# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 28 00:39:16 2020
#   Inital geometry file: a 67 line input string
#   Ligand name: (quinolin-2-ylmethyl)phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P](O)(=O)Cc1ccc2ccccc2n1
#
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
 SYE  SYE  '(quinolin-2-ylmethyl)phosphonic acid'  ligand  25  15  .  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_SYE
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
 SYE  C1    C  CR16  0  -0.257   3.9918  -1.4180   0.1824
 SYE  C2    C  CR16  0  -0.296   2.6946  -1.5930  -0.2179
 SYE  C3    C  CR66  0   0.197   1.8141  -0.4893  -0.2833
 SYE  C4    C  CR66  0   0.080   2.2955   0.7950   0.0698
 SYE  C5    C  CR16  0  -0.312   3.6387   0.9477   0.4784
 SYE  C6    C  CR16  0  -0.255   4.4702  -0.1380   0.5336
 SYE  N11   N  N     0  -0.433   0.5379  -0.6986  -0.6839
 SYE  C12   C  CR6   0   0.224  -0.2810   0.3174  -0.7482
 SYE  C13   C  CR16  0  -0.322   0.1056   1.6392  -0.4172
 SYE  C14   C  CR16  0  -0.182   1.3870   1.8726  -0.0130
 SYE  C17   C  CH2   0  -0.831  -1.6932   0.0370  -1.1734
 SYE  P18   P  P     0   1.369  -2.7356  -0.2592   0.2755
 SYE  O21   O  O     0  -0.705  -2.2542  -1.3059   1.2045
 SYE  O22   O  OH1   0  -0.744  -2.8415   1.1377   1.0659
 SYE  O23   O  OH1   0  -0.743  -4.1574  -0.5117  -0.4250
 SYE  H1    H  HCR6  0   0.264   4.6607  -2.2671   0.2323
 SYE  H2    H  HCR6  0   0.261   2.3190  -2.5713  -0.4892
 SYE  H5    H  HCR6  0   0.263   3.9989   1.9332   0.7469
 SYE  H6    H  HCR6  0   0.264   5.4989  -0.0195   0.8474
 SYE  H13   H  HCR6  0   0.269  -0.6079   2.4481  -0.4950
 SYE  H14   H  HCR6  0   0.274   1.7151   2.8725   0.2433
 SYE  H17   H  HCH2  0   0.313  -2.1086   0.8629  -1.7544
 SYE  H17A  H  HCH2  0   0.318  -1.7232  -0.8602  -1.7935
 SYE  HO22  H  HOH1  0   0.490  -3.2658   1.8625   0.5888
 SYE  HO23  H  HOH1  0   0.497  -4.8601  -0.7766   0.1851

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
 SYE  C1   C2    aromatic  1.369  0.020  1.369
 SYE  C1   C6    aromatic  1.411  0.020  1.411
 SYE  C2   C3    aromatic  1.413  0.020  1.413
 SYE  C3   C4    aromatic  1.416  0.020  1.416
 SYE  C3   N11   aromatic  1.354  0.020  1.354
 SYE  C4   C5    aromatic  1.412  0.020  1.412
 SYE  C4   C14   aromatic  1.412  0.020  1.412
 SYE  C5   C6    aromatic  1.369  0.020  1.369
 SYE  N11  C12   aromatic  1.307  0.020  1.307
 SYE  C12  C13   aromatic  1.416  0.020  1.416
 SYE  C12  C17   single    1.501  0.020  1.501
 SYE  C13  C14   aromatic  1.364  0.020  1.364
 SYE  C17  P18   single    1.809  0.020  1.809
 SYE  P18  O21   double    1.480  0.020  1.480
 SYE  P18  O22   single    1.608  0.020  1.608
 SYE  P18  O23   single    1.605  0.020  1.605
 SYE  C1   H1    single    0.930  0.020  1.080
 SYE  C2   H2    single    0.930  0.020  1.080
 SYE  C5   H5    single    0.930  0.020  1.080
 SYE  C6   H6    single    0.930  0.020  1.080
 SYE  C13  H13   single    0.930  0.020  1.080
 SYE  C14  H14   single    0.930  0.020  1.080
 SYE  C17  H17   single    0.970  0.020  1.090
 SYE  C17  H17A  single    0.970  0.020  1.090
 SYE  O22  HO22  single    0.850  0.020  0.980
 SYE  O23  HO23  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
 SYE  H1    C1   C6   119.40  3.000
 SYE  H1    C1   C2   119.93  3.000
 SYE  C6    C1   C2   120.67  3.000
 SYE  H2    C2   C3   118.56  3.000
 SYE  H2    C2   C1   121.17  3.000
 SYE  C3    C2   C1   120.27  3.000
 SYE  N11   C3   C4   122.30  3.000
 SYE  N11   C3   C2   118.70  3.000
 SYE  C4    C3   C2   119.00  3.000
 SYE  C14   C4   C5   123.12  3.000
 SYE  C14   C4   C3   117.31  3.000
 SYE  C5    C4   C3   119.57  3.000
 SYE  H5    C5   C6   120.64  3.000
 SYE  H5    C5   C4   119.11  3.000
 SYE  C6    C5   C4   120.25  3.000
 SYE  H6    C6   C5   120.16  3.000
 SYE  H6    C6   C1   119.60  3.000
 SYE  C5    C6   C1   120.24  3.000
 SYE  C12   N11  C3   119.02  3.000
 SYE  C17   C12  C13  119.82  3.000
 SYE  C17   C12  N11  117.28  3.000
 SYE  C13   C12  N11  122.89  3.000
 SYE  H13   C13  C14  120.88  3.000
 SYE  H13   C13  C12  120.07  3.000
 SYE  C14   C13  C12  119.05  3.000
 SYE  H14   C14  C13  120.85  3.000
 SYE  H14   C14  C4   119.72  3.000
 SYE  C13   C14  C4   119.43  3.000
 SYE  H17A  C17  H17  108.01  3.000
 SYE  H17A  C17  P18  107.74  3.000
 SYE  H17   C17  P18  109.31  3.000
 SYE  H17A  C17  C12  109.91  3.000
 SYE  H17   C17  C12  111.55  3.000
 SYE  P18   C17  C12  110.22  3.000
 SYE  O23   P18  O22  107.02  3.000
 SYE  O23   P18  O21  116.80  3.000
 SYE  O22   P18  O21  109.10  3.000
 SYE  O23   P18  C17  100.76  3.000
 SYE  O22   P18  C17  106.82  3.000
 SYE  O21   P18  C17  115.54  3.000
 SYE  HO22  O22  P18  115.97  3.000
 SYE  HO23  O23  P18  114.28  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
 SYE  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 SYE  CONST_02  N11  C3   C2   C1   180.00   0.0  0
 SYE  CONST_03  C4   C5   C6   C1     0.00   0.0  0
 SYE  CONST_04  C5   C6   C1   C2     0.00   0.0  0
 SYE  CONST_05  C5   C4   C3   C2     0.00   0.0  0
 SYE  CONST_06  C14  C4   C3   C2   180.00   0.0  0
 SYE  CONST_07  C12  N11  C3   C2   180.00   0.0  0
 SYE  CONST_08  C6   C1   C2   C3     0.00   0.0  0
 SYE  CONST_09  C6   C5   C4   C3     0.00   0.0  0
 SYE  CONST_10  C13  C14  C4   C3     0.00   0.0  0
 SYE  CONST_11  C13  C12  N11  C3     0.00   0.0  0
 SYE  CONST_12  C12  N11  C3   C4     0.00   0.0  0
 SYE  CONST_13  C12  C13  C14  C4     0.00   0.0  0
 SYE  CONST_14  N11  C3   C4   C5   180.00   0.0  0
 SYE  CONST_15  C13  C14  C4   C5   180.00   0.0  0
 SYE  CONST_16  C14  C4   C5   C6   180.00   0.0  0
 SYE  CONST_17  C14  C4   C3   N11    0.00   0.0  0
 SYE  CONST_18  C14  C13  C12  N11    0.00   0.0  0
 SYE  CONST_19  C17  C12  N11  C3   180.00   0.0  0
 SYE  CONST_20  C17  C12  C13  C14  180.00   0.0  0
 SYE  CONST_21  H5   C5   C6   C1   180.00   0.0  0
 SYE  CONST_22  H6   C6   C1   C2   180.00   0.0  0
 SYE  CONST_23  H1   C1   C2   C3   180.00   0.0  0
 SYE  CONST_24  H14  C14  C4   C3   180.00   0.0  0
 SYE  CONST_25  H2   C2   C3   C4   180.00   0.0  0
 SYE  CONST_26  H13  C13  C14  C4   180.00   0.0  0
 SYE  Var_01    P18  C17  C12  N11   92.47  30.0  2
 SYE  Var_02    O21  P18  C17  C12  -53.75  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
 SYE  plan-1  C1   0.020
 SYE  plan-1  C2   0.020
 SYE  plan-1  C3   0.020
 SYE  plan-1  C4   0.020
 SYE  plan-1  C5   0.020
 SYE  plan-1  C6   0.020
 SYE  plan-1  N11  0.020
 SYE  plan-1  C12  0.020
 SYE  plan-1  C13  0.020
 SYE  plan-1  C14  0.020
 SYE  plan-1  C17  0.020
 SYE  plan-1  H1   0.020
 SYE  plan-1  H2   0.020
 SYE  plan-1  H5   0.020
 SYE  plan-1  H6   0.020
 SYE  plan-1  H13  0.020
 SYE  plan-1  H14  0.020

