# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 18:25:36 2022
#   Inital geometry file: a 68 line input string
#   Ligand name: 3-cyclohexyl-D-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](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
 ZAL  ZAL  '3-cyclohexyl-D-alanine   '  D-peptide  28  12  .  2016-04-26  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_ZAL
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
 ZAL  C1   C  CH1    0  -0.224  19.4079  15.0050  24.5746
 ZAL  C2   C  CH2    0  -0.408  19.7375  15.2874  26.0414
 ZAL  C3   C  CH2    0  -0.428  21.1572  15.8110  26.2300
 ZAL  C4   C  CH2    0  -0.426  22.1812  14.8516  25.6344
 ZAL  C5   C  CH2    0  -0.426  21.8751  14.5744  24.1675
 ZAL  C6   C  CH2    0  -0.417  20.4510  14.0614  23.9744
 ZAL  N    N  NH2    0  -0.799  16.1147  13.6044  23.0471
 ZAL  CA   C  CH1    0  -0.182  17.4543  14.1848  23.0354
 ZAL  CB   C  CH2    0  -0.427  17.9845  14.4616  24.4524
 ZAL  C    C  C      0   0.403  17.4463  15.4943  22.2161
 ZAL  O    O  O      0  -0.608  16.4479  16.2302  22.3655
 ZAL  H1   H  HCH1   0   0.203  19.4681  15.9564  24.0316
 ZAL  H2   H  HCH2   0   0.217  19.0165  16.0014  26.4512
 ZAL  H2A  H  HCH2   0   0.198  19.6174  14.3619  26.6185
 ZAL  H3   H  HCH2   0   0.204  21.2528  16.7886  25.7449
 ZAL  H3A  H  HCH2   0   0.220  21.3607  15.9729  27.2918
 ZAL  H4   H  HCH2   0   0.220  23.1910  15.2555  25.7433
 ZAL  H4A  H  HCH2   0   0.203  22.1614  13.9096  26.1943
 ZAL  H5   H  HCH2   0   0.204  22.0042  15.4984  23.5930
 ZAL  H5A  H  HCH2   0   0.220  22.5902  13.8558  23.7585
 ZAL  H6   H  HCH2   0   0.195  20.3511  13.0739  24.4423
 ZAL  H6A  H  HCH2   0   0.223  20.2582  13.9210  22.9092
 ZAL  HA   H  HCH1   0   0.195  18.1213  13.4708  22.5433
 ZAL  HB   H  HCH2   0   0.200  17.9226  13.5299  25.0303
 ZAL  HBA  H  HCH2   0   0.203  17.2942  15.1628  24.9373
 ZAL  OXT  O  OC    -1  -0.608  18.4462  15.7299  21.5083
 ZAL  HN   H  HNH2   0   0.325  16.0662  12.8765  23.7512
 ZAL  HNA  H  HNH2   0   0.321  15.4694  14.3268  23.3441

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
 ZAL  C1  C2   single  1.530  0.020  1.530
 ZAL  C1  C6   single  1.529  0.020  1.529
 ZAL  C1  CB   single  1.529  0.020  1.529
 ZAL  C1  H1   single  0.970  0.020  1.090
 ZAL  C2  C3   single  1.525  0.020  1.525
 ZAL  C2  H2   single  0.970  0.020  1.090
 ZAL  C2  H2A  single  0.970  0.020  1.090
 ZAL  C3  C4   single  1.524  0.020  1.524
 ZAL  C3  H3   single  0.970  0.020  1.090
 ZAL  C3  H3A  single  0.970  0.020  1.090
 ZAL  C4  C5   single  1.524  0.020  1.524
 ZAL  C4  H4   single  0.970  0.020  1.090
 ZAL  C4  H4A  single  0.970  0.020  1.090
 ZAL  C5  C6   single  1.526  0.020  1.526
 ZAL  C5  H5   single  0.970  0.020  1.090
 ZAL  C5  H5A  single  0.970  0.020  1.090
 ZAL  C6  H6   single  0.970  0.020  1.090
 ZAL  C6  H6A  single  0.970  0.020  1.090
 ZAL  N   CA   single  1.458  0.019  1.458
 ZAL  N   HN   single  0.890  0.020  1.040
 ZAL  N   HNA  single  0.890  0.020  1.040
 ZAL  CA  CB   single  1.521  0.033  1.521
 ZAL  CA  C    single  1.525  0.021  1.525
 ZAL  CA  HA   single  0.970  0.020  0.970
 ZAL  CB  HB   single  0.970  0.020  1.090
 ZAL  CB  HBA  single  0.970  0.020  1.090
 ZAL  C   O    deloc   1.231  0.020  1.231
 ZAL  C   OXT  deloc   1.247  0.020  1.247

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
 ZAL  H1   C1  CB  108.65  3.000
 ZAL  H1   C1  C6  107.66  3.000
 ZAL  CB   C1  C6  112.61  3.000
 ZAL  H1   C1  C2  107.62  3.000
 ZAL  CB   C1  C2  110.06  3.000
 ZAL  C6   C1  C2  110.08  3.000
 ZAL  H2A  C2  H2  106.34  3.000
 ZAL  H2A  C2  C3  109.05  3.000
 ZAL  H2   C2  C3  110.06  3.000
 ZAL  H2A  C2  C1  108.97  3.000
 ZAL  H2   C2  C1  109.73  3.000
 ZAL  C3   C2  C1  112.49  3.000
 ZAL  H3A  C3  H3  106.36  3.000
 ZAL  H3A  C3  C4  110.34  3.000
 ZAL  H3   C3  C4  109.27  3.000
 ZAL  H3A  C3  C2  110.14  3.000
 ZAL  H3   C3  C2  109.45  3.000
 ZAL  C4   C3  C2  111.16  3.000
 ZAL  H4A  C4  H4  106.46  3.000
 ZAL  H4A  C4  C5  109.38  3.000
 ZAL  H4   C4  C5  110.41  3.000
 ZAL  H4A  C4  C3  109.22  3.000
 ZAL  H4   C4  C3  110.43  3.000
 ZAL  C5   C4  C3  110.83  3.000
 ZAL  H5A  C5  H5  106.32  3.000
 ZAL  H5A  C5  C6  110.01  3.000
 ZAL  H5   C5  C6  109.10  3.000
 ZAL  H5A  C5  C4  110.38  3.000
 ZAL  H5   C5  C4  109.12  3.000
 ZAL  C6   C5  C4  111.74  3.000
 ZAL  H6A  C6  H6  106.51  3.000
 ZAL  H6A  C6  C5  109.36  3.000
 ZAL  H6   C6  C5  109.49  3.000
 ZAL  H6A  C6  C1  109.99  3.000
 ZAL  H6   C6  C1  109.02  3.000
 ZAL  C5   C6  C1  112.30  3.000
 ZAL  HNA  N   HN  106.13  3.000
 ZAL  HNA  N   CA  107.66  3.000
 ZAL  HN   N   CA  109.57  3.000
 ZAL  HA   CA  C   110.00  3.000
 ZAL  HA   CA  CB  109.00  3.000
 ZAL  C    CA  CB  110.50  1.500
 ZAL  HA   CA  N   110.00  3.000
 ZAL  C    CA  N   111.00  2.800
 ZAL  CB   CA  N   110.40  1.500
 ZAL  HBA  CB  HB  105.92  3.000
 ZAL  HBA  CB  CA  107.78  3.000
 ZAL  HB   CB  CA  108.22  3.000
 ZAL  HBA  CB  C1  108.87  3.000
 ZAL  HB   CB  C1  108.18  3.000
 ZAL  CA   CB  C1  117.30  3.000
 ZAL  OXT  C   O   126.67  3.000
 ZAL  OXT  C   CA  120.80  1.700
 ZAL  O    C   CA  120.80  1.700

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
 ZAL  Var_01  C4  C3  C2  C1  -55.81  30.0  1
 ZAL  Var_02  C4  C5  C6  C1   54.95  30.0  1
 ZAL  Var_03  C5  C4  C3  C2   55.24  30.0  1
 ZAL  Var_04  C6  C5  C4  C3  -55.03  30.0  1

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
 ZAL  chir_01  C1  C2  C6  CB  negativ
 ZAL  chir_02  CA  N   C   CB  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
 ZAL  plan-1  CA   0.020
 ZAL  plan-1  C    0.020
 ZAL  plan-1  O    0.020
 ZAL  plan-1  OXT  0.020

