# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar  7 21:06:35 2022
#   Inital geometry file: a 108 line input string
#   Ligand name: N-[(2S)-2-benzyl-3-sulfanylpropanoyl]-L-alanylglycinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](NC(=O)[C@@H](CS)Cc1ccccc1)C(=O)NCC(N)=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
 0D3  0D3  N-[(2S)-2-benzyl-3-sulfanylpropanoyl]-L-alanylglycinamide  peptide  43  22  .  2019-03-22  2022-03-08
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_0D3
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
 0D3  C1   C  C     0   0.585  28.0124  59.2294  50.3907
 0D3  O1   O  O     0  -0.484  27.7155  60.0104  49.4981
 0D3  C2   C  CH1   0  -0.371  26.9871  58.7364  51.3992
 0D3  C3   C  CH2   0  -0.474  25.7691  58.1645  50.6678
 0D3  C1'  C  CR6   0   0.124  26.1106  57.0422  49.7253
 0D3  C2'  C  CR16  0  -0.309  26.6236  55.8379  50.2064
 0D3  C3'  C  CR16  0  -0.237  26.9392  54.8011  49.3398
 0D3  C4'  C  CR16  0  -0.271  26.7418  54.9487  47.9721
 0D3  C5'  C  CR16  0  -0.236  26.2297  56.1413  47.4811
 0D3  C6'  C  CR16  0  -0.312  25.9205  57.1785  48.3525
 0D3  C'   C  CH2   0  -0.565  26.6176  59.9117  52.3078
 0D3  S'   S  S2    0  -0.230  25.4781  59.4815  53.6582
 0D3  N    N  NH1   0  -0.626  29.2647  58.7761  50.5596
 0D3  CA   C  CH1   0  -0.191  30.3307  59.1396  49.6594
 0D3  C    C  C     0   0.561  30.0747  58.5282  48.2818
 0D3  O    O  O     0  -0.492  29.7286  57.3615  48.1641
 0D3  CB   C  CH3   0  -0.682  31.6621  58.6265  50.1929
 0D3  N1   N  NH1   0  -0.621  30.3042  59.3363  47.2385
 0D3  CA1  C  CH2   0  -0.418  30.1016  58.9376  45.8644
 0D3  C4   C  C     0   0.494  31.3322  58.2840  45.2375
 0D3  O2   O  O     0  -0.476  31.9267  58.8050  44.3080
 0D3  N2   N  NH2   0  -0.797  31.6862  57.1137  45.7874
 0D3  H2   H  HCH1  0   0.268  27.4346  57.9523  52.0180
 0D3  H31  H  HCH2  0   0.259  25.0605  57.8122  51.4203
 0D3  H32  H  HCH2  0   0.246  25.2712  58.9670  50.1195
 0D3  H2'  H  HCR6  0   0.247  26.7720  55.7059  51.2723
 0D3  H3'  H  HCR6  0   0.251  27.3348  53.8732  49.7331
 0D3  H4'  H  HCR6  0   0.251  26.9851  54.1393  47.2959
 0D3  H5'  H  HCR6  0   0.251  26.0718  56.2676  46.4174
 0D3  H6'  H  HCR6  0   0.245  25.5226  58.1070  47.9602
 0D3  H'1  H  HCH2  0   0.292  27.5130  60.3604  52.7385
 0D3  H'2  H  HCH2  0   0.283  26.1086  60.6878  51.7343
 0D3  HS'  H  HSH1  0   0.222  26.3213  58.7060  54.3502
 0D3  H    H  HNH1  0   0.408  29.4501  58.0883  51.2725
 0D3  HA   H  HCH1  0   0.273  30.3776  60.2293  49.5815
 0D3  HB1  H  HCH3  0   0.255  32.4722  58.8973  49.5174
 0D3  HB2  H  HCH3  0   0.257  31.8743  59.0657  51.1672
 0D3  HB3  H  HCH3  0   0.242  31.6518  57.5410  50.2959
 0D3  H1   H  HNH1  0   0.412  30.5845  60.2891  47.4076
 0D3  HA2  H  HCH2  0   0.275  29.2509  58.2554  45.8068
 0D3  HA3  H  HCH2  0   0.284  29.8548  59.8247  45.2859
 0D3  HN1  H  HNH2  0   0.409  31.1462  56.6945  46.5273
 0D3  HN2  H  HNH2  0   0.399  32.4982  56.6195  45.4543

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
 0D3  C1   O1   double    1.223  0.020  1.223
 0D3  C1   C2   single    1.520  0.020  1.520
 0D3  C2   C3   single    1.532  0.020  1.532
 0D3  C2   C'   single    1.531  0.020  1.531
 0D3  C2   H2   single    0.970  0.020  1.090
 0D3  C3   C1'  single    1.505  0.020  1.505
 0D3  C3   H31  single    0.970  0.020  1.090
 0D3  C3   H32  single    0.970  0.020  1.090
 0D3  C1'  C2'  aromatic  1.395  0.020  1.395
 0D3  C1'  C6'  aromatic  1.393  0.020  1.393
 0D3  C2'  C3'  aromatic  1.388  0.020  1.388
 0D3  C2'  H2'  single    0.930  0.020  1.080
 0D3  C3'  C4'  aromatic  1.390  0.020  1.390
 0D3  C3'  H3'  single    0.930  0.020  1.080
 0D3  C4'  C5'  aromatic  1.388  0.020  1.388
 0D3  C4'  H4'  single    0.930  0.020  1.080
 0D3  C5'  C6'  aromatic  1.390  0.020  1.390
 0D3  C5'  H5'  single    0.930  0.020  1.080
 0D3  C6'  H6'  single    0.930  0.020  1.080
 0D3  C'   S'   single    1.819  0.020  1.819
 0D3  C'   H'1  single    0.970  0.020  1.090
 0D3  C'   H'2  single    0.970  0.020  1.090
 0D3  S'   HS'  single    1.200  0.020  1.300
 0D3  N    CA   single    1.458  0.019  1.458
 0D3  N    H    single    0.860  0.020  0.860
 0D3  CA   C    single    1.525  0.021  1.525
 0D3  CA   CB   single    1.521  0.033  1.521
 0D3  CA   HA   single    0.970  0.020  0.970
 0D3  C    O    double    1.231  0.020  1.231
 0D3  CB   HB1  single    0.970  0.020  1.090
 0D3  CB   HB2  single    0.970  0.020  1.090
 0D3  CB   HB3  single    0.970  0.020  1.090
 0D3  N1   CA1  single    1.445  0.020  1.445
 0D3  N1   H1   single    0.860  0.020  1.020
 0D3  CA1  C4   single    1.528  0.020  1.528
 0D3  CA1  HA2  single    0.970  0.020  1.090
 0D3  CA1  HA3  single    0.970  0.020  1.090
 0D3  C4   O2   double    1.220  0.020  1.220
 0D3  N2   HN1  single    0.860  0.020  1.020
 0D3  N2   HN2  single    0.860  0.020  1.020
 0D3  C1   N    single    1.342  0.020  1.342
 0D3  C    N1   single    1.339  0.020  1.339
 0D3  C4   N2   single    1.341  0.020  1.341

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
 0D3  N    C1   C2   115.86  3.000
 0D3  N    C1   O1   122.28  3.000
 0D3  C2   C1   O1   121.85  3.000
 0D3  H2   C2   C'   108.25  3.000
 0D3  H2   C2   C3   109.13  3.000
 0D3  C'   C2   C3   112.22  3.000
 0D3  H2   C2   C1   109.37  3.000
 0D3  C'   C2   C1   107.91  3.000
 0D3  C3   C2   C1   109.91  3.000
 0D3  H32  C3   H31  106.69  3.000
 0D3  H32  C3   C1'  109.70  3.000
 0D3  H31  C3   C1'  109.77  3.000
 0D3  H32  C3   C2   109.14  3.000
 0D3  H31  C3   C2   107.90  3.000
 0D3  C1'  C3   C2   113.40  3.000
 0D3  C6'  C1'  C2'  118.35  3.000
 0D3  C6'  C1'  C3   120.89  3.000
 0D3  C2'  C1'  C3   120.76  3.000
 0D3  H2'  C2'  C3'  119.46  3.000
 0D3  H2'  C2'  C1'  119.64  3.000
 0D3  C3'  C2'  C1'  120.89  3.000
 0D3  H3'  C3'  C4'  120.03  3.000
 0D3  H3'  C3'  C2'  119.78  3.000
 0D3  C4'  C3'  C2'  120.19  3.000
 0D3  H4'  C4'  C5'  120.30  3.000
 0D3  H4'  C4'  C3'  120.23  3.000
 0D3  C5'  C4'  C3'  119.47  3.000
 0D3  H5'  C5'  C6'  119.77  3.000
 0D3  H5'  C5'  C4'  120.11  3.000
 0D3  C6'  C5'  C4'  120.11  3.000
 0D3  H6'  C6'  C5'  119.62  3.000
 0D3  H6'  C6'  C1'  119.40  3.000
 0D3  C5'  C6'  C1'  120.98  3.000
 0D3  H'2  C'   H'1  107.34  3.000
 0D3  H'2  C'   S'   105.44  3.000
 0D3  H'1  C'   S'   108.58  3.000
 0D3  H'2  C'   C2   110.29  3.000
 0D3  H'1  C'   C2   110.62  3.000
 0D3  S'   C'   C2   114.23  3.000
 0D3  HS'  S'   C'    97.25  3.000
 0D3  H    N    CA   114.00  3.000
 0D3  H    N    C1   119.41  3.000
 0D3  CA   N    C1   121.73  3.000
 0D3  HA   CA   CB   109.00  3.000
 0D3  HA   CA   C    110.00  3.000
 0D3  CB   CA   C    110.50  1.500
 0D3  HA   CA   N    110.00  3.000
 0D3  CB   CA   N    110.40  1.500
 0D3  C    CA   N    111.00  2.800
 0D3  N1   C    O    123.32  3.000
 0D3  N1   C    CA   115.59  3.000
 0D3  O    C    CA   120.80  1.700
 0D3  HB3  CB   HB2  108.59  3.000
 0D3  HB3  CB   HB1  108.25  3.000
 0D3  HB2  CB   HB1  108.04  3.000
 0D3  HB3  CB   CA   111.11  3.000
 0D3  HB2  CB   CA   110.34  3.000
 0D3  HB1  CB   CA   110.43  3.000
 0D3  H1   N1   CA1  117.36  3.000
 0D3  H1   N1   C    119.18  3.000
 0D3  CA1  N1   C    123.38  3.000
 0D3  HA3  CA1  HA2  107.75  3.000
 0D3  HA3  CA1  C4   108.26  3.000
 0D3  HA2  CA1  C4   109.79  3.000
 0D3  HA3  CA1  N1   108.22  3.000
 0D3  HA2  CA1  N1   109.38  3.000
 0D3  C4   CA1  N1   113.28  3.000
 0D3  N2   C4   O2   123.81  3.000
 0D3  N2   C4   CA1  114.70  3.000
 0D3  O2   C4   CA1  121.49  3.000
 0D3  HN2  N2   HN1  118.09  3.000
 0D3  HN2  N2   C4   120.37  3.000
 0D3  HN1  N2   C4   121.53  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
 0D3  CONST_01  C4'  C3'  C2'  C1'     0.00   0.0  0
 0D3  CONST_02  C4'  C5'  C6'  C1'     0.00   0.0  0
 0D3  CONST_03  C5'  C6'  C1'  C2'     0.00   0.0  0
 0D3  CONST_04  C5'  C4'  C3'  C2'     0.00   0.0  0
 0D3  CONST_05  C6'  C1'  C2'  C3'     0.00   0.0  0
 0D3  CONST_06  C6'  C5'  C4'  C3'     0.00   0.0  0
 0D3  CONST_07  C3'  C2'  C1'  C3    180.00   0.0  0
 0D3  CONST_08  C5'  C6'  C1'  C3    180.00   0.0  0
 0D3  CONST_09  H3'  C3'  C2'  C1'   180.00   0.0  0
 0D3  CONST_10  H5'  C5'  C6'  C1'   180.00   0.0  0
 0D3  CONST_11  H6'  C6'  C1'  C2'   180.00   0.0  0
 0D3  CONST_12  H4'  C4'  C3'  C2'   180.00   0.0  0
 0D3  CONST_13  H2'  C2'  C3'  C4'   180.00   0.0  0
 0D3  CONST_14  CA   N    C1   O1      0.00   0.0  0
 0D3  CONST_15  CA   N    C1   C2    180.00   0.0  0
 0D3  CONST_16  CA1  N1   C    CA    180.00   0.0  0
 0D3  CONST_17  CA1  N1   C    O       0.00   0.0  0
 0D3  CONST_18  H    N    C1   O1    180.00   0.0  0
 0D3  CONST_19  H1   N1   C    CA      0.00   0.0  0
 0D3  CONST_20  HN1  N2   C4   CA1     0.00   0.0  0
 0D3  CONST_21  HN2  N2   C4   CA1   180.00   0.0  0
 0D3  Var_01    C2'  C1'  C3   C2     64.63  30.0  2
 0D3  Var_02    C4   CA1  N1   C     -88.66  30.0  3
 0D3  Var_03    O2   C4   CA1  N1   -115.06  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
 0D3  chir_01  C2  C1  C3  C'  positiv
 0D3  chir_02  CA  N   C   CB  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
 0D3  plan-1  C3   0.020
 0D3  plan-1  C1'  0.020
 0D3  plan-1  C2'  0.020
 0D3  plan-1  C3'  0.020
 0D3  plan-1  C4'  0.020
 0D3  plan-1  C5'  0.020
 0D3  plan-1  C6'  0.020
 0D3  plan-1  H2'  0.020
 0D3  plan-1  H3'  0.020
 0D3  plan-1  H4'  0.020
 0D3  plan-1  H5'  0.020
 0D3  plan-1  H6'  0.020
 0D3  plan-2  C1   0.020
 0D3  plan-2  O1   0.020
 0D3  plan-2  C2   0.020
 0D3  plan-2  N    0.020
 0D3  plan-2  CA   0.020
 0D3  plan-2  H    0.020
 0D3  plan-3  CA   0.020
 0D3  plan-3  C    0.020
 0D3  plan-3  O    0.020
 0D3  plan-3  N1   0.020
 0D3  plan-3  CA1  0.020
 0D3  plan-3  H1   0.020
 0D3  plan-4  CA1  0.020
 0D3  plan-4  C4   0.020
 0D3  plan-4  O2   0.020
 0D3  plan-4  N2   0.020
 0D3  plan-4  HN1  0.020
 0D3  plan-4  HN2  0.020

