# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 21:01:02 2022
#   Inital geometry file: a 96 line input string
#   Ligand name: 3-{[(1-hydroxy-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl]disulfanyl}-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(C)C=C(CSSC[C@H](N)C(O)=O)C(C)(C)N1O
#
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
 3X9  3X9  3-{[(1-hydroxy-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl]disulfanyl}-L-alanine  L-peptide  40  19  .  2016-04-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_3X9
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
 3X9  CAC  C  CH3    0  -0.644  -2.8003   1.8663  -16.5723
 3X9  CAS  C  CT     0   0.068  -2.3984   1.0295  -15.3582
 3X9  CAD  C  CH3    0  -0.650  -2.9066  -0.4051  -15.5453
 3X9  NAQ  N  NT     0  -0.234  -0.9453   1.1601  -15.1556
 3X9  OAH  O  OH1    0  -0.567  -0.2118   0.2103  -15.8627
 3X9  CAR  C  CT     0   0.085  -0.6080   1.1947  -13.7257
 3X9  CAA  C  CH3    0  -0.639   0.5487   2.1661  -13.4969
 3X9  CAB  C  CH3    0  -0.646  -0.2617  -0.1623  -13.0977
 3X9  CAI  C  C1     0  -0.253  -1.9051   1.7030  -13.1718
 3X9  CAO  C  C      0   0.122  -2.8951   1.6127  -14.0539
 3X9  CAJ  C  CH2    0  -0.633  -4.3234   1.9538  -13.7954
 3X9  SAL  S  S2     0  -0.060  -5.0623   0.5549  -12.8652
 3X9  N    N  NH2    0  -0.785  -6.8619   0.3638   -9.5196
 3X9  CA   C  CH1    0  -0.224  -7.7412   1.4046  -10.0386
 3X9  CB   C  CH2    0  -0.541  -7.0877   2.1260  -11.2000
 3X9  SG   S  S2     0  -0.066  -7.0427   1.0769  -12.7014
 3X9  C    C  C      0   0.411  -9.1734   0.9211  -10.3966
 3X9  O    O  O      0  -0.598  -9.7256   1.4728  -11.3709
 3X9  H1   H  HCH3   0   0.221  -3.8744   1.8191  -16.7574
 3X9  H2   H  HCH3   0   0.227  -2.5196   2.9111  -16.4367
 3X9  H3   H  HCH3   0   0.233  -2.3007   1.4927  -17.4682
 3X9  H4   H  HCH3   0   0.233  -2.6131  -1.0584  -14.7243
 3X9  H5   H  HCH3   0   0.227  -3.9963  -0.4062  -15.5911
 3X9  H6   H  HCH3   0   0.231  -2.5408  -0.8371  -16.4769
 3X9  HAA  H  HOH1   0   0.460   0.2984   0.7251  -16.4958
 3X9  H7   H  HCH3   0   0.220   0.7709   2.2652  -12.4332
 3X9  H8   H  HCH3   0   0.227   1.4543   1.8094  -13.9915
 3X9  H9   H  HCH3   0   0.226   0.3107   3.1541  -13.8915
 3X9  H10  H  HCH3   0   0.226  -0.1305  -0.0402  -12.0215
 3X9  H11  H  HCH3   0   0.233  -1.0484  -0.9001  -13.2509
 3X9  H12  H  HCH3   0   0.229   0.6699  -0.5625  -13.4984
 3X9  H13  H  H      0   0.253  -1.9966   2.0669  -12.1552
 3X9  H16  H  HCH2   0   0.291  -4.4105   2.8541  -13.1878
 3X9  H17  H  HCH2   0   0.285  -4.8888   2.0970  -14.7154
 3X9  HA   H  HCH1   0   0.236  -7.8560   2.1536   -9.2414
 3X9  HB2  H  HCH2   0   0.272  -6.0641   2.4203  -10.9673
 3X9  HB3  H  HCH2   0   0.271  -7.6445   3.0223  -11.4642
 3X9  OXT  O  OC    -1  -0.601  -9.6549   0.0410   -9.6581
 3X9  H    H  HNH2   0   0.334  -7.3921  -0.1598   -8.8329
 3X9  HN   H  HNH2   0   0.323  -6.6879  -0.3050  -10.2638

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
 3X9  CAC  CAS  single  1.528  0.020  1.528
 3X9  OAH  NAQ  single  1.393  0.020  1.393
 3X9  NAQ  CAS  single  1.473  0.020  1.473
 3X9  NAQ  CAR  single  1.470  0.020  1.470
 3X9  CAS  CAD  single  1.533  0.020  1.533
 3X9  CAS  CAO  single  1.513  0.020  1.513
 3X9  CAO  CAJ  single  1.491  0.020  1.491
 3X9  CAO  CAI  double  1.329  0.020  1.329
 3X9  CAR  CAA  single  1.528  0.020  1.528
 3X9  CAR  CAI  single  1.499  0.020  1.499
 3X9  CAR  CAB  single  1.535  0.020  1.535
 3X9  CAJ  SAL  single  1.835  0.020  1.835
 3X9  SAL  SG   single  2.055  0.020  2.055
 3X9  SG   CB   single  1.832  0.020  1.832
 3X9  O    C    deloc   1.231  0.020  1.231
 3X9  CB   CA   single  1.530  0.020  1.530
 3X9  N    CA   single  1.458  0.019  1.458
 3X9  C    CA   single  1.525  0.021  1.525
 3X9  CAC  H1   single  0.970  0.020  1.090
 3X9  CAC  H2   single  0.970  0.020  1.090
 3X9  CAC  H3   single  0.970  0.020  1.090
 3X9  CAD  H4   single  0.970  0.020  1.090
 3X9  CAD  H5   single  0.970  0.020  1.090
 3X9  CAD  H6   single  0.970  0.020  1.090
 3X9  OAH  HAA  single  0.850  0.020  0.980
 3X9  CAA  H7   single  0.970  0.020  1.090
 3X9  CAA  H8   single  0.970  0.020  1.090
 3X9  CAA  H9   single  0.970  0.020  1.090
 3X9  CAB  H10  single  0.970  0.020  1.090
 3X9  CAB  H11  single  0.970  0.020  1.090
 3X9  CAB  H12  single  0.970  0.020  1.090
 3X9  CAI  H13  single  0.930  0.020  1.080
 3X9  CAJ  H16  single  0.970  0.020  1.090
 3X9  CAJ  H17  single  0.970  0.020  1.090
 3X9  N    H    single  0.860  0.020  0.860
 3X9  N    HN   single  0.890  0.020  1.040
 3X9  CA   HA   single  0.970  0.020  0.970
 3X9  CB   HB2  single  0.970  0.020  1.090
 3X9  CB   HB3  single  0.970  0.020  1.090
 3X9  C    OXT  deloc   1.246  0.020  1.246

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
 3X9  H3   CAC  H2   108.19  3.000
 3X9  H3   CAC  H1   107.25  3.000
 3X9  H2   CAC  H1   108.42  3.000
 3X9  H3   CAC  CAS  110.13  3.000
 3X9  H2   CAC  CAS  110.98  3.000
 3X9  H1   CAC  CAS  111.72  3.000
 3X9  CAO  CAS  NAQ   99.85  3.000
 3X9  CAO  CAS  CAD  110.92  3.000
 3X9  NAQ  CAS  CAD  115.26  3.000
 3X9  CAO  CAS  CAC  112.80  3.000
 3X9  CAD  CAS  CAC  109.16  3.000
 3X9  NAQ  CAS  CAC  108.67  3.000
 3X9  H6   CAD  H5   107.40  3.000
 3X9  H6   CAD  H4   108.41  3.000
 3X9  H5   CAD  H4   107.47  3.000
 3X9  H6   CAD  CAS  111.33  3.000
 3X9  H5   CAD  CAS  109.71  3.000
 3X9  H4   CAD  CAS  112.32  3.000
 3X9  CAR  NAQ  OAH  112.91  3.000
 3X9  CAR  NAQ  CAS  111.24  3.000
 3X9  OAH  NAQ  CAS  112.90  3.000
 3X9  HAA  OAH  NAQ  104.38  3.000
 3X9  CAI  CAR  CAB  110.11  3.000
 3X9  CAB  CAR  CAA  109.27  3.000
 3X9  CAI  CAR  CAA  112.59  3.000
 3X9  CAB  CAR  NAQ  115.41  3.000
 3X9  CAI  CAR  NAQ   99.72  3.000
 3X9  CAA  CAR  NAQ  109.54  3.000
 3X9  H9   CAA  H8   108.25  3.000
 3X9  H9   CAA  H7   108.36  3.000
 3X9  H8   CAA  H7   107.60  3.000
 3X9  H9   CAA  CAR  110.90  3.000
 3X9  H8   CAA  CAR  110.64  3.000
 3X9  H7   CAA  CAR  110.98  3.000
 3X9  H12  CAB  H11  108.46  3.000
 3X9  H12  CAB  H10  107.52  3.000
 3X9  H11  CAB  H10  107.54  3.000
 3X9  H12  CAB  CAR  111.53  3.000
 3X9  H11  CAB  CAR  112.23  3.000
 3X9  H10  CAB  CAR  109.38  3.000
 3X9  H13  CAI  CAO  125.64  3.000
 3X9  H13  CAI  CAR  122.24  3.000
 3X9  CAO  CAI  CAR  112.10  3.000
 3X9  CAJ  CAO  CAI  125.66  3.000
 3X9  CAI  CAO  CAS  110.73  3.000
 3X9  CAJ  CAO  CAS  123.52  3.000
 3X9  H17  CAJ  H16  108.71  3.000
 3X9  H17  CAJ  SAL  108.62  3.000
 3X9  H16  CAJ  SAL  108.36  3.000
 3X9  H17  CAJ  CAO  112.39  3.000
 3X9  H16  CAJ  CAO  111.24  3.000
 3X9  SAL  CAJ  CAO  107.41  3.000
 3X9  SG   SAL  CAJ  103.58  3.000
 3X9  HN   N    H    104.24  3.000
 3X9  HN   N    CA   108.22  3.000
 3X9  H    N    CA   114.00  3.000
 3X9  HA   CA   C    109.00  3.000
 3X9  HA   CA   CB   109.00  3.000
 3X9  C    CA   CB   110.10  1.900
 3X9  HA   CA   N    110.00  3.000
 3X9  C    CA   N    111.00  2.800
 3X9  CB   CA   N    110.50  1.700
 3X9  HB3  CB   HB2  108.06  3.000
 3X9  HB3  CB   SG   106.58  3.000
 3X9  HB2  CB   SG   107.84  3.000
 3X9  HB3  CB   CA   110.96  3.000
 3X9  HB2  CB   CA   111.70  3.000
 3X9  SG   CB   CA   111.48  3.000
 3X9  CB   SG   SAL  103.56  3.000
 3X9  OXT  C    O    127.15  3.000
 3X9  OXT  C    CA   116.08  3.000
 3X9  O    C    CA   120.80  1.700

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
 3X9  Var_01  CAI  CAR  NAQ  CAS   -24.81  30.0  1
 3X9  Var_02  CAI  CAO  CAS  NAQ   -14.35  30.0  1
 3X9  Var_03  CAO  CAI  CAR  NAQ    15.05  30.0  1
 3X9  Var_04  CAO  CAS  NAQ  CAR    24.63  30.0  1
 3X9  Var_05  SAL  CAJ  CAO  CAS    97.96  30.0  3
 3X9  Var_06  H1   CAC  CAS  NAQ  -178.98  30.0  3
 3X9  Var_07  H4   CAD  CAS  NAQ    55.13  30.0  3
 3X9  Var_08  H7   CAA  CAR  NAQ   175.87  30.0  3
 3X9  Var_09  H10  CAB  CAR  NAQ  -174.16  30.0  3
 3X9  Var_10  CA   CB   SG   SAL  -107.36  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
 3X9  chir_01  CA  CB  N  C  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
 3X9  plan-1  CA   0.020
 3X9  plan-1  C    0.020
 3X9  plan-1  O    0.020
 3X9  plan-1  OXT  0.020

