# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 18:26:22 2020
#   Inital geometry file: a 57 line input string
#   Ligand name: N-(3-sulfanylpropanoyl)-D-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](NC(=O)CCS)C(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
 I38  I38  N-(3-sulfanylpropanoyl)-D-alanine  ligand  21  11  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_I38
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
 I38  S     S  S2     0  -0.256   4.4130  -0.6553   0.1944
 I38  C1    C  CH2    0  -0.547   2.9583   0.2710  -0.4000
 I38  C2    C  CH2    0  -0.564   1.7603  -0.1230   0.4479
 I38  C3    C  C      0   0.560   0.5166   0.6605   0.0646
 I38  O3    O  O      0  -0.515   0.5789   1.8372  -0.2768
 I38  N4    N  NH1    0  -0.633  -0.6261  -0.0221   0.1582
 I38  C5    C  CH1    0  -0.204  -1.9385   0.5182  -0.1188
 I38  C51   C  CH3    0  -0.658  -2.4175   1.4537   0.9904
 I38  C6    C  C      0   0.418  -2.9395  -0.6479  -0.3082
 I38  O62   O  O      0  -0.599  -2.5254  -1.8012  -0.0757
 I38  O61   O  OC    -1  -0.604  -4.0837  -0.3165  -0.6626
 I38  HS    H  HSH1   0   0.224   5.3030  -0.1659  -0.6755
 I38  H11   H  HCH2   0   0.272   3.1501   1.3387  -0.3183
 I38  H12   H  HCH2   0   0.272   2.7823   0.0302  -1.4480
 I38  H21   H  HCH2   0   0.261   1.5802  -1.1975   0.3735
 I38  H22   H  HCH2   0   0.277   1.9679   0.0862   1.5024
 I38  HN4   H  HNH1   0   0.384  -0.6150  -1.0107   0.3657
 I38  H5    H  HCH1   0   0.237  -1.8992   1.0838  -1.0555
 I38  H511  H  HCH3   0   0.227  -3.3956   1.8640   0.7444
 I38  H512  H  HCH3   0   0.218  -2.4989   0.9209   1.9396
 I38  H513  H  HCH3   0   0.231  -1.7276   2.2857   1.1257

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
 I38  S    C1    single  1.824  0.020  1.824
 I38  S    HS    single  1.200  0.020  1.300
 I38  C1   C2    single  1.520  0.020  1.520
 I38  C1   H11   single  0.970  0.020  1.090
 I38  C1   H12   single  0.970  0.020  1.090
 I38  C2   C3    single  1.519  0.020  1.519
 I38  C2   H21   single  0.970  0.020  1.090
 I38  C2   H22   single  0.970  0.020  1.090
 I38  C3   O3    double  1.227  0.020  1.227
 I38  C3   N4    single  1.334  0.020  1.334
 I38  N4   C5    single  1.446  0.020  1.446
 I38  N4   HN4   single  0.860  0.020  1.020
 I38  C5   C51   single  1.528  0.020  1.528
 I38  C5   C6    single  1.548  0.020  1.548
 I38  C5   H5    single  0.970  0.020  1.090
 I38  C51  H511  single  0.970  0.020  1.090
 I38  C51  H512  single  0.970  0.020  1.090
 I38  C51  H513  single  0.970  0.020  1.090
 I38  C6   O62   deloc   1.247  0.020  1.247
 I38  C6   O61   deloc   1.243  0.020  1.243

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
 I38  HS    S    C1     97.64  3.000
 I38  H12   C1   H11   108.51  3.000
 I38  H12   C1   C2    110.61  3.000
 I38  H11   C1   C2    110.58  3.000
 I38  H12   C1   S     109.27  3.000
 I38  H11   C1   S     109.48  3.000
 I38  C2    C1   S     108.37  3.000
 I38  H22   C2   H21   106.56  3.000
 I38  H22   C2   C3    107.44  3.000
 I38  H21   C2   C3    110.81  3.000
 I38  H22   C2   C1    109.78  3.000
 I38  H21   C2   C1    110.31  3.000
 I38  C3    C2   C1    111.77  3.000
 I38  N4    C3   O3    123.62  3.000
 I38  N4    C3   C2    114.81  3.000
 I38  O3    C3   C2    121.56  3.000
 I38  HN4   N4   C5    114.52  3.000
 I38  HN4   N4   C3    120.37  3.000
 I38  C5    N4   C3    124.94  3.000
 I38  H5    C5   C6    107.91  3.000
 I38  H5    C5   C51   108.42  3.000
 I38  C6    C5   C51   110.32  3.000
 I38  H5    C5   N4    108.92  3.000
 I38  C6    C5   N4    109.19  3.000
 I38  C51   C5   N4    111.98  3.000
 I38  H513  C51  H512  108.18  3.000
 I38  H513  C51  H511  108.01  3.000
 I38  H512  C51  H511  108.27  3.000
 I38  H513  C51  C5    111.05  3.000
 I38  H512  C51  C5    110.84  3.000
 I38  H511  C51  C5    110.38  3.000
 I38  O61   C6   O62   127.25  3.000
 I38  O61   C6   C5    115.42  3.000
 I38  O62   C6   C5    117.32  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
 I38  CONST_01  C5   N4  C3  C2  180.00   0.0  0
 I38  CONST_02  C5   N4  C3  O3    0.00   0.0  0
 I38  CONST_03  HN4  N4  C3  C2    0.00   0.0  0
 I38  Var_01    C3   C2  C1  S   177.01  30.0  3
 I38  Var_02    O3   C3  C2  C1  -36.26  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
 I38  chir_01  C5  N4  C51  C6  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
 I38  plan-1  C2   0.020
 I38  plan-1  C3   0.020
 I38  plan-1  O3   0.020
 I38  plan-1  N4   0.020
 I38  plan-1  C5   0.020
 I38  plan-1  HN4  0.020
 I38  plan-2  C5   0.020
 I38  plan-2  C6   0.020
 I38  plan-2  O62  0.020
 I38  plan-2  O61  0.020

