# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 07:51:50 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: (4S)-3-{4-[6-amino-5-(pyrimidin-2-yl)pyridin-3-yl]phenyl}-5,5-dimethyl-4-phenyl-1,3-oxazolidin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(C)OC(=O)N([C@H]1c2ccccc2)c3ccc(cc3)c4cnc(N)c(c4)c5ncccn5
#
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
 2GV  2GV  (4S)-3-{4-[6-amino-5-(pyrimidin-2-yl)pyridin-3-yl]phenyl}-5,5-dimethyl-4-phenyl-1,3-oxazolidin-2-one  ligand  56  33  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_2GV
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
 2GV  C12  C  CR16  0  -0.310   3.6898  -2.8049  -0.1701
 2GV  C13  C  CR16  0  -0.241   3.5975  -3.7316  -1.1997
 2GV  C14  C  CR16  0  -0.265   3.6324  -3.3062  -2.5202
 2GV  C15  C  CR16  0  -0.238   3.7605  -1.9522  -2.8035
 2GV  C16  C  CR16  0  -0.304   3.8567  -1.0290  -1.7724
 2GV  C17  C  CR6   0   0.174   3.8256  -1.4486  -0.4456
 2GV  C7   C  CR15  0  -0.200   3.9587  -0.4787   0.7010
 2GV  C8   C  CR5   0   0.191   5.3998  -0.0025   1.0458
 2GV  C9   C  CH3   0  -0.670   6.5134  -0.8448   0.4645
 2GV  C10  C  CH3   0  -0.658   5.5491   0.1580   2.5501
 2GV  O1   O  O     0  -0.471   5.4608   1.3107   0.4468
 2GV  C11  C  CR5   0   0.679   4.2330   1.7889   0.2333
 2GV  O2   O  O     0  -0.472   4.0236   2.9332  -0.0819
 2GV  N2   N  NR5   0  -0.614   3.3246   0.7960   0.4303
 2GV  C18  C  CR16  0  -0.281   1.0650   0.3704   1.1728
 2GV  C19  C  CR6   0   0.342   1.9358   0.9386   0.2492
 2GV  C20  C  CR16  0  -0.265   1.4112   1.6138  -0.8482
 2GV  C21  C  CR16  0  -0.321   0.0398   1.7300  -1.0011
 2GV  C5   C  CR6   0   0.091  -0.8473   1.1734  -0.0781
 2GV  C22  C  CR16  0  -0.319  -0.3044   0.4846   1.0077
 2GV  C1   C  CR6   0   0.004  -2.3024   1.3097  -0.2403
 2GV  C23  C  CR16  0  -0.228  -3.1939   0.3186   0.1496
 2GV  C24  C  CR6   0  -0.158  -4.5676   0.4631   0.0061
 2GV  C25  C  CR6   0   0.443  -5.0320   1.6867  -0.5595
 2GV  N3   N  N     0  -0.451  -4.1712   2.6462  -0.9303
 2GV  C26  C  CR16  0  -0.098  -2.8776   2.4593  -0.7811
 2GV  N1   N  N     0  -0.433  -4.8672  -1.7185   0.9482
 2GV  C2   C  CR16  0  -0.007  -5.6469  -2.7118   1.3343
 2GV  C3   C  CR16  0  -0.367  -7.0281  -2.6637   1.2152
 2GV  C4   C  CR16  0   0.005  -7.5433  -1.5066   0.6656
 2GV  N5   N  N     0  -0.484  -6.7678  -0.5030   0.2766
 2GV  C6   C  CR6   0   0.466  -5.4501  -0.6362   0.4288
 2GV  N4   N  NH2   0  -0.834  -6.3276   1.9661  -0.7492
 2GV  H1   H  HCR6  0   0.255   3.6522  -3.1424   0.8595
 2GV  H2   H  HCR6  0   0.259   3.4910  -4.7838  -0.9700
 2GV  H3   H  HCR6  0   0.259   3.5552  -4.0250  -3.3253
 2GV  H4   H  HCR6  0   0.259   3.7848  -1.6135  -3.8312
 2GV  H5   H  HCR6  0   0.249   3.9542   0.0219  -2.0160
 2GV  H6   H  HCR5  0   0.289   3.5329  -0.9441   1.5941
 2GV  H7   H  HCH3  0   0.253   6.4850  -0.8681  -0.6237
 2GV  H8   H  HCH3  0   0.253   7.4819  -0.4555   0.7793
 2GV  H9   H  HCH3  0   0.246   6.4354  -1.8701   0.8250
 2GV  H10  H  HCH3  0   0.246   5.5341  -0.8185   3.0345
 2GV  H11  H  HCH3  0   0.253   6.4954   0.6400   2.7958
 2GV  H12  H  HCH3  0   0.244   4.7375   0.7524   2.9736
 2GV  H14  H  HCR6  0   0.268   2.0616   2.0407  -1.5982
 2GV  H15  H  HCR6  0   0.256  -0.3396   2.2391  -1.8781
 2GV  H16  H  HCR6  0   0.257  -0.9536   0.0522   1.7588
 2GV  H17  H  HCR6  0   0.263  -2.8217  -0.6095   0.5626
 2GV  H18  H  HCR6  0   0.260  -2.2477   3.2877  -1.0918
 2GV  H19  H  HCR6  0   0.279  -5.1563  -3.5801   1.7594
 2GV  H20  H  HCR6  0   0.287  -7.6593  -3.4792   1.5345
 2GV  H21  H  HCR6  0   0.282  -8.6105  -1.3742   0.5322
 2GV  H22  H  HNH2  0   0.417  -7.0274   1.2769  -0.5199
 2GV  H23  H  HNH2  0   0.389  -6.5768   2.8312  -1.1948
 2GV  H13  H  HCR6  0   0.271   1.4496  -0.1502   2.0403

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
 2GV  C14  C15  aromatic  1.389  0.020  1.389
 2GV  C14  C13  aromatic  1.388  0.020  1.388
 2GV  C15  C16  aromatic  1.387  0.020  1.387
 2GV  C2   C3   aromatic  1.387  0.020  1.387
 2GV  C2   N1   aromatic  1.320  0.020  1.320
 2GV  C3   C4   aromatic  1.381  0.020  1.381
 2GV  N1   C6   aromatic  1.335  0.020  1.335
 2GV  C4   N5   aromatic  1.327  0.020  1.327
 2GV  C13  C12  aromatic  1.388  0.020  1.388
 2GV  C16  C17  aromatic  1.392  0.020  1.392
 2GV  C6   N5   aromatic  1.333  0.020  1.333
 2GV  C6   C24  single    1.472  0.020  1.472
 2GV  C24  C23  aromatic  1.389  0.020  1.389
 2GV  C24  C25  aromatic  1.426  0.020  1.426
 2GV  C12  C17  aromatic  1.391  0.020  1.391
 2GV  C23  C1   aromatic  1.389  0.020  1.389
 2GV  C17  C7   single    1.508  0.020  1.508
 2GV  N4   C25  single    1.339  0.020  1.339
 2GV  C25  N3   aromatic  1.341  0.020  1.341
 2GV  C21  C5   aromatic  1.396  0.020  1.396
 2GV  C21  C20  aromatic  1.385  0.020  1.385
 2GV  C1   C5   single    1.470  0.020  1.470
 2GV  C1   C26  aromatic  1.395  0.020  1.395
 2GV  C5   C22  aromatic  1.396  0.020  1.396
 2GV  C20  C19  aromatic  1.391  0.020  1.391
 2GV  C22  C18  aromatic  1.384  0.020  1.384
 2GV  C19  C18  aromatic  1.391  0.020  1.391
 2GV  C19  N2   single    1.408  0.020  1.408
 2GV  N2   C7   single    1.449  0.020  1.449
 2GV  N2   C11  single    1.360  0.020  1.360
 2GV  N3   C26  aromatic  1.316  0.020  1.316
 2GV  C7   C8   single    1.556  0.020  1.556
 2GV  O2   C11  double    1.205  0.020  1.205
 2GV  C11  O1   single    1.335  0.020  1.335
 2GV  C9   C8   single    1.512  0.020  1.512
 2GV  O1   C8   single    1.445  0.020  1.445
 2GV  C8   C10  single    1.520  0.020  1.520
 2GV  C12  H1   single    0.930  0.020  1.080
 2GV  C13  H2   single    0.930  0.020  1.080
 2GV  C14  H3   single    0.930  0.020  1.080
 2GV  C15  H4   single    0.930  0.020  1.080
 2GV  C16  H5   single    0.930  0.020  1.080
 2GV  C7   H6   single    0.970  0.020  1.090
 2GV  C9   H7   single    0.970  0.020  1.090
 2GV  C9   H8   single    0.970  0.020  1.090
 2GV  C9   H9   single    0.970  0.020  1.090
 2GV  C10  H10  single    0.970  0.020  1.090
 2GV  C10  H11  single    0.970  0.020  1.090
 2GV  C10  H12  single    0.970  0.020  1.090
 2GV  C18  H13  single    0.930  0.020  1.080
 2GV  C20  H14  single    0.930  0.020  1.080
 2GV  C21  H15  single    0.930  0.020  1.080
 2GV  C22  H16  single    0.930  0.020  1.080
 2GV  C23  H17  single    0.930  0.020  1.080
 2GV  C26  H18  single    0.930  0.020  1.080
 2GV  C2   H19  single    0.930  0.020  1.080
 2GV  C3   H20  single    0.930  0.020  1.080
 2GV  C4   H21  single    0.930  0.020  1.080
 2GV  N4   H22  single    0.860  0.020  1.020
 2GV  N4   H23  single    0.860  0.020  1.020

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
 2GV  H1   C12  C17  119.68  3.000
 2GV  H1   C12  C13  119.61  3.000
 2GV  C17  C12  C13  120.70  3.000
 2GV  H2   C13  C14  120.16  3.000
 2GV  H2   C13  C12  119.87  3.000
 2GV  C14  C13  C12  119.96  3.000
 2GV  H3   C14  C15  120.15  3.000
 2GV  H3   C14  C13  120.17  3.000
 2GV  C15  C14  C13  119.68  3.000
 2GV  H4   C15  C16  119.73  3.000
 2GV  H4   C15  C14  120.05  3.000
 2GV  C16  C15  C14  120.22  3.000
 2GV  H5   C16  C17  120.59  3.000
 2GV  H5   C16  C15  118.99  3.000
 2GV  C17  C16  C15  120.42  3.000
 2GV  C7   C17  C16  121.94  3.000
 2GV  C7   C17  C12  119.04  3.000
 2GV  C16  C17  C12  119.01  3.000
 2GV  H6   C7   N2   110.89  3.000
 2GV  H6   C7   C8   108.05  3.000
 2GV  N2   C7   C8   100.22  3.000
 2GV  H6   C7   C17  108.24  3.000
 2GV  C8   C7   C17  116.56  3.000
 2GV  N2   C7   C17  112.66  3.000
 2GV  O1   C8   C10  108.07  3.000
 2GV  C10  C8   C9   111.52  3.000
 2GV  O1   C8   C9   108.41  3.000
 2GV  C10  C8   C7   110.03  3.000
 2GV  O1   C8   C7   103.02  3.000
 2GV  C9   C8   C7   115.22  3.000
 2GV  H9   C9   H8   107.70  3.000
 2GV  H9   C9   H7   107.98  3.000
 2GV  H8   C9   H7   108.62  3.000
 2GV  H9   C9   C8   110.13  3.000
 2GV  H8   C9   C8   110.14  3.000
 2GV  H7   C9   C8   112.14  3.000
 2GV  H12  C10  H11  108.50  3.000
 2GV  H12  C10  H10  107.77  3.000
 2GV  H11  C10  H10  107.93  3.000
 2GV  H12  C10  C8   111.62  3.000
 2GV  H11  C10  C8   110.79  3.000
 2GV  H10  C10  C8   110.11  3.000
 2GV  C11  O1   C8   110.68  3.000
 2GV  N2   C11  O2   127.95  3.000
 2GV  O2   C11  O1   122.80  3.000
 2GV  N2   C11  O1   109.25  3.000
 2GV  C19  N2   C11  124.50  3.000
 2GV  C11  N2   C7   112.14  3.000
 2GV  C19  N2   C7   123.01  3.000
 2GV  H13  C18  C22  119.13  3.000
 2GV  H13  C18  C19  120.42  3.000
 2GV  C22  C18  C19  120.44  3.000
 2GV  C20  C19  C18  119.08  3.000
 2GV  C18  C19  N2   119.40  3.000
 2GV  C20  C19  N2   121.51  3.000
 2GV  H14  C20  C21  119.09  3.000
 2GV  H14  C20  C19  120.82  3.000
 2GV  C21  C20  C19  120.09  3.000
 2GV  H15  C21  C5   120.03  3.000
 2GV  H15  C21  C20  118.42  3.000
 2GV  C5   C21  C20  121.52  3.000
 2GV  C1   C5   C22  121.09  3.000
 2GV  C22  C5   C21  117.64  3.000
 2GV  C1   C5   C21  121.26  3.000
 2GV  H16  C22  C5   120.23  3.000
 2GV  H16  C22  C18  118.52  3.000
 2GV  C5   C22  C18  121.22  3.000
 2GV  C26  C1   C23  115.62  3.000
 2GV  C26  C1   C5   121.83  3.000
 2GV  C23  C1   C5   122.55  3.000
 2GV  H17  C23  C24  117.97  3.000
 2GV  H17  C23  C1   119.90  3.000
 2GV  C24  C23  C1   122.12  3.000
 2GV  C6   C24  C25  124.03  3.000
 2GV  C25  C24  C23  116.90  3.000
 2GV  C6   C24  C23  119.06  3.000
 2GV  N4   C25  N3   115.64  3.000
 2GV  N3   C25  C24  120.96  3.000
 2GV  N4   C25  C24  123.40  3.000
 2GV  C26  N3   C25  119.88  3.000
 2GV  H18  C26  N3   115.44  3.000
 2GV  H18  C26  C1   120.03  3.000
 2GV  N3   C26  C1   124.52  3.000
 2GV  C6   N1   C2   117.78  3.000
 2GV  H19  C2   C3   120.79  3.000
 2GV  H19  C2   N1   116.74  3.000
 2GV  C3   C2   N1   122.46  3.000
 2GV  H20  C3   C4   122.18  3.000
 2GV  H20  C3   C2   122.05  3.000
 2GV  C4   C3   C2   115.77  3.000
 2GV  H21  C4   N5   116.56  3.000
 2GV  H21  C4   C3   121.26  3.000
 2GV  N5   C4   C3   122.18  3.000
 2GV  C6   N5   C4   117.95  3.000
 2GV  N5   C6   N1   123.86  3.000
 2GV  N5   C6   C24  119.03  3.000
 2GV  N1   C6   C24  117.11  3.000
 2GV  H23  N4   H22  121.15  3.000
 2GV  H23  N4   C25  118.85  3.000
 2GV  H22  N4   C25  119.78  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
 2GV  CONST_01  C15  C14  C13  C12     0.00   0.0  0
 2GV  CONST_02  C15  C16  C17  C12     0.00   0.0  0
 2GV  CONST_03  C16  C15  C14  C13     0.00   0.0  0
 2GV  CONST_04  C16  C17  C12  C13     0.00   0.0  0
 2GV  CONST_05  C17  C16  C15  C14     0.00   0.0  0
 2GV  CONST_06  C17  C12  C13  C14     0.00   0.0  0
 2GV  CONST_07  C21  C5   C22  C18     0.00   0.0  0
 2GV  CONST_08  C1   C5   C22  C18   180.00   0.0  0
 2GV  CONST_09  C21  C20  C19  C18     0.00   0.0  0
 2GV  CONST_10  C5   C21  C20  C19     0.00   0.0  0
 2GV  CONST_11  C5   C22  C18  C19     0.00   0.0  0
 2GV  CONST_12  C1   C5   C21  C20   180.00   0.0  0
 2GV  CONST_13  C22  C5   C21  C20     0.00   0.0  0
 2GV  CONST_14  C22  C18  C19  C20     0.00   0.0  0
 2GV  CONST_17  C24  C23  C1   C5    180.00   0.0  0
 2GV  CONST_18  N3   C26  C1   C5    180.00   0.0  0
 2GV  CONST_21  C6   C24  C23  C1    180.00   0.0  0
 2GV  CONST_22  C25  C24  C23  C1      0.00   0.0  0
 2GV  CONST_23  C25  N3   C26  C1      0.00   0.0  0
 2GV  CONST_24  N1   C6   C24  C23     0.00   0.0  0
 2GV  CONST_25  N5   C6   C24  C23   180.00   0.0  0
 2GV  CONST_26  N3   C25  C24  C23     0.00   0.0  0
 2GV  CONST_27  N3   C26  C1   C23     0.00   0.0  0
 2GV  CONST_28  C2   N1   C6   C24   180.00   0.0  0
 2GV  CONST_29  C4   N5   C6   C24   180.00   0.0  0
 2GV  CONST_30  C26  C1   C23  C24     0.00   0.0  0
 2GV  CONST_31  C26  N3   C25  C24     0.00   0.0  0
 2GV  CONST_32  N1   C6   C24  C25   180.00   0.0  0
 2GV  CONST_33  N5   C6   C24  C25     0.00   0.0  0
 2GV  CONST_34  C6   C24  C25  N3    180.00   0.0  0
 2GV  CONST_35  C4   C3   C2   N1      0.00   0.0  0
 2GV  CONST_36  C4   N5   C6   N1      0.00   0.0  0
 2GV  CONST_37  N5   C4   C3   C2      0.00   0.0  0
 2GV  CONST_38  N5   C6   N1   C2      0.00   0.0  0
 2GV  CONST_39  C6   N1   C2   C3      0.00   0.0  0
 2GV  CONST_40  C6   N5   C4   C3      0.00   0.0  0
 2GV  CONST_41  C7   C17  C12  C13   180.00   0.0  0
 2GV  CONST_42  C7   C17  C16  C15   180.00   0.0  0
 2GV  CONST_43  C21  C20  C19  N2    180.00   0.0  0
 2GV  CONST_44  C22  C18  C19  N2    180.00   0.0  0
 2GV  CONST_45  N4   C25  C24  C23   180.00   0.0  0
 2GV  CONST_46  N4   C25  N3   C26   180.00   0.0  0
 2GV  CONST_47  N4   C25  C24  C6      0.00   0.0  0
 2GV  CONST_48  H3   C14  C13  C12   180.00   0.0  0
 2GV  CONST_49  H5   C16  C17  C12   180.00   0.0  0
 2GV  CONST_50  H4   C15  C14  C13   180.00   0.0  0
 2GV  CONST_51  H1   C12  C13  C14   180.00   0.0  0
 2GV  CONST_52  H2   C13  C14  C15   180.00   0.0  0
 2GV  CONST_53  H14  C20  C19  N2      0.00   0.0  0
 2GV  CONST_54  H13  C18  C19  N2      0.00   0.0  0
 2GV  CONST_55  H15  C21  C20  C19   180.00   0.0  0
 2GV  CONST_56  H16  C22  C18  C19   180.00   0.0  0
 2GV  CONST_57  H17  C23  C1   C5      0.00   0.0  0
 2GV  CONST_58  H18  C26  C1   C5      0.00   0.0  0
 2GV  CONST_59  H20  C3   C2   N1    180.00   0.0  0
 2GV  CONST_60  H21  C4   C3   C2    180.00   0.0  0
 2GV  CONST_61  H19  C2   C3   C4    180.00   0.0  0
 2GV  CONST_62  H22  N4   C25  C24     0.00   0.0  0
 2GV  CONST_63  H23  N4   C25  C24   180.00   0.0  0
 2GV  Var_01    C20  C19  N2   C7   -129.47  30.0  2
 2GV  Var_02    O1   C11  N2   C7     -4.55  30.0  1
 2GV  Var_03    N2   C11  O1   C8    -10.58  30.0  1
 2GV  Var_04    H7   C9   C8   C7     60.49  30.0  3
 2GV  Var_05    H10  C10  C8   C7     69.70  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
 2GV  chir_01  C7  C17  N2  C8  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
 2GV  plan-1  C12  0.020
 2GV  plan-1  C13  0.020
 2GV  plan-1  C14  0.020
 2GV  plan-1  C15  0.020
 2GV  plan-1  C16  0.020
 2GV  plan-1  C17  0.020
 2GV  plan-1  C7   0.020
 2GV  plan-1  H1   0.020
 2GV  plan-1  H2   0.020
 2GV  plan-1  H3   0.020
 2GV  plan-1  H4   0.020
 2GV  plan-1  H5   0.020
 2GV  plan-2  N2   0.020
 2GV  plan-2  C18  0.020
 2GV  plan-2  C19  0.020
 2GV  plan-2  C20  0.020
 2GV  plan-2  C21  0.020
 2GV  plan-2  C5   0.020
 2GV  plan-2  C22  0.020
 2GV  plan-2  C1   0.020
 2GV  plan-2  H14  0.020
 2GV  plan-2  H15  0.020
 2GV  plan-2  H16  0.020
 2GV  plan-2  H13  0.020
 2GV  plan-3  C5   0.020
 2GV  plan-3  C1   0.020
 2GV  plan-3  C23  0.020
 2GV  plan-3  C24  0.020
 2GV  plan-3  C25  0.020
 2GV  plan-3  N3   0.020
 2GV  plan-3  C26  0.020
 2GV  plan-3  C6   0.020
 2GV  plan-3  N4   0.020
 2GV  plan-3  H17  0.020
 2GV  plan-3  H18  0.020
 2GV  plan-4  C24  0.020
 2GV  plan-4  N1   0.020
 2GV  plan-4  C2   0.020
 2GV  plan-4  C3   0.020
 2GV  plan-4  C4   0.020
 2GV  plan-4  N5   0.020
 2GV  plan-4  C6   0.020
 2GV  plan-4  H19  0.020
 2GV  plan-4  H20  0.020
 2GV  plan-4  H21  0.020
 2GV  plan-5  C25  0.020
 2GV  plan-5  N4   0.020
 2GV  plan-5  H22  0.020
 2GV  plan-5  H23  0.020
 2GV  plan-6  C7   0.020
 2GV  plan-6  C11  0.020
 2GV  plan-6  N2   0.020
 2GV  plan-6  C19  0.020
 2GV  plan-7  O1   0.020
 2GV  plan-7  C11  0.020
 2GV  plan-7  O2   0.020
 2GV  plan-7  N2   0.020

