# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 20 23:46:16 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: (6S)-8-[(aminomethyl)sulfanyl]-6-[(2-hydroxyethyl)disulfanyl]octanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCSCC[C@H](CCCCC(O)=O)SSCCO
#
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
 OSS  OSS  '(6S)-8-[(aminomethyl)sulfanyl]-6-[(2-hydroxyethyl)disulfanyl]octanoic acid'  ligand  41  18  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_OSS
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
 OSS  C1    C  C     0   0.550   0.5414  -0.3903  -6.1427
 OSS  O1    O  O     0  -0.446  -0.2662   0.4190  -6.5272
 OSS  O2    O  OH1   0  -0.598   1.2626  -1.1409  -6.9715
 OSS  C2    C  CH2   0  -0.580   0.8618  -0.6820  -4.7031
 OSS  C3    C  CH2   0  -0.417   0.0696   0.1594  -3.7170
 OSS  C4    C  CH2   0  -0.429   0.4294  -0.1704  -2.2727
 OSS  C5    C  CH2   0  -0.388  -0.3597   0.6894  -1.2897
 OSS  C6    C  CH1   0  -0.375  -0.1393   0.3210   0.1720
 OSS  C7    C  CH2   0  -0.432   1.2806   0.6125   0.6546
 OSS  C8    C  CH2   0  -0.551   1.5546   0.1370   2.0754
 OSS  S9    S  S2    0  -0.046   3.3254   0.3016   2.4411
 OSS  C10   C  CH2   0  -0.369   3.3366  -0.2918   4.1673
 OSS  N11   N  NH2   0  -0.795   4.7012  -0.5932   4.5187
 OSS  S12   S  S2    0  -0.044  -1.2824   1.2723   1.2556
 OSS  S13   S  S2    0  -0.043  -3.1205   0.4961   0.7849
 OSS  C14   C  CH2   0  -0.587  -3.2544  -0.9398   1.8883
 OSS  C15   C  CH2   0  -0.122  -3.4567  -0.5316   3.3334
 OSS  O16   O  OH1   0  -0.670  -3.5971  -1.7074   4.0990
 OSS  HO2   H  HOH1  0   0.478   1.0342  -0.9330  -7.8898
 OSS  H21   H  HCH2  0   0.276   1.9370  -0.5354  -4.5583
 OSS  H22   H  HCH2  0   0.276   0.6869  -1.7486  -4.5277
 OSS  H31   H  HCH2  0   0.229  -1.0011  -0.0006  -3.8674
 OSS  H32   H  HCH2  0   0.229   0.2560   1.2204  -3.9014
 OSS  H41   H  HCH2  0   0.226   1.5045  -0.0287  -2.1305
 OSS  H42   H  HCH2  0   0.222   0.2287  -1.2291  -2.0781
 OSS  H51   H  HCH2  0   0.235  -1.4243   0.5833  -1.5178
 OSS  H52   H  HCH2  0   0.227  -0.1109   1.7453  -1.4341
 OSS  H6    H  HCH1  0   0.274  -0.3593  -0.7397   0.3272
 OSS  H71   H  HCH2  0   0.249   1.4928   1.6822   0.5637
 OSS  H72   H  HCH2  0   0.265   1.9677   0.1037  -0.0261
 OSS  H81   H  HCH2  0   0.260   1.2625  -0.9106   2.1858
 OSS  H82   H  HCH2  0   0.265   0.9851   0.7171   2.8025
 OSS  H101  H  HCH2  0   0.236   2.6381  -1.1343   4.2323
 OSS  H102  H  HCH2  0   0.260   2.9630   0.4982   4.8191
 OSS  HN11  H  HNH2  0   0.361   4.7875  -0.6612   5.5239
 OSS  HN12  H  HNH2  0   0.353   4.9707  -1.4900   4.1373
 OSS  H141  H  HCH2  0   0.287  -4.1203  -1.4927   1.5149
 OSS  H142  H  HCH2  0   0.277  -2.3755  -1.5749   1.7671
 OSS  H151  H  HCH2  0   0.203  -2.5970   0.0647   3.6619
 OSS  H152  H  HCH2  0   0.201  -4.3436   0.1102   3.4018
 OSS  HO6   H  HOH1  0   0.457  -3.6546  -1.4551   5.0249

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
 OSS  C1   O1    double  1.206  0.020  1.206
 OSS  C1   O2    single  1.331  0.020  1.331
 OSS  C1   C2    single  1.503  0.020  1.503
 OSS  O2   HO2   single  0.850  0.020  0.980
 OSS  C2   C3    single  1.519  0.020  1.519
 OSS  C2   H21   single  0.970  0.020  1.090
 OSS  C2   H22   single  0.970  0.020  1.090
 OSS  C3   C4    single  1.525  0.020  1.525
 OSS  C3   H31   single  0.970  0.020  1.090
 OSS  C3   H32   single  0.970  0.020  1.090
 OSS  C4   C5    single  1.526  0.020  1.526
 OSS  C4   H41   single  0.970  0.020  1.090
 OSS  C4   H42   single  0.970  0.020  1.090
 OSS  C5   C6    single  1.523  0.020  1.523
 OSS  C5   H51   single  0.970  0.020  1.090
 OSS  C5   H52   single  0.970  0.020  1.090
 OSS  C6   C7    single  1.528  0.020  1.528
 OSS  C6   S12   single  1.840  0.020  1.840
 OSS  C6   H6    single  0.970  0.020  1.090
 OSS  C7   C8    single  1.523  0.020  1.523
 OSS  C7   H71   single  0.970  0.020  1.090
 OSS  C7   H72   single  0.970  0.020  1.090
 OSS  C8   S9    single  1.816  0.020  1.816
 OSS  C8   H81   single  0.970  0.020  1.090
 OSS  C8   H82   single  0.970  0.020  1.090
 OSS  S9   C10   single  1.825  0.020  1.825
 OSS  C10  N11   single  1.441  0.020  1.441
 OSS  C10  H101  single  0.970  0.020  1.090
 OSS  C10  H102  single  0.970  0.020  1.090
 OSS  N11  HN11  single  0.890  0.020  1.040
 OSS  N11  HN12  single  0.890  0.020  1.040
 OSS  S12  S13   single  2.050  0.020  2.050
 OSS  S13  C14   single  1.816  0.020  1.816
 OSS  C14  C15   single  1.515  0.020  1.515
 OSS  C14  H141  single  0.970  0.020  1.090
 OSS  C14  H142  single  0.970  0.020  1.090
 OSS  C15  O16   single  1.410  0.020  1.410
 OSS  C15  H151  single  0.970  0.020  1.090
 OSS  C15  H152  single  0.970  0.020  1.090
 OSS  O16  HO6   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
 OSS  C2    C1   O2    111.81  3.000
 OSS  C2    C1   O1    125.32  3.000
 OSS  O2    C1   O1    122.88  3.000
 OSS  HO2   O2   C1    109.97  3.000
 OSS  H22   C2   H21   105.44  3.000
 OSS  H22   C2   C3    110.62  3.000
 OSS  H21   C2   C3    110.62  3.000
 OSS  H22   C2   C1    107.96  3.000
 OSS  H21   C2   C1    108.06  3.000
 OSS  C3    C2   C1    113.76  3.000
 OSS  H32   C3   H31   106.62  3.000
 OSS  H32   C3   C4    109.24  3.000
 OSS  H31   C3   C4    109.26  3.000
 OSS  H32   C3   C2    109.83  3.000
 OSS  H31   C3   C2    109.91  3.000
 OSS  C4    C3   C2    111.84  3.000
 OSS  H42   C4   H41   106.40  3.000
 OSS  H42   C4   C5    109.60  3.000
 OSS  H41   C4   C5    110.59  3.000
 OSS  H42   C4   C3    109.52  3.000
 OSS  H41   C4   C3    109.10  3.000
 OSS  C5    C4   C3    111.49  3.000
 OSS  H52   C5   H51   106.69  3.000
 OSS  H52   C5   C6    109.09  3.000
 OSS  H51   C5   C6    108.51  3.000
 OSS  H52   C5   C4    109.95  3.000
 OSS  H51   C5   C4    108.32  3.000
 OSS  C6    C5   C4    114.02  3.000
 OSS  H6    C6   S12   107.02  3.000
 OSS  H6    C6   C7    109.09  3.000
 OSS  S12   C6   C7    107.02  3.000
 OSS  H6    C6   C5    109.96  3.000
 OSS  S12   C6   C5    110.49  3.000
 OSS  C7    C6   C5    113.04  3.000
 OSS  H72   C7   H71   106.35  3.000
 OSS  H72   C7   C8    108.82  3.000
 OSS  H71   C7   C8    110.35  3.000
 OSS  H72   C7   C6    107.39  3.000
 OSS  H71   C7   C6    109.90  3.000
 OSS  C8    C7   C6    113.72  3.000
 OSS  H82   C8   H81   107.63  3.000
 OSS  H82   C8   S9    109.07  3.000
 OSS  H81   C8   S9    109.10  3.000
 OSS  H82   C8   C7    111.22  3.000
 OSS  H81   C8   C7    110.20  3.000
 OSS  S9    C8   C7    109.57  3.000
 OSS  C10   S9   C8     99.61  3.000
 OSS  H102  C10  H101  107.65  3.000
 OSS  H102  C10  N11   109.29  3.000
 OSS  H101  C10  N11   115.35  3.000
 OSS  H102  C10  S9    109.13  3.000
 OSS  H101  C10  S9    107.57  3.000
 OSS  N11   C10  S9    107.72  3.000
 OSS  HN12  N11  HN11  107.01  3.000
 OSS  HN12  N11  C10   110.24  3.000
 OSS  HN11  N11  C10   109.71  3.000
 OSS  S13   S12  C6    103.06  3.000
 OSS  C14   S13  S12   103.06  3.000
 OSS  H142  C14  H141  107.80  3.000
 OSS  H142  C14  C15   111.73  3.000
 OSS  H141  C14  C15   110.87  3.000
 OSS  H142  C14  S13   109.48  3.000
 OSS  H141  C14  S13   104.53  3.000
 OSS  C15   C14  S13   112.11  3.000
 OSS  H152  C15  H151  107.28  3.000
 OSS  H152  C15  O16   111.93  3.000
 OSS  H151  C15  O16   111.65  3.000
 OSS  H152  C15  C14   108.97  3.000
 OSS  H151  C15  C14   109.12  3.000
 OSS  O16   C15  C14   107.85  3.000
 OSS  HO6   O16  C15   108.06  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
 OSS  CONST_01  HO2   O2   C1   O1      0.00   0.0  0
 OSS  Var_01    C4    C3   C2   C1   -179.93  30.0  3
 OSS  Var_02    C3    C2   C1   O1     -0.48  30.0  3
 OSS  Var_03    C5    C4   C3   C2    179.39  30.0  3
 OSS  Var_04    C6    C5   C4   C3    174.72  30.0  3
 OSS  Var_05    S9    C8   C7   C6    171.27  30.0  3
 OSS  Var_06    N11   C10  S9   C8    164.03  30.0  3
 OSS  Var_07    C15   C14  S13  S12    71.50  30.0  3
 OSS  Var_08    O16   C15  C14  S13   177.90  30.0  3
 OSS  Var_09    HN11  N11  C10  S9    163.50  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
 OSS  chir_01  C6  C5  C7  S12  negativ

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
 OSS  plan-1  C1   0.020
 OSS  plan-1  O1   0.020
 OSS  plan-1  O2   0.020
 OSS  plan-1  C2   0.020
 OSS  plan-1  HO2  0.020

