# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 10:25:52 2022
#   Inital geometry file: a 68 line input string
#   Ligand name: 3-cyclohexyl-L-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
 ALC  ALC  '3-cyclohexyl-L-alanine   '  L-peptide  28  12  .  2012-08-28  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_ALC
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
 ALC  N     N  NH2    0  -0.811  5.2360  20.1929  15.0102
 ALC  CA    C  CH1    0  -0.197  4.2246  20.4786  16.0217
 ALC  C     C  C      0   0.395  2.8169  20.1783  15.4575
 ALC  O     O  O      0  -0.606  2.6439  20.3816  14.2382
 ALC  CB    C  CH2    0  -0.422  4.2436  21.9258  16.5617
 ALC  CG    C  CH1    0  -0.220  5.1364  22.1605  17.7825
 ALC  CD2   C  CH2    0  -0.411  5.0809  23.6287  18.2086
 ALC  CE2   C  CH2    0  -0.429  5.9228  23.9103  19.4483
 ALC  CZ    C  CH2    0  -0.427  7.3686  23.4713  19.2442
 ALC  CE1   C  CH2    0  -0.422  7.4347  22.0051  18.8339
 ALC  CD1   C  CH2    0  -0.435  6.5910  21.7293  17.5926
 ALC  OXT   O  OC    -1  -0.613  1.9597  19.8022  16.2817
 ALC  H     H  HNH2   0   0.337  6.1153  20.6283  15.2566
 ALC  H2    H  HNH2   0   0.322  4.9328  20.6312  14.1487
 ALC  HA    H  HCH1   0   0.194  4.3873  19.8038  16.8705
 ALC  HB2   H  HCH2   0   0.202  4.5431  22.6000  15.7508
 ALC  HB3   H  HCH2   0   0.214  3.2317  22.2303  16.8497
 ALC  HG    H  HCH1   0   0.200  4.7243  21.5588  18.6054
 ALC  HD23  H  HCH2   0   0.201  5.4424  24.2494  17.3795
 ALC  HD22  H  HCH2   0   0.218  4.0419  23.9232  18.3834
 ALC  HE23  H  HCH2   0   0.221  5.8789  24.9732  19.6993
 ALC  HE22  H  HCH2   0   0.205  5.5007  23.3712  20.3036
 ALC  HZ3   H  HCH2   0   0.205  7.8284  24.0873  18.4638
 ALC  HZ2   H  HCH2   0   0.222  7.9507  23.6380  20.1543
 ALC  HE13  H  HCH2   0   0.222  8.4704  21.7057  18.6552
 ALC  HE12  H  HCH2   0   0.206  7.0710  21.3843  19.6603
 ALC  HD12  H  HCH2   0   0.226  6.6467  20.6630  17.3568
 ALC  HD13  H  HCH2   0   0.202  7.0192  22.2675  16.7377

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
 ALC  N    CA    single  1.458  0.019  1.458
 ALC  N    H     single  0.860  0.020  0.860
 ALC  N    H2    single  0.890  0.020  1.040
 ALC  CA   C     single  1.525  0.021  1.525
 ALC  CA   CB    single  1.521  0.033  1.521
 ALC  CA   HA    single  0.970  0.020  0.970
 ALC  C    O     deloc   1.231  0.020  1.231
 ALC  C    OXT   deloc   1.247  0.020  1.247
 ALC  CB   CG    single  1.531  0.020  1.531
 ALC  CB   HB2   single  0.970  0.020  1.090
 ALC  CB   HB3   single  0.970  0.020  1.090
 ALC  CG   CD2   single  1.530  0.020  1.530
 ALC  CG   CD1   single  1.529  0.020  1.529
 ALC  CG   HG    single  0.970  0.020  1.090
 ALC  CD2  CE2   single  1.525  0.020  1.525
 ALC  CD2  HD23  single  0.970  0.020  1.090
 ALC  CD2  HD22  single  0.970  0.020  1.090
 ALC  CE2  CZ    single  1.525  0.020  1.525
 ALC  CE2  HE23  single  0.970  0.020  1.090
 ALC  CE2  HE22  single  0.970  0.020  1.090
 ALC  CZ   CE1   single  1.524  0.020  1.524
 ALC  CZ   HZ3   single  0.970  0.020  1.090
 ALC  CZ   HZ2   single  0.970  0.020  1.090
 ALC  CE1  CD1   single  1.526  0.020  1.526
 ALC  CE1  HE13  single  0.970  0.020  1.090
 ALC  CE1  HE12  single  0.970  0.020  1.090
 ALC  CD1  HD12  single  0.970  0.020  1.090
 ALC  CD1  HD13  single  0.970  0.020  1.090

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
 ALC  H2    N    H     106.32  3.000
 ALC  H2    N    CA    107.30  3.000
 ALC  H     N    CA    114.00  3.000
 ALC  HA    CA   CB    109.00  3.000
 ALC  HA    CA   C     109.00  3.000
 ALC  CB    CA   C     110.50  1.500
 ALC  HA    CA   N     110.00  3.000
 ALC  CB    CA   N     110.40  1.500
 ALC  C     CA   N     111.00  2.800
 ALC  OXT   C    O     126.82  3.000
 ALC  OXT   C    CA    116.31  3.000
 ALC  O     C    CA    120.80  1.700
 ALC  HB3   CB   HB2   106.02  3.000
 ALC  HB3   CB   CG    106.65  3.000
 ALC  HB2   CB   CG    109.65  3.000
 ALC  HB3   CB   CA    109.94  3.000
 ALC  HB2   CB   CA    108.72  3.000
 ALC  CG    CB   CA    115.45  3.000
 ALC  HG    CG   CD1   107.17  3.000
 ALC  HG    CG   CD2   107.65  3.000
 ALC  CD1   CG   CD2   109.87  3.000
 ALC  HG    CG   CB    107.12  3.000
 ALC  CD1   CG   CB    114.37  3.000
 ALC  CD2   CG   CB    110.38  3.000
 ALC  HD22  CD2  HD23  106.34  3.000
 ALC  HD22  CD2  CE2   110.17  3.000
 ALC  HD23  CD2  CE2   109.15  3.000
 ALC  HD22  CD2  CG    109.71  3.000
 ALC  HD23  CD2  CG    108.70  3.000
 ALC  CE2   CD2  CG    112.56  3.000
 ALC  HE22  CE2  HE23  106.48  3.000
 ALC  HE22  CE2  CZ    109.16  3.000
 ALC  HE23  CE2  CZ    110.41  3.000
 ALC  HE22  CE2  CD2   109.34  3.000
 ALC  HE23  CE2  CD2   110.13  3.000
 ALC  CZ    CE2  CD2   111.20  3.000
 ALC  HZ2   CZ   HZ3   106.50  3.000
 ALC  HZ2   CZ   CE1   110.35  3.000
 ALC  HZ3   CZ   CE1   109.33  3.000
 ALC  HZ2   CZ   CE2   110.47  3.000
 ALC  HZ3   CZ   CE2   109.36  3.000
 ALC  CE1   CZ   CE2   110.74  3.000
 ALC  HE12  CE1  HE13  106.42  3.000
 ALC  HE12  CE1  CD1   109.12  3.000
 ALC  HE13  CE1  CD1   109.96  3.000
 ALC  HE12  CE1  CZ    109.13  3.000
 ALC  HE13  CE1  CZ    110.41  3.000
 ALC  CD1   CE1  CZ    111.65  3.000
 ALC  HD13  CD1  HD12  106.89  3.000
 ALC  HD13  CD1  CE1   109.23  3.000
 ALC  HD12  CD1  CE1   108.88  3.000
 ALC  HD13  CD1  CG    109.25  3.000
 ALC  HD12  CD1  CG    110.51  3.000
 ALC  CE1   CD1  CG    111.96  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
 ALC  Var_01  CZ   CE2  CD2  CG    55.58  30.0  1
 ALC  Var_02  CZ   CE1  CD1  CG   -55.84  30.0  1
 ALC  Var_03  CD1  CE1  CZ   CE2   55.37  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
 ALC  chir_01  CA  N   C    CB   positiv
 ALC  chir_02  CG  CB  CD2  CD1  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
 ALC  plan-1  CA   0.020
 ALC  plan-1  C    0.020
 ALC  plan-1  O    0.020
 ALC  plan-1  OXT  0.020

