# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 11:21:49 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: 7-[(4-fluoranylphenoxy)methyl]-3-[(1~{S},2~{S})-2-(hydroxymethyl)cyclopropyl]-2-methyl-[1,3]thiazolo[3,2-a]pyrimidin-5-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=C([C@H]2C[C@@H]2CO)N3C(=O)C=C(COc4ccc(F)cc4)N=C3S1
#
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
 5YF  5YF  7-[(4-fluoranylphenoxy)methyl]-3-[(1~{S},2~{S})-2-(hydroxymethyl)cyclopropyl]-2-methyl-[1,3]thiazolo[3,2-a]pyrimidin-5-one  ligand  42  25  .  2022-09-22  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_5YF
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
 5YF  C4   C  CR16  0  -0.496  -0.2033   1.2087  -1.2811
 5YF  C14  C  CH1   0  -0.315  -4.4446   0.3011  -0.2867
 5YF  C5   C  CR6   0   0.264   0.6727   0.2439  -0.8874
 5YF  C6   C  CR56  0   0.308  -0.9949  -1.0788  -0.1875
 5YF  C11  C  CR6   0   0.500   6.8806  -0.1137   0.4194
 5YF  C7   C  CH2   0  -0.244   2.1486   0.4091  -1.0890
 5YF  C8   C  CR6   0   0.383   4.1339   0.0498   0.1602
 5YF  C9   C  CR16  0  -0.330   4.7057  -0.3670   1.3632
 5YF  C10  C  CR16  0  -0.392   6.0799  -0.4491   1.4967
 5YF  C12  C  CR16  0  -0.395   6.3407   0.3008  -0.7778
 5YF  C13  C  CR16  0  -0.363   4.9582   0.3848  -0.9097
 5YF  N1   N  N     0  -0.469   0.2802  -0.9329  -0.3555
 5YF  C3   C  CR6   0   0.592  -1.6188   1.0267  -1.1709
 5YF  O1   O  O2    0  -0.469   2.7846   0.1012   0.1308
 5YF  O    O  O     0  -0.457  -2.4711   1.7810  -1.5985
 5YF  S    S  S2    0   0.268  -1.6875  -2.5184   0.4527
 5YF  C1   C  CR5   0  -0.335  -3.2897  -1.8472   0.3205
 5YF  C    C  CH3   0  -0.730  -4.4445  -2.6871   0.7431
 5YF  N    N  N     0  -0.624  -1.9657  -0.1706  -0.4955
 5YF  C2   C  CR5   0   0.534  -3.2733  -0.5910  -0.1640
 5YF  C16  C  CH1   0  -0.257  -4.5807   1.4883   0.6194
 5YF  C15  C  CH2   0  -0.485  -5.4871   0.3172   0.7978
 5YF  C17  C  CH2   0  -0.143  -5.1087   2.7727   0.0572
 5YF  O2   O  OH1   0  -0.674  -5.7706   3.4713   1.0910
 5YF  H1   H  HCR6  0   0.283   0.1436   2.1327  -1.7223
 5YF  H2   H  HCH1  0   0.286  -4.8130   0.4396  -1.2978
 5YF  H3   H  HCH2  0   0.254   2.4725  -0.2746  -1.8837
 5YF  H4   H  HCH2  0   0.253   2.3756   1.4292  -1.4144
 5YF  H5   H  HCR6  0   0.275   4.0663  -0.6295   2.1964
 5YF  H6   H  HCR6  0   0.282   6.5197  -0.7762   2.4295
 5YF  H7   H  HCR6  0   0.284   6.9812   0.5615  -1.6101
 5YF  H8   H  HCR6  0   0.291   4.5552   0.7192  -1.8556
 5YF  H10  H  HCH3  0   0.269  -4.3182  -3.7127   0.3967
 5YF  H11  H  HCH3  0   0.268  -4.5387  -2.7177   1.8295
 5YF  H12  H  HCH3  0   0.275  -5.3747  -2.3107   0.3279
 5YF  H13  H  HCH1  0   0.261  -3.8055   1.6034   1.3714
 5YF  H14  H  HCH2  0   0.259  -6.5196   0.4113   0.4836
 5YF  H15  H  HCH2  0   0.263  -5.3466  -0.3016   1.6738
 5YF  H16  H  HCH2  0   0.209  -4.2801   3.3581  -0.3555
 5YF  H17  H  HCH2  0   0.187  -5.7889   2.5485  -0.7763
 5YF  H18  H  HOH1  0   0.452  -6.0165   4.3382   0.7556
 5YF  F    F  F     0  -0.321   8.2179  -0.1974   0.5473

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
 5YF  C15  C16  single    1.492  0.020  1.492
 5YF  C15  C14  single    1.504  0.020  1.504
 5YF  C16  C17  single    1.498  0.020  1.498
 5YF  C16  C14  single    1.500  0.020  1.500
 5YF  O    C3   double    1.216  0.020  1.216
 5YF  C17  O2   single    1.412  0.020  1.412
 5YF  C14  C2   single    1.477  0.020  1.477
 5YF  C3   N    single    1.418  0.020  1.418
 5YF  C3   C4   single    1.431  0.020  1.431
 5YF  C    C1   single    1.489  0.020  1.489
 5YF  C2   N    single    1.413  0.020  1.413
 5YF  C2   C1   double    1.346  0.020  1.346
 5YF  N    C6   single    1.365  0.020  1.365
 5YF  C1   S    single    1.742  0.020  1.742
 5YF  C4   C5   double    1.361  0.020  1.361
 5YF  C6   S    single    1.721  0.020  1.721
 5YF  C6   N1   double    1.294  0.020  1.294
 5YF  C5   N1   single    1.350  0.020  1.350
 5YF  C5   C7   single    1.499  0.020  1.499
 5YF  C7   O1   single    1.410  0.020  1.410
 5YF  O1   C8   single    1.351  0.020  1.351
 5YF  C8   C9   aromatic  1.396  0.020  1.396
 5YF  C8   C13  aromatic  1.392  0.020  1.392
 5YF  C9   C10  aromatic  1.383  0.020  1.383
 5YF  C13  C12  aromatic  1.391  0.020  1.391
 5YF  C10  C11  aromatic  1.384  0.020  1.384
 5YF  C12  C11  aromatic  1.377  0.020  1.377
 5YF  C11  F    single    1.346  0.020  1.346
 5YF  C4   H1   single    0.930  0.020  1.080
 5YF  C14  H2   single    0.970  0.020  1.090
 5YF  C7   H3   single    0.970  0.020  1.090
 5YF  C7   H4   single    0.970  0.020  1.090
 5YF  C9   H5   single    0.930  0.020  1.080
 5YF  C10  H6   single    0.930  0.020  1.080
 5YF  C12  H7   single    0.930  0.020  1.080
 5YF  C13  H8   single    0.930  0.020  1.080
 5YF  C    H10  single    0.970  0.020  1.090
 5YF  C    H11  single    0.970  0.020  1.090
 5YF  C    H12  single    0.970  0.020  1.090
 5YF  C16  H13  single    0.970  0.020  1.090
 5YF  C15  H14  single    0.970  0.020  1.090
 5YF  C15  H15  single    0.970  0.020  1.090
 5YF  C17  H16  single    0.970  0.020  1.090
 5YF  C17  H17  single    0.970  0.020  1.090
 5YF  O2   H18  single    0.850  0.020  0.980

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
 5YF  H1   C4   C3   117.22  3.000
 5YF  H1   C4   C5   121.15  3.000
 5YF  C3   C4   C5   121.60  3.000
 5YF  H2   C14  C15  115.79  3.000
 5YF  H2   C14  C16  115.54  3.000
 5YF  C15  C14  C16   59.54  3.000
 5YF  H2   C14  C2   115.07  3.000
 5YF  C16  C14  C2   119.99  3.000
 5YF  C15  C14  C2   119.73  3.000
 5YF  N1   C5   C7   115.82  3.000
 5YF  C7   C5   C4   121.11  3.000
 5YF  N1   C5   C4   123.01  3.000
 5YF  N    C6   S    110.75  3.000
 5YF  S    C6   N1   122.61  3.000
 5YF  N    C6   N1   126.63  3.000
 5YF  F    C11  C12  119.40  3.000
 5YF  F    C11  C10  119.08  3.000
 5YF  C12  C11  C10  121.53  3.000
 5YF  H4   C7   H3   107.71  3.000
 5YF  H4   C7   O1   111.55  3.000
 5YF  H3   C7   O1   110.94  3.000
 5YF  H4   C7   C5   110.30  3.000
 5YF  H3   C7   C5   108.63  3.000
 5YF  O1   C7   C5   107.68  3.000
 5YF  O1   C8   C13  124.47  3.000
 5YF  C13  C8   C9   119.46  3.000
 5YF  O1   C8   C9   116.07  3.000
 5YF  H5   C9   C10  119.88  3.000
 5YF  H5   C9   C8   119.59  3.000
 5YF  C10  C9   C8   120.53  3.000
 5YF  H6   C10  C9   120.34  3.000
 5YF  H6   C10  C11  120.62  3.000
 5YF  C9   C10  C11  119.05  3.000
 5YF  H7   C12  C13  120.04  3.000
 5YF  H7   C12  C11  120.60  3.000
 5YF  C13  C12  C11  119.36  3.000
 5YF  H8   C13  C12  118.16  3.000
 5YF  H8   C13  C8   121.76  3.000
 5YF  C12  C13  C8   120.08  3.000
 5YF  C6   N1   C5   115.84  3.000
 5YF  N    C3   O    121.33  3.000
 5YF  N    C3   C4   112.71  3.000
 5YF  O    C3   C4   125.96  3.000
 5YF  C8   O1   C7   118.54  3.000
 5YF  C1   S    C6    91.12  3.000
 5YF  C2   C1   C    129.62  3.000
 5YF  C2   C1   S    112.06  3.000
 5YF  C    C1   S    118.32  3.000
 5YF  H12  C    H11  108.46  3.000
 5YF  H12  C    H10  107.69  3.000
 5YF  H11  C    H10  107.47  3.000
 5YF  H12  C    C1   111.12  3.000
 5YF  H11  C    C1   111.43  3.000
 5YF  H10  C    C1   110.52  3.000
 5YF  C2   N    C3   126.12  3.000
 5YF  C2   N    C6   114.04  3.000
 5YF  C3   N    C6   119.70  3.000
 5YF  N    C2   C1   111.92  3.000
 5YF  C1   C2   C14  125.70  3.000
 5YF  N    C2   C14  122.31  3.000
 5YF  H13  C16  C17  114.87  3.000
 5YF  H13  C16  C15  115.73  3.000
 5YF  C17  C16  C15  120.25  3.000
 5YF  H13  C16  C14  115.94  3.000
 5YF  C17  C16  C14  118.94  3.000
 5YF  C15  C16  C14   60.39  3.000
 5YF  H15  C15  H14  114.10  3.000
 5YF  H15  C15  C16  117.85  3.000
 5YF  H14  C15  C16  118.44  3.000
 5YF  H15  C15  C14  119.19  3.000
 5YF  H14  C15  C14  116.89  3.000
 5YF  C16  C15  C14   60.07  3.000
 5YF  H17  C17  H16  106.95  3.000
 5YF  H17  C17  O2   111.46  3.000
 5YF  H16  C17  O2   111.46  3.000
 5YF  H17  C17  C16  109.14  3.000
 5YF  H16  C17  C16  109.45  3.000
 5YF  O2   C17  C16  108.34  3.000
 5YF  H18  O2   C17  108.09  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
 5YF  CONST_01  C8   C9   C10  C11     0.00   0.0  0
 5YF  CONST_02  C8   C13  C12  C11     0.00   0.0  0
 5YF  CONST_03  C12  C13  C8   C9      0.00   0.0  0
 5YF  CONST_04  C12  C11  C10  C9      0.00   0.0  0
 5YF  CONST_05  C13  C8   C9   C10     0.00   0.0  0
 5YF  CONST_06  C13  C12  C11  C10     0.00   0.0  0
 5YF  CONST_07  C2   N    C3   C4    180.00   0.0  0
 5YF  CONST_08  C6   N    C3   C4      0.00   0.0  0
 5YF  CONST_09  N    C6   N1   C5      0.00   0.0  0
 5YF  CONST_10  S    C6   N1   C5    180.00   0.0  0
 5YF  CONST_11  C3   N    C6   N1      0.00   0.0  0
 5YF  CONST_12  C2   N    C6   N1    180.00   0.0  0
 5YF  CONST_13  S    C6   N    C3    180.00   0.0  0
 5YF  CONST_14  C2   N    C6   S       0.00   0.0  0
 5YF  CONST_15  F    C11  C10  C9    180.00   0.0  0
 5YF  CONST_16  O1   C8   C9   C10   180.00   0.0  0
 5YF  CONST_17  O1   C8   C13  C12   180.00   0.0  0
 5YF  CONST_18  F    C11  C12  C13   180.00   0.0  0
 5YF  CONST_19  O    C3   N    C6    180.00   0.0  0
 5YF  CONST_20  C2   N    C3   O       0.00   0.0  0
 5YF  CONST_21  H5   C9   C10  C11   180.00   0.0  0
 5YF  CONST_22  H8   C13  C12  C11   180.00   0.0  0
 5YF  CONST_23  H6   C10  C9   C8    180.00   0.0  0
 5YF  CONST_24  H7   C12  C13  C8    180.00   0.0  0
 5YF  Var_01    C15  C14  C2   C1     39.09  30.0  2
 5YF  Var_02    C16  C15  C14  C2    109.38  30.0  1
 5YF  Var_03    C17  C16  C15  C14   108.24  30.0  1
 5YF  Var_04    O1   C7   C5   C4    131.31  30.0  3
 5YF  Var_05    O2   C17  C16  C14   150.66  30.0  3
 5YF  Var_06    C9   C8   O1   C7   -174.88  30.0  2
 5YF  Var_07    H10  C    C1   S     -42.14  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
 5YF  chir_01  C14  C15  C16  C2   both
 5YF  chir_02  C16  C14  C17  C15  both

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
 5YF  plan-1  C11  0.020
 5YF  plan-1  C8   0.020
 5YF  plan-1  C9   0.020
 5YF  plan-1  C10  0.020
 5YF  plan-1  C12  0.020
 5YF  plan-1  C13  0.020
 5YF  plan-1  O1   0.020
 5YF  plan-1  H5   0.020
 5YF  plan-1  H6   0.020
 5YF  plan-1  H7   0.020
 5YF  plan-1  H8   0.020
 5YF  plan-1  F    0.020
 5YF  plan-2  C4   0.020
 5YF  plan-2  C14  0.020
 5YF  plan-2  C5   0.020
 5YF  plan-2  C6   0.020
 5YF  plan-2  C7   0.020
 5YF  plan-2  N1   0.020
 5YF  plan-2  C3   0.020
 5YF  plan-2  O    0.020
 5YF  plan-2  S    0.020
 5YF  plan-2  C1   0.020
 5YF  plan-2  C    0.020
 5YF  plan-2  N    0.020
 5YF  plan-2  C2   0.020
 5YF  plan-2  H1   0.020

