# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 10:08:15 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: (E)-N-{2-hydroxy-3-methyl-6-[(phosphonooxy)methyl]benzylidene}-L-aspartic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(CO[P](O)(O)=O)c(C=N[C@@H](CC(O)=O)C(O)=O)c1O
#
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
 3QP  3QP  '(E)-N-{2-hydroxy-3-methyl-6-[(phosphonooxy)methyl]benzylidene}-L-aspartic acid'  peptide  36  24  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_3QP
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
 3QP  C01   C  CH3    0  -0.665   0.5345   4.7770  -0.7924
 3QP  C02   C  CR6    0  -0.082  -0.0910   3.4691  -0.4102
 3QP  C03   C  CR6    0   0.295   0.7141   2.3558  -0.1286
 3QP  O04   O  OH1    0  -0.679   2.0367   2.5037  -0.2065
 3QP  C05   C  CR6    0   0.121   0.1347   1.1192   0.2263
 3QP  C06   C  CR6    0  -0.145  -1.2665   0.9963   0.3183
 3QP  C07   C  CH2    0  -0.156  -1.9019  -0.3109   0.7472
 3QP  O08   O  O2     0  -0.662  -3.2718  -0.2109   0.9365
 3QP  P09   P  P      0   1.217  -4.2816  -0.9878  -0.2102
 3QP  O10   O  OP    -1  -0.958  -3.8198  -0.4649  -1.5645
 3QP  O11   O  O      0  -0.857  -4.0214  -2.4767   0.0029
 3QP  O12   O  OP    -1  -0.921  -5.6473  -0.4990   0.2502
 3QP  C13   C  CR16   0  -0.249  -2.0515   2.0998   0.0340
 3QP  C14   C  CR16   0  -0.294  -1.4602   3.3085  -0.3236
 3QP  C15   C  C1     0  -0.123   0.9967  -0.0279   0.4656
 3QP  N16   N  N      0  -0.323   2.2645   0.0547   0.4206
 3QP  C17   C  CH1    0  -0.182   3.0614  -1.1255   0.6213
 3QP  C18   C  CH2    0  -0.590   3.8785  -1.3773  -0.6420
 3QP  C19   C  C      0   0.431   3.0238  -1.6523  -1.8921
 3QP  O20   O  O      0  -0.552   1.9817  -2.3292  -1.7302
 3QP  O21   O  OC    -1  -0.667   3.4490  -1.2178  -2.9828
 3QP  C22   C  C      0   0.395   3.9806  -0.9975   1.8671
 3QP  O23   O  O      0  -0.674   3.9237   0.0539   2.5288
 3QP  O24   O  OC    -1  -0.575   4.6787  -2.0038   2.0926
 3QP  H01   H  HCH3   0   0.278   1.1209   4.6984  -1.7111
 3QP  H01A  H  HCH3   0   0.220  -0.2308   5.5354  -0.9574
 3QP  H01B  H  HCH3   0   0.234   1.2076   5.1486  -0.0181
 3QP  HO04  H  HOH1   0   0.464   2.4515   1.6219   0.0374
 3QP  H07   H  HCH2   0   0.199  -1.6419  -1.0871   0.0142
 3QP  H07A  H  HCH2   0   0.226  -1.4342  -0.6284   1.6891
 3QP  H13   H  HCR6   0   0.258  -3.1267   2.0217   0.0912
 3QP  H14   H  HCR6   0   0.241  -2.0947   4.1610  -0.5402
 3QP  H15   H  H      0   0.220   0.5193  -0.9882   0.6756
 3QP  H17   H  HCH1   0   0.141   2.4092  -1.9978   0.7765
 3QP  H18   H  HCH2   0   0.213   4.5502  -0.5343  -0.8211
 3QP  H18A  H  HCH2   0   0.202   4.5128  -2.2495  -0.4629

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
 3QP  C02  C01   single    1.499  0.020  1.499
 3QP  C01  H01   single    0.970  0.020  1.090
 3QP  C01  H01A  single    0.970  0.020  1.090
 3QP  C01  H01B  single    0.970  0.020  1.090
 3QP  C14  C02   aromatic  1.381  0.020  1.381
 3QP  C03  C02   aromatic  1.402  0.020  1.402
 3QP  C05  C03   aromatic  1.411  0.020  1.411
 3QP  C03  O04   single    1.333  0.020  1.333
 3QP  O04  HO04  single    0.850  0.020  0.980
 3QP  C06  C05   aromatic  1.410  0.020  1.410
 3QP  C15  C05   single    1.455  0.020  1.455
 3QP  C07  C06   single    1.515  0.020  1.515
 3QP  C06  C13   aromatic  1.384  0.020  1.384
 3QP  O08  C07   single    1.386  0.020  1.386
 3QP  C07  H07   single    0.970  0.020  1.090
 3QP  C07  H07A  single    0.970  0.020  1.090
 3QP  P09  O08   single    1.714  0.020  1.714
 3QP  O11  P09   deloc     1.526  0.020  1.526
 3QP  O10  P09   deloc     1.523  0.020  1.523
 3QP  P09  O12   deloc     1.522  0.020  1.522
 3QP  C13  C14   aromatic  1.392  0.020  1.392
 3QP  C13  H13   single    0.930  0.020  1.080
 3QP  C14  H14   single    0.930  0.020  1.080
 3QP  C15  N16   double    1.271  0.020  1.271
 3QP  C15  H15   single    0.930  0.020  1.080
 3QP  C17  N16   single    1.438  0.020  1.438
 3QP  C18  C17   single    1.526  0.020  1.526
 3QP  C17  C22   single    1.553  0.020  1.553
 3QP  C17  H17   single    0.970  0.020  1.090
 3QP  C19  C18   single    1.539  0.020  1.539
 3QP  C18  H18   single    0.970  0.020  1.090
 3QP  C18  H18A  single    0.970  0.020  1.090
 3QP  O20  C19   deloc     1.253  0.020  1.253
 3QP  C19  O21   deloc     1.249  0.020  1.249
 3QP  O23  C22   deloc     1.244  0.020  1.244
 3QP  C22  O24   deloc     1.245  0.020  1.245

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
 3QP  H01B  C01  H01A  107.67  3.000
 3QP  H01B  C01  H01   106.86  3.000
 3QP  H01A  C01  H01   107.43  3.000
 3QP  H01B  C01  C02   111.93  3.000
 3QP  H01A  C01  C02   110.65  3.000
 3QP  H01   C01  C02   112.05  3.000
 3QP  C14   C02  C03   117.66  3.000
 3QP  C03   C02  C01   120.28  3.000
 3QP  C14   C02  C01   122.06  3.000
 3QP  C05   C03  O04   121.29  3.000
 3QP  O04   C03  C02   118.02  3.000
 3QP  C05   C03  C02   120.70  3.000
 3QP  HO04  O04  C03   107.34  3.000
 3QP  C15   C05  C06   120.63  3.000
 3QP  C15   C05  C03   119.28  3.000
 3QP  C06   C05  C03   120.07  3.000
 3QP  C13   C06  C07   120.54  3.000
 3QP  C13   C06  C05   118.75  3.000
 3QP  C07   C06  C05   120.70  3.000
 3QP  H07A  C07  H07   105.49  3.000
 3QP  H07A  C07  O08   108.93  3.000
 3QP  H07   C07  O08   112.08  3.000
 3QP  H07A  C07  C06   108.27  3.000
 3QP  H07   C07  C06   108.74  3.000
 3QP  O08   C07  C06   113.00  3.000
 3QP  P09   O08  C07   117.26  3.000
 3QP  O12   P09  O11   115.09  3.000
 3QP  O12   P09  O10   115.51  3.000
 3QP  O11   P09  O10   114.03  3.000
 3QP  O12   P09  O08   100.41  3.000
 3QP  O10   P09  O08   105.10  3.000
 3QP  O11   P09  O08   104.37  3.000
 3QP  H13   C13  C14   119.96  3.000
 3QP  H13   C13  C06   119.77  3.000
 3QP  C14   C13  C06   120.27  3.000
 3QP  H14   C14  C13   119.03  3.000
 3QP  H14   C14  C02   118.43  3.000
 3QP  C13   C14  C02   122.54  3.000
 3QP  H15   C15  N16   119.97  3.000
 3QP  H15   C15  C05   117.75  3.000
 3QP  N16   C15  C05   122.27  3.000
 3QP  C17   N16  C15   119.63  3.000
 3QP  H17   C17  C22   107.64  3.000
 3QP  H17   C17  C18   107.67  3.000
 3QP  C22   C17  C18   111.15  3.000
 3QP  H17   C17  N16   109.99  3.000
 3QP  C22   C17  N16   111.85  3.000
 3QP  C18   C17  N16   108.46  3.000
 3QP  H18A  C18  H18   106.60  3.000
 3QP  H18A  C18  C19   108.23  3.000
 3QP  H18   C18  C19   110.25  3.000
 3QP  H18A  C18  C17   107.87  3.000
 3QP  H18   C18  C17   109.73  3.000
 3QP  C19   C18  C17   113.87  3.000
 3QP  O21   C19  O20   125.73  3.000
 3QP  O21   C19  C18   117.27  3.000
 3QP  O20   C19  C18   116.96  3.000
 3QP  O24   C22  O23   127.77  3.000
 3QP  O24   C22  C17   114.22  3.000
 3QP  O23   C22  C17   117.99  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
 3QP  CONST_01  C06  C13  C14  C02    0.00   0.0  0
 3QP  CONST_02  C06  C05  C03  C02    0.00   0.0  0
 3QP  CONST_03  C13  C14  C02  C03    0.00   0.0  0
 3QP  CONST_04  C13  C06  C05  C03    0.00   0.0  0
 3QP  CONST_05  C14  C02  C03  C05    0.00   0.0  0
 3QP  CONST_06  C14  C13  C06  C05    0.00   0.0  0
 3QP  CONST_07  C13  C14  C02  C01  180.00   0.0  0
 3QP  CONST_08  C05  C03  C02  C01  180.00   0.0  0
 3QP  CONST_09  C15  C05  C03  C02  180.00   0.0  0
 3QP  CONST_10  C07  C06  C05  C03  180.00   0.0  0
 3QP  CONST_11  C14  C02  C03  O04  180.00   0.0  0
 3QP  CONST_12  C06  C05  C03  O04  180.00   0.0  0
 3QP  CONST_13  C14  C13  C06  C07  180.00   0.0  0
 3QP  CONST_14  C15  C05  C06  C13  180.00   0.0  0
 3QP  CONST_15  H13  C13  C14  C02  180.00   0.0  0
 3QP  CONST_16  H14  C14  C02  C03  180.00   0.0  0
 3QP  Var_01    N16  C15  C05  C03    2.97  30.0  2
 3QP  Var_02    O08  C07  C06  C05  172.81  30.0  1
 3QP  Var_03    H01  C01  C02  C03   61.20  30.0  2
 3QP  Var_04    O11  P09  O08  C07   67.22  30.0  3
 3QP  Var_05    O20  C19  C18  C17  -37.49  30.0  2

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
 3QP  chir_01  C17  N16  C18  C22  negativ

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
 3QP  plan-1  C01  0.020
 3QP  plan-1  C02  0.020
 3QP  plan-1  C03  0.020
 3QP  plan-1  O04  0.020
 3QP  plan-1  C05  0.020
 3QP  plan-1  C06  0.020
 3QP  plan-1  C07  0.020
 3QP  plan-1  C13  0.020
 3QP  plan-1  C14  0.020
 3QP  plan-1  C15  0.020
 3QP  plan-1  H13  0.020
 3QP  plan-1  H14  0.020
 3QP  plan-2  C18  0.020
 3QP  plan-2  C19  0.020
 3QP  plan-2  O20  0.020
 3QP  plan-2  O21  0.020
 3QP  plan-3  C17  0.020
 3QP  plan-3  C22  0.020
 3QP  plan-3  O23  0.020
 3QP  plan-3  O24  0.020
 3QP  plan-4  C05  0.020
 3QP  plan-4  C15  0.020
 3QP  plan-4  N16  0.020
 3QP  plan-4  C17  0.020
 3QP  plan-4  H15  0.020

