# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 07:49:21 2021
#   Inital geometry file: a 107 line input string
#   Ligand name: (5R)-3-{3-fluoro-4-[6-(1-methyl-1H-tetrazol-5-yl)pyridin-3-yl]phenyl}-5-(hydroxymethyl)-1,3-oxazolidin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1nnnc1c2ccc(cn2)c3ccc(cc3F)N4C[C@H](CO)OC4=O
#
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
 U7Y  U7Y  (5R)-3-{3-fluoro-4-[6-(1-methyl-1H-tetrazol-5-yl)pyridin-3-yl]phenyl}-5-(hydroxymethyl)-1,3-oxazolidin-2-one  ligand  42  27  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_U7Y
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
 U7Y  C1    C  CR5   0   0.510  191.6533  208.5103  223.2440
 U7Y  N1    N  NR5   0  -0.337  190.9163  208.1199  222.1954
 U7Y  O1    O  O     0  -0.463  190.7625  202.8690  232.2377
 U7Y  C2    C  CR6   0   0.205  191.5287  208.0730  224.6317
 U7Y  N2    N  N     0  -0.082  191.3626  208.7586  221.1257
 U7Y  C3    C  CR16  0  -0.283  192.4015  208.5667  225.5960
 U7Y  N3    N  N     0  -0.140  192.3272  209.5027  221.5032
 U7Y  C4    C  CR16  0  -0.184  192.2573  208.1300  226.8989
 U7Y  N4    N  N     0  -0.344  192.5387  209.3783  222.8047
 U7Y  C5    C  CR6   0   0.025  191.2535  207.2149  227.2107
 U7Y  C6    C  CR16  0  -0.087  190.4350  206.7918  226.1625
 U7Y  C7    C  CR6   0   0.567  191.0024  207.4731  229.6945
 U7Y  C8    C  CR6   0  -0.172  191.0501  206.6738  228.5632
 U7Y  C9    C  CR16  0  -0.272  190.8594  205.3083  228.7793
 U7Y  C10   C  CR16  0  -0.309  190.6477  204.7728  230.0352
 U7Y  C11   C  CR6   0   0.401  190.6204  205.6113  231.1550
 U7Y  C12   C  CR16  0  -0.511  190.7966  206.9830  230.9660
 U7Y  C13   C  CR5   0   0.716  190.4938  203.8517  232.8787
 U7Y  C14   C  CH2   0  -0.337  190.2221  206.0484  233.5725
 U7Y  C15   C  CR15  0  -0.014  189.8397  205.0795  234.6861
 U7Y  C16   C  CH2   0  -0.163  190.5345  205.3921  235.9854
 U7Y  C17   C  CH3   0  -0.517  189.8014  207.1986  222.0802
 U7Y  N5    N  N     0  -0.419  190.5668  207.2035  224.9143
 U7Y  N6    N  NR5   0  -0.628  190.3946  205.1482  232.4490
 U7Y  O2    O  O     0  -0.461  190.2443  203.7971  234.1869
 U7Y  O3    O  OH1   0  -0.664  190.0939  204.4938  236.9679
 U7Y  H3    H  HCR6  0   0.283  193.1808  209.2679  225.3328
 U7Y  H4    H  HCR6  0   0.275  192.9430  208.4817  227.6574
 U7Y  H6    H  HCR6  0   0.273  189.6271  206.0938  226.3531
 U7Y  H9    H  HCR6  0   0.275  190.8905  204.6334  227.9335
 U7Y  H10   H  HCR6  0   0.289  190.5091  203.7093  230.1282
 U7Y  H12   H  HCR6  0   0.308  190.7729  207.6863  231.7866
 U7Y  H14B  H  HCH2  0   0.273  191.1528  206.5818  233.7927
 U7Y  H14A  H  HCH2  0   0.293  189.4376  206.7807  233.3872
 U7Y  H15   H  HCR5  0   0.278  188.7562  205.0558  234.8296
 U7Y  H16A  H  HCH2  0   0.212  191.6205  205.3423  235.8282
 U7Y  H16B  H  HCH2  0   0.221  190.2932  206.4336  236.2361
 U7Y  H17A  H  HCH3  0   0.277  189.5267  207.1558  221.0313
 U7Y  H17C  H  HCH3  0   0.275  190.0907  206.2124  222.4275
 U7Y  H17B  H  HCH3  0   0.275  188.9597  207.5525  222.6671
 U7Y  H1    H  HOH1  0   0.462  190.4954  204.7439  237.8049
 U7Y  F1    F  F     0  -0.306  191.1405  208.8005  229.5600

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
 U7Y  N2   N3    aromatic  1.275  0.020  1.275
 U7Y  N2   N1    aromatic  1.323  0.020  1.323
 U7Y  N3   N4    aromatic  1.324  0.020  1.324
 U7Y  N1   C17   single    1.451  0.020  1.451
 U7Y  N1   C1    aromatic  1.340  0.020  1.340
 U7Y  N4   C1    aromatic  1.315  0.020  1.315
 U7Y  C1   C2    single    1.460  0.020  1.460
 U7Y  C2   N5    aromatic  1.327  0.020  1.327
 U7Y  C2   C3    aromatic  1.391  0.020  1.391
 U7Y  N5   C6    aromatic  1.321  0.020  1.321
 U7Y  C3   C4    aromatic  1.382  0.020  1.382
 U7Y  C6   C5    aromatic  1.396  0.020  1.396
 U7Y  C4   C5    aromatic  1.394  0.020  1.394
 U7Y  C5   C8    single    1.471  0.020  1.471
 U7Y  C8   C9    aromatic  1.396  0.020  1.396
 U7Y  C8   C7    aromatic  1.386  0.020  1.386
 U7Y  C9   C10   aromatic  1.382  0.020  1.382
 U7Y  F1   C7    single    1.341  0.020  1.341
 U7Y  C7   C12   aromatic  1.378  0.020  1.378
 U7Y  C10  C11   aromatic  1.399  0.020  1.399
 U7Y  C12  C11   aromatic  1.396  0.020  1.396
 U7Y  C11  N6    single    1.393  0.020  1.393
 U7Y  O1   C13   double    1.204  0.020  1.204
 U7Y  N6   C13   single    1.370  0.020  1.370
 U7Y  N6   C14   single    1.450  0.020  1.450
 U7Y  C13  O2    single    1.333  0.020  1.333
 U7Y  C14  C15   single    1.525  0.020  1.525
 U7Y  O2   C15   single    1.434  0.020  1.434
 U7Y  C15  C16   single    1.506  0.020  1.506
 U7Y  C16  O3    single    1.402  0.020  1.402
 U7Y  C3   H3    single    0.930  0.020  1.080
 U7Y  C4   H4    single    0.930  0.020  1.080
 U7Y  C6   H6    single    0.930  0.020  1.080
 U7Y  C9   H9    single    0.930  0.020  1.080
 U7Y  C10  H10   single    0.930  0.020  1.080
 U7Y  C12  H12   single    0.930  0.020  1.080
 U7Y  C14  H14B  single    0.970  0.020  1.090
 U7Y  C14  H14A  single    0.970  0.020  1.090
 U7Y  C15  H15   single    0.970  0.020  1.090
 U7Y  C16  H16A  single    0.970  0.020  1.090
 U7Y  C16  H16B  single    0.970  0.020  1.090
 U7Y  C17  H17A  single    0.970  0.020  1.090
 U7Y  C17  H17C  single    0.970  0.020  1.090
 U7Y  C17  H17B  single    0.970  0.020  1.090
 U7Y  O3   H1    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
 U7Y  N4    C1   C2    124.92  3.000
 U7Y  C2    C1   N1    127.55  3.000
 U7Y  N4    C1   N1    107.52  3.000
 U7Y  C17   N1   N2    120.09  3.000
 U7Y  C17   N1   C1    132.06  3.000
 U7Y  N2    N1   C1    107.85  3.000
 U7Y  N5    C2   C3    122.66  3.000
 U7Y  C3    C2   C1    119.92  3.000
 U7Y  N5    C2   C1    117.42  3.000
 U7Y  N3    N2   N1    107.30  3.000
 U7Y  H3    C3   C4    120.66  3.000
 U7Y  H3    C3   C2    120.91  3.000
 U7Y  C4    C3   C2    118.42  3.000
 U7Y  N4    N3   N2    110.91  3.000
 U7Y  H4    C4   C5    120.89  3.000
 U7Y  H4    C4   C3    119.50  3.000
 U7Y  C5    C4   C3    119.59  3.000
 U7Y  N3    N4   C1    106.42  3.000
 U7Y  C8    C5   C6    119.87  3.000
 U7Y  C8    C5   C4    123.16  3.000
 U7Y  C6    C5   C4    116.96  3.000
 U7Y  H6    C6   N5    116.17  3.000
 U7Y  H6    C6   C5    120.00  3.000
 U7Y  N5    C6   C5    123.83  3.000
 U7Y  F1    C7   C12   117.38  3.000
 U7Y  C12   C7   C8    123.58  3.000
 U7Y  F1    C7   C8    119.03  3.000
 U7Y  C9    C8   C7    115.67  3.000
 U7Y  C7    C8   C5    122.90  3.000
 U7Y  C9    C8   C5    121.41  3.000
 U7Y  H9    C9   C10   118.23  3.000
 U7Y  H9    C9   C8    119.02  3.000
 U7Y  C10   C9   C8    122.75  3.000
 U7Y  H10   C10  C11   121.36  3.000
 U7Y  H10   C10  C9    118.76  3.000
 U7Y  C11   C10  C9    119.88  3.000
 U7Y  N6    C11  C12   118.23  3.000
 U7Y  N6    C11  C10   123.19  3.000
 U7Y  C12   C11  C10   118.56  3.000
 U7Y  H12   C12  C11   122.26  3.000
 U7Y  H12   C12  C7    118.18  3.000
 U7Y  C11   C12  C7    119.56  3.000
 U7Y  O2    C13  N6    109.46  3.000
 U7Y  O2    C13  O1    122.08  3.000
 U7Y  N6    C13  O1    128.46  3.000
 U7Y  H14A  C14  H14B  108.59  3.000
 U7Y  H14A  C14  N6    111.79  3.000
 U7Y  H14B  C14  N6    110.92  3.000
 U7Y  H14A  C14  C15   111.77  3.000
 U7Y  H14B  C14  C15   112.07  3.000
 U7Y  N6    C14  C15   101.61  3.000
 U7Y  H15   C15  O2    107.81  3.000
 U7Y  H15   C15  C16   110.39  3.000
 U7Y  O2    C15  C16   110.83  3.000
 U7Y  H15   C15  C14   110.99  3.000
 U7Y  C16   C15  C14   112.49  3.000
 U7Y  O2    C15  C14   104.08  3.000
 U7Y  H16B  C16  H16A  107.04  3.000
 U7Y  H16B  C16  O3    112.24  3.000
 U7Y  H16A  C16  O3    112.45  3.000
 U7Y  H16B  C16  C15   107.00  3.000
 U7Y  H16A  C16  C15   108.86  3.000
 U7Y  O3    C16  C15   109.06  3.000
 U7Y  H17B  C17  H17C  109.27  3.000
 U7Y  H17B  C17  H17A  109.83  3.000
 U7Y  H17C  C17  H17A  109.95  3.000
 U7Y  H17B  C17  N1    110.24  3.000
 U7Y  H17C  C17  N1    110.30  3.000
 U7Y  H17A  C17  N1    107.24  3.000
 U7Y  C6    N5   C2    118.54  3.000
 U7Y  C14   N6   C13   110.68  3.000
 U7Y  C14   N6   C11   122.19  3.000
 U7Y  C13   N6   C11   126.48  3.000
 U7Y  C15   O2   C13   110.96  3.000
 U7Y  H1    O3   C16   108.18  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
 U7Y  CONST_01  N3    N2   N1   C1      0.00   0.0  0
 U7Y  CONST_02  N2    N3   N4   C1      0.00   0.0  0
 U7Y  CONST_03  C6    N5   C2   C1    180.00   0.0  0
 U7Y  CONST_04  C4    C3   C2   C1    180.00   0.0  0
 U7Y  CONST_05  N4    N3   N2   N1      0.00   0.0  0
 U7Y  CONST_06  N3    N4   C1   N1      0.00   0.0  0
 U7Y  CONST_07  N5    C2   C1   N1      0.00   0.0  0
 U7Y  CONST_08  C3    C2   C1   N1    180.00   0.0  0
 U7Y  CONST_09  N2    N1   C1   C2    180.00   0.0  0
 U7Y  CONST_10  N3    N4   C1   C2    180.00   0.0  0
 U7Y  CONST_11  C5    C6   N5   C2      0.00   0.0  0
 U7Y  CONST_12  C5    C4   C3   C2      0.00   0.0  0
 U7Y  CONST_13  N4    C1   N1   N2      0.00   0.0  0
 U7Y  CONST_14  N4    C1   C2   C3      0.00   0.0  0
 U7Y  CONST_15  C6    N5   C2   C3      0.00   0.0  0
 U7Y  CONST_16  C6    C5   C4   C3      0.00   0.0  0
 U7Y  CONST_17  C8    C5   C4   C3    180.00   0.0  0
 U7Y  CONST_18  N5    C2   C3   C4      0.00   0.0  0
 U7Y  CONST_19  N5    C6   C5   C4      0.00   0.0  0
 U7Y  CONST_22  N5    C2   C1   N4    180.00   0.0  0
 U7Y  CONST_23  C10   C9   C8   C5    180.00   0.0  0
 U7Y  CONST_24  C12   C7   C8   C5    180.00   0.0  0
 U7Y  CONST_27  C10   C9   C8   C7      0.00   0.0  0
 U7Y  CONST_28  C10   C11  C12  C7      0.00   0.0  0
 U7Y  CONST_29  N5    C6   C5   C8    180.00   0.0  0
 U7Y  CONST_30  C11   C10  C9   C8      0.00   0.0  0
 U7Y  CONST_31  C11   C12  C7   C8      0.00   0.0  0
 U7Y  CONST_32  C12   C7   C8   C9      0.00   0.0  0
 U7Y  CONST_33  C12   C11  C10  C9      0.00   0.0  0
 U7Y  CONST_34  N6    C11  C12  C7    180.00   0.0  0
 U7Y  CONST_35  N6    C11  C10  C9    180.00   0.0  0
 U7Y  CONST_36  C17   N1   C1   C2      0.00   0.0  0
 U7Y  CONST_37  C17   N1   N2   N3    180.00   0.0  0
 U7Y  CONST_38  C17   N1   C1   N4    180.00   0.0  0
 U7Y  CONST_39  F1    C7   C8   C5      0.00   0.0  0
 U7Y  CONST_40  F1    C7   C8   C9    180.00   0.0  0
 U7Y  CONST_41  F1    C7   C12  C11   180.00   0.0  0
 U7Y  CONST_42  H3    C3   C2   C1      0.00   0.0  0
 U7Y  CONST_43  H6    C6   N5   C2    180.00   0.0  0
 U7Y  CONST_44  H4    C4   C3   C2    180.00   0.0  0
 U7Y  CONST_45  H9    C9   C8   C5      0.00   0.0  0
 U7Y  CONST_46  H10   C10  C9   C8    180.00   0.0  0
 U7Y  CONST_47  H12   C12  C7   C8    180.00   0.0  0
 U7Y  Var_01    C13   N6   C11  C10    17.10  30.0  2
 U7Y  Var_02    O2    C13  N6   C11   178.16  30.0  1
 U7Y  Var_03    C15   C14  N6   C11   173.26  30.0  1
 U7Y  Var_04    N6    C13  O2   C15     5.19  30.0  1
 U7Y  Var_05    H17A  C17  N1   C1   -178.12  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
 U7Y  chir_01  C15  C14  O2  C16  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
 U7Y  plan-1  C1   0.020
 U7Y  plan-1  N1   0.020
 U7Y  plan-1  C2   0.020
 U7Y  plan-1  N2   0.020
 U7Y  plan-1  N3   0.020
 U7Y  plan-1  N4   0.020
 U7Y  plan-1  C17  0.020
 U7Y  plan-2  C11  0.020
 U7Y  plan-2  C13  0.020
 U7Y  plan-2  C14  0.020
 U7Y  plan-2  N6   0.020
 U7Y  plan-3  C1   0.020
 U7Y  plan-3  C2   0.020
 U7Y  plan-3  C3   0.020
 U7Y  plan-3  C4   0.020
 U7Y  plan-3  C5   0.020
 U7Y  plan-3  C6   0.020
 U7Y  plan-3  C8   0.020
 U7Y  plan-3  N5   0.020
 U7Y  plan-3  H3   0.020
 U7Y  plan-3  H4   0.020
 U7Y  plan-3  H6   0.020
 U7Y  plan-4  C5   0.020
 U7Y  plan-4  C7   0.020
 U7Y  plan-4  C8   0.020
 U7Y  plan-4  C9   0.020
 U7Y  plan-4  C10  0.020
 U7Y  plan-4  C11  0.020
 U7Y  plan-4  C12  0.020
 U7Y  plan-4  N6   0.020
 U7Y  plan-4  H9   0.020
 U7Y  plan-4  H10  0.020
 U7Y  plan-4  H12  0.020
 U7Y  plan-4  F1   0.020
 U7Y  plan-5  O1   0.020
 U7Y  plan-5  C13  0.020
 U7Y  plan-5  N6   0.020
 U7Y  plan-5  O2   0.020

