# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 20:56:44 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  30  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  -0.580   0.7251   0.1158  -3.3479
 KAP  C    C  C     0   0.550   0.0257  -0.0674  -4.6656
 KAP  OI1  O  OH1   0  -0.599   0.8679   0.0336  -5.6911
 KAP  OI2  O  O     0  -0.446  -1.1528  -0.2819  -4.8058
 KAP  CB   C  CH2   0  -0.418  -0.1936   0.0074  -2.1421
 KAP  CG   C  CH2   0  -0.417   0.5648   0.2081  -0.8364
 KAP  CD   C  CH2   0  -0.413  -0.3319   0.0731   0.3875
 KAP  CE   C  CH2   0  -0.568   0.4324   0.3042   1.6804
 KAP  CZ   C  C     0   0.410  -0.3823   0.1524   2.9375
 KAP  CH   C  CH1   0  -0.201   0.3729   0.2643   4.2519
 KAP  CS   C  CH3   0  -0.675   1.1141  -1.0570   4.5083
 KAP  O    O  O     0  -0.405  -1.5725  -0.0658   2.9173
 KAP  N    N  NH2   0  -0.784  -0.5325   0.6587   5.3127
 KAP  HA2  H  HCH2  0   0.275   1.2274   1.0888  -3.3624
 KAP  HA1  H  HCH2  0   0.276   1.5293  -0.6244  -3.2858
 KAP  HO1  H  HOH1  0   0.478   0.3879  -0.0806  -6.5248
 KAP  HB2  H  HCH2  0   0.226  -0.6798  -0.9720  -2.1339
 KAP  HB1  H  HCH2  0   0.226  -0.9930   0.7497  -2.2154
 KAP  HG2  H  HCH2  0   0.217   1.0388   1.1957  -0.8376
 KAP  HG1  H  HCH2  0   0.217   1.3806  -0.5203  -0.7728
 KAP  HD2  H  HCH2  0   0.224  -0.7844  -0.9224   0.3969
 KAP  HD1  H  HCH2  0   0.224  -1.1575   0.7861   0.3153
 KAP  HE2  H  HCH2  0   0.270   0.8651   1.3117   1.6965
 KAP  HE1  H  HCH2  0   0.264   1.2968  -0.3668   1.7405
 KAP  HH   H  HCH1  0   0.253   1.1247   1.0518   4.1361
 KAP  HS3  H  HCH3  0   0.246   1.6634  -0.9896   5.4482
 KAP  HS2  H  HCH3  0   0.231   0.4116  -1.8886   4.5870
 KAP  HS1  H  HCH3  0   0.231   1.8340  -1.2927   3.7239
 KAP  H1   H  HNH2  0   0.340  -1.2375  -0.0568   5.4442
 KAP  H2   H  HNH2  0   0.350  -0.0166   0.7020   6.1828

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  1.503  0.020  1.503
 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  single  1.331  0.020  1.331
 KAP  C    OI2  double  1.206  0.020  1.206
 KAP  OI1  HO1  single  0.850  0.020  0.980
 KAP  CB   CG   single  1.523  0.020  1.523
 KAP  CB   HB2  single  0.970  0.020  1.090
 KAP  CB   HB1  single  0.970  0.020  1.090
 KAP  CG   CD   single  1.523  0.020  1.523
 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  105.35  3.000
 KAP  HA1  CA   CB   110.54  3.000
 KAP  HA2  CA   CB   110.56  3.000
 KAP  HA1  CA   C    108.00  3.000
 KAP  HA2  CA   C    108.06  3.000
 KAP  CB   CA   C    113.93  3.000
 KAP  OI2  C    OI1  122.84  3.000
 KAP  OI2  C    CA   125.33  3.000
 KAP  OI1  C    CA   111.83  3.000
 KAP  HO1  OI1  C    109.91  3.000
 KAP  HB1  CB   HB2  106.48  3.000
 KAP  HB1  CB   CG   109.39  3.000
 KAP  HB2  CB   CG   109.45  3.000
 KAP  HB1  CB   CA   109.90  3.000
 KAP  HB2  CB   CA   109.79  3.000
 KAP  CG   CB   CA   111.69  3.000
 KAP  HG1  CG   HG2  106.10  3.000
 KAP  HG1  CG   CD   109.44  3.000
 KAP  HG2  CG   CD   109.60  3.000
 KAP  HG1  CG   CB   109.45  3.000
 KAP  HG2  CG   CB   109.47  3.000
 KAP  CD   CG   CB   112.58  3.000
 KAP  HD1  CD   HD2  106.37  3.000
 KAP  HD1  CD   CE   109.69  3.000
 KAP  HD2  CD   CE   109.83  3.000
 KAP  HD1  CD   CG   109.49  3.000
 KAP  HD2  CD   CG   109.33  3.000
 KAP  CE   CD   CG   111.97  3.000
 KAP  HE1  CE   HE2  104.51  3.000
 KAP  HE1  CE   CZ   108.62  3.000
 KAP  HE2  CE   CZ   107.09  3.000
 KAP  HE1  CE   CD   110.50  3.000
 KAP  HE2  CE   CD   110.53  3.000
 KAP  CZ   CE   CD   115.01  3.000
 KAP  O    CZ   CH   121.08  3.000
 KAP  O    CZ   CE   122.44  3.000
 KAP  CH   CZ   CE   116.47  3.000
 KAP  HH   CH   N    108.10  3.000
 KAP  HH   CH   CS   107.76  3.000
 KAP  N    CH   CS   114.40  3.000
 KAP  HH   CH   CZ   107.61  3.000
 KAP  N    CH   CZ   110.03  3.000
 KAP  CS   CH   CZ   108.70  3.000
 KAP  HS1  CS   HS2  108.19  3.000
 KAP  HS1  CS   HS3  107.50  3.000
 KAP  HS2  CS   HS3  108.01  3.000
 KAP  HS1  CS   CH   112.59  3.000
 KAP  HS2  CS   CH   110.90  3.000
 KAP  HS3  CS   CH   109.49  3.000
 KAP  H2   N    H1   105.86  3.000
 KAP  H2   N    CH   108.80  3.000
 KAP  H1   N    CH   109.73  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  CONST_01  HO1  OI1  C   CA    180.00   0.0  0
 KAP  Var_01    CD   CG   CB  CA   -178.74  30.0  3
 KAP  Var_02    CG   CB   CA  C    -179.70  30.0  3
 KAP  Var_03    CB   CA   C   OI1  -179.91  30.0  2
 KAP  Var_04    CE   CD   CG  CB   -178.82  30.0  3
 KAP  Var_05    CZ   CE   CD  CG   -178.51  30.0  3
 KAP  Var_06    CH   CZ   CE  CD    175.18  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
 KAP  plan-2  HO1  0.020

