# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 05:01:05 2022
#   Inital geometry file: a 68 line input string
#   Ligand name: (1~{S},2~{R},3~{R},4~{S},5~{S})-4-[[(azanylidyne-$l^{4}-azanyl)amino]methyl]cyclohexane-1,2,3,5-tetrol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1C[C@H](O)[C@H](CN[N]#N)[C@@H](O)[C@@H]1O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 PN8  PN8  (1~{S},2~{R},3~{R},4~{S},5~{S})-4-[[(azanylidyne-$l^{4}-azanyl)amino]methyl]cyclohexane-1,2,3,5-tetrol  ligand  28  14  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PN8
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
 PN8  C3   C  CR16  0   0.039  -66.6331  -41.6375  -5.2318
 PN8  C2   C  CH2   0  -0.305  -66.1484  -42.8419  -7.4085
 PN8  C6   C  CR16  0   0.028  -69.2694  -40.8360  -6.2912
 PN8  C4   C  C     0  -0.522  -67.7447  -41.1140  -4.3300
 PN8  C1   C  CR16  0  -0.323  -67.2189  -42.2583  -6.4934
 PN8  O1   O  OH1   0  -0.680  -65.7376  -40.6249  -5.6465
 PN8  N    N  NC1   0  -0.457  -65.4943  -41.8504  -8.2876
 PN8  N1   N  N     1   0.527  -64.4612  -41.2350  -7.9449
 PN8  N2   N  N     0  -0.003  -63.5359  -40.7184  -7.6370
 PN8  C5   C  CR16  0   0.041  -68.6863  -40.1605  -5.0560
 PN8  O2   O  OH1   0  -0.674  -69.7774  -39.7785  -4.2444
 PN8  O3   O  OH1   0  -0.675  -70.0888  -39.9667  -7.0356
 PN8  C    C  CR16  0   0.060  -68.1496  -41.2906  -7.2200
 PN8  O    O  OH1   0  -0.670  -68.6404  -41.9539  -8.3600
 PN8  H2   H  HCR6  0   0.242  -66.0909  -42.4242  -4.6902
 PN8  H7   H  HCH2  0   0.325  -66.5711  -43.5612  -8.1045
 PN8  H6   H  HCH2  0   0.315  -65.3682  -43.3499  -6.8425
 PN8  H4   H  HCR6  0   0.205  -69.8336  -41.7262  -5.9655
 PN8  H10  H  H     0   0.239  -68.3174  -41.9698  -3.9588
 PN8  H9   H  H     0   0.255  -67.3111  -40.6236  -3.4529
 PN8  H1   H  HCR6  0   0.288  -67.8112  -43.1242  -6.1736
 PN8  H8   H  HOH1  0   0.461  -65.2856  -40.2724  -4.8726
 PN8  HN   H  HNC1  0   0.501  -65.8686  -41.5834  -9.1955
 PN8  H3   H  HCR6  0   0.208  -68.1236  -39.2755  -5.3846
 PN8  H11  H  HOH1  0   0.453  -69.4615  -39.1684  -3.5707
 PN8  H12  H  HOH1  0   0.451  -70.8103  -39.6721  -6.4705
 PN8  H    H  HCR6  0   0.218  -67.5852  -40.3929  -7.5160
 PN8  H5   H  HOH1  0   0.453  -69.1958  -41.3402  -8.8522

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
 PN8  O   C    single  1.407  0.020  1.407
 PN8  N   N1   single  1.250  0.020  1.250
 PN8  N   C2   single  1.478  0.020  1.478
 PN8  N1  N2   triple  1.104  0.020  1.104
 PN8  C2  C1   single  1.524  0.020  1.524
 PN8  C   C1   single  1.527  0.020  1.527
 PN8  C   C6   single  1.524  0.020  1.524
 PN8  O3  C6   single  1.408  0.020  1.408
 PN8  C1  C3   single  1.523  0.020  1.523
 PN8  C6  C5   single  1.524  0.020  1.524
 PN8  O1  C3   single  1.414  0.020  1.414
 PN8  C3  C4   single  1.524  0.020  1.524
 PN8  C5  C4   single  1.524  0.020  1.524
 PN8  C5  O2   single  1.412  0.020  1.412
 PN8  C3  H2   single  0.970  0.020  1.090
 PN8  C2  H7   single  0.970  0.020  1.090
 PN8  C2  H6   single  0.970  0.020  1.090
 PN8  C6  H4   single  0.970  0.020  1.090
 PN8  C4  H10  single  0.970  0.020  1.090
 PN8  C4  H9   single  0.970  0.020  1.090
 PN8  C1  H1   single  0.970  0.020  1.090
 PN8  O1  H8   single  0.850  0.020  0.980
 PN8  N   HN   single  0.860  0.020  1.020
 PN8  C5  H3   single  0.970  0.020  1.090
 PN8  O2  H11  single  0.850  0.020  0.980
 PN8  O3  H12  single  0.850  0.020  0.980
 PN8  C   H    single  0.970  0.020  1.090
 PN8  O   H5   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
 PN8  H2   C3  O1   110.18  3.000
 PN8  H2   C3  C1   107.84  3.000
 PN8  O1   C3  C1   107.01  3.000
 PN8  H2   C3  C4   108.32  3.000
 PN8  O1   C3  C4   112.92  3.000
 PN8  C1   C3  C4   110.46  3.000
 PN8  H6   C2  H7   107.61  3.000
 PN8  H6   C2  N    107.75  3.000
 PN8  H7   C2  N    103.61  3.000
 PN8  H6   C2  C1   111.69  3.000
 PN8  H7   C2  C1   111.39  3.000
 PN8  N    C2  C1   114.27  3.000
 PN8  H4   C6  C    108.36  3.000
 PN8  H4   C6  O3   110.91  3.000
 PN8  C    C6  O3   106.83  3.000
 PN8  H4   C6  C5   108.31  3.000
 PN8  O3   C6  C5   112.19  3.000
 PN8  C    C6  C5   110.18  3.000
 PN8  H9   C4  H10  106.61  3.000
 PN8  H9   C4  C5   110.26  3.000
 PN8  H10  C4  C5   109.12  3.000
 PN8  H9   C4  C3   109.82  3.000
 PN8  H10  C4  C3   108.28  3.000
 PN8  C5   C4  C3   112.56  3.000
 PN8  H1   C1  C    108.06  3.000
 PN8  H1   C1  C2   104.60  3.000
 PN8  C    C1  C2   112.65  3.000
 PN8  H1   C1  C3   106.73  3.000
 PN8  C    C1  C3   111.73  3.000
 PN8  C2   C1  C3   112.53  3.000
 PN8  H8   O1  C3   108.88  3.000
 PN8  HN   N   N1   114.78  3.000
 PN8  HN   N   C2   122.95  3.000
 PN8  N1   N   C2   122.20  3.000
 PN8  N2   N1  N    180.00  3.000
 PN8  H3   C5  O2   110.46  3.000
 PN8  H3   C5  C4   109.26  3.000
 PN8  O2   C5  C4   111.89  3.000
 PN8  H3   C5  C6   108.09  3.000
 PN8  O2   C5  C6   106.86  3.000
 PN8  C4   C5  C6   110.19  3.000
 PN8  H11  O2  C5   108.67  3.000
 PN8  H12  O3  C6   108.35  3.000
 PN8  H    C   O    110.20  3.000
 PN8  H    C   C1   109.41  3.000
 PN8  O    C   C1   107.42  3.000
 PN8  H    C   C6   107.29  3.000
 PN8  C1   C   C6   110.30  3.000
 PN8  O    C   C6   112.21  3.000
 PN8  H5   O   C    108.35  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
 PN8  Var_01  N1  N  C2  C1  90.61  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
 PN8  chir_01  C3  C1  O1  C4  negativ
 PN8  chir_02  C6  O3  C   C5  negativ
 PN8  chir_03  C1  C3  C   C2  negativ
 PN8  chir_04  C5  O2  C4  C6  negativ
 PN8  chir_05  C   O   C6  C1  negativ

