# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 23:14:41 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 5-amino-6-cyclohexyl-2,5,6-trideoxy-2-(1-methylethyl)-L-idonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@H]([C@@H](O)[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
 CAV  CAV  '5-amino-6-cyclohexyl-2,5,6-trideoxy-2-(1-methylethyl)-L-idonic acid'  peptide  48  20  .  2022-03-15  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CAV
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
 CAV  N     N  NH2    0  -0.795   2.0391  -0.5175  -1.0173
 CAV  CA    C  CH1    0  -0.133   0.6003  -0.3733  -0.8305
 CAV  CB    C  CH2    0  -0.410  -0.2406  -0.8705  -2.0116
 CAV  CG    C  CH1    0  -0.232   0.0821  -0.2302  -3.3612
 CAV  CD1   C  CH2    0  -0.410  -0.7275  -0.8934  -4.4767
 CAV  CD2   C  CH2    0  -0.422  -0.1522   1.2809  -3.3705
 CAV  CE1   C  CH2    0  -0.431  -0.4299  -0.2874  -5.8441
 CAV  CE2   C  CH2    0  -0.427   0.1354   1.8978  -4.7365
 CAV  CZ    C  CH2    0  -0.428  -0.6661   1.2191  -5.8419
 CAV  CH    C  CH1    0   0.042   0.1626  -1.0429   0.4757
 CAV  OH    O  OH1    0  -0.681   0.3274  -2.4451   0.4403
 CAV  CB1   C  CH1    0   0.066   0.8824  -0.4368   1.7111
 CAV  CA'   C  CH1    0  -0.398  -0.0630  -0.3053   2.9054
 CAV  CB'   C  CH1    0  -0.229   0.6528   0.1261   4.2069
 CAV  CG1   C  CH3    0  -0.654   1.4197   1.4400   4.0912
 CAV  CG2   C  CH3    0  -0.645  -0.3134   0.1770   5.3887
 CAV  OB1   O  OH1    0  -0.679   2.0379  -1.2080   2.0161
 CAV  C     C  C      0   0.415  -1.2360   0.6407   2.5630
 CAV  O     O  O      0  -0.602  -0.9593   1.6828   1.9321
 CAV  OXT   O  OC    -1  -0.614  -2.3718   0.2982   2.9492
 CAV  H     H  HNH2   0   0.346   2.3450   0.0723  -1.7808
 CAV  H2    H  HNH2   0   0.332   2.2481  -1.4643  -1.3139
 CAV  HA    H  HCH1   0   0.224   0.3991   0.6932  -0.6810
 CAV  HB2   H  HCH2   0   0.214  -0.1117  -1.9551  -2.1002
 CAV  HB3   H  HCH2   0   0.202  -1.3029  -0.7049  -1.7921
 CAV  HG    H  HCH1   0   0.193   1.1437  -0.4059  -3.5851
 CAV  HD12  H  HCH2   0   0.220  -0.5260  -1.9689  -4.4874
 CAV  HD13  H  HCH2   0   0.202  -1.7975  -0.7831  -4.2591
 CAV  HD23  H  HCH2   0   0.203  -1.1934   1.4799  -3.0877
 CAV  HD22  H  HCH2   0   0.226   0.4669   1.7706  -2.6137
 CAV  HE12  H  HCH2   0   0.206   0.6129  -0.4903  -6.1121
 CAV  HE13  H  HCH2   0   0.223  -1.0438  -0.7664  -6.6113
 CAV  HE23  H  HCH2   0   0.206   1.2051   1.8024  -4.9551
 CAV  HE22  H  HCH2   0   0.223  -0.0788   2.9694  -4.7157
 CAV  HZ2   H  HCH2   0   0.223  -0.4081   1.6463  -6.8144
 CAV  HZ3   H  HCH2   0   0.206  -1.7331   1.4160  -5.6889
 CAV  HH    H  HCH1   0   0.218  -0.9152  -0.8732   0.5701
 CAV  HO    H  HOH1   0   0.433   1.2461  -2.6131   0.6846
 CAV  HB1   H  HCH1   0   0.214   1.2437   0.5558   1.4393
 CAV  HA'   H  HCH1   0   0.203  -0.4893  -1.2987   3.1049
 CAV  HB'   H  HCH1   0   0.204   1.3860  -0.6544   4.4414
 CAV  HG11  H  HCH3   0   0.214   1.9318   1.6597   5.0303
 CAV  HG12  H  HCH3   0   0.223   2.1794   1.4046   3.3101
 CAV  HG13  H  HCH3   0   0.216   0.7533   2.2742   3.8723
 CAV  HG21  H  HCH3   0   0.214  -1.0108   1.0111   5.3039
 CAV  HG22  H  HCH3   0   0.218  -0.9014  -0.7388   5.4653
 CAV  HG23  H  HCH3   0   0.216   0.2346   0.3001   6.3246
 CAV  HOB1  H  HOH1   0   0.445   1.8227  -1.8263   2.7220

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
 CAV  N    CA    single  1.458  0.019  1.458
 CAV  N    H     single  0.860  0.020  0.860
 CAV  N    H2    single  0.890  0.020  1.040
 CAV  CA   CB    single  1.521  0.033  1.521
 CAV  CA   CH    single  1.532  0.020  1.532
 CAV  CA   HA    single  0.970  0.020  0.970
 CAV  CB   CG    single  1.528  0.020  1.528
 CAV  CB   HB2   single  0.970  0.020  1.090
 CAV  CB   HB3   single  0.970  0.020  1.090
 CAV  CG   CD1   single  1.530  0.020  1.530
 CAV  CG   CD2   single  1.529  0.020  1.529
 CAV  CG   HG    single  0.970  0.020  1.090
 CAV  CD1  CE1   single  1.525  0.020  1.525
 CAV  CD1  HD12  single  0.970  0.020  1.090
 CAV  CD1  HD13  single  0.970  0.020  1.090
 CAV  CD2  CE2   single  1.526  0.020  1.526
 CAV  CD2  HD23  single  0.970  0.020  1.090
 CAV  CD2  HD22  single  0.970  0.020  1.090
 CAV  CE1  CZ    single  1.525  0.020  1.525
 CAV  CE1  HE12  single  0.970  0.020  1.090
 CAV  CE1  HE13  single  0.970  0.020  1.090
 CAV  CE2  CZ    single  1.525  0.020  1.525
 CAV  CE2  HE23  single  0.970  0.020  1.090
 CAV  CE2  HE22  single  0.970  0.020  1.090
 CAV  CZ   HZ2   single  0.970  0.020  1.090
 CAV  CZ   HZ3   single  0.970  0.020  1.090
 CAV  CH   OH    single  1.412  0.020  1.412
 CAV  CH   CB1   single  1.553  0.020  1.553
 CAV  CH   HH    single  0.970  0.020  1.090
 CAV  OH   HO    single  0.850  0.020  0.980
 CAV  CB1  CA'   single  1.529  0.020  1.529
 CAV  CB1  OB1   single  1.422  0.020  1.422
 CAV  CB1  HB1   single  0.970  0.020  1.090
 CAV  CA'  CB'   single  1.547  0.020  1.547
 CAV  CA'  C     single  1.545  0.020  1.545
 CAV  CA'  HA'   single  0.970  0.020  1.090
 CAV  CB'  CG1   single  1.526  0.020  1.526
 CAV  CB'  CG2   single  1.527  0.020  1.527
 CAV  CB'  HB'   single  0.970  0.020  1.090
 CAV  CG1  HG11  single  0.970  0.020  1.090
 CAV  CG1  HG12  single  0.970  0.020  1.090
 CAV  CG1  HG13  single  0.970  0.020  1.090
 CAV  CG2  HG21  single  0.970  0.020  1.090
 CAV  CG2  HG22  single  0.970  0.020  1.090
 CAV  CG2  HG23  single  0.970  0.020  1.090
 CAV  OB1  HOB1  single  0.850  0.020  0.980
 CAV  C    O     deloc   1.231  0.020  1.231
 CAV  C    OXT   deloc   1.248  0.020  1.248

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
 CAV  H2    N    H     105.14  3.000
 CAV  H2    N    CA    109.46  3.000
 CAV  H     N    CA    114.00  3.000
 CAV  HA    CA   CH    104.87  3.000
 CAV  HA    CA   CB    109.00  3.000
 CAV  CH    CA   CB    111.01  3.000
 CAV  HA    CA   N     110.00  3.000
 CAV  CH    CA   N     110.37  3.000
 CAV  CB    CA   N     110.40  1.500
 CAV  HB3   CB   HB2   106.23  3.000
 CAV  HB3   CB   CG    108.53  3.000
 CAV  HB2   CB   CG    108.57  3.000
 CAV  HB3   CB   CA    109.15  3.000
 CAV  HB2   CB   CA    108.59  3.000
 CAV  CG    CB   CA    115.39  3.000
 CAV  HG    CG   CD2   107.74  3.000
 CAV  HG    CG   CD1   107.06  3.000
 CAV  CD2   CG   CD1   110.05  3.000
 CAV  HG    CG   CB    108.47  3.000
 CAV  CD2   CG   CB    112.77  3.000
 CAV  CD1   CG   CB    110.52  3.000
 CAV  HD13  CD1  HD12  106.27  3.000
 CAV  HD13  CD1  CE1   109.15  3.000
 CAV  HD12  CD1  CE1   110.23  3.000
 CAV  HD13  CD1  CG    109.14  3.000
 CAV  HD12  CD1  CG    109.62  3.000
 CAV  CE1   CD1  CG    112.23  3.000
 CAV  HD22  CD2  HD23  106.12  3.000
 CAV  HD22  CD2  CE2   109.37  3.000
 CAV  HD23  CD2  CE2   109.64  3.000
 CAV  HD22  CD2  CG    110.59  3.000
 CAV  HD23  CD2  CG    108.85  3.000
 CAV  CE2   CD2  CG    112.09  3.000
 CAV  HE13  CE1  HE12  106.36  3.000
 CAV  HE13  CE1  CZ    110.30  3.000
 CAV  HE12  CE1  CZ    109.32  3.000
 CAV  HE13  CE1  CD1   110.22  3.000
 CAV  HE12  CE1  CD1   109.36  3.000
 CAV  CZ    CE1  CD1   111.16  3.000
 CAV  HE22  CE2  HE23  106.29  3.000
 CAV  HE22  CE2  CZ    110.32  3.000
 CAV  HE23  CE2  CZ    109.25  3.000
 CAV  HE22  CE2  CD2   110.02  3.000
 CAV  HE23  CE2  CD2   109.10  3.000
 CAV  CZ    CE2  CD2   111.71  3.000
 CAV  HZ3   CZ   HZ2   106.49  3.000
 CAV  HZ3   CZ   CE2   109.31  3.000
 CAV  HZ2   CZ   CE2   110.30  3.000
 CAV  HZ3   CZ   CE1   109.19  3.000
 CAV  HZ2   CZ   CE1   110.38  3.000
 CAV  CE2   CZ   CE1   111.06  3.000
 CAV  HH    CH   CB1   109.10  3.000
 CAV  HH    CH   OH    105.71  3.000
 CAV  CB1   CH   OH    110.69  3.000
 CAV  HH    CH   CA    106.68  3.000
 CAV  CB1   CH   CA    112.05  3.000
 CAV  OH    CH   CA    112.29  3.000
 CAV  HO    OH   CH    106.11  3.000
 CAV  HB1   CB1  OB1   106.13  3.000
 CAV  HB1   CB1  CA'   108.73  3.000
 CAV  OB1   CB1  CA'   112.43  3.000
 CAV  HB1   CB1  CH    108.09  3.000
 CAV  OB1   CB1  CH    109.61  3.000
 CAV  CA'   CB1  CH    111.62  3.000
 CAV  HA'   CA'  C     107.40  3.000
 CAV  HA'   CA'  CB'   106.19  3.000
 CAV  C     CA'  CB'   111.53  3.000
 CAV  HA'   CA'  CB1   107.69  3.000
 CAV  C     CA'  CB1   110.42  3.000
 CAV  CB'   CA'  CB1   113.28  3.000
 CAV  HB'   CB'  CG2   106.33  3.000
 CAV  HB'   CB'  CG1   107.04  3.000
 CAV  CG2   CB'  CG1   110.36  3.000
 CAV  HB'   CB'  CA'   106.91  3.000
 CAV  CG2   CB'  CA'   111.57  3.000
 CAV  CG1   CB'  CA'   114.15  3.000
 CAV  HG13  CG1  HG12  107.88  3.000
 CAV  HG13  CG1  HG11  107.78  3.000
 CAV  HG12  CG1  HG11  107.21  3.000
 CAV  HG13  CG1  CB'   111.53  3.000
 CAV  HG12  CG1  CB'   112.13  3.000
 CAV  HG11  CG1  CB'   110.11  3.000
 CAV  HG23  CG2  HG22  107.77  3.000
 CAV  HG23  CG2  HG21  107.55  3.000
 CAV  HG22  CG2  HG21  107.63  3.000
 CAV  HG23  CG2  CB'   110.47  3.000
 CAV  HG22  CG2  CB'   111.55  3.000
 CAV  HG21  CG2  CB'   111.70  3.000
 CAV  HOB1  OB1  CB1   108.90  3.000
 CAV  OXT   C    O     125.94  3.000
 CAV  OXT   C    CA'   117.03  3.000
 CAV  O     C    CA'   117.03  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
 CAV  Var_01  CZ    CE1  CD1  CG    -55.90  30.0  1
 CAV  Var_02  CZ    CE2  CD2  CG     54.99  30.0  1
 CAV  Var_03  CE1   CZ   CE2  CD2   -54.64  30.0  1
 CAV  Var_04  HG11  CG1  CB'  CA'  -177.63  30.0  3
 CAV  Var_05  HG21  CG2  CB'  CA'   -70.81  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
 CAV  chir_01  CA   N    CB   CH   negativ
 CAV  chir_02  CG   CB   CD1  CD2  negativ
 CAV  chir_03  CH   OH   CA   CB1  positiv
 CAV  chir_04  CB1  OB1  CH   CA'  negativ
 CAV  chir_05  CA'  CB1  CB'  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
 CAV  plan-1  CA'  0.020
 CAV  plan-1  C    0.020
 CAV  plan-1  O    0.020
 CAV  plan-1  OXT  0.020

