# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 12:16:46 2020
#   Inital geometry file: a 62 line input string
#   Ligand name: 3-(piperidin-4-yl)propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCC1CCNCC1
#
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
 BV7  BV7  '3-(piperidin-4-yl)propanoic acid'  ligand  25  11  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BV7
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
 BV7  C1    C  CH2    0  -0.408  -1.7740  -1.3131  -0.0587
 BV7  C2    C  CH2    0  -0.292  -3.1977  -0.9038  -0.4052
 BV7  N3    N  NH1    0  -0.595  -3.5673   0.2834   0.3451
 BV7  C4    C  CH2    0  -0.289  -2.7074   1.4076   0.0206
 BV7  C5    C  CH2    0  -0.417  -1.2636   1.0861   0.3782
 BV7  C6    C  CH1    0  -0.228  -0.7833  -0.1813  -0.3296
 BV7  C7    C  CH2    0  -0.389   0.6381  -0.5810   0.0600
 BV7  C8    C  CH2    0  -0.592   1.7011   0.4183  -0.3679
 BV7  C9    C  C      0   0.413   3.1565   0.0387  -0.0419
 BV7  O10   O  O      0  -0.609   3.3629  -1.0390   0.5503
 BV7  O11   O  OC    -1  -0.635   4.0275   0.8594  -0.4033
 BV7  H11C  H  HCH2   0   0.204  -1.7275  -1.5923   0.9998
 BV7  H12C  H  HCH2   0   0.219  -1.4941  -2.2005  -0.6336
 BV7  H21C  H  HCH2   0   0.180  -3.2669  -0.7481  -1.4958
 BV7  H22C  H  HCH2   0   0.225  -3.8931  -1.7092  -0.1573
 BV7  H6    H  HCH1   0   0.195  -0.8000   0.0163  -1.4113
 BV7  H3    H  HNH1   0   0.347  -4.5286   0.5249   0.1425
 BV7  H41C  H  HCH2   0   0.180  -2.7539   1.6765  -1.0489
 BV7  H42C  H  HCH2   0   0.225  -3.0467   2.2830   0.5793
 BV7  H51C  H  HCH2   0   0.226  -0.6316   1.9396   0.1204
 BV7  H52C  H  HCH2   0   0.203  -1.1824   0.9463   1.4624
 BV7  H71C  H  HCH2   0   0.196   0.6812  -0.7314   1.1440
 BV7  H72C  H  HCH2   0   0.205   0.8632  -1.5552  -0.3848
 BV7  H81C  H  HCH2   0   0.215   1.6271   0.5853  -1.4495
 BV7  H82C  H  HCH2   0   0.222   1.5042   1.3992   0.0782

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
 BV7  C1  C2    single  1.521  0.020  1.521
 BV7  C1  C6    single  1.528  0.020  1.528
 BV7  C2  N3    single  1.452  0.020  1.452
 BV7  N3  C4    single  1.452  0.020  1.452
 BV7  C4  C5    single  1.522  0.020  1.522
 BV7  C5  C6    single  1.529  0.020  1.529
 BV7  C6  C7    single  1.527  0.020  1.527
 BV7  C7  C8    single  1.520  0.020  1.520
 BV7  C8  C9    single  1.539  0.020  1.539
 BV7  C9  O10   deloc   1.247  0.020  1.247
 BV7  C9  O11   deloc   1.250  0.020  1.250
 BV7  C1  H11C  single  0.970  0.020  1.090
 BV7  C1  H12C  single  0.970  0.020  1.090
 BV7  C2  H21C  single  0.970  0.020  1.090
 BV7  C2  H22C  single  0.970  0.020  1.090
 BV7  C6  H6    single  0.970  0.020  1.090
 BV7  N3  H3    single  0.890  0.020  1.040
 BV7  C4  H41C  single  0.970  0.020  1.090
 BV7  C4  H42C  single  0.970  0.020  1.090
 BV7  C5  H51C  single  0.970  0.020  1.090
 BV7  C5  H52C  single  0.970  0.020  1.090
 BV7  C7  H71C  single  0.970  0.020  1.090
 BV7  C7  H72C  single  0.970  0.020  1.090
 BV7  C8  H81C  single  0.970  0.020  1.090
 BV7  C8  H82C  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
 BV7  H12C  C1  H11C  106.87  3.000
 BV7  H12C  C1  C6    109.98  3.000
 BV7  H11C  C1  C6    109.41  3.000
 BV7  H12C  C1  C2    109.76  3.000
 BV7  H11C  C1  C2    109.17  3.000
 BV7  C6    C1  C2    111.53  3.000
 BV7  H22C  C2  H21C  106.76  3.000
 BV7  H22C  C2  N3    108.87  3.000
 BV7  H21C  C2  N3    112.28  3.000
 BV7  H22C  C2  C1    110.22  3.000
 BV7  H21C  C2  C1    108.76  3.000
 BV7  N3    C2  C1    109.90  3.000
 BV7  H3    N3  C4    109.46  3.000
 BV7  H3    N3  C2    109.48  3.000
 BV7  C4    N3  C2    111.51  3.000
 BV7  H42C  C4  H41C  106.70  3.000
 BV7  H42C  C4  C5    110.11  3.000
 BV7  H41C  C4  C5    108.61  3.000
 BV7  H42C  C4  N3    108.79  3.000
 BV7  H41C  C4  N3    112.35  3.000
 BV7  C5    C4  N3    110.23  3.000
 BV7  H52C  C5  H51C  106.86  3.000
 BV7  H52C  C5  C6    109.20  3.000
 BV7  H51C  C5  C6    110.89  3.000
 BV7  H52C  C5  C4    109.24  3.000
 BV7  H51C  C5  C4    109.16  3.000
 BV7  C6    C5  C4    111.37  3.000
 BV7  H6    C6  C7    108.19  3.000
 BV7  H6    C6  C5    107.55  3.000
 BV7  C7    C6  C5    113.03  3.000
 BV7  H6    C6  C1    107.31  3.000
 BV7  C7    C6  C1    111.37  3.000
 BV7  C5    C6  C1    109.16  3.000
 BV7  H72C  C7  H71C  105.78  3.000
 BV7  H72C  C7  C8    109.08  3.000
 BV7  H71C  C7  C8    109.96  3.000
 BV7  H72C  C7  C6    108.71  3.000
 BV7  H71C  C7  C6    108.97  3.000
 BV7  C8    C7  C6    114.01  3.000
 BV7  H82C  C8  H81C  104.66  3.000
 BV7  H82C  C8  C9    107.73  3.000
 BV7  H81C  C8  C9    108.08  3.000
 BV7  H82C  C8  C7    110.38  3.000
 BV7  H81C  C8  C7    109.29  3.000
 BV7  C9    C8  C7    116.07  3.000
 BV7  O11   C9  O10   126.12  3.000
 BV7  O11   C9  C8    115.83  3.000
 BV7  O10   C9  C8    118.05  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
 BV7  Var_01  C4   N3  C2  C1    61.32  30.0  1
 BV7  Var_02  C5   C4  N3  C2   -61.27  30.0  1
 BV7  Var_03  C6   C1  C2  N3   -57.20  30.0  1
 BV7  Var_04  C6   C5  C4  N3    56.82  30.0  1
 BV7  Var_05  C9   C8  C7  C6  -177.97  30.0  3
 BV7  Var_06  O10  C9  C8  C7    -0.54  30.0  3

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
 BV7  chir_01  C6  C1  C5  C7  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
 BV7  plan-1  C8   0.020
 BV7  plan-1  C9   0.020
 BV7  plan-1  O10  0.020
 BV7  plan-1  O11  0.020

