# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 01:24:15 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: (3S,4S)-3-(carboxymethyl)-4-(1-methylethenyl)-L-proline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=C)[C@H]1CN[C@@H]([C@H]1CC(O)=O)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
 KAI  KAI  (3S,4S)-3-(carboxymethyl)-4-(1-methylethenyl)-L-proline  ligand  30  15  .  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_KAI
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
 KAI  N     N  NH1   0  -0.606   0.3594  -1.3656  -1.4970
 KAI  CD    C  CH2   0  -0.255  -1.0549  -1.5712  -1.1765
 KAI  CD1   C  C2    0  -0.598  -3.6763  -0.3974  -0.3573
 KAI  CD2   C  CH3   0  -0.717  -2.7533   0.3593   1.8067
 KAI  CA    C  CH1   0  -0.186   1.0171  -0.6759  -0.4128
 KAI  CB    C  CH1   0  -0.294  -0.1163   0.1512   0.2186
 KAI  CB1   C  CH2   0  -0.583  -0.4111   1.4003  -0.6000
 KAI  CG    C  CH1   0  -0.313  -1.2724  -0.8705   0.1672
 KAI  CG1   C  C     0   0.558   0.6017   2.4963  -0.4103
 KAI  CG2   C  C     0   0.154  -2.6320  -0.3013   0.4633
 KAI  C     C  C     0   0.529   1.6444  -1.6080   0.6116
 KAI  O     O  O     0  -0.438   1.5075  -2.8061   0.6247
 KAI  OD1   O  OH1   0  -0.596   0.3888   3.5095  -1.2445
 KAI  OD2   O  O     0  -0.439   1.4910   2.4919   0.4040
 KAI  OXT   O  OH1   0  -0.587   2.3826  -0.9457   1.4926
 KAI  HN1   H  HNH1  0   0.357   0.8277  -2.2213  -1.7555
 KAI  HD1   H  HCH2  0   0.212  -1.6776  -1.1341  -1.9624
 KAI  HD2   H  HCH2  0   0.237  -1.3185  -2.6290  -1.1121
 KAI  HD11  H  H     0   0.234  -4.6410   0.0101  -0.0804
 KAI  HD12  H  H     0   0.234  -3.6230  -0.8840  -1.3221
 KAI  HD21  H  HCH3  0   0.241  -2.4925  -0.3393   2.6058
 KAI  HD22  H  HCH3  0   0.238  -2.0700   1.2067   1.9009
 KAI  HD23  H  HCH3  0   0.245  -3.7640   0.7210   1.9895
 KAI  HA    H  HCH1  0   0.281   1.8201  -0.0309  -0.7869
 KAI  HB    H  HCH1  0   0.277   0.1153   0.4369   1.2448
 KAI  HB11  H  HCH2  0   0.290  -0.4880   1.1689  -1.6659
 KAI  HB12  H  HCH2  0   0.298  -1.3865   1.8157  -0.3243
 KAI  HG    H  HCH1  0   0.266  -1.0731  -1.5993   0.9635
 KAI  HOD1  H  HOH1  0   0.479   1.0332   4.2140  -1.0789
 KAI  HXT   H  HOH1  0   0.481   2.7705  -1.5611   2.1329

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
 KAI  N    CD    single  1.465  0.020  1.465
 KAI  N    CA    single  1.444  0.020  1.444
 KAI  N    HN1   single  0.890  0.020  1.040
 KAI  CD   CG    single  1.531  0.020  1.531
 KAI  CD   HD1   single  0.970  0.020  1.090
 KAI  CD   HD2   single  0.970  0.020  1.090
 KAI  CD1  CG2   double  1.332  0.020  1.332
 KAI  CD1  HD11  single  0.930  0.020  1.080
 KAI  CD1  HD12  single  0.930  0.020  1.080
 KAI  CD2  CG2   single  1.502  0.020  1.502
 KAI  CD2  HD21  single  0.970  0.020  1.090
 KAI  CD2  HD22  single  0.970  0.020  1.090
 KAI  CD2  HD23  single  0.970  0.020  1.090
 KAI  CA   CB    single  1.539  0.020  1.539
 KAI  CA   C     single  1.520  0.020  1.520
 KAI  CA   HA    single  0.970  0.020  1.090
 KAI  CB   CB1   single  1.522  0.020  1.522
 KAI  CB   CG    single  1.544  0.020  1.544
 KAI  CB   HB    single  0.970  0.020  1.090
 KAI  CB1  CG1   single  1.504  0.020  1.504
 KAI  CB1  HB11  single  0.970  0.020  1.090
 KAI  CB1  HB12  single  0.970  0.020  1.090
 KAI  CG   CG2   single  1.503  0.020  1.503
 KAI  CG   HG    single  0.970  0.020  1.090
 KAI  CG1  OD1   single  1.330  0.020  1.330
 KAI  CG1  OD2   double  1.206  0.020  1.206
 KAI  C    O     double  1.206  0.020  1.206
 KAI  C    OXT   single  1.327  0.020  1.327
 KAI  OD1  HOD1  single  0.850  0.020  0.980
 KAI  OXT  HXT   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
 KAI  HN1   N    CA    112.71  3.000
 KAI  HN1   N    CD    112.65  3.000
 KAI  CA    N    CD    110.04  3.000
 KAI  HD2   CD   HD1   106.98  3.000
 KAI  HD2   CD   CG    110.93  3.000
 KAI  HD1   CD   CG    111.52  3.000
 KAI  HD2   CD   N     112.46  3.000
 KAI  HD1   CD   N     109.66  3.000
 KAI  CG    CD   N     105.37  3.000
 KAI  HD12  CD1  HD11  116.17  3.000
 KAI  HD12  CD1  CG2   122.92  3.000
 KAI  HD11  CD1  CG2   120.91  3.000
 KAI  HD23  CD2  HD22  107.96  3.000
 KAI  HD23  CD2  HD21  108.12  3.000
 KAI  HD22  CD2  HD21  106.46  3.000
 KAI  HD23  CD2  CG2   111.79  3.000
 KAI  HD22  CD2  CG2   111.58  3.000
 KAI  HD21  CD2  CG2   110.71  3.000
 KAI  HA    CA   C     106.77  3.000
 KAI  HA    CA   CB    111.32  3.000
 KAI  C     CA   CB    110.91  3.000
 KAI  HA    CA   N     111.02  3.000
 KAI  C     CA   N     113.65  3.000
 KAI  CB    CA   N     103.26  3.000
 KAI  HB    CB   CG    111.34  3.000
 KAI  HB    CB   CB1   109.41  3.000
 KAI  CG    CB   CB1   112.34  3.000
 KAI  HB    CB   CA    111.76  3.000
 KAI  CG    CB   CA    100.50  3.000
 KAI  CB1   CB   CA    111.29  3.000
 KAI  HB12  CB1  HB11  105.24  3.000
 KAI  HB12  CB1  CG1   106.94  3.000
 KAI  HB11  CB1  CG1   108.94  3.000
 KAI  HB12  CB1  CB    110.38  3.000
 KAI  HB11  CB1  CB    111.36  3.000
 KAI  CG1   CB1  CB    113.56  3.000
 KAI  HG    CG   CG2   105.83  3.000
 KAI  HG    CG   CB    106.22  3.000
 KAI  CG2   CG   CB    114.85  3.000
 KAI  HG    CG   CD    107.88  3.000
 KAI  CG2   CG   CD    118.34  3.000
 KAI  CB    CG   CD    103.04  3.000
 KAI  OD2   CG1  OD1   123.00  3.000
 KAI  OD2   CG1  CB1   125.38  3.000
 KAI  OD1   CG1  CB1   111.61  3.000
 KAI  CG    CG2  CD2   114.56  3.000
 KAI  CG    CG2  CD1   124.09  3.000
 KAI  CD2   CG2  CD1   121.31  3.000
 KAI  OXT   C    O     123.50  3.000
 KAI  OXT   C    CA    111.77  3.000
 KAI  O     C    CA    124.72  3.000
 KAI  HOD1  OD1  CG1   109.89  3.000
 KAI  HXT   OXT  C     110.15  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
 KAI  CONST_01  HXT   OXT  C    CA   180.00   0.0  0
 KAI  CONST_02  HOD1  OD1  CG1  CB1  180.00   0.0  0
 KAI  Var_01    CG    CD   N    CA     3.71  30.0  1
 KAI  Var_02    OD1   CG1  CB1  CB   173.36  30.0  3
 KAI  Var_03    HD11  CD1  CG2  CG   178.40   0.0  2
 KAI  Var_04    HD21  CD2  CG2  CG   -57.21  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
 KAI  chir_01  CA  N    CB   C   negativ
 KAI  chir_02  CB  CA   CB1  CG  negativ
 KAI  chir_03  CG  CG2  CB   CD  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
 KAI  plan-1  CB1   0.020
 KAI  plan-1  CG1   0.020
 KAI  plan-1  OD1   0.020
 KAI  plan-1  OD2   0.020
 KAI  plan-1  HOD1  0.020
 KAI  plan-2  CA    0.020
 KAI  plan-2  C     0.020
 KAI  plan-2  O     0.020
 KAI  plan-2  OXT   0.020
 KAI  plan-2  HXT   0.020
 KAI  plan-3  CD1   0.020
 KAI  plan-3  CD2   0.020
 KAI  plan-3  CG    0.020
 KAI  plan-3  CG2   0.020
 KAI  plan-3  HD11  0.020
 KAI  plan-3  HD12  0.020

