# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 11:25:51 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: 1-(3,5-difluoro-3'-methoxybiphenyl-4-yl)-3-(1,3-thiazol-5-yl)urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(c1)c2cc(F)c(NC(=O)Nc3scnc3)c(F)c2
#
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
 4R5  4R5  1-(3,5-difluoro-3'-methoxybiphenyl-4-yl)-3-(1,3-thiazol-5-yl)urea  ligand  38  25  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4R5
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
 4R5  C2   C  CR5   0   0.060  -5.1545  -0.1617  -0.0651
 4R5  C3   C  CR15  0  -0.112  -6.4595  -0.0924  -0.4580
 4R5  C5   C  CR15  0  -0.234  -6.7718  -1.0454   1.4885
 4R5  C11  C  CR16  0  -0.502   1.7611  -0.1967  -1.3289
 4R5  C13  C  CR16  0  -0.505   1.3830   1.3507   0.4745
 4R5  C15  C  CR6   0   0.103   3.6938   0.5248   0.0755
 4R5  C16  C  CR16  0  -0.405   4.4016  -0.6684   0.0116
 4R5  C17  C  CR6   0   0.408   5.7548  -0.7140   0.3500
 4R5  C18  C  CR16  0  -0.389   6.4056   0.4503   0.7511
 4R5  C19  C  CR16  0  -0.227   5.6923   1.6420   0.8068
 4R5  C26  C  CH3   0  -0.438   7.7002  -2.0386   0.6468
 4R5  S1   S  S2    0   0.227  -5.0527  -0.8938   1.4942
 4R5  N4   N  N     0  -0.348  -7.3616  -0.5964   0.4318
 4R5  N6   N  NH1   0  -0.741  -4.0655   0.2848  -0.7793
 4R5  C7   C  C     0   0.750  -2.7760   0.1640  -0.3489
 4R5  N8   N  NH1   0  -0.764  -1.8477   0.6597  -1.2131
 4R5  C9   C  CR6   0  -0.045  -0.4857   0.6259  -0.8972
 4R5  C10  C  CR6   0   0.572   0.4125  -0.1551  -1.6122
 4R5  C12  C  CR6   0   0.116   2.2577   0.5582  -0.2679
 4R5  C14  C  CR6   0   0.582   0.0462   1.3770   0.1433
 4R5  C20  C  CR16  0  -0.327   4.3499   1.6911   0.4777
 4R5  O21  O  O     0  -0.495  -2.4947  -0.3417   0.7234
 4R5  F22  F  F     0  -0.296  -0.0644  -0.8810  -2.6262
 4R5  F24  F  F     0  -0.296  -0.7824   2.1470   0.8491
 4R5  O25  O  O2    0  -0.472   6.3424  -1.9220   0.2688
 4R5  H1   H  HCR5  0   0.277  -6.7929   0.3249  -1.3980
 4R5  H2   H  HCR5  0   0.295  -7.2851  -1.4935   2.3280
 4R5  H3   H  HCR6  0   0.286   2.4140  -0.8070  -1.9388
 4R5  H4   H  HCR6  0   0.285   1.7337   1.9346   1.3151
 4R5  H5   H  HCR6  0   0.264   3.9062  -1.5878  -0.2771
 4R5  H6   H  HCR6  0   0.282   7.4526   0.4490   1.0208
 4R5  H7   H  HCR6  0   0.264   6.2028   2.5468   1.1097
 4R5  H8   H  HCH3  0   0.229   8.3556  -1.4371   0.0120
 4R5  H9   H  HCH3  0   0.230   7.8590  -1.7509   1.6891
 4R5  H10  H  HCH3  0   0.261   7.9645  -3.0863   0.5283
 4R5  H11  H  HNH1  0   0.428  -4.2641   0.7350  -1.6603
 4R5  H12  H  HNH1  0   0.420  -2.1203   0.9572  -2.1381
 4R5  H13  H  HCR6  0   0.256   3.8195   2.6338   0.5113

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
 4R5  F24  C14  single    1.333  0.020  1.333
 4R5  C14  C13  aromatic  1.377  0.020  1.377
 4R5  C14  C9   aromatic  1.389  0.020  1.389
 4R5  N8   C9   single    1.399  0.020  1.399
 4R5  N8   C7   single    1.362  0.020  1.362
 4R5  C13  C12  aromatic  1.394  0.020  1.394
 4R5  O25  C26  single    1.414  0.020  1.414
 4R5  O25  C17  single    1.346  0.020  1.346
 4R5  N6   C7   single    1.365  0.020  1.365
 4R5  N6   C2   single    1.377  0.020  1.377
 4R5  C9   C10  aromatic  1.389  0.020  1.389
 4R5  S1   C2   aromatic  1.726  0.020  1.726
 4R5  S1   C5   aromatic  1.726  0.020  1.726
 4R5  C16  C17  aromatic  1.396  0.020  1.396
 4R5  C16  C15  aromatic  1.389  0.020  1.389
 4R5  C7   O21  double    1.218  0.020  1.218
 4R5  C2   C3   aromatic  1.365  0.020  1.365
 4R5  C17  C18  aromatic  1.393  0.020  1.393
 4R5  C12  C15  single    1.477  0.020  1.477
 4R5  C12  C11  aromatic  1.394  0.020  1.394
 4R5  C10  C11  aromatic  1.379  0.020  1.379
 4R5  C10  F22  single    1.335  0.020  1.335
 4R5  C15  C20  aromatic  1.397  0.020  1.397
 4R5  C5   N4   aromatic  1.291  0.020  1.291
 4R5  C3   N4   aromatic  1.364  0.020  1.364
 4R5  C18  C19  aromatic  1.390  0.020  1.390
 4R5  C20  C19  aromatic  1.383  0.020  1.383
 4R5  C3   H1   single    0.930  0.020  1.080
 4R5  C5   H2   single    0.930  0.020  1.080
 4R5  C11  H3   single    0.930  0.020  1.080
 4R5  C13  H4   single    0.930  0.020  1.080
 4R5  C16  H5   single    0.930  0.020  1.080
 4R5  C18  H6   single    0.930  0.020  1.080
 4R5  C19  H7   single    0.930  0.020  1.080
 4R5  C26  H8   single    0.970  0.020  1.090
 4R5  C26  H9   single    0.970  0.020  1.090
 4R5  C26  H10  single    0.970  0.020  1.090
 4R5  N6   H11  single    0.860  0.020  1.020
 4R5  N8   H12  single    0.860  0.020  1.020
 4R5  C20  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
 4R5  N6   C2   S1   124.03  3.000
 4R5  S1   C2   C3   109.76  3.000
 4R5  N6   C2   C3   126.20  3.000
 4R5  H1   C3   N4   120.39  3.000
 4R5  H1   C3   C2   124.39  3.000
 4R5  N4   C3   C2   115.22  3.000
 4R5  H2   C5   N4   124.26  3.000
 4R5  H2   C5   S1   120.44  3.000
 4R5  N4   C5   S1   115.30  3.000
 4R5  H3   C11  C12  121.30  3.000
 4R5  H3   C11  C10  119.44  3.000
 4R5  C12  C11  C10  119.26  3.000
 4R5  H4   C13  C14  119.41  3.000
 4R5  H4   C13  C12  121.13  3.000
 4R5  C14  C13  C12  119.45  3.000
 4R5  C20  C15  C12  120.30  3.000
 4R5  C20  C15  C16  119.41  3.000
 4R5  C12  C15  C16  120.29  3.000
 4R5  H5   C16  C17  118.70  3.000
 4R5  H5   C16  C15  120.55  3.000
 4R5  C17  C16  C15  120.74  3.000
 4R5  O25  C17  C18  124.31  3.000
 4R5  C18  C17  C16  119.70  3.000
 4R5  O25  C17  C16  115.98  3.000
 4R5  H6   C18  C19  119.21  3.000
 4R5  H6   C18  C17  121.55  3.000
 4R5  C19  C18  C17  119.24  3.000
 4R5  H7   C19  C20  119.66  3.000
 4R5  H7   C19  C18  119.08  3.000
 4R5  C20  C19  C18  121.26  3.000
 4R5  H10  C26  H9   108.81  3.000
 4R5  H10  C26  H8   108.75  3.000
 4R5  H9   C26  H8   108.78  3.000
 4R5  H10  C26  O25  106.49  3.000
 4R5  H9   C26  O25  111.88  3.000
 4R5  H8   C26  O25  112.03  3.000
 4R5  C5   S1   C2    88.59  3.000
 4R5  C5   N4   C3   111.13  3.000
 4R5  H11  N6   C7   120.05  3.000
 4R5  H11  N6   C2   116.23  3.000
 4R5  C7   N6   C2   123.72  3.000
 4R5  O21  C7   N8   123.52  3.000
 4R5  O21  C7   N6   122.16  3.000
 4R5  N8   C7   N6   114.32  3.000
 4R5  H12  N8   C9   118.51  3.000
 4R5  H12  N8   C7   120.33  3.000
 4R5  C9   N8   C7   120.78  3.000
 4R5  C14  C9   C10  116.24  3.000
 4R5  C10  C9   N8   121.82  3.000
 4R5  C14  C9   N8   121.94  3.000
 4R5  F22  C10  C9   117.77  3.000
 4R5  F22  C10  C11  119.28  3.000
 4R5  C9   C10  C11  122.95  3.000
 4R5  C15  C12  C13  119.94  3.000
 4R5  C15  C12  C11  120.75  3.000
 4R5  C13  C12  C11  119.31  3.000
 4R5  F24  C14  C9   118.09  3.000
 4R5  C9   C14  C13  122.77  3.000
 4R5  F24  C14  C13  119.14  3.000
 4R5  H13  C20  C19  119.95  3.000
 4R5  H13  C20  C15  120.39  3.000
 4R5  C19  C20  C15  119.65  3.000
 4R5  C26  O25  C17  118.50  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
 4R5  CONST_01  N4   C5   S1   C2     0.00   0.0  0
 4R5  CONST_02  C5   N4   C3   C2     0.00   0.0  0
 4R5  CONST_03  C5   S1   C2   C3     0.00   0.0  0
 4R5  CONST_04  S1   C5   N4   C3     0.00   0.0  0
 4R5  CONST_05  C14  C13  C12  C11    0.00   0.0  0
 4R5  CONST_08  C14  C9   C10  C11    0.00   0.0  0
 4R5  CONST_09  C10  C9   C14  C13    0.00   0.0  0
 4R5  CONST_12  C10  C11  C12  C13    0.00   0.0  0
 4R5  CONST_13  C18  C17  C16  C15    0.00   0.0  0
 4R5  CONST_14  C14  C13  C12  C15  180.00   0.0  0
 4R5  CONST_15  C10  C11  C12  C15  180.00   0.0  0
 4R5  CONST_16  C18  C19  C20  C15    0.00   0.0  0
 4R5  CONST_17  C19  C18  C17  C16    0.00   0.0  0
 4R5  CONST_18  C19  C20  C15  C16    0.00   0.0  0
 4R5  CONST_19  C12  C15  C16  C17  180.00   0.0  0
 4R5  CONST_20  C20  C15  C16  C17    0.00   0.0  0
 4R5  CONST_21  C20  C19  C18  C17    0.00   0.0  0
 4R5  CONST_22  C12  C15  C20  C19  180.00   0.0  0
 4R5  CONST_23  N4   C3   C2   S1     0.00   0.0  0
 4R5  CONST_24  C12  C13  C14  C9     0.00   0.0  0
 4R5  CONST_25  C12  C11  C10  C9     0.00   0.0  0
 4R5  CONST_26  N6   C2   S1   C5   180.00   0.0  0
 4R5  CONST_27  N8   C9   C10  C11  180.00   0.0  0
 4R5  CONST_28  N8   C9   C14  C13  180.00   0.0  0
 4R5  CONST_29  O25  C17  C16  C15  180.00   0.0  0
 4R5  CONST_30  O25  C17  C18  C19  180.00   0.0  0
 4R5  CONST_31  N6   C2   C3   N4   180.00   0.0  0
 4R5  CONST_32  F24  C14  C9   C10  180.00   0.0  0
 4R5  CONST_33  F24  C14  C13  C12  180.00   0.0  0
 4R5  CONST_34  F22  C10  C11  C12  180.00   0.0  0
 4R5  CONST_35  F22  C10  C9   C14  180.00   0.0  0
 4R5  CONST_36  H2   C5   S1   C2   180.00   0.0  0
 4R5  CONST_37  H1   C3   N4   C5   180.00   0.0  0
 4R5  CONST_38  H4   C13  C12  C11  180.00   0.0  0
 4R5  CONST_39  H3   C11  C12  C13  180.00   0.0  0
 4R5  CONST_40  H7   C19  C20  C15  180.00   0.0  0
 4R5  CONST_41  H6   C18  C17  C16  180.00   0.0  0
 4R5  CONST_42  H13  C20  C15  C16  180.00   0.0  0
 4R5  CONST_43  H5   C16  C17  C18  180.00   0.0  0
 4R5  CONST_44  C7   N6   C2   C3   180.00   0.0  0
 4R5  CONST_45  C7   N6   C2   S1     0.00   0.0  0
 4R5  CONST_48  H11  N6   C2   C3     0.00   0.0  0
 4R5  CONST_50  O21  C7   N6   C2     0.00   0.0  0
 4R5  CONST_51  O21  C7   N8   C9     0.00   0.0  0
 4R5  CONST_52  N8   C7   N6   C2   180.00   0.0  0
 4R5  CONST_53  C9   N8   C7   N6   180.00   0.0  0
 4R5  Var_01    H8   C26  O25  C17  -62.50  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
 4R5  plan-1  C2   0.020
 4R5  plan-1  C3   0.020
 4R5  plan-1  C5   0.020
 4R5  plan-1  S1   0.020
 4R5  plan-1  N4   0.020
 4R5  plan-1  N6   0.020
 4R5  plan-1  H1   0.020
 4R5  plan-1  H2   0.020
 4R5  plan-2  C15  0.020
 4R5  plan-2  C16  0.020
 4R5  plan-2  C17  0.020
 4R5  plan-2  C18  0.020
 4R5  plan-2  C19  0.020
 4R5  plan-2  C12  0.020
 4R5  plan-2  C20  0.020
 4R5  plan-2  O25  0.020
 4R5  plan-2  H5   0.020
 4R5  plan-2  H6   0.020
 4R5  plan-2  H7   0.020
 4R5  plan-2  H13  0.020
 4R5  plan-3  C11  0.020
 4R5  plan-3  C13  0.020
 4R5  plan-3  C15  0.020
 4R5  plan-3  N8   0.020
 4R5  plan-3  C9   0.020
 4R5  plan-3  C10  0.020
 4R5  plan-3  C12  0.020
 4R5  plan-3  C14  0.020
 4R5  plan-3  F22  0.020
 4R5  plan-3  F24  0.020
 4R5  plan-3  H3   0.020
 4R5  plan-3  H4   0.020
 4R5  plan-4  C2   0.020
 4R5  plan-4  N6   0.020
 4R5  plan-4  C7   0.020
 4R5  plan-4  N8   0.020
 4R5  plan-4  C9   0.020
 4R5  plan-4  O21  0.020
 4R5  plan-4  H11  0.020
 4R5  plan-4  H12  0.020

