# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 14:06:12 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: (3R,12R)-3-amino-12-methyltetradecanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@@H](C)CCCCCCCC[C@@H](N)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
 AFC  AFC  '(3R,12R)-3-amino-12-methyltetradecanoic acid'  peptide  48  18  .  2022-03-11  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_AFC
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
 AFC  N     N  NH2    0  -0.797    4.8259  -1.5156  -0.2047
 AFC  CA    C  CH1    0  -0.082    4.7292  -0.0804   0.0488
 AFC  CB    C  CH2    0  -0.405    3.3808   0.4424  -0.4397
 AFC  O     O  O      0  -0.609    7.4091  -0.3444   0.9184
 AFC  CD    C  CH2    0  -0.404    2.1662  -0.2351   0.1809
 AFC  CE    C  CH2    0  -0.413    0.8548   0.3998  -0.2649
 AFC  CF    C  CH2    0  -0.411   -0.3854  -0.3411   0.2206
 AFC  CI    C  CH2    0  -0.411   -1.6799   0.4015  -0.0904
 AFC  CJ    C  CH2    0  -0.409   -2.9361  -0.4143   0.1889
 AFC  CK    C  CH2    0  -0.420   -4.2221   0.3760  -0.0232
 AFC  CL    C  CH2    0  -0.397   -5.4752  -0.4687   0.1716
 AFC  CM    C  CH1    0  -0.219   -6.7976   0.2510  -0.1064
 AFC  CN2   C  CH3    0  -0.669   -7.0260   1.4097   0.8605
 AFC  CN1   C  CH2    0  -0.405   -7.9538  -0.7535  -0.0658
 AFC  CO1   C  CH3    0  -0.670   -9.2970  -0.1977  -0.5193
 AFC  CG    C  CH2    0  -0.583    5.8674   0.7290  -0.5687
 AFC  H     H  HNH2   0   0.320    4.8118  -1.6700  -1.2079
 AFC  HA    H  HCH1   0   0.196    4.7656   0.0525   1.1361
 AFC  HG1   H  HCH2   0   0.208    5.8309   0.6233  -1.6601
 AFC  HG2   H  HCH2   0   0.220    5.7027   1.7977  -0.3808
 AFC  HB2   H  HCH2   0   0.208    3.3332   1.5189  -0.2422
 AFC  HB3   H  HCH2   0   0.199    3.3317   0.3409  -1.5318
 AFC  HD1   H  HCH2   0   0.209    2.1700  -1.2984  -0.0726
 AFC  HD2   H  HCH2   0   0.200    2.2394  -0.1855   1.2733
 AFC  HE1   H  HCH2   0   0.204    0.8191   1.4386   0.0826
 AFC  HE2   H  HCH2   0   0.204    0.8288   0.4515  -1.3593
 AFC  HF1   H  HCH2   0   0.205   -0.4118  -1.3360  -0.2370
 AFC  HF2   H  HCH2   0   0.206   -0.3166  -0.5081   1.3012
 AFC  HI1   H  HCH2   0   0.206   -1.7078   1.3280   0.4934
 AFC  HI2   H  HCH2   0   0.205   -1.6816   0.7079  -1.1423
 AFC  HJ1   H  HCH2   0   0.205   -2.9399  -1.2976  -0.4593
 AFC  HJ2   H  HCH2   0   0.206   -2.9096  -0.7927   1.2169
 AFC  HK1   H  HCH2   0   0.212   -4.2269   1.2287   0.6624
 AFC  HK2   H  HCH2   0   0.204   -4.2266   0.7997  -1.0341
 AFC  HL1   H  HCH2   0   0.210   -5.4122  -1.3397  -0.4904
 AFC  HL2   H  HCH2   0   0.201   -5.4935  -0.8674   1.1935
 AFC  HM    H  HCH1   0   0.201   -6.7490   0.6603  -1.1246
 AFC  HN21  H  HCH3   0   0.229   -7.9638   1.9277   0.6578
 AFC  HN22  H  HCH3   0   0.210   -7.0647   1.0468   1.8913
 AFC  HN23  H  HCH3   0   0.230   -6.2314   2.1534   0.8008
 AFC  HN11  H  HCH2   0   0.215   -7.6938  -1.6068  -0.6999
 AFC  HN12  H  HCH2   0   0.205   -8.0449  -1.1508   0.9515
 AFC  HO11  H  HCH3   0   0.220   -9.6470   0.6104   0.1238
 AFC  HO12  H  HCH3   0   0.215   -9.2373   0.1948  -1.5365
 AFC  HO13  H  HCH3   0   0.227  -10.0643  -0.9726  -0.5114
 AFC  OXT   O  OC    -1  -0.626    8.2245   0.9106  -0.7276
 AFC  H2    H  HNH2   0   0.337    5.7396  -1.8213   0.1084
 AFC  C     C  C      0   0.414    7.2890   0.3926  -0.0836

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
 AFC  N    H     single  0.860  0.020  0.860
 AFC  N    CA    single  1.458  0.019  1.458
 AFC  CA   HA    single  0.970  0.020  0.970
 AFC  CA   CG    single  1.527  0.020  1.527
 AFC  CA   CB    single  1.521  0.033  1.521
 AFC  CB   HB2   single  0.970  0.020  1.090
 AFC  CB   HB3   single  0.970  0.020  1.090
 AFC  CB   CD    single  1.523  0.020  1.523
 AFC  C    CG    single  1.539  0.020  1.539
 AFC  C    O     deloc   1.231  0.020  1.231
 AFC  CD   HD1   single  0.970  0.020  1.090
 AFC  CD   HD2   single  0.970  0.020  1.090
 AFC  CD   CE    single  1.524  0.020  1.524
 AFC  CE   HE1   single  0.970  0.020  1.090
 AFC  CE   HE2   single  0.970  0.020  1.090
 AFC  CE   CF    single  1.524  0.020  1.524
 AFC  CF   HF1   single  0.970  0.020  1.090
 AFC  CF   HF2   single  0.970  0.020  1.090
 AFC  CF   CI    single  1.524  0.020  1.524
 AFC  CI   HI1   single  0.970  0.020  1.090
 AFC  CI   HI2   single  0.970  0.020  1.090
 AFC  CI   CJ    single  1.524  0.020  1.524
 AFC  CJ   HJ1   single  0.970  0.020  1.090
 AFC  CJ   HJ2   single  0.970  0.020  1.090
 AFC  CJ   CK    single  1.524  0.020  1.524
 AFC  CK   HK1   single  0.970  0.020  1.090
 AFC  CK   HK2   single  0.970  0.020  1.090
 AFC  CK   CL    single  1.524  0.020  1.524
 AFC  CL   HL1   single  0.970  0.020  1.090
 AFC  CL   HL2   single  0.970  0.020  1.090
 AFC  CL   CM    single  1.531  0.020  1.531
 AFC  CM   HM    single  0.970  0.020  1.090
 AFC  CM   CN2   single  1.526  0.020  1.526
 AFC  CM   CN1   single  1.532  0.020  1.532
 AFC  CN2  HN21  single  0.970  0.020  1.090
 AFC  CN2  HN22  single  0.970  0.020  1.090
 AFC  CN2  HN23  single  0.970  0.020  1.090
 AFC  CN1  HN11  single  0.970  0.020  1.090
 AFC  CN1  HN12  single  0.970  0.020  1.090
 AFC  CN1  CO1   single  1.523  0.020  1.523
 AFC  CO1  HO11  single  0.970  0.020  1.090
 AFC  CO1  HO12  single  0.970  0.020  1.090
 AFC  CO1  HO13  single  0.970  0.020  1.090
 AFC  CG   HG1   single  0.970  0.020  1.090
 AFC  CG   HG2   single  0.970  0.020  1.090
 AFC  OXT  C     deloc   1.248  0.020  1.248
 AFC  H2   N     single  0.890  0.020  1.040

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
 AFC  H2    N    H     105.79  3.000
 AFC  H2    N    CA    107.62  3.000
 AFC  H     N    CA    114.00  3.000
 AFC  HA    CA   CG    108.18  3.000
 AFC  CG    CA   CB    110.33  3.000
 AFC  HA    CA   CB    109.00  3.000
 AFC  CB    CA   N     110.40  1.500
 AFC  CG    CA   N     113.66  3.000
 AFC  HA    CA   N     110.00  3.000
 AFC  HB3   CB   HB2   105.56  3.000
 AFC  HB3   CB   CD    109.18  3.000
 AFC  HB2   CB   CD    109.21  3.000
 AFC  CD    CB   CA    114.94  3.000
 AFC  HB3   CB   CA    109.04  3.000
 AFC  HB2   CB   CA    108.50  3.000
 AFC  HD2   CD   HD1   105.96  3.000
 AFC  HD2   CD   CE    109.28  3.000
 AFC  HD1   CD   CE    109.91  3.000
 AFC  CE    CD   CB    112.44  3.000
 AFC  HD2   CD   CB    109.44  3.000
 AFC  HD1   CD   CB    109.61  3.000
 AFC  HE2   CE   HE1   105.74  3.000
 AFC  HE2   CE   CF    108.76  3.000
 AFC  HE1   CE   CF    109.47  3.000
 AFC  CF    CE   CD    113.86  3.000
 AFC  HE2   CE   CD    109.41  3.000
 AFC  HE1   CE   CD    109.28  3.000
 AFC  HF2   CF   HF1   105.97  3.000
 AFC  HF2   CF   CI    109.20  3.000
 AFC  HF1   CF   CI    109.68  3.000
 AFC  CI    CF   CE    112.90  3.000
 AFC  HF2   CF   CE    109.70  3.000
 AFC  HF1   CF   CE    109.15  3.000
 AFC  HI2   CI   HI1   105.97  3.000
 AFC  HI2   CI   CJ    108.93  3.000
 AFC  HI1   CI   CJ    109.52  3.000
 AFC  CJ    CI   CF    113.69  3.000
 AFC  HI2   CI   CF    109.48  3.000
 AFC  HI1   CI   CF    108.96  3.000
 AFC  HJ2   CJ   HJ1   106.07  3.000
 AFC  HJ2   CJ   CK    109.27  3.000
 AFC  HJ1   CJ   CK    109.43  3.000
 AFC  CK    CJ   CI    113.11  3.000
 AFC  HJ2   CJ   CI    109.69  3.000
 AFC  HJ1   CJ   CI    109.03  3.000
 AFC  HK2   CK   HK1   106.06  3.000
 AFC  HK2   CK   CL    109.20  3.000
 AFC  HK1   CK   CL    110.39  3.000
 AFC  CL    CK   CJ    112.87  3.000
 AFC  HK2   CK   CJ    109.40  3.000
 AFC  HK1   CK   CJ    108.70  3.000
 AFC  HL2   CL   HL1   105.95  3.000
 AFC  HL2   CL   CM    109.00  3.000
 AFC  HL1   CL   CM    108.28  3.000
 AFC  CM    CL   CK    115.24  3.000
 AFC  HL2   CL   CK    109.53  3.000
 AFC  HL1   CL   CK    108.43  3.000
 AFC  HM    CM   CN1   107.59  3.000
 AFC  CN1   CM   CN2   111.59  3.000
 AFC  HM    CM   CN2   108.12  3.000
 AFC  CN1   CM   CL    109.80  3.000
 AFC  CN2   CM   CL    111.79  3.000
 AFC  HM    CM   CL    107.77  3.000
 AFC  HN23  CN2  HN22  107.69  3.000
 AFC  HN23  CN2  HN21  107.02  3.000
 AFC  HN22  CN2  HN21  107.61  3.000
 AFC  HN23  CN2  CM    111.97  3.000
 AFC  HN22  CN2  CM    110.52  3.000
 AFC  HN21  CN2  CM    111.81  3.000
 AFC  HN12  CN1  HN11  105.96  3.000
 AFC  HN12  CN1  CO1   109.60  3.000
 AFC  HN11  CN1  CO1   108.76  3.000
 AFC  CO1   CN1  CM    114.74  3.000
 AFC  HN12  CN1  CM    108.97  3.000
 AFC  HN11  CN1  CM    108.45  3.000
 AFC  HO13  CO1  HO12  107.50  3.000
 AFC  HO13  CO1  HO11  107.24  3.000
 AFC  HO12  CO1  HO11  107.49  3.000
 AFC  HO13  CO1  CN1   111.05  3.000
 AFC  HO12  CO1  CN1   111.13  3.000
 AFC  HO11  CO1  CN1   112.21  3.000
 AFC  HG2   CG   HG1   105.02  3.000
 AFC  HG2   CG   C     107.31  3.000
 AFC  HG1   CG   C     108.85  3.000
 AFC  HG2   CG   CA    109.58  3.000
 AFC  HG1   CG   CA    109.05  3.000
 AFC  C     CG   CA    116.43  3.000
 AFC  OXT   C    CG    116.04  3.000
 AFC  OXT   C    O     125.89  3.000
 AFC  CG    C    O     118.06  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
 AFC  Var_01  O     C    CG   CA   -11.44  30.0  2
 AFC  Var_02  CE    CD   CB   CA   175.63  30.0  3
 AFC  Var_03  CF    CE   CD   CB   174.00  30.0  3
 AFC  Var_04  CI    CF   CE   CD   172.97  30.0  3
 AFC  Var_05  CJ    CI   CF   CE   171.03  30.0  3
 AFC  Var_06  CK    CJ   CI   CF   175.53  30.0  3
 AFC  Var_07  CL    CK   CJ   CI   176.36  30.0  3
 AFC  Var_08  CM    CL   CK   CJ  -176.67  30.0  3
 AFC  Var_09  HO11  CO1  CN1  CM   -62.66  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
 AFC  chir_01  CA  N   CG   CB   negativ
 AFC  chir_02  CM  CL  CN2  CN1  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
 AFC  plan-1  O    0.020
 AFC  plan-1  CG   0.020
 AFC  plan-1  OXT  0.020
 AFC  plan-1  C    0.020

