# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:28:06 2022
#   Inital geometry file: a 65 line input string
#   Ligand name: (1R,2R,3R,6S,7S,7aR)-3-(hydroxymethyl)hexahydro-1H-pyrrolizine-1,2,6,7-tetrol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H]1[C@@H](O)[C@H](O)[C@H]2[C@H](O)[C@@H](O)CN12
#
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
 3CU  3CU  (1R,2R,3R,6S,7S,7aR)-3-(hydroxymethyl)hexahydro-1H-pyrrolizine-1,2,6,7-tetrol  ligand  29  14  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3CU
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
 3CU  O7    O  OH1   0  -0.669   2.7870   1.3901  -0.6950
 3CU  C7    C  CH1   0   0.021   1.9572   0.5375   0.0464
 3CU  C7A   C  CR15  0  -0.077   0.5246   0.5832  -0.4713
 3CU  C1    C  CR15  0   0.017  -0.4402   1.5666   0.1789
 3CU  O1    O  OH1   0  -0.670  -0.4456   2.7904  -0.5087
 3CU  C2    C  CR15  0   0.009  -1.7558   0.7881   0.1470
 3CU  O2    O  OH1   0  -0.673  -2.7336   1.2372   1.0502
 3CU  C3    C  CR15  0  -0.094  -1.2970  -0.6201   0.5144
 3CU  C8    C  CH2   0  -0.155  -2.2825  -1.7230   0.1836
 3CU  O8    O  OH1   0  -0.669  -2.5902  -1.7005  -1.1893
 3CU  N4    N  NR5   0  -0.459  -0.0329  -0.7462  -0.1849
 3CU  C5    C  CH2   0  -0.298   0.9833  -1.5821   0.4243
 3CU  C6    C  CH1   0   0.000   2.2868  -0.9483  -0.0558
 3CU  OXT   O  OH1   0  -0.668   3.4200  -1.2572   0.7114
 3CU  H7    H  HOH1  0   0.452   3.6725   1.3510  -0.3202
 3CU  HA    H  HCH1  0   0.206   1.9677   0.8047   1.1155
 3CU  H7A   H  HCR5  0   0.226   0.5470   0.7704  -1.5547
 3CU  H6    H  HCH1  0   0.214   2.4433  -1.1987  -1.1151
 3CU  H1    H  HCR5  0   0.203  -0.1614   1.7093   1.2347
 3CU  HB    H  HOH1  0   0.451  -0.9930   3.4130  -0.0208
 3CU  H2    H  HCR5  0   0.219  -2.1357   0.7926  -0.8832
 3CU  HC    H  HOH1  0   0.456  -3.2333   1.9474   0.6388
 3CU  H3    H  HCR5  0   0.211  -1.1509  -0.6600   1.6094
 3CU  H8C1  H  HCH2  0   0.203  -1.8464  -2.6866   0.4828
 3CU  H8C2  H  HCH2  0   0.199  -3.1749  -1.5803   0.8067
 3CU  H8    H  HOH1  0   0.455  -3.2815  -2.3484  -1.3495
 3CU  H5C1  H  HCH2  0   0.199   0.9467  -1.5502   1.5249
 3CU  H5C2  H  HCH2  0   0.233   0.8899  -2.6301   0.1266
 3CU  HOT   H  HOH1  0   0.457   3.7004  -2.1527   0.5012

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
 3CU  O7   C7    single  1.402  0.020  1.402
 3CU  C7   C7A   single  1.524  0.020  1.524
 3CU  C7   C6    single  1.525  0.020  1.525
 3CU  C7A  C1    single  1.523  0.020  1.523
 3CU  C7A  N4    single  1.470  0.020  1.470
 3CU  C1   O1    single  1.404  0.020  1.404
 3CU  C1   C2    single  1.529  0.020  1.529
 3CU  C2   O2    single  1.405  0.020  1.405
 3CU  C2   C3    single  1.526  0.020  1.526
 3CU  C3   C8    single  1.516  0.020  1.516
 3CU  C3   N4    single  1.450  0.020  1.450
 3CU  C8   O8    single  1.407  0.020  1.407
 3CU  N4   C5    single  1.450  0.020  1.450
 3CU  C5   C6    single  1.527  0.020  1.527
 3CU  C6   OXT   single  1.403  0.020  1.403
 3CU  O7   H7    single  0.850  0.020  0.980
 3CU  C7   HA    single  0.970  0.020  1.090
 3CU  C7A  H7A   single  0.970  0.020  1.090
 3CU  C6   H6    single  0.970  0.020  1.090
 3CU  C1   H1    single  0.970  0.020  1.090
 3CU  O1   HB    single  0.850  0.020  0.980
 3CU  C2   H2    single  0.970  0.020  1.090
 3CU  O2   HC    single  0.850  0.020  0.980
 3CU  C3   H3    single  0.970  0.020  1.090
 3CU  C8   H8C1  single  0.970  0.020  1.090
 3CU  C8   H8C2  single  0.970  0.020  1.090
 3CU  O8   H8    single  0.850  0.020  0.980
 3CU  C5   H5C1  single  0.970  0.020  1.090
 3CU  C5   H5C2  single  0.970  0.020  1.090
 3CU  OXT  HOT   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
 3CU  H7    O7   C7    108.30  3.000
 3CU  HA    C7   C6    107.40  3.000
 3CU  HA    C7   C7A   109.35  3.000
 3CU  C6    C7   C7A   102.10  3.000
 3CU  HA    C7   O7    111.09  3.000
 3CU  C6    C7   O7    115.41  3.000
 3CU  C7A   C7   O7    111.01  3.000
 3CU  H7A   C7A  N4    110.71  3.000
 3CU  H7A   C7A  C1    108.88  3.000
 3CU  N4    C7A  C1    105.10  3.000
 3CU  H7A   C7A  C7    108.70  3.000
 3CU  N4    C7A  C7    105.26  3.000
 3CU  C1    C7A  C7    118.02  3.000
 3CU  H1    C1   C2    107.69  3.000
 3CU  H1    C1   O1    110.96  3.000
 3CU  C2    C1   O1    115.49  3.000
 3CU  H1    C1   C7A   109.42  3.000
 3CU  C2    C1   C7A   101.97  3.000
 3CU  O1    C1   C7A   110.86  3.000
 3CU  HB    O1   C1    108.54  3.000
 3CU  H2    C2   C3    109.49  3.000
 3CU  H2    C2   O2    111.17  3.000
 3CU  C3    C2   O2    110.45  3.000
 3CU  H2    C2   C1    108.37  3.000
 3CU  C3    C2   C1    101.90  3.000
 3CU  O2    C2   C1    115.00  3.000
 3CU  HC    O2   C2    108.84  3.000
 3CU  H3    C3   N4    111.06  3.000
 3CU  H3    C3   C8    106.02  3.000
 3CU  N4    C3   C8    113.47  3.000
 3CU  H3    C3   C2    108.15  3.000
 3CU  N4    C3   C2    103.07  3.000
 3CU  C8    C3   C2    115.05  3.000
 3CU  H8C2  C8   H8C1  106.38  3.000
 3CU  H8C2  C8   O8    111.96  3.000
 3CU  H8C1  C8   O8    111.49  3.000
 3CU  H8C2  C8   C3    108.07  3.000
 3CU  H8C1  C8   C3    108.70  3.000
 3CU  O8    C8   C3    110.09  3.000
 3CU  H8    O8   C8    108.02  3.000
 3CU  C5    N4   C3    117.28  3.000
 3CU  C5    N4   C7A   109.72  3.000
 3CU  C3    N4   C7A   110.24  3.000
 3CU  H5C2  C5   H5C1  107.27  3.000
 3CU  H5C2  C5   C6    112.66  3.000
 3CU  H5C1  C5   C6    109.29  3.000
 3CU  H5C2  C5   N4    112.23  3.000
 3CU  H5C1  C5   N4    112.32  3.000
 3CU  C6    C5   N4    103.11  3.000
 3CU  H6    C6   OXT   111.21  3.000
 3CU  H6    C6   C5    109.26  3.000
 3CU  OXT   C6   C5    115.23  3.000
 3CU  H6    C6   C7    108.49  3.000
 3CU  OXT   C6   C7    110.63  3.000
 3CU  C5    C6   C7    101.47  3.000
 3CU  HOT   OXT  C6    108.72  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
 3CU  Var_01  C6  C5  N4  C7A  -24.06  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
 3CU  chir_01  C7   O7   C7A  C6  negativ
 3CU  chir_02  C7A  N4   C1   C7  negativ
 3CU  chir_03  C1   O1   C7A  C2  positiv
 3CU  chir_04  C2   O2   C1   C3  negativ
 3CU  chir_05  C3   N4   C2   C8  negativ
 3CU  chir_06  C6   OXT  C7   C5  positiv

