# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 21:21:43 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: (2R,4S,5S)-5-amino-6-cyclohexyl-4-hydroxy-2-(2-methylpropyl)hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](C[C@H](O)[C@@H](N)CC1CCCCC1)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
 CAL  CAL  '(2R,4S,5S)-5-amino-6-cyclohexyl-4-hydroxy-2-(2-methylpropyl)hexanoic acid'  peptide  51  20  .  2022-03-15  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_CAL
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
 CAL  N     N  NH2   0  -0.809  -1.8669   0.6367  -0.9221
 CAL  CA    C  CH1   0  -0.116  -0.4758   0.2006  -0.9952
 CAL  CB    C  CH2   0  -0.419   0.2786   0.7408  -2.2123
 CAL  CG    C  CH1   0  -0.225  -0.2652   0.3076  -3.5724
 CAL  CD1   C  CH2   0  -0.412   0.5064   1.0043  -4.6950
 CAL  CD2   C  CH2   0  -0.423  -0.2200  -1.2090  -3.7640
 CAL  CE1   C  CH2   0  -0.431   0.0247   0.5879  -6.0808
 CAL  CE2   C  CH2   0  -0.427  -0.6999  -1.6292  -5.1504
 CAL  CZ    C  CH2   0  -0.429   0.0830  -0.9258  -6.2531
 CAL  CH    C  CH1   0   0.055   0.2434   0.5741   0.3091
 CAL  OH    O  OH1   0  -0.673   0.1448   1.9619   0.5703
 CAL  CM    C  CH2   0  -0.454  -0.2671  -0.2494   1.4884
 CAL  CA2   C  CH1   0  -0.378   0.4760   0.0131   2.7942
 CAL  CB2   C  CH2   0  -0.406  -0.1925  -0.6766   3.9993
 CAL  CG2   C  CH1   0  -0.242  -1.5514  -0.0993   4.4048
 CAL  CD3   C  CH3   0  -0.650  -2.1515  -0.9502   5.5204
 CAL  CD4   C  CH3   0  -0.660  -1.4484   1.3598   4.8382
 CAL  C     C  C     0   0.553   1.9005  -0.4851   2.7236
 CAL  O     O  O     0  -0.447   2.2699  -1.4407   2.0850
 CAL  OXT   O  OH1   0  -0.593   2.7209   0.2242   3.4934
 CAL  H     H  HNH2  0   0.354  -2.4534   0.0478  -1.4972
 CAL  H2    H  HNH2  0   0.342  -1.9602   1.5716  -1.3019
 CAL  HA    H  HCH1  0   0.228  -0.4761  -0.8929  -1.0407
 CAL  HB2   H  HCH2  0   0.217   0.2814   1.8360  -2.1613
 CAL  HB3   H  HCH2  0   0.208   1.3289   0.4335  -2.1416
 CAL  HG    H  HCH1  0   0.198  -1.3139   0.6258  -3.6520
 CAL  HD12  H  HCH2  0   0.221   0.4249   2.0893  -4.5779
 CAL  HD13  H  HCH2  0   0.202   1.5724   0.7645  -4.5958
 CAL  HD23  H  HCH2  0   0.203   0.8099  -1.5558  -3.6118
 CAL  HD22  H  HCH2  0   0.226  -0.8269  -1.7107  -3.0054
 CAL  HE12  H  HCH2  0   0.206  -1.0065   0.9290  -6.2254
 CAL  HE13  H  HCH2  0   0.223   0.6234   1.0817  -6.8505
 CAL  HE23  H  HCH2  0   0.206  -1.7636  -1.3857  -5.2511
 CAL  HE22  H  HCH2  0   0.223  -0.6210  -2.7140  -5.2597
 CAL  HZ2   H  HCH2  0   0.224  -0.3010  -1.2134  -7.2350
 CAL  HZ3   H  HCH2  0   0.206   1.1283  -1.2527  -6.2193
 CAL  HH    H  HCH1  0   0.221   1.3114   0.3768   0.1660
 CAL  HO    H  HOH1  0   0.437  -0.7889   2.1565   0.7139
 CAL  HM1   H  HCH2  0   0.229  -0.2016  -1.3130   1.2439
 CAL  HM2   H  HCH2  0   0.242  -1.3311  -0.0347   1.6211
 CAL  HA2   H  HCH1  0   0.262   0.5105   1.0880   2.9846
 CAL  HB21  H  HCH2  0   0.233   0.4690  -0.6147   4.8702
 CAL  HB22  H  HCH2  0   0.232  -0.3063  -1.7421   3.7735
 CAL  HG2   H  HCH1  0   0.223  -2.2289  -0.1529   3.5466
 CAL  HD31  H  HCH3  0   0.227  -3.1238  -0.5639   5.8304
 CAL  HD32  H  HCH3  0   0.226  -2.2913  -1.9842   5.2003
 CAL  HD33  H  HCH3  0   0.214  -1.5020  -0.9606   6.3994
 CAL  HD41  H  HCH3  0   0.215  -0.7459   1.4725   5.6681
 CAL  HD42  H  HCH3  0   0.227  -1.1103   2.0112   4.0306
 CAL  HD43  H  HCH3  0   0.230  -2.4169   1.7367   5.1699
 CAL  HXT   H  HOH1  0   0.477   3.6102  -0.1605   3.4711

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
 CAL  N    CA    single  1.458  0.019  1.458
 CAL  N    H     single  0.860  0.020  0.860
 CAL  N    H2    single  0.890  0.020  1.040
 CAL  CA   CB    single  1.521  0.033  1.521
 CAL  CA   CH    single  1.536  0.020  1.536
 CAL  CA   HA    single  0.970  0.020  0.970
 CAL  CB   CG    single  1.527  0.020  1.527
 CAL  CB   HB2   single  0.970  0.020  1.090
 CAL  CB   HB3   single  0.970  0.020  1.090
 CAL  CG   CD1   single  1.530  0.020  1.530
 CAL  CG   CD2   single  1.529  0.020  1.529
 CAL  CG   HG    single  0.970  0.020  1.090
 CAL  CD1  CE1   single  1.525  0.020  1.525
 CAL  CD1  HD12  single  0.970  0.020  1.090
 CAL  CD1  HD13  single  0.970  0.020  1.090
 CAL  CD2  CE2   single  1.526  0.020  1.526
 CAL  CD2  HD23  single  0.970  0.020  1.090
 CAL  CD2  HD22  single  0.970  0.020  1.090
 CAL  CE1  CZ    single  1.525  0.020  1.525
 CAL  CE1  HE12  single  0.970  0.020  1.090
 CAL  CE1  HE13  single  0.970  0.020  1.090
 CAL  CE2  CZ    single  1.524  0.020  1.524
 CAL  CE2  HE23  single  0.970  0.020  1.090
 CAL  CE2  HE22  single  0.970  0.020  1.090
 CAL  CZ   HZ2   single  0.970  0.020  1.090
 CAL  CZ   HZ3   single  0.970  0.020  1.090
 CAL  CH   OH    single  1.416  0.020  1.416
 CAL  CH   CM    single  1.526  0.020  1.526
 CAL  CH   HH    single  0.970  0.020  1.090
 CAL  OH   HO    single  0.850  0.020  0.980
 CAL  CM   CA2   single  1.525  0.020  1.525
 CAL  CM   HM1   single  0.970  0.020  1.090
 CAL  CM   HM2   single  0.970  0.020  1.090
 CAL  CA2  CB2   single  1.541  0.020  1.541
 CAL  CA2  C     single  1.511  0.020  1.511
 CAL  CA2  HA2   single  0.970  0.020  1.090
 CAL  CB2  CG2   single  1.531  0.020  1.531
 CAL  CB2  HB21  single  0.970  0.020  1.090
 CAL  CB2  HB22  single  0.970  0.020  1.090
 CAL  CG2  CD3   single  1.526  0.020  1.526
 CAL  CG2  CD4   single  1.526  0.020  1.526
 CAL  CG2  HG2   single  0.970  0.020  1.090
 CAL  CD3  HD31  single  0.970  0.020  1.090
 CAL  CD3  HD32  single  0.970  0.020  1.090
 CAL  CD3  HD33  single  0.970  0.020  1.090
 CAL  CD4  HD41  single  0.970  0.020  1.090
 CAL  CD4  HD42  single  0.970  0.020  1.090
 CAL  CD4  HD43  single  0.970  0.020  1.090
 CAL  C    O     double  1.231  0.020  1.231
 CAL  C    OXT   single  1.330  0.020  1.330
 CAL  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
 CAL  H2    N    H     105.71  3.000
 CAL  H2    N    CA    110.16  3.000
 CAL  H     N    CA    114.00  3.000
 CAL  HA    CA   CH    106.17  3.000
 CAL  HA    CA   CB    109.00  3.000
 CAL  CH    CA   CB    111.03  3.000
 CAL  HA    CA   N     110.00  3.000
 CAL  CH    CA   N     109.33  3.000
 CAL  CB    CA   N     110.40  1.500
 CAL  HB3   CB   HB2   105.93  3.000
 CAL  HB3   CB   CG    108.59  3.000
 CAL  HB2   CB   CG    109.00  3.000
 CAL  HB3   CB   CA    108.78  3.000
 CAL  HB2   CB   CA    108.47  3.000
 CAL  CG    CB   CA    115.63  3.000
 CAL  HG    CG   CD2   107.83  3.000
 CAL  HG    CG   CD1   107.24  3.000
 CAL  CD2   CG   CD1   110.17  3.000
 CAL  HG    CG   CB    108.79  3.000
 CAL  CD2   CG   CB    112.47  3.000
 CAL  CD1   CG   CB    110.16  3.000
 CAL  HD13  CD1  HD12  106.23  3.000
 CAL  HD13  CD1  CE1   109.23  3.000
 CAL  HD12  CD1  CE1   110.15  3.000
 CAL  HD13  CD1  CG    108.91  3.000
 CAL  HD12  CD1  CG    109.60  3.000
 CAL  CE1   CD1  CG    112.52  3.000
 CAL  HD22  CD2  HD23  106.24  3.000
 CAL  HD22  CD2  CE2   109.24  3.000
 CAL  HD23  CD2  CE2   109.52  3.000
 CAL  HD22  CD2  CG    110.59  3.000
 CAL  HD23  CD2  CG    108.89  3.000
 CAL  CE2   CD2  CG    112.18  3.000
 CAL  HE13  CE1  HE12  106.37  3.000
 CAL  HE13  CE1  CZ    110.36  3.000
 CAL  HE12  CE1  CZ    109.28  3.000
 CAL  HE13  CE1  CD1   110.09  3.000
 CAL  HE12  CE1  CD1   109.40  3.000
 CAL  CZ    CE1  CD1   111.21  3.000
 CAL  HE22  CE2  HE23  106.34  3.000
 CAL  HE22  CE2  CZ    110.40  3.000
 CAL  HE23  CE2  CZ    109.24  3.000
 CAL  HE22  CE2  CD2   109.96  3.000
 CAL  HE23  CE2  CD2   109.12  3.000
 CAL  CZ    CE2  CD2   111.63  3.000
 CAL  HZ3   CZ   HZ2   106.53  3.000
 CAL  HZ3   CZ   CE2   109.27  3.000
 CAL  HZ2   CZ   CE2   110.37  3.000
 CAL  HZ3   CZ   CE1   109.22  3.000
 CAL  HZ2   CZ   CE1   110.45  3.000
 CAL  CE2   CZ   CE1   110.90  3.000
 CAL  HH    CH   CM    109.26  3.000
 CAL  HH    CH   OH    105.58  3.000
 CAL  CM    CH   OH    111.29  3.000
 CAL  HH    CH   CA    107.57  3.000
 CAL  CM    CH   CA    111.62  3.000
 CAL  OH    CH   CA    111.26  3.000
 CAL  HO    OH   CH    107.02  3.000
 CAL  HM2   CM   HM1   106.04  3.000
 CAL  HM2   CM   CA2   109.65  3.000
 CAL  HM1   CM   CA2   109.25  3.000
 CAL  HM2   CM   CH    108.26  3.000
 CAL  HM1   CM   CH    109.39  3.000
 CAL  CA2   CM   CH    113.94  3.000
 CAL  HA2   CA2  C     107.63  3.000
 CAL  HA2   CA2  CB2   108.54  3.000
 CAL  C     CA2  CB2   107.34  3.000
 CAL  HA2   CA2  CM    109.51  3.000
 CAL  C     CA2  CM    111.26  3.000
 CAL  CB2   CA2  CM    112.40  3.000
 CAL  HB22  CB2  HB21  106.36  3.000
 CAL  HB22  CB2  CG2   109.22  3.000
 CAL  HB21  CB2  CG2   107.71  3.000
 CAL  HB22  CB2  CA2   108.62  3.000
 CAL  HB21  CB2  CA2   109.53  3.000
 CAL  CG2   CB2  CA2   115.05  3.000
 CAL  HG2   CG2  CD4   108.14  3.000
 CAL  HG2   CG2  CD3   107.61  3.000
 CAL  CD4   CG2  CD3   110.62  3.000
 CAL  HG2   CG2  CB2   108.86  3.000
 CAL  CD4   CG2  CB2   112.08  3.000
 CAL  CD3   CG2  CB2   109.41  3.000
 CAL  HD33  CD3  HD32  107.64  3.000
 CAL  HD33  CD3  HD31  107.72  3.000
 CAL  HD32  CD3  HD31  107.73  3.000
 CAL  HD33  CD3  CG2   111.07  3.000
 CAL  HD32  CD3  CG2   111.36  3.000
 CAL  HD31  CD3  CG2   111.14  3.000
 CAL  HD43  CD4  HD42  107.09  3.000
 CAL  HD43  CD4  HD41  107.69  3.000
 CAL  HD42  CD4  HD41  107.53  3.000
 CAL  HD43  CD4  CG2   110.91  3.000
 CAL  HD42  CD4  CG2   112.44  3.000
 CAL  HD41  CD4  CG2   110.96  3.000
 CAL  OXT   C    O     122.65  3.000
 CAL  OXT   C    CA2   112.26  3.000
 CAL  O     C    CA2   125.05  3.000
 CAL  HXT   OXT  C     109.94  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
 CAL  CONST_01  HXT   OXT  C    CA2   180.00   0.0  0
 CAL  Var_01    CZ    CE1  CD1  CG    -55.45  30.0  1
 CAL  Var_02    CZ    CE2  CD2  CG     55.22  30.0  1
 CAL  Var_03    CE1   CZ   CE2  CD2   -55.21  30.0  1
 CAL  Var_04    CD3   CG2  CB2  CA2   174.93  30.0  3
 CAL  Var_05    HD31  CD3  CG2  CB2  -179.90  30.0  3
 CAL  Var_06    HD41  CD4  CG2  CB2   -57.51  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
 CAL  chir_01  CA   N   CB   CH   negativ
 CAL  chir_02  CG   CB  CD1  CD2  negativ
 CAL  chir_03  CH   OH  CA   CM   positiv
 CAL  chir_04  CA2  CM  CB2  C    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
 CAL  plan-1  CA2  0.020
 CAL  plan-1  C    0.020
 CAL  plan-1  O    0.020
 CAL  plan-1  OXT  0.020
 CAL  plan-1  HXT  0.020

