# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 08:57:20 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: methyl 3-(7~{H}-purin-6-ylcarbamoyl)benzoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)c1cccc(c1)C(=O)Nc2ncnc3nc[nH]c23
#
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
 5XS  5XS  'methyl 3-(7~{H}-purin-6-ylcarbamoyl)benzoate'  ligand  33  22  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5XS
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
 5XS  C10  C  C     0   0.550  -0.0880  -0.6471   0.3481
 5XS  N12  N  NH1   0  -0.748  -1.2372   0.1003   0.2502
 5XS  C13  C  CR6   0   0.538  -2.5322  -0.3816   0.2507
 5XS  C15  C  CR16  0   0.026  -4.0868  -1.9540   0.8358
 5XS  C17  C  CR56  0   0.303  -4.8671  -0.1843  -0.2505
 5XS  C21  C  CR56  0   0.165  -3.5725   0.3439  -0.3246
 5XS  C22  C  CR16  0  -0.275   2.3436  -0.4180   0.0127
 5XS  C01  C  CH3   0  -0.424   7.0967  -0.1998  -0.7047
 5XS  O02  O  O2    0  -0.455   5.8580   0.3346  -0.2353
 5XS  O04  O  O     0  -0.442   4.7698  -1.4839  -0.9307
 5XS  C05  C  CR6   0  -0.065   3.5492   0.2621   0.1261
 5XS  C06  C  CR16  0  -0.260   3.5785   1.5183   0.7309
 5XS  C07  C  CR16  0  -0.225   2.4072   2.0814   1.2107
 5XS  C08  C  CR16  0  -0.280   1.2022   1.4068   1.0831
 5XS  C09  C  CR6   0  -0.044   1.1647   0.1530   0.4772
 5XS  O11  O  O     0  -0.416  -0.0679  -1.8559   0.3108
 5XS  N14  N  N     0  -0.428  -2.8201  -1.5318   0.8298
 5XS  N16  N  N     0  -0.420  -5.1429  -1.3496   0.3330
 5XS  N18  N  N     0  -0.452  -5.7529   0.6511  -0.8609
 5XS  C19  C  CR15  0   0.126  -5.0217   1.6465  -1.2904
 5XS  N20  N  NR15  0  -0.654  -3.7093   1.5234  -1.0005
 5XS  H1   H  HNH1  0   0.430  -1.1260   1.0856   0.0639
 5XS  H2   H  HCR6  0   0.261  -4.2565  -2.9076   1.3226
 5XS  H3   H  HCR6  0   0.272   2.3202  -1.3953  -0.4503
 5XS  H4   H  HCH3  0   0.243   7.3475  -1.1271  -0.1906
 5XS  H5   H  HCH3  0   0.243   7.0696  -0.3783  -1.7790
 5XS  H6   H  HCH3  0   0.256   7.8476   0.5515  -0.4806
 5XS  H7   H  HCR6  0   0.276   4.5074   2.0610   0.8368
 5XS  H8   H  HCR6  0   0.278   2.4328   3.0486   1.6934
 5XS  H9   H  HCR6  0   0.278   0.3051   1.8594   1.4865
 5XS  H11  H  HCR5  0   0.302  -5.3929   2.5032  -1.8317
 5XS  H12  H  HNR5  0   0.437  -2.9913   2.1779  -1.2701
 5XS  C03  C  C     0   0.605   4.7725  -0.3976  -0.4048

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
 5XS  C01  O02  single    1.428  0.020  1.428
 5XS  O04  C03  double    1.207  0.020  1.207
 5XS  O02  C03  single    1.320  0.020  1.320
 5XS  C03  C05  single    1.488  0.020  1.488
 5XS  C05  C06  aromatic  1.395  0.020  1.395
 5XS  C05  C22  aromatic  1.389  0.020  1.389
 5XS  C06  C07  aromatic  1.385  0.020  1.385
 5XS  C22  C09  aromatic  1.390  0.020  1.390
 5XS  C07  C08  aromatic  1.387  0.020  1.387
 5XS  C09  C08  aromatic  1.393  0.020  1.393
 5XS  C09  C10  single    1.492  0.020  1.492
 5XS  C19  N20  aromatic  1.350  0.020  1.350
 5XS  C19  N18  aromatic  1.308  0.020  1.308
 5XS  N20  C21  aromatic  1.366  0.020  1.366
 5XS  O11  C10  double    1.210  0.020  1.210
 5XS  C10  N12  single    1.374  0.020  1.374
 5XS  N18  C17  aromatic  1.362  0.020  1.362
 5XS  N12  C13  single    1.382  0.020  1.382
 5XS  C21  C17  aromatic  1.400  0.020  1.400
 5XS  C21  C13  aromatic  1.393  0.020  1.393
 5XS  C17  N16  aromatic  1.332  0.020  1.332
 5XS  C13  N14  aromatic  1.319  0.020  1.319
 5XS  N16  C15  aromatic  1.317  0.020  1.317
 5XS  N14  C15  aromatic  1.335  0.020  1.335
 5XS  N12  H1   single    0.860  0.020  1.020
 5XS  C15  H2   single    0.930  0.020  1.080
 5XS  C22  H3   single    0.930  0.020  1.080
 5XS  C01  H4   single    0.970  0.020  1.090
 5XS  C01  H5   single    0.970  0.020  1.090
 5XS  C01  H6   single    0.970  0.020  1.090
 5XS  C06  H7   single    0.930  0.020  1.080
 5XS  C07  H8   single    0.930  0.020  1.080
 5XS  C08  H9   single    0.930  0.020  1.080
 5XS  C19  H11  single    0.930  0.020  1.080
 5XS  N20  H12  single    0.860  0.020  1.020

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
 5XS  O11  C10  C09  121.65  3.000
 5XS  O11  C10  N12  123.72  3.000
 5XS  C09  C10  N12  114.62  3.000
 5XS  H1   N12  C13  116.35  3.000
 5XS  H1   N12  C10  116.88  3.000
 5XS  C13  N12  C10  126.44  3.000
 5XS  N14  C13  C21  118.19  3.000
 5XS  N14  C13  N12  120.57  3.000
 5XS  C21  C13  N12  121.21  3.000
 5XS  H2   C15  N16  116.73  3.000
 5XS  H2   C15  N14  115.38  3.000
 5XS  N16  C15  N14  127.89  3.000
 5XS  N18  C17  N16  126.74  3.000
 5XS  N16  C17  C21  123.00  3.000
 5XS  N18  C17  C21  110.26  3.000
 5XS  N20  C21  C17  105.02  3.000
 5XS  C17  C21  C13  118.18  3.000
 5XS  N20  C21  C13  136.79  3.000
 5XS  H3   C22  C09  119.73  3.000
 5XS  H3   C22  C05  119.75  3.000
 5XS  C09  C22  C05  120.52  3.000
 5XS  H6   C01  H5   109.52  3.000
 5XS  H6   C01  H4   109.41  3.000
 5XS  H5   C01  H4   109.37  3.000
 5XS  H6   C01  O02  105.85  3.000
 5XS  H5   C01  O02  111.34  3.000
 5XS  H4   C01  O02  111.28  3.000
 5XS  C03  O02  C01  117.60  3.000
 5XS  C06  C05  C03  122.47  3.000
 5XS  C06  C05  C22  119.66  3.000
 5XS  C03  C05  C22  117.87  3.000
 5XS  H7   C06  C07  119.25  3.000
 5XS  H7   C06  C05  120.85  3.000
 5XS  C07  C06  C05  119.90  3.000
 5XS  H8   C07  C08  119.79  3.000
 5XS  H8   C07  C06  119.88  3.000
 5XS  C08  C07  C06  120.33  3.000
 5XS  H9   C08  C09  121.07  3.000
 5XS  H9   C08  C07  118.83  3.000
 5XS  C09  C08  C07  120.08  3.000
 5XS  C08  C09  C22  119.49  3.000
 5XS  C08  C09  C10  122.88  3.000
 5XS  C22  C09  C10  117.58  3.000
 5XS  C15  N14  C13  118.98  3.000
 5XS  C17  N16  C15  113.75  3.000
 5XS  C19  N18  C17  104.50  3.000
 5XS  H11  C19  N20  120.97  3.000
 5XS  H11  C19  N18  125.22  3.000
 5XS  N20  C19  N18  113.82  3.000
 5XS  H12  N20  C19  125.16  3.000
 5XS  H12  N20  C21  128.41  3.000
 5XS  C19  N20  C21  106.40  3.000
 5XS  C05  C03  O04  123.56  3.000
 5XS  C05  C03  O02  112.60  3.000
 5XS  O04  C03  O02  123.84  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
 5XS  CONST_01  C19  N20  C21  C13   180.00   0.0  0
 5XS  CONST_02  N18  C17  C21  C13   180.00   0.0  0
 5XS  CONST_03  N16  C17  C21  C13     0.00   0.0  0
 5XS  CONST_04  N16  C15  N14  C13     0.00   0.0  0
 5XS  CONST_05  N18  C17  N16  C15   180.00   0.0  0
 5XS  CONST_06  C21  C17  N16  C15     0.00   0.0  0
 5XS  CONST_07  C21  C13  N14  C15     0.00   0.0  0
 5XS  CONST_08  N20  C19  N18  C17     0.00   0.0  0
 5XS  CONST_09  C19  N20  C21  C17     0.00   0.0  0
 5XS  CONST_10  N14  C13  C21  C17     0.00   0.0  0
 5XS  CONST_11  N14  C15  N16  C17     0.00   0.0  0
 5XS  CONST_12  N18  C19  N20  C21     0.00   0.0  0
 5XS  CONST_13  C19  N18  C17  C21     0.00   0.0  0
 5XS  CONST_14  C07  C06  C05  C22     0.00   0.0  0
 5XS  CONST_15  C07  C08  C09  C22     0.00   0.0  0
 5XS  CONST_16  C08  C07  C06  C05     0.00   0.0  0
 5XS  CONST_17  C08  C09  C22  C05     0.00   0.0  0
 5XS  CONST_18  C09  C22  C05  C06     0.00   0.0  0
 5XS  CONST_19  C09  C08  C07  C06     0.00   0.0  0
 5XS  CONST_20  N20  C21  C13  N14   180.00   0.0  0
 5XS  CONST_21  C19  N18  C17  N16   180.00   0.0  0
 5XS  CONST_22  N20  C21  C17  N16   180.00   0.0  0
 5XS  CONST_23  N20  C21  C17  N18     0.00   0.0  0
 5XS  CONST_24  C05  C22  C09  C10   180.00   0.0  0
 5XS  CONST_25  C07  C08  C09  C10   180.00   0.0  0
 5XS  CONST_26  N20  C21  C13  N12     0.00   0.0  0
 5XS  CONST_27  C17  C21  C13  N12   180.00   0.0  0
 5XS  CONST_28  C15  N14  C13  N12   180.00   0.0  0
 5XS  CONST_29  C07  C06  C05  C03   180.00   0.0  0
 5XS  CONST_30  C09  C22  C05  C03   180.00   0.0  0
 5XS  CONST_31  H12  N20  C21  C13     0.00   0.0  0
 5XS  CONST_32  H2   C15  N14  C13   180.00   0.0  0
 5XS  CONST_33  H11  C19  N18  C17   180.00   0.0  0
 5XS  CONST_34  H7   C06  C05  C22   180.00   0.0  0
 5XS  CONST_35  H9   C08  C09  C22   180.00   0.0  0
 5XS  CONST_36  H8   C07  C06  C05   180.00   0.0  0
 5XS  CONST_37  H3   C22  C05  C06   180.00   0.0  0
 5XS  CONST_38  C09  C10  N12  C13   180.00   0.0  0
 5XS  CONST_42  O11  C10  N12  C13     0.00   0.0  0
 5XS  Var_01    C22  C09  C10  N12  -152.69  30.0  2
 5XS  Var_02    O04  C03  C05  C22     0.32  30.0  2
 5XS  Var_03    C05  C03  O02  C01   179.87  30.0  3
 5XS  Var_04    H4   C01  O02  C03   -61.80  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
 5XS  plan-1  C10  0.020
 5XS  plan-1  C22  0.020
 5XS  plan-1  C05  0.020
 5XS  plan-1  C06  0.020
 5XS  plan-1  C07  0.020
 5XS  plan-1  C08  0.020
 5XS  plan-1  C09  0.020
 5XS  plan-1  H3   0.020
 5XS  plan-1  H7   0.020
 5XS  plan-1  H8   0.020
 5XS  plan-1  H9   0.020
 5XS  plan-1  C03  0.020
 5XS  plan-2  N12  0.020
 5XS  plan-2  C13  0.020
 5XS  plan-2  C15  0.020
 5XS  plan-2  C17  0.020
 5XS  plan-2  C21  0.020
 5XS  plan-2  N14  0.020
 5XS  plan-2  N16  0.020
 5XS  plan-2  N18  0.020
 5XS  plan-2  C19  0.020
 5XS  plan-2  N20  0.020
 5XS  plan-2  H2   0.020
 5XS  plan-2  H11  0.020
 5XS  plan-2  H12  0.020
 5XS  plan-3  C10  0.020
 5XS  plan-3  N12  0.020
 5XS  plan-3  C13  0.020
 5XS  plan-3  C09  0.020
 5XS  plan-3  O11  0.020
 5XS  plan-3  H1   0.020
 5XS  plan-4  O02  0.020
 5XS  plan-4  O04  0.020
 5XS  plan-4  C05  0.020
 5XS  plan-4  C03  0.020

