# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 04:49:22 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: trans-4-({[(E)-1-amino-2-sulfanylethenyl]carbamoyl}oxy)cyclohexanecarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N\C(NC(=O)O[C@H]1CC[C@@H](CC1)C(O)=O)=C/S
#
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
 9BB  9BB  'trans-4-({[(E)-1-amino-2-sulfanylethenyl]carbamoyl}oxy)cyclohexanecarboxylic acid'  peptide  32  17  .  2022-03-11  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9BB
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
 9BB  N     N  NH2    0  -0.841   3.9895   1.0081   0.8103
 9BB  O8    O  O      0  -0.501   1.2367   1.1378   0.7691
 9BB  O9    O  OC    -1  -0.618  -6.1270  -0.7575   0.1129
 9BB  CA    C  C      0   0.633   3.8002  -0.1422   0.1269
 9BB  CB    C  C1     0  -0.646   4.7953  -0.9101  -0.3940
 9BB  SG    S  S2     0  -0.235   6.4837  -0.4925  -0.1841
 9BB  O10   O  O      0  -0.604  -5.7062   1.3190  -0.5613
 9BB  O11   O  O2     0  -0.492   0.3084  -0.7779   0.0348
 9BB  N13   N  NH1    0  -0.735   2.4959  -0.6134  -0.0057
 9BB  C48   C  C      0   0.764   1.3300   0.0204   0.3073
 9BB  C49   C  CH1    0   0.059  -1.0334  -0.2976   0.2624
 9BB  C50   C  CH2    0  -0.461  -1.5137   0.5458  -0.9063
 9BB  C51   C  CH2    0  -0.421  -2.9663   0.9683  -0.6930
 9BB  C52   C  CH1    0  -0.387  -3.8840  -0.2313  -0.4813
 9BB  C53   C  CH2    0  -0.431  -3.3647  -1.0962   0.6675
 9BB  C54   C  CH2    0  -0.454  -1.9132  -1.5187   0.4562
 9BB  C55   C  C      0   0.432  -5.3679   0.1500  -0.2869
 9BB  HN    H  HNH2   0   0.408   3.2173   1.6413   0.9293
 9BB  H2    H  HNH2   0   0.392   4.9077   1.4148   0.7454
 9BB  HB    H  H      0   0.266   4.5509  -1.8450  -0.8807
 9BB  HSG   H  HSH1   0   0.210   6.7380   0.1548  -1.3346
 9BB  HN13  H  HNH1   0   0.421   2.4113  -1.5228  -0.4351
 9BB  H49   H  HCH1   0   0.233  -1.0449   0.3020   1.1782
 9BB  H50   H  HCH2   0   0.239  -0.8799   1.4274  -1.0253
 9BB  H50A  H  HCH2   0   0.220  -1.4323  -0.0416  -1.8275
 9BB  H51   H  HCH2   0   0.207  -3.0282   1.6321   0.1758
 9BB  H51A  H  HCH2   0   0.226  -3.2996   1.5536  -1.5498
 9BB  H52   H  HCH1   0   0.216  -3.8425  -0.8486  -1.3925
 9BB  H53   H  HCH2   0   0.208  -3.4427  -0.5382   1.6082
 9BB  H53A  H  HCH2   0   0.232  -3.9894  -1.9815   0.7800
 9BB  H54   H  HCH2   0   0.222  -1.8424  -2.1612  -0.4277
 9BB  H54A  H  HCH2   0   0.239  -1.5606  -2.1009   1.3110

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
 9BB  N    HN    single  0.890  0.020  1.040
 9BB  O8   C48   double  1.213  0.020  1.213
 9BB  CA   N     single  1.458  0.019  1.458
 9BB  CA   N13   single  1.393  0.020  1.393
 9BB  CB   CA    double  1.521  0.033  1.521
 9BB  CB   SG    single  1.752  0.020  1.752
 9BB  O10  C55   deloc   1.247  0.020  1.247
 9BB  O11  C49   single  1.443  0.020  1.443
 9BB  C48  O11   single  1.325  0.020  1.325
 9BB  C48  N13   single  1.363  0.020  1.363
 9BB  C49  C54   single  1.517  0.020  1.517
 9BB  C50  C49   single  1.519  0.020  1.519
 9BB  C50  C51   single  1.528  0.020  1.528
 9BB  C51  C52   single  1.525  0.020  1.525
 9BB  C52  C55   single  1.544  0.020  1.544
 9BB  C52  C53   single  1.529  0.020  1.529
 9BB  C54  C53   single  1.526  0.020  1.526
 9BB  C55  O9    deloc   1.249  0.020  1.249
 9BB  N    H2    single  0.890  0.020  1.040
 9BB  CB   HB    single  0.930  0.020  1.080
 9BB  SG   HSG   single  1.200  0.020  1.300
 9BB  N13  HN13  single  0.860  0.020  1.020
 9BB  C49  H49   single  0.970  0.020  1.090
 9BB  C50  H50   single  0.970  0.020  1.090
 9BB  C50  H50A  single  0.970  0.020  1.090
 9BB  C51  H51   single  0.970  0.020  1.090
 9BB  C51  H51A  single  0.970  0.020  1.090
 9BB  C52  H52   single  0.970  0.020  1.090
 9BB  C53  H53   single  0.970  0.020  1.090
 9BB  C53  H53A  single  0.970  0.020  1.090
 9BB  C54  H54   single  0.970  0.020  1.090
 9BB  C54  H54A  single  0.970  0.020  1.090

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
 9BB  H2    N    HN   116.99  3.000
 9BB  H2    N    CA   116.05  3.000
 9BB  HN    N    CA   119.23  3.000
 9BB  N13   CA   CB   117.22  3.000
 9BB  CB    CA   N    110.40  1.500
 9BB  N13   CA   N    117.85  3.000
 9BB  HB    CB   SG   118.52  3.000
 9BB  HB    CB   CA   119.65  3.000
 9BB  SG    CB   CA   121.64  3.000
 9BB  HSG   SG   CB   101.22  3.000
 9BB  C49   O11  C48  118.95  3.000
 9BB  HN13  N13  C48  116.41  3.000
 9BB  HN13  N13  CA   115.07  3.000
 9BB  C48   N13  CA   128.43  3.000
 9BB  N13   C48  O11  109.40  3.000
 9BB  N13   C48  O8   125.56  3.000
 9BB  O11   C48  O8   125.04  3.000
 9BB  H49   C49  C54  109.13  3.000
 9BB  H49   C49  C50  109.64  3.000
 9BB  C54   C49  C50  111.21  3.000
 9BB  H49   C49  O11  108.91  3.000
 9BB  C50   C49  O11  110.94  3.000
 9BB  C54   C49  O11  106.94  3.000
 9BB  H50A  C50  H50  107.34  3.000
 9BB  H50A  C50  C51  109.65  3.000
 9BB  H50   C50  C51  110.10  3.000
 9BB  H50A  C50  C49  109.01  3.000
 9BB  H50   C50  C49  110.40  3.000
 9BB  C51   C50  C49  110.29  3.000
 9BB  H51A  C51  H51  106.31  3.000
 9BB  H51A  C51  C52  110.34  3.000
 9BB  H51   C51  C52  109.43  3.000
 9BB  H51A  C51  C50  109.24  3.000
 9BB  H51   C51  C50  109.39  3.000
 9BB  C52   C51  C50  111.96  3.000
 9BB  H52   C52  C55  106.18  3.000
 9BB  H52   C52  C53  106.96  3.000
 9BB  C55   C52  C53  111.80  3.000
 9BB  H52   C52  C51  107.66  3.000
 9BB  C53   C52  C51  110.18  3.000
 9BB  C55   C52  C51  113.67  3.000
 9BB  H53A  C53  H53  106.51  3.000
 9BB  H53A  C53  C54  109.55  3.000
 9BB  H53   C53  C54  109.10  3.000
 9BB  H53A  C53  C52  110.04  3.000
 9BB  H53   C53  C52  109.43  3.000
 9BB  C54   C53  C52  112.06  3.000
 9BB  H54A  C54  H54  107.34  3.000
 9BB  H54A  C54  C53  110.25  3.000
 9BB  H54   C54  C53  109.61  3.000
 9BB  H54A  C54  C49  109.97  3.000
 9BB  H54   C54  C49  109.36  3.000
 9BB  C53   C54  C49  110.26  3.000
 9BB  C52   C55  O10  117.66  3.000
 9BB  C52   C55  O9   116.42  3.000
 9BB  O10   C55  O9   125.91  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
 9BB  CONST_01  C48   N13  CA   N      0.00   0.0  0
 9BB  CONST_02  C48   N13  CA   CB   180.00   0.0  0
 9BB  CONST_03  HN13  N13  CA   N    180.00   0.0  0
 9BB  CONST_05  H2    N    CA   CB     0.00   0.0  0
 9BB  Var_01    C52   C53  C54  C49   56.14  30.0  1
 9BB  Var_02    C52   C51  C50  C49  -56.27  30.0  1
 9BB  Var_03    SG    CB   CA   N      1.81   0.0  2
 9BB  Var_04    CA    N13  C48  O8    -0.03  30.0  2

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
 9BB  chir_01  C49  O11  C54  C50  positiv
 9BB  chir_02  C52  C53  C55  C51  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
 9BB  plan-1  N     0.020
 9BB  plan-1  CA    0.020
 9BB  plan-1  CB    0.020
 9BB  plan-1  SG    0.020
 9BB  plan-1  N13   0.020
 9BB  plan-1  C48   0.020
 9BB  plan-1  HN    0.020
 9BB  plan-1  H2    0.020
 9BB  plan-1  HB    0.020
 9BB  plan-1  HN13  0.020
 9BB  plan-2  O9    0.020
 9BB  plan-2  O10   0.020
 9BB  plan-2  C52   0.020
 9BB  plan-2  C55   0.020
 9BB  plan-3  O8    0.020
 9BB  plan-3  O11   0.020
 9BB  plan-3  N13   0.020
 9BB  plan-3  C48   0.020

