# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 01:12:12 2022
#   Inital geometry file: a 115 line input string
#   Ligand name: N-cyclopropyl-1-(4-phenylpyridin-3-yl)piperidine-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NC1CC1)C2CCN(CC2)c3cnccc3c4ccccc4
#
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
 04Y  04Y  "N-cyclopropyl-1-(4-phenylpyridin-3-yl)piperidine-4-carboxamide"  ligand  47  24  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_04Y
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
 04Y  C4   C  CR16  0  -0.265  17.8356  -2.6663  -23.8384
 04Y  C5   C  CR16  0  -0.288  17.8497  -4.4676  -22.2505
 04Y  C6   C  CR16  0  -0.369  14.8405  -4.1466  -22.5116
 04Y  C7   C  CR16  0  -0.083  13.5059  -3.8823  -22.2497
 04Y  C8   C  CR16  0  -0.139  13.9435  -1.6780  -21.9271
 04Y  C10  C  CR6   0   0.137  15.7722  -3.1155  -22.4947
 04Y  C13  C  CH2   0  -0.512  20.2998   5.6749  -20.6292
 04Y  C15  C  CH2   0  -0.417  16.7636   1.5640  -22.6140
 04Y  C17  C  CH2   0  -0.315  15.6516   0.5859  -22.2653
 04Y  C20  C  CH1   0  -0.078  19.8819   4.7299  -21.7076
 04Y  C1   C  CR16  0  -0.262  19.7969  -4.0432  -23.5971
 04Y  C2   C  CR16  0  -0.242  19.1323  -2.9872  -24.2094
 04Y  C3   C  CR16  0  -0.240  19.1518  -4.7819  -22.6158
 04Y  C9   C  CR6   0   0.031  17.1780  -3.4056  -22.8540
 04Y  C11  C  CR6   0   0.222  15.3125  -1.8260  -22.1670
 04Y  C12  C  C     0   0.571  18.9798   2.4865  -21.9504
 04Y  C14  C  CH2   0  -0.481  21.2768   4.6753  -21.1675
 04Y  C16  C  CH2   0  -0.420  18.3545   0.1258  -21.3360
 04Y  C18  C  CH2   0  -0.308  17.1925  -0.8052  -21.0367
 04Y  C19  C  CH1   0  -0.399  17.8577   1.5529  -21.5424
 04Y  N21  N  N     0  -0.396  13.0590  -2.6657  -21.9754
 04Y  N22  N  NT    0  -0.509  16.1974  -0.7479  -22.1012
 04Y  O24  O  O     0  -0.487  19.8211   2.1689  -22.7781
 04Y  H1   H  HCR6  0   0.252  17.3289  -1.8418  -24.3211
 04Y  H2   H  HCR6  0   0.254  17.3563  -5.0470  -21.4794
 04Y  H3   H  HCR6  0   0.264  15.1482  -5.1528  -22.7658
 04Y  H4   H  HCR6  0   0.257  12.7750  -4.6828  -22.2725
 04Y  H5   H  HCR6  0   0.267  13.5432  -0.7009  -21.6808
 04Y  H7   H  HCH2  0   0.257  19.9052   5.5088  -19.6342
 04Y  H8   H  HCH2  0   0.233  17.1925   1.2907  -23.5817
 04Y  H9   H  HCH2  0   0.246  16.3369   2.5646  -22.7141
 04Y  H10  H  HCH2  0   0.211  15.1353   0.9362  -21.3575
 04Y  H11  H  HCH2  0   0.255  14.9178   0.5766  -23.0730
 04Y  H12  H  HCH1  0   0.264  19.7586   5.1442  -22.7037
 04Y  H13  H  HCR6  0   0.256  20.8110  -4.2879  -23.8853
 04Y  H14  H  HCR6  0   0.256  19.6257  -2.4101  -24.9808
 04Y  H15  H  HCR6  0   0.256  19.6608  -5.6054  -22.1321
 04Y  H16  H  HCH2  0   0.253  21.5347   3.8343  -20.5372
 04Y  H17  H  HCH2  0   0.253  22.0779   5.0230  -21.8064
 04Y  H18  H  HCH2  0   0.231  18.8691  -0.2249  -22.2330
 04Y  H19  H  HCH2  0   0.243  19.0665   0.0825  -20.5088
 04Y  H20  H  HCH2  0   0.218  16.7343  -0.5324  -20.0729
 04Y  H21  H  HCH2  0   0.261  17.5628  -1.8238  -20.9328
 04Y  H22  H  HCH1  0   0.250  17.4117   1.9026  -20.6036
 04Y  N23  N  NH1   0  -0.643  18.9610   3.6983  -21.3637
 04Y  H6   H  HCH2  0   0.257  20.4206   6.7170  -20.8934
 04Y  H23  H  HNH1  0   0.400  18.2023   3.9241  -20.7397

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
 04Y  C2   C4   aromatic  1.386  0.020  1.386
 04Y  C2   C1   aromatic  1.390  0.020  1.390
 04Y  C4   C9   aromatic  1.396  0.020  1.396
 04Y  C1   C3   aromatic  1.387  0.020  1.387
 04Y  C9   C10  single    1.480  0.020  1.480
 04Y  C9   C5   aromatic  1.394  0.020  1.394
 04Y  C3   C5   aromatic  1.388  0.020  1.388
 04Y  C10  C6   aromatic  1.390  0.020  1.390
 04Y  C10  C11  aromatic  1.408  0.020  1.408
 04Y  C6   C7   aromatic  1.386  0.020  1.386
 04Y  C15  C17  single    1.521  0.020  1.521
 04Y  C15  C19  single    1.531  0.020  1.531
 04Y  O24  C12  double    1.222  0.020  1.222
 04Y  C7   N21  aromatic  1.325  0.020  1.325
 04Y  C11  N22  single    1.396  0.020  1.396
 04Y  C11  C8   aromatic  1.398  0.020  1.398
 04Y  C17  N22  single    1.450  0.020  1.450
 04Y  N22  C18  single    1.458  0.020  1.458
 04Y  N21  C8   aromatic  1.327  0.020  1.327
 04Y  C20  N23  single    1.425  0.020  1.425
 04Y  C20  C13  single    1.494  0.020  1.494
 04Y  C20  C14  single    1.497  0.020  1.497
 04Y  C12  N23  single    1.347  0.020  1.347
 04Y  C12  C19  single    1.516  0.020  1.516
 04Y  C19  C16  single    1.525  0.020  1.525
 04Y  C16  C18  single    1.519  0.020  1.519
 04Y  C13  C14  single    1.498  0.020  1.498
 04Y  C4   H1   single    0.930  0.020  1.080
 04Y  C5   H2   single    0.930  0.020  1.080
 04Y  C6   H3   single    0.930  0.020  1.080
 04Y  C7   H4   single    0.930  0.020  1.080
 04Y  C8   H5   single    0.930  0.020  1.080
 04Y  C13  H6   single    0.970  0.020  1.090
 04Y  C13  H7   single    0.970  0.020  1.090
 04Y  C15  H8   single    0.970  0.020  1.090
 04Y  C15  H9   single    0.970  0.020  1.090
 04Y  C17  H10  single    0.970  0.020  1.090
 04Y  C17  H11  single    0.970  0.020  1.090
 04Y  C20  H12  single    0.970  0.020  1.090
 04Y  C1   H13  single    0.930  0.020  1.080
 04Y  C2   H14  single    0.930  0.020  1.080
 04Y  C3   H15  single    0.930  0.020  1.080
 04Y  C14  H16  single    0.970  0.020  1.090
 04Y  C14  H17  single    0.970  0.020  1.090
 04Y  C16  H18  single    0.970  0.020  1.090
 04Y  C16  H19  single    0.970  0.020  1.090
 04Y  C18  H20  single    0.970  0.020  1.090
 04Y  C18  H21  single    0.970  0.020  1.090
 04Y  C19  H22  single    0.970  0.020  1.090
 04Y  N23  H23  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
 04Y  H1   C4   C9   119.86  3.000
 04Y  H1   C4   C2   119.69  3.000
 04Y  C9   C4   C2   120.45  3.000
 04Y  H2   C5   C9   119.74  3.000
 04Y  H2   C5   C3   119.56  3.000
 04Y  C9   C5   C3   120.69  3.000
 04Y  H3   C6   C10  120.13  3.000
 04Y  H3   C6   C7   119.70  3.000
 04Y  C10  C6   C7   120.13  3.000
 04Y  H4   C7   N21  117.06  3.000
 04Y  H4   C7   C6   120.30  3.000
 04Y  N21  C7   C6   122.64  3.000
 04Y  H5   C8   N21  115.65  3.000
 04Y  H5   C8   C11  119.74  3.000
 04Y  N21  C8   C11  124.61  3.000
 04Y  C11  C10  C9   123.12  3.000
 04Y  C11  C10  C6   117.61  3.000
 04Y  C9   C10  C6   119.24  3.000
 04Y  H7   C13  H6   114.38  3.000
 04Y  H7   C13  C14  117.73  3.000
 04Y  H6   C13  C14  118.83  3.000
 04Y  H7   C13  C20  117.66  3.000
 04Y  H6   C13  C20  117.67  3.000
 04Y  C14  C13  C20   60.05  3.000
 04Y  H9   C15  H8   107.52  3.000
 04Y  H9   C15  C19  110.48  3.000
 04Y  H8   C15  C19  109.71  3.000
 04Y  H9   C15  C17  108.92  3.000
 04Y  H8   C15  C17  109.20  3.000
 04Y  C19  C15  C17  110.92  3.000
 04Y  H11  C17  H10  107.31  3.000
 04Y  H11  C17  N22  109.20  3.000
 04Y  H10  C17  N22  112.06  3.000
 04Y  H11  C17  C15  109.11  3.000
 04Y  H10  C17  C15  109.09  3.000
 04Y  N22  C17  C15  110.00  3.000
 04Y  H12  C20  N23  115.11  3.000
 04Y  H12  C20  C14  116.79  3.000
 04Y  N23  C20  C14  119.26  3.000
 04Y  H12  C20  C13  116.92  3.000
 04Y  C14  C20  C13   60.12  3.000
 04Y  N23  C20  C13  117.68  3.000
 04Y  H13  C1   C3   120.24  3.000
 04Y  H13  C1   C2   120.17  3.000
 04Y  C3   C1   C2   119.59  3.000
 04Y  H14  C2   C1   120.07  3.000
 04Y  H14  C2   C4   119.58  3.000
 04Y  C1   C2   C4   120.35  3.000
 04Y  H15  C3   C1   120.17  3.000
 04Y  H15  C3   C5   119.72  3.000
 04Y  C1   C3   C5   120.11  3.000
 04Y  C10  C9   C5   120.13  3.000
 04Y  C5   C9   C4   118.81  3.000
 04Y  C10  C9   C4   121.00  3.000
 04Y  N22  C11  C10  120.75  3.000
 04Y  N22  C11  C8   122.07  3.000
 04Y  C10  C11  C8   117.18  3.000
 04Y  O24  C12  N23  122.59  3.000
 04Y  N23  C12  C19  115.26  3.000
 04Y  O24  C12  C19  122.13  3.000
 04Y  H17  C14  H16  114.66  3.000
 04Y  H17  C14  C20  117.73  3.000
 04Y  H16  C14  C20  117.42  3.000
 04Y  H17  C14  C13  118.73  3.000
 04Y  H16  C14  C13  117.69  3.000
 04Y  C20  C14  C13   59.83  3.000
 04Y  H19  C16  H18  107.59  3.000
 04Y  H19  C16  C19  110.61  3.000
 04Y  H18  C16  C19  110.05  3.000
 04Y  H19  C16  C18  108.98  3.000
 04Y  H18  C16  C18  109.00  3.000
 04Y  C19  C16  C18  110.55  3.000
 04Y  H21  C18  H20  106.84  3.000
 04Y  H21  C18  N22  109.78  3.000
 04Y  H20  C18  N22  110.19  3.000
 04Y  H21  C18  C16  109.40  3.000
 04Y  H20  C18  C16  109.81  3.000
 04Y  N22  C18  C16  110.74  3.000
 04Y  H22  C19  C16  108.36  3.000
 04Y  H22  C19  C12  109.58  3.000
 04Y  C16  C19  C12  111.82  3.000
 04Y  H22  C19  C15  107.82  3.000
 04Y  C16  C19  C15  109.52  3.000
 04Y  C12  C19  C15  109.64  3.000
 04Y  C8   N21  C7   117.79  3.000
 04Y  C18  N22  C11  115.88  3.000
 04Y  C18  N22  C17  112.06  3.000
 04Y  C11  N22  C17  117.78  3.000
 04Y  H23  N23  C12  118.80  3.000
 04Y  H23  N23  C20  118.28  3.000
 04Y  C12  N23  C20  122.50  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
 04Y  CONST_01  C3   C1   C2   C4      0.00   0.0  0
 04Y  CONST_04  C3   C5   C9   C4      0.00   0.0  0
 04Y  CONST_05  C2   C4   C9   C5      0.00   0.0  0
 04Y  CONST_08  C2   C1   C3   C5      0.00   0.0  0
 04Y  CONST_09  C8   C11  C10  C6      0.00   0.0  0
 04Y  CONST_10  C8   N21  C7   C6      0.00   0.0  0
 04Y  CONST_11  C9   C10  C6   C7    180.00   0.0  0
 04Y  CONST_12  C11  C10  C6   C7      0.00   0.0  0
 04Y  CONST_13  C11  C8   N21  C7      0.00   0.0  0
 04Y  CONST_14  C9   C10  C11  C8    180.00   0.0  0
 04Y  CONST_15  C2   C4   C9   C10   180.00   0.0  0
 04Y  CONST_16  C3   C5   C9   C10   180.00   0.0  0
 04Y  CONST_17  N21  C7   C6   C10     0.00   0.0  0
 04Y  CONST_18  N21  C8   C11  C10     0.00   0.0  0
 04Y  CONST_19  C9   C4   C2   C1      0.00   0.0  0
 04Y  CONST_20  C9   C5   C3   C1      0.00   0.0  0
 04Y  CONST_21  N22  C11  C10  C6    180.00   0.0  0
 04Y  CONST_22  N22  C11  C10  C9      0.00   0.0  0
 04Y  CONST_23  N22  C11  C8   N21   180.00   0.0  0
 04Y  CONST_24  H13  C1   C2   C4    180.00   0.0  0
 04Y  CONST_25  H2   C5   C9   C4    180.00   0.0  0
 04Y  CONST_26  H1   C4   C9   C5    180.00   0.0  0
 04Y  CONST_27  H13  C1   C3   C5    180.00   0.0  0
 04Y  CONST_28  H5   C8   N21  C7    180.00   0.0  0
 04Y  CONST_29  H4   C7   N21  C8    180.00   0.0  0
 04Y  CONST_30  H1   C4   C9   C10     0.00   0.0  0
 04Y  CONST_31  H2   C5   C9   C10     0.00   0.0  0
 04Y  CONST_32  H4   C7   C6   C10   180.00   0.0  0
 04Y  CONST_33  H5   C8   C11  C10   180.00   0.0  0
 04Y  CONST_34  H1   C4   C2   C1    180.00   0.0  0
 04Y  CONST_35  H2   C5   C3   C1    180.00   0.0  0
 04Y  CONST_36  H15  C3   C1   C2    180.00   0.0  0
 04Y  CONST_37  H14  C2   C1   C3    180.00   0.0  0
 04Y  CONST_38  H14  C2   C4   C9    180.00   0.0  0
 04Y  CONST_39  H3   C6   C10  C9      0.00   0.0  0
 04Y  CONST_40  H15  C3   C5   C9    180.00   0.0  0
 04Y  CONST_41  H3   C6   C10  C11   180.00   0.0  0
 04Y  CONST_42  H3   C6   C7   N21   180.00   0.0  0
 04Y  CONST_43  H5   C8   C11  N22     0.00   0.0  0
 04Y  CONST_44  C19  C12  N23  C20   180.00   0.0  0
 04Y  CONST_45  O24  C12  N23  C20     0.00   0.0  0
 04Y  CONST_46  H23  N23  C12  C19     0.00   0.0  0
 04Y  CONST_47  H23  N23  C12  O24   180.00   0.0  0
 04Y  Var_01    C17  N22  C11  C8    -22.23  30.0  2
 04Y  Var_02    C18  N22  C11  C8    114.44  30.0  2
 04Y  Var_03    C17  N22  C11  C10   157.14  30.0  2
 04Y  Var_04    C18  N22  C11  C10   -66.19  30.0  2
 04Y  Var_05    C11  N22  C17  C15  -161.70  30.0  1
 04Y  Var_06    C18  N22  C17  C15    60.06  30.0  1
 04Y  Var_07    C16  C18  N22  C17   -60.18  30.0  1
 04Y  Var_08    C16  C18  N22  C11   160.74  30.0  1
 04Y  Var_09    N22  C17  C15  C19   -57.09  30.0  1
 04Y  Var_10    N22  C18  C16  C19    56.59  30.0  1
 04Y  Var_11    N23  C20  C14  C13  -106.99  30.0  1
 04Y  Var_12    H16  C14  C20  C13   107.70  30.0  1
 04Y  Var_13    H17  C14  C20  C13  -108.82  30.0  1
 04Y  Var_14    H12  C20  C14  C13   107.14  30.0  1
 04Y  Var_15    H20  C18  N22  C17    61.52  30.0  1
 04Y  Var_16    H21  C18  N22  C17   178.92  30.0  1
 04Y  Var_17    H6   C13  C14  C20  -107.14  30.0  1
 04Y  Var_18    H7   C13  C14  C20   107.60  30.0  1
 04Y  Var_19    H10  C17  N22  C11    76.76  30.0  1
 04Y  Var_20    H11  C17  N22  C11   -41.99  30.0  1
 04Y  Var_21    H20  C18  N22  C11   -77.57  30.0  1
 04Y  Var_22    H21  C18  N22  C11    39.84  30.0  1
 04Y  Var_23    H10  C17  N22  C18   -61.47  30.0  1
 04Y  Var_24    H11  C17  N22  C18   179.77  30.0  1
 04Y  Var_25    H10  C17  C15  C19    66.20  30.0  1
 04Y  Var_26    H11  C17  C15  C19  -176.86  30.0  1
 04Y  Var_27    H20  C18  C16  C19   -65.32  30.0  1
 04Y  Var_28    H21  C18  C16  C19   177.72  30.0  1
 04Y  Var_29    H8   C15  C17  N22    63.94  30.0  1
 04Y  Var_30    H9   C15  C17  N22  -178.90  30.0  1
 04Y  Var_31    H18  C16  C18  N22   -64.50  30.0  1
 04Y  Var_32    H19  C16  C18  N22   178.35  30.0  1
 04Y  Var_33    C12  N23  C20  C13  -147.59  30.0  3
 04Y  Var_34    C14  C20  N23  C12   -78.14  30.0  2
 04Y  Var_35    H23  N23  C20  C13    39.91  30.0  3
 04Y  Var_36    H23  N23  C20  C14   109.36  30.0  3
 04Y  Var_37    H6   C13  C20  N23  -141.38  30.0  1
 04Y  Var_38    H7   C13  C20  N23     1.86  30.0  1
 04Y  Var_39    H16  C14  C20  N23     0.70  30.0  1
 04Y  Var_40    H17  C14  C20  N23   144.18  30.0  1
 04Y  Var_41    H12  C20  N23  C12    68.28  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
 04Y  chir_02  C19  C15  C12  C16  positiv
 04Y  chir_03  C20  N23  C13  C14  both

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
 04Y  plan-1  C6   0.020
 04Y  plan-1  C7   0.020
 04Y  plan-1  C8   0.020
 04Y  plan-1  C10  0.020
 04Y  plan-1  C9   0.020
 04Y  plan-1  C11  0.020
 04Y  plan-1  N21  0.020
 04Y  plan-1  N22  0.020
 04Y  plan-1  H3   0.020
 04Y  plan-1  H4   0.020
 04Y  plan-1  H5   0.020
 04Y  plan-2  C20  0.020
 04Y  plan-2  C12  0.020
 04Y  plan-2  C19  0.020
 04Y  plan-2  O24  0.020
 04Y  plan-2  N23  0.020
 04Y  plan-2  H23  0.020
 04Y  plan-3  C4   0.020
 04Y  plan-3  C5   0.020
 04Y  plan-3  C10  0.020
 04Y  plan-3  C1   0.020
 04Y  plan-3  C2   0.020
 04Y  plan-3  C3   0.020
 04Y  plan-3  C9   0.020
 04Y  plan-3  H1   0.020
 04Y  plan-3  H2   0.020
 04Y  plan-3  H13  0.020
 04Y  plan-3  H14  0.020
 04Y  plan-3  H15  0.020

