# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 10:12:45 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: ~{N}-[3-[(3~{R})-5-azanyl-3-methyl-2,6-dihydro-1,4-oxazin-3-yl]phenyl]-5-bromanyl-pyridine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@]1(COCC(=N1)N)c2cccc(NC(=O)c3ccc(Br)cn3)c2
#
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
 D9W  D9W  ~{N}-[3-[(3~{R})-5-azanyl-3-methyl-2,6-dihydro-1,4-oxazin-3-yl]phenyl]-5-bromanyl-pyridine-2-carboxamide  ligand  41  24  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_D9W
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
 D9W  C2   C   CR6   0  -0.183  -4.3256   0.8983   0.1522
 D9W  C3   C   CR16  0  -0.032  -3.0134   1.3244  -0.0294
 D9W  C11  C   C     0   0.539  -1.0550  -1.7457   0.1694
 D9W  C15  C   CR6   0   0.424   1.4151  -1.6314  -0.0559
 D9W  C16  C   CR16  0  -0.442   2.4430  -0.7040  -0.2499
 D9W  C18  C   CR6   0   0.150   3.7713  -1.0939  -0.3039
 D9W  C19  C   CR16  0  -0.325   4.0734  -2.4495  -0.1585
 D9W  C21  C   CR16  0  -0.232   3.0575  -3.3703   0.0327
 D9W  C23  C   CR16  0  -0.335   1.7252  -2.9823   0.0859
 D9W  C25  C   CR6   0  -0.031   4.8869  -0.0725  -0.4753
 D9W  C27  C   CR6   0   0.365   4.8306   2.2565  -0.1678
 D9W  C28  C   C     0  -0.249   6.0044   2.2252   0.7825
 D9W  BR1  BR  BR    0   0.001  -5.7197   2.1516   0.1314
 D9W  N5   N   N     0  -0.436  -2.0029   0.4759  -0.0204
 D9W  C6   C   CR6   0   0.129  -2.2374  -0.8178   0.1646
 D9W  C7   C   CR16  0  -0.286  -3.5135  -1.3270   0.3514
 D9W  C9   C   CR16  0  -0.114  -4.5848  -0.4481   0.3459
 D9W  O12  O   O     0  -0.456  -1.2034  -2.9449   0.3314
 D9W  N13  N   NH1   0  -0.762   0.1188  -1.1121  -0.0168
 D9W  N26  N   N     0  -0.429   4.3153   1.2357  -0.7275
 D9W  O31  O   O     0  -0.474   6.6456   0.9825   0.7948
 D9W  C32  C   C     0  -0.170   5.7120  -0.0720   0.8171
 D9W  N35  N   NH2   0  -0.816   4.3515   3.5047  -0.4207
 D9W  C38  C   CH3   0  -0.633   5.7610  -0.4450  -1.6798
 D9W  H1   H   HCR6  0   0.293  -2.7781   2.3707  -0.1842
 D9W  H2   H   HCR6  0   0.266   2.2019   0.3454  -0.3668
 D9W  H3   H   HCR6  0   0.247   5.0982  -2.7972  -0.1946
 D9W  H4   H   HCR6  0   0.256   3.3004  -4.4193   0.1438
 D9W  H5   H   HCR6  0   0.277   0.9577  -3.7236   0.2334
 D9W  H6   H   H     0   0.270   6.7383   2.9782   0.4869
 D9W  H7   H   H     0   0.242   5.6408   2.5010   1.7845
 D9W  H8   H   HCR6  0   0.290  -3.6751  -2.3849   0.4992
 D9W  H9   H   HCR6  0   0.303  -5.5920  -0.8145   0.4908
 D9W  H10  H   HNH1  0   0.422   0.0383  -0.1090  -0.1318
 D9W  H11  H   H     0   0.221   5.0427   0.0178   1.6856
 D9W  H12  H   H     0   0.241   6.2767  -0.9990   0.9270
 D9W  H13  H   HNH2  0   0.383   3.4312   3.5631  -0.8261
 D9W  H14  H   HNH2  0   0.393   4.5675   4.2417   0.2302
 D9W  H15  H   HCH3  0   0.235   5.1705  -0.4206  -2.5962
 D9W  H16  H   HCH3  0   0.234   6.5813   0.2649  -1.7864
 D9W  H17  H   HCH3  0   0.223   6.1893  -1.4428  -1.5835

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
 D9W  BR1  C2   single    1.875  0.020  1.875
 D9W  C2   C9   aromatic  1.385  0.020  1.385
 D9W  C2   C3   aromatic  1.392  0.020  1.392
 D9W  C9   C7   aromatic  1.386  0.020  1.386
 D9W  C3   N5   aromatic  1.319  0.020  1.319
 D9W  C7   C6   aromatic  1.387  0.020  1.387
 D9W  C28  O31  single    1.398  0.020  1.398
 D9W  C28  C27  single    1.511  0.020  1.511
 D9W  N5   C6   aromatic  1.328  0.020  1.328
 D9W  N35  C27  single    1.361  0.020  1.361
 D9W  C6   C11  single    1.503  0.020  1.503
 D9W  O31  C32  single    1.409  0.020  1.409
 D9W  C27  N26  double    1.273  0.020  1.273
 D9W  C11  N13  single    1.347  0.020  1.347
 D9W  C11  O12  double    1.219  0.020  1.219
 D9W  N13  C15  single    1.397  0.020  1.397
 D9W  C32  C25  single    1.533  0.020  1.533
 D9W  N26  C25  single    1.450  0.020  1.450
 D9W  C16  C15  aromatic  1.398  0.020  1.398
 D9W  C16  C18  aromatic  1.385  0.020  1.385
 D9W  C15  C23  aromatic  1.393  0.020  1.393
 D9W  C25  C18  single    1.522  0.020  1.522
 D9W  C25  C38  single    1.534  0.020  1.534
 D9W  C18  C19  aromatic  1.397  0.020  1.397
 D9W  C23  C21  aromatic  1.389  0.020  1.389
 D9W  C19  C21  aromatic  1.384  0.020  1.384
 D9W  C3   H1   single    0.930  0.020  1.080
 D9W  C16  H2   single    0.930  0.020  1.080
 D9W  C19  H3   single    0.930  0.020  1.080
 D9W  C21  H4   single    0.930  0.020  1.080
 D9W  C23  H5   single    0.930  0.020  1.080
 D9W  C28  H6   single    0.970  0.020  1.090
 D9W  C28  H7   single    0.970  0.020  1.090
 D9W  C7   H8   single    0.930  0.020  1.080
 D9W  C9   H9   single    0.930  0.020  1.080
 D9W  N13  H10  single    0.860  0.020  1.020
 D9W  C32  H11  single    0.970  0.020  1.090
 D9W  C32  H12  single    0.970  0.020  1.090
 D9W  N35  H13  single    0.890  0.020  1.040
 D9W  N35  H14  single    0.890  0.020  1.040
 D9W  C38  H15  single    0.970  0.020  1.090
 D9W  C38  H16  single    0.970  0.020  1.090
 D9W  C38  H17  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
 D9W  C9   C2   BR1  120.82  3.000
 D9W  C9   C2   C3   119.51  3.000
 D9W  BR1  C2   C3   119.67  3.000
 D9W  H1   C3   N5   117.10  3.000
 D9W  H1   C3   C2   121.28  3.000
 D9W  N5   C3   C2   121.62  3.000
 D9W  N13  C11  O12  125.95  3.000
 D9W  O12  C11  C6   120.80  3.000
 D9W  N13  C11  C6   113.25  3.000
 D9W  N13  C15  C23  124.33  3.000
 D9W  C23  C15  C16  119.58  3.000
 D9W  N13  C15  C16  116.08  3.000
 D9W  H2   C16  C18  118.80  3.000
 D9W  H2   C16  C15  119.61  3.000
 D9W  C18  C16  C15  121.59  3.000
 D9W  C25  C18  C19  120.30  3.000
 D9W  C19  C18  C16  118.46  3.000
 D9W  C25  C18  C16  121.22  3.000
 D9W  H3   C19  C21  119.05  3.000
 D9W  H3   C19  C18  120.86  3.000
 D9W  C21  C19  C18  120.09  3.000
 D9W  H4   C21  C23  118.82  3.000
 D9W  H4   C21  C19  119.61  3.000
 D9W  C23  C21  C19  121.57  3.000
 D9W  H5   C23  C21  119.77  3.000
 D9W  H5   C23  C15  121.51  3.000
 D9W  C21  C23  C15  118.72  3.000
 D9W  C38  C25  C32  110.81  3.000
 D9W  C38  C25  N26  107.89  3.000
 D9W  C32  C25  N26  111.01  3.000
 D9W  C38  C25  C18  110.06  3.000
 D9W  N26  C25  C18  109.64  3.000
 D9W  C32  C25  C18  107.44  3.000
 D9W  N35  C27  N26  120.75  3.000
 D9W  N26  C27  C28  125.07  3.000
 D9W  N35  C27  C28  114.18  3.000
 D9W  H7   C28  H6   107.19  3.000
 D9W  H7   C28  O31  111.47  3.000
 D9W  H6   C28  O31  107.87  3.000
 D9W  H7   C28  C27  108.10  3.000
 D9W  H6   C28  C27  109.73  3.000
 D9W  O31  C28  C27  112.35  3.000
 D9W  C6   N5   C3   119.49  3.000
 D9W  C7   C6   N5   122.62  3.000
 D9W  N5   C6   C11  117.59  3.000
 D9W  C7   C6   C11  119.79  3.000
 D9W  H8   C7   C9   120.40  3.000
 D9W  H8   C7   C6   121.05  3.000
 D9W  C9   C7   C6   118.56  3.000
 D9W  H9   C9   C7   120.30  3.000
 D9W  H9   C9   C2   121.50  3.000
 D9W  C7   C9   C2   118.20  3.000
 D9W  H10  N13  C15  116.01  3.000
 D9W  H10  N13  C11  114.35  3.000
 D9W  C15  N13  C11  129.63  3.000
 D9W  C27  N26  C25  119.17  3.000
 D9W  C32  O31  C28  111.19  3.000
 D9W  H12  C32  H11  107.74  3.000
 D9W  H12  C32  O31  107.13  3.000
 D9W  H11  C32  O31  110.77  3.000
 D9W  H12  C32  C25  111.29  3.000
 D9W  H11  C32  C25  109.75  3.000
 D9W  O31  C32  C25  110.10  3.000
 D9W  H14  N35  H13  114.44  3.000
 D9W  H14  N35  C27  118.42  3.000
 D9W  H13  N35  C27  116.73  3.000
 D9W  H17  C38  H16  108.00  3.000
 D9W  H17  C38  H15  107.91  3.000
 D9W  H16  C38  H15  108.11  3.000
 D9W  H17  C38  C25  112.13  3.000
 D9W  H16  C38  C25  110.33  3.000
 D9W  H15  C38  C25  110.23  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
 D9W  CONST_01  C6   C7   C9   C2     0.00   0.0  0
 D9W  CONST_02  C6   N5   C3   C2     0.00   0.0  0
 D9W  CONST_03  C7   C9   C2   C3     0.00   0.0  0
 D9W  CONST_04  C7   C6   N5   C3     0.00   0.0  0
 D9W  CONST_05  C19  C18  C16  C15    0.00   0.0  0
 D9W  CONST_06  C19  C21  C23  C15    0.00   0.0  0
 D9W  CONST_07  C21  C23  C15  C16    0.00   0.0  0
 D9W  CONST_08  C21  C19  C18  C16    0.00   0.0  0
 D9W  CONST_09  C23  C15  C16  C18    0.00   0.0  0
 D9W  CONST_10  C23  C21  C19  C18    0.00   0.0  0
 D9W  CONST_11  C9   C2   C3   N5     0.00   0.0  0
 D9W  CONST_12  C9   C7   C6   N5     0.00   0.0  0
 D9W  CONST_13  C25  C18  C16  C15  180.00   0.0  0
 D9W  CONST_14  C25  C18  C19  C21  180.00   0.0  0
 D9W  CONST_15  C28  C27  N26  C25    0.00   0.0  0
 D9W  CONST_16  C11  C6   N5   C3   180.00   0.0  0
 D9W  CONST_17  C9   C7   C6   C11  180.00   0.0  0
 D9W  CONST_18  N13  C15  C16  C18  180.00   0.0  0
 D9W  CONST_19  N13  C15  C23  C21  180.00   0.0  0
 D9W  CONST_20  C7   C9   C2   BR1  180.00   0.0  0
 D9W  CONST_21  N5   C3   C2   BR1  180.00   0.0  0
 D9W  CONST_22  N35  C27  N26  C25  180.00   0.0  0
 D9W  CONST_23  H8   C7   C9   C2   180.00   0.0  0
 D9W  CONST_24  H9   C9   C2   C3   180.00   0.0  0
 D9W  CONST_25  H4   C21  C23  C15  180.00   0.0  0
 D9W  CONST_26  H5   C23  C15  C16  180.00   0.0  0
 D9W  CONST_27  H3   C19  C18  C16  180.00   0.0  0
 D9W  CONST_28  H2   C16  C18  C19  180.00   0.0  0
 D9W  CONST_29  H1   C3   N5   C6   180.00   0.0  0
 D9W  CONST_30  C6   C11  N13  C15  180.00   0.0  0
 D9W  CONST_31  C16  C15  N13  C11  180.00   0.0  0
 D9W  CONST_32  C23  C15  N13  C11    0.00   0.0  0
 D9W  CONST_33  H10  N13  C15  C16    0.00   0.0  0
 D9W  CONST_36  O12  C11  N13  C15    0.00   0.0  0
 D9W  Var_01    O31  C28  C27  N26   11.63  30.0  1
 D9W  Var_02    H11  C32  O31  C28  -57.16  30.0  1
 D9W  Var_03    N13  C11  C6   N5     0.22  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
 D9W  chir_01  C25  N26  C18  C32  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
 D9W  plan-1  C2   0.020
 D9W  plan-1  C3   0.020
 D9W  plan-1  C11  0.020
 D9W  plan-1  BR1  0.020
 D9W  plan-1  N5   0.020
 D9W  plan-1  C6   0.020
 D9W  plan-1  C7   0.020
 D9W  plan-1  C9   0.020
 D9W  plan-1  H1   0.020
 D9W  plan-1  H8   0.020
 D9W  plan-1  H9   0.020
 D9W  plan-2  C15  0.020
 D9W  plan-2  C16  0.020
 D9W  plan-2  C18  0.020
 D9W  plan-2  C19  0.020
 D9W  plan-2  C21  0.020
 D9W  plan-2  C23  0.020
 D9W  plan-2  C25  0.020
 D9W  plan-2  N13  0.020
 D9W  plan-2  H2   0.020
 D9W  plan-2  H3   0.020
 D9W  plan-2  H4   0.020
 D9W  plan-2  H5   0.020
 D9W  plan-3  C11  0.020
 D9W  plan-3  C15  0.020
 D9W  plan-3  C6   0.020
 D9W  plan-3  O12  0.020
 D9W  plan-3  N13  0.020
 D9W  plan-3  H10  0.020
 D9W  plan-4  C25  0.020
 D9W  plan-4  C27  0.020
 D9W  plan-4  C28  0.020
 D9W  plan-4  N26  0.020
 D9W  plan-4  N35  0.020
 D9W  plan-4  H13  0.020
 D9W  plan-4  H14  0.020

