# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 27 23:54:50 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: (pyridin-2-ylmethyl)phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P](O)(=O)Cc1ccccn1
#
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
 SYC  SYC  '(pyridin-2-ylmethyl)phosphonic acid'  ligand  19  11  .  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_SYC
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
 SYC  C1    C  CR16  0  -0.077   2.7411  -1.1481   0.1706
 SYC  N2    N  N     0  -0.404   1.5163  -1.1834  -0.3399
 SYC  C3    C  CR6   0   0.245   0.9061  -0.0322  -0.6019
 SYC  C4    C  CR16  0  -0.326   1.5059   1.2000  -0.3592
 SYC  C5    C  CR16  0  -0.151   2.7842   1.2286   0.1735
 SYC  C6    C  CR16  0  -0.326   3.4206   0.0278   0.4493
 SYC  C11   C  CH2   0  -0.826  -0.4840  -0.1135  -1.1645
 SYC  P12   P  P     0   1.369  -1.7113  -0.0684   0.1628
 SYC  O15   O  O     0  -0.706  -1.5474  -1.0835   1.2278
 SYC  O16   O  OH1   0  -0.745  -1.6357   1.4003   0.8155
 SYC  O17   O  OH1   0  -0.744  -3.0727  -0.1313  -0.6862
 SYC  H1    H  HCR6  0   0.265   3.2081  -2.1072   0.3652
 SYC  H4    H  HCR6  0   0.267   0.9864   2.1194  -0.5935
 SYC  H5    H  HCR6  0   0.276   3.2751   2.1731   0.3679
 SYC  H6    H  HCR6  0   0.272   4.4182  -0.0016   0.8649
 SYC  H11   H  HCH2  0   0.312  -0.6780   0.6994  -1.8672
 SYC  H11A  H  HCH2  0   0.315  -0.6116  -1.0548  -1.7017
 SYC  HO16  H  HOH1  0   0.490  -1.8093   2.1361   0.2142
 SYC  HO17  H  HOH1  0   0.496  -3.8736  -0.2185  -0.1504

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
 SYC  C1   N2    aromatic  1.328  0.020  1.328
 SYC  C1   C6    aromatic  1.386  0.020  1.386
 SYC  N2   C3    aromatic  1.329  0.020  1.329
 SYC  C3   C4    aromatic  1.392  0.020  1.392
 SYC  C3   C11   single    1.502  0.020  1.502
 SYC  C4   C5    aromatic  1.385  0.020  1.385
 SYC  C5   C6    aromatic  1.387  0.020  1.387
 SYC  C11  P12   single    1.808  0.020  1.808
 SYC  P12  O15   double    1.480  0.020  1.480
 SYC  P12  O16   single    1.609  0.020  1.609
 SYC  P12  O17   single    1.606  0.020  1.606
 SYC  C1   H1    single    0.930  0.020  1.080
 SYC  C4   H4    single    0.930  0.020  1.080
 SYC  C5   H5    single    0.930  0.020  1.080
 SYC  C6   H6    single    0.930  0.020  1.080
 SYC  C11  H11   single    0.970  0.020  1.090
 SYC  C11  H11A  single    0.970  0.020  1.090
 SYC  O16  HO16  single    0.850  0.020  0.980
 SYC  O17  HO17  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
 SYC  H1    C1   C6   120.21  3.000
 SYC  H1    C1   N2   116.28  3.000
 SYC  C6    C1   N2   123.51  3.000
 SYC  C3    N2   C1   118.45  3.000
 SYC  C11   C3   C4   120.81  3.000
 SYC  C11   C3   N2   116.87  3.000
 SYC  C4    C3   N2   122.32  3.000
 SYC  H4    C4   C5   120.59  3.000
 SYC  H4    C4   C3   120.52  3.000
 SYC  C5    C4   C3   118.89  3.000
 SYC  H5    C5   C6   120.80  3.000
 SYC  H5    C5   C4   120.38  3.000
 SYC  C6    C5   C4   118.82  3.000
 SYC  H6    C6   C5   121.56  3.000
 SYC  H6    C6   C1   120.43  3.000
 SYC  C5    C6   C1   118.01  3.000
 SYC  H11A  C11  H11  107.73  3.000
 SYC  H11A  C11  P12  107.67  3.000
 SYC  H11   C11  P12  109.46  3.000
 SYC  H11A  C11  C3   109.84  3.000
 SYC  H11   C11  C3   111.43  3.000
 SYC  P12   C11  C3   110.60  3.000
 SYC  O17   P12  O16  106.87  3.000
 SYC  O17   P12  O15  116.58  3.000
 SYC  O16   P12  O15  109.20  3.000
 SYC  O17   P12  C11  100.74  3.000
 SYC  O16   P12  C11  106.77  3.000
 SYC  O15   P12  C11  115.83  3.000
 SYC  HO16  O16  P12  115.74  3.000
 SYC  HO17  O17  P12  114.36  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
 SYC  CONST_01  C4   C3   N2   C1    0.00   0.0  0
 SYC  CONST_02  C4   C5   C6   C1    0.00   0.0  0
 SYC  CONST_03  C5   C6   C1   N2    0.00   0.0  0
 SYC  CONST_04  C5   C4   C3   N2    0.00   0.0  0
 SYC  CONST_05  C6   C1   N2   C3    0.00   0.0  0
 SYC  CONST_06  C6   C5   C4   C3    0.00   0.0  0
 SYC  CONST_07  C11  C3   N2   C1  180.00   0.0  0
 SYC  CONST_08  C11  C3   C4   C5  180.00   0.0  0
 SYC  CONST_09  H5   C5   C6   C1  180.00   0.0  0
 SYC  CONST_10  H6   C6   C1   N2  180.00   0.0  0
 SYC  CONST_11  H4   C4   C3   N2  180.00   0.0  0
 SYC  CONST_12  H1   C1   N2   C3  180.00   0.0  0
 SYC  Var_01    P12  C11  C3   N2   92.03  30.0  2
 SYC  Var_02    O15  P12  C11  C3  -54.58  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
 SYC  plan-1  C1   0.020
 SYC  plan-1  N2   0.020
 SYC  plan-1  C3   0.020
 SYC  plan-1  C4   0.020
 SYC  plan-1  C5   0.020
 SYC  plan-1  C6   0.020
 SYC  plan-1  C11  0.020
 SYC  plan-1  H1   0.020
 SYC  plan-1  H4   0.020
 SYC  plan-1  H5   0.020
 SYC  plan-1  H6   0.020

