# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 28 18:10:45 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: [[(4-hexoxypyridin-2-yl)amino]-phosphono-methyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCOc1ccnc(NC([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
 T93  T93  '[[(4-hexoxypyridin-2-yl)amino]-phosphono-methyl]phosphonic acid'  ligand  45  23  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_T93
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
 T93  O1    O  O     0  -0.687  -5.1198   0.9147   0.7040
 T93  P2    P  P     0   1.410  -4.1353  -0.0611   1.2124
 T93  O3    O  OH1   0  -0.730  -3.6481   0.3657   2.6732
 T93  O4    O  OH1   0  -0.754  -4.5810  -1.6005   1.2810
 T93  C5    C  CH1   0  -0.668  -2.6166  -0.2208   0.2005
 T93  P6    P  P     0   1.375  -2.7463  -1.2710  -1.3012
 T93  O7    O  OH1   0  -0.741  -2.8779  -2.7884  -0.8082
 T93  O8    O  OH1   0  -0.739  -4.1764  -0.8034  -1.8508
 T93  O9    O  O     0  -0.684  -1.6040  -1.1258  -2.2285
 T93  N10   N  NH1   0  -0.680  -2.2055   1.1126  -0.1297
 T93  C11   C  CR6   0   0.519  -0.9031   1.5015  -0.3251
 T93  N12   N  N     0  -0.474  -0.7709   2.7009  -0.8961
 T93  C13   C  CR16  0  -0.062   0.4569   3.1613  -1.0786
 T93  C14   C  CR16  0  -0.469   1.6153   2.4938  -0.7243
 T93  C15   C  CR6   0   0.483   1.4668   1.2381  -0.1304
 T93  O16   O  O2    0  -0.468   2.4808   0.4645   0.2638
 T93  C17   C  CH2   0  -0.174   3.8173   0.8764  -0.0084
 T93  C18   C  CH2   0  -0.456   4.7538  -0.2096   0.4749
 T93  C19   C  CH2   0  -0.425   6.2067   0.1237   0.1564
 T93  C20   C  CH2   0  -0.407   7.1737  -0.9526   0.6325
 T93  C21   C  CH2   0  -0.419   8.6264  -0.6486   0.2875
 T93  C22   C  CH3   0  -0.662   9.5849  -1.7308   0.7645
 T93  C23   C  CR16  0  -0.497   0.1874   0.7306   0.0705
 T93  H1    H  HOH1  0   0.498  -3.0797  -0.2604   3.1415
 T93  H2    H  HOH1  0   0.510  -5.4660  -1.7653   1.6382
 T93  H051  H  HCH1  0   0.345  -1.8680  -0.6998   0.8369
 T93  H3    H  HOH1  0   0.493  -3.6066  -2.9632  -0.1950
 T93  H4    H  HOH1  0   0.501  -4.3822  -1.0955  -2.7505
 T93  H101  H  HNH1  0   0.393  -2.8808   1.6907  -0.6083
 T93  H131  H  HCR6  0   0.262   0.5332   4.1371  -1.5464
 T93  H141  H  HCR6  0   0.282   2.5757   2.9482  -0.9155
 T93  H171  H  HCH2  0   0.227   3.9466   1.0388  -1.0842
 T93  H172  H  HCH2  0   0.227   4.0342   1.8225   0.4996
 T93  H182  H  HCH2  0   0.231   4.6337  -0.3460   1.5536
 T93  H181  H  HCH2  0   0.230   4.4833  -1.1572   0.0002
 T93  H192  H  HCH2  0   0.216   6.3202   0.2612  -0.9243
 T93  H191  H  HCH2  0   0.217   6.4763   1.0809   0.6152
 T93  H202  H  HCH2  0   0.210   7.0757  -1.0757   1.7167
 T93  H201  H  HCH2  0   0.210   6.8905  -1.9146   0.1914
 T93  H212  H  HCH2  0   0.211   8.7221  -0.5242  -0.7956
 T93  H211  H  HCH2  0   0.211   8.9104   0.3117   0.7288
 T93  H223  H  HCH3  0   0.226  10.6156  -1.5038   0.4899
 T93  H221  H  HCH3  0   0.216   9.5478  -1.8390   1.8501
 T93  H222  H  HCH3  0   0.216   9.3328  -2.6999   0.3295
 T93  H231  H  HCR6  0   0.275   0.0764  -0.2463   0.5208

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
 T93  C22  C21   single    1.522  0.020  1.522
 T93  C21  C20   single    1.524  0.020  1.524
 T93  C20  C19   single    1.523  0.020  1.523
 T93  C19  C18   single    1.524  0.020  1.524
 T93  C18  C17   single    1.513  0.020  1.513
 T93  O1   P2    double    1.477  0.020  1.477
 T93  C17  O16   single    1.425  0.020  1.425
 T93  O4   P2    single    1.604  0.020  1.604
 T93  O16  C15   single    1.335  0.020  1.335
 T93  C23  C15   aromatic  1.391  0.020  1.391
 T93  C23  C11   aromatic  1.393  0.020  1.393
 T93  P2   O3    single    1.598  0.020  1.598
 T93  P2   C5    single    1.832  0.020  1.832
 T93  N10  C11   single    1.373  0.020  1.373
 T93  N10  C5    single    1.434  0.020  1.434
 T93  C15  C14   aromatic  1.397  0.020  1.397
 T93  C11  N12   aromatic  1.335  0.020  1.335
 T93  C5   P6    single    1.837  0.020  1.837
 T93  C14  C13   aromatic  1.383  0.020  1.383
 T93  N12  C13   aromatic  1.324  0.020  1.324
 T93  O9   P6    double    1.478  0.020  1.478
 T93  P6   O8    single    1.602  0.020  1.602
 T93  P6   O7    single    1.601  0.020  1.601
 T93  O3   H1    single    0.850  0.020  0.980
 T93  O4   H2    single    0.850  0.020  0.980
 T93  C5   H051  single    0.970  0.020  1.090
 T93  O7   H3    single    0.850  0.020  0.980
 T93  O8   H4    single    0.850  0.020  0.980
 T93  N10  H101  single    0.890  0.020  1.040
 T93  C13  H131  single    0.930  0.020  1.080
 T93  C14  H141  single    0.930  0.020  1.080
 T93  C17  H171  single    0.970  0.020  1.090
 T93  C17  H172  single    0.970  0.020  1.090
 T93  C18  H182  single    0.970  0.020  1.090
 T93  C18  H181  single    0.970  0.020  1.090
 T93  C19  H192  single    0.970  0.020  1.090
 T93  C19  H191  single    0.970  0.020  1.090
 T93  C20  H202  single    0.970  0.020  1.090
 T93  C20  H201  single    0.970  0.020  1.090
 T93  C21  H212  single    0.970  0.020  1.090
 T93  C21  H211  single    0.970  0.020  1.090
 T93  C22  H223  single    0.970  0.020  1.090
 T93  C22  H221  single    0.970  0.020  1.090
 T93  C22  H222  single    0.970  0.020  1.090
 T93  C23  H231  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
 T93  C5    P2   O4     99.81  3.000
 T93  C5    P2   O3    105.99  3.000
 T93  O4    P2   O3    107.58  3.000
 T93  C5    P2   O1    114.85  3.000
 T93  O3    P2   O1    109.97  3.000
 T93  O4    P2   O1    117.62  3.000
 T93  H1    O3   P2    116.69  3.000
 T93  H2    O4   P2    115.66  3.000
 T93  H051  C5   N10   110.19  3.000
 T93  H051  C5   P6    105.89  3.000
 T93  N10   C5   P6    111.32  3.000
 T93  H051  C5   P2    106.52  3.000
 T93  P6    C5   P2    116.29  3.000
 T93  N10   C5   P2    106.49  3.000
 T93  O9    P6   O8    116.49  3.000
 T93  O8    P6   O7    108.00  3.000
 T93  O9    P6   O7    110.47  3.000
 T93  O7    P6   C5    107.21  3.000
 T93  O8    P6   C5    100.17  3.000
 T93  O9    P6   C5    113.71  3.000
 T93  H3    O7   P6    115.34  3.000
 T93  H4    O8   P6    114.87  3.000
 T93  H101  N10  C11   113.87  3.000
 T93  H101  N10  C5    116.74  3.000
 T93  C11   N10  C5    124.62  3.000
 T93  C23   C11  N12   122.77  3.000
 T93  N12   C11  N10   114.16  3.000
 T93  C23   C11  N10   123.06  3.000
 T93  C13   N12  C11   117.59  3.000
 T93  H131  C13  C14   119.05  3.000
 T93  H131  C13  N12   115.94  3.000
 T93  C14   C13  N12   125.01  3.000
 T93  H141  C14  C15   123.24  3.000
 T93  H141  C14  C13   119.78  3.000
 T93  C15   C14  C13   116.98  3.000
 T93  C23   C15  O16   116.40  3.000
 T93  C23   C15  C14   119.15  3.000
 T93  O16   C15  C14   124.45  3.000
 T93  C17   O16  C15   119.25  3.000
 T93  H172  C17  H171  107.69  3.000
 T93  H172  C17  C18   110.44  3.000
 T93  H171  C17  C18   110.30  3.000
 T93  H172  C17  O16   110.29  3.000
 T93  H171  C17  O16   109.94  3.000
 T93  C18   C17  O16   108.18  3.000
 T93  H181  C18  H182  107.03  3.000
 T93  H181  C18  C19   109.54  3.000
 T93  H182  C18  C19   109.75  3.000
 T93  H181  C18  C17   109.27  3.000
 T93  H182  C18  C17   109.66  3.000
 T93  C19   C18  C17   111.48  3.000
 T93  H191  C19  H192  106.15  3.000
 T93  H191  C19  C20   109.29  3.000
 T93  H192  C19  C20   109.34  3.000
 T93  H191  C19  C18   109.77  3.000
 T93  H192  C19  C18   109.42  3.000
 T93  C20   C19  C18   112.66  3.000
 T93  H201  C20  H202  106.06  3.000
 T93  H201  C20  C21   109.31  3.000
 T93  H202  C20  C21   109.38  3.000
 T93  H201  C20  C19   109.30  3.000
 T93  H202  C20  C19   109.38  3.000
 T93  C21   C20  C19   113.17  3.000
 T93  H211  C21  H212  106.06  3.000
 T93  H211  C21  C22   109.52  3.000
 T93  H212  C21  C22   109.62  3.000
 T93  H211  C21  C20   109.35  3.000
 T93  H212  C21  C20   109.27  3.000
 T93  C22   C21  C20   112.80  3.000
 T93  H222  C22  H221  107.48  3.000
 T93  H222  C22  H223  107.62  3.000
 T93  H221  C22  H223  107.65  3.000
 T93  H222  C22  C21   111.15  3.000
 T93  H221  C22  C21   111.14  3.000
 T93  H223  C22  C21   111.61  3.000
 T93  H231  C23  C15   118.96  3.000
 T93  H231  C23  C11   122.54  3.000
 T93  C15   C23  C11   118.50  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
 T93  CONST_01  C14   C15  C23  C11     0.00   0.0  0
 T93  CONST_02  C14   C13  N12  C11     0.00   0.0  0
 T93  CONST_03  C15   C23  C11  N12     0.00   0.0  0
 T93  CONST_04  C15   C14  C13  N12     0.00   0.0  0
 T93  CONST_05  C23   C15  C14  C13     0.00   0.0  0
 T93  CONST_06  C23   C11  N12  C13     0.00   0.0  0
 T93  CONST_07  C15   C23  C11  N10   180.00   0.0  0
 T93  CONST_08  C13   N12  C11  N10   180.00   0.0  0
 T93  CONST_09  O16   C15  C23  C11   180.00   0.0  0
 T93  CONST_10  O16   C15  C14  C13   180.00   0.0  0
 T93  CONST_11  H131  C13  N12  C11   180.00   0.0  0
 T93  CONST_12  H231  C23  C11  N12   180.00   0.0  0
 T93  CONST_13  H141  C14  C13  N12   180.00   0.0  0
 T93  CONST_15  N12   C11  N10  C5    180.00   0.0  0
 T93  CONST_16  H101  N10  C11  N12     0.00   0.0  0
 T93  Var_01    C23   C15  O16  C17   175.08  30.0  2
 T93  Var_02    C11   N10  C5   P2    149.36  30.0  3
 T93  Var_03    C18   C17  O16  C15  -176.99  30.0  1
 T93  Var_04    N10   C5   P2   O1     44.37  30.0  3
 T93  Var_05    O9    P6   C5   P2    167.15  30.0  3
 T93  Var_06    C19   C18  C17  O16   177.15  30.0  1
 T93  Var_07    C20   C19  C18  C17   179.97  30.0  1
 T93  Var_08    C21   C20  C19  C18   178.49  30.0  1
 T93  Var_09    C22   C21  C20  C19  -179.88  30.0  1
 T93  Var_10    H223  C22  C21  C20   178.83  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
 T93  plan-1  N10   0.020
 T93  plan-1  C11   0.020
 T93  plan-1  N12   0.020
 T93  plan-1  C13   0.020
 T93  plan-1  C14   0.020
 T93  plan-1  C15   0.020
 T93  plan-1  O16   0.020
 T93  plan-1  C23   0.020
 T93  plan-1  H131  0.020
 T93  plan-1  H141  0.020
 T93  plan-1  H231  0.020
 T93  plan-2  C5    0.020
 T93  plan-2  N10   0.020
 T93  plan-2  C11   0.020
 T93  plan-2  H101  0.020

