# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 20:25:51 2022
#   Inital geometry file: a 57 line input string
#   Ligand name: (1~{R},2~{R},3~{S},4~{R},5~{R},6~{R})-5-(hydroxymethyl)-7-azabicyclo[4.1.0]heptane-2,3,4-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H]1[C@@H](O)[C@H](O)[C@H](O)[C@@H]2N[C@H]12
#
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
 JIT  JIT  "beta-D-manno-configured cyclophellitol aziridine"  ligand  25  12  .  2022-08-10  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_JIT
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
 JIT  C1   C  CH1   0  -0.172  -20.0405  57.9402  49.2393
 JIT  C2   C  CH1   0   0.039  -19.6363  57.1303  48.0390
 JIT  C3   C  CH1   0   0.019  -19.8433  57.8409  46.6835
 JIT  C4   C  CH1   0   0.059  -19.6938  59.3715  46.7202
 JIT  C5   C  CH1   0  -0.313  -18.9847  59.8913  47.9764
 JIT  C6   C  CH2   0  -0.176  -18.8589  61.4068  48.0004
 JIT  C7   C  CH1   0  -0.135  -19.6784  59.3642  49.2142
 JIT  N8   N  NH1   0  -0.590  -21.0725  58.9522  49.0816
 JIT  O2   O  OH1   0  -0.679  -20.3009  55.8867  47.9507
 JIT  O3   O  OH1   0  -0.672  -21.1059  57.5644  46.1242
 JIT  O4   O  OH1   0  -0.682  -19.0172  59.7549  45.5367
 JIT  O6   O  OH1   0  -0.667  -20.1433  61.9866  47.9883
 JIT  H1   H  HCH1  0   0.257  -19.9768  57.4195  50.1920
 JIT  H2   H  HCH1  0   0.213  -18.5538  56.9693  48.1443
 JIT  H3   H  HCH1  0   0.206  -19.0491  57.4586  46.0252
 JIT  H4   H  HCH1  0   0.220  -20.7074  59.7793  46.7207
 JIT  H5   H  HCH1  0   0.243  -17.9562  59.5068  47.9879
 JIT  H6   H  HCH2  0   0.207  -18.2999  61.6900  48.9028
 JIT  H7   H  HCH2  0   0.204  -18.2541  61.7413  47.1474
 JIT  H8   H  HCH1  0   0.252  -19.3745  59.8199  50.1526
 JIT  H9   H  HNH1  0   0.360  -21.5696  59.0923  49.9524
 JIT  H11  H  HOH1  0   0.457  -19.9847  55.3154  48.6569
 JIT  H12  H  HOH1  0   0.444  -21.2349  56.6103  46.1458
 JIT  H13  H  HOH1  0   0.450  -19.2748  60.6546  45.3170
 JIT  H14  H  HOH1  0   0.453  -20.0424  62.9424  47.9898

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
 JIT  O4  C4   single  1.416  0.020  1.416
 JIT  O3  C3   single  1.408  0.020  1.408
 JIT  C3  C4   single  1.538  0.020  1.538
 JIT  C3  C2   single  1.544  0.020  1.544
 JIT  C4  C5   single  1.533  0.020  1.533
 JIT  C5  C6   single  1.521  0.020  1.521
 JIT  C5  C7   single  1.514  0.020  1.514
 JIT  C6  O6   single  1.409  0.020  1.409
 JIT  C2  O2   single  1.413  0.020  1.413
 JIT  C2  C1   single  1.503  0.020  1.503
 JIT  N8  C7   single  1.460  0.020  1.460
 JIT  N8  C1   single  1.454  0.020  1.454
 JIT  C7  C1   single  1.470  0.020  1.470
 JIT  C1  H1   single  0.970  0.020  1.090
 JIT  C2  H2   single  0.970  0.020  1.090
 JIT  C3  H3   single  0.970  0.020  1.090
 JIT  C4  H4   single  0.970  0.020  1.090
 JIT  C5  H5   single  0.970  0.020  1.090
 JIT  C6  H6   single  0.970  0.020  1.090
 JIT  C6  H7   single  0.970  0.020  1.090
 JIT  C7  H8   single  0.970  0.020  1.090
 JIT  N8  H9   single  0.890  0.020  1.040
 JIT  O2  H11  single  0.850  0.020  0.980
 JIT  O3  H12  single  0.850  0.020  0.980
 JIT  O4  H13  single  0.850  0.020  0.980
 JIT  O6  H14  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
 JIT  H1   C1  N8  118.02  3.000
 JIT  H1   C1  C7  117.67  3.000
 JIT  N8   C1  C7   59.90  3.000
 JIT  H1   C1  C2  115.20  3.000
 JIT  C7   C1  C2  116.24  3.000
 JIT  N8   C1  C2  118.63  3.000
 JIT  H2   C2  O2  109.89  3.000
 JIT  H2   C2  C3  106.46  3.000
 JIT  O2   C2  C3  106.68  3.000
 JIT  H2   C2  C1  105.50  3.000
 JIT  O2   C2  C1  113.43  3.000
 JIT  C3   C2  C1  114.64  3.000
 JIT  H3   C3  O3  109.96  3.000
 JIT  H3   C3  C4  106.85  3.000
 JIT  O3   C3  C4  106.98  3.000
 JIT  H3   C3  C2  105.58  3.000
 JIT  C4   C3  C2  115.08  3.000
 JIT  O3   C3  C2  112.23  3.000
 JIT  H4   C4  O4  110.03  3.000
 JIT  H4   C4  C5  107.59  3.000
 JIT  O4   C4  C5  111.84  3.000
 JIT  H4   C4  C3  106.33  3.000
 JIT  C5   C4  C3  113.69  3.000
 JIT  O4   C4  C3  107.21  3.000
 JIT  H5   C5  C7  107.38  3.000
 JIT  H5   C5  C6  105.74  3.000
 JIT  C7   C5  C6  111.84  3.000
 JIT  H5   C5  C4  108.85  3.000
 JIT  C7   C5  C4  109.87  3.000
 JIT  C6   C5  C4  112.89  3.000
 JIT  H7   C6  H6  106.22  3.000
 JIT  H7   C6  O6  111.72  3.000
 JIT  H6   C6  O6  111.39  3.000
 JIT  H7   C6  C5  109.69  3.000
 JIT  H6   C6  C5  108.17  3.000
 JIT  O6   C6  C5  109.53  3.000
 JIT  H8   C7  N8  117.64  3.000
 JIT  H8   C7  C5  115.59  3.000
 JIT  N8   C7  C5  117.50  3.000
 JIT  H8   C7  C1  117.42  3.000
 JIT  N8   C7  C1   59.52  3.000
 JIT  C5   C7  C1  117.67  3.000
 JIT  H9   N8  C7  110.59  3.000
 JIT  H9   N8  C1  110.58  3.000
 JIT  C7   N8  C1   60.58  3.000
 JIT  H11  O2  C2  108.80  3.000
 JIT  H12  O3  C3  107.80  3.000
 JIT  H13  O4  C4  108.45  3.000
 JIT  H14  O6  C6  108.27  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
 JIT  Var_01  C5  C7  N8  C1   107.52  30.0  1
 JIT  Var_02  C7  N8  C1  C2  -105.41  30.0  1
 JIT  Var_03  C5  C7  C1  C2     2.14  30.0  1
 JIT  Var_04  H8  C7  N8  C1  -107.16  30.0  1
 JIT  Var_05  H9  N8  C7  C1   102.66  30.0  1
 JIT  Var_06  H9  N8  C1  C2   151.90  30.0  1
 JIT  Var_07  H8  C7  C1  C2  -143.10  30.0  1
 JIT  Var_08  H9  N8  C7  C5  -149.81  30.0  1
 JIT  Var_09  H1  C1  C7  C5   144.75  30.0  1
 JIT  Var_10  H1  C1  N8  C7   107.44  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
 JIT  chir_02  C2  C3  O2  C1  positiv
 JIT  chir_03  C3  O3  C2  C4  positiv
 JIT  chir_04  C4  O4  C3  C5  negativ
 JIT  chir_05  C5  C4  C6  C7  negativ
 JIT  chir_06  C1  C2  N8  C7  both
 JIT  chir_07  C7  N8  C1  C5  both

