# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 07:46:53 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  29  12  .  2022-07-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.140   0.8730   0.5433   0.0710
 4SF  O6   O  O     0  -0.443  -3.1267  -0.7813  -0.8606
 4SF  C5   C  C     0   0.496  -2.2203  -0.0782  -0.4781
 4SF  O7   O  OH1   0  -0.589  -1.8626   1.0313  -1.1111
 4SF  C3   C  C     0  -0.063  -1.4549  -0.3712   0.7620
 4SF  C4   C  CH3   0  -0.701  -2.2471  -1.1279   1.7926
 4SF  C2   C  C1    0  -0.175  -0.1620  -0.0902   0.9569
 4SF  C11  C  CH1   0  -0.239   1.7160  -0.5338  -0.6614
 4SF  C12  C  CH3   0  -0.675   2.5126  -1.4203   0.2899
 4SF  C13  C  CH3   0  -0.660   0.8603  -1.3748  -1.6015
 4SF  N    N  NH1   0  -0.596   1.6311   1.4660   0.9076
 4SF  CN   C  CH3   0  -0.523   2.6068   2.2688   0.1998
 4SF  H2   H  HCH1  0   0.254   0.4008   1.1475  -0.7040
 4SF  H7   H  HOH1  0   0.482  -2.3942   1.1321  -1.9153
 4SF  H8   H  HCH3  0   0.245  -2.5353  -2.1143   1.4270
 4SF  H9   H  HCH3  0   0.244  -1.6632  -1.2655   2.7009
 4SF  H10  H  HCH3  0   0.243  -3.1662  -0.6039   2.0597
 4SF  H11  H  H     0   0.251   0.2390  -0.4260   1.9113
 4SF  H12  H  HCH1  0   0.231   2.4315   0.0147  -1.2841
 4SF  H13  H  HCH3  0   0.222   1.8581  -2.0320   0.9142
 4SF  H14  H  HCH3  0   0.235   3.1553  -2.1010  -0.2705
 4SF  H15  H  HCH3  0   0.223   3.1614  -0.8413   0.9502
 4SF  H16  H  HCH3  0   0.225   0.2743  -0.7507  -2.2781
 4SF  H17  H  HCH3  0   0.233   1.4891  -2.0205  -2.2161
 4SF  H18  H  HCH3  0   0.219   0.1692  -2.0178  -1.0529
 4SF  H19  H  HCH3  0   0.200   3.4132   1.7058  -0.2863
 4SF  H20  H  HCH3  0   0.223   2.1070   2.8579  -0.5720
 4SF  H21  H  HCH3  0   0.235   3.0706   2.9695   0.8945
 4SF  H1   H  HNH1  0   0.342   2.0863   0.9621   1.6596

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   double  1.209  0.020  1.209
 4SF  C5   O7   single  1.327  0.020  1.327
 4SF  C5   C3   single  1.486  0.020  1.486
 4SF  C4   C3   single  1.504  0.020  1.504
 4SF  C3   C2   double  1.337  0.020  1.337
 4SF  CN   N    single  1.448  0.020  1.448
 4SF  N    C1   single  1.458  0.020  1.458
 4SF  C2   C1   single  1.502  0.020  1.502
 4SF  C1   C11  single  1.552  0.020  1.552
 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  O7   H7   single  0.850  0.020  0.980
 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    106.40  3.000
 4SF  H2   C1   C11  106.53  3.000
 4SF  N    C1   C11  115.31  3.000
 4SF  H2   C1   C2   110.76  3.000
 4SF  C11  C1   C2   111.09  3.000
 4SF  N    C1   C2   106.66  3.000
 4SF  C3   C5   O7   115.09  3.000
 4SF  C3   C5   O6   122.36  3.000
 4SF  O7   C5   O6   122.52  3.000
 4SF  H7   O7   C5   109.57  3.000
 4SF  C2   C3   C4   121.00  3.000
 4SF  C2   C3   C5   125.31  3.000
 4SF  C4   C3   C5   113.55  3.000
 4SF  H10  C4   H9   107.96  3.000
 4SF  H10  C4   H8   107.08  3.000
 4SF  H9   C4   H8   107.89  3.000
 4SF  H10  C4   C3   111.70  3.000
 4SF  H9   C4   C3   110.66  3.000
 4SF  H8   C4   C3   111.38  3.000
 4SF  H11  C2   C3   114.78  3.000
 4SF  H11  C2   C1   113.16  3.000
 4SF  C3   C2   C1   131.96  3.000
 4SF  H12  C11  C13  107.00  3.000
 4SF  H12  C11  C12  107.72  3.000
 4SF  C13  C11  C12  110.93  3.000
 4SF  H12  C11  C1   105.99  3.000
 4SF  C13  C11  C1   111.66  3.000
 4SF  C12  C11  C1   113.14  3.000
 4SF  H15  C12  H14  106.94  3.000
 4SF  H15  C12  H13  107.90  3.000
 4SF  H14  C12  H13  107.29  3.000
 4SF  H15  C12  C11  112.30  3.000
 4SF  H14  C12  C11  110.49  3.000
 4SF  H13  C12  C11  111.67  3.000
 4SF  H18  C13  H17  107.41  3.000
 4SF  H18  C13  H16  107.96  3.000
 4SF  H17  C13  H16  107.38  3.000
 4SF  H18  C13  C11  111.74  3.000
 4SF  H17  C13  C11  110.52  3.000
 4SF  H16  C13  C11  111.62  3.000
 4SF  H1   N    CN   109.62  3.000
 4SF  H1   N    C1   110.17  3.000
 4SF  CN   N    C1   114.87  3.000
 4SF  H21  CN   H20  107.36  3.000
 4SF  H21  CN   H19  107.42  3.000
 4SF  H20  CN   H19  107.46  3.000
 4SF  H21  CN   N    109.36  3.000
 4SF  H20  CN   N    109.65  3.000
 4SF  H19  CN   N    115.29  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
 4SF  CONST_01  H7   O7   C5   O6    0.00   0.0  0
 4SF  Var_01    C5   C3   C2   C1   -0.77   0.0  2
 4SF  Var_02    C4   C3   C5   O6  -27.88  30.0  2
 4SF  Var_03    H19  CN   N    C1  -62.68  30.0  3
 4SF  Var_04    H13  C12  C11  C1   65.69  30.0  3
 4SF  Var_05    H16  C13  C11  C1   51.98  30.0  3
 4SF  Var_06    H8   C4   C3   C5   63.33  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-1  H7   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

