# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 21 00:06:53 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  28  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  OP    -1  -0.889   3.6202  -0.2819  -0.2053
 11P  O6    O  O      0  -0.885   2.5392   1.8725   0.6520
 11P  O7    O  OP    -1  -0.923   2.5213   1.3400  -1.8587
 11P  O8    O  OP    -1  -0.920   1.2205  -1.4031   1.8981
 11P  P4    P  P      0   1.161   2.5183   0.7591  -0.4025
 11P  C1    C  CT     0  -0.297   0.8203  -0.0849  -0.4648
 11P  O2    O  OH1    0  -0.748   0.6557  -0.3662  -1.8645
 11P  P1    P  P      0   1.181   0.6753  -1.6900   0.4853
 11P  O10   O  O      0  -0.919   1.4889  -2.7414  -0.2804
 11P  O9    O  OP    -1  -0.906  -0.8287  -2.0312   0.5049
 11P  C3    C  CH1    0  -0.287  -0.2721   0.9312  -0.0800
 11P  C16   C  CH2    0  -0.460  -0.3471   1.3680   1.3962
 11P  C17   C  CH2    0  -0.502  -1.7747   1.8874   1.6029
 11P  C23   C  CR6    0   0.149  -2.5582   1.1012   0.5950
 11P  C26   C  CR16   0  -0.411  -3.9260   0.8867   0.5151
 11P  C29   C  CR16   0  -0.097  -4.3929   0.1161  -0.5384
 11P  N25   N  N      0  -0.430  -3.5988  -0.4026  -1.4723
 11P  C28   C  CR16   0  -0.130  -2.2884  -0.1850  -1.3836
 11P  C27   C  CR6    0   0.112  -1.7097   0.5465  -0.3556
 11P  HO2   H  HOH1   0   0.400   1.2766   0.3032  -2.2507
 11P  H3    H  HCH1   0   0.187  -0.0822   1.8371  -0.6806
 11P  H161  H  HCH2   0   0.229  -0.1664   0.4974   2.0251
 11P  H162  H  HCH2   0   0.218   0.4220   2.0996   1.6216
 11P  H171  H  HCH2   0   0.231  -2.1422   1.7637   2.6243
 11P  H172  H  HCH2   0   0.227  -1.8496   2.9570   1.3719
 11P  H26   H  HCR6   0   0.240  -4.6147   1.2935   1.2460
 11P  H29   H  HCR6   0   0.237  -5.4544  -0.0907  -0.6349
 11P  H28   H  HCR6   0   0.231  -1.6728  -0.6233  -2.1565

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    1.533  0.020  1.533
 11P  C17  C23   single    1.499  0.020  1.499
 11P  C16  C3    single    1.541  0.020  1.541
 11P  O10  P1    deloc     1.534  0.020  1.534
 11P  O9   P1    deloc     1.542  0.020  1.542
 11P  C23  C26   aromatic  1.387  0.020  1.387
 11P  C23  C27   aromatic  1.390  0.020  1.390
 11P  C3   C27   single    1.514  0.020  1.514
 11P  C3   C1    single    1.541  0.020  1.541
 11P  P1   C1    single    1.871  0.020  1.871
 11P  P1   O8    deloc     1.541  0.020  1.541
 11P  C26  C29   aromatic  1.386  0.020  1.386
 11P  C27  C28   aromatic  1.388  0.020  1.388
 11P  C1   O2    single    1.437  0.020  1.437
 11P  C1   P4    single    1.897  0.020  1.897
 11P  O6   P4    deloc     1.534  0.020  1.534
 11P  C29  N25   aromatic  1.331  0.020  1.331
 11P  C28  N25   aromatic  1.331  0.020  1.331
 11P  P4   O5    deloc     1.529  0.020  1.529
 11P  P4   O7    deloc     1.568  0.020  1.568
 11P  O2   HO2   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  C1    P4   O7     97.82  3.000
 11P  O7    P4   O6    111.69  3.000
 11P  C1    P4   O6    110.97  3.000
 11P  O7    P4   O5    111.76  3.000
 11P  O6    P4   O5    113.32  3.000
 11P  C1    P4   O5    110.27  3.000
 11P  C3    C1   P1    112.59  3.000
 11P  P1    C1   O2    108.53  3.000
 11P  C3    C1   O2    106.92  3.000
 11P  O2    C1   P4    102.80  3.000
 11P  P1    C1   P4    115.75  3.000
 11P  C3    C1   P4    109.45  3.000
 11P  HO2   O2   C1    100.11  3.000
 11P  O9    P1   O10   111.83  3.000
 11P  O9    P1   C1    105.78  3.000
 11P  O10   P1   C1    107.07  3.000
 11P  C1    P1   O8    106.16  3.000
 11P  O9    P1   O8    111.98  3.000
 11P  O10   P1   O8    113.42  3.000
 11P  H3    C3   C27   105.85  3.000
 11P  H3    C3   C16   107.28  3.000
 11P  C27   C3   C16   101.54  3.000
 11P  H3    C3   C1    106.47  3.000
 11P  C27   C3   C1    117.41  3.000
 11P  C16   C3   C1    117.43  3.000
 11P  H162  C16  H161  107.53  3.000
 11P  H162  C16  C17   113.80  3.000
 11P  H161  C16  C17   110.33  3.000
 11P  H162  C16  C3    110.82  3.000
 11P  H161  C16  C3    108.57  3.000
 11P  C17   C16  C3    105.70  3.000
 11P  H172  C17  H171  106.52  3.000
 11P  H172  C17  C23   109.52  3.000
 11P  H171  C17  C23   113.16  3.000
 11P  H172  C17  C16   111.45  3.000
 11P  H171  C17  C16   113.64  3.000
 11P  C23   C17  C16   102.61  3.000
 11P  C27   C23  C26   120.07  3.000
 11P  C27   C23  C17   110.49  3.000
 11P  C26   C23  C17   129.44  3.000
 11P  H26   C26  C29   120.48  3.000
 11P  H26   C26  C23   122.00  3.000
 11P  C29   C26  C23   117.52  3.000
 11P  H29   C29  N25   116.53  3.000
 11P  H29   C29  C26   120.18  3.000
 11P  N25   C29  C26   123.29  3.000
 11P  C28   N25  C29   118.47  3.000
 11P  H28   C28  C27   120.39  3.000
 11P  H28   C28  N25   116.53  3.000
 11P  C27   C28  N25   123.08  3.000
 11P  C28   C27  C23   117.54  3.000
 11P  C28   C27  C3    131.66  3.000
 11P  C23   C27  C3    110.73  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    28.45  30.0  1
 11P  Var_02    C26  C23  C17  C16  162.69  30.0  1
 11P  Var_03    C3   C1   P4   O5   156.74  30.0  3

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

