# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 06:54:25 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  40  24  .  2022-09-22  2022-11-17
;
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  -0.708   0.6927   4.9107  -0.5334
 3QP  C02   C  CR6   0  -0.014   0.0048   3.5960  -0.3247
 3QP  C03   C  CR6   0   0.345   0.7581   2.4348  -0.0879
 3QP  O04   O  OH1   0  -0.626   2.0810   2.5560  -0.0517
 3QP  C05   C  CR6   0  -0.112   0.1231   1.1904   0.1046
 3QP  C06   C  CR6   0  -0.001  -1.2848   1.1094   0.0633
 3QP  C07   C  CH2   0  -0.213  -1.9490  -0.2267   0.2717
 3QP  O08   O  O2    0  -0.592  -3.3619  -0.0670   0.2601
 3QP  P09   P  P     0   1.463  -4.2880  -1.3700   0.2021
 3QP  O10   O  OH1   0  -0.739  -4.2207  -1.9148  -1.2975
 3QP  O11   O  O     0  -0.708  -3.9467  -2.4554   1.1394
 3QP  O12   O  OH1   0  -0.728  -5.6779  -0.6187   0.3931
 3QP  C13   C  CR16  0  -0.329  -2.0197   2.2531  -0.1672
 3QP  C14   C  CR16  0  -0.272  -1.3697   3.4735  -0.3580
 3QP  C15   C  C1    0   0.069   0.9274   0.0004   0.3327
 3QP  N16   N  N     0  -0.462   2.1993   0.0451   0.3718
 3QP  C17   C  CH1   0  -0.246   2.9359  -1.1721   0.5711
 3QP  C18   C  CH2   0  -0.582   3.8388  -1.4207  -0.6364
 3QP  C19   C  C     0   0.564   3.0425  -1.6697  -1.8903
 3QP  O20   O  O     0  -0.435   1.8945  -2.0350  -1.9138
 3QP  O21   O  OH1   0  -0.590   3.7725  -1.4735  -2.9796
 3QP  C22   C  C     0   0.568   3.7552  -1.0462   1.8458
 3QP  O23   O  O     0  -0.419   3.7331  -0.0939   2.5778
 3QP  O24   O  OH1   0  -0.590   4.4777  -2.1352   2.0609
 3QP  H01   H  HCH3  0   0.244   1.3448   4.8913  -1.4085
 3QP  H01A  H  HCH3  0   0.243  -0.0369   5.7056  -0.6810
 3QP  H01B  H  HCH3  0   0.243   1.3144   5.1832   0.3211
 3QP  HO04  H  HOH1  0   0.469   2.4677   1.6521   0.1308
 3QP  H07   H  HCH2  0   0.255  -1.6396  -0.9195  -0.5184
 3QP  H07A  H  HCH2  0   0.265  -1.6425  -0.6605   1.2274
 3QP  HO10  H  HOH1  0   0.497  -4.4606  -1.2825  -1.9885
 3QP  HO12  H  HOH1  0   0.506  -6.4332  -1.2119   0.5067
 3QP  H13   H  HCR6  0   0.256  -3.0984   2.2239  -0.2047
 3QP  H14   H  HCR6  0   0.256  -1.9677   4.3587  -0.5390
 3QP  H15   H  H     0   0.258   0.4105  -0.9499   0.4756
 3QP  H17   H  HCH1  0   0.285   2.2678  -2.0349   0.7048
 3QP  H18   H  HCH2  0   0.295   4.5197  -0.5799  -0.7828
 3QP  H18A  H  HCH2  0   0.313   4.4641  -2.3030  -0.4749
 3QP  HO21  H  HOH1  0   0.483   3.2507  -1.6765  -3.7707
 3QP  HO24  H  HOH1  0   0.489   4.9815  -2.0496   2.8847

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    1.498  0.020  1.498
 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  1.380  0.020  1.380
 3QP  C03  C02   aromatic  1.404  0.020  1.404
 3QP  C05  C03   aromatic  1.410  0.020  1.410
 3QP  C03  O04   single    1.329  0.020  1.329
 3QP  O04  HO04  single    0.850  0.020  0.980
 3QP  C06  C05   aromatic  1.411  0.020  1.411
 3QP  C15  C05   single    1.454  0.020  1.454
 3QP  C07  C06   single    1.507  0.020  1.507
 3QP  C06  C13   aromatic  1.379  0.020  1.379
 3QP  O08  C07   single    1.422  0.020  1.422
 3QP  C07  H07   single    0.970  0.020  1.090
 3QP  C07  H07A  single    0.970  0.020  1.090
 3QP  P09  O08   single    1.600  0.020  1.600
 3QP  O11  P09   double    1.474  0.020  1.474
 3QP  O10  P09   single    1.597  0.020  1.597
 3QP  P09  O12   single    1.591  0.020  1.591
 3QP  O10  HO10  single    0.850  0.020  0.980
 3QP  O12  HO12  single    0.850  0.020  0.980
 3QP  C13  C14   aromatic  1.396  0.020  1.396
 3QP  C13  H13   single    0.930  0.020  1.080
 3QP  C14  H14   single    0.930  0.020  1.080
 3QP  C15  N16   double    1.273  0.020  1.273
 3QP  C15  H15   single    0.930  0.020  1.080
 3QP  C17  N16   single    1.437  0.020  1.437
 3QP  C18  C17   single    1.528  0.020  1.528
 3QP  C17  C22   single    1.520  0.020  1.520
 3QP  C17  H17   single    0.970  0.020  1.090
 3QP  C19  C18   single    1.506  0.020  1.506
 3QP  C18  H18   single    0.970  0.020  1.090
 3QP  C18  H18A  single    0.970  0.020  1.090
 3QP  O20  C19   double    1.205  0.020  1.205
 3QP  C19  O21   single    1.326  0.020  1.326
 3QP  O21  HO21  single    0.850  0.020  0.980
 3QP  O23  C22   double    1.201  0.020  1.201
 3QP  C22  O24   single    1.324  0.020  1.324
 3QP  O24  HO24  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
 3QP  H01B  C01  H01A  107.79  3.000
 3QP  H01B  C01  H01   106.97  3.000
 3QP  H01A  C01  H01   107.73  3.000
 3QP  H01B  C01  C02   111.82  3.000
 3QP  H01A  C01  C02   110.59  3.000
 3QP  H01   C01  C02   111.73  3.000
 3QP  C14   C02  C03   117.70  3.000
 3QP  C03   C02  C01   120.18  3.000
 3QP  C14   C02  C01   122.12  3.000
 3QP  C05   C03  O04   121.67  3.000
 3QP  O04   C03  C02   117.59  3.000
 3QP  C05   C03  C02   120.74  3.000
 3QP  HO04  O04  C03   107.91  3.000
 3QP  C15   C05  C06   120.63  3.000
 3QP  C15   C05  C03   119.63  3.000
 3QP  C06   C05  C03   119.73  3.000
 3QP  C13   C06  C07   121.58  3.000
 3QP  C13   C06  C05   119.29  3.000
 3QP  C07   C06  C05   119.13  3.000
 3QP  H07A  C07  H07   107.48  3.000
 3QP  H07A  C07  O08   109.28  3.000
 3QP  H07   C07  O08   110.23  3.000
 3QP  H07A  C07  C06   110.43  3.000
 3QP  H07   C07  C06   109.67  3.000
 3QP  O08   C07  C06   109.71  3.000
 3QP  P09   O08  C07   118.95  3.000
 3QP  O12   P09  O11   118.26  3.000
 3QP  O12   P09  O10   108.09  3.000
 3QP  O11   P09  O10   109.64  3.000
 3QP  O12   P09  O08    96.70  3.000
 3QP  O10   P09  O08   106.71  3.000
 3QP  O11   P09  O08   116.27  3.000
 3QP  HO10  O10  P09   115.95  3.000
 3QP  HO12  O12  P09   113.99  3.000
 3QP  H13   C13  C14   118.95  3.000
 3QP  H13   C13  C06   121.06  3.000
 3QP  C14   C13  C06   119.99  3.000
 3QP  H14   C14  C13   118.70  3.000
 3QP  H14   C14  C02   118.75  3.000
 3QP  C13   C14  C02   122.55  3.000
 3QP  H15   C15  N16   119.98  3.000
 3QP  H15   C15  C05   118.11  3.000
 3QP  N16   C15  C05   121.91  3.000
 3QP  C17   N16  C15   119.13  3.000
 3QP  H17   C17  C22   106.88  3.000
 3QP  H17   C17  C18   109.12  3.000
 3QP  C22   C17  C18   110.95  3.000
 3QP  H17   C17  N16   111.73  3.000
 3QP  C22   C17  N16   108.81  3.000
 3QP  C18   C17  N16   109.34  3.000
 3QP  H18A  C18  H18   106.53  3.000
 3QP  H18A  C18  C19   106.97  3.000
 3QP  H18   C18  C19   110.21  3.000
 3QP  H18A  C18  C17   110.64  3.000
 3QP  H18   C18  C17   110.44  3.000
 3QP  C19   C18  C17   111.86  3.000
 3QP  O21   C19  O20   123.60  3.000
 3QP  O21   C19  C18   111.62  3.000
 3QP  O20   C19  C18   124.76  3.000
 3QP  HO21  O21  C19   110.07  3.000
 3QP  O24   C22  O23   124.25  3.000
 3QP  O24   C22  C17   111.23  3.000
 3QP  O23   C22  C17   124.51  3.000
 3QP  HO24  O24  C22   110.42  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  CONST_17  HO24  O24  C22  C17  180.00   0.0  0
 3QP  CONST_18  HO21  O21  C19  C18  180.00   0.0  0
 3QP  Var_01    N16   C15  C05  C03    0.36  30.0  2
 3QP  Var_02    O08   C07  C06  C05  176.96  30.0  2
 3QP  Var_03    H01   C01  C02  C03   61.26  30.0  2
 3QP  Var_04    O11   P09  O08  C07   47.29  30.0  3
 3QP  Var_05    O20   C19  C18  C17  -21.28  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-2  HO21  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-3  HO24  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

