# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 04:57:49 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-3-[(2-hydroxyphenyl)amino]-D-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(CN[C@H](CNc2ccccc2O)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
 AQ3  AQ3  N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-3-[(2-hydroxyphenyl)amino]-D-alanine  ligand  51  29  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_AQ3
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
 AQ3  O    O  OH1   0  -0.638  -5.2487   1.1517  -0.5608
 AQ3  C2   C  CR6   0   0.281  -5.3472   0.2033   0.4009
 AQ3  C3   C  CR16  0  -0.378  -6.3760   0.1687   1.3247
 AQ3  C4   C  CR16  0  -0.278  -6.4254  -0.8295   2.2950
 AQ3  C5   C  CR16  0  -0.273  -5.4381  -1.7964   2.3228
 AQ3  C6   C  CR16  0  -0.344  -4.4072  -1.7740   1.3864
 AQ3  C1   C  CR6   0   0.290  -4.3330  -0.7765   0.4174
 AQ3  N    N  NH1   0  -0.696  -3.3027  -0.6726  -0.5070
 AQ3  O3P  O  OH1   0  -0.730   5.3237  -0.9845   2.3509
 AQ3  P    P  P     0   1.464   4.3565  -1.5084   1.1981
 AQ3  O1P  O  O     0  -0.710   4.9703  -2.1653   0.0300
 AQ3  O2P  O  OH1   0  -0.740   3.2820  -2.4858   1.8614
 AQ3  O4P  O  O2    0  -0.594   3.6192  -0.1173   0.9307
 AQ3  C51  C  CR6   0  -0.061   2.0924   1.3680  -0.1516
 AQ3  C61  C  CR16  0  -0.138   2.6340   2.4058   0.5894
 AQ3  N1   N  N     0  -0.407   2.1667   3.6489   0.5457
 AQ3  C41  C  CR6   0   0.069   1.0080   1.6445  -0.9889
 AQ3  C31  C  CR6   0   0.251   0.5239   2.9477  -1.0162
 AQ3  O3   O  OH1   0  -0.620  -0.5377   3.2165  -1.8008
 AQ3  C21  C  CR6   0   0.127   1.1372   3.9366  -0.2320
 AQ3  C2A  C  CH3   0  -0.786   0.6400   5.3511  -0.2571
 AQ3  N2   N  NH1   0  -0.587  -0.5010  -0.2412  -0.9077
 AQ3  CA   C  CH1   0  -0.211  -1.2184  -1.2935  -1.5792
 AQ3  C    C  C     0   0.542  -0.3094  -2.4814  -1.8500
 AQ3  OXT  O  OH1   0  -0.592  -0.8251  -3.2765  -2.7795
 AQ3  O1   O  O     0  -0.417   0.7314  -2.7000  -1.2877
 AQ3  CB   C  CH2   0  -0.279  -2.3785  -1.7647  -0.6928
 AQ3  H1   H  HOH1  0   0.476  -6.0197   1.7289  -0.5394
 AQ3  H2   H  HCR6  0   0.266  -7.1459   0.9318   1.2916
 AQ3  H3   H  HCR6  0   0.250  -7.2342  -0.8414   3.0130
 AQ3  H4   H  HCR6  0   0.248  -5.4620  -2.5841   3.0642
 AQ3  H5   H  HCR6  0   0.265  -3.6590  -2.5540   1.4226
 AQ3  H6   H  HNH1  0   0.379  -3.5946  -0.2564  -1.3803
 AQ3  H7   H  HOH1  0   0.504   5.9953  -1.6259   2.6191
 AQ3  H8   H  HOH1  0   0.496   2.8625  -2.1644   2.6710
 AQ3  H9   H  HCH2  0   0.254   3.0999  -0.2798  -1.0653
 AQ3  H10  H  HCH2  0   0.270   1.8292  -0.7387   0.0696
 AQ3  H11  H  HCR6  0   0.257   3.4757   2.2413   1.2496
 AQ3  H12  H  HOH1  0   0.486  -0.7853   4.1460  -1.7494
 AQ3  H13  H  HCH3  0   0.255  -0.4120   5.4262   0.0302
 AQ3  H14  H  HCH3  0   0.272   1.2131   5.9555   0.4418
 AQ3  H15  H  HCH3  0   0.259   0.7435   5.8031  -1.2471
 AQ3  H16  H  HCH2  0   0.248  -0.2071   0.9725  -2.6350
 AQ3  H17  H  HCH2  0   0.250   1.1109  -0.0936  -2.2213
 AQ3  H18  H  HNH1  0   0.362  -1.1790   0.3644  -0.4598
 AQ3  H20  H  HCH1  0   0.253  -1.6374  -0.9751  -2.5495
 AQ3  H21  H  HOH1  0   0.484  -0.2574  -4.0512  -2.9082
 AQ3  H22  H  HCH2  0   0.251  -1.9650  -2.0572   0.2746
 AQ3  H23  H  HCH2  0   0.248  -2.8545  -2.6517  -1.1273
 AQ3  C4A  C  CH2   0  -0.363   0.3448   0.5529  -1.7860
 AQ3  C5A  C  CH2   0  -0.215   2.6414  -0.0279  -0.1034

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
 AQ3  O1   C    double    1.203  0.020  1.203
 AQ3  OXT  C    single    1.327  0.020  1.327
 AQ3  C    CA   single    1.520  0.020  1.520
 AQ3  O3   C31  single    1.347  0.020  1.347
 AQ3  C2A  C21  single    1.500  0.020  1.500
 AQ3  CA   N2   single    1.440  0.020  1.440
 AQ3  CA   CB   single    1.534  0.020  1.534
 AQ3  N2   C4A  single    1.455  0.020  1.455
 AQ3  O    C2   single    1.354  0.020  1.354
 AQ3  C31  C21  aromatic  1.403  0.020  1.403
 AQ3  C31  C41  aromatic  1.391  0.020  1.391
 AQ3  C21  N1   aromatic  1.322  0.020  1.322
 AQ3  N    CB   single    1.443  0.020  1.443
 AQ3  N    C1   single    1.388  0.020  1.388
 AQ3  C4A  C41  single    1.506  0.020  1.506
 AQ3  C41  C51  aromatic  1.398  0.020  1.398
 AQ3  C2   C1   aromatic  1.410  0.020  1.410
 AQ3  C2   C3   aromatic  1.383  0.020  1.383
 AQ3  N1   C61  aromatic  1.329  0.020  1.329
 AQ3  C1   C6   aromatic  1.393  0.020  1.393
 AQ3  C3   C4   aromatic  1.393  0.020  1.393
 AQ3  C51  C61  aromatic  1.385  0.020  1.385
 AQ3  C51  C5A  single    1.501  0.020  1.501
 AQ3  O4P  C5A  single    1.426  0.020  1.426
 AQ3  O4P  P    single    1.597  0.020  1.597
 AQ3  C6   C5   aromatic  1.393  0.020  1.393
 AQ3  O1P  P    double    1.474  0.020  1.474
 AQ3  O3P  P    single    1.593  0.020  1.593
 AQ3  C4   C5   aromatic  1.382  0.020  1.382
 AQ3  P    O2P  single    1.597  0.020  1.597
 AQ3  O    H1   single    0.850  0.020  0.980
 AQ3  C3   H2   single    0.930  0.020  1.080
 AQ3  C4   H3   single    0.930  0.020  1.080
 AQ3  C5   H4   single    0.930  0.020  1.080
 AQ3  C6   H5   single    0.930  0.020  1.080
 AQ3  N    H6   single    0.890  0.020  1.040
 AQ3  O3P  H7   single    0.850  0.020  0.980
 AQ3  O2P  H8   single    0.850  0.020  0.980
 AQ3  C5A  H9   single    0.970  0.020  1.090
 AQ3  C5A  H10  single    0.970  0.020  1.090
 AQ3  C61  H11  single    0.930  0.020  1.080
 AQ3  O3   H12  single    0.850  0.020  0.980
 AQ3  C2A  H13  single    0.970  0.020  1.090
 AQ3  C2A  H14  single    0.970  0.020  1.090
 AQ3  C2A  H15  single    0.970  0.020  1.090
 AQ3  C4A  H16  single    0.970  0.020  1.090
 AQ3  C4A  H17  single    0.970  0.020  1.090
 AQ3  N2   H18  single    0.890  0.020  1.040
 AQ3  CA   H20  single    0.970  0.020  1.090
 AQ3  OXT  H21  single    0.850  0.020  0.980
 AQ3  CB   H22  single    0.970  0.020  1.090
 AQ3  CB   H23  single    0.970  0.020  1.090

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
 AQ3  H1   O    C2   110.22  3.000
 AQ3  C1   C2   C3   120.65  3.000
 AQ3  C3   C2   O    123.09  3.000
 AQ3  C1   C2   O    116.26  3.000
 AQ3  H2   C3   C4   120.02  3.000
 AQ3  H2   C3   C2   119.35  3.000
 AQ3  C4   C3   C2   120.63  3.000
 AQ3  H3   C4   C5   120.88  3.000
 AQ3  H3   C4   C3   119.78  3.000
 AQ3  C5   C4   C3   119.34  3.000
 AQ3  H4   C5   C6   119.25  3.000
 AQ3  H4   C5   C4   120.49  3.000
 AQ3  C6   C5   C4   120.26  3.000
 AQ3  H5   C6   C1   120.20  3.000
 AQ3  H5   C6   C5   118.55  3.000
 AQ3  C1   C6   C5   121.25  3.000
 AQ3  N    C1   C6   123.81  3.000
 AQ3  C6   C1   C2   117.87  3.000
 AQ3  N    C1   C2   118.30  3.000
 AQ3  H6   N    CB   112.68  3.000
 AQ3  H6   N    C1   113.07  3.000
 AQ3  CB   N    C1   120.31  3.000
 AQ3  H7   O3P  P    113.85  3.000
 AQ3  O4P  P    O2P  106.98  3.000
 AQ3  O2P  P    O1P  109.67  3.000
 AQ3  O4P  P    O1P  116.60  3.000
 AQ3  O2P  P    O3P  108.01  3.000
 AQ3  O1P  P    O3P  117.85  3.000
 AQ3  O4P  P    O3P   96.60  3.000
 AQ3  H8   O2P  P    115.87  3.000
 AQ3  C5A  O4P  P    119.51  3.000
 AQ3  C41  C51  C61  118.39  3.000
 AQ3  C61  C51  C5A  122.45  3.000
 AQ3  C41  C51  C5A  119.15  3.000
 AQ3  H11  C61  N1   115.83  3.000
 AQ3  H11  C61  C51  121.09  3.000
 AQ3  N1   C61  C51  123.08  3.000
 AQ3  C21  N1   C61  119.79  3.000
 AQ3  C4A  C41  C31  121.05  3.000
 AQ3  C4A  C41  C51  121.03  3.000
 AQ3  C31  C41  C51  117.86  3.000
 AQ3  C21  C31  O3   121.96  3.000
 AQ3  C21  C31  C41  119.83  3.000
 AQ3  O3   C31  C41  118.21  3.000
 AQ3  H12  O3   C31  111.34  3.000
 AQ3  C2A  C21  C31  120.70  3.000
 AQ3  C31  C21  N1   121.05  3.000
 AQ3  C2A  C21  N1   118.25  3.000
 AQ3  H15  C2A  H14  107.60  3.000
 AQ3  H15  C2A  H13  107.50  3.000
 AQ3  H14  C2A  H13  107.46  3.000
 AQ3  H15  C2A  C21  111.95  3.000
 AQ3  H14  C2A  C21  109.81  3.000
 AQ3  H13  C2A  C21  112.30  3.000
 AQ3  H18  N2   CA   108.03  3.000
 AQ3  H18  N2   C4A  109.24  3.000
 AQ3  CA   N2   C4A  114.01  3.000
 AQ3  H20  CA   CB   108.02  3.000
 AQ3  H20  CA   C    107.20  3.000
 AQ3  CB   CA   C    108.37  3.000
 AQ3  H20  CA   N2   112.85  3.000
 AQ3  CB   CA   N2   109.38  3.000
 AQ3  C    CA   N2   110.88  3.000
 AQ3  O1   C    OXT  123.68  3.000
 AQ3  OXT  C    CA   111.13  3.000
 AQ3  O1   C    CA   125.17  3.000
 AQ3  H21  OXT  C    110.13  3.000
 AQ3  H23  CB   H22  107.39  3.000
 AQ3  H23  CB   CA   110.35  3.000
 AQ3  H22  CB   CA   107.92  3.000
 AQ3  H23  CB   N    112.67  3.000
 AQ3  H22  CB   N    109.34  3.000
 AQ3  CA   CB   N    109.05  3.000
 AQ3  H17  C4A  H16  105.72  3.000
 AQ3  H17  C4A  N2   108.97  3.000
 AQ3  H16  C4A  N2   112.56  3.000
 AQ3  H17  C4A  C41  109.33  3.000
 AQ3  H16  C4A  C41  110.76  3.000
 AQ3  N2   C4A  C41  109.40  3.000
 AQ3  H10  C5A  H9   107.50  3.000
 AQ3  H10  C5A  C51  109.76  3.000
 AQ3  H9   C5A  C51  109.81  3.000
 AQ3  H10  C5A  O4P  110.73  3.000
 AQ3  H9   C5A  O4P  109.61  3.000
 AQ3  C51  C5A  O4P  109.41  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
 AQ3  CONST_01  C5   C6   C1   C2      0.00   0.0  0
 AQ3  CONST_02  C5   C4   C3   C2      0.00   0.0  0
 AQ3  CONST_03  C6   C1   C2   C3      0.00   0.0  0
 AQ3  CONST_04  C6   C5   C4   C3      0.00   0.0  0
 AQ3  CONST_05  C1   C2   C3   C4      0.00   0.0  0
 AQ3  CONST_06  C1   C6   C5   C4      0.00   0.0  0
 AQ3  CONST_07  C21  C31  C41  C51     0.00   0.0  0
 AQ3  CONST_08  C21  N1   C61  C51     0.00   0.0  0
 AQ3  CONST_09  C31  C21  N1   C61     0.00   0.0  0
 AQ3  CONST_10  C31  C41  C51  C61     0.00   0.0  0
 AQ3  CONST_11  C41  C31  C21  N1      0.00   0.0  0
 AQ3  CONST_12  C41  C51  C61  N1      0.00   0.0  0
 AQ3  CONST_13  C6   C1   C2   O     180.00   0.0  0
 AQ3  CONST_14  C4   C3   C2   O     180.00   0.0  0
 AQ3  CONST_15  N    C1   C2   C3    180.00   0.0  0
 AQ3  CONST_16  N    C1   C6   C5    180.00   0.0  0
 AQ3  CONST_17  C31  C41  C51  C5A   180.00   0.0  0
 AQ3  CONST_18  N1   C61  C51  C5A   180.00   0.0  0
 AQ3  CONST_19  O3   C31  C41  C51   180.00   0.0  0
 AQ3  CONST_20  C2A  C21  N1   C61   180.00   0.0  0
 AQ3  CONST_21  C4A  C41  C51  C61   180.00   0.0  0
 AQ3  CONST_22  O3   C31  C21  N1    180.00   0.0  0
 AQ3  CONST_23  C2A  C21  C31  C41   180.00   0.0  0
 AQ3  CONST_24  C4A  C41  C31  C21   180.00   0.0  0
 AQ3  CONST_25  H5   C6   C1   C2    180.00   0.0  0
 AQ3  CONST_26  H3   C4   C3   C2    180.00   0.0  0
 AQ3  CONST_27  H4   C5   C4   C3    180.00   0.0  0
 AQ3  CONST_28  H2   C3   C4   C5    180.00   0.0  0
 AQ3  CONST_29  H11  C61  C51  C41   180.00   0.0  0
 AQ3  CONST_30  CB   N    C1   C2    180.00   0.0  0
 AQ3  CONST_31  CB   N    C1   C6      0.00   0.0  0
 AQ3  CONST_33  H21  OXT  C    CA    180.00   0.0  0
 AQ3  Var_01    C41  C51  C5A  O4P  -172.65  30.0  1
 AQ3  Var_02    N2   C4A  C41  C51    76.42  30.0  1
 AQ3  Var_03    H13  C2A  C21  N1   -121.86  30.0  2
 AQ3  Var_04    CA   CB   N    C1   -170.28  30.0  3
 AQ3  Var_05    C51  C5A  O4P  P     179.70  30.0  3
 AQ3  Var_06    CA   N2   C4A  C41   178.19  30.0  1

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
 AQ3  chir_01  CA  C  N2  CB  positiv

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
 AQ3  plan-1  O    0.020
 AQ3  plan-1  C2   0.020
 AQ3  plan-1  C3   0.020
 AQ3  plan-1  C4   0.020
 AQ3  plan-1  C5   0.020
 AQ3  plan-1  C6   0.020
 AQ3  plan-1  C1   0.020
 AQ3  plan-1  N    0.020
 AQ3  plan-1  H2   0.020
 AQ3  plan-1  H3   0.020
 AQ3  plan-1  H4   0.020
 AQ3  plan-1  H5   0.020
 AQ3  plan-2  C51  0.020
 AQ3  plan-2  C61  0.020
 AQ3  plan-2  N1   0.020
 AQ3  plan-2  C41  0.020
 AQ3  plan-2  C31  0.020
 AQ3  plan-2  O3   0.020
 AQ3  plan-2  C21  0.020
 AQ3  plan-2  C2A  0.020
 AQ3  plan-2  H11  0.020
 AQ3  plan-2  C4A  0.020
 AQ3  plan-2  C5A  0.020
 AQ3  plan-3  C1   0.020
 AQ3  plan-3  N    0.020
 AQ3  plan-3  CB   0.020
 AQ3  plan-3  H6   0.020
 AQ3  plan-4  CA   0.020
 AQ3  plan-4  C    0.020
 AQ3  plan-4  OXT  0.020
 AQ3  plan-4  O1   0.020
 AQ3  plan-4  H21  0.020

