# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 15:50:01 2022
#   Inital geometry file: a 149 line input string
#   Ligand name: 2-(5-amino-6-oxo-2-phenylpyrimidin-1(6H)-yl)-N-{(1S)-1-[(S)-(5-tert-butyl-1,3,4-oxadiazol-2-yl)(hydroxy)methyl]-2-methylpropyl}acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@H](NC(=O)CN1C(=O)C(=CN=C1c2ccccc2)N)[C@H](O)c3oc(nn3)C(C)(C)C
#
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
 681  681  2-(5-amino-6-oxo-2-phenylpyrimidin-1(6H)-yl)-N-{(1S)-1-[(S)-(5-tert-butyl-1,3,4-oxadiazol-2-yl)(hydroxy)methyl]-2-methylpropyl}acetamide  ligand  63  33  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_681
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
 681  C1    C  CH1   0  -0.047   2.5971  -0.0923   2.3158
 681  O1    O  OH1   0  -0.637   3.6234  -0.8569   2.8735
 681  C2    C  CR5   0   0.454   1.2841  -0.5029   2.9142
 681  N1    N  N     0  -0.315   0.9834  -1.6567   3.3844
 681  O2    O  O     0  -0.415   0.2497   0.3461   2.9858
 681  N2    N  N     0  -0.318  -0.3272  -1.5876   3.7815
 681  C3    C  CR5   0   0.539  -0.7347  -0.3960   3.5255
 681  C4    C  CT    0  -0.241  -2.1083   0.1687   3.7308
 681  C5    C  CH3   0  -0.631  -2.5806  -0.2100   5.1385
 681  C6    C  CH3   0  -0.650  -2.1116   1.6890   3.5742
 681  C7    C  CH3   0  -0.634  -3.0411  -0.4663   2.6892
 681  CVA   C  CH1   0  -0.121   2.5301  -0.1869   0.7722
 681  CVB   C  CH1   0  -0.255   3.8561   0.1020   0.0405
 681  CV1   C  CH3   0  -0.684   4.5530   1.3705   0.5251
 681  CV2   C  CH3   0  -0.659   4.8128  -1.0861   0.0197
 681  NV    N  NH1   0  -0.642   1.5193   0.7309   0.2850
 681  COG   C  C     0   0.572   0.2578   0.3864  -0.0018
 681  OCG   O  O     0  -0.471  -0.2251  -0.7137   0.2023
 681  CAG   C  CH2   0  -0.474  -0.5723   1.5213  -0.5839
 681  N2X   N  NR6   0  -0.523  -1.5974   0.9966  -1.4686
 681  C1X   C  CR6   0   0.449  -1.2476   0.2002  -2.5328
 681  N1X   N  N     0  -0.417  -2.1177  -0.4482  -3.2238
 681  C2X   C  CR16  0  -0.165  -3.4329  -0.3268  -2.9052
 681  C3X   C  CR6   0   0.147  -3.8910   0.4867  -1.9151
 681  C4X   C  CR6   0   0.547  -2.9183   1.2033  -1.1099
 681  O1X   O  OC    0  -0.484  -3.2334   1.9187  -0.1678
 681  N3X   N  NH2   0  -0.843  -5.2112   0.7101  -1.6231
 681  C5X   C  CR6   0  -0.037   0.1810   0.0958  -2.9108
 681  C6X   C  CR16  0  -0.244   0.8004  -1.1513  -2.9066
 681  C7X   C  CR16  0  -0.242   2.1288  -1.2711  -3.2861
 681  C8X   C  CR16  0  -0.253   2.8439  -0.1489  -3.6834
 681  C9X   C  CR16  0  -0.242   2.2263   1.0944  -3.7033
 681  C0X   C  CR16  0  -0.272   0.8996   1.2176  -3.3176
 681  H11   H  HCH1  0   0.283   2.7923   0.9482   2.5920
 681  HO1   H  HOH1  0   0.456   3.4747  -1.7882   2.6724
 681  H51   H  HCH3  0   0.237  -3.5952   0.1579   5.2943
 681  H52   H  HCH3  0   0.239  -2.5890  -1.2905   5.2795
 681  H53   H  HCH3  0   0.237  -1.9418   0.2308   5.9050
 681  H61   H  HCH3  0   0.238  -1.4346   2.1745   4.2781
 681  H62   H  HCH3  0   0.243  -1.8445   2.0020   2.5645
 681  H63   H  HCH3  0   0.242  -3.1170   2.0628   3.7715
 681  H71   H  HCH3  0   0.236  -3.0564  -1.5520   2.7865
 681  H72   H  HCH3  0   0.235  -4.0582  -0.0985   2.8325
 681  H73   H  HCH3  0   0.246  -2.7342  -0.2166   1.6744
 681  HVA1  H  HCH1  0   0.273   2.2050  -1.1969   0.5037
 681  HVB1  H  HCH1  0   0.257   3.5542   0.2662  -0.9991
 681  HV11  H  HCH3  0   0.245   5.3910   1.6099  -0.1303
 681  HV12  H  HCH3  0   0.229   3.8938   2.2419   0.5257
 681  HV13  H  HCH3  0   0.232   4.9512   1.2567   1.5341
 681  HV21  H  HCH3  0   0.228   5.2436  -1.2934   0.9973
 681  HV22  H  HCH3  0   0.228   4.3121  -1.9892  -0.3335
 681  HV23  H  HCH3  0   0.230   5.6354  -0.8805  -0.6665
 681  HNV1  H  HNH1  0   0.406   1.8207   1.6648   0.0510
 681  HAG1  H  HCH2  0   0.334  -1.0723   2.0347   0.2364
 681  HAG2  H  HCH2  0   0.300   0.0410   2.2657  -1.0887
 681  H2X1  H  HCR6  0   0.270  -4.1248  -0.9077  -3.5048
 681  H3X1  H  HNH2  0   0.385  -5.8558   0.0040  -1.9410
 681  H3X2  H  HNH2  0   0.382  -5.3986   1.0061  -0.6781
 681  H6X1  H  HCR6  0   0.257   0.2452  -2.0254  -2.5927
 681  H7X1  H  HCR6  0   0.261   2.6066  -2.2420  -3.2695
 681  H8X1  H  HCR6  0   0.263   3.8817  -0.2446  -3.9752
 681  H9X1  H  HCR6  0   0.263   2.7743   1.9709  -4.0229
 681  H0X1  H  HCR6  0   0.270   0.4223   2.1894  -3.3502

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
 681  C1   O1    single    1.396  0.020  1.396
 681  C1   C2    single    1.500  0.020  1.500
 681  C1   CVA   single    1.548  0.020  1.548
 681  C1   H11   single    0.970  0.020  1.090
 681  O1   HO1   single    0.850  0.020  0.980
 681  C2   N1    aromatic  1.282  0.020  1.282
 681  C2   O2    aromatic  1.340  0.020  1.340
 681  N1   N2    aromatic  1.371  0.020  1.371
 681  O2   C3    aromatic  1.346  0.020  1.346
 681  N2   C3    aromatic  1.285  0.020  1.285
 681  C3   C4    single    1.499  0.020  1.499
 681  C4   C5    single    1.532  0.020  1.532
 681  C4   C6    single    1.528  0.020  1.528
 681  C4   C7    single    1.536  0.020  1.536
 681  C5   H51   single    0.970  0.020  1.090
 681  C5   H52   single    0.970  0.020  1.090
 681  C5   H53   single    0.970  0.020  1.090
 681  C6   H61   single    0.970  0.020  1.090
 681  C6   H62   single    0.970  0.020  1.090
 681  C6   H63   single    0.970  0.020  1.090
 681  C7   H71   single    0.970  0.020  1.090
 681  C7   H72   single    0.970  0.020  1.090
 681  C7   H73   single    0.970  0.020  1.090
 681  CVA  CVB   single    1.542  0.020  1.542
 681  CVA  NV    single    1.450  0.020  1.450
 681  CVA  HVA1  single    0.970  0.020  1.090
 681  CVB  CV1   single    1.526  0.020  1.526
 681  CVB  CV2   single    1.525  0.020  1.525
 681  CVB  HVB1  single    0.970  0.020  1.090
 681  CV1  HV11  single    0.970  0.020  1.090
 681  CV1  HV12  single    0.970  0.020  1.090
 681  CV1  HV13  single    0.970  0.020  1.090
 681  CV2  HV21  single    0.970  0.020  1.090
 681  CV2  HV22  single    0.970  0.020  1.090
 681  CV2  HV23  single    0.970  0.020  1.090
 681  NV   COG   single    1.339  0.020  1.339
 681  NV   HNV1  single    0.860  0.020  1.020
 681  COG  OCG   double    1.219  0.020  1.219
 681  COG  CAG   single    1.522  0.020  1.522
 681  CAG  N2X   single    1.452  0.020  1.452
 681  CAG  HAG1  single    0.970  0.020  1.090
 681  CAG  HAG2  single    0.970  0.020  1.090
 681  N2X  C1X   aromatic  1.374  0.020  1.374
 681  N2X  C4X   aromatic  1.384  0.020  1.384
 681  C1X  N1X   aromatic  1.287  0.020  1.287
 681  C1X  C5X   single    1.481  0.020  1.481
 681  N1X  C2X   aromatic  1.359  0.020  1.359
 681  C2X  C3X   aromatic  1.361  0.020  1.361
 681  C2X  H2X1  single    0.930  0.020  1.080
 681  C3X  C4X   aromatic  1.452  0.020  1.452
 681  C3X  N3X   single    1.370  0.020  1.370
 681  C4X  O1X   double    1.224  0.020  1.224
 681  N3X  H3X1  single    0.890  0.020  1.040
 681  N3X  H3X2  single    0.890  0.020  1.040
 681  C5X  C6X   aromatic  1.392  0.020  1.392
 681  C5X  C0X   aromatic  1.393  0.020  1.393
 681  C6X  C7X   aromatic  1.387  0.020  1.387
 681  C6X  H6X1  single    0.930  0.020  1.080
 681  C7X  C8X   aromatic  1.389  0.020  1.389
 681  C7X  H7X1  single    0.930  0.020  1.080
 681  C8X  C9X   aromatic  1.388  0.020  1.388
 681  C8X  H8X1  single    0.930  0.020  1.080
 681  C9X  C0X   aromatic  1.387  0.020  1.387
 681  C9X  H9X1  single    0.930  0.020  1.080
 681  C0X  H0X1  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
 681  H11   C1   CVA   108.52  3.000
 681  H11   C1   C2    108.41  3.000
 681  CVA   C1   C2    110.07  3.000
 681  H11   C1   O1    106.79  3.000
 681  CVA   C1   O1    113.38  3.000
 681  C2    C1   O1    109.52  3.000
 681  HO1   O1   C1    109.40  3.000
 681  O2    C2   N1    111.69  3.000
 681  O2    C2   C1    121.57  3.000
 681  N1    C2   C1    126.73  3.000
 681  N2    N1   C2    106.57  3.000
 681  C3    O2   C2    103.69  3.000
 681  C3    N2   N1    106.98  3.000
 681  C4    C3   N2    127.77  3.000
 681  C4    C3   O2    121.16  3.000
 681  N2    C3   O2    111.05  3.000
 681  C7    C4   C6    109.91  3.000
 681  C7    C4   C5    109.50  3.000
 681  C6    C4   C5    109.83  3.000
 681  C7    C4   C3    107.94  3.000
 681  C6    C4   C3    111.26  3.000
 681  C5    C4   C3    108.36  3.000
 681  H53   C5   H52   108.32  3.000
 681  H53   C5   H51   107.95  3.000
 681  H52   C5   H51   107.99  3.000
 681  H53   C5   C4    111.42  3.000
 681  H52   C5   C4    111.49  3.000
 681  H51   C5   C4    109.55  3.000
 681  H63   C6   H62   107.16  3.000
 681  H63   C6   H61   107.63  3.000
 681  H62   C6   H61   108.54  3.000
 681  H63   C6   C4    108.93  3.000
 681  H62   C6   C4    112.32  3.000
 681  H61   C6   C4    112.04  3.000
 681  H73   C7   H72   107.93  3.000
 681  H73   C7   H71   108.39  3.000
 681  H72   C7   H71   108.11  3.000
 681  H73   C7   C4    111.47  3.000
 681  H72   C7   C4    109.74  3.000
 681  H71   C7   C4    111.08  3.000
 681  HVA1  CVA  NV    107.14  3.000
 681  HVA1  CVA  CVB   108.18  3.000
 681  NV    CVA  CVB   108.76  3.000
 681  HVA1  CVA  C1    108.29  3.000
 681  NV    CVA  C1    109.06  3.000
 681  CVB   CVA  C1    115.12  3.000
 681  HVB1  CVB  CV2   106.07  3.000
 681  HVB1  CVB  CV1   107.62  3.000
 681  CV2   CVB  CV1   111.42  3.000
 681  HVB1  CVB  CVA   103.98  3.000
 681  CV2   CVB  CVA   113.57  3.000
 681  CV1   CVB  CVA   113.44  3.000
 681  HV13  CV1  HV12  107.64  3.000
 681  HV13  CV1  HV11  107.35  3.000
 681  HV12  CV1  HV11  106.79  3.000
 681  HV13  CV1  CVB   111.94  3.000
 681  HV12  CV1  CVB   112.80  3.000
 681  HV11  CV1  CVB   110.03  3.000
 681  HV23  CV2  HV22  107.36  3.000
 681  HV23  CV2  HV21  107.60  3.000
 681  HV22  CV2  HV21  108.34  3.000
 681  HV23  CV2  CVB   109.56  3.000
 681  HV22  CV2  CVB   111.17  3.000
 681  HV21  CV2  CVB   112.61  3.000
 681  HNV1  NV   COG   118.04  3.000
 681  HNV1  NV   CVA   117.12  3.000
 681  COG   NV   CVA   124.48  3.000
 681  CAG   COG  OCG   121.41  3.000
 681  CAG   COG  NV    113.83  3.000
 681  OCG   COG  NV    124.74  3.000
 681  HAG2  CAG  HAG1  106.59  3.000
 681  HAG2  CAG  N2X   111.24  3.000
 681  HAG1  CAG  N2X   107.76  3.000
 681  HAG2  CAG  COG   112.33  3.000
 681  HAG1  CAG  COG   108.29  3.000
 681  N2X   CAG  COG   110.40  3.000
 681  C4X   N2X  C1X   122.01  3.000
 681  C4X   N2X  CAG   117.50  3.000
 681  C1X   N2X  CAG   120.10  3.000
 681  C5X   C1X  N1X   118.66  3.000
 681  C5X   C1X  N2X   118.94  3.000
 681  N1X   C1X  N2X   122.40  3.000
 681  C2X   N1X  C1X   118.93  3.000
 681  H2X1  C2X  C3X   120.52  3.000
 681  H2X1  C2X  N1X   116.11  3.000
 681  C3X   C2X  N1X   123.36  3.000
 681  N3X   C3X  C4X   116.54  3.000
 681  N3X   C3X  C2X   125.22  3.000
 681  C4X   C3X  C2X   118.23  3.000
 681  O1X   C4X  C3X   122.88  3.000
 681  O1X   C4X  N2X   122.16  3.000
 681  C3X   C4X  N2X   114.95  3.000
 681  H3X2  N3X  H3X1  112.49  3.000
 681  H3X2  N3X  C3X   115.26  3.000
 681  H3X1  N3X  C3X   115.78  3.000
 681  C0X   C5X  C6X   119.52  3.000
 681  C0X   C5X  C1X   121.02  3.000
 681  C6X   C5X  C1X   119.43  3.000
 681  H6X1  C6X  C7X   120.07  3.000
 681  H6X1  C6X  C5X   119.74  3.000
 681  C7X   C6X  C5X   120.18  3.000
 681  H7X1  C7X  C8X   120.13  3.000
 681  H7X1  C7X  C6X   119.76  3.000
 681  C8X   C7X  C6X   120.11  3.000
 681  H8X1  C8X  C9X   120.12  3.000
 681  H8X1  C8X  C7X   119.96  3.000
 681  C9X   C8X  C7X   119.91  3.000
 681  H9X1  C9X  C0X   119.64  3.000
 681  H9X1  C9X  C8X   120.29  3.000
 681  C0X   C9X  C8X   120.06  3.000
 681  H0X1  C0X  C9X   119.52  3.000
 681  H0X1  C0X  C5X   120.27  3.000
 681  C9X   C0X  C5X   120.21  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
 681  CONST_01  C3    N2   N1   C2      0.00   0.0  0
 681  CONST_02  N2    C3   O2   C2      0.00   0.0  0
 681  CONST_03  C3    O2   C2   N1      0.00   0.0  0
 681  CONST_04  O2    C3   N2   N1      0.00   0.0  0
 681  CONST_05  N2    N1   C2   O2      0.00   0.0  0
 681  CONST_06  C2X   N1X  C1X  N2X     0.00   0.0  0
 681  CONST_09  C2X   C3X  C4X  N2X     0.00   0.0  0
 681  CONST_10  C3X   C4X  N2X  C1X     0.00   0.0  0
 681  CONST_11  C3X   C2X  N1X  C1X     0.00   0.0  0
 681  CONST_12  C7X   C6X  C5X  C1X   180.00   0.0  0
 681  CONST_13  C9X   C0X  C5X  C1X   180.00   0.0  0
 681  CONST_14  C4X   N2X  C1X  N1X     0.00   0.0  0
 681  CONST_17  C4X   C3X  C2X  N1X     0.00   0.0  0
 681  CONST_18  C5X   C1X  N1X  C2X   180.00   0.0  0
 681  CONST_19  C5X   C1X  N2X  C4X   180.00   0.0  0
 681  CONST_20  C8X   C7X  C6X  C5X     0.00   0.0  0
 681  CONST_21  C8X   C9X  C0X  C5X     0.00   0.0  0
 681  CONST_22  C9X   C0X  C5X  C6X     0.00   0.0  0
 681  CONST_23  C9X   C8X  C7X  C6X     0.00   0.0  0
 681  CONST_24  C0X   C5X  C6X  C7X     0.00   0.0  0
 681  CONST_25  C0X   C9X  C8X  C7X     0.00   0.0  0
 681  CONST_26  N2    N1   C2   C1    180.00   0.0  0
 681  CONST_27  C3    O2   C2   C1    180.00   0.0  0
 681  CONST_28  C4    C3   O2   C2    180.00   0.0  0
 681  CONST_29  C4    C3   N2   N1    180.00   0.0  0
 681  CONST_30  N1X   C1X  N2X  CAG   180.00   0.0  0
 681  CONST_31  C5X   C1X  N2X  CAG     0.00   0.0  0
 681  CONST_32  C3X   C4X  N2X  CAG   180.00   0.0  0
 681  CONST_33  N3X   C3X  C4X  N2X   180.00   0.0  0
 681  CONST_34  O1X   C4X  N2X  C1X   180.00   0.0  0
 681  CONST_35  N3X   C3X  C2X  N1X   180.00   0.0  0
 681  CONST_36  O1X   C4X  C3X  C2X   180.00   0.0  0
 681  CONST_37  H2X1  C2X  N1X  C1X   180.00   0.0  0
 681  CONST_38  H6X1  C6X  C5X  C1X     0.00   0.0  0
 681  CONST_39  H0X1  C0X  C5X  C1X     0.00   0.0  0
 681  CONST_40  H7X1  C7X  C6X  C5X   180.00   0.0  0
 681  CONST_41  H9X1  C9X  C0X  C5X   180.00   0.0  0
 681  CONST_42  H8X1  C8X  C7X  C6X   180.00   0.0  0
 681  CONST_43  O1X   C4X  N2X  CAG     0.00   0.0  0
 681  CONST_46  OCG   COG  NV   CVA     0.00   0.0  0
 681  CONST_47  CAG   COG  NV   CVA   180.00   0.0  0
 681  CONST_48  HNV1  NV   COG  OCG   180.00   0.0  0
 681  Var_01    C5    C4   C3   O2   -134.29  30.0  2
 681  Var_02    C1X   N2X  CAG  COG   -56.33  30.0  2
 681  Var_03    N2X   CAG  COG  NV    150.72  30.0  3
 681  Var_04    H51   C5   C4   C3   -177.77  30.0  3
 681  Var_05    H61   C6   C4   C3    -58.69  30.0  3
 681  Var_06    H71   C7   C4   C3     58.73  30.0  3
 681  Var_07    HV11  CV1  CVB  CVA  -170.86  30.0  3
 681  Var_08    HV21  CV2  CVB  CVA   -71.02  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
 681  chir_01  C1   O1  C2  CVA  positiv
 681  chir_02  CVA  NV  C1  CVB  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
 681  plan-1  C1    0.020
 681  plan-1  C2    0.020
 681  plan-1  N1    0.020
 681  plan-1  O2    0.020
 681  plan-1  N2    0.020
 681  plan-1  C3    0.020
 681  plan-1  C4    0.020
 681  plan-2  CAG   0.020
 681  plan-2  N2X   0.020
 681  plan-2  C1X   0.020
 681  plan-2  N1X   0.020
 681  plan-2  C2X   0.020
 681  plan-2  C3X   0.020
 681  plan-2  C4X   0.020
 681  plan-2  O1X   0.020
 681  plan-2  N3X   0.020
 681  plan-2  C5X   0.020
 681  plan-2  H2X1  0.020
 681  plan-3  C1X   0.020
 681  plan-3  C5X   0.020
 681  plan-3  C6X   0.020
 681  plan-3  C7X   0.020
 681  plan-3  C8X   0.020
 681  plan-3  C9X   0.020
 681  plan-3  C0X   0.020
 681  plan-3  H6X1  0.020
 681  plan-3  H7X1  0.020
 681  plan-3  H8X1  0.020
 681  plan-3  H9X1  0.020
 681  plan-3  H0X1  0.020
 681  plan-4  CVA   0.020
 681  plan-4  NV    0.020
 681  plan-4  COG   0.020
 681  plan-4  OCG   0.020
 681  plan-4  CAG   0.020
 681  plan-4  HNV1  0.020
 681  plan-5  C3X   0.020
 681  plan-5  N3X   0.020
 681  plan-5  H3X1  0.020
 681  plan-5  H3X2  0.020

