# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 03:31:19 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: 2-amino-4-fluoro-5-[(1-methyl-1H-imidazol-2-yl)sulfanyl]-N-1,3-thiazol-2-ylbenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1ccnc1Sc2cc(c(N)cc2F)C(=O)Nc3sccn3
#
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
 MRK  MRK  2-amino-4-fluoro-5-[(1-methyl-1H-imidazol-2-yl)sulfanyl]-N-1,3-thiazol-2-ylbenzamide  ligand  35  23  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MRK
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
 MRK  S1    S  S2    0   0.210   1.4756  -1.1401  -4.9361
 MRK  C2    C  CR15  0  -0.508   1.3875  -0.1791  -6.3592
 MRK  C3    C  CR15  0  -0.010   0.5751   0.8810  -6.1386
 MRK  N4    N  N     0  -0.390   0.0316   0.9766  -4.8877
 MRK  C5    C  CR5   0   0.290   0.4146  -0.0097  -4.1504
 MRK  N6    N  NH1   0  -0.725   0.0721  -0.2250  -2.8335
 MRK  C7    C  C     0   0.568  -1.0427   0.2738  -2.2011
 MRK  O8    O  O     0  -0.446  -1.8994   0.9004  -2.7954
 MRK  C9    C  CR6   0   0.380  -2.3817  -0.1346  -0.1110
 MRK  C10   C  CR6   0  -0.154  -1.1199  -0.0372  -0.7565
 MRK  C11   C  CR16  0  -0.267   0.0443  -0.2003  -0.0046
 MRK  C12   C  CR6   0  -0.369   0.0246  -0.5057   1.3426
 MRK  C13   C  CR6   0   0.646  -1.2277  -0.6476   1.9393
 MRK  F14   F  F     0  -0.296  -1.2827  -0.9516   3.2360
 MRK  C15   C  CR16  0  -0.498  -2.3990  -0.4635   1.2588
 MRK  S16   S  S2    0   0.070   1.5180  -0.7789   2.2351
 MRK  N17   N  NR5   0  -0.405   1.5672   0.4286   4.6756
 MRK  C18   C  CR5   0   0.260   1.5081   0.5893   3.3323
 MRK  N19   N  N     0  -0.416   1.4623   1.8524   2.9907
 MRK  C20   C  CR15  0  -0.217   1.4817   2.5440   4.1629
 MRK  C21   C  CR15  0  -0.102   1.5574   1.6791   5.2191
 MRK  N23   N  NH2   0  -0.860  -3.5529   0.0220  -0.7553
 MRK  H2    H  HCR5  0   0.311   1.9332  -0.4400  -7.2513
 MRK  H3    H  HCR5  0   0.276   0.3470   1.6390  -6.8741
 MRK  HN6   H  HNH1  0   0.434   0.6171  -0.9132  -2.3373
 MRK  H11   H  HCR6  0   0.288   1.0114  -0.0631  -0.4723
 MRK  H15   H  HCR6  0   0.294  -3.3441  -0.5695   1.7771
 MRK  H20   H  HCR5  0   0.256   1.4481   3.6220   4.1902
 MRK  H21   H  HCR5  0   0.294   1.6078   1.8388   6.2832
 MRK  H221  H  HCH3  0   0.262   0.7596  -1.4376   5.1767
 MRK  H222  H  HCH3  0   0.265   2.5302  -1.3724   5.1607
 MRK  H223  H  HCH3  0   0.269   1.6295  -0.6018   6.4684
 MRK  H231  H  HNH2  0   0.402  -4.4045   0.0337  -0.2212
 MRK  H232  H  HNH2  0   0.409  -3.5714   0.4763  -1.6517
 MRK  C22   C  CH3   0  -0.523   1.6254  -0.8204   5.4049

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
 MRK  S1   C2    aromatic  1.719  0.020  1.719
 MRK  S1   C5    aromatic  1.738  0.020  1.738
 MRK  C2   C3    aromatic  1.354  0.020  1.354
 MRK  C2   H2    single    0.930  0.020  1.080
 MRK  C3   N4    aromatic  1.367  0.020  1.367
 MRK  C3   H3    single    0.930  0.020  1.080
 MRK  N4   C5    aromatic  1.290  0.020  1.290
 MRK  C5   N6    single    1.378  0.020  1.378
 MRK  N6   C7    single    1.375  0.020  1.375
 MRK  N6   HN6   single    0.860  0.020  1.020
 MRK  C7   O8    double    1.216  0.020  1.216
 MRK  C7   C10   single    1.480  0.020  1.480
 MRK  C9   C10   aromatic  1.421  0.020  1.421
 MRK  C9   C15   aromatic  1.409  0.020  1.409
 MRK  C9   N23   single    1.346  0.020  1.346
 MRK  C10  C11   aromatic  1.395  0.020  1.395
 MRK  C11  C12   aromatic  1.381  0.020  1.381
 MRK  C11  H11   single    0.930  0.020  1.080
 MRK  C12  C13   aromatic  1.394  0.020  1.394
 MRK  C12  S16   single    1.761  0.020  1.761
 MRK  C13  F14   single    1.333  0.020  1.333
 MRK  C13  C15   aromatic  1.367  0.020  1.367
 MRK  C15  H15   single    0.930  0.020  1.080
 MRK  S16  C18   single    1.754  0.020  1.754
 MRK  N17  C18   aromatic  1.354  0.020  1.354
 MRK  N17  C21   aromatic  1.364  0.020  1.364
 MRK  N17  C22   single    1.447  0.020  1.447
 MRK  C18  N19   aromatic  1.309  0.020  1.309
 MRK  N19  C20   aromatic  1.361  0.020  1.361
 MRK  C20  C21   aromatic  1.367  0.020  1.367
 MRK  C20  H20   single    0.930  0.020  1.080
 MRK  C21  H21   single    0.930  0.020  1.080
 MRK  C22  H221  single    0.970  0.020  1.090
 MRK  C22  H222  single    0.970  0.020  1.090
 MRK  C22  H223  single    0.970  0.020  1.090
 MRK  N23  H231  single    0.890  0.020  1.040
 MRK  N23  H232  single    0.890  0.020  1.040

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
 MRK  C5    S1   C2     88.82  3.000
 MRK  H2    C2   C3    128.93  3.000
 MRK  H2    C2   S1    121.59  3.000
 MRK  C3    C2   S1    109.48  3.000
 MRK  H3    C3   N4    119.32  3.000
 MRK  H3    C3   C2    124.41  3.000
 MRK  N4    C3   C2    116.26  3.000
 MRK  C5    N4   C3    110.58  3.000
 MRK  N6    C5   N4    126.31  3.000
 MRK  N6    C5   S1    118.83  3.000
 MRK  N4    C5   S1    114.85  3.000
 MRK  HN6   N6   C7    117.34  3.000
 MRK  HN6   N6   C5    116.28  3.000
 MRK  C7    N6   C5    125.76  3.000
 MRK  C10   C7   O8    123.26  3.000
 MRK  C10   C7   N6    114.52  3.000
 MRK  O8    C7   N6    122.21  3.000
 MRK  N23   C9   C15   118.82  3.000
 MRK  N23   C9   C10   123.19  3.000
 MRK  C15   C9   C10   117.95  3.000
 MRK  C11   C10  C9    119.22  3.000
 MRK  C11   C10  C7    120.47  3.000
 MRK  C9    C10  C7    120.29  3.000
 MRK  H11   C11  C12   117.51  3.000
 MRK  H11   C11  C10   119.83  3.000
 MRK  C12   C11  C10   122.65  3.000
 MRK  S16   C12  C13   121.93  3.000
 MRK  S16   C12  C11   121.09  3.000
 MRK  C13   C12  C11   116.91  3.000
 MRK  C15   C13  F14   118.66  3.000
 MRK  C15   C13  C12   122.87  3.000
 MRK  F14   C13  C12   118.46  3.000
 MRK  H15   C15  C13   119.75  3.000
 MRK  H15   C15  C9    119.92  3.000
 MRK  C13   C15  C9    120.33  3.000
 MRK  C18   S16  C12   101.02  3.000
 MRK  C22   N17  C21   126.21  3.000
 MRK  C22   N17  C18   127.15  3.000
 MRK  C21   N17  C18   106.63  3.000
 MRK  N19   C18  N17   112.02  3.000
 MRK  N19   C18  S16   126.13  3.000
 MRK  N17   C18  S16   121.85  3.000
 MRK  C20   N19  C18   105.36  3.000
 MRK  H20   C20  C21   127.89  3.000
 MRK  H20   C20  N19   121.94  3.000
 MRK  C21   C20  N19   110.16  3.000
 MRK  H21   C21  C20   132.21  3.000
 MRK  H21   C21  N17   121.97  3.000
 MRK  C20   C21  N17   105.82  3.000
 MRK  H232  N23  H231  116.93  3.000
 MRK  H232  N23  C9    119.71  3.000
 MRK  H231  N23  C9    118.96  3.000
 MRK  H223  C22  H222  108.60  3.000
 MRK  H223  C22  H221  108.83  3.000
 MRK  H222  C22  H221  109.10  3.000
 MRK  H223  C22  N17   108.66  3.000
 MRK  H222  C22  N17   110.99  3.000
 MRK  H221  C22  N17   110.61  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
 MRK  CONST_01  N4    C3   C2   S1      0.00   0.0  0
 MRK  CONST_02  C3    N4   C5   S1      0.00   0.0  0
 MRK  CONST_03  N4    C5   S1   C2      0.00   0.0  0
 MRK  CONST_04  C5    N4   C3   C2      0.00   0.0  0
 MRK  CONST_05  C5    S1   C2   C3      0.00   0.0  0
 MRK  CONST_06  C12   C11  C10  C9      0.00   0.0  0
 MRK  CONST_07  C12   C13  C15  C9      0.00   0.0  0
 MRK  CONST_08  C13   C15  C9   C10     0.00   0.0  0
 MRK  CONST_09  C13   C12  C11  C10     0.00   0.0  0
 MRK  CONST_10  C15   C9   C10  C11     0.00   0.0  0
 MRK  CONST_11  C15   C13  C12  C11     0.00   0.0  0
 MRK  CONST_12  C20   N19  C18  N17     0.00   0.0  0
 MRK  CONST_13  N19   C20  C21  N17     0.00   0.0  0
 MRK  CONST_14  C20   C21  N17  C18     0.00   0.0  0
 MRK  CONST_15  C21   C20  N19  C18     0.00   0.0  0
 MRK  CONST_16  C21   N17  C18  N19     0.00   0.0  0
 MRK  CONST_17  N6    C5   S1   C2    180.00   0.0  0
 MRK  CONST_18  N6    C5   N4   C3    180.00   0.0  0
 MRK  CONST_19  C15   C9   C10  C7    180.00   0.0  0
 MRK  CONST_20  C12   C11  C10  C7    180.00   0.0  0
 MRK  CONST_21  F14   C13  C15  C9    180.00   0.0  0
 MRK  CONST_22  S16   C12  C11  C10   180.00   0.0  0
 MRK  CONST_23  N23   C9   C10  C11   180.00   0.0  0
 MRK  CONST_24  F14   C13  C12  C11   180.00   0.0  0
 MRK  CONST_25  N23   C9   C15  C13   180.00   0.0  0
 MRK  CONST_26  S16   C12  C13  C15   180.00   0.0  0
 MRK  CONST_27  C21   N17  C18  S16   180.00   0.0  0
 MRK  CONST_28  C20   N19  C18  S16   180.00   0.0  0
 MRK  CONST_29  C22   N17  C18  N19   180.00   0.0  0
 MRK  CONST_30  C22   N17  C21  C20   180.00   0.0  0
 MRK  CONST_31  H3    C3   C2   S1    180.00   0.0  0
 MRK  CONST_32  H2    C2   C3   N4    180.00   0.0  0
 MRK  CONST_33  H11   C11  C10  C9    180.00   0.0  0
 MRK  CONST_34  H15   C15  C9   C10   180.00   0.0  0
 MRK  CONST_35  H20   C20  C21  N17   180.00   0.0  0
 MRK  CONST_36  H21   C21  N17  C18   180.00   0.0  0
 MRK  CONST_37  C10   C7   N6   C5    180.00   0.0  0
 MRK  CONST_40  HN6   N6   C5   S1      0.00   0.0  0
 MRK  CONST_41  H231  N23  C9   C10   180.00   0.0  0
 MRK  CONST_43  O8    C7   N6   C5      0.00   0.0  0
 MRK  Var_01    N17   C18  S16  C12   123.25  30.0  2
 MRK  Var_02    C9    C10  C7   N6   -152.16  30.0  2
 MRK  Var_03    H221  C22  N17  C18   -58.65  30.0  2

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
 MRK  plan-1  S1    0.020
 MRK  plan-1  C2    0.020
 MRK  plan-1  C3    0.020
 MRK  plan-1  N4    0.020
 MRK  plan-1  C5    0.020
 MRK  plan-1  N6    0.020
 MRK  plan-1  H2    0.020
 MRK  plan-1  H3    0.020
 MRK  plan-2  S16   0.020
 MRK  plan-2  N17   0.020
 MRK  plan-2  C18   0.020
 MRK  plan-2  N19   0.020
 MRK  plan-2  C20   0.020
 MRK  plan-2  C21   0.020
 MRK  plan-2  H20   0.020
 MRK  plan-2  H21   0.020
 MRK  plan-2  C22   0.020
 MRK  plan-3  C7    0.020
 MRK  plan-3  C9    0.020
 MRK  plan-3  C10   0.020
 MRK  plan-3  C11   0.020
 MRK  plan-3  C12   0.020
 MRK  plan-3  C13   0.020
 MRK  plan-3  F14   0.020
 MRK  plan-3  C15   0.020
 MRK  plan-3  S16   0.020
 MRK  plan-3  N23   0.020
 MRK  plan-3  H11   0.020
 MRK  plan-3  H15   0.020
 MRK  plan-4  C5    0.020
 MRK  plan-4  N6    0.020
 MRK  plan-4  C7    0.020
 MRK  plan-4  O8    0.020
 MRK  plan-4  C10   0.020
 MRK  plan-4  HN6   0.020
 MRK  plan-5  C9    0.020
 MRK  plan-5  N23   0.020
 MRK  plan-5  H231  0.020
 MRK  plan-5  H232  0.020

