# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 16:47:32 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: {2-[3-(hex-1-yn-1-yl)pyridinium-1-yl]ethane-1,1-diyl}bis(phosphonate)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC#Cc1ccc[n+](CC([P]([O-])([O-])=O)[P]([O-])([O-])=O)c1
#
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
 QAF  QAF  {2-[3-(hex-1-yn-1-yl)pyridinium-1-yl]ethane-1,1-diyl}bis(phosphonate)  ligand  38  22  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QAF
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
 QAF  C01   C  CH3    0  -0.662   7.7011   2.8228   0.7702
 QAF  C02   C  CH2    0  -0.424   7.4947   1.3456   0.4681
 QAF  C03   C  CH2    0  -0.414   6.0314   0.9931   0.2342
 QAF  C04   C  CH2    0  -0.607   5.8397  -0.4921  -0.0845
 QAF  C05   C  CSP    0   0.029   4.4391  -0.8610  -0.2566
 QAF  C06   C  CSP    0   0.100   3.2682  -1.1412  -0.3692
 QAF  C07   C  CR6    0  -0.285   1.9017  -1.5110  -0.4720
 QAF  C08   C  CR16   0  -0.204   1.4603  -2.8612  -0.2003
 QAF  C09   C  CR16   0  -0.358   0.1573  -3.1734  -0.1971
 QAF  C10   C  CR16   0   0.166  -0.8869  -2.1166  -0.3316
 QAF  N11   N  NR6    1  -0.443  -0.3481  -0.9557  -1.0050
 QAF  C12   C  CH2    0  -0.319  -1.3489   0.0594  -1.3123
 QAF  C13   C  CH1    0  -0.778  -2.0151   0.6415  -0.0685
 QAF  P14   P  P      0   1.185  -3.2851   1.9334  -0.5722
 QAF  O15   O  O      0  -0.913  -2.4297   3.1312  -1.0104
 QAF  O16   O  OP    -1  -0.902  -4.0741   1.3073  -1.7262
 QAF  O17   O  OP    -1  -0.895  -4.1113   2.1934   0.6903
 QAF  P18   P  P      0   1.266  -2.6742  -0.6847   0.9864
 QAF  O19   O  O      0  -0.819  -3.8280  -1.3866   0.3193
 QAF  O20   O  OP    -1  -0.635  -1.3624  -1.7557   0.9522
 QAF  O21   O  OP    -1  -0.811  -2.7573  -0.2941   2.4361
 QAF  C22   C  CR16   0   0.006   0.9472  -0.6239  -0.8845
 QAF  H01   H  HCH3   0   0.228   8.7532   3.0511   0.9433
 QAF  H01A  H  HCH3   0   0.218   7.3584   3.4469  -0.0572
 QAF  H01B  H  HCH3   0   0.218   7.1462   3.1250   1.6603
 QAF  H02   H  HCH2   0   0.215   8.0810   1.0647  -0.4121
 QAF  H02A  H  HCH2   0   0.216   7.8818   0.7427   1.2952
 QAF  H03   H  HCH2   0   0.223   5.4440   1.2519   1.1195
 QAF  H03A  H  HCH2   0   0.223   5.6330   1.5941  -0.5881
 QAF  H04   H  HCH2   0   0.250   6.4096  -0.7470  -0.9839
 QAF  H04A  H  HCH2   0   0.253   6.2688  -1.0938   0.7231
 QAF  H08   H  HCR6   0   0.241   2.2081  -3.6280  -0.0364
 QAF  H09   H  HCR6   0   0.250  -0.1762  -4.1900  -0.0345
 QAF  H10   H  HCR6   0   0.217  -1.7298  -2.4740  -0.9353
 QAF  H12   H  HCH2   0   0.237  -0.8729   0.8542  -1.8890
 QAF  H12A  H  HCH2   0   0.241  -2.1071  -0.3959  -1.9511
 QAF  H13   H  HCH1   0   0.213  -1.2456   1.1576   0.5197
 QAF  H22   H  HCR6   0   0.277   1.2104   0.3838  -1.1838

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
 QAF  C01  C02   single    1.522  0.020  1.522
 QAF  C02  C03   single    1.523  0.020  1.523
 QAF  C03  C04   single    1.531  0.020  1.531
 QAF  C04  C05   single    1.459  0.020  1.459
 QAF  C05  C06   triple    1.209  0.020  1.209
 QAF  C06  C07   single    1.419  0.020  1.419
 QAF  C07  C08   aromatic  1.446  0.020  1.446
 QAF  C07  C22   aromatic  1.367  0.020  1.367
 QAF  C08  C09   aromatic  1.340  0.020  1.340
 QAF  C09  C10   aromatic  1.492  0.020  1.492
 QAF  C10  N11   aromatic  1.446  0.020  1.446
 QAF  N11  C12   single    1.458  0.020  1.458
 QAF  N11  C22   aromatic  1.343  0.020  1.343
 QAF  C12  C13   single    1.526  0.020  1.526
 QAF  C13  P14   single    1.880  0.020  1.880
 QAF  C13  P18   single    1.818  0.020  1.818
 QAF  P14  O15   deloc     1.536  0.020  1.536
 QAF  P14  O16   deloc     1.532  0.020  1.532
 QAF  P14  O17   deloc     1.531  0.020  1.531
 QAF  P18  O19   deloc     1.506  0.020  1.506
 QAF  P18  O20   deloc     1.694  0.020  1.694
 QAF  P18  O21   deloc     1.504  0.020  1.504
 QAF  C01  H01   single    0.939  0.020  1.096
 QAF  C01  H01A  single    0.939  0.020  1.096
 QAF  C01  H01B  single    0.939  0.020  1.096
 QAF  C02  H02   single    0.939  0.020  1.096
 QAF  C02  H02A  single    0.939  0.020  1.096
 QAF  C03  H03   single    0.939  0.020  1.096
 QAF  C03  H03A  single    0.939  0.020  1.096
 QAF  C04  H04   single    0.939  0.020  1.096
 QAF  C04  H04A  single    0.939  0.020  1.096
 QAF  C08  H08   single    0.929  0.020  1.085
 QAF  C09  H09   single    0.929  0.020  1.085
 QAF  C10  H10   single    0.929  0.020  1.085
 QAF  C12  H12   single    0.939  0.020  1.096
 QAF  C12  H12A  single    0.939  0.020  1.096
 QAF  C13  H13   single    0.939  0.020  1.096
 QAF  C22  H22   single    0.929  0.020  1.085

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
 QAF  H01B  C01  H01A  107.48  3.000
 QAF  H01B  C01  H01   107.65  3.000
 QAF  H01A  C01  H01   107.67  3.000
 QAF  H01B  C01  C02   111.20  3.000
 QAF  H01A  C01  C02   111.21  3.000
 QAF  H01   C01  C02   111.44  3.000
 QAF  H02A  C02  H02   106.08  3.000
 QAF  H02A  C02  C03   109.17  3.000
 QAF  H02   C02  C03   109.38  3.000
 QAF  H02A  C02  C01   109.68  3.000
 QAF  H02   C02  C01   109.65  3.000
 QAF  C03   C02  C01   112.67  3.000
 QAF  H03A  C03  H03   106.44  3.000
 QAF  H03A  C03  C04   109.33  3.000
 QAF  H03   C03  C04   109.32  3.000
 QAF  H03A  C03  C02   109.77  3.000
 QAF  H03   C03  C02   109.69  3.000
 QAF  C04   C03  C02   112.13  3.000
 QAF  H04A  C04  H04   105.91  3.000
 QAF  H04A  C04  C05   108.93  3.000
 QAF  H04   C04  C05   110.13  3.000
 QAF  H04A  C04  C03   109.30  3.000
 QAF  H04   C04  C03   109.37  3.000
 QAF  C05   C04  C03   112.96  3.000
 QAF  C06   C05  C04   180.00  3.000
 QAF  C07   C06  C05   180.00  3.000
 QAF  C22   C07  C08   116.71  3.000
 QAF  C22   C07  C06   121.67  3.000
 QAF  C08   C07  C06   121.57  3.000
 QAF  H08   C08  C09   120.39  3.000
 QAF  H08   C08  C07   118.58  3.000
 QAF  C09   C08  C07   120.98  3.000
 QAF  H09   C09  C10   117.61  3.000
 QAF  H09   C09  C08   121.25  3.000
 QAF  C10   C09  C08   121.03  3.000
 QAF  H10   C10  N11   106.96  3.000
 QAF  H10   C10  C09   110.90  3.000
 QAF  N11   C10  C09   110.48  3.000
 QAF  C22   N11  C12   120.60  3.000
 QAF  C22   N11  C10   121.07  3.000
 QAF  C12   N11  C10   113.66  3.000
 QAF  H12A  C12  H12   107.32  3.000
 QAF  H12A  C12  C13   109.44  3.000
 QAF  H12   C12  C13   110.07  3.000
 QAF  H12A  C12  N11   108.05  3.000
 QAF  H12   C12  N11   108.61  3.000
 QAF  C13   C12  N11   113.16  3.000
 QAF  H13   C13  P18   106.63  3.000
 QAF  H13   C13  P14   107.10  3.000
 QAF  P18   C13  P14   114.31  3.000
 QAF  H13   C13  C12   108.06  3.000
 QAF  P18   C13  C12   110.66  3.000
 QAF  P14   C13  C12   109.79  3.000
 QAF  O17   P14  O16   114.37  3.000
 QAF  O17   P14  O15   113.79  3.000
 QAF  O16   P14  O15   113.00  3.000
 QAF  O17   P14  C13   105.09  3.000
 QAF  O16   P14  C13   105.59  3.000
 QAF  O15   P14  C13   103.66  3.000
 QAF  O21   P18  O20   103.09  3.000
 QAF  O21   P18  O19   120.37  3.000
 QAF  O20   P18  O19   106.84  3.000
 QAF  O21   P18  C13   112.95  3.000
 QAF  O20   P18  C13    99.71  3.000
 QAF  O19   P18  C13   111.14  3.000
 QAF  H22   C22  N11   116.06  3.000
 QAF  H22   C22  C07   121.15  3.000
 QAF  N11   C22  C07   122.71  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
 QAF  CONST_01  C10  C09  C08  C07     0.00   0.0  0
 QAF  CONST_03  N11  C22  C07  C08     0.00   0.0  0
 QAF  CONST_05  C22  C07  C08  C09     0.00   0.0  0
 QAF  CONST_07  C09  C08  C07  C06   180.00   0.0  0
 QAF  CONST_08  N11  C22  C07  C06   180.00   0.0  0
 QAF  CONST_09  C12  N11  C22  C07   180.00   0.0  0
 QAF  CONST_10  C12  N11  C10  C09   180.00   0.0  0
 QAF  CONST_11  H09  C09  C08  C07   180.00   0.0  0
 QAF  CONST_12  H22  C22  C07  C08   180.00   0.0  0
 QAF  CONST_14  H08  C08  C09  C10   180.00   0.0  0
 QAF  Var_01    C13  C12  N11  C10    62.13  30.0  2
 QAF  Var_02    P14  C13  C12  N11  -179.92  30.0  3
 QAF  Var_03    C04  C03  C02  C01   179.34  30.0  3
 QAF  Var_04    C05  C04  C03  C02   177.58  30.0  3
 QAF  Var_05    O15  P14  C13  C12   -73.60  30.0  3
 QAF  Var_06    O19  P18  C13  C12   -67.68  30.0  3
 QAF  Var_07    H01  C01  C02  C03   179.47  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
 QAF  plan-1  C05  0.020
 QAF  plan-1  C06  0.020
 QAF  plan-1  C07  0.020
 QAF  plan-1  C08  0.020
 QAF  plan-1  C09  0.020
 QAF  plan-1  C10  0.020
 QAF  plan-1  N11  0.020
 QAF  plan-1  C12  0.020
 QAF  plan-1  C22  0.020
 QAF  plan-1  H08  0.020
 QAF  plan-1  H09  0.020
 QAF  plan-1  H10  0.020
 QAF  plan-1  H22  0.020

