# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 12:44:17 2020
#   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  51  26  .  2021-08-12  2021-08-12  
;
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  -0.102  -2.9205  -0.0012   0.9583
 J13  O1    O  O      0  -0.507  -0.4726   1.1223   1.7854
 J13  C2    C  CH1    0   0.015  -3.5641   1.3825   1.1225
 J13  C3    C  CH1    0   0.020  -4.1337   1.8848  -0.1984
 J13  C4    C  CH1    0  -0.004  -5.1430   0.8966  -0.7646
 J13  C5    C  CH1    0   0.059  -4.4725  -0.4530  -0.9959
 J13  C6    C  CH1    0  -0.443  -3.8916  -0.9999   0.3019
 J13  N7    N  NH1    0  -0.660  -1.6937   0.0900   0.1881
 J13  C9    C  C      0   0.562  -0.5487   0.5928   0.6836
 J13  C10   C  CH2    0  -0.578   0.6431   0.4999  -0.2476
 J13  C11   C  CH2    0  -0.414   1.9728   0.3812   0.4835
 J13  C12   C  CH2    0  -0.416   3.1576   0.3701  -0.4739
 J13  C13   C  CH2    0  -0.413   4.4957   0.2570   0.2452
 J13  C14   C  CH2    0  -0.423   5.6851   0.2621  -0.7070
 J13  C15   C  CH2    0  -0.435   7.0216   0.1526   0.0169
 J13  C16   C  CH2    0  -0.302   8.1872   0.1673  -0.9613
 J13  N17   N  N      0  -0.363   9.4973   0.1295  -0.2962
 J13  N18   N  N      1   0.353   9.8366  -0.9392   0.1732
 J13  N19   N  N     -1  -0.232  10.2425  -1.8821   0.6352
 J13  C20   C  C      0   0.450  -3.2097  -2.3679   0.0737
 J13  O21   O  O      0  -0.593  -3.4930  -3.2873   0.8594
 J13  O22   O  OC    -1  -0.604  -2.4002  -2.4296  -0.8808
 J13  O23   O  OH1    0  -0.677  -5.3972  -1.4078  -1.4735
 J13  O24   O  OH1    0  -0.686  -5.6393   1.4417  -1.9767
 J13  O25   O  OH1    0  -0.682  -4.7183   3.1461   0.0428
 J13  H1    H  HCH1   0   0.262  -2.6819  -0.3701   1.9627
 J13  H12   H  HCH1   0   0.237  -2.7921   2.0876   1.4547
 J13  H3    H  HCH1   0   0.209  -3.3001   1.9769  -0.9119
 J13  H4    H  HCH1   0   0.216  -5.9611   0.7714  -0.0437
 J13  H5    H  HCH1   0   0.199  -3.6661  -0.3072  -1.7292
 J13  H6    H  HCH1   0   0.239  -4.7125  -1.1354   1.0121
 J13  HN7   H  HNH1   0   0.398  -1.6320  -0.5408  -0.6028
 J13  H110  H  HCH2   0   0.245   0.5195  -0.3330  -0.9454
 J13  H210  H  HCH2   0   0.264   0.6431   1.4065  -0.8638
 J13  H111  H  HCH2   0   0.222   2.0825   1.2121   1.1839
 J13  H211  H  HCH2   0   0.221   1.9824  -0.5331   1.0852
 J13  H112  H  HCH2   0   0.212   3.0522  -0.4606  -1.1801
 J13  H212  H  HCH2   0   0.212   3.1451   1.2852  -1.0767
 J13  H113  H  HCH2   0   0.212   4.5978   1.0840   0.9561
 J13  H213  H  HCH2   0   0.212   4.5120  -0.6615   0.8423
 J13  H114  H  HCH2   0   0.218   5.5844  -0.5653  -1.4174
 J13  H214  H  HCH2   0   0.217   5.6677   1.1806  -1.3037
 J13  H115  H  HCH2   0   0.230   7.1323   0.9802   0.7232
 J13  H215  H  HCH2   0   0.226   7.0432  -0.7704   0.6057
 J13  H116  H  HCH2   0   0.246   8.0969  -0.6581  -1.6738
 J13  H216  H  HCH2   0   0.253   8.1829   1.0924  -1.5353
 J13  HO23  H  HOH1   0   0.445  -5.6405  -1.1705  -2.3735
 J13  HO24  H  HOH1   0   0.458  -6.5601   1.1870  -2.0799
 J13  HO25  H  HOH1   0   0.449  -5.2735   3.3597  -0.7156
 J13  O2    O  OH1    0  -0.675  -4.5655   1.2593   2.1078
 J13  HO2   H  HOH1   0   0.449  -5.0558   2.0881   2.1352

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  1.419  0.020  1.419
 J13  O25  C3    single  1.411  0.020  1.411
 J13  C3   C4    single  1.522  0.020  1.522
 J13  C3   C2    single  1.524  0.020  1.524
 J13  C4   C5    single  1.525  0.020  1.525
 J13  N17  N18   double  1.216  0.020  1.216
 J13  N17  C16   single  1.470  0.020  1.470
 J13  C5   O23   single  1.412  0.020  1.412
 J13  C5   C6    single  1.523  0.020  1.523
 J13  N18  N19   double  1.126  0.020  1.126
 J13  C2   C1    single  1.535  0.020  1.535
 J13  C10  C9    single  1.515  0.020  1.515
 J13  C10  C11   single  1.522  0.020  1.522
 J13  N7   C1    single  1.451  0.020  1.451
 J13  N7   C9    single  1.345  0.020  1.345
 J13  C16  C15   single  1.522  0.020  1.522
 J13  C1   C6    single  1.540  0.020  1.540
 J13  C9   O1    double  1.225  0.020  1.225
 J13  C14  C13   single  1.524  0.020  1.524
 J13  C14  C15   single  1.524  0.020  1.524
 J13  C11  C12   single  1.523  0.020  1.523
 J13  C6   C20   single  1.546  0.020  1.546
 J13  C13  C12   single  1.523  0.020  1.523
 J13  O22  C20   deloc   1.253  0.020  1.253
 J13  C20  O21   deloc   1.242  0.020  1.242
 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  0.890  0.020  1.040
 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  C2   O2    single  1.410  0.020  1.410
 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    108.87  3.000
 J13  H1    C1   C6    108.03  3.000
 J13  N7    C1   C6    110.34  3.000
 J13  H1    C1   C2    107.25  3.000
 J13  C6    C1   C2    111.46  3.000
 J13  N7    C1   C2    110.77  3.000
 J13  O2    C2   H12   110.14  3.000
 J13  O2    C2   C3    111.66  3.000
 J13  H12   C2   C3    108.28  3.000
 J13  O2    C2   C1    107.08  3.000
 J13  H12   C2   C1    108.47  3.000
 J13  C3    C2   C1    111.18  3.000
 J13  H3    C3   O25   110.47  3.000
 J13  H3    C3   C4    108.38  3.000
 J13  O25   C3   C4    111.67  3.000
 J13  H3    C3   C2    107.84  3.000
 J13  C4    C3   C2    110.88  3.000
 J13  O25   C3   C2    107.54  3.000
 J13  H4    C4   O24   110.14  3.000
 J13  H4    C4   C5    109.06  3.000
 J13  O24   C4   C5    111.37  3.000
 J13  H4    C4   C3    108.91  3.000
 J13  C5    C4   C3    109.85  3.000
 J13  O24   C4   C3    107.48  3.000
 J13  H5    C5   O23   110.13  3.000
 J13  H5    C5   C6    109.64  3.000
 J13  O23   C5   C6    107.16  3.000
 J13  H5    C5   C4    107.84  3.000
 J13  C6    C5   C4    110.87  3.000
 J13  O23   C5   C4    111.21  3.000
 J13  H6    C6   C20   108.50  3.000
 J13  H6    C6   C5    108.15  3.000
 J13  C20   C6   C5    111.11  3.000
 J13  H6    C6   C1    106.07  3.000
 J13  C20   C6   C1    111.02  3.000
 J13  C5    C6   C1    111.76  3.000
 J13  HN7   N7   C9    117.92  3.000
 J13  HN7   N7   C1    115.25  3.000
 J13  C9    N7   C1    123.20  3.000
 J13  C10   C9   N7    114.85  3.000
 J13  N7    C9   O1    123.08  3.000
 J13  C10   C9   O1    122.04  3.000
 J13  H210  C10  H110  105.74  3.000
 J13  H210  C10  C11   109.54  3.000
 J13  H110  C10  C11   110.23  3.000
 J13  H210  C10  C9    107.15  3.000
 J13  H110  C10  C9    110.48  3.000
 J13  C11   C10  C9    113.37  3.000
 J13  H211  C11  H111  106.38  3.000
 J13  H211  C11  C12   109.43  3.000
 J13  H111  C11  C12   109.30  3.000
 J13  H211  C11  C10   109.69  3.000
 J13  H111  C11  C10   109.66  3.000
 J13  C12   C11  C10   112.22  3.000
 J13  H212  C12  H112  106.11  3.000
 J13  H212  C12  C13   109.37  3.000
 J13  H112  C12  C13   109.42  3.000
 J13  H212  C12  C11   109.32  3.000
 J13  H112  C12  C11   109.63  3.000
 J13  C13   C12  C11   112.77  3.000
 J13  H213  C13  H113  106.13  3.000
 J13  H213  C13  C14   109.38  3.000
 J13  H113  C13  C14   109.29  3.000
 J13  H213  C13  C12   109.43  3.000
 J13  H113  C13  C12   109.40  3.000
 J13  C14   C13  C12   112.98  3.000
 J13  H214  C14  H114  106.18  3.000
 J13  H214  C14  C15   109.45  3.000
 J13  H114  C14  C15   109.54  3.000
 J13  H214  C14  C13   109.32  3.000
 J13  H114  C14  C13   109.33  3.000
 J13  C15   C14  C13   112.80  3.000
 J13  H215  C15  H115  106.78  3.000
 J13  H215  C15  C16   109.80  3.000
 J13  H115  C15  C16   109.28  3.000
 J13  H215  C15  C14   109.47  3.000
 J13  H115  C15  C14   109.95  3.000
 J13  C16   C15  C14   111.45  3.000
 J13  H216  C16  H116  107.30  3.000
 J13  H216  C16  N17   105.30  3.000
 J13  H116  C16  N17   110.41  3.000
 J13  H216  C16  C15   110.13  3.000
 J13  H116  C16  C15   110.37  3.000
 J13  N17   C16  C15   113.06  3.000
 J13  N18   N17  C16   116.50  3.000
 J13  N19   N18  N17   174.57  3.000
 J13  O22   C20  O21   126.35  3.000
 J13  O21   C20  C6    117.46  3.000
 J13  O22   C20  C6    116.17  3.000
 J13  HO23  O23  C5    108.37  3.000
 J13  HO24  O24  C4    108.97  3.000
 J13  HO25  O25  C3    107.59  3.000
 J13  HO2   O2   C2    107.83  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  Var_01    C11  C10  C9   O1     31.56  30.0  1
 J13  Var_02    C12  C11  C10  C9   -176.72  30.0  3
 J13  Var_03    C13  C12  C11  C10   179.78  30.0  3
 J13  Var_04    C14  C13  C12  C11  -179.32  30.0  1
 J13  Var_05    C15  C14  C13  C12   179.85  30.0  1
 J13  Var_06    C16  C15  C14  C13  -179.72  30.0  3
 J13  Var_07    N17  C16  C15  C14   177.19  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-3  C16  0.020
 J13  plan-3  N17  0.020
 J13  plan-3  N18  0.020
 J13  plan-3  N19  0.020

