# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 12:48:38 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  49  18  .  2022-03-11  2022-11-17
;
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  -0.788    4.8063  -1.5831  -0.1922
 AFC  CA    C  CH1   0  -0.095    4.7163  -0.1602   0.0981
 AFC  CB    C  CH2   0  -0.411    3.3912   0.3961  -0.4173
 AFC  O     O  O     0  -0.448    7.4091  -0.3245   1.0917
 AFC  CD    C  CH2   0  -0.405    2.1589  -0.2876   0.1591
 AFC  CE    C  CH2   0  -0.414    0.8623   0.3976  -0.2563
 AFC  CF    C  CH2   0  -0.411   -0.3881  -0.3759   0.1461
 AFC  CI    C  CH2   0  -0.412   -1.6772   0.3949  -0.1127
 AFC  CJ    C  CH2   0  -0.409   -2.9358  -0.4275   0.1324
 AFC  CK    C  CH2   0  -0.420   -4.2211   0.3693  -0.0581
 AFC  CL    C  CH2   0  -0.397   -5.4742  -0.4751   0.1399
 AFC  CM    C  CH1   0  -0.219   -6.7974   0.2470  -0.1278
 AFC  CN2   C  CH3   0  -0.669   -7.0149   1.4073   0.8395
 AFC  CN1   C  CH2   0  -0.405   -7.9554  -0.7548  -0.0759
 AFC  CO1   C  CH3   0  -0.670   -9.2995  -0.1981  -0.5259
 AFC  CG    C  CH2   0  -0.582    5.8686   0.6693  -0.4750
 AFC  H     H  HNH2  0   0.333    4.8621  -1.7228  -1.1950
 AFC  HA    H  HCH1  0   0.226    4.7229  -0.0494   1.1874
 AFC  HG1   H  HCH2  0   0.268    5.9002   0.5699  -1.5645
 AFC  HG2   H  HCH2  0   0.281    5.7042   1.7356  -0.2804
 AFC  HB2   H  HCH2  0   0.218    3.3519   1.4667  -0.1906
 AFC  HB3   H  HCH2  0   0.210    3.3699   0.3222  -1.5117
 AFC  HD1   H  HCH2  0   0.213    2.1420  -1.3350  -0.1515
 AFC  HD2   H  HCH2  0   0.204    2.2267  -0.2983   1.2526
 AFC  HE1   H  HCH2  0   0.206    0.8287   1.4028   0.1777
 AFC  HE2   H  HCH2  0   0.206    0.8549   0.5398  -1.3427
 AFC  HF1   H  HCH2  0   0.206   -0.4116  -1.3237  -0.4024
 AFC  HF2   H  HCH2  0   0.206   -0.3335  -0.6411   1.2076
 AFC  HI1   H  HCH2  0   0.206   -1.6940   1.2863   0.5240
 AFC  HI2   H  HCH2  0   0.205   -1.6831   0.7612  -1.1453
 AFC  HJ1   H  HCH2  0   0.205   -2.9388  -1.2899  -0.5436
 AFC  HJ2   H  HCH2  0   0.206   -2.9131  -0.8392   1.1477
 AFC  HK1   H  HCH2  0   0.212   -4.2172   1.2147   0.6367
 AFC  HK2   H  HCH2  0   0.204   -4.2336   0.8041  -1.0643
 AFC  HL1   H  HCH2  0   0.210   -5.4153  -1.3436  -0.5255
 AFC  HL2   H  HCH2  0   0.202   -5.4869  -0.8774   1.1605
 AFC  HM    H  HCH1  0   0.201   -6.7560   0.6548  -1.1470
 AFC  HN21  H  HCH3  0   0.229   -7.9540   1.9261   0.6453
 AFC  HN22  H  HCH3  0   0.210   -7.0439   1.0460   1.8711
 AFC  HN23  H  HCH3  0   0.230   -6.2199   2.1497   0.7708
 AFC  HN11  H  HCH2  0   0.215   -7.7008  -1.6123  -0.7065
 AFC  HN12  H  HCH2  0   0.205   -8.0422  -1.1462   0.9441
 AFC  HO11  H  HCH3  0   0.220   -9.6427   0.6168   0.1124
 AFC  HO12  H  HCH3  0   0.215   -9.2442   0.1855  -1.5467
 AFC  HO13  H  HCH3  0   0.227  -10.0696  -0.9701  -0.5065
 AFC  OXT   O  OH1   0  -0.595    8.2069   0.8595  -0.6177
 AFC  H2    H  HNH2  0   0.345    5.6569  -1.9685   0.1971
 AFC  HXT   H  HOH1  0   0.478    9.0592   0.6483  -0.2080
 AFC  C     C  C     0   0.548    7.2177   0.3287   0.0944

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  1.531  0.020  1.531
 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  1.503  0.020  1.503
 AFC  C    O     double  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  1.523  0.020  1.523
 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     single  1.329  0.020  1.329
 AFC  H2   N     single  0.890  0.020  1.040
 AFC  OXT  HXT   single  0.850  0.020  0.980

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     106.37  3.000
 AFC  H2    N    CA    110.35  3.000
 AFC  H     N    CA    114.00  3.000
 AFC  HA    CA   CG    108.24  3.000
 AFC  CG    CA   CB    109.24  3.000
 AFC  HA    CA   CB    109.00  3.000
 AFC  CB    CA   N     110.40  1.500
 AFC  CG    CA   N     114.12  3.000
 AFC  HA    CA   N     110.00  3.000
 AFC  HB3   CB   HB2   105.77  3.000
 AFC  HB3   CB   CD    109.37  3.000
 AFC  HB2   CB   CD    109.37  3.000
 AFC  CD    CB   CA    114.27  3.000
 AFC  HB3   CB   CA    109.21  3.000
 AFC  HB2   CB   CA    108.51  3.000
 AFC  HD2   CD   HD1   105.98  3.000
 AFC  HD2   CD   CE    109.21  3.000
 AFC  HD1   CD   CE    109.90  3.000
 AFC  CE    CD   CB    112.55  3.000
 AFC  HD2   CD   CB    109.40  3.000
 AFC  HD1   CD   CB    109.59  3.000
 AFC  HE2   CE   HE1   105.87  3.000
 AFC  HE2   CE   CF    108.79  3.000
 AFC  HE1   CE   CF    109.62  3.000
 AFC  CF    CE   CD    113.44  3.000
 AFC  HE2   CE   CD    109.53  3.000
 AFC  HE1   CE   CD    109.31  3.000
 AFC  HF2   CF   HF1   106.07  3.000
 AFC  HF2   CF   CI    109.21  3.000
 AFC  HF1   CF   CI    109.54  3.000
 AFC  CI    CF   CE    113.10  3.000
 AFC  HF2   CF   CE    109.74  3.000
 AFC  HF1   CF   CE    108.94  3.000
 AFC  HI2   CI   HI1   106.00  3.000
 AFC  HI2   CI   CJ    109.13  3.000
 AFC  HI1   CI   CJ    109.46  3.000
 AFC  CJ    CI   CF    113.48  3.000
 AFC  HI2   CI   CF    109.49  3.000
 AFC  HI1   CI   CF    109.01  3.000
 AFC  HJ2   CJ   HJ1   106.02  3.000
 AFC  HJ2   CJ   CK    109.25  3.000
 AFC  HJ1   CJ   CK    109.39  3.000
 AFC  CK    CJ   CI    113.22  3.000
 AFC  HJ2   CJ   CI    109.56  3.000
 AFC  HJ1   CJ   CI    109.14  3.000
 AFC  HK2   CK   HK1   106.05  3.000
 AFC  HK2   CK   CL    109.25  3.000
 AFC  HK1   CK   CL    110.39  3.000
 AFC  CL    CK   CJ    112.80  3.000
 AFC  HK2   CK   CJ    109.38  3.000
 AFC  HK1   CK   CJ    108.76  3.000
 AFC  HL2   CL   HL1   105.95  3.000
 AFC  HL2   CL   CM    109.00  3.000
 AFC  HL1   CL   CM    108.31  3.000
 AFC  CM    CL   CK    115.26  3.000
 AFC  HL2   CL   CK    109.49  3.000
 AFC  HL1   CL   CK    108.43  3.000
 AFC  HM    CM   CN1   107.62  3.000
 AFC  CN1   CM   CN2   111.59  3.000
 AFC  HM    CM   CN2   108.13  3.000
 AFC  CN1   CM   CL    109.81  3.000
 AFC  CN2   CM   CL    111.77  3.000
 AFC  HM    CM   CL    107.74  3.000
 AFC  HN23  CN2  HN22  107.69  3.000
 AFC  HN23  CN2  HN21  107.03  3.000
 AFC  HN22  CN2  HN21  107.60  3.000
 AFC  HN23  CN2  CM    111.96  3.000
 AFC  HN22  CN2  CM    110.52  3.000
 AFC  HN21  CN2  CM    111.82  3.000
 AFC  HN12  CN1  HN11  105.95  3.000
 AFC  HN12  CN1  CO1   109.62  3.000
 AFC  HN11  CN1  CO1   108.75  3.000
 AFC  CO1   CN1  CM    114.71  3.000
 AFC  HN12  CN1  CM    108.96  3.000
 AFC  HN11  CN1  CM    108.48  3.000
 AFC  HO13  CO1  HO12  107.52  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   111.10  3.000
 AFC  HO11  CO1  CN1   112.21  3.000
 AFC  HG2   CG   HG1   105.63  3.000
 AFC  HG2   CG   C     106.72  3.000
 AFC  HG1   CG   C     109.30  3.000
 AFC  HG2   CG   CA    110.34  3.000
 AFC  HG1   CG   CA    110.19  3.000
 AFC  C     CG   CA    114.26  3.000
 AFC  HXT   OXT  C     109.93  3.000
 AFC  OXT   C    CG    111.98  3.000
 AFC  OXT   C    O     122.72  3.000
 AFC  CG    C    O     125.29  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  CONST_01  HXT   OXT  C    O      0.00   0.0  0
 AFC  Var_01    O     C    CG   CA   -14.58  30.0  2
 AFC  Var_02    CE    CD   CB   CA   173.48  30.0  3
 AFC  Var_03    CF    CE   CD   CB   172.02  30.0  3
 AFC  Var_04    CI    CF   CE   CD   172.69  30.0  3
 AFC  Var_05    CJ    CI   CF   CE   173.26  30.0  3
 AFC  Var_06    CK    CJ   CI   CF   177.02  30.0  3
 AFC  Var_07    CL    CK   CJ   CI   177.92  30.0  3
 AFC  Var_08    CM    CL   CK   CJ  -176.18  30.0  3
 AFC  Var_09    HO11  CO1  CN1  CM   -62.45  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  HXT  0.020
 AFC  plan-1  C    0.020

