# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 22:32:46 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: 4-aminopiperidine-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1CCN(CC1)C(O)=O
#
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
 MRM  MRM  '4-aminopiperidine-1-carboxylic acid'  ligand  21  10  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MRM
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
 MRM  NB    N  NH2    0  -0.792  -0.0163   0.5496   3.4407
 MRM  CM1   C  CH1    0  -0.088   0.0140  -0.1685   2.1727
 MRM  CM2   C  CH2    0  -0.422  -1.2444   0.1376   1.3700
 MRM  CM5   C  CH2    0  -0.433   1.2496   0.1059   1.3153
 MRM  CM3   C  CH2    0  -0.279  -1.2407  -0.5896   0.0278
 MRM  NM    N  NT     0  -0.478  -0.0430  -0.3173  -0.7218
 MRM  CM4   C  CH2    0  -0.280   1.1766  -0.6254  -0.0229
 MRM  C     C  C      0   0.518  -0.0635   0.1818  -2.0328
 MRM  O     O  O      0  -0.655  -1.1859   0.4100  -2.5374
 MRM  OXT   O  OC    -1  -0.656   1.0424   0.3584  -2.5918
 MRM  HNB1  H  HNH2   0   0.338   0.8148   0.3225   3.9743
 MRM  HNB2  H  HNH2   0   0.330   0.0498   1.5450   3.2551
 MRM  HM1   H  HCH1   0   0.204   0.0039  -1.2400   2.4128
 MRM  HM21  H  HCH2   0   0.219  -2.1298  -0.1501   1.9433
 MRM  HM22  H  HCH2   0   0.204  -1.3091   1.2181   1.1952
 MRM  HM51  H  HCH2   0   0.203   1.3296   1.1845   1.1362
 MRM  HM52  H  HCH2   0   0.216   2.1530  -0.1999   1.8523
 MRM  HM31  H  HCH2   0   0.188  -1.3352  -1.6702   0.2188
 MRM  HM32  H  HCH2   0   0.237  -2.1038  -0.2980  -0.5639
 MRM  HM41  H  HCH2   0   0.187   1.2470  -1.7083   0.1668
 MRM  HM42  H  HCH2   0   0.236   2.0222  -0.3617  -0.6519

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
 MRM  NB   CM1   single  1.458  0.020  1.458
 MRM  NB   HNB1  single  0.890  0.020  1.040
 MRM  NB   HNB2  single  0.890  0.020  1.040
 MRM  CM1  CM2   single  1.524  0.020  1.524
 MRM  CM1  CM5   single  1.529  0.020  1.529
 MRM  CM1  HM1   single  0.970  0.020  1.090
 MRM  CM2  CM3   single  1.527  0.020  1.527
 MRM  CM2  HM21  single  0.970  0.020  1.090
 MRM  CM2  HM22  single  0.970  0.020  1.090
 MRM  CM5  CM4   single  1.527  0.020  1.527
 MRM  CM5  HM51  single  0.970  0.020  1.090
 MRM  CM5  HM52  single  0.970  0.020  1.090
 MRM  CM3  NM    single  1.439  0.020  1.439
 MRM  CM3  HM31  single  0.970  0.020  1.090
 MRM  CM3  HM32  single  0.970  0.020  1.090
 MRM  NM   CM4   single  1.439  0.020  1.439
 MRM  NM   C     single  1.403  0.020  1.403
 MRM  CM4  HM41  single  0.970  0.020  1.090
 MRM  CM4  HM42  single  0.970  0.020  1.090
 MRM  C    O     deloc   1.252  0.020  1.252
 MRM  C    OXT   deloc   1.252  0.020  1.252

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
 MRM  HNB2  NB   HNB1  105.23  3.000
 MRM  HNB2  NB   CM1   108.83  3.000
 MRM  HNB1  NB   CM1   109.30  3.000
 MRM  HM1   CM1  CM5   107.77  3.000
 MRM  HM1   CM1  CM2   107.67  3.000
 MRM  CM5   CM1  CM2   109.63  3.000
 MRM  HM1   CM1  NB    106.88  3.000
 MRM  CM5   CM1  NB    114.60  3.000
 MRM  CM2   CM1  NB    110.01  3.000
 MRM  HM22  CM2  HM21  107.17  3.000
 MRM  HM22  CM2  CM3   109.23  3.000
 MRM  HM21  CM2  CM3   109.73  3.000
 MRM  HM22  CM2  CM1   109.31  3.000
 MRM  HM21  CM2  CM1   109.86  3.000
 MRM  CM3   CM2  CM1   111.44  3.000
 MRM  HM52  CM5  HM51  107.14  3.000
 MRM  HM52  CM5  CM4   109.61  3.000
 MRM  HM51  CM5  CM4   109.37  3.000
 MRM  HM52  CM5  CM1   109.98  3.000
 MRM  HM51  CM5  CM1   109.10  3.000
 MRM  CM4   CM5  CM1   111.53  3.000
 MRM  HM32  CM3  HM31  106.83  3.000
 MRM  HM32  CM3  NM    109.07  3.000
 MRM  HM31  CM3  NM    110.33  3.000
 MRM  HM32  CM3  CM2   110.44  3.000
 MRM  HM31  CM3  CM2   108.34  3.000
 MRM  NM    CM3  CM2   111.71  3.000
 MRM  C     NM   CM4   122.85  3.000
 MRM  C     NM   CM3   122.82  3.000
 MRM  CM4   NM   CM3   114.32  3.000
 MRM  HM42  CM4  HM41  106.77  3.000
 MRM  HM42  CM4  NM    109.06  3.000
 MRM  HM41  CM4  NM    110.39  3.000
 MRM  HM42  CM4  CM5   110.73  3.000
 MRM  HM41  CM4  CM5   108.47  3.000
 MRM  NM    CM4  CM5   111.32  3.000
 MRM  OXT   C    O     125.91  3.000
 MRM  OXT   C    NM    117.04  3.000
 MRM  O     C    NM    117.05  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
 MRM  Var_01  NM   CM3  CM2  CM1  -53.85  30.0  1
 MRM  Var_02  NM   CM4  CM5  CM1   54.15  30.0  1
 MRM  Var_03  CM3  NM   CM4  CM5  -55.90  30.0  1
 MRM  Var_04  O    C    NM   CM3    1.16  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
 MRM  chir_01  CM1  NB  CM2  CM5  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
 MRM  plan-1  NM   0.020
 MRM  plan-1  C    0.020
 MRM  plan-1  O    0.020
 MRM  plan-1  OXT  0.020

