# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 00:33:07 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: [(7R)-6,7-dihydro-5H-cyclopenta[c]pyridin-7-yl(hydroxy)methanediyl]bis(phosphonic acid)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC([C@@H]1CCc2ccncc12)([P](O)(O)=O)[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
 11P  11P  '[(7R)-6,7-dihydro-5H-cyclopenta[c]pyridin-7-yl(hydroxy)methanediyl]bis(phosphonic acid)'  ligand  32  19  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_11P
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
 11P  O5    O  OH1   0  -0.738   3.3892  -0.5130  -0.5140
 11P  O6    O  O     0  -0.685   2.6974   1.4162   1.1327
 11P  O7    O  OH1   0  -0.745   2.6016   1.7882  -1.3589
 11P  O8    O  OH1   0  -0.739   1.3560  -1.3385   1.7825
 11P  P4    P  P     0   1.404   2.4535   0.7331  -0.1550
 11P  C1    C  CT    0  -0.293   0.7762  -0.0249  -0.4509
 11P  O2    O  OH1   0  -0.651   0.7251  -0.3616  -1.8207
 11P  P1    P  P     0   1.391   0.6646  -1.6849   0.3817
 11P  O10   O  O     0  -0.682   1.2343  -2.7954  -0.4056
 11P  O9    O  OH1   0  -0.726  -0.8759  -1.9993   0.6892
 11P  C3    C  CR15  0  -0.384  -0.3252   0.9905  -0.0936
 11P  C16   C  CH2   0  -0.470  -0.4165   1.4641   1.3733
 11P  C17   C  CH2   0  -0.492  -1.8494   1.9848   1.5257
 11P  C23   C  CR56  0   0.179  -2.6142   1.1719   0.5286
 11P  C26   C  CR16  0  -0.393  -3.9792   0.9684   0.4222
 11P  C29   C  CR16  0  -0.066  -4.4277   0.1795  -0.6268
 11P  N25   N  N     0  -0.411  -3.6224  -0.3757  -1.5258
 11P  C28   C  CR16  0  -0.106  -2.3129  -0.1722  -1.4200
 11P  C27   C  CR56  0   0.012  -1.7580   0.5875  -0.3992
 11P  HO5   H  HOH1  0   0.501   4.3194  -0.3967  -0.2730
 11P  HO7   H  HOH1  0   0.495   2.7486   1.4229  -2.2412
 11P  HO8   H  HOH1  0   0.503   1.4914  -2.0983   2.3680
 11P  HO2   H  HOH1  0   0.470   0.4784   0.4195  -2.3316
 11P  HO9   H  HOH1  0   0.490  -1.3407  -1.4157   1.3034
 11P  H3    H  HCR5  0   0.301  -0.1136   1.8802  -0.7062
 11P  H161  H  HCH2  0   0.244  -0.2583   0.6364   2.0664
 11P  H162  H  HCH2  0   0.272   0.3300   2.2170   1.6060
 11P  H171  H  HCH2  0   0.268  -2.2291   1.8896   2.5429
 11P  H172  H  HCH2  0   0.267  -1.9128   3.0435   1.2565
 11P  H26   H  HCR6  0   0.266  -4.6789   1.3990   1.1265
 11P  H29   H  HCR6  0   0.264  -5.4883  -0.0135  -0.7454
 11P  H28   H  HCR6  0   0.255  -1.7006  -0.6522  -2.1726

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
 11P  C17  C16   single    1.532  0.020  1.532
 11P  C17  C23   single    1.497  0.020  1.497
 11P  C16  C3    single    1.544  0.020  1.544
 11P  O10  P1    double    1.476  0.020  1.476
 11P  O9   P1    single    1.602  0.020  1.602
 11P  C23  C26   aromatic  1.384  0.020  1.384
 11P  C23  C27   aromatic  1.391  0.020  1.391
 11P  C3   C27   single    1.519  0.020  1.519
 11P  C3   C1    single    1.540  0.020  1.540
 11P  P1   C1    single    1.860  0.020  1.860
 11P  P1   O8    single    1.600  0.020  1.600
 11P  C26  C29   aromatic  1.387  0.020  1.387
 11P  C27  C28   aromatic  1.388  0.020  1.388
 11P  C1   O2    single    1.412  0.020  1.412
 11P  C1   P4    single    1.864  0.020  1.864
 11P  O6   P4    double    1.478  0.020  1.478
 11P  C29  N25   aromatic  1.329  0.020  1.329
 11P  C28  N25   aromatic  1.329  0.020  1.329
 11P  P4   O5    single    1.599  0.020  1.599
 11P  P4   O7    single    1.608  0.020  1.608
 11P  O5   HO5   single    0.850  0.020  0.980
 11P  O7   HO7   single    0.850  0.020  0.980
 11P  O8   HO8   single    0.850  0.020  0.980
 11P  O2   HO2   single    0.850  0.020  0.980
 11P  O9   HO9   single    0.850  0.020  0.980
 11P  C3   H3    single    0.970  0.020  1.090
 11P  C16  H161  single    0.970  0.020  1.090
 11P  C16  H162  single    0.970  0.020  1.090
 11P  C17  H171  single    0.970  0.020  1.090
 11P  C17  H172  single    0.970  0.020  1.090
 11P  C26  H26   single    0.930  0.020  1.080
 11P  C29  H29   single    0.930  0.020  1.080
 11P  C28  H28   single    0.930  0.020  1.080

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
 11P  HO5   O5   P4    114.38  3.000
 11P  HO7   O7   P4    116.73  3.000
 11P  HO8   O8   P1    114.82  3.000
 11P  C1    P4   O7    103.35  3.000
 11P  O7    P4   O6    109.51  3.000
 11P  C1    P4   O6    118.34  3.000
 11P  O7    P4   O5    106.82  3.000
 11P  O6    P4   O5    117.33  3.000
 11P  C1    P4   O5    100.02  3.000
 11P  C3    C1   P1    116.21  3.000
 11P  P1    C1   O2    102.67  3.000
 11P  C3    C1   O2    110.89  3.000
 11P  O2    C1   P4    106.48  3.000
 11P  P1    C1   P4    110.23  3.000
 11P  C3    C1   P4    109.79  3.000
 11P  HO2   O2   C1    109.26  3.000
 11P  O9    P1   O10   109.02  3.000
 11P  O9    P1   C1    108.58  3.000
 11P  O10   P1   C1    114.17  3.000
 11P  C1    P1   O8     99.94  3.000
 11P  O9    P1   O8    106.86  3.000
 11P  O10   P1   O8    117.60  3.000
 11P  HO9   O9   P1    117.77  3.000
 11P  H3    C3   C27   106.48  3.000
 11P  H3    C3   C16   106.99  3.000
 11P  C27   C3   C16   102.52  3.000
 11P  H3    C3   C1    105.45  3.000
 11P  C27   C3   C1    116.92  3.000
 11P  C16   C3   C1    117.70  3.000
 11P  H162  C16  H161  106.88  3.000
 11P  H162  C16  C17   112.71  3.000
 11P  H161  C16  C17   109.28  3.000
 11P  H162  C16  C3    112.07  3.000
 11P  H161  C16  C3    111.23  3.000
 11P  C17   C16  C3    104.72  3.000
 11P  H172  C17  H171  107.09  3.000
 11P  H172  C17  C23   109.39  3.000
 11P  H171  C17  C23   113.35  3.000
 11P  H172  C17  C16   111.01  3.000
 11P  H171  C17  C16   112.89  3.000
 11P  C23   C17  C16   103.13  3.000
 11P  C27   C23  C26   119.60  3.000
 11P  C27   C23  C17   110.97  3.000
 11P  C26   C23  C17   129.42  3.000
 11P  H26   C26  C29   120.62  3.000
 11P  H26   C26  C23   121.95  3.000
 11P  C29   C26  C23   117.43  3.000
 11P  H29   C29  N25   116.39  3.000
 11P  H29   C29  C26   120.01  3.000
 11P  N25   C29  C26   123.60  3.000
 11P  C28   N25  C29   118.64  3.000
 11P  H28   C28  C27   121.86  3.000
 11P  H28   C28  N25   115.72  3.000
 11P  C27   C28  N25   122.42  3.000
 11P  C28   C27  C23   118.31  3.000
 11P  C28   C27  C3    132.07  3.000
 11P  C23   C27  C3    109.56  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
 11P  CONST_01  N25  C29  C26  C23    0.00   0.0  0
 11P  CONST_02  N25  C28  C27  C23    0.00   0.0  0
 11P  CONST_03  C28  C27  C23  C26    0.00   0.0  0
 11P  CONST_04  C28  N25  C29  C26    0.00   0.0  0
 11P  CONST_05  C27  C23  C26  C29    0.00   0.0  0
 11P  CONST_06  C27  C28  N25  C29    0.00   0.0  0
 11P  CONST_07  H28  C28  C27  C3     0.00   0.0  0
 11P  CONST_08  H26  C26  C23  C17    0.00   0.0  0
 11P  CONST_09  H29  C29  C26  C23  180.00   0.0  0
 11P  Var_01    C23  C17  C16  C3    28.61  30.0  1
 11P  Var_02    C26  C23  C17  C16  163.26  30.0  1
 11P  Var_03    C3   C1   P4   O5   177.12  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
 11P  chir_01  C3  C16  C27  C1  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
 11P  plan-1  C3   0.020
 11P  plan-1  C17  0.020
 11P  plan-1  C23  0.020
 11P  plan-1  C26  0.020
 11P  plan-1  C29  0.020
 11P  plan-1  N25  0.020
 11P  plan-1  C28  0.020
 11P  plan-1  C27  0.020
 11P  plan-1  H26  0.020
 11P  plan-1  H29  0.020
 11P  plan-1  H28  0.020

