# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 16:12:46 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: 5-[(2R,4S)-2-benzylpiperidin-4-yl]-1,2-oxazol-3(2H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1NOC(=C1)[C@H]2CCN[C@H](C2)Cc3ccccc3
#
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
 XO3  XO3  5-[(2R,4S)-2-benzylpiperidin-4-yl]-1,2-oxazol-3(2H)-one  ligand  37  19  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XO3
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
 XO3  C1    C  CH2   0  -0.412   1.2538  -1.7839  -0.6556
 XO3  C2    C  CH2   0  -0.300  -0.2045  -2.0033  -1.0233
 XO3  N3    N  NH1   0  -0.601  -1.0683  -1.3185  -0.0782
 XO3  C4    C  CH1   0  -0.069  -0.8727   0.1201  -0.0949
 XO3  C5    C  CH2   0  -0.398   0.5648   0.4362   0.3032
 XO3  C6    C  CH1   0  -0.389   1.5528  -0.2796  -0.6261
 XO3  C7    C  CR5   0   0.564   2.9636   0.0045  -0.2631
 XO3  O8    O  O     0  -0.348   3.3621  -0.3989   0.9544
 XO3  N9    N  NR15  0  -0.379   4.7078  -0.1305   1.0303
 XO3  C10   C  CR5   0   0.528   5.1193   0.5947  -0.0721
 XO3  C11   C  CR15  0  -0.632   3.9645   0.5948  -0.9418
 XO3  O12   O  O     0  -0.490   6.2387   1.0634  -0.2016
 XO3  C13   C  CH2   0  -0.505  -1.8506   0.8043   0.8633
 XO3  C14   C  CR6   0   0.113  -3.2891   0.5908   0.4818
 XO3  C15   C  CR16  0  -0.314  -4.0625  -0.3845   1.1080
 XO3  C16   C  CR16  0  -0.241  -5.3813  -0.6021   0.7279
 XO3  C17   C  CR16  0  -0.272  -5.9475   0.1559  -0.2874
 XO3  C18   C  CR16  0  -0.240  -5.1869   1.1327  -0.9194
 XO3  C19   C  CR16  0  -0.303  -3.8703   1.3456  -0.5369
 XO3  H11C  H  HCH2  0   0.232   1.4538  -2.2285   0.3223
 XO3  H12C  H  HCH2  0   0.248   1.8981  -2.2817  -1.3829
 XO3  H21C  H  HCH2  0   0.194  -0.3626  -1.6635  -2.0600
 XO3  H22C  H  HCH2  0   0.240  -0.4333  -3.0702  -1.0007
 XO3  H6    H  HCH1  0   0.273   1.4166   0.1132  -1.6391
 XO3  H3    H  HNH1  0   0.357  -2.0331  -1.5287  -0.3033
 XO3  H4    H  HCH1  0   0.202  -1.0399   0.5385  -1.1046
 XO3  H51C  H  HCH2  0   0.248   0.7238   1.5162   0.2612
 XO3  H52C  H  HCH2  0   0.231   0.7225   0.1193   1.3383
 XO3  H131  H  HCH2  0   0.241  -1.6727   0.4309   1.8754
 XO3  H132  H  HCH2  0   0.248  -1.6262   1.8742   0.8720
 XO3  H11   H  HCR5  0   0.289   3.9124   1.0145  -1.9323
 XO3  H9    H  HNR5  0   0.431   4.9980   0.0720   1.9785
 XO3  H15   H  HCR6  0   0.250  -3.6284  -0.9786   1.9040
 XO3  H19   H  HCR6  0   0.246  -3.2845   2.1123  -1.0311
 XO3  H16   H  HCR6  0   0.254  -5.9670  -1.3633   1.2274
 XO3  H17   H  HCR6  0   0.254  -6.9755  -0.0096  -0.5830
 XO3  H18   H  HCR6  0   0.253  -5.6226   1.7317  -1.7090

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
 XO3  C1   C2    single    1.520  0.020  1.520
 XO3  C1   C6    single    1.534  0.020  1.534
 XO3  C2   N3    single    1.452  0.020  1.452
 XO3  N3   C4    single    1.452  0.020  1.452
 XO3  C4   C5    single    1.525  0.020  1.525
 XO3  C4   C13   single    1.531  0.020  1.531
 XO3  C5   C6    single    1.534  0.020  1.534
 XO3  C6   C7    single    1.484  0.020  1.484
 XO3  C7   O8    single    1.343  0.020  1.343
 XO3  C7   C11   double    1.346  0.020  1.346
 XO3  O8   N9    single    1.374  0.020  1.374
 XO3  N9   C10   single    1.382  0.020  1.382
 XO3  C10  C11   single    1.446  0.020  1.446
 XO3  C10  O12   double    1.220  0.020  1.220
 XO3  C13  C14   single    1.503  0.020  1.503
 XO3  C14  C15   aromatic  1.393  0.020  1.393
 XO3  C14  C19   aromatic  1.395  0.020  1.395
 XO3  C15  C16   aromatic  1.390  0.020  1.390
 XO3  C16  C17   aromatic  1.388  0.020  1.388
 XO3  C17  C18   aromatic  1.390  0.020  1.390
 XO3  C18  C19   aromatic  1.387  0.020  1.387
 XO3  C1   H11C  single    0.970  0.020  1.090
 XO3  C1   H12C  single    0.970  0.020  1.090
 XO3  C2   H21C  single    0.970  0.020  1.090
 XO3  C2   H22C  single    0.970  0.020  1.090
 XO3  C6   H6    single    0.970  0.020  1.090
 XO3  N3   H3    single    0.890  0.020  1.040
 XO3  C4   H4    single    0.970  0.020  1.090
 XO3  C5   H51C  single    0.970  0.020  1.090
 XO3  C5   H52C  single    0.970  0.020  1.090
 XO3  C13  H131  single    0.970  0.020  1.090
 XO3  C13  H132  single    0.970  0.020  1.090
 XO3  C11  H11   single    0.930  0.020  1.080
 XO3  N9   H9    single    0.890  0.020  1.040
 XO3  C15  H15   single    0.930  0.020  1.080
 XO3  C19  H19   single    0.930  0.020  1.080
 XO3  C16  H16   single    0.930  0.020  1.080
 XO3  C17  H17   single    0.930  0.020  1.080
 XO3  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
 XO3  H12C  C1   H11C  107.61  3.000
 XO3  H12C  C1   C6    110.17  3.000
 XO3  H11C  C1   C6    110.25  3.000
 XO3  H12C  C1   C2    109.83  3.000
 XO3  H11C  C1   C2    109.48  3.000
 XO3  C6    C1   C2    109.47  3.000
 XO3  H22C  C2   H21C  106.91  3.000
 XO3  H22C  C2   N3    108.84  3.000
 XO3  H21C  C2   N3    112.42  3.000
 XO3  H22C  C2   C1    109.71  3.000
 XO3  H21C  C2   C1    108.70  3.000
 XO3  N3    C2   C1    110.19  3.000
 XO3  H3    N3   C4    109.35  3.000
 XO3  H3    N3   C2    108.91  3.000
 XO3  C4    N3   C2    112.31  3.000
 XO3  H4    C4   C13   107.81  3.000
 XO3  H4    C4   C5    107.61  3.000
 XO3  C13   C4   C5    110.25  3.000
 XO3  H4    C4   N3    111.42  3.000
 XO3  C13   C4   N3    110.47  3.000
 XO3  C5    C4   N3    109.23  3.000
 XO3  H52C  C5   H51C  107.56  3.000
 XO3  H52C  C5   C6    110.20  3.000
 XO3  H51C  C5   C6    110.14  3.000
 XO3  H52C  C5   C4    108.84  3.000
 XO3  H51C  C5   C4    109.40  3.000
 XO3  C6    C5   C4    110.64  3.000
 XO3  H6    C6   C7    106.02  3.000
 XO3  H6    C6   C5    108.24  3.000
 XO3  C7    C6   C5    112.02  3.000
 XO3  H6    C6   C1    108.04  3.000
 XO3  C7    C6   C1    112.19  3.000
 XO3  C5    C6   C1    110.10  3.000
 XO3  C11   C7   O8    111.61  3.000
 XO3  C11   C7   C6    131.88  3.000
 XO3  O8    C7   C6    116.50  3.000
 XO3  N9    O8   C7    106.37  3.000
 XO3  H9    N9   C10   123.84  3.000
 XO3  H9    N9   O8    111.81  3.000
 XO3  C10   N9   O8    110.48  3.000
 XO3  O12   C10  C11   131.97  3.000
 XO3  O12   C10  N9    124.00  3.000
 XO3  C11   C10  N9    104.01  3.000
 XO3  H11   C11  C10   126.29  3.000
 XO3  H11   C11  C7    126.79  3.000
 XO3  C10   C11  C7    106.90  3.000
 XO3  H132  C13  H131  107.07  3.000
 XO3  H132  C13  C14   109.72  3.000
 XO3  H131  C13  C14   110.01  3.000
 XO3  H132  C13  C4    108.14  3.000
 XO3  H131  C13  C4    108.84  3.000
 XO3  C14   C13  C4    112.89  3.000
 XO3  C19   C14  C15   118.41  3.000
 XO3  C19   C14  C13   120.48  3.000
 XO3  C15   C14  C13   121.09  3.000
 XO3  H15   C15  C16   119.67  3.000
 XO3  H15   C15  C14   119.43  3.000
 XO3  C16   C15  C14   120.90  3.000
 XO3  H16   C16  C17   120.06  3.000
 XO3  H16   C16  C15   119.83  3.000
 XO3  C17   C16  C15   120.12  3.000
 XO3  H17   C17  C18   120.20  3.000
 XO3  H17   C17  C16   120.25  3.000
 XO3  C18   C17  C16   119.55  3.000
 XO3  H18   C18  C19   119.87  3.000
 XO3  H18   C18  C17   120.01  3.000
 XO3  C19   C18  C17   120.12  3.000
 XO3  H19   C19  C18   119.71  3.000
 XO3  H19   C19  C14   119.37  3.000
 XO3  C18   C19  C14   120.91  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
 XO3  CONST_01  C17  C16  C15  C14    0.00   0.0  0
 XO3  CONST_02  C17  C18  C19  C14    0.00   0.0  0
 XO3  CONST_03  C18  C19  C14  C15    0.00   0.0  0
 XO3  CONST_04  C18  C17  C16  C15    0.00   0.0  0
 XO3  CONST_05  C19  C14  C15  C16    0.00   0.0  0
 XO3  CONST_06  C19  C18  C17  C16    0.00   0.0  0
 XO3  CONST_07  C11  C10  N9   O8     0.00   0.0  0
 XO3  CONST_08  C16  C15  C14  C13  180.00   0.0  0
 XO3  CONST_09  C18  C19  C14  C13  180.00   0.0  0
 XO3  CONST_10  O12  C10  N9   O8   180.00   0.0  0
 XO3  CONST_11  H16  C16  C15  C14  180.00   0.0  0
 XO3  CONST_12  H18  C18  C19  C14  180.00   0.0  0
 XO3  CONST_13  H19  C19  C14  C15  180.00   0.0  0
 XO3  CONST_14  H17  C17  C16  C15  180.00   0.0  0
 XO3  CONST_15  H15  C15  C16  C17  180.00   0.0  0
 XO3  Var_01    C4   N3   C2   C1    62.53  30.0  1
 XO3  Var_02    C6   C1   C2   N3   -57.60  30.0  1
 XO3  Var_03    C15  C14  C13  C4    98.92  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
 XO3  chir_01  C4  N3  C5  C13  positiv
 XO3  chir_02  C6  C7  C5  C1   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
 XO3  plan-1  C6   0.020
 XO3  plan-1  C7   0.020
 XO3  plan-1  O8   0.020
 XO3  plan-1  N9   0.020
 XO3  plan-1  C10  0.020
 XO3  plan-1  C11  0.020
 XO3  plan-1  O12  0.020
 XO3  plan-1  H11  0.020
 XO3  plan-1  H9   0.020
 XO3  plan-2  C13  0.020
 XO3  plan-2  C14  0.020
 XO3  plan-2  C15  0.020
 XO3  plan-2  C16  0.020
 XO3  plan-2  C17  0.020
 XO3  plan-2  C18  0.020
 XO3  plan-2  C19  0.020
 XO3  plan-2  H15  0.020
 XO3  plan-2  H19  0.020
 XO3  plan-2  H16  0.020
 XO3  plan-2  H17  0.020
 XO3  plan-2  H18  0.020

