# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 04:59:52 2022
#   Inital geometry file: a 123 line input string
#   Ligand name: 6-{4-[(2-chloro-4-fluorophenoxy)methyl]piperidine-1-carbonyl}-2H-1,4-benzoxazin-3(4H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc(OCC2CCN(CC2)C(=O)c3ccc4OCC(=O)Nc4c3)c(Cl)c1
#
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
 XPD  XPD  6-{4-[(2-chloro-4-fluorophenoxy)methyl]piperidine-1-carbonyl}-2H-1,4-benzoxazin-3(4H)-one  ligand  49  29  .  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_XPD
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
 XPD  C4    C   CR16  0  -0.393  -30.0397   9.9571  -61.4352
 XPD  C5    C   CR16  0  -0.349  -19.2397  11.9342  -57.5145
 XPD  C6    C   CR16  0  -0.364  -31.1454  11.0994  -59.6237
 XPD  C7    C   CR6   0  -0.077  -20.4800  11.4542  -57.9241
 XPD  C8    C   CR66  0   0.332  -18.0847  11.5117  -58.1497
 XPD  C10   C   CR6   0   0.466  -28.7383  11.2904  -59.8913
 XPD  C13   C   CR6   0   0.480  -15.6757  11.4053  -58.1754
 XPD  C15   C   C     0  -0.311  -15.8748  10.1405  -58.9864
 XPD  C17   C   CH2   0  -0.419  -25.1927  11.8270  -57.8169
 XPD  C20   C   CH1   0  -0.295  -25.2783  12.2575  -59.2792
 XPD  C21   C   CH2   0  -0.161  -26.3739  11.5330  -60.0355
 XPD  C1    C   CR16  0  -0.270  -20.5470  10.5144  -58.9476
 XPD  C2    C   CR16  0  -0.345  -19.3885  10.0627  -59.5636
 XPD  C3    C   CR16  0  -0.372  -28.8182  10.4622  -61.0069
 XPD  C9    C   CR66  0   0.340  -18.1607  10.5681  -59.1748
 XPD  C11   C   CR6   0   0.504  -31.1823  10.2842  -60.7396
 XPD  C12   C   CR6   0  -0.147  -29.9223  11.5927  -59.2094
 XPD  C16   C   CH2   0  -0.426  -23.9337  12.0306  -59.9680
 XPD  C18   C   CH2   0  -0.318  -22.8125  12.7077  -59.1950
 XPD  C19   C   CH2   0  -0.307  -24.0314  12.5056  -57.1041
 XPD  N22   N   NR16  0  -0.720  -16.8287  12.0161  -57.8170
 XPD  N23   N   NT    0  -0.452  -22.7862  12.2564  -57.8126
 XPD  O24   O   O     0  -0.444  -14.5756  11.7960  -57.8442
 XPD  O25   O   O     0  -0.483  -21.6453  11.7891  -55.9151
 XPD  O26   O   O     0  -0.469  -17.0296  10.1788  -59.8041
 XPD  O27   O   O2    0  -0.462  -27.6129  11.8307  -59.4103
 XPD  F28   F   F     0  -0.315  -32.3687   9.8062  -61.1481
 XPD  CL29  CL  CL    0  -0.100  -29.8422  12.6108  -57.8173
 XPD  H1    H   HCR6  0   0.287  -30.0874   9.3160  -62.3053
 XPD  H3    H   HCR6  0   0.299  -32.0514  11.3452  -59.0859
 XPD  H4    H   H     0   0.270  -15.9159   9.2902  -58.2931
 XPD  H5    H   H     0   0.284  -15.0205   9.9992  -59.6450
 XPD  H6    H   HCH2  0   0.246  -26.1140  12.0707  -57.2855
 XPD  H7    H   HCH2  0   0.225  -25.0649  10.7407  -57.7614
 XPD  H8    H   HCH1  0   0.239  -25.4927  13.3335  -59.3133
 XPD  H9    H   HCH2  0   0.226  -26.1914  10.4513  -60.0219
 XPD  H10   H   HCH2  0   0.239  -26.3889  11.8585  -61.0821
 XPD  H11   H   HCR6  0   0.275  -21.5011  10.1081  -59.2579
 XPD  H12   H   HCR6  0   0.275  -19.4370   9.3240  -60.3530
 XPD  H13   H   HCR6  0   0.299  -27.9296  10.1984  -61.5635
 XPD  H14   H   HCH2  0   0.234  -23.7277  10.9580  -60.0474
 XPD  H15   H   HCH2  0   0.247  -23.9545  12.4309  -60.9842
 XPD  H16   H   HCH2  0   0.275  -21.8523  12.5325  -59.6705
 XPD  H17   H   HCH2  0   0.249  -22.9746  13.7921  -59.1977
 XPD  H18   H   HCH2  0   0.265  -23.9440  12.1410  -56.0846
 XPD  H19   H   HCH2  0   0.235  -24.2059  13.5866  -57.0512
 XPD  H20   H   HNR6  0   0.416  -16.7712  12.8256  -57.2130
 XPD  C14   C   C     0   0.514  -21.6869  11.8603  -57.1373
 XPD  H2    H   HCR6  0   0.277  -19.1677  12.6545  -56.7084

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
 XPD  C4   C3    aromatic  1.389  0.020  1.389
 XPD  C4   C11   aromatic  1.377  0.020  1.377
 XPD  F28  C11   single    1.343  0.020  1.343
 XPD  C3   C10   aromatic  1.392  0.020  1.392
 XPD  C11  C6    aromatic  1.382  0.020  1.382
 XPD  C16  C20   single    1.528  0.020  1.528
 XPD  C16  C18   single    1.521  0.020  1.521
 XPD  C10  O27   single    1.338  0.020  1.338
 XPD  C10  C12   aromatic  1.399  0.020  1.399
 XPD  C21  O27   single    1.419  0.020  1.419
 XPD  C21  C20   single    1.516  0.020  1.516
 XPD  O26  C9    single    1.352  0.020  1.352
 XPD  O26  C15   single    1.416  0.020  1.416
 XPD  C6   C12   aromatic  1.382  0.020  1.382
 XPD  C2   C9    aromatic  1.384  0.020  1.384
 XPD  C2   C1    aromatic  1.388  0.020  1.388
 XPD  C12  CL29  single    1.726  0.020  1.726
 XPD  C20  C17   single    1.527  0.020  1.527
 XPD  C18  N23   single    1.455  0.020  1.455
 XPD  C9   C8    aromatic  1.395  0.020  1.395
 XPD  C15  C13   single    1.516  0.020  1.516
 XPD  C1   C7    aromatic  1.391  0.020  1.391
 XPD  C13  O24   double    1.213  0.020  1.213
 XPD  C13  N22   single    1.353  0.020  1.353
 XPD  C8   N22   single    1.394  0.020  1.394
 XPD  C8   C5    aromatic  1.384  0.020  1.384
 XPD  C7   C5    aromatic  1.392  0.020  1.392
 XPD  C7   C14   single    1.497  0.020  1.497
 XPD  N23  C19   single    1.454  0.020  1.454
 XPD  N23  C14   single    1.350  0.020  1.350
 XPD  C17  C19   single    1.522  0.020  1.522
 XPD  C14  O25   double    1.225  0.020  1.225
 XPD  C4   H1    single    0.930  0.020  1.080
 XPD  C5   H2    single    0.930  0.020  1.080
 XPD  C6   H3    single    0.930  0.020  1.080
 XPD  C15  H4    single    0.970  0.020  1.090
 XPD  C15  H5    single    0.970  0.020  1.090
 XPD  C17  H6    single    0.970  0.020  1.090
 XPD  C17  H7    single    0.970  0.020  1.090
 XPD  C20  H8    single    0.970  0.020  1.090
 XPD  C21  H9    single    0.970  0.020  1.090
 XPD  C21  H10   single    0.970  0.020  1.090
 XPD  C1   H11   single    0.930  0.020  1.080
 XPD  C2   H12   single    0.930  0.020  1.080
 XPD  C3   H13   single    0.930  0.020  1.080
 XPD  C16  H14   single    0.970  0.020  1.090
 XPD  C16  H15   single    0.970  0.020  1.090
 XPD  C18  H16   single    0.970  0.020  1.090
 XPD  C18  H17   single    0.970  0.020  1.090
 XPD  C19  H18   single    0.970  0.020  1.090
 XPD  C19  H19   single    0.970  0.020  1.090
 XPD  N22  H20   single    0.860  0.020  1.020

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
 XPD  H1    C4   C11  120.69  3.000
 XPD  H1    C4   C3   120.14  3.000
 XPD  C11   C4   C3   119.17  3.000
 XPD  H2    C5   C8   119.27  3.000
 XPD  H2    C5   C7   120.50  3.000
 XPD  C8    C5   C7   120.22  3.000
 XPD  H3    C6   C12  120.72  3.000
 XPD  H3    C6   C11  120.85  3.000
 XPD  C12   C6   C11  118.43  3.000
 XPD  C14   C7   C1   122.09  3.000
 XPD  C14   C7   C5   118.06  3.000
 XPD  C1    C7   C5   119.50  3.000
 XPD  N22   C8   C9   117.98  3.000
 XPD  N22   C8   C5   122.14  3.000
 XPD  C9    C8   C5   119.87  3.000
 XPD  O27   C10  C12  116.70  3.000
 XPD  C12   C10  C3   118.07  3.000
 XPD  O27   C10  C3   125.23  3.000
 XPD  O24   C13  N22  123.71  3.000
 XPD  N22   C13  C15  113.98  3.000
 XPD  O24   C13  C15  122.26  3.000
 XPD  H5    C15  H4   108.13  3.000
 XPD  H5    C15  O26  107.12  3.000
 XPD  H4    C15  O26  110.80  3.000
 XPD  H5    C15  C13  109.22  3.000
 XPD  H4    C15  C13  108.26  3.000
 XPD  O26   C15  C13  113.19  3.000
 XPD  H7    C17  H6   107.17  3.000
 XPD  H7    C17  C19  109.23  3.000
 XPD  H6    C17  C19  108.45  3.000
 XPD  H7    C17  C20  109.56  3.000
 XPD  H6    C17  C20  110.86  3.000
 XPD  C19   C17  C20  111.45  3.000
 XPD  H8    C20  C16  107.67  3.000
 XPD  H8    C20  C21  108.18  3.000
 XPD  C16   C20  C21  109.89  3.000
 XPD  H8    C20  C17  108.49  3.000
 XPD  C21   C20  C17  112.56  3.000
 XPD  C16   C20  C17  109.91  3.000
 XPD  H10   C21  H9   107.87  3.000
 XPD  H10   C21  O27  110.27  3.000
 XPD  H9    C21  O27  110.28  3.000
 XPD  H10   C21  C20  110.14  3.000
 XPD  H9    C21  C20  110.18  3.000
 XPD  O27   C21  C20  108.12  3.000
 XPD  H11   C1   C2   119.11  3.000
 XPD  H11   C1   C7   120.46  3.000
 XPD  C2    C1   C7   120.42  3.000
 XPD  H12   C2   C9   119.61  3.000
 XPD  H12   C2   C1   120.57  3.000
 XPD  C9    C2   C1   119.82  3.000
 XPD  H13   C3   C10  120.71  3.000
 XPD  H13   C3   C4   118.37  3.000
 XPD  C10   C3   C4   120.93  3.000
 XPD  O26   C9   C2   120.44  3.000
 XPD  C2    C9   C8   120.12  3.000
 XPD  O26   C9   C8   119.42  3.000
 XPD  F28   C11  C6   118.63  3.000
 XPD  C6    C11  C4   121.71  3.000
 XPD  F28   C11  C4   119.66  3.000
 XPD  CL29  C12  C10  118.75  3.000
 XPD  CL29  C12  C6   119.55  3.000
 XPD  C10   C12  C6   121.70  3.000
 XPD  H15   C16  H14  107.16  3.000
 XPD  H15   C16  C18  108.89  3.000
 XPD  H14   C16  C18  109.53  3.000
 XPD  H15   C16  C20  110.38  3.000
 XPD  H14   C16  C20  110.11  3.000
 XPD  C18   C16  C20  110.71  3.000
 XPD  H17   C18  H16  106.81  3.000
 XPD  H17   C18  N23  108.17  3.000
 XPD  H16   C18  N23  110.50  3.000
 XPD  H17   C18  C16  109.28  3.000
 XPD  H16   C18  C16  110.95  3.000
 XPD  N23   C18  C16  110.99  3.000
 XPD  H19   C19  H18  107.37  3.000
 XPD  H19   C19  N23  109.20  3.000
 XPD  H18   C19  N23  109.32  3.000
 XPD  H19   C19  C17  109.92  3.000
 XPD  H18   C19  C17  110.57  3.000
 XPD  N23   C19  C17  110.41  3.000
 XPD  H20   N22  C13  118.09  3.000
 XPD  H20   N22  C8   118.90  3.000
 XPD  C13   N22  C8   122.78  3.000
 XPD  C19   N23  C18  113.23  3.000
 XPD  C19   N23  C14  120.27  3.000
 XPD  C18   N23  C14  125.55  3.000
 XPD  C9    O26  C15  114.93  3.000
 XPD  C21   O27  C10  119.42  3.000
 XPD  O25   C14  N23  122.95  3.000
 XPD  O25   C14  C7   118.77  3.000
 XPD  N23   C14  C7   118.25  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
 XPD  CONST_01  C12   C10  C3   C4      0.00   0.0  0
 XPD  CONST_02  C12   C6   C11  C4      0.00   0.0  0
 XPD  CONST_03  C2    C9   C8   C5      0.00   0.0  0
 XPD  CONST_04  C2    C1   C7   C5      0.00   0.0  0
 XPD  CONST_05  C3    C4   C11  C6      0.00   0.0  0
 XPD  CONST_06  C3    C10  C12  C6      0.00   0.0  0
 XPD  CONST_07  C9    C2   C1   C7      0.00   0.0  0
 XPD  CONST_08  C9    C8   C5   C7      0.00   0.0  0
 XPD  CONST_09  C1    C2   C9   C8      0.00   0.0  0
 XPD  CONST_10  C1    C7   C5   C8      0.00   0.0  0
 XPD  CONST_11  C11   C4   C3   C10     0.00   0.0  0
 XPD  CONST_12  C11   C6   C12  C10     0.00   0.0  0
 XPD  CONST_13  C15   C13  N22  C8      0.00   0.0  0
 XPD  CONST_14  O27   C10  C3   C4    180.00   0.0  0
 XPD  CONST_15  O27   C10  C12  C6    180.00   0.0  0
 XPD  CONST_16  C14   C7   C5   C8    180.00   0.0  0
 XPD  CONST_17  C14   C7   C1   C2    180.00   0.0  0
 XPD  CONST_18  F28   C11  C4   C3    180.00   0.0  0
 XPD  CONST_19  CL29  C12  C10  C3    180.00   0.0  0
 XPD  CONST_20  CL29  C12  C6   C11   180.00   0.0  0
 XPD  CONST_21  F28   C11  C6   C12   180.00   0.0  0
 XPD  CONST_23  C19   N23  C14  C7    180.00   0.0  0
 XPD  CONST_24  O24   C13  N22  C8    180.00   0.0  0
 XPD  CONST_25  H3    C6   C11  C4    180.00   0.0  0
 XPD  CONST_26  H11   C1   C7   C5    180.00   0.0  0
 XPD  CONST_27  H1    C4   C11  C6    180.00   0.0  0
 XPD  CONST_28  H12   C2   C1   C7    180.00   0.0  0
 XPD  CONST_29  H2    C5   C7   C1    180.00   0.0  0
 XPD  CONST_30  H13   C3   C4   C11   180.00   0.0  0
 XPD  CONST_31  H20   N22  C13  C15   180.00   0.0  0
 XPD  CONST_33  O25   C14  N23  C19     0.00   0.0  0
 XPD  Var_01    C13   N22  C8   C5    163.42  30.0  1
 XPD  Var_02    C2    C9   O26  C15  -147.99  30.0  1
 XPD  Var_03    C18   N23  C19  C17    57.86  30.0  1
 XPD  Var_04    N23   C18  C16  C20    55.62  30.0  1
 XPD  Var_05    N23   C19  C17  C20   -55.20  30.0  1
 XPD  Var_06    C19   N23  C18  C16   -58.47  30.0  1
 XPD  Var_07    O26   C15  C13  N22    31.72  30.0  1
 XPD  Var_08    N23   C14  C7   C5    134.97  30.0  2
 XPD  Var_09    H4    C15  O26  C9     72.71  30.0  1
 XPD  Var_10    C20   C21  O27  C10  -179.25  30.0  1
 XPD  Var_11    C3    C10  O27  C21    -1.83  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
 XPD  chir_01  C20  C16  C21  C17  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
 XPD  plan-1  C4    0.020
 XPD  plan-1  C6    0.020
 XPD  plan-1  C10   0.020
 XPD  plan-1  C3    0.020
 XPD  plan-1  C11   0.020
 XPD  plan-1  C12   0.020
 XPD  plan-1  O27   0.020
 XPD  plan-1  F28   0.020
 XPD  plan-1  CL29  0.020
 XPD  plan-1  H1    0.020
 XPD  plan-1  H3    0.020
 XPD  plan-1  H13   0.020
 XPD  plan-2  C5    0.020
 XPD  plan-2  C7    0.020
 XPD  plan-2  C8    0.020
 XPD  plan-2  C1    0.020
 XPD  plan-2  C2    0.020
 XPD  plan-2  C9    0.020
 XPD  plan-2  N22   0.020
 XPD  plan-2  O26   0.020
 XPD  plan-2  H11   0.020
 XPD  plan-2  H12   0.020
 XPD  plan-2  C14   0.020
 XPD  plan-2  H2    0.020
 XPD  plan-3  C7    0.020
 XPD  plan-3  C18   0.020
 XPD  plan-3  C19   0.020
 XPD  plan-3  N23   0.020
 XPD  plan-3  O25   0.020
 XPD  plan-3  C14   0.020
 XPD  plan-4  C8    0.020
 XPD  plan-4  C13   0.020
 XPD  plan-4  C15   0.020
 XPD  plan-4  N22   0.020
 XPD  plan-4  O24   0.020
 XPD  plan-4  H20   0.020

