# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 24 05:46:33 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: benzyl 2-formylphenyl hydrogen (R)-phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P@](=O)(OCc1ccccc1)Oc2ccccc2C=O
#
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
 PSN  PSN  'benzyl 2-formylphenyl hydrogen (R)-phosphate'  ligand  33  20  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PSN
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
 PSN  C1    C  CR16  0  -0.237  17.3403  26.0377  21.5314
 PSN  C2    C  CR16  0  -0.243  17.4421  24.6979  21.1865
 PSN  C3    C  CR16  0  -0.290  16.9212  24.2743  19.9768
 PSN  C4    C  CR6   0  -0.067  16.3137  25.1664  19.0923
 PSN  C5    C  CR6   0   0.382  16.2497  26.5187  19.4465
 PSN  C6    C  CR16  0  -0.330  16.7442  26.9458  20.6664
 PSN  C7    C  C1    0   0.128  15.7368  24.5918  17.8677
 PSN  O8    O  O2    0  -0.618  15.6345  27.4424  18.6461
 PSN  P9    P  P     0   1.489  16.1650  28.0863  17.2650
 PSN  O10   O  O2    0  -0.566  16.7369  29.5262  17.6457
 PSN  O11   O  O     0  -0.674  15.1004  28.2486  16.2658
 PSN  C12   C  CH2   0  -0.258  17.7998  29.7935  18.5719
 PSN  C13   C  CR6   0   0.045  19.1315  29.2905  18.0942
 PSN  C16   C  CR16  0  -0.277  19.8685  28.4034  18.8695
 PSN  C17   C  CR16  0  -0.242  21.1022  27.9396  18.4307
 PSN  C18   C  CR16  0  -0.260  21.6019  28.3513  17.2036
 PSN  C19   C  CR16  0  -0.240  20.8682  29.2354  16.4206
 PSN  C20   C  CR16  0  -0.292  19.6417  29.7065  16.8656
 PSN  O32   O  OH1   0  -0.738  17.4025  27.1417  16.9487
 PSN  O25   O  O     0  -0.374  15.1449  25.1946  17.0050
 PSN  H1    H  HCR6  0   0.281  17.7260  26.3872  22.4796
 PSN  H2    H  HCR6  0   0.273  17.9093  23.9917  21.8586
 PSN  H3    H  HCR6  0   0.279  16.9751  23.2271  19.7028
 PSN  H6    H  HCR6  0   0.291  16.6539  27.9859  20.9516
 PSN  H7    H  H     0   0.208  15.8794  23.4990  17.7943
 PSN  H121  H  HCH2  0   0.250  17.5645  29.3841  19.5554
 PSN  H122  H  HCH2  0   0.275  17.8105  30.8788  18.6692
 PSN  H16   H  HCR6  0   0.253  19.4751  28.0640  19.8205
 PSN  H17   H  HCR6  0   0.261  21.6661  27.2486  19.0435
 PSN  H18   H  HCR6  0   0.260  22.5599  27.9857  16.8578
 PSN  H19   H  HCR6  0   0.261  21.2545  29.5621  15.4639
 PSN  H20   H  HCR6  0   0.264  19.0804  30.4014  16.2520
 PSN  H32   H  HOH1  0   0.504  18.0048  27.4553  16.2600

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
 PSN  C1   C2    aromatic  1.387  0.020  1.387
 PSN  C1   C6    aromatic  1.389  0.020  1.389
 PSN  C1   H1    single    0.930  0.020  1.080
 PSN  C2   C3    aromatic  1.383  0.020  1.383
 PSN  C2   H2    single    0.930  0.020  1.080
 PSN  C3   C4    aromatic  1.395  0.020  1.395
 PSN  C3   H3    single    0.930  0.020  1.080
 PSN  C4   C5    aromatic  1.399  0.020  1.399
 PSN  C4   C7    single    1.471  0.020  1.471
 PSN  C5   C6    aromatic  1.384  0.020  1.384
 PSN  C5   O8    single    1.368  0.020  1.368
 PSN  C6   H6    single    0.930  0.020  1.080
 PSN  C7   O25   double    1.207  0.020  1.207
 PSN  C7   H7    single    0.930  0.020  1.080
 PSN  O8   P9    single    1.614  0.020  1.614
 PSN  P9   O10   single    1.595  0.020  1.595
 PSN  P9   O11   double    1.469  0.020  1.469
 PSN  P9   O32   single    1.589  0.020  1.589
 PSN  O10  C12   single    1.435  0.020  1.435
 PSN  C12  C13   single    1.502  0.020  1.502
 PSN  C12  H121  single    0.970  0.020  1.090
 PSN  C12  H122  single    0.970  0.020  1.090
 PSN  C13  C16   aromatic  1.390  0.020  1.390
 PSN  C13  C20   aromatic  1.394  0.020  1.394
 PSN  C16  C17   aromatic  1.389  0.020  1.389
 PSN  C16  H16   single    0.930  0.020  1.080
 PSN  C17  C18   aromatic  1.387  0.020  1.387
 PSN  C17  H17   single    0.930  0.020  1.080
 PSN  C18  C19   aromatic  1.390  0.020  1.390
 PSN  C18  H18   single    0.930  0.020  1.080
 PSN  C19  C20   aromatic  1.387  0.020  1.387
 PSN  C19  H19   single    0.930  0.020  1.080
 PSN  C20  H20   single    0.930  0.020  1.080
 PSN  O32  H32   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
 PSN  H1    C1   C6    119.20  3.000
 PSN  H1    C1   C2    120.25  3.000
 PSN  C6    C1   C2    120.54  3.000
 PSN  H2    C2   C3    120.42  3.000
 PSN  H2    C2   C1    120.53  3.000
 PSN  C3    C2   C1    119.04  3.000
 PSN  H3    C3   C4    118.63  3.000
 PSN  H3    C3   C2    119.88  3.000
 PSN  C4    C3   C2    121.49  3.000
 PSN  C7    C4   C5    124.78  3.000
 PSN  C7    C4   C3    116.67  3.000
 PSN  C5    C4   C3    118.51  3.000
 PSN  O8    C5   C6    117.90  3.000
 PSN  O8    C5   C4    121.66  3.000
 PSN  C6    C5   C4    120.33  3.000
 PSN  H6    C6   C5    119.94  3.000
 PSN  H6    C6   C1    120.01  3.000
 PSN  C5    C6   C1    120.04  3.000
 PSN  H7    C7   O25   120.65  3.000
 PSN  H7    C7   C4    113.03  3.000
 PSN  O25   C7   C4    126.31  3.000
 PSN  P9    O8   C5    128.48  3.000
 PSN  O32   P9   O11   119.65  3.000
 PSN  O32   P9   O10   107.75  3.000
 PSN  O11   P9   O10   108.81  3.000
 PSN  O32   P9   O8    100.91  3.000
 PSN  O11   P9   O8    112.83  3.000
 PSN  O10   P9   O8    105.89  3.000
 PSN  C12   O10  P9    125.99  3.000
 PSN  H122  C12  H121  107.18  3.000
 PSN  H122  C12  C13   110.69  3.000
 PSN  H121  C12  C13   110.64  3.000
 PSN  H122  C12  O10   104.50  3.000
 PSN  H121  C12  O10   110.62  3.000
 PSN  C13   C12  O10   112.90  3.000
 PSN  C20   C13  C16   119.22  3.000
 PSN  C20   C13  C12   120.34  3.000
 PSN  C16   C13  C12   120.44  3.000
 PSN  H16   C16  C17   119.67  3.000
 PSN  H16   C16  C13   119.80  3.000
 PSN  C17   C16  C13   120.52  3.000
 PSN  H17   C17  C18   120.18  3.000
 PSN  H17   C17  C16   119.81  3.000
 PSN  C18   C17  C16   120.01  3.000
 PSN  H18   C18  C19   120.13  3.000
 PSN  H18   C18  C17   120.08  3.000
 PSN  C19   C18  C17   119.79  3.000
 PSN  H19   C19  C20   119.78  3.000
 PSN  H19   C19  C18   120.10  3.000
 PSN  C20   C19  C18   120.12  3.000
 PSN  H20   C20  C19   119.61  3.000
 PSN  H20   C20  C13   120.06  3.000
 PSN  C19   C20  C13   120.33  3.000
 PSN  H32   O32  P9    115.73  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
 PSN  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 PSN  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 PSN  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 PSN  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 PSN  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 PSN  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 PSN  CONST_07  C18  C17  C16  C13     0.00   0.0  0
 PSN  CONST_08  C18  C19  C20  C13     0.00   0.0  0
 PSN  CONST_09  C19  C20  C13  C16     0.00   0.0  0
 PSN  CONST_10  C19  C18  C17  C16     0.00   0.0  0
 PSN  CONST_11  C20  C13  C16  C17     0.00   0.0  0
 PSN  CONST_12  C20  C19  C18  C17     0.00   0.0  0
 PSN  CONST_13  O8   C5   C6   C1    180.00   0.0  0
 PSN  CONST_14  C7   C4   C3   C2    180.00   0.0  0
 PSN  CONST_15  O8   C5   C4   C3    180.00   0.0  0
 PSN  CONST_16  C7   C4   C5   C6    180.00   0.0  0
 PSN  CONST_17  C17  C16  C13  C12   180.00   0.0  0
 PSN  CONST_18  C19  C20  C13  C12   180.00   0.0  0
 PSN  CONST_19  H3   C3   C2   C1    180.00   0.0  0
 PSN  CONST_20  H6   C6   C1   C2    180.00   0.0  0
 PSN  CONST_21  H1   C1   C2   C3    180.00   0.0  0
 PSN  CONST_22  H2   C2   C3   C4    180.00   0.0  0
 PSN  CONST_23  H17  C17  C16  C13   180.00   0.0  0
 PSN  CONST_24  H19  C19  C20  C13   180.00   0.0  0
 PSN  CONST_25  H20  C20  C13  C16   180.00   0.0  0
 PSN  CONST_26  H18  C18  C17  C16   180.00   0.0  0
 PSN  CONST_27  H16  C16  C17  C18   180.00   0.0  0
 PSN  Var_01    O25  C7   C4   C3    178.02  30.0  2
 PSN  Var_02    C16  C13  C12  O10  -123.37  30.0  2
 PSN  Var_03    O10  P9   O8   C5   -100.57  30.0  3
 PSN  Var_04    C13  C12  O10  P9     67.19  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 PSN  chir_01  P9  O10  O11  O32  both

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
 PSN  plan-1  C1   0.020
 PSN  plan-1  C2   0.020
 PSN  plan-1  C3   0.020
 PSN  plan-1  C4   0.020
 PSN  plan-1  C5   0.020
 PSN  plan-1  C6   0.020
 PSN  plan-1  C7   0.020
 PSN  plan-1  O8   0.020
 PSN  plan-1  H1   0.020
 PSN  plan-1  H2   0.020
 PSN  plan-1  H3   0.020
 PSN  plan-1  H6   0.020
 PSN  plan-2  C12  0.020
 PSN  plan-2  C13  0.020
 PSN  plan-2  C16  0.020
 PSN  plan-2  C17  0.020
 PSN  plan-2  C18  0.020
 PSN  plan-2  C19  0.020
 PSN  plan-2  C20  0.020
 PSN  plan-2  H16  0.020
 PSN  plan-2  H17  0.020
 PSN  plan-2  H18  0.020
 PSN  plan-2  H19  0.020
 PSN  plan-2  H20  0.020
 PSN  plan-3  C4   0.020
 PSN  plan-3  C7   0.020
 PSN  plan-3  O25  0.020
 PSN  plan-3  H7   0.020

