# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 28 03:14:16 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: [(5-phenylpyridin-2-yl)methyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P](O)(=O)Cc1ccc(cn1)c2ccccc2
#
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
 SYD  SYD  '[(5-phenylpyridin-2-yl)methyl]phosphonic acid'  ligand  29  17  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_SYD
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
 SYD  C1    C  CR16  0  -0.239   5.1207  -1.0687  -0.1363
 SYD  C2    C  CR16  0  -0.308   3.7584  -1.0816  -0.3979
 SYD  C3    C  CR6   0   0.082   2.9508  -0.0077  -0.0196
 SYD  C4    C  CR16  0  -0.308   3.5428   1.0791   0.6258
 SYD  C5    C  CR16  0  -0.239   4.9048   1.0916   0.8870
 SYD  C6    C  CR16  0  -0.264   5.6991   0.0174   0.5075
 SYD  C12   C  CR6   0  -0.001   1.5043  -0.0148  -0.2994
 SYD  C13   C  CR16  0  -0.115   0.7443  -1.1766  -0.1720
 SYD  N14   N  N     0  -0.398  -0.5552  -1.2450  -0.4184
 SYD  C15   C  CR6   0   0.241  -1.1910  -0.1469  -0.8123
 SYD  C16   C  CR16  0  -0.314  -0.5311   1.0685  -0.9626
 SYD  C17   C  CR16  0  -0.191   0.8258   1.1317  -0.7062
 SYD  C21   C  CH2   0  -0.829  -2.6640  -0.2652  -1.0716
 SYD  P22   P  P     0   1.370  -3.6016   0.1286   0.4240
 SYD  O25   O  O     0  -0.706  -3.2654  -0.6648   1.6274
 SYD  O26   O  OH1   0  -0.746  -3.3423   1.6872   0.7275
 SYD  O27   O  OH1   0  -0.744  -5.1069   0.0033  -0.1199
 SYD  H1    H  HCR6  0   0.260   5.7325  -1.9064  -0.4451
 SYD  H2    H  HCR6  0   0.256   3.3266  -1.9266  -0.9197
 SYD  H4    H  HCR6  0   0.256   2.9330   1.9155   0.9450
 SYD  H5    H  HCR6  0   0.260   5.3448   1.9409   1.3931
 SYD  H6    H  HCR6  0   0.259   6.7617   0.0267   0.7119
 SYD  H13   H  HCR6  0   0.262   1.2131  -2.0967   0.1616
 SYD  H16   H  HCR6  0   0.269  -1.0650   1.9482  -1.2961
 SYD  H17   H  HCR6  0   0.271   1.3574   2.0654  -0.8418
 SYD  H21   H  HCH2  0   0.313  -2.9807   0.3999  -1.8779
 SYD  H21A  H  HCH2  0   0.317  -2.9105  -1.2872  -1.3634
 SYD  HO26  H  HOH1  0   0.490  -3.5996   2.3007   0.0270
 SYD  HO27  H  HOH1  0   0.496  -5.7848   0.0731   0.5670

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
 SYD  C1   C2    aromatic  1.387  0.020  1.387
 SYD  C1   C6    aromatic  1.389  0.020  1.389
 SYD  C2   C3    aromatic  1.396  0.020  1.396
 SYD  C3   C4    aromatic  1.396  0.020  1.396
 SYD  C3   C12   single    1.473  0.020  1.473
 SYD  C4   C5    aromatic  1.387  0.020  1.387
 SYD  C5   C6    aromatic  1.389  0.020  1.389
 SYD  C12  C13   aromatic  1.394  0.020  1.394
 SYD  C12  C17   aromatic  1.393  0.020  1.393
 SYD  C13  N14   aromatic  1.324  0.020  1.324
 SYD  N14  C15   aromatic  1.329  0.020  1.329
 SYD  C15  C16   aromatic  1.391  0.020  1.391
 SYD  C15  C21   single    1.500  0.020  1.500
 SYD  C16  C17   aromatic  1.382  0.020  1.382
 SYD  C21  P22   single    1.809  0.020  1.809
 SYD  P22  O25   double    1.480  0.020  1.480
 SYD  P22  O26   single    1.609  0.020  1.609
 SYD  P22  O27   single    1.605  0.020  1.605
 SYD  C1   H1    single    0.930  0.020  1.080
 SYD  C2   H2    single    0.930  0.020  1.080
 SYD  C4   H4    single    0.930  0.020  1.080
 SYD  C5   H5    single    0.930  0.020  1.080
 SYD  C6   H6    single    0.930  0.020  1.080
 SYD  C13  H13   single    0.930  0.020  1.080
 SYD  C16  H16   single    0.930  0.020  1.080
 SYD  C17  H17   single    0.930  0.020  1.080
 SYD  C21  H21   single    0.970  0.020  1.090
 SYD  C21  H21A  single    0.970  0.020  1.090
 SYD  O26  HO26  single    0.850  0.020  0.980
 SYD  O27  HO27  single    0.850  0.020  0.980

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
 SYD  H1    C1   C6   120.14  3.000
 SYD  H1    C1   C2   119.61  3.000
 SYD  C6    C1   C2   120.24  3.000
 SYD  H2    C2   C3   120.01  3.000
 SYD  H2    C2   C1   119.32  3.000
 SYD  C3    C2   C1   120.66  3.000
 SYD  C12   C3   C4   120.53  3.000
 SYD  C12   C3   C2   120.86  3.000
 SYD  C4    C3   C2   118.62  3.000
 SYD  H4    C4   C5   119.37  3.000
 SYD  H4    C4   C3   119.92  3.000
 SYD  C5    C4   C3   120.71  3.000
 SYD  H5    C5   C6   120.15  3.000
 SYD  H5    C5   C4   119.63  3.000
 SYD  C6    C5   C4   120.21  3.000
 SYD  H6    C6   C5   120.22  3.000
 SYD  H6    C6   C1   120.22  3.000
 SYD  C5    C6   C1   119.56  3.000
 SYD  C17   C12  C13  116.56  3.000
 SYD  C17   C12  C3   121.99  3.000
 SYD  C13   C12  C3   121.46  3.000
 SYD  H13   C13  N14  115.93  3.000
 SYD  H13   C13  C12  119.94  3.000
 SYD  N14   C13  C12  124.12  3.000
 SYD  C15   N14  C13  118.81  3.000
 SYD  C21   C15  C16  121.06  3.000
 SYD  C21   C15  N14  117.12  3.000
 SYD  C16   C15  N14  121.81  3.000
 SYD  H16   C16  C17  120.30  3.000
 SYD  H16   C16  C15  120.64  3.000
 SYD  C17   C16  C15  119.05  3.000
 SYD  H17   C17  C16  119.87  3.000
 SYD  H17   C17  C12  120.47  3.000
 SYD  C16   C17  C12  119.65  3.000
 SYD  H21A  C21  H21  107.91  3.000
 SYD  H21A  C21  P22  107.94  3.000
 SYD  H21   C21  P22  109.12  3.000
 SYD  H21A  C21  C15  109.99  3.000
 SYD  H21   C21  C15  111.36  3.000
 SYD  P22   C21  C15  110.42  3.000
 SYD  O27   P22  O26  106.89  3.000
 SYD  O27   P22  O25  116.53  3.000
 SYD  O26   P22  O25  109.22  3.000
 SYD  O27   P22  C21  100.89  3.000
 SYD  O26   P22  C21  106.46  3.000
 SYD  O25   P22  C21  115.97  3.000
 SYD  HO26  O26  P22  115.82  3.000
 SYD  HO27  O27  P22  114.26  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
 SYD  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 SYD  CONST_02  C12  C3   C2   C1   180.00   0.0  0
 SYD  CONST_03  C4   C5   C6   C1     0.00   0.0  0
 SYD  CONST_04  C5   C6   C1   C2     0.00   0.0  0
 SYD  CONST_05  C5   C4   C3   C2     0.00   0.0  0
 SYD  CONST_08  C6   C1   C2   C3     0.00   0.0  0
 SYD  CONST_09  C6   C5   C4   C3     0.00   0.0  0
 SYD  CONST_10  N14  C13  C12  C3   180.00   0.0  0
 SYD  CONST_11  C16  C17  C12  C3   180.00   0.0  0
 SYD  CONST_14  C12  C3   C4   C5   180.00   0.0  0
 SYD  CONST_15  C15  N14  C13  C12    0.00   0.0  0
 SYD  CONST_16  C15  C16  C17  C12    0.00   0.0  0
 SYD  CONST_17  C16  C17  C12  C13    0.00   0.0  0
 SYD  CONST_18  C16  C15  N14  C13    0.00   0.0  0
 SYD  CONST_19  C17  C12  C13  N14    0.00   0.0  0
 SYD  CONST_20  C17  C16  C15  N14    0.00   0.0  0
 SYD  CONST_21  C21  C15  N14  C13  180.00   0.0  0
 SYD  CONST_22  C21  C15  C16  C17  180.00   0.0  0
 SYD  CONST_23  H5   C5   C6   C1   180.00   0.0  0
 SYD  CONST_24  H6   C6   C1   C2   180.00   0.0  0
 SYD  CONST_25  H4   C4   C3   C2   180.00   0.0  0
 SYD  CONST_26  H1   C1   C2   C3   180.00   0.0  0
 SYD  CONST_27  H13  C13  C12  C3     0.00   0.0  0
 SYD  CONST_28  H17  C17  C12  C3     0.00   0.0  0
 SYD  CONST_29  H2   C2   C3   C4   180.00   0.0  0
 SYD  CONST_30  H16  C16  C17  C12  180.00   0.0  0
 SYD  Var_01    P22  C21  C15  N14   91.63  30.0  2
 SYD  Var_02    O25  P22  C21  C15  -55.76  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
 SYD  plan-1  C1   0.020
 SYD  plan-1  C2   0.020
 SYD  plan-1  C3   0.020
 SYD  plan-1  C4   0.020
 SYD  plan-1  C5   0.020
 SYD  plan-1  C6   0.020
 SYD  plan-1  C12  0.020
 SYD  plan-1  H1   0.020
 SYD  plan-1  H2   0.020
 SYD  plan-1  H4   0.020
 SYD  plan-1  H5   0.020
 SYD  plan-1  H6   0.020
 SYD  plan-2  C3   0.020
 SYD  plan-2  C12  0.020
 SYD  plan-2  C13  0.020
 SYD  plan-2  N14  0.020
 SYD  plan-2  C15  0.020
 SYD  plan-2  C16  0.020
 SYD  plan-2  C17  0.020
 SYD  plan-2  C21  0.020
 SYD  plan-2  H13  0.020
 SYD  plan-2  H16  0.020
 SYD  plan-2  H17  0.020

