# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 20:19:15 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: (8S)-8-amino-7-oxononanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](N)C(=O)CCCCCC(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
 KAP  KAP  '(8S)-8-amino-7-oxononanoic acid'  ligand  29  13  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_KAP
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
 KAP  CA   C  CH2    0  -0.581   0.7503   0.1090  -3.3607
 KAP  C    C  C      0   0.410   0.0714  -0.0826  -4.7283
 KAP  OI1  O  OC    -1  -0.635   0.7861   0.1369  -5.7300
 KAP  OI2  O  O      0  -0.610  -1.1211  -0.4469  -4.7422
 KAP  CB   C  CH2    0  -0.403  -0.1515  -0.0145  -2.1436
 KAP  CG   C  CH2    0  -0.411   0.5970   0.1921  -0.8323
 KAP  CD   C  CH2    0  -0.410  -0.3007   0.0586   0.3918
 KAP  CE   C  CH2    0  -0.567   0.4582   0.2952   1.6870
 KAP  CZ   C  C      0   0.410  -0.3591   0.1488   2.9429
 KAP  CH   C  CH1    0  -0.201   0.3914   0.2744   4.2592
 KAP  CS   C  CH3    0  -0.676   1.1397  -1.0407   4.5269
 KAP  O    O  O      0  -0.405  -1.5484  -0.0750   2.9218
 KAP  N    N  NH2    0  -0.784  -0.5197   0.6708   5.3145
 KAP  HA2  H  HCH2   0   0.213   1.2484   1.0855  -3.3558
 KAP  HA1  H  HCH2   0   0.218   1.5654  -0.6217  -3.2868
 KAP  HB2  H  HCH2   0   0.201  -0.6291  -0.9985  -2.1355
 KAP  HB1  H  HCH2   0   0.201  -0.9659   0.7136  -2.2097
 KAP  HG2  H  HCH2   0   0.205   1.0691   1.1813  -0.8327
 KAP  HG1  H  HCH2   0   0.206   1.4168  -0.5318  -0.7626
 KAP  HD2  H  HCH2   0   0.219  -0.7522  -0.9375   0.4031
 KAP  HD1  H  HCH2   0   0.219  -1.1279   0.7696   0.3153
 KAP  HE2  H  HCH2   0   0.268   0.8908   1.3030   1.7002
 KAP  HE1  H  HCH2   0   0.262   1.3230  -0.3748   1.7528
 KAP  HH   H  HCH1   0   0.252   1.1390   1.0653   4.1400
 KAP  HS3  H  HCH3   0   0.246   1.6833  -0.9650   5.4693
 KAP  HS2  H  HCH3   0   0.231   0.4425  -1.8767   4.6060
 KAP  HS1  H  HCH3   0   0.231   1.8656  -1.2753   3.7478
 KAP  H1   H  HNH2   0   0.340  -1.2232  -0.0463   5.4457
 KAP  H2   H  HNH2   0   0.350  -0.0077   0.7189   6.1866

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
 KAP  CA  C    single  1.539  0.020  1.539
 KAP  CA  CB   single  1.520  0.020  1.520
 KAP  CA  HA2  single  0.970  0.020  1.090
 KAP  CA  HA1  single  0.970  0.020  1.090
 KAP  C   OI1  deloc   1.250  0.020  1.250
 KAP  C   OI2  deloc   1.247  0.020  1.247
 KAP  CB  CG   single  1.524  0.020  1.524
 KAP  CB  HB2  single  0.970  0.020  1.090
 KAP  CB  HB1  single  0.970  0.020  1.090
 KAP  CG  CD   single  1.524  0.020  1.524
 KAP  CG  HG2  single  0.970  0.020  1.090
 KAP  CG  HG1  single  0.970  0.020  1.090
 KAP  CD  CE   single  1.520  0.020  1.520
 KAP  CD  HD2  single  0.970  0.020  1.090
 KAP  CD  HD1  single  0.970  0.020  1.090
 KAP  CE  CZ   single  1.506  0.020  1.506
 KAP  CE  HE2  single  0.970  0.020  1.090
 KAP  CE  HE1  single  0.970  0.020  1.090
 KAP  CZ  CH   single  1.520  0.020  1.520
 KAP  CZ  O    double  1.210  0.020  1.210
 KAP  CH  CS   single  1.537  0.020  1.537
 KAP  CH  N    single  1.449  0.020  1.449
 KAP  CH  HH   single  0.970  0.020  1.090
 KAP  CS  HS3  single  0.970  0.020  1.090
 KAP  CS  HS2  single  0.970  0.020  1.090
 KAP  CS  HS1  single  0.970  0.020  1.090
 KAP  N   H1   single  0.890  0.020  1.040
 KAP  N   H2   single  0.890  0.020  1.040

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
 KAP  HA1  CA  HA2  104.80  3.000
 KAP  HA1  CA  CB   109.44  3.000
 KAP  HA2  CA  CB   109.78  3.000
 KAP  HA1  CA  C    107.74  3.000
 KAP  HA2  CA  C    108.38  3.000
 KAP  CB   CA  C    116.09  3.000
 KAP  OI2  C   OI1  126.09  3.000
 KAP  OI2  C   CA   117.92  3.000
 KAP  OI1  C   CA   115.99  3.000
 KAP  HB1  CB  HB2  105.91  3.000
 KAP  HB1  CB  CG   109.10  3.000
 KAP  HB2  CB  CG   109.27  3.000
 KAP  HB1  CB  CA   109.82  3.000
 KAP  HB2  CB  CA   109.76  3.000
 KAP  CG   CB  CA   112.75  3.000
 KAP  HG1  CG  HG2  105.90  3.000
 KAP  HG1  CG  CD   109.37  3.000
 KAP  HG2  CG  CD   109.46  3.000
 KAP  HG1  CG  CB   109.43  3.000
 KAP  HG2  CG  CB   109.49  3.000
 KAP  CD   CG  CB   112.96  3.000
 KAP  HD1  CD  HD2  106.29  3.000
 KAP  HD1  CD  CE   109.64  3.000
 KAP  HD2  CD  CE   109.82  3.000
 KAP  HD1  CD  CG   109.42  3.000
 KAP  HD2  CD  CG   109.35  3.000
 KAP  CE   CD  CG   112.14  3.000
 KAP  HE1  CE  HE2  104.47  3.000
 KAP  HE1  CE  CZ   108.59  3.000
 KAP  HE2  CE  CZ   107.07  3.000
 KAP  HE1  CE  CD   110.49  3.000
 KAP  HE2  CE  CD   110.50  3.000
 KAP  CZ   CE  CD   115.13  3.000
 KAP  O    CZ  CH   121.02  3.000
 KAP  O    CZ  CE   122.47  3.000
 KAP  CH   CZ  CE   116.50  3.000
 KAP  HH   CH  N    108.11  3.000
 KAP  HH   CH  CS   107.74  3.000
 KAP  N    CH  CS   114.41  3.000
 KAP  HH   CH  CZ   107.61  3.000
 KAP  N    CH  CZ   110.04  3.000
 KAP  CS   CH  CZ   108.70  3.000
 KAP  HS1  CS  HS2  108.20  3.000
 KAP  HS1  CS  HS3  107.49  3.000
 KAP  HS2  CS  HS3  107.99  3.000
 KAP  HS1  CS  CH   112.57  3.000
 KAP  HS2  CS  CH   110.92  3.000
 KAP  HS3  CS  CH   109.51  3.000
 KAP  H2   N   H1   105.86  3.000
 KAP  H2   N   CH   108.80  3.000
 KAP  H1   N   CH   109.71  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
 KAP  Var_01  CD  CG  CB  CA   -179.55  30.0  3
 KAP  Var_02  CG  CB  CA  C    -179.85  30.0  3
 KAP  Var_03  CB  CA  C   OI1   173.82  30.0  2
 KAP  Var_04  CE  CD  CG  CB   -178.86  30.0  3
 KAP  Var_05  CZ  CE  CD  CG   -178.67  30.0  3
 KAP  Var_06  CH  CZ  CE  CD    175.50  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
 KAP  chir_01  CH  CZ  CS  N  positiv

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
 KAP  plan-1  CE   0.020
 KAP  plan-1  CZ   0.020
 KAP  plan-1  CH   0.020
 KAP  plan-1  O    0.020
 KAP  plan-2  CA   0.020
 KAP  plan-2  C    0.020
 KAP  plan-2  OI1  0.020
 KAP  plan-2  OI2  0.020

