# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 28 21:39:50 2022
#   Inital geometry file: a 75 line input string
#   Ligand name: 4-acetyl-L-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)c1ccc(C[C@H](N)C(O)=O)cc1
#
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
 4AF  4AF  "4-ACETYL-L-PHENYLALANINE"  L-peptide  27  15  .  2022-09-15  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_4AF
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
 4AF  C11   C  CH3    0  -0.801   4.7906   1.2304   0.5764
 4AF  C8    C  C      0   0.363   4.0715  -0.0376   0.2008
 4AF  O2    O  O      0  -0.404   4.6698  -1.0903   0.0971
 4AF  C7    C  CR6    0  -0.048   2.6081   0.0295  -0.0477
 4AF  C9    C  CR16   0  -0.253   1.9236  -1.1252  -0.4350
 4AF  C10   C  CR16   0  -0.291   0.5644  -1.0895  -0.6858
 4AF  C6    C  CR16   0  -0.273   1.8884   1.2172   0.0810
 4AF  C5    C  CR16   0  -0.294   0.5274   1.2466  -0.1748
 4AF  C4    C  CR6    0   0.168  -0.1574   0.0983  -0.5667
 4AF  C3    C  CH2    0  -0.527  -1.6315   0.1525  -0.8266
 4AF  C1    C  CH1    0  -0.205  -2.4709  -0.0734   0.4417
 4AF  C2    C  C      0   0.383  -3.9555   0.2503   0.1244
 4AF  OX1   O  OC    -1  -0.621  -4.2028   1.4418  -0.1559
 4AF  O     O  O      0  -0.603  -4.7721  -0.6897   0.1612
 4AF  N     N  NH2    0  -0.774  -2.2105  -1.3967   0.9763
 4AF  H111  H  HCH3   0   0.268   5.8544   1.0396   0.6964
 4AF  H112  H  HCH3   0   0.266   4.6533   1.9974  -0.1872
 4AF  H113  H  HCH3   0   0.267   4.4006   1.6380   1.5108
 4AF  H9    H  HCR6   0   0.257   2.4626  -2.0574  -0.5445
 4AF  H10   H  HCR6   0   0.244   0.0549  -1.9937  -0.9935
 4AF  H6    H  HCR6   0   0.258   2.3818   2.1332   0.3774
 4AF  H5    H  HCR6   0   0.250  -0.0129   2.1811  -0.0765
 4AF  H31   H  HCH2   0   0.249  -1.8918   1.1264  -1.2426
 4AF  H32   H  HCH2   0   0.238  -1.9052  -0.6009  -1.5725
 4AF  H1    H  HCH1   0   0.224  -2.1344   0.6565   1.1878
 4AF  HN1   H  HNH2   0   0.336  -2.7111  -1.4957   1.8513
 4AF  HN2   H  HNH2   0   0.324  -2.6424  -2.0786   0.3625

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
 4AF  C11  C8    single    1.505  0.020  1.505
 4AF  C11  H111  single    0.970  0.020  1.090
 4AF  C11  H112  single    0.970  0.020  1.090
 4AF  C11  H113  single    0.970  0.020  1.090
 4AF  C8   O2    double    1.215  0.020  1.215
 4AF  C8   C7    single    1.486  0.020  1.486
 4AF  C7   C9    aromatic  1.397  0.020  1.397
 4AF  C7   C6    aromatic  1.395  0.020  1.395
 4AF  C9   C10   aromatic  1.383  0.020  1.383
 4AF  C9   H9    single    0.930  0.020  1.080
 4AF  C10  C4    aromatic  1.395  0.020  1.395
 4AF  C10  H10   single    0.930  0.020  1.080
 4AF  C6   C5    aromatic  1.385  0.020  1.385
 4AF  C6   H6    single    0.930  0.020  1.080
 4AF  C5   C4    aromatic  1.393  0.020  1.393
 4AF  C5   H5    single    0.930  0.020  1.080
 4AF  C4   C3    single    1.498  0.020  1.498
 4AF  C3   C1    single    1.538  0.020  1.538
 4AF  C3   H31   single    0.970  0.020  1.090
 4AF  C3   H32   single    0.970  0.020  1.090
 4AF  C1   C2    single    1.552  0.020  1.552
 4AF  C1   N     single    1.451  0.020  1.451
 4AF  C1   H1    single    0.970  0.020  1.090
 4AF  C2   OX1   deloc     1.249  0.020  1.249
 4AF  C2   O     deloc     1.246  0.020  1.246
 4AF  N    HN1   single    0.890  0.020  1.040
 4AF  N    HN2   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
 4AF  H113  C11  H112  106.96  3.000
 4AF  H113  C11  H111  108.70  3.000
 4AF  H112  C11  H111  108.88  3.000
 4AF  H113  C11  C8    110.95  3.000
 4AF  H112  C11  C8    110.94  3.000
 4AF  H111  C11  C8    110.31  3.000
 4AF  C7    C8   O2    120.65  3.000
 4AF  C7    C8   C11   118.31  3.000
 4AF  O2    C8   C11   121.04  3.000
 4AF  C6    C7   C9    118.46  3.000
 4AF  C6    C7   C8    122.09  3.000
 4AF  C9    C7   C8    119.45  3.000
 4AF  H9    C9   C10   119.57  3.000
 4AF  H9    C9   C7    119.73  3.000
 4AF  C10   C9   C7    120.70  3.000
 4AF  H10   C10  C4    119.47  3.000
 4AF  H10   C10  C9    119.52  3.000
 4AF  C4    C10  C9    121.01  3.000
 4AF  H6    C6   C5    118.73  3.000
 4AF  H6    C6   C7    120.73  3.000
 4AF  C5    C6   C7    120.53  3.000
 4AF  H5    C5   C4    119.42  3.000
 4AF  H5    C5   C6    119.42  3.000
 4AF  C4    C5   C6    121.16  3.000
 4AF  C3    C4   C5    120.18  3.000
 4AF  C3    C4   C10   121.68  3.000
 4AF  C5    C4   C10   118.13  3.000
 4AF  H32   C3   H31   107.15  3.000
 4AF  H32   C3   C1    108.93  3.000
 4AF  H31   C3   C1    108.39  3.000
 4AF  H32   C3   C4    109.84  3.000
 4AF  H31   C3   C4    109.48  3.000
 4AF  C1    C3   C4    112.88  3.000
 4AF  H1    C1   N     107.54  3.000
 4AF  H1    C1   C2    107.08  3.000
 4AF  N     C1   C2    115.93  3.000
 4AF  H1    C1   C3    107.21  3.000
 4AF  N     C1   C3    109.87  3.000
 4AF  C2    C1   C3    108.84  3.000
 4AF  O     C2   OX1   126.64  3.000
 4AF  O     C2   C1    117.61  3.000
 4AF  OX1   C2   C1    115.74  3.000
 4AF  HN2   N    HN1   104.28  3.000
 4AF  HN2   N    C1    108.29  3.000
 4AF  HN1   N    C1    108.58  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
 4AF  CONST_01  C4    C10  C9   C7      0.00   0.0  0
 4AF  CONST_02  C4    C5   C6   C7      0.00   0.0  0
 4AF  CONST_03  C5    C6   C7   C9      0.00   0.0  0
 4AF  CONST_04  C5    C4   C10  C9      0.00   0.0  0
 4AF  CONST_05  C6    C7   C9   C10     0.00   0.0  0
 4AF  CONST_06  C6    C5   C4   C10     0.00   0.0  0
 4AF  CONST_07  C10   C9   C7   C8    180.00   0.0  0
 4AF  CONST_08  C5    C6   C7   C8    180.00   0.0  0
 4AF  CONST_09  C3    C4   C10  C9    180.00   0.0  0
 4AF  CONST_10  C3    C4   C5   C6    180.00   0.0  0
 4AF  CONST_11  H10   C10  C9   C7    180.00   0.0  0
 4AF  CONST_12  H5    C5   C6   C7    180.00   0.0  0
 4AF  CONST_13  H6    C6   C7   C9    180.00   0.0  0
 4AF  CONST_14  H5    C5   C4   C10   180.00   0.0  0
 4AF  CONST_15  H9    C9   C7   C6    180.00   0.0  0
 4AF  CONST_16  H10   C10  C4   C5    180.00   0.0  0
 4AF  CONST_17  H9    C9   C10  C4    180.00   0.0  0
 4AF  CONST_18  H6    C6   C5   C4    180.00   0.0  0
 4AF  Var_01    C9    C7   C8   C11   178.18  30.0  2
 4AF  Var_02    C6    C7   C8   C11    -1.21  30.0  2
 4AF  Var_03    C9    C7   C8   O2     -1.53  30.0  2
 4AF  Var_04    C6    C7   C8   O2    179.08  30.0  2
 4AF  Var_05    C1    C3   C4   C10    91.73  30.0  2
 4AF  Var_06    C1    C3   C4   C5    -87.26  30.0  2
 4AF  Var_07    H31   C3   C4   C10  -147.44  30.0  2
 4AF  Var_08    H32   C3   C4   C10   -30.04  30.0  2
 4AF  Var_09    H31   C3   C4   C5     33.57  30.0  2
 4AF  Var_10    H32   C3   C4   C5    150.97  30.0  2
 4AF  Var_11    H111  C11  C8   C7   -178.21  30.0  3
 4AF  Var_12    H112  C11  C8   C7    -57.47  30.0  3
 4AF  Var_13    H113  C11  C8   C7     61.27  30.0  3
 4AF  Var_14    H111  C11  C8   O2      1.50  30.0  3
 4AF  Var_15    H112  C11  C8   O2    122.24  30.0  3
 4AF  Var_16    H113  C11  C8   O2   -119.02  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
 4AF  chir_01  C1  C3  C2  N  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
 4AF  plan-1  C8   0.020
 4AF  plan-1  C7   0.020
 4AF  plan-1  C9   0.020
 4AF  plan-1  C10  0.020
 4AF  plan-1  C6   0.020
 4AF  plan-1  C5   0.020
 4AF  plan-1  C4   0.020
 4AF  plan-1  C3   0.020
 4AF  plan-1  H9   0.020
 4AF  plan-1  H10  0.020
 4AF  plan-1  H6   0.020
 4AF  plan-1  H5   0.020
 4AF  plan-2  C11  0.020
 4AF  plan-2  C8   0.020
 4AF  plan-2  O2   0.020
 4AF  plan-2  C7   0.020
 4AF  plan-3  C1   0.020
 4AF  plan-3  C2   0.020
 4AF  plan-3  OX1  0.020
 4AF  plan-3  O    0.020

