# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 13:44:55 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: (2S)-2-(3'-chlorobiphenyl-3-yl)-2-methyl-5,6-dihydro-2H-1,3-oxazin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@]1(OCCC(=N1)N)c2cccc(c2)c3cccc(Cl)c3
#
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
 WM9  WM9  (2S)-2-(3'-chlorobiphenyl-3-yl)-2-methyl-5,6-dihydro-2H-1,3-oxazin-4-amine  ligand  38  21  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_WM9
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
 WM9  C1    C   CH3   0  -0.656   3.0671  -0.1781  -2.0736
 WM9  C2    C   CT    0   0.318   2.6999  -0.1507  -0.5831
 WM9  N3    N   N     0  -0.448   2.3247   1.1878  -0.2363
 WM9  C4    C   C     0   0.415   3.0363   1.8804   0.5634
 WM9  C5    C   CH2   0  -0.553   4.3235   1.4080   1.1804
 WM9  C6    C   CH2   0  -0.198   4.8242   0.2049   0.4085
 WM9  O7    O   O2    0  -0.500   3.7559  -0.6900   0.1969
 WM9  N8    N   NH2   0  -0.814   2.6214   3.1158   0.9512
 WM9  C9    C   CR6   0   0.094   1.5225  -1.0968  -0.3631
 WM9  C10   C   CR16  0  -0.302   1.7267  -2.4758  -0.3810
 WM9  C11   C   CR16  0  -0.229   0.6566  -3.3422  -0.2186
 WM9  C12   C   CR16  0  -0.323  -0.6278  -2.8500  -0.0391
 WM9  C13   C   CR6   0   0.118  -0.8526  -1.4751  -0.0223
 WM9  C14   C   CR16  0  -0.378   0.2340  -0.6134  -0.1863
 WM9  C15   C   CR6   0   0.085  -2.2150  -0.9351   0.1644
 WM9  C16   C   CR16  0  -0.303  -3.1262  -1.5588   1.0177
 WM9  C17   C   CR16  0  -0.246  -4.4023  -1.0445   1.1867
 WM9  C18   C   CR16  0  -0.229  -4.8016   0.1007   0.5125
 WM9  C19   C   CR6   0  -0.021  -3.8926   0.7162  -0.3332
 WM9  C20   C   CR16  0  -0.272  -2.6147   0.2158  -0.5156
 WM9  CL    CL  CL    0  -0.130  -4.3670   2.1443  -1.1968
 WM9  H11C  H   HCH3  0   0.234   3.9179   0.4714  -2.2856
 WM9  H12C  H   HCH3  0   0.229   3.3130  -1.1896  -2.3988
 WM9  H13C  H   HCH3  0   0.237   2.2271   0.1753  -2.6711
 WM9  H51C  H   HCH2  0   0.264   5.0656   2.2092   1.1711
 WM9  H52C  H   HCH2  0   0.275   4.1453   1.1526   2.2285
 WM9  H81N  H   HNH2  0   0.380   1.8539   3.5223   0.4406
 WM9  H82N  H   HNH2  0   0.390   3.3142   3.7730   1.2680
 WM9  H61C  H   HCH2  0   0.215   5.2816   0.5231  -0.5362
 WM9  H62C  H   HCH2  0   0.251   5.5858  -0.3349   0.9711
 WM9  H10   H   HCR6  0   0.250   2.7189  -2.8831  -0.5263
 WM9  H14   H   HCR6  0   0.251   0.0852   0.4579  -0.1560
 WM9  H11   H   HCR6  0   0.256   0.8217  -4.4117  -0.2397
 WM9  H12   H   HCR6  0   0.254  -1.4552  -3.5408   0.0631
 WM9  H16   H   HCR6  0   0.261  -2.8334  -2.4426   1.5692
 WM9  H20   H   HCR6  0   0.277  -1.9372   0.7079  -1.2007
 WM9  H17   H   HCR6  0   0.270  -5.0947  -1.5347   1.8579
 WM9  H18   H   HCR6  0   0.281  -5.7968   0.5024   0.6449

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
 WM9  C1   C2    single    1.535  0.020  1.535
 WM9  C2   N3    single    1.433  0.020  1.433
 WM9  C2   O7    single    1.419  0.020  1.419
 WM9  C2   C9    single    1.526  0.020  1.526
 WM9  N3   C4    double    1.275  0.020  1.275
 WM9  C4   C5    single    1.504  0.020  1.504
 WM9  C4   N8    single    1.360  0.020  1.360
 WM9  C5   C6    single    1.515  0.020  1.515
 WM9  C6   O7    single    1.409  0.020  1.409
 WM9  C9   C10   aromatic  1.394  0.020  1.394
 WM9  C9   C14   aromatic  1.388  0.020  1.388
 WM9  C10  C11   aromatic  1.386  0.020  1.386
 WM9  C11  C12   aromatic  1.387  0.020  1.387
 WM9  C12  C13   aromatic  1.393  0.020  1.393
 WM9  C13  C14   aromatic  1.396  0.020  1.396
 WM9  C13  C15   single    1.477  0.020  1.477
 WM9  C15  C16   aromatic  1.396  0.020  1.396
 WM9  C15  C20   aromatic  1.395  0.020  1.395
 WM9  C16  C17   aromatic  1.386  0.020  1.386
 WM9  C17  C18   aromatic  1.388  0.020  1.388
 WM9  C18  C19   aromatic  1.386  0.020  1.386
 WM9  C19  C20   aromatic  1.384  0.020  1.384
 WM9  C19  CL    single    1.735  0.020  1.735
 WM9  C1   H11C  single    0.970  0.020  1.090
 WM9  C1   H12C  single    0.970  0.020  1.090
 WM9  C1   H13C  single    0.970  0.020  1.090
 WM9  C5   H51C  single    0.970  0.020  1.090
 WM9  C5   H52C  single    0.970  0.020  1.090
 WM9  N8   H81N  single    0.890  0.020  1.040
 WM9  N8   H82N  single    0.890  0.020  1.040
 WM9  C6   H61C  single    0.970  0.020  1.090
 WM9  C6   H62C  single    0.970  0.020  1.090
 WM9  C10  H10   single    0.930  0.020  1.080
 WM9  C14  H14   single    0.930  0.020  1.080
 WM9  C11  H11   single    0.930  0.020  1.080
 WM9  C12  H12   single    0.930  0.020  1.080
 WM9  C16  H16   single    0.930  0.020  1.080
 WM9  C20  H20   single    0.930  0.020  1.080
 WM9  C17  H17   single    0.930  0.020  1.080
 WM9  C18  H18   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
 WM9  H13C  C1   H12C  108.13  3.000
 WM9  H13C  C1   H11C  107.54  3.000
 WM9  H12C  C1   H11C  108.56  3.000
 WM9  H13C  C1   C2    110.01  3.000
 WM9  H12C  C1   C2    111.10  3.000
 WM9  H11C  C1   C2    111.37  3.000
 WM9  C9    C2   O7    105.02  3.000
 WM9  C9    C2   N3    110.01  3.000
 WM9  O7    C2   N3    114.63  3.000
 WM9  C9    C2   C1    108.26  3.000
 WM9  O7    C2   C1    110.42  3.000
 WM9  N3    C2   C1    108.32  3.000
 WM9  C4    N3   C2    120.88  3.000
 WM9  N8    C4   C5    115.45  3.000
 WM9  N8    C4   N3    120.15  3.000
 WM9  C5    C4   N3    124.37  3.000
 WM9  H52C  C5   H51C  106.87  3.000
 WM9  H52C  C5   C6    110.91  3.000
 WM9  H51C  C5   C6    110.72  3.000
 WM9  H52C  C5   C4    109.10  3.000
 WM9  H51C  C5   C4    110.35  3.000
 WM9  C6    C5   C4    108.87  3.000
 WM9  H62C  C6   H61C  107.27  3.000
 WM9  H62C  C6   O7    107.01  3.000
 WM9  H61C  C6   O7    111.78  3.000
 WM9  H62C  C6   C5    111.18  3.000
 WM9  H61C  C6   C5    110.26  3.000
 WM9  O7    C6   C5    109.29  3.000
 WM9  C6    O7   C2    113.90  3.000
 WM9  H82N  N8   H81N  114.86  3.000
 WM9  H82N  N8   C4    118.24  3.000
 WM9  H81N  N8   C4    117.04  3.000
 WM9  C14   C9   C10   118.83  3.000
 WM9  C14   C9   C2    121.25  3.000
 WM9  C10   C9   C2    119.89  3.000
 WM9  H10   C10  C11   119.22  3.000
 WM9  H10   C10  C9    120.54  3.000
 WM9  C11   C10  C9    120.24  3.000
 WM9  H11   C11  C12   119.63  3.000
 WM9  H11   C11  C10   119.83  3.000
 WM9  C12   C11  C10   120.53  3.000
 WM9  H12   C12  C13   120.34  3.000
 WM9  H12   C12  C11   119.56  3.000
 WM9  C13   C12  C11   120.08  3.000
 WM9  C15   C13  C14   120.45  3.000
 WM9  C15   C13  C12   120.73  3.000
 WM9  C14   C13  C12   118.82  3.000
 WM9  H14   C14  C13   120.05  3.000
 WM9  H14   C14  C9    118.44  3.000
 WM9  C13   C14  C9    121.50  3.000
 WM9  C20   C15  C16   118.66  3.000
 WM9  C20   C15  C13   120.27  3.000
 WM9  C16   C15  C13   121.07  3.000
 WM9  H16   C16  C17   119.34  3.000
 WM9  H16   C16  C15   120.00  3.000
 WM9  C17   C16  C15   120.65  3.000
 WM9  H17   C17  C18   119.43  3.000
 WM9  H17   C17  C16   119.78  3.000
 WM9  C18   C17  C16   120.79  3.000
 WM9  H18   C18  C19   120.89  3.000
 WM9  H18   C18  C17   120.79  3.000
 WM9  C19   C18  C17   118.32  3.000
 WM9  CL    C19  C20   118.97  3.000
 WM9  CL    C19  C18   119.34  3.000
 WM9  C20   C19  C18   121.69  3.000
 WM9  H20   C20  C19   119.80  3.000
 WM9  H20   C20  C15   120.29  3.000
 WM9  C19   C20  C15   119.89  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
 WM9  CONST_01  C12   C11  C10  C9     0.00   0.0  0
 WM9  CONST_02  C12   C13  C14  C9     0.00   0.0  0
 WM9  CONST_03  C15   C13  C14  C9   180.00   0.0  0
 WM9  CONST_04  C13   C14  C9   C10    0.00   0.0  0
 WM9  CONST_05  C13   C12  C11  C10    0.00   0.0  0
 WM9  CONST_06  C14   C9   C10  C11    0.00   0.0  0
 WM9  CONST_07  C14   C13  C12  C11    0.00   0.0  0
 WM9  CONST_08  C15   C13  C12  C11  180.00   0.0  0
 WM9  CONST_11  C17   C16  C15  C13  180.00   0.0  0
 WM9  CONST_12  C19   C20  C15  C13  180.00   0.0  0
 WM9  CONST_15  C18   C17  C16  C15    0.00   0.0  0
 WM9  CONST_16  C18   C19  C20  C15    0.00   0.0  0
 WM9  CONST_17  C19   C20  C15  C16    0.00   0.0  0
 WM9  CONST_18  C19   C18  C17  C16    0.00   0.0  0
 WM9  CONST_19  C20   C15  C16  C17    0.00   0.0  0
 WM9  CONST_20  C20   C19  C18  C17    0.00   0.0  0
 WM9  CONST_21  C11   C10  C9   C2   180.00   0.0  0
 WM9  CONST_22  C13   C14  C9   C2   180.00   0.0  0
 WM9  CONST_23  C5    C4   N3   C2     0.00   0.0  0
 WM9  CONST_24  CL    C19  C20  C15  180.00   0.0  0
 WM9  CONST_25  CL    C19  C18  C17  180.00   0.0  0
 WM9  CONST_26  N8    C4   N3   C2   180.00   0.0  0
 WM9  CONST_27  H10   C10  C9   C2     0.00   0.0  0
 WM9  CONST_28  H14   C14  C9   C2     0.00   0.0  0
 WM9  CONST_29  H11   C11  C10  C9   180.00   0.0  0
 WM9  CONST_30  H12   C12  C11  C10  180.00   0.0  0
 WM9  CONST_31  H16   C16  C15  C13    0.00   0.0  0
 WM9  CONST_32  H20   C20  C15  C13    0.00   0.0  0
 WM9  CONST_33  H17   C17  C16  C15  180.00   0.0  0
 WM9  CONST_34  H18   C18  C17  C16  180.00   0.0  0
 WM9  CONST_35  H81N  N8   C4   N3     0.00   0.0  0
 WM9  Var_01    C5    C6   O7   C2    62.27  30.0  1
 WM9  Var_02    C6    C5   C4   N3    16.40  30.0  1
 WM9  Var_03    O7    C6   C5   C4   -46.24  30.0  1

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
 WM9  chir_01  C2  N3  O7  C9  negativ

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
 WM9  plan-1  C2    0.020
 WM9  plan-1  C9    0.020
 WM9  plan-1  C10   0.020
 WM9  plan-1  C11   0.020
 WM9  plan-1  C12   0.020
 WM9  plan-1  C13   0.020
 WM9  plan-1  C14   0.020
 WM9  plan-1  C15   0.020
 WM9  plan-1  H10   0.020
 WM9  plan-1  H14   0.020
 WM9  plan-1  H11   0.020
 WM9  plan-1  H12   0.020
 WM9  plan-2  C2    0.020
 WM9  plan-2  N3    0.020
 WM9  plan-2  C4    0.020
 WM9  plan-2  C5    0.020
 WM9  plan-2  N8    0.020
 WM9  plan-2  H81N  0.020
 WM9  plan-2  H82N  0.020
 WM9  plan-3  C13   0.020
 WM9  plan-3  C15   0.020
 WM9  plan-3  C16   0.020
 WM9  plan-3  C17   0.020
 WM9  plan-3  C18   0.020
 WM9  plan-3  C19   0.020
 WM9  plan-3  C20   0.020
 WM9  plan-3  CL    0.020
 WM9  plan-3  H16   0.020
 WM9  plan-3  H20   0.020
 WM9  plan-3  H17   0.020
 WM9  plan-3  H18   0.020

