# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  3 02:18:39 2022
#   Inital geometry file: a 140 line input string
#   Ligand name: (2~{R})-2-azanyl-5-[[(2~{R})-3-(hexylcarbamothioylsulfanyl)-1-(2-hydroxy-2-oxoethylamino)-1-oxidanylidene-propan-2-yl]amino]-5-oxidanylidene-pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCNC(=S)SC[C@H](NC(=O)CC[C@@H](N)C(O)=O)C(=O)NCC(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
 TZ8  TZ8  "(2~{R})-2-azanyl-5-[[(2~{R})-3-(hexylcarbamothioylsulfanyl)-1-(2-hydroxy-2-oxoethylamino)-1-oxidanylidene-propan-2-yl]amino]-5-oxidanylidene-pentanoic acid"  ligand  57  29  .  2022-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_TZ8
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
 TZ8  N1   N  NH1    0  -0.542  35.5192   9.3414  15.6738
 TZ8  C7   C  CH2    0  -0.472  35.9923   6.9454  15.6852
 TZ8  C8   C  CH2    0  -0.427  34.8733   6.6072  16.6661
 TZ8  C9   C  CH2    0  -0.427  33.5330   6.3076  16.0049
 TZ8  C1   C  CH2    0  -0.586  28.8597   9.1103  13.7948
 TZ8  O5   O  OC    -1  -0.606  31.4483   7.2122  13.0467
 TZ8  C5   C  C      0   0.080  34.7498  10.3948  15.4539
 TZ8  C6   C  CH2    0  -0.297  35.7281   8.1764  14.8306
 TZ8  N3   N  NH2    0  -0.798  29.2334   5.4987  15.1275
 TZ8  C4   C  CH2    0  -0.604  32.8440  11.8008  13.9929
 TZ8  O4   O  O      0  -0.604  29.9036   5.7114  12.4668
 TZ8  C3   C  CH1    0  -0.181  31.5747  11.5269  14.7955
 TZ8  O3   O  OC    -1  -0.601  31.4662  16.6131  17.9260
 TZ8  N    N  NH1    0  -0.624  30.7469  10.5867  14.0986
 TZ8  C    C  CH2    0  -0.441  28.4856   7.7391  14.3459
 TZ8  O    O  O      0  -0.494  29.5920   9.9525  15.9242
 TZ8  C10  C  CH2    0  -0.442  32.4521   5.8768  16.9936
 TZ8  C11  C  CH3    0  -0.669  31.9876   6.9988  17.9149
 TZ8  C12  C  C      0   0.538  30.8324  12.8489  15.0557
 TZ8  C13  C  CH2    0  -0.410  30.9265  14.9011  16.3988
 TZ8  C14  C  C      0   0.397  31.8002  15.4831  17.5332
 TZ8  C15  C  CH1    0  -0.190  29.6618   6.7780  14.5731
 TZ8  C16  C  C      0   0.406  30.4163   6.5397  13.2475
 TZ8  O2   O  O      0  -0.593  32.7411  14.7753  17.9405
 TZ8  S    S  S2     0   0.078  33.9304  10.3647  13.8938
 TZ8  S1   S  S1     0  -0.337  34.6183  11.6350  16.5650
 TZ8  H1   H  HNH1   0   0.414  36.0457   9.3715  16.5374
 TZ8  H2   H  HCH2   0   0.245  36.1558   6.1074  15.0029
 TZ8  H3   H  HCH2   0   0.244  36.9307   7.0822  16.2306
 TZ8  H4   H  HCH2   0   0.226  35.1842   5.7316  17.2437
 TZ8  H5   H  HCH2   0   0.221  34.7618   7.4157  17.3942
 TZ8  H6   H  HNH1   0   0.387  32.2122  13.2686  16.5032
 TZ8  H7   H  HCH2   0   0.210  33.1691   7.1795  15.4519
 TZ8  H8   H  HCH2   0   0.215  33.6791   5.5184  15.2604
 TZ8  H9   H  HCH2   0   0.249  29.3036   9.0227  12.8021
 TZ8  H10  H  HCH2   0   0.270  27.9472   9.7010  13.6649
 TZ8  H12  H  HCH2   0   0.260  34.8454   8.0182  14.2097
 TZ8  H13  H  HCH2   0   0.271  36.5677   8.3551  14.1537
 TZ8  H14  H  HNH2   0   0.330  28.5659   5.6547  15.8740
 TZ8  H15  H  HNH2   0   0.327  28.7383   4.9935  14.4017
 TZ8  H17  H  HCH2   0   0.311  33.4099  12.6325  14.4087
 TZ8  H18  H  HCH2   0   0.313  32.6052  12.0476  12.9555
 TZ8  H19  H  HCH1   0   0.283  31.8585  11.1013  15.7603
 TZ8  H21  H  HNH1   0   0.400  30.7681  10.5883  13.0910
 TZ8  H22  H  HCH2   0   0.221  27.9507   7.8661  15.2913
 TZ8  H23  H  HCH2   0   0.222  27.7802   7.2704  13.6537
 TZ8  H24  H  HCH2   0   0.231  31.5916   5.4969  16.4371
 TZ8  H25  H  HCH2   0   0.209  32.8230   5.0383  17.5919
 TZ8  H26  H  HCH3   0   0.224  31.1829   6.6638  18.5705
 TZ8  H27  H  HCH3   0   0.220  32.7917   7.3694  18.5520
 TZ8  H28  H  HCH3   0   0.214  31.6085   7.8457  17.3380
 TZ8  H29  H  HCH2   0   0.236  30.9427  15.5901  15.5484
 TZ8  H30  H  HCH2   0   0.237  29.8875  14.8564  16.7396
 TZ8  H31  H  HCH1   0   0.214  30.3504   7.2374  15.2888
 TZ8  C2   C  C      0   0.559  29.7588   9.9073  14.7131
 TZ8  N2   N  NH1    0  -0.630  31.3908  13.5953  16.0076
 TZ8  O1   O  O      0  -0.488  29.8376  13.1652  14.4206

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
 TZ8  O4   C16  deloc   1.248  0.020  1.248
 TZ8  O5   C16  deloc   1.248  0.020  1.248
 TZ8  C16  C15  single  1.544  0.020  1.544
 TZ8  C1   C    single  1.524  0.020  1.524
 TZ8  C1   C2   single  1.512  0.020  1.512
 TZ8  C15  C    single  1.536  0.020  1.536
 TZ8  C15  N3   single  1.459  0.020  1.459
 TZ8  N    C2   single  1.347  0.020  1.347
 TZ8  N    C3   single  1.434  0.020  1.434
 TZ8  S    C4   single  1.803  0.020  1.803
 TZ8  S    C5   single  1.762  0.020  1.762
 TZ8  C4   C3   single  1.527  0.020  1.527
 TZ8  C2   O    double  1.223  0.020  1.223
 TZ8  O1   C12  double  1.222  0.020  1.222
 TZ8  C3   C12  single  1.538  0.020  1.538
 TZ8  N1   C6   single  1.453  0.020  1.453
 TZ8  N1   C5   single  1.323  0.020  1.323
 TZ8  C6   C7   single  1.522  0.020  1.522
 TZ8  C12  N2   single  1.332  0.020  1.332
 TZ8  C5   S1   double  1.670  0.020  1.670
 TZ8  C7   C8   single  1.526  0.020  1.526
 TZ8  N2   C13  single  1.440  0.020  1.440
 TZ8  C13  C14  single  1.546  0.020  1.546
 TZ8  C8   C9   single  1.524  0.020  1.524
 TZ8  C14  O2   deloc   1.246  0.020  1.246
 TZ8  C14  O3   deloc   1.242  0.020  1.242
 TZ8  C9   C10  single  1.527  0.020  1.527
 TZ8  C11  C10  single  1.524  0.020  1.524
 TZ8  N1   H1   single  0.860  0.020  1.020
 TZ8  C7   H2   single  0.970  0.020  1.090
 TZ8  C7   H3   single  0.970  0.020  1.090
 TZ8  C8   H4   single  0.970  0.020  1.090
 TZ8  C8   H5   single  0.970  0.020  1.090
 TZ8  N2   H6   single  0.860  0.020  1.020
 TZ8  C9   H7   single  0.970  0.020  1.090
 TZ8  C9   H8   single  0.970  0.020  1.090
 TZ8  C1   H9   single  0.970  0.020  1.090
 TZ8  C1   H10  single  0.970  0.020  1.090
 TZ8  C6   H12  single  0.970  0.020  1.090
 TZ8  C6   H13  single  0.970  0.020  1.090
 TZ8  N3   H14  single  0.890  0.020  1.040
 TZ8  N3   H15  single  0.890  0.020  1.040
 TZ8  C4   H17  single  0.970  0.020  1.090
 TZ8  C4   H18  single  0.970  0.020  1.090
 TZ8  C3   H19  single  0.970  0.020  1.090
 TZ8  N    H21  single  0.860  0.020  1.020
 TZ8  C    H22  single  0.970  0.020  1.090
 TZ8  C    H23  single  0.970  0.020  1.090
 TZ8  C10  H24  single  0.970  0.020  1.090
 TZ8  C10  H25  single  0.970  0.020  1.090
 TZ8  C11  H26  single  0.970  0.020  1.090
 TZ8  C11  H27  single  0.970  0.020  1.090
 TZ8  C11  H28  single  0.970  0.020  1.090
 TZ8  C13  H29  single  0.970  0.020  1.090
 TZ8  C13  H30  single  0.970  0.020  1.090
 TZ8  C15  H31  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
 TZ8  H1   N1   C6   116.38  3.000
 TZ8  H1   N1   C5   114.89  3.000
 TZ8  C6   N1   C5   128.72  3.000
 TZ8  H3   C7   H2   106.18  3.000
 TZ8  H3   C7   C6   109.14  3.000
 TZ8  H2   C7   C6   107.20  3.000
 TZ8  H3   C7   C8   109.65  3.000
 TZ8  H2   C7   C8   109.94  3.000
 TZ8  C6   C7   C8   114.39  3.000
 TZ8  H5   C8   H4   105.61  3.000
 TZ8  H5   C8   C9   110.14  3.000
 TZ8  H4   C8   C9   108.76  3.000
 TZ8  H5   C8   C7   109.80  3.000
 TZ8  H4   C8   C7   107.96  3.000
 TZ8  C9   C8   C7   114.18  3.000
 TZ8  H8   C9   H7   105.96  3.000
 TZ8  H8   C9   C10  109.35  3.000
 TZ8  H7   C9   C10  108.45  3.000
 TZ8  H8   C9   C8   108.62  3.000
 TZ8  H7   C9   C8   110.79  3.000
 TZ8  C10  C9   C8   113.40  3.000
 TZ8  H10  C1   H9   105.93  3.000
 TZ8  H10  C1   C    108.88  3.000
 TZ8  H9   C1   C    110.89  3.000
 TZ8  H10  C1   C2   106.45  3.000
 TZ8  H9   C1   C2   110.67  3.000
 TZ8  C    C1   C2   113.61  3.000
 TZ8  S1   C5   S    124.39  3.000
 TZ8  S1   C5   N1   121.77  3.000
 TZ8  S    C5   N1   113.83  3.000
 TZ8  H13  C6   H12  107.02  3.000
 TZ8  H13  C6   C7   110.28  3.000
 TZ8  H12  C6   C7   110.06  3.000
 TZ8  H13  C6   N1   109.79  3.000
 TZ8  H12  C6   N1   109.28  3.000
 TZ8  C7   C6   N1   110.34  3.000
 TZ8  H15  N3   H14  106.40  3.000
 TZ8  H15  N3   C15  107.97  3.000
 TZ8  H14  N3   C15  109.78  3.000
 TZ8  H18  C4   H17  107.68  3.000
 TZ8  H18  C4   S    105.03  3.000
 TZ8  H17  C4   S    108.44  3.000
 TZ8  H18  C4   C3   110.97  3.000
 TZ8  H17  C4   C3   111.62  3.000
 TZ8  S    C4   C3   112.76  3.000
 TZ8  H19  C3   C12  108.11  3.000
 TZ8  H19  C3   N    108.90  3.000
 TZ8  C12  C3   N    111.55  3.000
 TZ8  H19  C3   C4   108.56  3.000
 TZ8  C12  C3   C4   109.63  3.000
 TZ8  N    C3   C4   110.01  3.000
 TZ8  H21  N    C2   118.18  3.000
 TZ8  H21  N    C3   118.22  3.000
 TZ8  C2   N    C3   122.17  3.000
 TZ8  H23  C    H22  106.34  3.000
 TZ8  H23  C    C15  108.63  3.000
 TZ8  H22  C    C15  108.62  3.000
 TZ8  H23  C    C1   108.35  3.000
 TZ8  H22  C    C1   109.15  3.000
 TZ8  C15  C    C1   115.37  3.000
 TZ8  H25  C10  H24  106.19  3.000
 TZ8  H25  C10  C11  109.67  3.000
 TZ8  H24  C10  C11  108.89  3.000
 TZ8  H25  C10  C9   109.28  3.000
 TZ8  H24  C10  C9   109.01  3.000
 TZ8  C11  C10  C9   113.54  3.000
 TZ8  H28  C11  H27  107.50  3.000
 TZ8  H28  C11  H26  107.42  3.000
 TZ8  H27  C11  H26  107.29  3.000
 TZ8  H28  C11  C10  110.93  3.000
 TZ8  H27  C11  C10  112.24  3.000
 TZ8  H26  C11  C10  111.22  3.000
 TZ8  C3   C12  O1   121.83  3.000
 TZ8  C3   C12  N2   113.58  3.000
 TZ8  O1   C12  N2   124.58  3.000
 TZ8  H30  C13  H29  106.36  3.000
 TZ8  H30  C13  C14  108.88  3.000
 TZ8  H29  C13  C14  108.96  3.000
 TZ8  H30  C13  N2   110.71  3.000
 TZ8  H29  C13  N2   110.79  3.000
 TZ8  C14  C13  N2   111.01  3.000
 TZ8  O2   C14  C13  116.93  3.000
 TZ8  O2   C14  O3   128.07  3.000
 TZ8  C13  C14  O3   115.00  3.000
 TZ8  H31  C15  C16  108.59  3.000
 TZ8  H31  C15  C    108.42  3.000
 TZ8  C16  C15  C    110.11  3.000
 TZ8  H31  C15  N3   107.73  3.000
 TZ8  C    C15  N3   112.35  3.000
 TZ8  C16  C15  N3   109.54  3.000
 TZ8  C15  C16  O4   116.02  3.000
 TZ8  C15  C16  O5   117.33  3.000
 TZ8  O4   C16  O5   126.62  3.000
 TZ8  C4   S    C5   102.58  3.000
 TZ8  O    C2   N    122.20  3.000
 TZ8  O    C2   C1   122.65  3.000
 TZ8  N    C2   C1   115.14  3.000
 TZ8  H6   N2   C13  114.89  3.000
 TZ8  H6   N2   C12  120.56  3.000
 TZ8  C13  N2   C12  124.54  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
 TZ8  CONST_01  C13  N2   C12  O1      0.00   0.0  0
 TZ8  CONST_02  C3   N    C2   C1    180.00   0.0  0
 TZ8  CONST_03  O    C2   N    C3      0.00   0.0  0
 TZ8  CONST_04  C13  N2   C12  C3    180.00   0.0  0
 TZ8  CONST_05  H6   N2   C12  O1    180.00   0.0  0
 TZ8  CONST_06  H21  N    C2   C1      0.00   0.0  0
 TZ8  CONST_07  H6   N2   C12  C3      0.00   0.0  0
 TZ8  CONST_08  H21  N    C2   O     180.00   0.0  0
 TZ8  Var_01    C8   C7   C6   N1     58.66  30.0  3
 TZ8  Var_02    C4   S    C5   N1    173.65  30.0  2
 TZ8  Var_03    C5   N1   C6   C7   -148.10  30.0  2
 TZ8  Var_04    C10  C9   C8   C7    175.97  30.0  3
 TZ8  Var_05    C11  C10  C9   C8     69.30  30.0  3
 TZ8  Var_06    O2   C14  C13  N2     -0.25  30.0  3
 TZ8  Var_07    O3   C14  C13  N2    179.80  30.0  3
 TZ8  Var_08    C6   C7   C8   C9     60.71  30.0  2
 TZ8  Var_09    C3   C4   S    C5    -79.76  30.0  3
 TZ8  Var_10    S    C5   N1   C6     -2.29  30.0  2
 TZ8  Var_11    S1   C5   N1   C6    178.91  30.0  2
 TZ8  Var_12    S1   C5   S    C4     -7.59  30.0  3
 TZ8  Var_13    C15  C    C1   C2    -62.14  30.0  3
 TZ8  Var_14    C    C1   C2   N     139.23  30.0  1
 TZ8  Var_15    O    C2   C1   C     -41.90  30.0  3
 TZ8  Var_16    C14  C13  N2   C12   179.87  30.0  3
 TZ8  Var_17    H2   C7   C6   N1   -179.18  30.0  3
 TZ8  Var_18    H3   C7   C6   N1    -64.58  30.0  3
 TZ8  Var_19    H1   N1   C6   C7     33.55  30.0  2
 TZ8  Var_20    H7   C9   C8   C7    -61.81  30.0  3
 TZ8  Var_21    H8   C9   C8   C7     54.18  30.0  3
 TZ8  Var_22    H12  C6   C7   C8    -62.03  30.0  1
 TZ8  Var_23    H13  C6   C7   C8   -179.88  30.0  1
 TZ8  Var_24    H24  C10  C9   C8   -169.13  30.0  3
 TZ8  Var_25    H25  C10  C9   C8    -53.48  30.0  3
 TZ8  Var_26    H2   C7   C8   C9    -59.94  30.0  2
 TZ8  Var_27    H3   C7   C8   C9   -176.32  30.0  2
 TZ8  Var_28    H26  C11  C10  C9    177.20  30.0  3
 TZ8  Var_29    H27  C11  C10  C9    -62.59  30.0  3
 TZ8  Var_30    H28  C11  C10  C9     57.70  30.0  3
 TZ8  Var_31    H17  C4   S    C5     44.38  30.0  3
 TZ8  Var_32    H18  C4   S    C5    159.28  30.0  3
 TZ8  Var_33    H12  C6   N1   C5    -26.96  30.0  3
 TZ8  Var_34    H13  C6   N1   C5     90.14  30.0  3
 TZ8  Var_35    H4   C8   C7   C6   -178.22  30.0  3
 TZ8  Var_36    H5   C8   C7   C6    -63.54  30.0  3
 TZ8  Var_37    H29  C13  C14  O3     57.53  30.0  2
 TZ8  Var_38    H30  C13  C14  O3    -58.08  30.0  2
 TZ8  Var_39    H22  C    C1   C2     60.46  30.0  3
 TZ8  Var_40    H23  C    C1   C2    175.87  30.0  3
 TZ8  Var_41    H9   C1   C2   N      13.72  30.0  1
 TZ8  Var_42    H10  C1   C2   N    -100.94  30.0  1
 TZ8  Var_43    H9   C1   C2   O    -167.41  30.0  1
 TZ8  Var_44    H10  C1   C2   O      77.92  30.0  1
 TZ8  Var_45    H4   C8   C9   C10    55.34  30.0  1
 TZ8  Var_46    H5   C8   C9   C10   -59.96  30.0  1
 TZ8  Var_47    H7   C9   C10  C11   -54.21  30.0  2
 TZ8  Var_48    H8   C9   C10  C11  -169.32  30.0  2
 TZ8  Var_49    H29  C13  N2   C12   -58.93  30.0  3
 TZ8  Var_50    H30  C13  N2   C12    58.83  30.0  3
 TZ8  Var_51    H6   N2   C13  C14    -1.40  30.0  2
 TZ8  Var_52    H9   C1   C    C15    63.25  30.0  1
 TZ8  Var_53    H10  C1   C    C15   179.42  30.0  1
 TZ8  Var_54    H29  C13  C14  O2   -122.52  30.0  2
 TZ8  Var_55    H30  C13  C14  O2    121.87  30.0  2
 TZ8  Var_56    H1   N1   C5   S     176.08  30.0  2
 TZ8  Var_57    H1   N1   C5   S1     -2.72  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
 TZ8  chir_01  C3   N   C4   C12  negativ
 TZ8  chir_02  C15  N3  C16  C    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
 TZ8  plan-1  C3   0.020
 TZ8  plan-1  C12  0.020
 TZ8  plan-1  C13  0.020
 TZ8  plan-1  H6   0.020
 TZ8  plan-1  N2   0.020
 TZ8  plan-1  O1   0.020
 TZ8  plan-2  N1   0.020
 TZ8  plan-2  C5   0.020
 TZ8  plan-2  S    0.020
 TZ8  plan-2  S1   0.020
 TZ8  plan-3  C1   0.020
 TZ8  plan-3  C3   0.020
 TZ8  plan-3  N    0.020
 TZ8  plan-3  O    0.020
 TZ8  plan-3  H21  0.020
 TZ8  plan-3  C2   0.020
 TZ8  plan-4  O3   0.020
 TZ8  plan-4  C13  0.020
 TZ8  plan-4  C14  0.020
 TZ8  plan-4  O2   0.020
 TZ8  plan-5  O5   0.020
 TZ8  plan-5  O4   0.020
 TZ8  plan-5  C15  0.020
 TZ8  plan-5  C16  0.020

