# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 04:25:31 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: (2R,3E,5R)-5-amino-2,4-dimethylhex-3-enal
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](N)/C(C)=C/[C@@H](C)C=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
 CFD  CFD  (2R,3E,5R)-5-amino-2,4-dimethylhex-3-enal  ligand  25  10  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_CFD
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
 CFD  N     N  NH2   0  -0.789   2.6683  -1.2060  -0.7343
 CFD  CA    C  CH1   0  -0.190   2.1307   0.1269  -0.4664
 CFD  C     C  C1    0   0.212  -2.3134  -0.6056  -0.2904
 CFD  O     O  O     0  -0.383  -2.6390  -1.5371   0.4034
 CFD  CB2   C  CH3   0  -0.664   3.0678   1.0170   0.3544
 CFD  CB1   C  C     0   0.183   0.7718   0.0141   0.1901
 CFD  CG1   C  C1    0  -0.290  -0.2688   0.6695  -0.3294
 CFD  CG2   C  CH3   0  -0.751   0.6902  -0.8474   1.4135
 CFD  CD    C  CH1   0  -0.421  -1.6824   0.6696   0.2014
 CFD  CE    C  CH3   0  -0.667  -2.4663   1.8743  -0.3161
 CFD  HN    H  HNH2  0   0.349   3.5232  -1.1058  -1.2689
 CFD  HA    H  HCH1  0   0.238   1.9868   0.6067  -1.4387
 CFD  H1G1  H  H     0   0.233  -0.1139   1.2396  -1.2422
 CFD  HD    H  HCH1  0   0.269  -1.6957   0.6614   1.2941
 CFD  HNA   H  HNH2  0   0.342   2.9549  -1.6406   0.1363
 CFD  HB2   H  HCH3  0   0.233   4.0173   1.1476  -0.1682
 CFD  HB2A  H  HCH3  0   0.226   2.6378   2.0057   0.5203
 CFD  HB2B  H  HCH3  0   0.218   3.2883   0.5767   1.3291
 CFD  HG2   H  HCH3  0   0.243   1.5493  -0.6951   2.0694
 CFD  HG2A  H  HCH3  0   0.250  -0.2080  -0.6707   2.0014
 CFD  HG2B  H  HCH3  0   0.251   0.6909  -1.9043   1.1364
 CFD  HE    H  HCH3  0   0.249  -1.9993   2.7997   0.0199
 CFD  HEA   H  HCH3  0   0.230  -2.4889   1.8909  -1.4073
 CFD  HEB   H  HCH3  0   0.245  -3.4953   1.8656   0.0431
 CFD  H     H  H     0   0.184  -2.4413  -0.6455  -1.3892

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
 CFD  N     CA    single  1.462  0.020  1.462
 CFD  N     HN    single  0.890  0.020  1.040
 CFD  N     HNA   single  0.890  0.020  1.040
 CFD  HA    CA    single  0.970  0.020  1.090
 CFD  CA    CB2   single  1.531  0.020  1.531
 CFD  CA    CB1   single  1.513  0.020  1.513
 CFD  C     CD    single  1.505  0.020  1.505
 CFD  C     O     double  1.206  0.020  1.206
 CFD  C     H     single  0.930  0.020  1.080
 CFD  CB2   HB2   single  0.970  0.020  1.090
 CFD  CB2   HB2A  single  0.970  0.020  1.090
 CFD  CB2   HB2B  single  0.970  0.020  1.090
 CFD  CG1   CB1   double  1.335  0.020  1.335
 CFD  CB1   CG2   single  1.498  0.020  1.498
 CFD  H1G1  CG1   single  0.930  0.020  1.080
 CFD  CG1   CD    single  1.510  0.020  1.510
 CFD  CG2   HG2   single  0.970  0.020  1.090
 CFD  CG2   HG2A  single  0.970  0.020  1.090
 CFD  CG2   HG2B  single  0.970  0.020  1.090
 CFD  CE    CD    single  1.528  0.020  1.528
 CFD  CD    HD    single  0.970  0.020  1.090
 CFD  CE    HE    single  0.970  0.020  1.090
 CFD  CE    HEA   single  0.970  0.020  1.090
 CFD  CE    HEB   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
 CFD  HNA   N    HN    104.88  3.000
 CFD  HNA   N    CA    109.71  3.000
 CFD  HN    N    CA    108.46  3.000
 CFD  HA    CA   CB1   107.47  3.000
 CFD  CB1   CA   CB2   111.12  3.000
 CFD  HA    CA   CB2   107.59  3.000
 CFD  CB1   CA   N     109.98  3.000
 CFD  CB2   CA   N     113.78  3.000
 CFD  HA    CA   N     106.59  3.000
 CFD  H     C    CD    113.78  3.000
 CFD  H     C    O     120.79  3.000
 CFD  CD    C    O     125.41  3.000
 CFD  HB2B  CB2  HB2A  108.01  3.000
 CFD  HB2B  CB2  HB2   107.45  3.000
 CFD  HB2A  CB2  HB2   107.89  3.000
 CFD  HB2B  CB2  CA    111.58  3.000
 CFD  HB2A  CB2  CA    111.54  3.000
 CFD  HB2   CB2  CA    110.20  3.000
 CFD  CG2   CB1  CG1   123.88  3.000
 CFD  CG2   CB1  CA    116.48  3.000
 CFD  CG1   CB1  CA    119.64  3.000
 CFD  H1G1  CG1  CD    115.37  3.000
 CFD  CD    CG1  CB1   126.37  3.000
 CFD  H1G1  CG1  CB1   118.23  3.000
 CFD  HG2B  CG2  HG2A  107.13  3.000
 CFD  HG2B  CG2  HG2   106.67  3.000
 CFD  HG2A  CG2  HG2   107.60  3.000
 CFD  HG2B  CG2  CB1   110.43  3.000
 CFD  HG2A  CG2  CB1   113.13  3.000
 CFD  HG2   CG2  CB1   111.57  3.000
 CFD  HD    CD   CE    109.78  3.000
 CFD  HD    CD   CG1   111.28  3.000
 CFD  CE    CD   CG1   111.18  3.000
 CFD  HD    CD   C     108.37  3.000
 CFD  CE    CD   C     110.02  3.000
 CFD  CG1   CD   C     106.11  3.000
 CFD  HEB   CE   HEA   108.06  3.000
 CFD  HEB   CE   HE    108.04  3.000
 CFD  HEA   CE   HE    107.71  3.000
 CFD  HEB   CE   CD    111.50  3.000
 CFD  HEA   CE   CD    111.18  3.000
 CFD  HE    CE   CD    110.21  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
 CFD  Var_01  CD   CG1  CB1  CA  -179.74   0.0  2
 CFD  Var_02  HG2  CG2  CB1  CA    41.82  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
 CFD  chir_01  CA  N  CB2  CB1  positiv
 CFD  chir_02  CD  C  CG1  CE   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
 CFD  plan-1  C     0.020
 CFD  plan-1  O     0.020
 CFD  plan-1  CD    0.020
 CFD  plan-1  H     0.020
 CFD  plan-2  CA    0.020
 CFD  plan-2  CB1   0.020
 CFD  plan-2  CG1   0.020
 CFD  plan-2  CG2   0.020
 CFD  plan-2  CD    0.020
 CFD  plan-2  H1G1  0.020

