -7.1543   1.9540   0.5642
 ZVX  C5    C  CR16  0  -0.396   -8.6849  -0.1058  -0.4921
 ZVX  C4    C  CR16  0  -0.364   -7.3044  -0.2489  -0.3954
 ZVX  C3    C  CR6   0   0.379   -6.5327   0.7811   0.1333
 ZVX  O2    O  O2    0  -0.474   -5.1888   0.7358   0.2669
 ZVX  C1    C  CH2   0  -0.174   -4.5106  -0.4393  -0.1232
 ZVX  C10   C  CH2   0  -0.576   -3.0392  -0.1914   0.1543
 ZVX  S11   S  S2    0   0.055   -2.1414  -1.6997  -0.3141
 ZVX  C12   C  CR5   0   0.289   -0.5162  -1.1741   0.0040
 ZVX  N13   N  N     0  -0.327   -0.1297  -0.0528   0.5396
 ZVX  N14   N  N     0  -0.341    1.2285  -0.0879   0.5929
 ZVX  N16   N  NR5   0  -0.490    0.5519  -1.9520  -0.3045
 ZVX  C17   C  CH3   0  -0.553    0.5240  -3.2653  -0.9122
 ZVX  C15   C  CR5   0   0.465    1.6237  -1.2195   0.0937
 ZVX  C18   C  CH1   0  -0.181    3.0413  -1.6883   0.0221
 ZVX  C19   C  CH3   0  -0.648    3.3261  -2.7385   1.0981
 ZVX  N20   N  NH1   0  -0.617    3.8977  -0.5304   0.1577
 ZVX  C21   C  C     0   0.537    5.1359  -0.4899  -0.3461
 ZVX  O28   O  O     0  -0.464    5.6631  -1.4055  -0.9530
 ZVX  C22   C  CR6   0  -0.456    5.8605   0.8023  -0.1057
 ZVX  C27   C  CR6   0   0.585    5.5230   1.9721  -0.7660
 ZVX  F30   F  F     0  -0.296    4.4782   1.9416  -1.6012
 ZVX  C23   C  CR6   0   0.567    6.9588   0.8546   0.7376
 ZVX  F29   F  F     0  -0.296    7.2966  -0.2622   1.3909
 ZVX  C24   C  CR16  0  -0.419    7.6915   2.0058   0.9393
 ZVX  C25   C  CR16  0  -0.225    7.3140   3.1530   0.2546
 ZVX  C26   C  CR16  0  -0.417    6.2269   3.1491  -0.6072
 ZVX  H7    H  HCR6  0   0.283   -9.0059   3.0073   0.8057
 ZVX  H5    H  HCR6  0   0.283   -9.2842  -0.9072  -0.9041
 ZVX  H8    H  HCR6  0   0.276   -6.5565   2.7566   0.9767
 ZVX  H4    H  HCR6  0   0.292   -6.8605  -1.1713  -0.7430
 ZVX  H11C  H  HCH2  0   0.243   -4.8678  -1.3035   0.4481
 ZVX  H12C  H  HCH2  0   0.243   -4.6677  -0.6482  -1.1871
 ZVX  H101  H  HCH2  0   0.298   -2.6662   0.6444  -0.4366
 ZVX  H102  H  HCH2  0   0.297   -2.8720   0.0129   1.2110
 ZVX  H171  H  HCH3  0   0.281   -0.1871  -3.2775  -1.7356
 ZVX  H172  H  HCH3  0   0.283    1.5051  -3.5018  -1.3133
 ZVX  H173  H  HCH3  0   0.279    0.2468  -4.0234  -0.1820
 ZVX  H18   H  HCH1  0   0.289    3.2233  -2.1266  -0.9628
 ZVX  H191  H  HCH3  0   0.242    3.1773  -2.3168   2.0918
 ZVX  H192  H  HCH3  0   0.244    2.6693  -3.6023   0.9922
 ZVX  H193  H  HCH3  0   0.255    4.3528  -3.0913   1.0162
 ZVX  H20   H  HNH1  0   0.418    3.5484   0.2516   0.6927
 ZVX  H26   H  HCR6  0   0.291    5.9340   4.0388  -1.1478
 ZVX  H24   H  HCR6  0   0.292    8.5366   2.0058   1.6140
 ZVX  H25   H  HCR6  0   0.287    7.8774   4.0650   0.3950

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
 ZVX  F9   C6    single    1.346  0.020  1.346
 ZVX  C6   C7    aromatic  1.383  0.020  1.383
 ZVX  C6   C5    aromatic  1.377  0.020  1.377
 ZVX  C7   C8    aromatic  1.383  0.020  1.383
 ZVX  C8   C3    aromatic  1.396  0.020  1.396
 ZVX  C5   C4    aromatic  1.391  0.020  1.391
 ZVX  C4   C3    aromatic  1.391  0.020  1.391
 ZVX  C3   O2    single    1.351  0.020  1.351
 ZVX  O2   C1    single    1.412  0.020  1.412
 ZVX  C1   C10   single    1.518  0.020  1.518
 ZVX  C10  S11   single    1.817  0.020  1.817
 ZVX  S11  C12   single    1.737  0.020  1.737
 ZVX  C12  N13   aromatic  1.301  0.020  1.301
 ZVX  C12  N16   aromatic  1.357  0.020  1.357
 ZVX  N13  N14   aromatic  1.360  0.020  1.360
 ZVX  N14  C15   aromatic  1.298  0.020  1.298
 ZVX  N16  C17   single    1.447  0.020  1.447
 ZVX  N16  C15   aromatic  1.358  0.020  1.358
 ZVX  C15  C18   single    1.495  0.020  1.495
 ZVX  C18  C19   single    1.530  0.020  1.530
 ZVX  C18  N20   single    1.447  0.020  1.447
 ZVX  N20  C21   single    1.337  0.020  1.337
 ZVX  C21  O28   double    1.218  0.020  1.218
 ZVX  C21  C22   single    1.501  0.020  1.501
 ZVX  C22  C27   aromatic  1.385  0.020  1.385
 ZVX  C22  C23   aromatic  1.386  0.020  1.386
 ZVX  C27  F30   single    1.338  0.020  1.338
 ZVX  C27  C26   aromatic  1.381  0.020  1.381
 ZVX  C23  F29   single    1.337  0.020  1.337
 ZVX  C23  C24   aromatic  1.379  0.020  1.379
 ZVX  C24  C25   aromatic  1.388  0.020  1.388
 ZVX  C25  C26   aromatic  1.387  0.020  1.387
 ZVX  C7   H7    single    0.930  0.020  1.080
 ZVX  C5   H5    single    0.930  0.020  1.080
 ZVX  C8   H8    single    0.930  0.020  1.080
 ZVX  C4   H4    single    0.930  0.020  1.080
 ZVX  C1   H11C  single    0.970  0.020  1.090
 ZVX  C1   H12C  single    0.970  0.020  1.090
 ZVX  C10  H101  single    0.970  0.020  1.090
 ZVX  C10  H102  single    0.970  0.020  1.090
 ZVX  C17  H171  single    0.970  0.020  1.090
 ZVX  C17  H172  single    0.970  0.020  1.090
 ZVX  C17  H173  single    0.970  0.020  1.090
 ZVX  C18  H18   single    0.970  0.020  1.090
 ZVX  C19  H191  single    0.970  0.020  1.090
 ZVX  C19  H192  single    0.970  0.020  1.090
 ZVX  C19  H193  single    0.970  0.020  1.090
 ZVX  N20  H20   single    0.860  0.020  1.020
 ZVX  C26  H26   single    0.930  0.020  1.080
 ZVX  C24  H24   single    0.930  0.020  1.080
 ZVX  C25  H25   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
 ZVX  C5    C6   C7    121.52  3.000
 ZVX  C5    C6   F9    119.37  3.000
 ZVX  C7    C6   F9    119.12  3.000
 ZVX  H7    C7   C8    120.34  3.000
 ZVX  H7    C7   C6    120.63  3.000
 ZVX  C8    C7   C6    119.04  3.000
 ZVX  H8    C8   C3    119.65  3.000
 ZVX  H8    C8   C7    119.82  3.000
 ZVX  C3    C8   C7    120.52  3.000
 ZVX  H5    C5   C4    119.99  3.000
 ZVX  H5    C5   C6    120.62  3.000
 ZVX  C4    C5   C6    119.39  3.000
 ZVX  H4    C4   C3    121.74  3.000
 ZVX  H4    C4   C5    118.22  3.000
 ZVX  C3    C4   C5    120.04  3.000
 ZVX  O2    C3   C4    124.35  3.000
 ZVX  O2    C3   C8    116.15  3.000
 ZVX  C4    C3   C8    119.50  3.000
 ZVX  C1    O2   C3    118.58  3.000
 ZVX  H12C  C1   H11C  108.01  3.000
 ZVX  H12C  C1   C10   110.35  3.000
 ZVX  H11C  C1   C10   110.46  3.000
 ZVX  H12C  C1   O2    110.99  3.000
 ZVX  H11C  C1   O2    110.84  3.000
 ZVX  C10   C1   O2    106.22  3.000
 ZVX  H102  C10  H101  109.26  3.000
 ZVX  H102  C10  S11   109.27  3.000
 ZVX  H101  C10  S11   109.14  3.000
 ZVX  H102  C10  C1    110.91  3.000
 ZVX  H101  C10  C1    110.98  3.000
 ZVX  S11   C10  C1    107.24  3.000
 ZVX  C12   S11  C10    99.43  3.000
 ZVX  N16   C12  N13   110.71  3.000
 ZVX  N16   C12  S11   121.42  3.000
 ZVX  N13   C12  S11   127.87  3.000
 ZVX  N14   N13  C12   106.90  3.000
 ZVX  C15   N14  N13   108.15  3.000
 ZVX  C15   N16  C17   128.89  3.000
 ZVX  C15   N16  C12   104.20  3.000
 ZVX  C17   N16  C12   126.90  3.000
 ZVX  H173  C17  H172  109.04  3.000
 ZVX  H173  C17  H171  109.48  3.000
 ZVX  H172  C17  H171  107.96  3.000
 ZVX  H173  C17  N16   110.81  3.000
 ZVX  H172  C17  N16   109.59  3.000
 ZVX  H171  C17  N16   109.90  3.000
 ZVX  C18   C15  N16   124.42  3.000
 ZVX  C18   C15  N14   125.48  3.000
 ZVX  N16   C15  N14   110.04  3.000
 ZVX  H18   C18  N20   107.86  3.000
 ZVX  H18   C18  C19   109.11  3.000
 ZVX  N20   C18  C19   111.92  3.000
 ZVX  H18   C18  C15   109.07  3.000
 ZVX  N20   C18  C15   107.81  3.000
 ZVX  C19   C18  C15   110.98  3.000
 ZVX  H193  C19  H192  107.70  3.000
 ZVX  H193  C19  H191  108.83  3.000
 ZVX  H192  C19  H191  108.23  3.000
 ZVX  H193  C19  C18   110.18  3.000
 ZVX  H192  C19  C18   111.31  3.000
 ZVX  H191  C19  C18   110.50  3.000
 ZVX  H20   N20  C21   119.76  3.000
 ZVX  H20   N20  C18   117.69  3.000
 ZVX  C21   N20  C18   122.48  3.000
 ZVX  C22   C21  O28   121.19  3.000
 ZVX  C22   C21  N20   114.38  3.000
 ZVX  O28   C21  N20   124.43  3.000
 ZVX  C23   C22  C27   116.83  3.000
 ZVX  C23   C22  C21   120.84  3.000
 ZVX  C27   C22  C21   122.22  3.000
 ZVX  C26   C27  F30   119.30  3.000
 ZVX  C26   C27  C22   122.75  3.000
 ZVX  F30   C27  C22   117.94  3.000
 ZVX  C24   C23  F29   119.43  3.000
 ZVX  C24   C23  C22   122.79  3.000
 ZVX  F29   C23  C22   117.77  3.000
 ZVX  H24   C24  C25   121.35  3.000
 ZVX  H24   C24  C23   120.42  3.000
 ZVX  C25   C24  C23   118.23  3.000
 ZVX  H25   C25  C26   119.43  3.000
 ZVX  H25   C25  C24   119.43  3.000
 ZVX  C26   C25  C24   121.15  3.000
 ZVX  H26   C26  C25   121.36  3.000
 ZVX  H26   C26  C27   120.38  3.000
 ZVX  C25   C26  C27   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
 ZVX  CONST_01  C3    C8   C7   C6      0.00   0.0  0
 ZVX  CONST_02  C3    C4   C5   C6      0.00   0.0  0
 ZVX  CONST_03  C4    C5   C6   C7      0.00   0.0  0
 ZVX  CONST_04  C4    C3   C8   C7      0.00   0.0  0
 ZVX  CONST_05  C5    C6   C7   C8      0.00   0.0  0
 ZVX  CONST_06  C5    C4   C3   C8      0.00   0.0  0
 ZVX  CONST_07  C15   N14  N13  C12     0.00   0.0  0
 ZVX  CONST_08  N14   C15  N16  C12     0.00   0.0  0
 ZVX  CONST_09  C15   N16  C12  N13     0.00   0.0  0
 ZVX  CONST_10  N16   C15  N14  N13     0.00   0.0  0
 ZVX  CONST_11  N16   C12  N13  N14     0.00   0.0  0
 ZVX  CONST_12  C25   C26  C27  C22     0.00   0.0  0
 ZVX  CONST_13  C25   C24  C23  C22     0.00   0.0  0
 ZVX  CONST_14  C24   C23  C22  C27     0.00   0.0  0
 ZVX  CONST_15  C24   C25  C26  C27     0.00   0.0  0
 ZVX  CONST_16  C26   C27  C22  C23     0.00   0.0  0
 ZVX  CONST_17  C26   C25  C24  C23     0.00   0.0  0
 ZVX  CONST_18  C8    C7   C6   F9    180.00   0.0  0
 ZVX  CONST_19  C4    C5   C6   F9    180.00   0.0  0
 ZVX  CONST_20  O2    C3   C8   C7    180.00   0.0  0
 ZVX  CONST_21  O2    C3   C4   C5    180.00   0.0  0
 ZVX  CONST_22  N14   N13  C12  S11   180.00   0.0  0
 ZVX  CONST_23  C15   N16  C12  S11   180.00   0.0  0
 ZVX  CONST_24  C18   C15  N16  C12   180.00   0.0  0
 ZVX  CONST_25  C17   N16  C12  N13   180.00   0.0  0
 ZVX  CONST_26  C18   C15  N14  N13   180.00   0.0  0
 ZVX  CONST_27  C17   N16  C15  N14   180.00   0.0  0
 ZVX  CONST_28  C26   C27  C22  C21   180.00   0.0  0
 ZVX  CONST_29  C24   C23  C22  C21   180.00   0.0  0
 ZVX  CONST_30  F29   C23  C22  C27   180.00   0.0  0
 ZVX  CONST_31  C23   C22  C27  F30   180.00   0.0  0
 ZVX  CONST_32  C25   C26  C27  F30   180.00   0.0  0
 ZVX  CONST_33  C25   C24  C23  F29   180.00   0.0  0
 ZVX  CONST_34  H8    C8   C7   C6    180.00   0.0  0
 ZVX  CONST_35  H4    C4   C5   C6    180.00   0.0  0
 ZVX  CONST_36  H5    C5   C6   C7    180.00   0.0  0
 ZVX  CONST_37  H7    C7   C6   C5    180.00   0.0  0
 ZVX  CONST_38  H26   C26  C27  C22   180.00   0.0  0
 ZVX  CONST_39  H24   C24  C23  C22   180.00   0.0  0
 ZVX  CONST_40  H25   C25  C26  C27   180.00   0.0  0
 ZVX  CONST_41  C22   C21  N20  C18   180.00   0.0  0
 ZVX  CONST_42  H20   N20  C21  C22     0.00   0.0  0
 ZVX  CONST_43  O28   C21  N20  C18     0.00   0.0  0
 ZVX  Var_01    N13   C12  S11  C10     5.41  30.0  2
 ZVX  Var_02    C27   C22  C21  N20   -71.82  30.0  2
 ZVX  Var_03    H171  C17  N16  C12    44.05  30.0  2
 ZVX  Var_04    C10   C1   O2   C3   -179.52  30.0  3
 ZVX  Var_05    H101  C10  S11  C12    57.06  30.0  1
 ZVX  Var_06    S11   C10  C1   O2    179.12  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
 ZVX  chir_01  C18  C15  C19  N20  positiv

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
 ZVX  plan-1  S11  0.020
 ZVX  plan-1  C12  0.020
 ZVX  plan-1  N13  0.020
 ZVX  plan-1  N14  0.020
 ZVX  plan-1  N16  0.020
 ZVX  plan-1  C17  0.020
 ZVX  plan-1  C15  0.020
 ZVX  plan-1  C18  0.020
 ZVX  plan-2  F9   0.020
 ZVX  plan-2  C6   0.020
 ZVX  plan-2  C7   0.020
 ZVX  plan-2  C8   0.020
 ZVX  plan-2  C5   0.020
 ZVX  plan-2  C4   0.020
 ZVX  plan-2  C3   0.020
 ZVX  plan-2  O2   0.020
 ZVX  plan-2  H7   0.020
 ZVX  plan-2  H5   0.020
 ZVX  plan-2  H8   0.020
 ZVX  plan-2  H4   0.020
 ZVX  plan-3  C21  0.020
 ZVX  plan-3  C22  0.020
 ZVX  plan-3  C27  0.020
 ZVX  plan-3  F30  0.020
 ZVX  plan-3  C23  0.020
 ZVX  plan-3  F29  0.020
 ZVX  plan-3  C24  0.020
 ZVX  plan-3  C25  0.020
 ZVX  plan-3  C26  0.020
 ZVX  plan-3  H26  0.020
 ZVX  plan-3  H24  0.020
 ZVX  plan-3  H25  0.020
 ZVX  plan-4  C18  0.020
 ZVX  plan-4  N20  0.020
 ZVX  plan-4  C21  0.020
 ZVX  plan-4  O28  0.020
 ZVX  plan-4  C22  0.020
 ZVX  plan-4  H20  0.020

