# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 18 08:32:07 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: (3S)-N-(9H-xanthen-9-ylmethyl)piperidine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NCC1c2ccccc2Oc3ccccc13)[C@H]4CCCNC4
#
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
 0ME  0ME  (3S)-N-(9H-xanthen-9-ylmethyl)piperidine-3-carboxamide  ligand  46  24  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_0ME
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
 0ME  C1   C  CR66  0   0.088  -1.0649  -0.7754  -0.6429
 0ME  C2   C  CR66  0   0.346  -1.6991  -1.3518   0.4504
 0ME  O3   O  O     0  -0.506  -2.6679  -0.6798   1.1393
 0ME  C4   C  CR16  0  -0.389  -1.3685   0.6516  -0.9916
 0ME  C5   C  CR16  0  -0.250   0.2029  -2.8149  -0.9187
 0ME  C6   C  CR16  0  -0.268  -0.4226  -3.3584   0.1963
 0ME  C7   C  CR16  0  -0.344  -1.3868  -2.6337   0.8798
 0ME  C8   C  CR16  0  -0.324  -0.1235  -1.5317  -1.3316
 0ME  C9   C  CR66  0   0.077  -2.7769   0.9819  -0.5885
 0ME  C10  C  CR66  0   0.337  -3.3368   0.3213   0.4993
 0ME  C11  C  CR16  0  -0.341  -4.5999   0.6489   0.9741
 0ME  C12  C  CR16  0  -0.265  -5.3185   1.6551   0.3474
 0ME  C13  C  CR16  0  -0.255  -4.7861   2.3167  -0.7530
 0ME  C14  C  CR16  0  -0.326  -3.5225   1.9762  -1.2123
 0ME  C15  C  CH2   0  -0.258  -0.4045   1.6194  -0.2646
 0ME  N16  N  NH1   0  -0.638   0.9795   1.3242  -0.5137
 0ME  C17  C  C     0   0.594   1.7749   0.6699   0.3558
 0ME  O18  O  O     0  -0.495   1.4070   0.3394   1.4747
 0ME  C19  C  CH1   0  -0.408   3.1822   0.3980  -0.1291
 0ME  C20  C  CH2   0  -0.422   4.1822   1.3036   0.6004
 0ME  C21  C  CH2   0  -0.447   5.6109   0.9594   0.1934
 0ME  C22  C  CH2   0  -0.314   5.8857  -0.5282   0.3923
 0ME  N23  N  NH1   0  -0.579   4.9232  -1.3944  -0.2701
 0ME  C24  C  CH2   0  -0.288   3.5561  -1.0751   0.0961
 0ME  H1   H  HCR6  0   0.279  -1.2489   0.8007  -2.0687
 0ME  H2   H  HCR6  0   0.254   0.9429  -3.3880  -1.4614
 0ME  H3   H  HCR6  0   0.258  -0.1735  -4.3581   0.5271
 0ME  H4   H  HCR6  0   0.265  -1.9001  -3.0578   1.7337
 0ME  H5   H  HCR6  0   0.255   0.3652  -1.1034  -2.1984
 0ME  H6   H  HCR6  0   0.267  -5.0132   0.1141   1.8200
 0ME  H7   H  HCR6  0   0.262  -6.3035   1.9126   0.7135
 0ME  H8   H  HCR6  0   0.256  -5.3523   3.0943  -1.2478
 0ME  H9   H  HCR6  0   0.258  -3.0993   2.4938  -2.0654
 0ME  H10  H  HCH2  0   0.264  -0.6210   2.6373  -0.5940
 0ME  H11  H  HCH2  0   0.252  -0.5812   1.5789   0.8092
 0ME  H12  H  HNH1  0   0.399   1.3522   1.5608  -1.4189
 0ME  H13  H  HCH1  0   0.243   3.2492   0.6077  -1.2035
 0ME  H14  H  HCH2  0   0.240   3.9674   2.3533   0.3859
 0ME  H15  H  HCH2  0   0.223   4.0661   1.1707   1.6808
 0ME  H16  H  HCH2  0   0.216   5.7684   1.2221  -0.8580
 0ME  H17  H  HCH2  0   0.230   6.3212   1.5522   0.7750
 0ME  H18  H  HCH2  0   0.235   6.8859  -0.7832   0.0365
 0ME  H19  H  HCH2  0   0.214   5.8664  -0.7576   1.4637
 0ME  H20  H  HNH1  0   0.339   5.0300  -1.3022  -1.2742
 0ME  H22  H  HCH2  0   0.218   3.4172  -1.3184   1.1534
 0ME  H23  H  HCH2  0   0.246   2.8824  -1.7243  -0.4668

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
 0ME  C20  C21  single    1.525  0.020  1.525
 0ME  C20  C19  single    1.534  0.020  1.534
 0ME  O18  C17  double    1.223  0.020  1.223
 0ME  C21  C22  single    1.526  0.020  1.526
 0ME  C17  C19  single    1.513  0.020  1.513
 0ME  C17  N16  single    1.348  0.020  1.348
 0ME  C19  C24  single    1.536  0.020  1.536
 0ME  N16  C15  single    1.437  0.020  1.437
 0ME  C15  C4   single    1.547  0.020  1.547
 0ME  C22  N23  single    1.454  0.020  1.454
 0ME  C13  C14  aromatic  1.387  0.020  1.387
 0ME  C13  C12  aromatic  1.390  0.020  1.390
 0ME  C14  C9   aromatic  1.391  0.020  1.391
 0ME  C24  N23  single    1.451  0.020  1.451
 0ME  C12  C11  aromatic  1.386  0.020  1.386
 0ME  C9   C4   single    1.502  0.020  1.502
 0ME  C9   C10  aromatic  1.390  0.020  1.390
 0ME  C4   C1   single    1.500  0.020  1.500
 0ME  C11  C10  aromatic  1.389  0.020  1.389
 0ME  C10  O3   single    1.364  0.020  1.364
 0ME  O3   C2   single    1.366  0.020  1.366
 0ME  C1   C2   aromatic  1.389  0.020  1.389
 0ME  C1   C8   aromatic  1.390  0.020  1.390
 0ME  C2   C7   aromatic  1.388  0.020  1.388
 0ME  C8   C5   aromatic  1.387  0.020  1.387
 0ME  C7   C6   aromatic  1.386  0.020  1.386
 0ME  C5   C6   aromatic  1.389  0.020  1.389
 0ME  C4   H1   single    0.970  0.020  1.090
 0ME  C5   H2   single    0.930  0.020  1.080
 0ME  C6   H3   single    0.930  0.020  1.080
 0ME  C7   H4   single    0.930  0.020  1.080
 0ME  C8   H5   single    0.930  0.020  1.080
 0ME  C11  H6   single    0.930  0.020  1.080
 0ME  C12  H7   single    0.930  0.020  1.080
 0ME  C13  H8   single    0.930  0.020  1.080
 0ME  C14  H9   single    0.930  0.020  1.080
 0ME  C15  H10  single    0.970  0.020  1.090
 0ME  C15  H11  single    0.970  0.020  1.090
 0ME  N16  H12  single    0.860  0.020  1.020
 0ME  C19  H13  single    0.970  0.020  1.090
 0ME  C20  H14  single    0.970  0.020  1.090
 0ME  C20  H15  single    0.970  0.020  1.090
 0ME  C21  H16  single    0.970  0.020  1.090
 0ME  C21  H17  single    0.970  0.020  1.090
 0ME  C22  H18  single    0.970  0.020  1.090
 0ME  C22  H19  single    0.970  0.020  1.090
 0ME  N23  H20  single    0.890  0.020  1.040
 0ME  C24  H22  single    0.970  0.020  1.090
 0ME  C24  H23  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
 0ME  C8   C1   C4   122.65  3.000
 0ME  C8   C1   C2   118.25  3.000
 0ME  C4   C1   C2   119.03  3.000
 0ME  C7   C2   O3   117.27  3.000
 0ME  C7   C2   C1   121.61  3.000
 0ME  O3   C2   C1   121.12  3.000
 0ME  C10  O3   C2   118.20  3.000
 0ME  H1   C4   C15  108.01  3.000
 0ME  H1   C4   C9   109.69  3.000
 0ME  C15  C4   C9   108.70  3.000
 0ME  H1   C4   C1   109.66  3.000
 0ME  C9   C4   C1   109.67  3.000
 0ME  C15  C4   C1   111.08  3.000
 0ME  H2   C5   C8   120.12  3.000
 0ME  H2   C5   C6   120.22  3.000
 0ME  C8   C5   C6   119.66  3.000
 0ME  H3   C6   C7   119.49  3.000
 0ME  H3   C6   C5   120.21  3.000
 0ME  C7   C6   C5   120.29  3.000
 0ME  H4   C7   C6   120.92  3.000
 0ME  H4   C7   C2   119.95  3.000
 0ME  C6   C7   C2   119.14  3.000
 0ME  H5   C8   C5   119.86  3.000
 0ME  H5   C8   C1   119.12  3.000
 0ME  C5   C8   C1   121.02  3.000
 0ME  C14  C9   C10  118.35  3.000
 0ME  C10  C9   C4   118.89  3.000
 0ME  C14  C9   C4   122.66  3.000
 0ME  C11  C10  C9   121.45  3.000
 0ME  C11  C10  O3   117.32  3.000
 0ME  C9   C10  O3   121.23  3.000
 0ME  H6   C11  C12  120.92  3.000
 0ME  H6   C11  C10  119.86  3.000
 0ME  C12  C11  C10  119.22  3.000
 0ME  H7   C12  C13  120.22  3.000
 0ME  H7   C12  C11  119.46  3.000
 0ME  C13  C12  C11  120.32  3.000
 0ME  H8   C13  C14  120.13  3.000
 0ME  H8   C13  C12  120.25  3.000
 0ME  C14  C13  C12  119.62  3.000
 0ME  H9   C14  C13  119.94  3.000
 0ME  H9   C14  C9   119.03  3.000
 0ME  C13  C14  C9   121.03  3.000
 0ME  H11  C15  H10  107.46  3.000
 0ME  H11  C15  N16  108.64  3.000
 0ME  H10  C15  N16  109.29  3.000
 0ME  H11  C15  C4   109.81  3.000
 0ME  H10  C15  C4   108.53  3.000
 0ME  N16  C15  C4   112.96  3.000
 0ME  H12  N16  C17  118.39  3.000
 0ME  H12  N16  C15  117.64  3.000
 0ME  C17  N16  C15  123.80  3.000
 0ME  C19  C17  O18  121.62  3.000
 0ME  C19  C17  N16  115.42  3.000
 0ME  O18  C17  N16  122.94  3.000
 0ME  H13  C19  C24  108.18  3.000
 0ME  H13  C19  C20  108.25  3.000
 0ME  C24  C19  C20  109.74  3.000
 0ME  H13  C19  C17  109.66  3.000
 0ME  C24  C19  C17  110.59  3.000
 0ME  C20  C19  C17  110.36  3.000
 0ME  H15  C20  H14  106.83  3.000
 0ME  H15  C20  C21  109.60  3.000
 0ME  H14  C20  C21  110.40  3.000
 0ME  H15  C20  C19  109.18  3.000
 0ME  H14  C20  C19  110.22  3.000
 0ME  C21  C20  C19  110.52  3.000
 0ME  H17  C21  H16  106.70  3.000
 0ME  H17  C21  C22  110.03  3.000
 0ME  H16  C21  C22  109.46  3.000
 0ME  H17  C21  C20  110.15  3.000
 0ME  H16  C21  C20  109.69  3.000
 0ME  C22  C21  C20  110.73  3.000
 0ME  H19  C22  H18  106.61  3.000
 0ME  H19  C22  N23  108.00  3.000
 0ME  H18  C22  N23  108.59  3.000
 0ME  H19  C22  C21  109.17  3.000
 0ME  H18  C22  C21  110.50  3.000
 0ME  N23  C22  C21  113.71  3.000
 0ME  H20  N23  C24  109.22  3.000
 0ME  H20  N23  C22  109.10  3.000
 0ME  C24  N23  C22  112.18  3.000
 0ME  H23  C24  H22  106.72  3.000
 0ME  H23  C24  N23  108.69  3.000
 0ME  H22  C24  N23  108.34  3.000
 0ME  H23  C24  C19  110.15  3.000
 0ME  H22  C24  C19  108.91  3.000
 0ME  N23  C24  C19  113.79  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
 0ME  CONST_01  C6   C7   C2   C1      0.00   0.0  0
 0ME  CONST_02  C6   C5   C8   C1      0.00   0.0  0
 0ME  CONST_03  C5   C8   C1   C2      0.00   0.0  0
 0ME  CONST_04  C5   C6   C7   C2      0.00   0.0  0
 0ME  CONST_05  C8   C1   C2   C7      0.00   0.0  0
 0ME  CONST_06  C8   C5   C6   C7      0.00   0.0  0
 0ME  CONST_07  C12  C13  C14  C9      0.00   0.0  0
 0ME  CONST_08  C12  C11  C10  C9      0.00   0.0  0
 0ME  CONST_09  C13  C14  C9   C10     0.00   0.0  0
 0ME  CONST_10  C13  C12  C11  C10     0.00   0.0  0
 0ME  CONST_11  C14  C13  C12  C11     0.00   0.0  0
 0ME  CONST_12  C14  C9   C10  C11     0.00   0.0  0
 0ME  CONST_13  H4   C7   C2   C1    180.00   0.0  0
 0ME  CONST_14  H2   C5   C8   C1    180.00   0.0  0
 0ME  CONST_15  H5   C8   C1   C2    180.00   0.0  0
 0ME  CONST_16  H3   C6   C7   C2    180.00   0.0  0
 0ME  CONST_17  H6   C11  C10  O3      0.00   0.0  0
 0ME  CONST_18  H9   C14  C9   C4      0.00   0.0  0
 0ME  CONST_19  H8   C13  C14  C9    180.00   0.0  0
 0ME  CONST_20  H7   C12  C11  C10   180.00   0.0  0
 0ME  CONST_21  C19  C17  N16  C15   180.00   0.0  0
 0ME  CONST_22  H12  N16  C17  C19     0.00   0.0  0
 0ME  CONST_23  O18  C17  N16  C15     0.00   0.0  0
 0ME  Var_01    C9   C10  O3   C2    -23.40  30.0  1
 0ME  Var_02    C22  C21  C20  C19   -53.55  30.0  1
 0ME  Var_03    C22  N23  C24  C19    54.22  30.0  1
 0ME  Var_04    N23  C22  C21  C20    53.75  30.0  1
 0ME  Var_05    C24  N23  C22  C21   -53.60  30.0  1
 0ME  Var_06    C17  N16  C15  C4   -101.31  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
 0ME  chir_01  C4   C15  C9   C1   positiv
 0ME  chir_02  C19  C20  C17  C24  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
 0ME  plan-1  C15  0.020
 0ME  plan-1  N16  0.020
 0ME  plan-1  C17  0.020
 0ME  plan-1  O18  0.020
 0ME  plan-1  C19  0.020
 0ME  plan-1  H12  0.020
 0ME  plan-2  C1   0.020
 0ME  plan-2  C2   0.020
 0ME  plan-2  O3   0.020
 0ME  plan-2  C4   0.020
 0ME  plan-2  C5   0.020
 0ME  plan-2  C6   0.020
 0ME  plan-2  C7   0.020
 0ME  plan-2  C8   0.020
 0ME  plan-2  H2   0.020
 0ME  plan-2  H3   0.020
 0ME  plan-2  H4   0.020
 0ME  plan-2  H5   0.020
 0ME  plan-3  O3   0.020
 0ME  plan-3  C4   0.020
 0ME  plan-3  C9   0.020
 0ME  plan-3  C10  0.020
 0ME  plan-3  C11  0.020
 0ME  plan-3  C12  0.020
 0ME  plan-3  C13  0.020
 0ME  plan-3  C14  0.020
 0ME  plan-3  H6   0.020
 0ME  plan-3  H7   0.020
 0ME  plan-3  H8   0.020
 0ME  plan-3  H9   0.020

