# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 22:47:47 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: 6,7-dihydro-5H-cyclopenta[b]pyridine-6,6-diylbis(phosphonic acid)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P](O)(=O)C1(Cc2cccnc2C1)[P](O)(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
 UNV  UNV  '6,7-dihydro-5H-cyclopenta[b]pyridine-6,6-diylbis(phosphonic acid)'  ligand  24  17  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_UNV
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
 UNV  N1    N  N      0  -0.450  -2.9409  -0.3810  -1.3894
 UNV  C2    C  CR16   0  -0.253  -3.0374  -0.4076   1.4080
 UNV  C3    C  CR6    0   0.099  -1.8320  -0.4400   0.7433
 UNV  C4    C  CR16   0  -0.331  -4.2077  -0.3379   0.6457
 UNV  C5    C  CR16   0  -0.118  -4.1061  -0.3257  -0.7324
 UNV  C6    C  CR6    0   0.233  -1.8437  -0.4272  -0.6556
 UNV  C7    C  CH2    0  -0.507  -0.4249  -0.5174   1.2450
 UNV  C10   C  CH2    0  -0.507  -0.4488  -0.5263  -1.1876
 UNV  C14   C  CT     0  -0.537   0.4511  -0.1706   0.0150
 UNV  P17   P  P      0   1.177   1.9759  -1.2344   0.0010
 UNV  O18   O  OP    -1  -0.922   1.4600   2.0458  -1.2732
 UNV  O19   O  OP    -1  -0.916  -0.7689   2.2292  -0.0388
 UNV  O20   O  O      0  -0.922   1.4084   2.0773   1.2916
 UNV  O21   O  OP    -1  -0.933   1.4333  -2.6841   0.0273
 UNV  O22   O  OP    -1  -0.922   2.7372  -0.9352  -1.2994
 UNV  O23   O  O      0  -0.924   2.7769  -0.9038   1.2696
 UNV  H2    H  HCR6   0   0.239  -3.0896  -0.4199   2.4911
 UNV  H4    H  HCR6   0   0.246  -5.1810  -0.2939   1.1171
 UNV  H5    H  HCR6   0   0.235  -5.0012  -0.2712  -1.3439
 UNV  H7    H  HCH2   0   0.206  -0.2411   0.1500   2.0892
 UNV  H7A   H  HCH2   0   0.207  -0.2244  -1.5366   1.5960
 UNV  H10   H  HCH2   0   0.209  -0.2756  -1.5582  -1.5191
 UNV  H10A  H  HCH2   0   0.205  -0.2812   0.1169  -2.0530
 UNV  P11   P  P      0   1.187   0.6752   1.6843  -0.0018

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
 UNV  N1   C5    aromatic  1.339  0.020  1.339
 UNV  N1   C6    aromatic  1.321  0.020  1.321
 UNV  C4   C2    aromatic  1.398  0.020  1.398
 UNV  C3   C2    aromatic  1.377  0.020  1.377
 UNV  C2   H2    single    0.930  0.020  1.080
 UNV  C6   C3    aromatic  1.399  0.020  1.399
 UNV  C3   C7    single    1.496  0.020  1.496
 UNV  C5   C4    aromatic  1.382  0.020  1.382
 UNV  C4   H4    single    0.930  0.020  1.080
 UNV  C5   H5    single    0.930  0.020  1.080
 UNV  C10  C6    single    1.496  0.020  1.496
 UNV  C14  C7    single    1.549  0.020  1.549
 UNV  C7   H7    single    0.970  0.020  1.090
 UNV  C7   H7A   single    0.970  0.020  1.090
 UNV  C10  C14   single    1.544  0.020  1.544
 UNV  C10  H10   single    0.970  0.020  1.090
 UNV  C10  H10A  single    0.970  0.020  1.090
 UNV  O20  P11   deloc     1.538  0.020  1.538
 UNV  C14  P11   single    1.868  0.020  1.868
 UNV  P11  O18   deloc     1.537  0.020  1.537
 UNV  P11  O19   deloc     1.544  0.020  1.544
 UNV  P17  C14   single    1.859  0.020  1.859
 UNV  O23  P17   deloc     1.536  0.020  1.536
 UNV  O21  P17   deloc     1.548  0.020  1.548
 UNV  P17  O22   deloc     1.536  0.020  1.536

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
 UNV  C6    N1   C5   116.86  3.000
 UNV  H2    C2   C4   120.31  3.000
 UNV  H2    C2   C3   121.60  3.000
 UNV  C4    C2   C3   118.08  3.000
 UNV  C7    C3   C6   110.10  3.000
 UNV  C7    C3   C2   131.51  3.000
 UNV  C6    C3   C2   118.37  3.000
 UNV  H4    C4   C5   120.01  3.000
 UNV  H4    C4   C2   121.14  3.000
 UNV  C5    C4   C2   118.85  3.000
 UNV  H5    C5   C4   120.11  3.000
 UNV  H5    C5   N1   116.32  3.000
 UNV  C4    C5   N1   123.58  3.000
 UNV  C10   C6   C3   110.31  3.000
 UNV  C10   C6   N1   125.40  3.000
 UNV  C3    C6   N1   124.25  3.000
 UNV  H7A   C7   H7   106.86  3.000
 UNV  H7A   C7   C14  111.03  3.000
 UNV  H7    C7   C14  112.45  3.000
 UNV  H7A   C7   C3   109.12  3.000
 UNV  H7    C7   C3   112.71  3.000
 UNV  C14   C7   C3   104.71  3.000
 UNV  H10A  C10  H10  106.89  3.000
 UNV  H10A  C10  C14  113.11  3.000
 UNV  H10   C10  C14  111.10  3.000
 UNV  H10A  C10  C6   112.71  3.000
 UNV  H10   C10  C6   108.47  3.000
 UNV  C14   C10  C6   104.55  3.000
 UNV  P17   C14  P11  118.01  3.000
 UNV  P17   C14  C10  109.90  3.000
 UNV  P11   C14  C10  106.96  3.000
 UNV  P17   C14  C7   109.97  3.000
 UNV  P11   C14  C7   107.29  3.000
 UNV  C10   C14  C7   103.73  3.000
 UNV  O23   P17  O22  113.49  3.000
 UNV  O22   P17  O21  111.74  3.000
 UNV  O23   P17  O21  111.73  3.000
 UNV  O22   P17  C14  107.54  3.000
 UNV  O21   P17  C14  104.37  3.000
 UNV  O23   P17  C14  107.35  3.000
 UNV  O20   P11  O19  112.08  3.000
 UNV  O19   P11  O18  112.01  3.000
 UNV  O20   P11  O18  113.09  3.000
 UNV  O19   P11  C14  103.79  3.000
 UNV  O18   P11  C14  107.59  3.000
 UNV  O20   P11  C14  107.65  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
 UNV  CONST_01  C2   C4   C5   N1     0.00   0.0  0
 UNV  CONST_02  C2   C3   C6   N1     0.00   0.0  0
 UNV  CONST_03  C5   C4   C2   C3     0.00   0.0  0
 UNV  CONST_04  C5   N1   C6   C3     0.00   0.0  0
 UNV  CONST_05  C6   C3   C2   C4     0.00   0.0  0
 UNV  CONST_06  C6   N1   C5   C4     0.00   0.0  0
 UNV  CONST_07  H4   C4   C5   N1   180.00   0.0  0
 UNV  CONST_08  H5   C5   C4   C2   180.00   0.0  0
 UNV  CONST_09  H2   C2   C4   C5   180.00   0.0  0
 UNV  Var_01    C14  C10  C6   N1   165.42  30.0  1
 UNV  Var_02    C14  C7   C3   C2  -166.63  30.0  1
 UNV  Var_03    C10  C14  C7   C3   -24.04  30.0  1
 UNV  Var_04    C7   C14  C10  C6    24.71  30.0  1
 UNV  Var_05    O20  P11  C14  C7    61.72  30.0  3
 UNV  Var_06    O23  P17  C14  C7   -62.48  30.0  3

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
 UNV  plan-1  N1   0.020
 UNV  plan-1  C2   0.020
 UNV  plan-1  C3   0.020
 UNV  plan-1  C4   0.020
 UNV  plan-1  C5   0.020
 UNV  plan-1  C6   0.020
 UNV  plan-1  C7   0.020
 UNV  plan-1  C10  0.020
 UNV  plan-1  H2   0.020
 UNV  plan-1  H4   0.020
 UNV  plan-1  H5   0.020

