# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 05:37:27 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: 1,4'-bipiperidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CCN(CC1)C2CCNCC2
#
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
 4PN  4PN  '1,4'-bipiperidine        '  ligand  32  12  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_4PN
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
 4PN  C8    C  CH2   0  -0.284  -1.2006  -0.1371  -1.4393
 4PN  C9    C  CH2   0  -0.430  -1.1693   0.4450  -2.8467
 4PN  C10   C  CH2   0  -0.437  -0.0098  -0.1198  -3.6535
 4PN  C11   C  CH2   0  -0.435   1.2844   0.0664  -2.8760
 4PN  C12   C  CH2   0  -0.285   1.1545  -0.5009  -1.4706
 4PN  N7    N  NT    0  -0.431   0.0508   0.1036  -0.7372
 4PN  C4    C  CH1   0  -0.019   0.0630  -0.3186   0.6660
 4PN  C5    C  CH2   0  -0.437   1.1909   0.3907   1.4238
 4PN  C6    C  CH2   0  -0.294   1.2123   0.0029   2.8942
 4PN  N1    N  NH1   0  -0.592  -0.0632   0.3143   3.5097
 4PN  C2    C  CH2   0  -0.290  -1.1387  -0.4210   2.8742
 4PN  C3    C  CH2   0  -0.467  -1.2497  -0.0470   1.4021
 4PN  H81   H  HCH2  0   0.240  -2.0213   0.3296  -0.8961
 4PN  H82   H  HCH2  0   0.177  -1.4329  -1.2164  -1.5012
 4PN  H91   H  HCH2  0   0.211  -1.0758   1.5333  -2.7784
 4PN  H92   H  HCH2  0   0.226  -2.1240   0.2367  -3.3351
 4PN  H101  H  HCH2  0   0.208  -0.1770  -1.1879  -3.8296
 4PN  H102  H  HCH2  0   0.227   0.0517   0.3555  -4.6352
 4PN  H111  H  HCH2  0   0.227   2.1195  -0.4229  -3.3827
 4PN  H112  H  HCH2  0   0.213   1.5293   1.1309  -2.8121
 4PN  H121  H  HCH2  0   0.235   2.0871  -0.3310  -0.9326
 4PN  H122  H  HCH2  0   0.181   1.0279  -1.5978  -1.5340
 4PN  H4    H  HCH1  0   0.177   0.2431  -1.4099   0.7292
 4PN  H51   H  HCH2  0   0.231   2.1675   0.1596   0.9949
 4PN  H52   H  HCH2  0   0.212   1.0458   1.4714   1.3309
 4PN  H61   H  HCH2  0   0.184   1.4700  -1.0668   2.9770
 4PN  H62   H  HCH2  0   0.230   2.0015   0.5559   3.4078
 4PN  H1    H  HNH1  0   0.350  -0.0312   0.0833   4.4940
 4PN  H21   H  HCH2  0   0.185  -1.0042  -1.5135   2.9507
 4PN  H22   H  HCH2  0   0.232  -2.0780  -0.1844   3.3784
 4PN  H31   H  HCH2  0   0.218  -1.5117   1.0126   1.3145
 4PN  H32   H  HCH2  0   0.238  -2.0708  -0.6223   0.9710

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
 4PN  C8   C9    single  1.523  0.020  1.523
 4PN  C8   N7    single  1.455  0.020  1.455
 4PN  C8   H81   single  0.970  0.020  1.090
 4PN  C8   H82   single  0.970  0.020  1.090
 4PN  C9   C10   single  1.521  0.020  1.521
 4PN  C9   H91   single  0.970  0.020  1.090
 4PN  C9   H92   single  0.970  0.020  1.090
 4PN  C10  C11   single  1.521  0.020  1.521
 4PN  C10  H101  single  0.970  0.020  1.090
 4PN  C10  H102  single  0.970  0.020  1.090
 4PN  C11  C12   single  1.521  0.020  1.521
 4PN  C11  H111  single  0.970  0.020  1.090
 4PN  C11  H112  single  0.970  0.020  1.090
 4PN  C12  N7    single  1.457  0.020  1.457
 4PN  C12  H121  single  0.970  0.020  1.090
 4PN  C12  H122  single  0.970  0.020  1.090
 4PN  N7   C4    single  1.465  0.020  1.465
 4PN  C4   C5    single  1.533  0.020  1.533
 4PN  C4   C3    single  1.529  0.020  1.529
 4PN  C4   H4    single  0.970  0.020  1.090
 4PN  C5   C6    single  1.521  0.020  1.521
 4PN  C5   H51   single  0.970  0.020  1.090
 4PN  C5   H52   single  0.970  0.020  1.090
 4PN  C6   N1    single  1.450  0.020  1.450
 4PN  C6   H61   single  0.970  0.020  1.090
 4PN  C6   H62   single  0.970  0.020  1.090
 4PN  N1   C2    single  1.450  0.020  1.450
 4PN  N1   H1    single  0.890  0.020  1.040
 4PN  C2   C3    single  1.523  0.020  1.523
 4PN  C2   H21   single  0.970  0.020  1.090
 4PN  C2   H22   single  0.970  0.020  1.090
 4PN  C3   H31   single  0.970  0.020  1.090
 4PN  C3   H32   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
 4PN  H82   C8   H81   106.74  3.000
 4PN  H82   C8   N7    111.67  3.000
 4PN  H81   C8   N7    109.67  3.000
 4PN  H82   C8   C9    109.00  3.000
 4PN  H81   C8   C9    108.21  3.000
 4PN  N7    C8   C9    111.40  3.000
 4PN  H92   C9   H91   106.99  3.000
 4PN  H92   C9   C10   110.99  3.000
 4PN  H91   C9   C10   109.70  3.000
 4PN  H92   C9   C8    108.80  3.000
 4PN  H91   C9   C8    108.91  3.000
 4PN  C10   C9   C8    111.33  3.000
 4PN  H102  C10  H101  106.76  3.000
 4PN  H102  C10  C11   110.98  3.000
 4PN  H101  C10  C11   109.35  3.000
 4PN  H102  C10  C9    110.98  3.000
 4PN  H101  C10  C9    109.33  3.000
 4PN  C11   C10  C9    109.38  3.000
 4PN  H112  C11  H111  106.97  3.000
 4PN  H112  C11  C12   109.15  3.000
 4PN  H111  C11  C12   109.07  3.000
 4PN  H112  C11  C10   109.84  3.000
 4PN  H111  C11  C10   111.00  3.000
 4PN  C12   C11  C10   110.72  3.000
 4PN  H122  C12  H121  106.31  3.000
 4PN  H122  C12  N7    110.72  3.000
 4PN  H121  C12  N7    109.57  3.000
 4PN  H122  C12  C11   109.07  3.000
 4PN  H121  C12  C11   108.95  3.000
 4PN  N7    C12  C11   112.03  3.000
 4PN  C4    N7   C12   110.87  3.000
 4PN  C4    N7   C8    114.93  3.000
 4PN  C12   N7   C8    109.88  3.000
 4PN  H4    C4   C3    106.68  3.000
 4PN  H4    C4   C5    107.94  3.000
 4PN  C3    C4   C5    108.15  3.000
 4PN  H4    C4   N7    109.86  3.000
 4PN  C3    C4   N7    113.74  3.000
 4PN  C5    C4   N7    110.26  3.000
 4PN  H52   C5   H51   107.12  3.000
 4PN  H52   C5   C6    109.62  3.000
 4PN  H51   C5   C6    108.27  3.000
 4PN  H52   C5   C4    108.51  3.000
 4PN  H51   C5   C4    111.48  3.000
 4PN  C6    C5   C4    111.73  3.000
 4PN  H62   C6   H61   106.66  3.000
 4PN  H62   C6   N1    109.10  3.000
 4PN  H61   C6   N1    112.45  3.000
 4PN  H62   C6   C5    109.62  3.000
 4PN  H61   C6   C5    108.85  3.000
 4PN  N1    C6   C5    110.08  3.000
 4PN  H1    N1   C2    109.53  3.000
 4PN  H1    N1   C6    109.65  3.000
 4PN  C2    N1   C6    110.95  3.000
 4PN  H22   C2   H21   106.70  3.000
 4PN  H22   C2   C3    109.29  3.000
 4PN  H21   C2   C3    108.60  3.000
 4PN  H22   C2   N1    109.02  3.000
 4PN  H21   C2   N1    112.42  3.000
 4PN  C3    C2   N1    110.69  3.000
 4PN  H32   C3   H31   107.37  3.000
 4PN  H32   C3   C2    107.89  3.000
 4PN  H31   C3   C2    109.42  3.000
 4PN  H32   C3   C4    111.23  3.000
 4PN  H31   C3   C4    109.80  3.000
 4PN  C2    C3   C4    111.04  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
 4PN  Var_01  C11  C10  C9   C8   -53.01  30.0  1
 4PN  Var_02  C11  C12  N7   C8    59.82  30.0  1
 4PN  Var_03  C12  N7   C8   C9   -59.35  30.0  1
 4PN  Var_04  C12  C11  C10  C9    52.75  30.0  1
 4PN  Var_05  N7   C8   C9   C10   57.11  30.0  1
 4PN  Var_06  N7   C12  C11  C10  -57.24  30.0  1
 4PN  Var_07  N1   C6   C5   C4   -57.78  30.0  1
 4PN  Var_08  N1   C2   C3   C4    58.00  30.0  1
 4PN  Var_09  C2   N1   C6   C5    60.81  30.0  1
 4PN  Var_10  C3   C2   N1   C6   -61.28  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
 4PN  chir_01  C4  N7  C5  C3  negativ

