# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 17:28:10 2021
#   Inital geometry file: a 140 line input string
#   Ligand name: N-cyclopropyl-3-oxo-N-({4-[(pyrimidin-4-yl)carbamoyl]phenyl}methyl)-3,4-dihydro-2H-1,4-benzoxazine-7-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1COc2cc(ccc2N1)C(=O)N(Cc3ccc(cc3)C(=O)Nc4ccncn4)C5CC5
#
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
 V01  V01  N-cyclopropyl-3-oxo-N-({4-[(pyrimidin-4-yl)carbamoyl]phenyl}methyl)-3,4-dihydro-2H-1,4-benzoxazine-7-carboxamide  ligand  54  33  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_V01
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
 V01  O3   O  O     0  -0.452  17.3072  11.9743  21.9660
 V01  C4   C  CH2   0  -0.387  14.2824  15.5781  13.4691
 V01  C5   C  CR6   0   0.126  13.5123  16.7763  13.9603
 V01  C6   C  CR16  0  -0.293  12.2008  16.9991  13.5585
 V01  N1   N  NH1   0  -0.731  12.0225  21.2769  15.7118
 V01  C7   C  CR16  0  -0.245  11.4980  18.1039  14.0123
 V01  C8   C  CR6   0  -0.052  12.1021  19.0185  14.8705
 V01  N2   N  N     0  -0.408  11.0101  24.9370  17.2634
 V01  C9   C  C     0   0.547  11.2950  20.1832  15.3302
 V01  C10  C  CR6   0   0.525  11.5773  22.4759  16.2286
 V01  C11  C  CR16  0  -0.369  10.2500  22.7987  16.5142
 V01  C12  C  CR16  0  -0.032  10.0365  24.0590  17.0355
 V01  N3   N  N     0  -0.448  12.5582  23.3470  16.4527
 V01  C13  C  CR16  0   0.061  12.2278  24.5226  16.9546
 V01  C14  C  CR16  0  -0.273  13.4148  18.7907  15.2856
 V01  C15  C  CR16  0  -0.277  14.1068  17.6799  14.8371
 V01  N4   N  NH1   0  -0.717  17.6457  12.2323  19.7433
 V01  C20  C  C     0   0.486  16.9733  12.4457  20.8981
 V01  C19  C  CH2   0  -0.311  15.7195  13.2809  20.7372
 V01  O2   O  O2    0  -0.476  15.8222  14.2440  19.7058
 V01  C21  C  CR6   0   0.318  17.2209  12.7373  18.5187
 V01  C18  C  CR6   0   0.346  16.2777  13.7648  18.5237
 V01  C17  C  CR16  0  -0.353  15.8413  14.3203  17.3370
 V01  C22  C  CR16  0  -0.320  17.7368  12.2866  17.3125
 V01  C23  C  CR16  0  -0.283  17.3258  12.8678  16.1240
 V01  C16  C  CR6   0  -0.049  16.3656  13.8735  16.1274
 V01  C    C  C     0   0.521  16.0014  14.5224  14.8334
 V01  O    O  O     0  -0.479  16.8874  14.8656  14.0637
 V01  N    N  NT    0  -0.463  14.6849  14.7237  14.5733
 V01  C1   C  CH1   0  -0.108  13.6161  14.1381  15.3298
 V01  C3   C  CH2   0  -0.470  13.5903  12.6678  15.5843
 V01  C2   C  CH2   0  -0.493  12.6302  13.2686  14.6088
 V01  O1   O  O     0  -0.440  10.0807  20.1550  15.3448
 V01  H1   H  HCH2  0   0.268  13.6730  15.0080  12.7653
 V01  H2   H  HCH2  0   0.288  15.1745  15.9006  12.9349
 V01  H3   H  HCR6  0   0.262  11.7178  16.3023  12.8846
 V01  H4   H  HNH1  0   0.421  13.0226  21.2581  15.5717
 V01  H5   H  HCR6  0   0.266  10.4773  18.2575  13.6886
 V01  H6   H  HCR6  0   0.298   9.4280  22.1254  16.3457
 V01  H7   H  HCR6  0   0.283   9.0281  24.3732  17.2789
 V01  H8   H  HCR6  0   0.267  13.0433  25.2151  17.1310
 V01  H9   H  HCR6  0   0.266  13.9104  19.4561  15.9812
 V01  H10  H  HCR6  0   0.262  15.1237  17.5209  15.1746
 V01  H11  H  HNH1  0   0.419  18.4513  11.6215  19.7668
 V01  H12  H  HCH2  0   0.286  15.5275  13.8197  21.6626
 V01  H13  H  HCH2  0   0.272  14.8772  12.6003  20.5558
 V01  H14  H  HCR6  0   0.271  15.1138  15.1214  17.3759
 V01  H15  H  HCR6  0   0.281  18.4721  11.4922  17.3068
 V01  H16  H  HCR6  0   0.265  17.7481  12.5215  15.1904
 V01  H17  H  HCH1  0   0.274  13.1996  14.7700  16.1084
 V01  H18  H  HCH2  0   0.261  13.2298  12.3402  16.5502
 V01  H19  H  HCH2  0   0.262  14.3979  12.0693  15.1837
 V01  H20  H  HCH2  0   0.262  11.5883  13.3664  14.8833
 V01  H21  H  HCH2  0   0.262  12.8016  13.0705  13.5584

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
 V01  C6   C7   aromatic  1.386  0.020  1.386
 V01  C6   C5   aromatic  1.390  0.020  1.390
 V01  C7   C8   aromatic  1.392  0.020  1.392
 V01  C4   C5   single    1.507  0.020  1.507
 V01  C4   N    single    1.453  0.020  1.453
 V01  C5   C15  aromatic  1.392  0.020  1.392
 V01  O1   C9   double    1.215  0.020  1.215
 V01  O    C    double    1.223  0.020  1.223
 V01  C8   C9   single    1.490  0.020  1.490
 V01  C8   C14  aromatic  1.395  0.020  1.395
 V01  C2   C1   single    1.499  0.020  1.499
 V01  C2   C3   single    1.495  0.020  1.495
 V01  N    C    single    1.357  0.020  1.357
 V01  N    C1   single    1.434  0.020  1.434
 V01  C9   N1   single    1.368  0.020  1.368
 V01  C    C16  single    1.493  0.020  1.493
 V01  C15  C14  aromatic  1.383  0.020  1.383
 V01  C1   C3   single    1.492  0.020  1.492
 V01  N1   C10  single    1.379  0.020  1.379
 V01  C11  C10  aromatic  1.396  0.020  1.396
 V01  C11  C12  aromatic  1.381  0.020  1.381
 V01  C23  C16  aromatic  1.390  0.020  1.390
 V01  C23  C22  aromatic  1.385  0.020  1.385
 V01  C16  C17  aromatic  1.392  0.020  1.392
 V01  C10  N3   aromatic  1.331  0.020  1.331
 V01  C12  N2   aromatic  1.331  0.020  1.331
 V01  N3   C13  aromatic  1.320  0.020  1.320
 V01  C22  C21  aromatic  1.387  0.020  1.387
 V01  N2   C13  aromatic  1.323  0.020  1.323
 V01  C17  C18  aromatic  1.381  0.020  1.381
 V01  C21  C18  aromatic  1.395  0.020  1.395
 V01  C21  N4   single    1.391  0.020  1.391
 V01  C18  O2   single    1.354  0.020  1.354
 V01  N4   C20  single    1.353  0.020  1.353
 V01  O2   C19  single    1.415  0.020  1.415
 V01  C20  C19  single    1.515  0.020  1.515
 V01  C20  O3   double    1.214  0.020  1.214
 V01  C4   H1   single    0.970  0.020  1.090
 V01  C4   H2   single    0.970  0.020  1.090
 V01  C6   H3   single    0.930  0.020  1.080
 V01  N1   H4   single    0.860  0.020  1.020
 V01  C7   H5   single    0.930  0.020  1.080
 V01  C11  H6   single    0.930  0.020  1.080
 V01  C12  H7   single    0.930  0.020  1.080
 V01  C13  H8   single    0.930  0.020  1.080
 V01  C14  H9   single    0.930  0.020  1.080
 V01  C15  H10  single    0.930  0.020  1.080
 V01  N4   H11  single    0.860  0.020  1.020
 V01  C19  H12  single    0.970  0.020  1.090
 V01  C19  H13  single    0.970  0.020  1.090
 V01  C17  H14  single    0.930  0.020  1.080
 V01  C22  H15  single    0.930  0.020  1.080
 V01  C23  H16  single    0.930  0.020  1.080
 V01  C1   H17  single    0.970  0.020  1.090
 V01  C3   H18  single    0.970  0.020  1.090
 V01  C3   H19  single    0.970  0.020  1.090
 V01  C2   H20  single    0.970  0.020  1.090
 V01  C2   H21  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
 V01  H2   C4   H1   107.20  3.000
 V01  H2   C4   N    108.67  3.000
 V01  H1   C4   N    109.72  3.000
 V01  H2   C4   C5   110.07  3.000
 V01  H1   C4   C5   109.89  3.000
 V01  N    C4   C5   111.19  3.000
 V01  C15  C5   C6   118.74  3.000
 V01  C15  C5   C4   120.21  3.000
 V01  C6   C5   C4   121.04  3.000
 V01  H3   C6   C7   119.38  3.000
 V01  H3   C6   C5   119.84  3.000
 V01  C7   C6   C5   120.78  3.000
 V01  H4   N1   C10  112.81  3.000
 V01  H4   N1   C9   118.24  3.000
 V01  C10  N1   C9   128.89  3.000
 V01  H5   C7   C8   120.04  3.000
 V01  H5   C7   C6   119.59  3.000
 V01  C8   C7   C6   120.37  3.000
 V01  C14  C8   C9   123.06  3.000
 V01  C14  C8   C7   118.97  3.000
 V01  C9   C8   C7   117.95  3.000
 V01  C13  N2   C12  115.27  3.000
 V01  O1   C9   C8   121.81  3.000
 V01  C8   C9   N1   115.03  3.000
 V01  O1   C9   N1   123.16  3.000
 V01  N3   C10  C11  121.01  3.000
 V01  N3   C10  N1   113.21  3.000
 V01  C11  C10  N1   125.78  3.000
 V01  H6   C11  C12  120.82  3.000
 V01  H6   C11  C10  123.36  3.000
 V01  C12  C11  C10  115.82  3.000
 V01  H7   C12  C11  119.56  3.000
 V01  H7   C12  N2   116.81  3.000
 V01  C11  C12  N2   123.63  3.000
 V01  C13  N3   C10  117.54  3.000
 V01  H8   C13  N3   116.25  3.000
 V01  H8   C13  N2   117.02  3.000
 V01  N3   C13  N2   126.73  3.000
 V01  H9   C14  C15  118.21  3.000
 V01  H9   C14  C8   121.43  3.000
 V01  C15  C14  C8   120.34  3.000
 V01  H10  C15  C14  119.11  3.000
 V01  H10  C15  C5   120.11  3.000
 V01  C14  C15  C5   120.78  3.000
 V01  H11  N4   C21  118.89  3.000
 V01  H11  N4   C20  118.11  3.000
 V01  C21  N4   C20  122.84  3.000
 V01  C19  C20  N4   114.05  3.000
 V01  C19  C20  O3   122.34  3.000
 V01  N4   C20  O3   123.56  3.000
 V01  H13  C19  H12  108.19  3.000
 V01  H13  C19  O2   110.92  3.000
 V01  H12  C19  O2   107.20  3.000
 V01  H13  C19  C20  108.11  3.000
 V01  H12  C19  C20  109.19  3.000
 V01  O2   C19  C20  113.12  3.000
 V01  C18  O2   C19  114.82  3.000
 V01  C22  C21  C18  119.60  3.000
 V01  C18  C21  N4   118.09  3.000
 V01  C22  C21  N4   122.27  3.000
 V01  C17  C18  C21  120.46  3.000
 V01  C21  C18  O2   119.41  3.000
 V01  C17  C18  O2   120.09  3.000
 V01  H14  C17  C16  121.45  3.000
 V01  H14  C17  C18  118.62  3.000
 V01  C16  C17  C18  119.90  3.000
 V01  H15  C22  C23  120.32  3.000
 V01  H15  C22  C21  119.71  3.000
 V01  C23  C22  C21  119.96  3.000
 V01  H16  C23  C16  120.22  3.000
 V01  H16  C23  C22  119.36  3.000
 V01  C16  C23  C22  120.41  3.000
 V01  C    C16  C23  118.74  3.000
 V01  C23  C16  C17  119.63  3.000
 V01  C    C16  C17  121.45  3.000
 V01  N    C    O    122.73  3.000
 V01  N    C    C16  117.87  3.000
 V01  O    C    C16  119.40  3.000
 V01  C1   N    C    124.14  3.000
 V01  C1   N    C4   115.75  3.000
 V01  C    N    C4   120.11  3.000
 V01  H17  C1   C2   115.47  3.000
 V01  H17  C1   C3   116.38  3.000
 V01  C2   C1   C3    59.95  3.000
 V01  H17  C1   N    115.24  3.000
 V01  C3   C1   N    120.34  3.000
 V01  C2   C1   N    118.24  3.000
 V01  H19  C3   H18  114.31  3.000
 V01  H19  C3   C2   117.39  3.000
 V01  H18  C3   C2   119.36  3.000
 V01  H19  C3   C1   117.96  3.000
 V01  H18  C3   C1   117.16  3.000
 V01  C2   C3   C1    60.25  3.000
 V01  H21  C2   H20  114.53  3.000
 V01  H21  C2   C3   117.26  3.000
 V01  H20  C2   C3   119.30  3.000
 V01  H21  C2   C1   117.94  3.000
 V01  H20  C2   C1   117.31  3.000
 V01  C3   C2   C1    59.79  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
 V01  CONST_01  C8   C7   C6   C5      0.00   0.0  0
 V01  CONST_02  C8   C14  C15  C5      0.00   0.0  0
 V01  CONST_03  C14  C8   C7   C6      0.00   0.0  0
 V01  CONST_04  C14  C15  C5   C6      0.00   0.0  0
 V01  CONST_05  C15  C5   C6   C7      0.00   0.0  0
 V01  CONST_06  C15  C14  C8   C7      0.00   0.0  0
 V01  CONST_07  C10  C11  C12  N2      0.00   0.0  0
 V01  CONST_08  C10  N3   C13  N2      0.00   0.0  0
 V01  CONST_09  C13  N3   C10  C11     0.00   0.0  0
 V01  CONST_10  C13  N2   C12  C11     0.00   0.0  0
 V01  CONST_11  N3   C10  C11  C12     0.00   0.0  0
 V01  CONST_12  N3   C13  N2   C12     0.00   0.0  0
 V01  CONST_13  C16  C23  C22  C21     0.00   0.0  0
 V01  CONST_14  C16  C17  C18  C21     0.00   0.0  0
 V01  CONST_15  C23  C16  C17  C18     0.00   0.0  0
 V01  CONST_16  C23  C22  C21  C18     0.00   0.0  0
 V01  CONST_17  C22  C23  C16  C17     0.00   0.0  0
 V01  CONST_18  C22  C21  C18  C17     0.00   0.0  0
 V01  CONST_19  C21  N4   C20  C19     0.00   0.0  0
 V01  CONST_20  C7   C6   C5   C4    180.00   0.0  0
 V01  CONST_21  C14  C15  C5   C4    180.00   0.0  0
 V01  CONST_22  C9   C8   C7   C6    180.00   0.0  0
 V01  CONST_23  C12  C11  C10  N1    180.00   0.0  0
 V01  CONST_24  C13  N3   C10  N1    180.00   0.0  0
 V01  CONST_25  C15  C14  C8   C9    180.00   0.0  0
 V01  CONST_26  C    C16  C17  C18   180.00   0.0  0
 V01  CONST_27  C    C16  C23  C22   180.00   0.0  0
 V01  CONST_28  C21  N4   C20  O3    180.00   0.0  0
 V01  CONST_29  H5   C7   C6   C5    180.00   0.0  0
 V01  CONST_30  H9   C14  C15  C5    180.00   0.0  0
 V01  CONST_31  H10  C15  C5   C6    180.00   0.0  0
 V01  CONST_32  H3   C6   C7   C8    180.00   0.0  0
 V01  CONST_33  H6   C11  C12  N2    180.00   0.0  0
 V01  CONST_34  H7   C12  C11  C10   180.00   0.0  0
 V01  CONST_35  H8   C13  N3   C10   180.00   0.0  0
 V01  CONST_36  H15  C22  C21  N4      0.00   0.0  0
 V01  CONST_37  H14  C17  C18  O2      0.00   0.0  0
 V01  CONST_38  H16  C23  C22  C21   180.00   0.0  0
 V01  CONST_39  H11  N4   C20  C19   180.00   0.0  0
 V01  CONST_40  C10  N1   C9   C8    180.00   0.0  0
 V01  CONST_41  C1   N    C    C16     0.00   0.0  0
 V01  CONST_42  C11  C10  N1   C9      0.00   0.0  0
 V01  CONST_43  N3   C10  N1   C9    180.00   0.0  0
 V01  CONST_44  H4   N1   C10  C11   180.00   0.0  0
 V01  CONST_45  C16  C    N    C4    180.00   0.0  0
 V01  CONST_46  O1   C9   N1   C10     0.00   0.0  0
 V01  CONST_47  C1   N    C    O     180.00   0.0  0
 V01  CONST_48  O    C    N    C4      0.00   0.0  0
 V01  Var_01    O2   C19  C20  N4    -32.19  30.0  1
 V01  Var_02    C22  C21  N4   C20  -165.75  30.0  1
 V01  Var_03    C17  C18  O2   C19   148.11  30.0  1
 V01  Var_04    C3   C2   C1   N     110.59  30.0  1
 V01  Var_05    H18  C3   C2   C1    106.36  30.0  1
 V01  Var_06    C2   C1   N    C4     58.71  30.0  3
 V01  Var_07    C1   N    C4   C5     62.70  30.0  3
 V01  Var_08    N    C4   C5   C6   -119.14  30.0  3
 V01  Var_09    C7   C8   C9   N1   -155.75  30.0  2
 V01  Var_10    O    C    C16  C17   129.59  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
 V01  chir_01  C1  C2  N  C3  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
 V01  plan-1  O3   0.020
 V01  plan-1  N4   0.020
 V01  plan-1  C20  0.020
 V01  plan-1  C19  0.020
 V01  plan-1  C21  0.020
 V01  plan-1  H11  0.020
 V01  plan-2  C4   0.020
 V01  plan-2  C5   0.020
 V01  plan-2  C6   0.020
 V01  plan-2  C7   0.020
 V01  plan-2  C8   0.020
 V01  plan-2  C9   0.020
 V01  plan-2  C14  0.020
 V01  plan-2  C15  0.020
 V01  plan-2  H3   0.020
 V01  plan-2  H5   0.020
 V01  plan-2  H9   0.020
 V01  plan-2  H10  0.020
 V01  plan-3  N4   0.020
 V01  plan-3  O2   0.020
 V01  plan-3  C21  0.020
 V01  plan-3  C18  0.020
 V01  plan-3  C17  0.020
 V01  plan-3  C22  0.020
 V01  plan-3  C23  0.020
 V01  plan-3  C16  0.020
 V01  plan-3  C    0.020
 V01  plan-3  H14  0.020
 V01  plan-3  H15  0.020
 V01  plan-3  H16  0.020
 V01  plan-4  N1   0.020
 V01  plan-4  N2   0.020
 V01  plan-4  C10  0.020
 V01  plan-4  C11  0.020
 V01  plan-4  C12  0.020
 V01  plan-4  N3   0.020
 V01  plan-4  C13  0.020
 V01  plan-4  H6   0.020
 V01  plan-4  H7   0.020
 V01  plan-4  H8   0.020
 V01  plan-5  N1   0.020
 V01  plan-5  C8   0.020
 V01  plan-5  C9   0.020
 V01  plan-5  C10  0.020
 V01  plan-5  O1   0.020
 V01  plan-5  H4   0.020
 V01  plan-6  C4   0.020
 V01  plan-6  C16  0.020
 V01  plan-6  C    0.020
 V01  plan-6  O    0.020
 V01  plan-6  N    0.020
 V01  plan-6  C1   0.020

