# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 02:03:22 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: 4-amino-5-cyclohexyl-2,4,5-trideoxy-L-threo-pentonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC1CCCCC1)[C@@H](O)CC(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
 CHS  CHS  '4-amino-5-cyclohexyl-2,4,5-trideoxy-L-threo-pentonic acid'  peptide  36  15  .  2022-03-15  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CHS
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
 CHS  N     N  NH2   0  -0.829  -0.3367   1.7378   0.4238
 CHS  CA    C  CH1   0  -0.134  -0.2443   0.2801   0.3794
 CHS  CB    C  CH2   0  -0.407   0.6812  -0.1764  -0.7466
 CHS  CG    C  CH1   0  -0.249   0.2503   0.1883  -2.1675
 CHS  CD1   C  CH2   0  -0.409   1.3128  -0.2666  -3.1695
 CHS  CD2   C  CH2   0  -0.421  -1.1102  -0.3965  -2.5483
 CHS  CE1   C  CH2   0  -0.432   0.9352   0.0845  -4.6044
 CHS  CE2   C  CH2   0  -0.428  -1.4964  -0.0519  -3.9841
 CHS  CZ    C  CH2   0  -0.428  -0.4260  -0.4940  -4.9759
 CHS  CH    C  CH1   0   0.062   0.3144  -0.1705   1.7433
 CHS  OH    O  OH1   0  -0.681   1.4156   0.6340   2.0850
 CHS  CM    C  CH2   0  -0.595  -0.7569  -0.1032   2.8326
 CHS  C     C  C     0   0.548  -0.1975  -0.4993   4.1713
 CHS  O     O  O     0  -0.453   0.5203  -1.4522   4.3544
 CHS  OXT   O  OH1   0  -0.590  -0.5956   0.3027   5.1524
 CHS  H     H  HNH2  0   0.362  -1.2198   2.0342   0.8175
 CHS  H2    H  HNH2  0   0.366  -0.2895   2.1415  -0.5009
 CHS  HA    H  HCH1  0   0.227  -1.2253  -0.1922   0.2375
 CHS  HB2   H  HCH2  0   0.225   1.6841   0.2247  -0.5657
 CHS  HB3   H  HCH2  0   0.222   0.7721  -1.2659  -0.6818
 CHS  HG    H  HCH1  0   0.204   0.1812   1.2814  -2.2581
 CHS  HD12  H  HCH2  0   0.224   2.2770   0.1816  -2.9118
 CHS  HD13  H  HCH2  0   0.205   1.4423  -1.3523  -3.0808
 CHS  HD23  H  HCH2  0   0.205  -1.0698  -1.4872  -2.4347
 CHS  HD22  H  HCH2  0   0.229  -1.8866  -0.0420  -1.8652
 CHS  HE12  H  HCH2  0   0.207   0.9048   1.1746  -4.7119
 CHS  HE13  H  HCH2  0   0.224   1.7032  -0.2744  -5.2943
 CHS  HE23  H  HCH2  0   0.208  -1.6417   1.0307  -4.0697
 CHS  HE22  H  HCH2  0   0.225  -2.4560  -0.5116  -4.2339
 CHS  HZ2   H  HCH2  0   0.224  -0.7022  -0.1958  -5.9904
 CHS  HZ3   H  HCH2  0   0.207  -0.3662  -1.5880  -4.9794
 CHS  HH    H  HCH1  0   0.229   0.6590  -1.2057   1.6616
 CHS  HO    H  HOH1  0   0.435   1.1759   1.5033   1.7137
 CHS  HM1   H  HCH2  0   0.259  -1.2032   0.8919   2.8891
 CHS  HM2   H  HCH2  0   0.282  -1.5655  -0.8020   2.5944
 CHS  HXT   H  HOH1  0   0.477  -0.2356  -0.0061   5.9979

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
 CHS  N    CA    single  1.458  0.019  1.458
 CHS  N    H     single  0.860  0.020  0.860
 CHS  N    H2    single  0.890  0.020  1.040
 CHS  CA   CB    single  1.521  0.033  1.521
 CHS  CA   CH    single  1.541  0.020  1.541
 CHS  CA   HA    single  0.970  0.020  0.970
 CHS  CB   CG    single  1.529  0.020  1.529
 CHS  CB   HB2   single  0.970  0.020  1.090
 CHS  CB   HB3   single  0.970  0.020  1.090
 CHS  CG   CD1   single  1.530  0.020  1.530
 CHS  CG   CD2   single  1.529  0.020  1.529
 CHS  CG   HG    single  0.970  0.020  1.090
 CHS  CD1  CE1   single  1.525  0.020  1.525
 CHS  CD1  HD12  single  0.970  0.020  1.090
 CHS  CD1  HD13  single  0.970  0.020  1.090
 CHS  CD2  CE2   single  1.526  0.020  1.526
 CHS  CD2  HD23  single  0.970  0.020  1.090
 CHS  CD2  HD22  single  0.970  0.020  1.090
 CHS  CE1  CZ    single  1.525  0.020  1.525
 CHS  CE1  HE12  single  0.970  0.020  1.090
 CHS  CE1  HE13  single  0.970  0.020  1.090
 CHS  CE2  CZ    single  1.525  0.020  1.525
 CHS  CE2  HE23  single  0.970  0.020  1.090
 CHS  CE2  HE22  single  0.970  0.020  1.090
 CHS  CZ   HZ2   single  0.970  0.020  1.090
 CHS  CZ   HZ3   single  0.970  0.020  1.090
 CHS  CH   OH    single  1.406  0.020  1.406
 CHS  CH   CM    single  1.529  0.020  1.529
 CHS  CH   HH    single  0.970  0.020  1.090
 CHS  OH   HO    single  0.850  0.020  0.980
 CHS  CM   C     single  1.504  0.020  1.504
 CHS  CM   HM1   single  0.970  0.020  1.090
 CHS  CM   HM2   single  0.970  0.020  1.090
 CHS  C    O     double  1.231  0.020  1.231
 CHS  C    OXT   single  1.328  0.020  1.328
 CHS  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
 CHS  H2    N    H     106.26  3.000
 CHS  H2    N    CA    111.59  3.000
 CHS  H     N    CA    114.00  3.000
 CHS  HA    CA   CH    108.21  3.000
 CHS  HA    CA   CB    109.00  3.000
 CHS  CH    CA   CB    110.21  3.000
 CHS  HA    CA   N     110.00  3.000
 CHS  CH    CA   N     106.71  3.000
 CHS  CB    CA   N     110.40  1.500
 CHS  HB3   CB   HB2   106.18  3.000
 CHS  HB3   CB   CG    108.41  3.000
 CHS  HB2   CB   CG    108.92  3.000
 CHS  HB3   CB   CA    107.69  3.000
 CHS  HB2   CB   CA    108.88  3.000
 CHS  CG    CB   CA    116.30  3.000
 CHS  HG    CG   CD2   107.70  3.000
 CHS  HG    CG   CD1   106.59  3.000
 CHS  CD2   CG   CD1   109.95  3.000
 CHS  HG    CG   CB    109.36  3.000
 CHS  CD2   CG   CB    113.01  3.000
 CHS  CD1   CG   CB    110.00  3.000
 CHS  HD13  CD1  HD12  106.40  3.000
 CHS  HD13  CD1  CE1   109.46  3.000
 CHS  HD12  CD1  CE1   110.22  3.000
 CHS  HD13  CD1  CG    108.87  3.000
 CHS  HD12  CD1  CG    109.64  3.000
 CHS  CE1   CD1  CG    112.08  3.000
 CHS  HD22  CD2  HD23  106.48  3.000
 CHS  HD22  CD2  CE2   109.57  3.000
 CHS  HD23  CD2  CE2   109.34  3.000
 CHS  HD22  CD2  CG    110.63  3.000
 CHS  HD23  CD2  CG    108.76  3.000
 CHS  CE2   CD2  CG    111.91  3.000
 CHS  HE13  CE1  HE12  106.51  3.000
 CHS  HE13  CE1  CZ    110.42  3.000
 CHS  HE12  CE1  CZ    109.19  3.000
 CHS  HE13  CE1  CD1   110.14  3.000
 CHS  HE12  CE1  CD1   109.16  3.000
 CHS  CZ    CE1  CD1   111.28  3.000
 CHS  HE22  CE2  HE23  106.34  3.000
 CHS  HE22  CE2  CZ    110.23  3.000
 CHS  HE23  CE2  CZ    109.19  3.000
 CHS  HE22  CE2  CD2   110.01  3.000
 CHS  HE23  CE2  CD2   109.28  3.000
 CHS  CZ    CE2  CD2   111.64  3.000
 CHS  HZ3   CZ   HZ2   106.46  3.000
 CHS  HZ3   CZ   CE2   109.27  3.000
 CHS  HZ2   CZ   CE2   110.32  3.000
 CHS  HZ3   CZ   CE1   109.32  3.000
 CHS  HZ2   CZ   CE1   110.38  3.000
 CHS  CE2   CZ   CE1   110.99  3.000
 CHS  HH    CH   CM    108.39  3.000
 CHS  HH    CH   OH    108.23  3.000
 CHS  CM    CH   OH    110.51  3.000
 CHS  HH    CH   CA    108.94  3.000
 CHS  CM    CH   CA    111.32  3.000
 CHS  OH    CH   CA    109.38  3.000
 CHS  HO    OH   CH    103.00  3.000
 CHS  HM2   CM   HM1   106.91  3.000
 CHS  HM2   CM   C     107.47  3.000
 CHS  HM1   CM   C     110.24  3.000
 CHS  HM2   CM   CH    109.53  3.000
 CHS  HM1   CM   CH    111.30  3.000
 CHS  C     CM   CH    111.22  3.000
 CHS  OXT   C    O     122.88  3.000
 CHS  OXT   C    CM    112.76  3.000
 CHS  O     C    CM    124.34  3.000
 CHS  HXT   OXT  C     109.91  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
 CHS  CONST_01  HXT  OXT  C    CM   180.00   0.0  0
 CHS  Var_01    CZ   CE1  CD1  CG   -55.90  30.0  1
 CHS  Var_02    CZ   CE2  CD2  CG    55.43  30.0  1
 CHS  Var_03    CE1  CZ   CE2  CD2  -54.70  30.0  1
 CHS  Var_04    O    C    CM   CH   -44.67  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
 CHS  chir_01  CA  N   CB   CH   negativ
 CHS  chir_02  CG  CB  CD1  CD2  negativ
 CHS  chir_03  CH  OH  CA   CM   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
 CHS  plan-1  CM   0.020
 CHS  plan-1  C    0.020
 CHS  plan-1  O    0.020
 CHS  plan-1  OXT  0.020
 CHS  plan-1  HXT  0.020

