# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 06:31:18 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: 4-amino-5-cyclohexyl-2,4,5-trideoxy-2,2-difluoro-L-threo-pentonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC1CCCCC1)[C@@H](O)C(F)(F)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
 CFS  CFS  '4-amino-5-cyclohexyl-2,4,5-trideoxy-2,2-difluoro-L-threo-pentonic acid'  ligand  35  17  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CFS
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
 CFS  N     N  NH2    0  -0.828   0.5028   1.7469   0.0339
 CFS  CA    C  CH1    0  -0.150   0.1283   0.3361   0.0035
 CFS  CB    C  CH2    0  -0.418   0.8206  -0.3789  -1.1556
 CFS  CG    C  CH1    0  -0.247   0.4258   0.0812  -2.5601
 CFS  CD1   C  CH2    0  -0.410   1.2176  -0.7071  -3.6056
 CFS  CD2   C  CH2    0  -0.423  -1.0748  -0.0497  -2.8228
 CFS  CE1   C  CH2    0  -0.432   0.8519  -0.3054  -5.0304
 CFS  CE2   C  CH2    0  -0.428  -1.4452   0.3463  -4.2494
 CFS  CZ    C  CH2    0  -0.429  -0.6461  -0.4455  -5.2780
 CFS  CH    C  CH1    0  -0.056   0.5811  -0.2946   1.3455
 CFS  OH1   O  OH1    0  -0.684   1.7944   0.2792   1.7426
 CFS  CM    C  CT     0   0.633  -0.4452  -0.1472   2.4626
 CFS  F1    F  F      0  -0.359  -0.8600   1.1524   2.5586
 CFS  F2    F  F      0  -0.371  -1.5727  -0.8567   2.1131
 CFS  C     C  C      0   0.321   0.0554  -0.6661   3.8324
 CFS  O     O  O      0  -0.584   0.0747   0.1385   4.7719
 CFS  OXT   O  OC    -1  -0.603   0.3809  -1.8648   3.8199
 CFS  HN1   H  HNH2   0   0.367   0.7244   2.0934  -0.8885
 CFS  HN2   H  HNH2   0   0.364  -0.2420   2.3254   0.3961
 CFS  HA    H  HCH1   0   0.240  -0.9523   0.1972  -0.1066
 CFS  HB1   H  HCH2   0   0.228   1.9059  -0.2805  -1.0392
 CFS  HB2   H  HCH2   0   0.226   0.6000  -1.4478  -1.0696
 CFS  HG    H  HCH1   0   0.205   0.6980   1.1389  -2.6892
 CFS  HD11  H  HCH2   0   0.224   2.2898  -0.5675  -3.4384
 CFS  HD12  H  HCH2   0   0.205   1.0214  -1.7778  -3.4686
 CFS  HD21  H  HCH2   0   0.206  -1.3791  -1.0879  -2.6397
 CFS  HD22  H  HCH2   0   0.230  -1.6426   0.5654  -2.1201
 CFS  HE11  H  HCH2   0   0.208   1.1525   0.7342  -5.2017
 CFS  HE12  H  HCH2   0   0.225   1.4137  -0.9103  -5.7465
 CFS  HE21  H  HCH2   0   0.208  -1.2530   1.4165  -4.3863
 CFS  HE22  H  HCH2   0   0.225  -2.5172   0.2043  -4.4077
 CFS  HZ1   H  HCH2   0   0.225  -0.8970  -0.1155  -6.2891
 CFS  HZ2   H  HCH2   0   0.207  -0.9255  -1.5033  -5.2173
 CFS  HCH   H  HCH1   0   0.235   0.7220  -1.3709   1.2037
 CFS  HH1   H  HOH1   0   0.440   1.7655   1.1613   1.3154

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
 CFS  N    CA    single  1.460  0.020  1.460
 CFS  N    HN1   single  0.890  0.020  1.040
 CFS  N    HN2   single  0.890  0.020  1.040
 CFS  CA   CB    single  1.528  0.020  1.528
 CFS  CA   CH    single  1.550  0.020  1.550
 CFS  CA   HA    single  0.970  0.020  1.090
 CFS  CB   CG    single  1.530  0.020  1.530
 CFS  CB   HB1   single  0.970  0.020  1.090
 CFS  CB   HB2   single  0.970  0.020  1.090
 CFS  CG   CD1   single  1.530  0.020  1.530
 CFS  CG   CD2   single  1.529  0.020  1.529
 CFS  CG   HG    single  0.970  0.020  1.090
 CFS  CD1  CE1   single  1.525  0.020  1.525
 CFS  CD1  HD11  single  0.970  0.020  1.090
 CFS  CD1  HD12  single  0.970  0.020  1.090
 CFS  CD2  CE2   single  1.526  0.020  1.526
 CFS  CD2  HD21  single  0.970  0.020  1.090
 CFS  CD2  HD22  single  0.970  0.020  1.090
 CFS  CE1  CZ    single  1.525  0.020  1.525
 CFS  CE1  HE11  single  0.970  0.020  1.090
 CFS  CE1  HE12  single  0.970  0.020  1.090
 CFS  CE2  CZ    single  1.524  0.020  1.524
 CFS  CE2  HE21  single  0.970  0.020  1.090
 CFS  CE2  HE22  single  0.970  0.020  1.090
 CFS  CZ   HZ1   single  0.970  0.020  1.090
 CFS  CZ   HZ2   single  0.970  0.020  1.090
 CFS  CH   OH1   single  1.400  0.020  1.400
 CFS  CH   CM    single  1.524  0.020  1.524
 CFS  CH   HCH   single  0.970  0.020  1.090
 CFS  OH1  HH1   single  0.850  0.020  0.980
 CFS  CM   F1    single  1.368  0.020  1.368
 CFS  CM   F2    single  1.377  0.020  1.377
 CFS  CM   C     single  1.548  0.020  1.548
 CFS  C    O     deloc   1.237  0.020  1.237
 CFS  C    OXT   deloc   1.242  0.020  1.242

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
 CFS  HN2   N    HN1   107.02  3.000
 CFS  HN2   N    CA    111.82  3.000
 CFS  HN1   N    CA    111.64  3.000
 CFS  HA    CA   CH    108.89  3.000
 CFS  HA    CA   CB    108.16  3.000
 CFS  CH    CA   CB    109.51  3.000
 CFS  HA    CA   N     112.20  3.000
 CFS  CH    CA   N     107.46  3.000
 CFS  CB    CA   N     110.60  3.000
 CFS  HB2   CB   HB1   106.19  3.000
 CFS  HB2   CB   CG    108.28  3.000
 CFS  HB1   CB   CG    109.03  3.000
 CFS  HB2   CB   CA    107.82  3.000
 CFS  HB1   CB   CA    109.04  3.000
 CFS  CG    CB   CA    116.03  3.000
 CFS  HG    CG   CD2   107.77  3.000
 CFS  HG    CG   CD1   106.69  3.000
 CFS  CD2   CG   CD1   110.27  3.000
 CFS  HG    CG   CB    109.45  3.000
 CFS  CD2   CG   CB    112.66  3.000
 CFS  CD1   CG   CB    109.80  3.000
 CFS  HD12  CD1  HD11  106.30  3.000
 CFS  HD12  CD1  CE1   109.32  3.000
 CFS  HD11  CD1  CE1   110.13  3.000
 CFS  HD12  CD1  CG    108.96  3.000
 CFS  HD11  CD1  CG    109.69  3.000
 CFS  CE1   CD1  CG    112.25  3.000
 CFS  HD22  CD2  HD21  106.33  3.000
 CFS  HD22  CD2  CE2   109.20  3.000
 CFS  HD21  CD2  CE2   109.52  3.000
 CFS  HD22  CD2  CG    110.56  3.000
 CFS  HD21  CD2  CG    108.94  3.000
 CFS  CE2   CD2  CG    112.12  3.000
 CFS  HE12  CE1  HE11  106.37  3.000
 CFS  HE12  CE1  CZ    110.35  3.000
 CFS  HE11  CE1  CZ    109.35  3.000
 CFS  HE12  CE1  CD1   110.07  3.000
 CFS  HE11  CE1  CD1   109.28  3.000
 CFS  CZ    CE1  CD1   111.29  3.000
 CFS  HE22  CE2  HE21  106.31  3.000
 CFS  HE22  CE2  CZ    110.42  3.000
 CFS  HE21  CE2  CZ    109.33  3.000
 CFS  HE22  CE2  CD2   109.86  3.000
 CFS  HE21  CE2  CD2   109.13  3.000
 CFS  CZ    CE2  CD2   111.64  3.000
 CFS  HZ2   CZ   HZ1   106.51  3.000
 CFS  HZ2   CZ   CE2   109.29  3.000
 CFS  HZ1   CZ   CE2   110.31  3.000
 CFS  HZ2   CZ   CE1   109.29  3.000
 CFS  HZ1   CZ   CE1   110.37  3.000
 CFS  CE2   CZ   CE1   110.96  3.000
 CFS  HCH   CH   CM    106.06  3.000
 CFS  HCH   CH   OH1   109.16  3.000
 CFS  CM    CH   OH1   109.64  3.000
 CFS  HCH   CH   CA    108.99  3.000
 CFS  CM    CH   CA    113.48  3.000
 CFS  OH1   CH   CA    109.39  3.000
 CFS  HH1   OH1  CH    102.69  3.000
 CFS  C     CM   F2    108.46  3.000
 CFS  C     CM   F1    110.76  3.000
 CFS  F2    CM   F1    105.01  3.000
 CFS  C     CM   CH    113.48  3.000
 CFS  F2    CM   CH    108.39  3.000
 CFS  F1    CM   CH    110.34  3.000
 CFS  OXT   C    O     129.14  3.000
 CFS  OXT   C    CM    113.54  3.000
 CFS  O     C    CM    117.33  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
 CFS  Var_01  CZ   CE1  CD1  CG   -55.57  30.0  1
 CFS  Var_02  CZ   CE2  CD2  CG    55.08  30.0  1
 CFS  Var_03  CE1  CZ   CE2  CD2  -54.97  30.0  1
 CFS  Var_04  O    C    CM   CH   121.53  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
 CFS  chir_01  CA  N    CB   CH   negativ
 CFS  chir_02  CG  CB   CD1  CD2  negativ
 CFS  chir_03  CH  OH1  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
 CFS  plan-1  CM   0.020
 CFS  plan-1  C    0.020
 CFS  plan-1  O    0.020
 CFS  plan-1  OXT  0.020

