# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 00:03:52 2021
#   Inital geometry file: a 121 line input string
#   Ligand name: (1S,2R,3R,4S,6S)-6-[(8-azidooctanoyl)amino]-2,3,4-trihydroxycyclohexane-1-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1[C@@H](O)[C@H](O)[C@H]([C@@H](NC(=O)CCCCCCCN=[N+]=[N-])[C@@H]1O)C(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
 J13  J13  (1S,2R,3R,4S,6S)-6-[(8-azidooctanoyl)amino]-2,3,4-trihydroxycyclohexane-1-carboxylate  ligand  52  26  .  2021-08-12  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_J13
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
 J13  C1    C  CH1    0  -0.142  40.4301  11.0237  21.3411
 J13  O1    O  O      0  -0.486  38.5982  13.1325  21.1828
 J13  C2    C  CH1    0   0.002  39.9648  10.0623  20.2368
 J13  C3    C  CH1    0   0.039  41.1091   9.7259  19.2820
 J13  C4    C  CH1    0   0.040  42.2848   9.1140  20.0329
 J13  C5    C  CH1    0   0.025  42.7872  10.0890  21.0982
 J13  C6    C  CH1    0  -0.440  41.6602  10.4541  22.0665
 J13  N7    N  NH1    0  -0.646  40.6878  12.3552  20.8395
 J13  C9    C  C      0   0.542  39.7522  13.3336  20.8374
 J13  C10   C  CH2    0  -0.589  40.2687  14.6903  20.4170
 J13  C11   C  CH2    0  -0.453  41.2547  15.2770  21.4357
 J13  C12   C  CH2    0  -0.438  40.7076  15.3943  22.8577
 J13  C13   C  CH2    0  -0.441  39.3925  16.1594  22.9844
 J13  C14   C  CH2    0  -0.422  39.4730  17.6081  22.5203
 J13  C15   C  CH2    0  -0.458  38.1550  18.3679  22.6376
 J13  C16   C  CH2    0  -0.327  36.9977  17.7489  21.8617
 J13  N17   N  N      0  -0.359  37.3162  17.4641  20.4539
 J13  N18   N  N      1   0.358  37.5407  18.4223  19.7406
 J13  N19   N  N     -1  -0.229  37.7607  19.2400  18.9990
 J13  C20   C  C      0   0.576  42.0446  11.4137  23.1697
 J13  O21   O  O      0  -0.440  41.3945  11.5615  24.1736
 J13  O22   O  OH1    0  -0.588  43.1440  12.1089  22.9077
 J13  O23   O  OH1    0  -0.674  43.8489   9.4551  21.7776
 J13  O24   O  OH1    0  -0.670  43.3007   8.8372  19.1021
 J13  O25   O  OH1    0  -0.668  40.7087   8.8251  18.2830
 J13  H1    H  HCH1   0   0.289  39.6194  11.1154  22.0674
 J13  H12   H  HCH1   0   0.244  39.1760  10.5733  19.6654
 J13  H3    H  HCH1   0   0.216  41.4489  10.6740  18.8360
 J13  H4    H  HCH1   0   0.216  41.9534   8.1923  20.5352
 J13  H5    H  HCH1   0   0.227  43.1548  10.9801  20.5712
 J13  H6    H  HCH1   0   0.306  41.3307   9.5344  22.5596
 J13  HN7   H  HNH1   0   0.404  41.6028  12.5865  20.4865
 J13  H110  H  HCH2   0   0.272  40.7686  14.6075  19.4479
 J13  H210  H  HCH2   0   0.262  39.4155  15.3552  20.2802
 J13  H111  H  HCH2   0   0.232  42.1649  14.6711  21.4585
 J13  H211  H  HCH2   0   0.242  41.5674  16.2562  21.0680
 J13  H112  H  HCH2   0   0.223  40.5723  14.3934  23.2802
 J13  H212  H  HCH2   0   0.227  41.4696  15.8758  23.4781
 J13  H113  H  HCH2   0   0.224  39.0753  16.1378  24.0319
 J13  H213  H  HCH2   0   0.224  38.6146  15.6293  22.4297
 J13  H114  H  HCH2   0   0.226  40.2306  18.1333  23.1095
 J13  H214  H  HCH2   0   0.217  39.8195  17.6530  21.4844
 J13  H115  H  HCH2   0   0.237  38.3021  19.4018  22.3119
 J13  H215  H  HCH2   0   0.239  37.8439  18.4227  23.6850
 J13  H116  H  HCH2   0   0.264  36.1170  18.3942  21.9229
 J13  H216  H  HCH2   0   0.256  36.7182  16.7871  22.2847
 J13  HO23  H  HOH1   0   0.459  44.4813  10.1218  22.0606
 J13  HO24  H  HOH1   0   0.447  44.0573   8.4978  19.5925
 J13  HO25  H  HOH1   0   0.452  40.0776   9.2701  17.7087
 J13  HO22  H  HOH1   0   0.487  43.3392  12.7177  23.6369
 J13  O2    O  OH1    0  -0.662  39.4878   8.8633  20.7927
 J13  HO2   H  HOH1   0   0.458  38.6857   9.0546  21.2890

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
 J13  O24  C4    single  1.405  0.020  1.405
 J13  O25  C3    single  1.403  0.020  1.403
 J13  C3   C4    single  1.523  0.020  1.523
 J13  C3   C2    single  1.528  0.020  1.528
 J13  C4   C5    single  1.529  0.020  1.529
 J13  N17  N18   double  1.215  0.020  1.215
 J13  N17  C16   single  1.471  0.020  1.471
 J13  C5   O23   single  1.411  0.020  1.411
 J13  C5   C6    single  1.530  0.020  1.530
 J13  N18  N19   double  1.126  0.020  1.126
 J13  C2   C1    single  1.536  0.020  1.536
 J13  C10  C9    single  1.511  0.020  1.511
 J13  C10  C11   single  1.534  0.020  1.534
 J13  N7   C1    single  1.446  0.020  1.446
 J13  N7   C9    single  1.354  0.020  1.354
 J13  C16  C15   single  1.525  0.020  1.525
 J13  C1   C6    single  1.538  0.020  1.538
 J13  C9   O1    double  1.221  0.020  1.221
 J13  C14  C13   single  1.523  0.020  1.523
 J13  C14  C15   single  1.526  0.020  1.526
 J13  C11  C12   single  1.528  0.020  1.528
 J13  C6   C20   single  1.512  0.020  1.512
 J13  C13  C12   single  1.527  0.020  1.527
 J13  O22  C20   single  1.327  0.020  1.327
 J13  C20  O21   double  1.205  0.020  1.205
 J13  C1   H1    single  0.970  0.020  1.090
 J13  C2   H12   single  0.970  0.020  1.090
 J13  C3   H3    single  0.970  0.020  1.090
 J13  C4   H4    single  0.970  0.020  1.090
 J13  C5   H5    single  0.970  0.020  1.090
 J13  C6   H6    single  0.970  0.020  1.090
 J13  N7   HN7   single  0.860  0.020  1.020
 J13  C10  H110  single  0.970  0.020  1.090
 J13  C10  H210  single  0.970  0.020  1.090
 J13  C11  H111  single  0.970  0.020  1.090
 J13  C11  H211  single  0.970  0.020  1.090
 J13  C12  H112  single  0.970  0.020  1.090
 J13  C12  H212  single  0.970  0.020  1.090
 J13  C13  H113  single  0.970  0.020  1.090
 J13  C13  H213  single  0.970  0.020  1.090
 J13  C14  H114  single  0.970  0.020  1.090
 J13  C14  H214  single  0.970  0.020  1.090
 J13  C15  H115  single  0.970  0.020  1.090
 J13  C15  H215  single  0.970  0.020  1.090
 J13  C16  H116  single  0.970  0.020  1.090
 J13  C16  H216  single  0.970  0.020  1.090
 J13  O23  HO23  single  0.850  0.020  0.980
 J13  O24  HO24  single  0.850  0.020  0.980
 J13  O25  HO25  single  0.850  0.020  0.980
 J13  O22  HO22  single  0.850  0.020  0.980
 J13  C2   O2    single  1.405  0.020  1.405
 J13  O2   HO2   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
 J13  H1    C1   N7    106.60  3.000
 J13  H1    C1   C6    108.13  3.000
 J13  N7    C1   C6    111.24  3.000
 J13  H1    C1   C2    107.80  3.000
 J13  C6    C1   C2    110.46  3.000
 J13  N7    C1   C2    112.39  3.000
 J13  O2    C2   H12   111.01  3.000
 J13  O2    C2   C3    108.28  3.000
 J13  H12   C2   C3    108.35  3.000
 J13  O2    C2   C1    110.64  3.000
 J13  H12   C2   C1    107.45  3.000
 J13  C3    C2   C1    111.11  3.000
 J13  H3    C3   O25   110.62  3.000
 J13  H3    C3   C4    107.89  3.000
 J13  O25   C3   C4    108.26  3.000
 J13  H3    C3   C2    107.13  3.000
 J13  C4    C3   C2    111.01  3.000
 J13  O25   C3   C2    111.87  3.000
 J13  H4    C4   O24   110.79  3.000
 J13  H4    C4   C5    108.36  3.000
 J13  O24   C4   C5    110.46  3.000
 J13  H4    C4   C3    109.20  3.000
 J13  C5    C4   C3    109.93  3.000
 J13  O24   C4   C3    108.10  3.000
 J13  H5    C5   O23   110.10  3.000
 J13  H5    C5   C6    110.88  3.000
 J13  O23   C5   C6    110.90  3.000
 J13  H5    C5   C4    107.04  3.000
 J13  C6    C5   C4    110.55  3.000
 J13  O23   C5   C4    107.23  3.000
 J13  H6    C6   C20   106.33  3.000
 J13  H6    C6   C5    107.84  3.000
 J13  C20   C6   C5    115.21  3.000
 J13  H6    C6   C1    106.44  3.000
 J13  C20   C6   C1    108.21  3.000
 J13  C5    C6   C1    112.28  3.000
 J13  HN7   N7   C9    117.46  3.000
 J13  HN7   N7   C1    119.66  3.000
 J13  C9    N7   C1    122.88  3.000
 J13  C10   C9   N7    114.39  3.000
 J13  N7    C9   O1    122.25  3.000
 J13  C10   C9   O1    123.33  3.000
 J13  H210  C10  H110  107.02  3.000
 J13  H210  C10  C11   110.67  3.000
 J13  H110  C10  C11   108.88  3.000
 J13  H210  C10  C9    108.36  3.000
 J13  H110  C10  C9    109.56  3.000
 J13  C11   C10  C9    112.22  3.000
 J13  H211  C11  H111  105.40  3.000
 J13  H211  C11  C12   110.31  3.000
 J13  H111  C11  C12   108.73  3.000
 J13  H211  C11  C10   107.66  3.000
 J13  H111  C11  C10   109.68  3.000
 J13  C12   C11  C10   114.65  3.000
 J13  H212  C12  H112  105.64  3.000
 J13  H212  C12  C13   109.41  3.000
 J13  H112  C12  C13   108.64  3.000
 J13  H212  C12  C11   108.18  3.000
 J13  H112  C12  C11   109.47  3.000
 J13  C13   C12  C11   115.09  3.000
 J13  H213  C13  H113  105.66  3.000
 J13  H213  C13  C14   110.14  3.000
 J13  H113  C13  C14   109.00  3.000
 J13  H213  C13  C12   109.15  3.000
 J13  H113  C13  C12   108.61  3.000
 J13  C14   C13  C12   113.94  3.000
 J13  H214  C14  H114  105.73  3.000
 J13  H214  C14  C15   109.04  3.000
 J13  H114  C14  C15   108.52  3.000
 J13  H214  C14  C13   110.15  3.000
 J13  H114  C14  C13   109.21  3.000
 J13  C15   C14  C13   113.86  3.000
 J13  H215  C15  H115  106.02  3.000
 J13  H215  C15  C16   106.96  3.000
 J13  H115  C15  C16   109.53  3.000
 J13  H215  C15  C14   110.13  3.000
 J13  H115  C15  C14   109.36  3.000
 J13  C16   C15  C14   114.48  3.000
 J13  H216  C16  H116  107.05  3.000
 J13  H216  C16  N17   104.87  3.000
 J13  H116  C16  N17   110.00  3.000
 J13  H216  C16  C15   110.88  3.000
 J13  H116  C16  C15   110.07  3.000
 J13  N17   C16  C15   113.66  3.000
 J13  N18   N17  C16   116.68  3.000
 J13  N19   N18  N17   174.53  3.000
 J13  O22   C20  O21   123.18  3.000
 J13  O21   C20  C6    123.27  3.000
 J13  O22   C20  C6    113.52  3.000
 J13  HO22  O22  C20   110.31  3.000
 J13  HO23  O23  C5    108.97  3.000
 J13  HO24  O24  C4    107.46  3.000
 J13  HO25  O25  C3    108.36  3.000
 J13  HO2   O2   C2    108.50  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
 J13  CONST_01  C10   C9   N7   C1   180.00   0.0  0
 J13  CONST_02  O1    C9   N7   C1     0.00   0.0  0
 J13  CONST_03  HO22  O22  C20  C6   180.00   0.0  0
 J13  CONST_04  HN7   N7   C9   O1   180.00   0.0  0
 J13  Var_01    C11   C10  C9   O1   110.80  30.0  1
 J13  Var_02    C12   C11  C10  C9   -56.03  30.0  3
 J13  Var_03    C13   C12  C11  C10  -54.01  30.0  3
 J13  Var_04    C14   C13  C12  C11  -60.98  30.0  1
 J13  Var_05    C15   C14  C13  C12  179.55  30.0  1
 J13  Var_06    C16   C15  C14  C13  -58.19  30.0  3
 J13  Var_07    N17   C16  C15  C14  -51.12  30.0  1

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
 J13  chir_01  C1  C2   N7  C6   positiv
 J13  chir_02  C2  O2   C1  C3   negativ
 J13  chir_03  C3  O25  C2  C4   negativ
 J13  chir_04  C4  O24  C3  C5   positiv
 J13  chir_05  C5  O23  C4  C6   negativ
 J13  chir_06  C6  C5   C1  C20  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
 J13  plan-1  C1    0.020
 J13  plan-1  O1    0.020
 J13  plan-1  N7    0.020
 J13  plan-1  C9    0.020
 J13  plan-1  C10   0.020
 J13  plan-1  HN7   0.020
 J13  plan-2  C6    0.020
 J13  plan-2  C20   0.020
 J13  plan-2  O21   0.020
 J13  plan-2  O22   0.020
 J13  plan-2  HO22  0.020
 J13  plan-3  C16   0.020
 J13  plan-3  N17   0.020
 J13  plan-3  N18   0.020
 J13  plan-3  N19   0.020

