# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 07:23:53 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  26  11  .  2021-08-07  2021-08-07  
;
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  -0.409  -1.7657  -1.3127  -0.0830
 BV7  C2    C  CH2   0  -0.293  -3.1846  -0.8780  -0.4168
 BV7  N3    N  NH1   0  -0.595  -3.5423   0.2860   0.3739
 BV7  C4    C  CH2   0  -0.289  -2.6750   1.4132   0.0826
 BV7  C5    C  CH2   0  -0.421  -1.2343   1.0702   0.4323
 BV7  C6    C  CH1   0  -0.236  -0.7656  -0.1803  -0.3131
 BV7  C7    C  CH2   0  -0.407   0.6448  -0.6130   0.0801
 BV7  C8    C  CH2   0  -0.590   1.7083   0.4034  -0.3043
 BV7  C9    C  C     0   0.554   3.1084  -0.0310   0.0272
 BV7  O10   O  O     0  -0.446   3.4077  -1.0518   0.5956
 BV7  O11   O  OH1   0  -0.599   4.0108   0.8581  -0.3809
 BV7  H11C  H  HCH2  0   0.208  -1.7236  -1.6280   0.9654
 BV7  H12C  H  HCH2  0   0.224  -1.4927  -2.1815  -0.6882
 BV7  H21C  H  HCH2  0   0.182  -3.2519  -0.6855  -1.5015
 BV7  H22C  H  HCH2  0   0.228  -3.8865  -1.6852  -0.1961
 BV7  H6    H  HCH1  0   0.208  -0.7683   0.0486  -1.3880
 BV7  H3    H  HNH1  0   0.349  -4.5025   0.5417   0.1842
 BV7  H41C  H  HCH2  0   0.182  -2.7184   1.7144  -0.9782
 BV7  H42C  H  HCH2  0   0.228  -3.0070   2.2741   0.6672
 BV7  H51C  H  HCH2  0   0.230  -0.5971   1.9269   0.1989
 BV7  H52C  H  HCH2  0   0.209  -1.1544   0.8978   1.5117
 BV7  H71C  H  HCH2  0   0.221   0.6772  -0.7979   1.1581
 BV7  H72C  H  HCH2  0   0.230   0.8702  -1.5683  -0.4024
 BV7  H81C  H  HCH2  0   0.274   1.6615   0.6168  -1.3771
 BV7  H82C  H  HCH2  0   0.280   1.5352   1.3653   0.1881
 BV7  H11   H  HOH1  0   0.478   4.9011   0.5552  -0.1486

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  1.521  0.020  1.521
 BV7  C8   C9    single  1.503  0.020  1.503
 BV7  C9   O10   double  1.206  0.020  1.206
 BV7  C9   O11   single  1.331  0.020  1.331
 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
 BV7  O11  H11   single  0.850  0.020  0.980

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  106.94  3.000
 BV7  H12C  C1   C6    110.00  3.000
 BV7  H11C  C1   C6    109.40  3.000
 BV7  H12C  C1   C2    109.79  3.000
 BV7  H11C  C1   C2    109.15  3.000
 BV7  C6    C1   C2    111.45  3.000
 BV7  H22C  C2   H21C  106.75  3.000
 BV7  H22C  C2   N3    108.92  3.000
 BV7  H21C  C2   N3    112.36  3.000
 BV7  H22C  C2   C1    110.12  3.000
 BV7  H21C  C2   C1    108.81  3.000
 BV7  N3    C2   C1    109.84  3.000
 BV7  H3    N3   C4    109.46  3.000
 BV7  H3    N3   C2    109.53  3.000
 BV7  C4    N3   C2    111.47  3.000
 BV7  H42C  C4   H41C  106.70  3.000
 BV7  H42C  C4   C5    110.02  3.000
 BV7  H41C  C4   C5    108.64  3.000
 BV7  H42C  C4   N3    108.85  3.000
 BV7  H41C  C4   N3    112.41  3.000
 BV7  C5    C4   N3    110.15  3.000
 BV7  H52C  C5   H51C  106.93  3.000
 BV7  H52C  C5   C6    109.21  3.000
 BV7  H51C  C5   C6    110.99  3.000
 BV7  H52C  C5   C4    109.31  3.000
 BV7  H51C  C5   C4    109.04  3.000
 BV7  C6    C5   C4    111.25  3.000
 BV7  H6    C6   C7    108.25  3.000
 BV7  H6    C6   C5    107.79  3.000
 BV7  C7    C6   C5    112.91  3.000
 BV7  H6    C6   C1    107.46  3.000
 BV7  C7    C6   C1    110.84  3.000
 BV7  C5    C6   C1    109.39  3.000
 BV7  H72C  C7   H71C  106.32  3.000
 BV7  H72C  C7   C8    109.15  3.000
 BV7  H71C  C7   C8    109.96  3.000
 BV7  H72C  C7   C6    108.92  3.000
 BV7  H71C  C7   C6    109.21  3.000
 BV7  C8    C7   C6    113.05  3.000
 BV7  H82C  C8   H81C  105.24  3.000
 BV7  H82C  C8   C9    107.58  3.000
 BV7  H81C  C8   C9    108.20  3.000
 BV7  H82C  C8   C7    111.29  3.000
 BV7  H81C  C8   C7    110.38  3.000
 BV7  C9    C8   C7    113.74  3.000
 BV7  O11   C9   O10   122.80  3.000
 BV7  O11   C9   C8    111.77  3.000
 BV7  O10   C9   C8    125.43  3.000
 BV7  H11   O11  C9    109.92  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  CONST_01  H11  O11  C9  C8   180.00   0.0  0
 BV7  Var_01    C4   N3   C2  C1    61.66  30.0  1
 BV7  Var_02    C5   C4   N3  C2   -61.65  30.0  1
 BV7  Var_03    C6   C1   C2  N3   -57.15  30.0  1
 BV7  Var_04    C6   C5   C4  N3    56.82  30.0  1
 BV7  Var_05    C9   C8   C7  C6  -177.74  30.0  3
 BV7  Var_06    O10  C9   C8  C7    -3.10  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
 BV7  plan-1  H11  0.020

