# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 12:03:27 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: (2Z,4S)-2,5-dimethyl-4-(methylamino)hex-2-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN[C@H](\C=C(C)/C(O)=O)C(C)C
#
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
 4SF  4SF  '(2Z,4S)-2,5-dimethyl-4-(methylamino)hex-2-enoic acid'  peptide  28  12  .  2022-07-23  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_4SF
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
 4SF  C1   C  CH1    0  -0.122   0.8254   0.4646   0.0595
 4SF  O6   O  O      0  -0.606  -2.9954  -0.9912  -0.9520
 4SF  C5   C  C      0   0.369  -2.2118  -0.1081  -0.5478
 4SF  O7   O  OC    -1  -0.600  -2.0119   1.0000  -1.0847
 4SF  C3   C  C      0  -0.055  -1.4727  -0.4393   0.7408
 4SF  C4   C  CH3    0  -0.708  -2.2880  -1.1703   1.7710
 4SF  C2   C  C1     0  -0.242  -0.1819  -0.1821   0.9673
 4SF  C11  C  CH1    0  -0.236   1.7231  -0.5854  -0.6410
 4SF  C12  C  CH3    0  -0.673   2.5692  -1.3958   0.3360
 4SF  C13  C  CH3    0  -0.649   0.9020  -1.5014  -1.5412
 4SF  N    N  NH1    0  -0.598   1.5443   1.4649   0.8451
 4SF  CN   C  CH3    0  -0.520   2.5156   2.2452   0.1084
 4SF  H2   H  HCH1   0   0.238   0.2945   1.0034  -0.7276
 4SF  H8   H  HCH3   0   0.230  -2.6053  -2.1458   1.4000
 4SF  H9   H  HCH3   0   0.221  -1.7260  -1.3250   2.6927
 4SF  H10  H  HCH3   0   0.223  -3.1998  -0.6241   2.0252
 4SF  H11  H  H      0   0.215   0.2258  -0.5162   1.9219
 4SF  H12  H  HCH1   0   0.218   2.4100  -0.0307  -1.2911
 4SF  H13  H  HCH3   0   0.219   1.9475  -2.0098   0.9912
 4SF  H14  H  HCH3   0   0.228   3.2411  -2.0689  -0.1998
 4SF  H15  H  HCH3   0   0.218   3.1919  -0.7577   0.9664
 4SF  H16  H  HCH3   0   0.221   0.2893  -0.9285  -2.2395
 4SF  H17  H  HCH3   0   0.220   1.5525  -2.1522  -2.1282
 4SF  H18  H  HCH3   0   0.217   0.2310  -2.1361  -0.9601
 4SF  H19  H  HCH3   0   0.195   3.3651   1.6808  -0.2971
 4SF  H20  H  HCH3   0   0.218   2.0253   2.7424  -0.7317
 4SF  H21  H  HCH3   0   0.229   2.9224   3.0252   0.7538
 4SF  H1   H  HNH1   0   0.334   1.9972   1.0224   1.6358

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
 4SF  O6   C5   deloc   1.248  0.020  1.248
 4SF  C5   O7   deloc   1.247  0.020  1.247
 4SF  C5   C3   single  1.522  0.020  1.522
 4SF  C4   C3   single  1.503  0.020  1.503
 4SF  C3   C2   double  1.336  0.020  1.336
 4SF  CN   N    single  1.447  0.020  1.447
 4SF  N    C1   single  1.461  0.020  1.461
 4SF  C2   C1   single  1.502  0.020  1.502
 4SF  C1   C11  single  1.549  0.020  1.549
 4SF  C11  C12  single  1.525  0.020  1.525
 4SF  C11  C13  single  1.524  0.020  1.524
 4SF  C1   H2   single  0.970  0.020  1.090
 4SF  C4   H8   single  0.970  0.020  1.090
 4SF  C4   H9   single  0.970  0.020  1.090
 4SF  C4   H10  single  0.970  0.020  1.090
 4SF  C2   H11  single  0.930  0.020  1.080
 4SF  C11  H12  single  0.970  0.020  1.090
 4SF  C12  H13  single  0.970  0.020  1.090
 4SF  C12  H14  single  0.970  0.020  1.090
 4SF  C12  H15  single  0.970  0.020  1.090
 4SF  C13  H16  single  0.970  0.020  1.090
 4SF  C13  H17  single  0.970  0.020  1.090
 4SF  C13  H18  single  0.970  0.020  1.090
 4SF  CN   H19  single  0.970  0.020  1.090
 4SF  CN   H20  single  0.970  0.020  1.090
 4SF  CN   H21  single  0.970  0.020  1.090
 4SF  N    H1   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
 4SF  H2   C1   N    106.80  3.000
 4SF  H2   C1   C11  106.88  3.000
 4SF  N    C1   C11  114.97  3.000
 4SF  H2   C1   C2   108.79  3.000
 4SF  C11  C1   C2   111.72  3.000
 4SF  N    C1   C2   107.44  3.000
 4SF  C3   C5   O7   118.68  3.000
 4SF  C3   C5   O6   115.16  3.000
 4SF  O7   C5   O6   126.15  3.000
 4SF  C2   C3   C4   120.10  3.000
 4SF  C2   C3   C5   124.82  3.000
 4SF  C4   C3   C5   115.00  3.000
 4SF  H10  C4   H9   107.72  3.000
 4SF  H10  C4   H8   106.46  3.000
 4SF  H9   C4   H8   108.09  3.000
 4SF  H10  C4   C3   111.64  3.000
 4SF  H9   C4   C3   111.63  3.000
 4SF  H8   C4   C3   111.07  3.000
 4SF  H11  C2   C3   116.79  3.000
 4SF  H11  C2   C1   114.22  3.000
 4SF  C3   C2   C1   128.93  3.000
 4SF  H12  C11  C13  106.94  3.000
 4SF  H12  C11  C12  107.52  3.000
 4SF  C13  C11  C12  110.96  3.000
 4SF  H12  C11  C1   106.75  3.000
 4SF  C13  C11  C1   111.23  3.000
 4SF  C12  C11  C1   113.08  3.000
 4SF  H15  C12  H14  107.02  3.000
 4SF  H15  C12  H13  107.87  3.000
 4SF  H14  C12  H13  107.35  3.000
 4SF  H15  C12  C11  112.06  3.000
 4SF  H14  C12  C11  110.77  3.000
 4SF  H13  C12  C11  111.54  3.000
 4SF  H18  C13  H17  107.82  3.000
 4SF  H18  C13  H16  107.51  3.000
 4SF  H17  C13  H16  107.66  3.000
 4SF  H18  C13  C11  111.49  3.000
 4SF  H17  C13  C11  110.78  3.000
 4SF  H16  C13  C11  111.40  3.000
 4SF  H1   N    CN   109.43  3.000
 4SF  H1   N    C1   109.92  3.000
 4SF  CN   N    C1   115.19  3.000
 4SF  H21  CN   H20  107.27  3.000
 4SF  H21  CN   H19  107.31  3.000
 4SF  H20  CN   H19  107.29  3.000
 4SF  H21  CN   N    109.55  3.000
 4SF  H20  CN   N    109.61  3.000
 4SF  H19  CN   N    115.48  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
 4SF  Var_01  C5   C3   C2   C1   -0.08   0.0  2
 4SF  Var_02  C4   C3   C5   O6  -38.46  30.0  2
 4SF  Var_03  H19  CN   N    C1  -64.39  30.0  3
 4SF  Var_04  H13  C12  C11  C1   64.82  30.0  3
 4SF  Var_05  H16  C13  C11  C1   52.86  30.0  3
 4SF  Var_06  H8   C4   C3   C5   62.80  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
 4SF  chir_01  C1  N  C2  C11  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
 4SF  plan-1  O6   0.020
 4SF  plan-1  C5   0.020
 4SF  plan-1  O7   0.020
 4SF  plan-1  C3   0.020
 4SF  plan-2  C1   0.020
 4SF  plan-2  C5   0.020
 4SF  plan-2  C3   0.020
 4SF  plan-2  C4   0.020
 4SF  plan-2  C2   0.020
 4SF  plan-2  H11  0.020

