# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 13:10:23 2022
#   Inital geometry file: a 114 line input string
#   Ligand name: (4~{S})-3-[6-[2-azanyl-4-(trifluoromethyl)pyrimidin-5-yl]-2-morpholin-4-yl-pyrimidin-4-yl]-4-methyl-1,3-oxazolidin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1COC(=O)N1c2cc(nc(n2)N3CCOCC3)c4cnc(N)nc4C(F)(F)F
#
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
 H5I  H5I  "(4~{S})-3-[6-[2-azanyl-4-(trifluoromethyl)pyrimidin-5-yl]-2-morpholin-4-yl-pyrimidin-4-yl]-4-methyl-1,3-oxazolidin-2-one"
  ligand  48  30  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_H5I
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
 H5I  C1   C  CR15  0  -0.133   6.0785  -34.2532  -23.2545
 H5I  C2   C  CH2   0  -0.195   5.7663  -35.3232  -22.2128
 H5I  C3   C  CR5   0   0.727   7.9621  -34.8112  -21.9906
 H5I  O1   O  O     0  -0.451   9.0814  -34.8737  -21.5576
 H5I  O2   O  O     0  -0.478   5.9394  -29.0571  -27.6114
 H5I  C11  C  C     0  -0.329   5.6224  -30.3682  -25.5954
 H5I  C12  C  CR6   0  -0.051  11.0560  -30.5118  -23.0363
 H5I  C13  C  CR16  0  -0.006  11.7844  -30.0629  -24.1448
 H5I  C14  C  CR6   0   0.572  13.5754  -29.5559  -22.8712
 H5I  C15  C  CR6   0   0.003  11.7345  -30.3774  -21.8301
 H5I  C16  C  CT    0   1.048  11.1131  -30.7230  -20.4898
 H5I  F2   F  F     0  -0.311  11.2073  -32.0358  -20.2434
 H5I  F    F  F     0  -0.302   9.8219  -30.3911  -20.4432
 H5I  F1   F  F     0  -0.293  11.7204  -30.0938  -19.4902
 H5I  N6   N  N     0  -0.472  12.9627  -29.9138  -21.7389
 H5I  N5   N  NH2   0  -0.815  14.8347  -29.1216  -22.7880
 H5I  N4   N  N     0  -0.434  13.0102  -29.6007  -24.0870
 H5I  C6   C  CR6   0   0.246   9.6916  -31.0283  -23.2724
 H5I  C5   C  CR16  0  -0.456   9.2887  -32.2710  -22.8123
 H5I  N1   N  N     0  -0.507   8.9308  -30.2520  -24.0334
 H5I  C7   C  CR6   0   0.652   7.7205  -30.7196  -24.3501
 H5I  N3   N  NR6   0  -0.512   6.9386  -29.9606  -25.1466
 H5I  C10  C  C     0  -0.179   5.5678  -30.3228  -27.1135
 H5I  C9   C  C     0  -0.179   7.2382  -28.6987  -27.1973
 H5I  C8   C  C     0  -0.326   7.3599  -28.6815  -25.6827
 H5I  N2   N  N     0  -0.524   7.2239  -31.8848  -23.9271
 H5I  C4   C  CR6   0   0.576   7.9926  -32.6497  -23.1760
 H5I  N    N  NR5   0  -0.612   7.4011  -33.8374  -22.7836
 H5I  C    C  CH3   0  -0.662   6.1107  -34.7923  -24.6751
 H5I  O    O  O     0  -0.455   7.0500  -35.7510  -21.7475
 H5I  H1   H  HCR5  0   0.290   5.3790  -33.4229  -23.1785
 H5I  H2   H  HCH2  0   0.265   5.2003  -34.9246  -21.3691
 H5I  H3   H  HCH2  0   0.266   5.2389  -36.1808  -22.6257
 H5I  H5   H  H     0   0.278   5.4020  -31.3727  -25.2461
 H5I  H6   H  HCR6  0   0.281  11.3264  -30.0993  -25.1275
 H5I  H7   H  HNH2  0   0.408  15.3059  -28.7783  -23.6067
 H5I  H8   H  HNH2  0   0.408  15.2757  -29.0025  -21.8929
 H5I  H9   H  HCR6  0   0.287   9.9448  -32.9083  -22.2496
 H5I  H10  H  H     0   0.240   4.5502  -30.5208  -27.4537
 H5I  H11  H  H     0   0.205   6.2205  -31.1074  -27.5224
 H5I  H12  H  H     0   0.205   7.9829  -29.3923  -27.6132
 H5I  H13  H  H     0   0.240   7.4443  -27.7044  -27.5967
 H5I  H14  H  H     0   0.274   8.3867  -28.4773  -25.3950
 H5I  H15  H  H     0   0.241   6.7280  -27.8893  -25.2658
 H5I  H16  H  HCH3  0   0.246   5.1127  -35.1245  -24.9606
 H5I  H17  H  HCH3  0   0.251   6.4260  -34.0272  -25.3816
 H5I  H18  H  HCH3  0   0.235   6.7877  -35.6437  -24.7588
 H5I  H4   H  H     0   0.241   4.8701  -29.6924  -25.1734

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
 H5I  O2   C9   single    1.410  0.020  1.410
 H5I  O2   C10  single    1.410  0.020  1.410
 H5I  C9   C8   single    1.520  0.020  1.520
 H5I  C10  C11  single    1.520  0.020  1.520
 H5I  C8   N3   single    1.450  0.020  1.450
 H5I  C11  N3   single    1.449  0.020  1.449
 H5I  N3   C7   single    1.350  0.020  1.350
 H5I  C    C1   single    1.520  0.020  1.520
 H5I  C7   N1   aromatic  1.336  0.020  1.336
 H5I  C7   N2   aromatic  1.335  0.020  1.335
 H5I  N1   C6   aromatic  1.327  0.020  1.327
 H5I  C13  N4   aromatic  1.311  0.020  1.311
 H5I  C13  C12  aromatic  1.400  0.020  1.400
 H5I  N4   C14  aromatic  1.342  0.020  1.342
 H5I  N2   C4   aromatic  1.319  0.020  1.319
 H5I  C6   C12  single    1.478  0.020  1.478
 H5I  C6   C5   aromatic  1.385  0.020  1.385
 H5I  C1   N    single    1.464  0.020  1.464
 H5I  C1   C2   single    1.526  0.020  1.526
 H5I  C4   C5   aromatic  1.398  0.020  1.398
 H5I  C4   N    single    1.384  0.020  1.384
 H5I  C12  C15  aromatic  1.390  0.020  1.390
 H5I  C14  N5   single    1.335  0.020  1.335
 H5I  C14  N6   aromatic  1.336  0.020  1.336
 H5I  N    C3   single    1.375  0.020  1.375
 H5I  C2   O    single    1.431  0.020  1.431
 H5I  C15  N6   aromatic  1.316  0.020  1.316
 H5I  C15  C16  single    1.517  0.020  1.517
 H5I  C3   O    single    1.332  0.020  1.332
 H5I  C3   O1   double    1.202  0.020  1.202
 H5I  C16  F    single    1.334  0.020  1.334
 H5I  C16  F2   single    1.339  0.020  1.339
 H5I  C16  F1   single    1.328  0.020  1.328
 H5I  C1   H1   single    0.970  0.020  1.090
 H5I  C2   H2   single    0.970  0.020  1.090
 H5I  C2   H3   single    0.970  0.020  1.090
 H5I  C11  H4   single    0.970  0.020  1.090
 H5I  C11  H5   single    0.970  0.020  1.090
 H5I  C13  H6   single    0.930  0.020  1.080
 H5I  N5   H7   single    0.860  0.020  1.020
 H5I  N5   H8   single    0.860  0.020  1.020
 H5I  C5   H9   single    0.930  0.020  1.080
 H5I  C10  H10  single    0.970  0.020  1.090
 H5I  C10  H11  single    0.970  0.020  1.090
 H5I  C9   H12  single    0.970  0.020  1.090
 H5I  C9   H13  single    0.970  0.020  1.090
 H5I  C8   H14  single    0.970  0.020  1.090
 H5I  C8   H15  single    0.970  0.020  1.090
 H5I  C    H16  single    0.970  0.020  1.090
 H5I  C    H17  single    0.970  0.020  1.090
 H5I  C    H18  single    0.970  0.020  1.090

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
 H5I  H1   C1   C    110.45  3.000
 H5I  H1   C1   N    109.97  3.000
 H5I  C    C1   N    112.47  3.000
 H5I  H1   C1   C2   110.85  3.000
 H5I  N    C1   C2    99.47  3.000
 H5I  C    C1   C2   113.19  3.000
 H5I  H3   C2   H2   109.26  3.000
 H5I  H3   C2   O    108.82  3.000
 H5I  H2   C2   O    108.85  3.000
 H5I  H3   C2   C1   113.14  3.000
 H5I  H2   C2   C1   112.20  3.000
 H5I  O    C2   C1   104.37  3.000
 H5I  O    C3   N    108.99  3.000
 H5I  O    C3   O1   122.36  3.000
 H5I  N    C3   O1   128.64  3.000
 H5I  C9   O2   C10  111.55  3.000
 H5I  H5   C11  H4   107.89  3.000
 H5I  H5   C11  C10  109.97  3.000
 H5I  H4   C11  C10  109.97  3.000
 H5I  H5   C11  N3   110.17  3.000
 H5I  H4   C11  N3   109.32  3.000
 H5I  C10  C11  N3   109.49  3.000
 H5I  C6   C12  C15  128.53  3.000
 H5I  C15  C12  C13  113.70  3.000
 H5I  C6   C12  C13  117.76  3.000
 H5I  H6   C13  N4   116.52  3.000
 H5I  H6   C13  C12  119.12  3.000
 H5I  N4   C13  C12  124.36  3.000
 H5I  N4   C14  N5   117.70  3.000
 H5I  N5   C14  N6   117.84  3.000
 H5I  N4   C14  N6   124.46  3.000
 H5I  N6   C15  C16  113.66  3.000
 H5I  C16  C15  C12  122.99  3.000
 H5I  N6   C15  C12  123.34  3.000
 H5I  F1   C16  F    107.37  3.000
 H5I  F1   C16  F2   107.08  3.000
 H5I  F    C16  F2   107.79  3.000
 H5I  F1   C16  C15  111.70  3.000
 H5I  F2   C16  C15  110.92  3.000
 H5I  F    C16  C15  111.75  3.000
 H5I  C15  N6   C14  117.62  3.000
 H5I  H8   N5   H7   118.65  3.000
 H5I  H8   N5   C14  120.53  3.000
 H5I  H7   N5   C14  120.18  3.000
 H5I  C14  N4   C13  116.46  3.000
 H5I  N1   C6   C5   123.28  3.000
 H5I  C5   C6   C12  121.94  3.000
 H5I  N1   C6   C12  114.61  3.000
 H5I  H9   C5   C4   122.80  3.000
 H5I  H9   C5   C6   121.93  3.000
 H5I  C4   C5   C6   115.23  3.000
 H5I  C7   N1   C6   116.79  3.000
 H5I  N2   C7   N3   117.53  3.000
 H5I  N2   C7   N1   124.57  3.000
 H5I  N3   C7   N1   117.90  3.000
 H5I  C8   N3   C7   123.10  3.000
 H5I  C7   N3   C11  123.42  3.000
 H5I  C8   N3   C11  113.43  3.000
 H5I  H11  C10  H10  107.95  3.000
 H5I  H11  C10  C11  109.20  3.000
 H5I  H10  C10  C11  109.85  3.000
 H5I  H11  C10  O2   110.66  3.000
 H5I  H10  C10  O2   107.37  3.000
 H5I  C11  C10  O2   111.72  3.000
 H5I  H13  C9   H12  107.97  3.000
 H5I  H13  C9   C8   109.84  3.000
 H5I  H12  C9   C8   109.26  3.000
 H5I  H13  C9   O2   107.35  3.000
 H5I  H12  C9   O2   110.65  3.000
 H5I  C8   C9   O2   111.68  3.000
 H5I  H15  C8   H14  107.96  3.000
 H5I  H15  C8   C9   109.95  3.000
 H5I  H14  C8   C9   110.00  3.000
 H5I  H15  C8   N3   109.25  3.000
 H5I  H14  C8   N3   110.05  3.000
 H5I  C9   C8   N3   109.60  3.000
 H5I  C4   N2   C7   118.01  3.000
 H5I  N    C4   N2   114.21  3.000
 H5I  N    C4   C5   123.71  3.000
 H5I  N2   C4   C5   122.08  3.000
 H5I  C4   N    C3   126.64  3.000
 H5I  C3   N    C1   110.66  3.000
 H5I  C4   N    C1   122.60  3.000
 H5I  H18  C    H17  108.61  3.000
 H5I  H18  C    H16  108.07  3.000
 H5I  H17  C    H16  108.03  3.000
 H5I  H18  C    C1   111.20  3.000
 H5I  H17  C    C1   111.33  3.000
 H5I  H16  C    C1   109.49  3.000
 H5I  C3   O    C2   110.12  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
 H5I  CONST_01  C14  N4   C13  C12     0.00   0.0  0
 H5I  CONST_02  C7   N1   C6   C12   180.00   0.0  0
 H5I  CONST_03  C4   C5   C6   C12   180.00   0.0  0
 H5I  CONST_04  C14  N6   C15  C12     0.00   0.0  0
 H5I  CONST_05  N6   C14  N4   C13     0.00   0.0  0
 H5I  CONST_08  N6   C15  C12  C13     0.00   0.0  0
 H5I  CONST_09  N4   C13  C12  C15     0.00   0.0  0
 H5I  CONST_12  N4   C14  N6   C15     0.00   0.0  0
 H5I  CONST_13  C6   C12  C15  N6    180.00   0.0  0
 H5I  CONST_14  C6   C12  C13  N4    180.00   0.0  0
 H5I  CONST_15  N2   C7   N1   C6      0.00   0.0  0
 H5I  CONST_16  N2   C4   C5   C6      0.00   0.0  0
 H5I  CONST_17  C7   N1   C6   C5      0.00   0.0  0
 H5I  CONST_18  C7   N2   C4   C5      0.00   0.0  0
 H5I  CONST_19  C4   N2   C7   N1      0.00   0.0  0
 H5I  CONST_20  C4   C5   C6   N1      0.00   0.0  0
 H5I  CONST_21  N3   C7   N1   C6    180.00   0.0  0
 H5I  CONST_22  N    C4   C5   C6    180.00   0.0  0
 H5I  CONST_23  N    C4   N2   C7    180.00   0.0  0
 H5I  CONST_24  C4   N2   C7   N3    180.00   0.0  0
 H5I  CONST_25  N5   C14  N4   C13   180.00   0.0  0
 H5I  CONST_26  C16  C15  C12  C13   180.00   0.0  0
 H5I  CONST_27  C16  C15  N6   C14   180.00   0.0  0
 H5I  CONST_28  N5   C14  N6   C15   180.00   0.0  0
 H5I  CONST_29  C6   C12  C15  C16     0.00   0.0  0
 H5I  CONST_30  H9   C5   C6   C12     0.00   0.0  0
 H5I  CONST_31  H6   C13  N4   C14   180.00   0.0  0
 H5I  CONST_32  H6   C13  C12  C15   180.00   0.0  0
 H5I  CONST_33  H6   C13  C12  C6      0.00   0.0  0
 H5I  CONST_34  H9   C5   C6   N1    180.00   0.0  0
 H5I  CONST_35  H9   C5   C4   N2    180.00   0.0  0
 H5I  CONST_36  H9   C5   C4   N       0.00   0.0  0
 H5I  CONST_37  H7   N5   C14  N6    180.00   0.0  0
 H5I  CONST_38  H8   N5   C14  N6      0.00   0.0  0
 H5I  CONST_39  H7   N5   C14  N4      0.00   0.0  0
 H5I  CONST_40  H8   N5   C14  N4    180.00   0.0  0
 H5I  Var_01    N2   C4   N    C1      4.75  30.0  1
 H5I  Var_02    C5   C4   N    C1   -175.60  30.0  1
 H5I  Var_03    O    C3   N    C1     -8.51  30.0  1
 H5I  Var_04    C3   O    C2   C1     21.73  30.0  1
 H5I  Var_05    N    C3   O    C2     -8.95  30.0  1
 H5I  Var_06    N2   C4   N    C3   -179.24  30.0  1
 H5I  Var_07    C5   C4   N    C3      0.41  30.0  1
 H5I  Var_08    N3   C8   C9   O2     54.57  30.0  1
 H5I  Var_09    N3   C11  C10  O2    -54.71  30.0  1
 H5I  Var_10    C9   O2   C10  C11    58.23  30.0  1
 H5I  Var_11    C9   C8   N3   C11   -53.18  30.0  1
 H5I  Var_12    N1   C7   N3   C11   178.16  30.0  2
 H5I  Var_13    N2   C7   N3   C11    -2.23  30.0  2
 H5I  Var_14    C8   N3   C7   N1      0.90  30.0  2
 H5I  Var_15    C9   C8   N3   C7    124.32  30.0  1
 H5I  Var_16    C10  C11  N3   C7   -124.29  30.0  1
 H5I  Var_17    C8   C9   O2   C10   -58.12  30.0  1
 H5I  Var_18    C8   N3   C11  C10    53.20  30.0  1
 H5I  Var_19    N2   C7   N3   C8   -179.49  30.0  2
 H5I  Var_20    O    C3   N    C4    175.08  30.0  1
 H5I  Var_21    O1   C3   N    C1    171.13  30.0  1
 H5I  Var_22    O1   C3   O    C2    171.38  30.0  1
 H5I  Var_23    C4   N    C3   O1     -5.27  30.0  1
 H5I  Var_24    H2   C2   O    C3    -98.24  30.0  1
 H5I  Var_25    H3   C2   O    C3    142.78  30.0  1
 H5I  Var_26    H14  C8   C9   O2    175.69  30.0  1
 H5I  Var_27    H15  C8   C9   O2    -65.53  30.0  1
 H5I  Var_28    H4   C11  C10  O2     65.42  30.0  1
 H5I  Var_29    H5   C11  C10  O2   -175.90  30.0  1
 H5I  Var_30    H14  C8   N3   C11  -174.28  30.0  1
 H5I  Var_31    H15  C8   N3   C11    67.35  30.0  1
 H5I  Var_32    H14  C8   N3   C7      3.23  30.0  1
 H5I  Var_33    H15  C8   N3   C7   -115.14  30.0  1
 H5I  Var_34    H4   C11  N3   C7    115.18  30.0  1
 H5I  Var_35    H5   C11  N3   C7     -3.22  30.0  1
 H5I  Var_36    H12  C9   C8   N3    -68.18  30.0  1
 H5I  Var_37    H13  C9   C8   N3    173.56  30.0  1
 H5I  Var_38    H10  C10  C11  N3   -173.76  30.0  1
 H5I  Var_39    H11  C10  C11  N3     68.04  30.0  1
 H5I  Var_40    H12  C9   O2   C10    63.84  30.0  1
 H5I  Var_41    H13  C9   O2   C10  -178.57  30.0  1
 H5I  Var_42    H10  C10  O2   C9    178.73  30.0  1
 H5I  Var_43    H11  C10  O2   C9    -63.68  30.0  1
 H5I  Var_44    H4   C11  N3   C8    -67.33  30.0  1
 H5I  Var_45    H5   C11  N3   C8    174.27  30.0  1
 H5I  Var_46    F    C16  C15  C12   -37.30  30.0  2
 H5I  Var_47    F2   C16  C15  C12    83.02  30.0  2
 H5I  Var_48    F1   C16  C15  C12  -157.60  30.0  2
 H5I  Var_49    N6   C15  C16  F2    -98.31  30.0  3
 H5I  Var_50    N6   C15  C16  F     141.37  30.0  3
 H5I  Var_51    N6   C15  C16  F1     21.07  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
 H5I  chir_01  C1  C  N  C2  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
 H5I  plan-1  C14  0.020
 H5I  plan-1  N5   0.020
 H5I  plan-1  H7   0.020
 H5I  plan-1  H8   0.020
 H5I  plan-2  C12  0.020
 H5I  plan-2  C13  0.020
 H5I  plan-2  C14  0.020
 H5I  plan-2  C15  0.020
 H5I  plan-2  C16  0.020
 H5I  plan-2  N6   0.020
 H5I  plan-2  N5   0.020
 H5I  plan-2  N4   0.020
 H5I  plan-2  C6   0.020
 H5I  plan-2  H6   0.020
 H5I  plan-3  C12  0.020
 H5I  plan-3  C6   0.020
 H5I  plan-3  C5   0.020
 H5I  plan-3  N1   0.020
 H5I  plan-3  C7   0.020
 H5I  plan-3  N3   0.020
 H5I  plan-3  N2   0.020
 H5I  plan-3  C4   0.020
 H5I  plan-3  N    0.020
 H5I  plan-3  H9   0.020
 H5I  plan-4  C1   0.020
 H5I  plan-4  C3   0.020
 H5I  plan-4  C4   0.020
 H5I  plan-4  N    0.020
 H5I  plan-5  C3   0.020
 H5I  plan-5  O1   0.020
 H5I  plan-5  N    0.020
 H5I  plan-5  O    0.020

