# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 21:24:56 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  28  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  -0.616   0.3378  -1.7145  -1.3126
 KAI  CD    C  CH2    0  -0.292  -1.1114  -1.5640  -1.2214
 KAI  CD1   C  C2     0  -0.610  -3.7240  -0.3578  -0.4867
 KAI  CD2   C  CH3    0  -0.719  -2.8900   0.3169   1.7410
 KAI  CA    C  CH1    0  -0.189   0.9595  -0.7485  -0.3988
 KAI  CB    C  CH1    0  -0.282  -0.1911   0.0828   0.2186
 KAI  CB1   C  CH2    0  -0.529  -0.4441   1.3826  -0.5471
 KAI  CG    C  CH1    0  -0.283  -1.3688  -0.9096   0.1321
 KAI  CG1   C  C      0   0.404   0.7106   2.3794  -0.3681
 KAI  CG2   C  C      0   0.169  -2.7221  -0.3176   0.3909
 KAI  C     C  C      0   0.401   1.8022  -1.4390   0.6974
 KAI  O     O  O      0  -0.607   1.7276  -2.6840   0.7850
 KAI  OD1   O  OC    -1  -0.626   1.4144   2.6398  -1.3677
 KAI  OD2   O  O      0  -0.620   0.8586   2.8535   0.7776
 KAI  OXT   O  OC    -1  -0.609   2.4905  -0.6875   1.4130
 KAI  HN1   H  HNH1   0   0.333   0.5872  -2.6256  -0.9424
 KAI  HD1   H  HCH2   0   0.198  -1.4844  -0.9254  -2.0300
 KAI  HD2   H  HCH2   0   0.227  -1.6063  -2.5311  -1.3329
 KAI  HD11  H  H      0   0.225  -4.6912   0.0727  -0.2544
 KAI  HD12  H  H      0   0.227  -3.6266  -0.8161  -1.4626
 KAI  HD21  H  HCH3   0   0.235  -2.6921  -0.4062   2.5363
 KAI  HD22  H  HCH3   0   0.237  -2.1788   1.1346   1.8794
 KAI  HD23  H  HCH3   0   0.237  -3.8951   0.7123   1.8842
 KAI  HA    H  HCH1   0   0.211   1.6304  -0.0772  -0.9472
 KAI  HB    H  HCH1   0   0.230   0.0349   0.3435   1.2535
 KAI  HB11  H  HCH2   0   0.197  -0.6073   1.1714  -1.6076
 KAI  HB12  H  HCH2   0   0.214  -1.3637   1.8459  -0.1732
 KAI  HG    H  HCH1   0   0.235  -1.1973  -1.6712   0.9068

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  1.460  0.020  1.460
 KAI  N    CA    single  1.468  0.020  1.468
 KAI  N    HN1   single  0.890  0.020  1.040
 KAI  CD   CG    single  1.525  0.020  1.525
 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  1.501  0.020  1.501
 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  1.548  0.020  1.548
 KAI  CA   C     single  1.546  0.020  1.546
 KAI  CA   HA    single  0.970  0.020  1.090
 KAI  CB   CB1   single  1.530  0.020  1.530
 KAI  CB   CG    single  1.543  0.020  1.543
 KAI  CB   HB    single  0.970  0.020  1.090
 KAI  CB1  CG1   single  1.536  0.020  1.536
 KAI  CB1  HB11  single  0.970  0.020  1.090
 KAI  CB1  HB12  single  0.970  0.020  1.090
 KAI  CG   CG2   single  1.500  0.020  1.500
 KAI  CG   HG    single  0.970  0.020  1.090
 KAI  CG1  OD1   deloc   1.250  0.020  1.250
 KAI  CG1  OD2   deloc   1.249  0.020  1.249
 KAI  C    O     deloc   1.250  0.020  1.250
 KAI  C    OXT   deloc   1.245  0.020  1.245

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    105.06  3.000
 KAI  HN1   N    CD    108.28  3.000
 KAI  CA    N    CD    108.28  3.000
 KAI  HD2   CD   HD1   106.64  3.000
 KAI  HD2   CD   CG    113.21  3.000
 KAI  HD1   CD   CG    110.32  3.000
 KAI  HD2   CD   N     110.63  3.000
 KAI  HD1   CD   N     110.60  3.000
 KAI  CG    CD   N     105.50  3.000
 KAI  HD12  CD1  HD11  116.21  3.000
 KAI  HD12  CD1  CG2   122.60  3.000
 KAI  HD11  CD1  CG2   121.19  3.000
 KAI  HD23  CD2  HD22  108.20  3.000
 KAI  HD23  CD2  HD21  108.15  3.000
 KAI  HD22  CD2  HD21  106.57  3.000
 KAI  HD23  CD2  CG2   112.01  3.000
 KAI  HD22  CD2  CG2   110.94  3.000
 KAI  HD21  CD2  CG2   110.77  3.000
 KAI  HA    CA   C     107.14  3.000
 KAI  HA    CA   CB    109.01  3.000
 KAI  C     CA   CB    111.24  3.000
 KAI  HA    CA   N     110.53  3.000
 KAI  C     CA   N     112.23  3.000
 KAI  CB    CA   N     106.68  3.000
 KAI  HB    CB   CG    111.41  3.000
 KAI  HB    CB   CB1   107.82  3.000
 KAI  CG    CB   CB1   113.10  3.000
 KAI  HB    CB   CA    110.65  3.000
 KAI  CG    CB   CA    101.52  3.000
 KAI  CB1   CB   CA    112.31  3.000
 KAI  HB12  CB1  HB11  106.70  3.000
 KAI  HB12  CB1  CG1   108.47  3.000
 KAI  HB11  CB1  CG1   110.52  3.000
 KAI  HB12  CB1  CB    109.11  3.000
 KAI  HB11  CB1  CB    110.24  3.000
 KAI  CG1   CB1  CB    111.64  3.000
 KAI  HG    CG   CG2   107.01  3.000
 KAI  HG    CG   CB    106.68  3.000
 KAI  CG2   CG   CB    115.17  3.000
 KAI  HG    CG   CD    107.56  3.000
 KAI  CG2   CG   CD    118.35  3.000
 KAI  CB    CG   CD    101.36  3.000
 KAI  OD2   CG1  OD1   126.01  3.000
 KAI  OD2   CG1  CB1   116.26  3.000
 KAI  OD1   CG1  CB1   117.73  3.000
 KAI  CG    CG2  CD2   115.02  3.000
 KAI  CG    CG2  CD1   123.57  3.000
 KAI  CD2   CG2  CD1   121.40  3.000
 KAI  OXT   C    O     126.42  3.000
 KAI  OXT   C    CA    116.06  3.000
 KAI  O     C    CA    117.52  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  Var_01  CG    CD   N    CA  -22.21  30.0  1
 KAI  Var_02  OD1   CG1  CB1  CB  112.33  30.0  3
 KAI  Var_03  HD11  CD1  CG2  CG  179.26   0.0  2
 KAI  Var_04  HD21  CD2  CG2  CG  -58.00  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-2  CA    0.020
 KAI  plan-2  C     0.020
 KAI  plan-2  O     0.020
 KAI  plan-2  OXT   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

