# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 22:49:41 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: (3S)-4-oxo-3-[(sulfanylacetyl)amino]pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)[C@H](CC(O)=O)NC(=O)CS
#
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
 158  158  '(3S)-4-oxo-3-[(sulfanylacetyl)amino]pentanoic acid'  ligand  24  13  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_158
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
 158  O13   O  O     0  -0.479   0.7962   0.9644  -1.6514
 158  C5    C  C     0   0.578   0.0968  -0.0020  -1.3980
 158  C6    C  CH2   0  -0.689  -0.5922  -0.8070  -2.4777
 158  S7    S  S2    0  -0.222  -0.0059  -0.2177  -4.0892
 158  N4    N  NH1   0  -0.626  -0.1415  -0.4204  -0.1447
 158  C3    C  CH1   0  -0.176   0.4740   0.2273   0.9811
 158  C2    C  C     0   0.398   1.9809  -0.0401   1.0282
 158  O8    O  O     0  -0.383   2.4604  -1.0042   0.4852
 158  C1    C  CH3   0  -0.777   2.7946   0.9767   1.7714
 158  C9    C  CH2   0  -0.622  -0.1581  -0.2645   2.2775
 158  C10   C  C     0   0.565  -1.5891   0.1870   2.4367
 158  O11   O  O     0  -0.430  -2.1052   1.0745   1.8084
 158  O12   O  OH1   0  -0.589  -2.2060  -0.4983   3.3889
 158  H61   H  HCH2  0   0.304  -0.3748  -1.8685  -2.3544
 158  H62   H  HCH2  0   0.310  -1.6729  -0.6806  -2.3900
 158  H7    H  HSH1  0   0.222  -0.6743  -1.1233  -4.8120
 158  H4    H  HNH1  0   0.411  -0.6443  -1.2820   0.0001
 158  H3    H  HCH1  0   0.289   0.3268   1.3086   0.9067
 158  H11   H  HCH3  0   0.270   3.7857   0.5988   2.0111
 158  H12A  H  HCH3  0   0.280   2.8991   1.8594   1.1355
 158  H13   H  HCH3  0   0.260   2.3009   1.3112   2.6837
 158  H91   H  HCH2  0   0.302  -0.0948  -1.3529   2.3543
 158  H92   H  HCH2  0   0.319   0.3939   0.1254   3.1377
 158  H12   H  HOH1  0   0.484  -3.1103  -0.1694   3.5059

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
 158  O13  C5    double  1.220  0.020  1.220
 158  C5   C6    single  1.513  0.020  1.513
 158  C5   N4    single  1.343  0.020  1.343
 158  C6   S7    single  1.813  0.020  1.813
 158  C6   H61   single  0.970  0.020  1.090
 158  C6   H62   single  0.970  0.020  1.090
 158  S7   H7    single  1.200  0.020  1.300
 158  N4   C3    single  1.437  0.020  1.437
 158  N4   H4    single  0.860  0.020  1.020
 158  C3   C2    single  1.531  0.020  1.531
 158  C3   C9    single  1.524  0.020  1.524
 158  C3   H3    single  0.970  0.020  1.090
 158  C2   O8    double  1.206  0.020  1.206
 158  C2   C1    single  1.500  0.020  1.500
 158  C1   H11   single  0.970  0.020  1.090
 158  C1   H12A  single  0.970  0.020  1.090
 158  C1   H13   single  0.970  0.020  1.090
 158  C9   C10   single  1.509  0.020  1.509
 158  C9   H91   single  0.970  0.020  1.090
 158  C9   H92   single  0.970  0.020  1.090
 158  C10  O11   double  1.204  0.020  1.204
 158  C10  O12   single  1.325  0.020  1.325
 158  O12  H12   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
 158  N4    C5   C6    114.81  3.000
 158  N4    C5   O13   122.86  3.000
 158  C6    C5   O13   122.32  3.000
 158  H62   C6   H61   107.51  3.000
 158  H62   C6   S7    110.73  3.000
 158  H61   C6   S7    110.63  3.000
 158  H62   C6   C5    109.39  3.000
 158  H61   C6   C5    110.27  3.000
 158  S7    C6   C5    108.30  3.000
 158  H7    S7   C6     95.66  3.000
 158  H4    N4   C3    119.09  3.000
 158  H4    N4   C5    119.27  3.000
 158  C3    N4   C5    120.98  3.000
 158  H3    C3   C9    108.72  3.000
 158  H3    C3   C2    107.89  3.000
 158  C9    C3   C2    109.01  3.000
 158  H3    C3   N4    109.55  3.000
 158  C9    C3   N4    110.08  3.000
 158  C2    C3   N4    111.52  3.000
 158  C1    C2   O8    123.33  3.000
 158  C1    C2   C3    115.52  3.000
 158  O8    C2   C3    121.14  3.000
 158  H13   C1   H12A  106.41  3.000
 158  H13   C1   H11   109.57  3.000
 158  H12A  C1   H11   108.77  3.000
 158  H13   C1   C2    112.16  3.000
 158  H12A  C1   C2    108.13  3.000
 158  H11   C1   C2    111.60  3.000
 158  H92   C9   H91   105.69  3.000
 158  H92   C9   C10   106.80  3.000
 158  H91   C9   C10   110.21  3.000
 158  H92   C9   C3    110.16  3.000
 158  H91   C9   C3    110.92  3.000
 158  C10   C9   C3    112.74  3.000
 158  O12   C10  O11   123.82  3.000
 158  O12   C10  C9    111.25  3.000
 158  O11   C10  C9    124.91  3.000
 158  H12   O12  C10   110.21  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
 158  CONST_01  C3   N4   C5   O13    0.00   0.0  0
 158  CONST_02  C3   N4   C5   C6   180.00   0.0  0
 158  CONST_03  H4   N4   C5   O13  180.00   0.0  0
 158  CONST_04  H12  O12  C10  C9   180.00   0.0  0
 158  Var_01    S7   C6   C5   O13    7.48  30.0  3
 158  Var_02    O11  C10  C9   C3   -16.46  30.0  3
 158  Var_03    H11  C1   C2   C3   163.82  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
 158  chir_01  C3  N4  C2  C9  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
 158  plan-1  O13  0.020
 158  plan-1  C5   0.020
 158  plan-1  C6   0.020
 158  plan-1  N4   0.020
 158  plan-1  C3   0.020
 158  plan-1  H4   0.020
 158  plan-2  C3   0.020
 158  plan-2  C2   0.020
 158  plan-2  O8   0.020
 158  plan-2  C1   0.020
 158  plan-3  C9   0.020
 158  plan-3  C10  0.020
 158  plan-3  O11  0.020
 158  plan-3  O12  0.020
 158  plan-3  H12  0.020

