# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 12:34:47 2022
#   Inital geometry file: a 114 line input string
#   Ligand name: 4-(6-aminocarbonyl-8-oxidanylidene-9-phenyl-7~{H}-purin-2-yl)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1nc(nc2N(C(=O)Nc12)c3ccccc3)c4ccc(cc4)C(O)=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
 Y49  Y49  '4-(6-aminocarbonyl-8-oxidanylidene-9-phenyl-7~{H}-purin-2-yl)benzoic acid'  ligand  40  28  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_Y49
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
 Y49  C01  C  CR6    0   0.390   0.5975   8.5670  -24.5201
 Y49  N02  N  N      0  -0.476   0.4106   7.9742  -25.6853
 Y49  N03  N  N      0  -0.437   1.0699   9.8161  -24.3667
 Y49  C04  C  CR6    0   0.101   0.6918   8.6217  -26.8198
 Y49  C05  C  CR56   0   0.513   1.3465  10.4409  -25.4735
 Y49  C06  C  CR56   0   0.283   1.1802   9.9036  -26.7614
 Y49  N07  N  NR5    0  -0.700   1.8281  11.7115  -25.6240
 Y49  C08  C  CR5    0   0.656   1.9833  11.9956  -26.9853
 Y49  N09  N  NR15   0  -0.743   1.5710  10.8647  -27.6480
 Y49  C10  C  CR6    0   0.310   2.1621  12.6075  -24.5804
 Y49  C11  C  CR16   0  -0.269   3.1189  12.2377  -23.6449
 Y49  C12  C  CR16   0  -0.266   1.5247  13.8378  -24.4983
 Y49  C13  C  CR16   0  -0.255   3.4339  13.1088  -22.6126
 Y49  C14  C  CR16   0  -0.256   1.8589  14.7097  -23.4723
 Y49  C15  C  CR16   0  -0.245   2.8087  14.3458  -22.5271
 Y49  C16  C  CR6    0  -0.022   0.2661   7.8179  -23.2934
 Y49  C17  C  CR16   0  -0.275  -0.2827   6.5369  -23.3646
 Y49  C18  C  CR16   0  -0.273   0.4890   8.3779  -22.0349
 Y49  C19  C  CR16   0  -0.274  -0.6042   5.8438  -22.2099
 Y49  C20  C  CR16   0  -0.273   0.1672   7.6752  -20.8855
 Y49  C21  C  CR6    0  -0.099  -0.3881   6.3996  -20.9506
 Y49  O22  O  O      0  -0.441   2.4001  13.0234  -27.4582
 Y49  C23  C  C      0   0.520   0.4693   7.9415  -28.1317
 Y49  O24  O  O      0  -0.470   0.7202   8.5374  -29.1709
 Y49  N25  N  NH2    0  -0.808  -0.0013   6.6987  -28.0502
 Y49  C26  C  C      0   0.396  -0.7538   5.6364  -19.6785
 Y49  O27  O  OC    -1  -0.583  -0.5074   6.2106  -18.6015
 Y49  O28  O  O      0  -0.584  -1.2682   4.5132  -19.8358
 Y49  H1   H  HNR5   0   0.431   1.5616  10.7724  -28.6524
 Y49  H2   H  HCR6   0   0.274   3.6166  11.2801  -23.7234
 Y49  H3   H  HCR6   0   0.273   0.7695  14.1099  -25.2239
 Y49  H4   H  HCR6   0   0.266   4.1756  12.8218  -21.8792
 Y49  H5   H  HCR6   0   0.265   1.3668  15.6711  -23.4079
 Y49  H6   H  HCR6   0   0.264   3.0609  15.0260  -21.7243
 Y49  H7   H  HCR6   0   0.251  -0.4620   6.0827  -24.3299
 Y49  H8   H  HCR6   0   0.246   0.9156   9.3687  -21.9559
 Y49  H9   H  HCR6   0   0.242  -1.0332   4.8536  -22.2867
 Y49  H10  H  HCR6   0   0.242   0.3478   8.1268  -19.9192
 Y49  H11  H  HNH2   0   0.410  -0.1825   6.1625  -28.8830
 Y49  H12  H  HNH2   0   0.419  -0.1849   6.2769  -27.1541

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
 Y49  O24  C23  double    1.224  0.020  1.224
 Y49  N25  C23  single    1.331  0.020  1.331
 Y49  C23  C04  single    1.494  0.020  1.494
 Y49  N09  C08  single    1.374  0.020  1.374
 Y49  N09  C06  single    1.365  0.020  1.365
 Y49  O22  C08  double    1.206  0.020  1.206
 Y49  C08  N07  single    1.399  0.020  1.399
 Y49  C04  C06  aromatic  1.373  0.020  1.373
 Y49  C04  N02  aromatic  1.336  0.020  1.336
 Y49  C06  C05  aromatic  1.405  0.020  1.405
 Y49  N02  C01  aromatic  1.321  0.020  1.321
 Y49  N07  C05  single    1.367  0.020  1.367
 Y49  N07  C10  single    1.415  0.020  1.415
 Y49  C05  N03  aromatic  1.301  0.020  1.301
 Y49  C12  C10  aromatic  1.388  0.020  1.388
 Y49  C12  C14  aromatic  1.387  0.020  1.387
 Y49  C10  C11  aromatic  1.388  0.020  1.388
 Y49  C01  N03  aromatic  1.344  0.020  1.344
 Y49  C01  C16  single    1.475  0.020  1.475
 Y49  C14  C15  aromatic  1.389  0.020  1.389
 Y49  C17  C16  aromatic  1.395  0.020  1.395
 Y49  C17  C19  aromatic  1.385  0.020  1.385
 Y49  C11  C13  aromatic  1.387  0.020  1.387
 Y49  C16  C18  aromatic  1.395  0.020  1.395
 Y49  C15  C13  aromatic  1.389  0.020  1.389
 Y49  C19  C21  aromatic  1.393  0.020  1.393
 Y49  C18  C20  aromatic  1.385  0.020  1.385
 Y49  C21  C20  aromatic  1.393  0.020  1.393
 Y49  C21  C26  single    1.528  0.020  1.528
 Y49  C26  O28  deloc     1.245  0.020  1.245
 Y49  C26  O27  deloc     1.245  0.020  1.245
 Y49  N09  H1   single    0.860  0.020  1.020
 Y49  C11  H2   single    0.930  0.020  1.080
 Y49  C12  H3   single    0.930  0.020  1.080
 Y49  C13  H4   single    0.930  0.020  1.080
 Y49  C14  H5   single    0.930  0.020  1.080
 Y49  C15  H6   single    0.930  0.020  1.080
 Y49  C17  H7   single    0.930  0.020  1.080
 Y49  C18  H8   single    0.930  0.020  1.080
 Y49  C19  H9   single    0.930  0.020  1.080
 Y49  C20  H10  single    0.930  0.020  1.080
 Y49  N25  H11  single    0.860  0.020  1.020
 Y49  N25  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
 Y49  C16  C01  N03  117.12  3.000
 Y49  C16  C01  N02  118.30  3.000
 Y49  N03  C01  N02  124.58  3.000
 Y49  C04  N02  C01  120.12  3.000
 Y49  C05  N03  C01  115.08  3.000
 Y49  C23  C04  C06  121.01  3.000
 Y49  C06  C04  N02  119.42  3.000
 Y49  C23  C04  N02  119.57  3.000
 Y49  N07  C05  C06  107.22  3.000
 Y49  N07  C05  N03  127.95  3.000
 Y49  C06  C05  N03  124.82  3.000
 Y49  N09  C06  C05  106.99  3.000
 Y49  C05  C06  C04  115.97  3.000
 Y49  N09  C06  C04  137.03  3.000
 Y49  C10  N07  C08  124.24  3.000
 Y49  C10  N07  C05  126.18  3.000
 Y49  C08  N07  C05  109.56  3.000
 Y49  O22  C08  N09  128.04  3.000
 Y49  O22  C08  N07  126.36  3.000
 Y49  N09  C08  N07  105.60  3.000
 Y49  H1   N09  C08  123.94  3.000
 Y49  H1   N09  C06  125.44  3.000
 Y49  C08  N09  C06  110.62  3.000
 Y49  C12  C10  C11  120.84  3.000
 Y49  C11  C10  N07  119.40  3.000
 Y49  C12  C10  N07  119.76  3.000
 Y49  H2   C11  C13  120.36  3.000
 Y49  H2   C11  C10  120.25  3.000
 Y49  C13  C11  C10  119.39  3.000
 Y49  H3   C12  C14  120.40  3.000
 Y49  H3   C12  C10  120.24  3.000
 Y49  C14  C12  C10  119.35  3.000
 Y49  H4   C13  C15  120.21  3.000
 Y49  H4   C13  C11  119.58  3.000
 Y49  C15  C13  C11  120.20  3.000
 Y49  H5   C14  C15  120.23  3.000
 Y49  H5   C14  C12  119.53  3.000
 Y49  C15  C14  C12  120.23  3.000
 Y49  H6   C15  C14  119.98  3.000
 Y49  H6   C15  C13  120.05  3.000
 Y49  C14  C15  C13  119.97  3.000
 Y49  C18  C16  C17  118.51  3.000
 Y49  C18  C16  C01  120.69  3.000
 Y49  C17  C16  C01  120.80  3.000
 Y49  H7   C17  C19  119.70  3.000
 Y49  H7   C17  C16  119.75  3.000
 Y49  C19  C17  C16  120.55  3.000
 Y49  H8   C18  C20  119.72  3.000
 Y49  H8   C18  C16  119.77  3.000
 Y49  C20  C18  C16  120.52  3.000
 Y49  H9   C19  C21  119.39  3.000
 Y49  H9   C19  C17  119.41  3.000
 Y49  C21  C19  C17  121.20  3.000
 Y49  H10  C20  C21  119.39  3.000
 Y49  H10  C20  C18  119.39  3.000
 Y49  C21  C20  C18  121.23  3.000
 Y49  C26  C21  C20  120.93  3.000
 Y49  C26  C21  C19  121.07  3.000
 Y49  C20  C21  C19  118.00  3.000
 Y49  N25  C23  O24  125.37  3.000
 Y49  N25  C23  C04  115.07  3.000
 Y49  O24  C23  C04  119.56  3.000
 Y49  H12  N25  H11  118.69  3.000
 Y49  H12  N25  C23  120.65  3.000
 Y49  H11  N25  C23  120.66  3.000
 Y49  O28  C26  O27  127.36  3.000
 Y49  O27  C26  C21  116.26  3.000
 Y49  O28  C26  C21  116.37  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
 Y49  CONST_01  C06  C04  N02  C01     0.00   0.0  0
 Y49  CONST_02  C06  C05  N03  C01     0.00   0.0  0
 Y49  CONST_03  C19  C17  C16  C01   180.00   0.0  0
 Y49  CONST_04  C20  C18  C16  C01   180.00   0.0  0
 Y49  CONST_05  C05  C06  C04  N02     0.00   0.0  0
 Y49  CONST_06  C05  N03  C01  N02     0.00   0.0  0
 Y49  CONST_07  C17  C16  C01  N02     0.00   0.0  0
 Y49  CONST_08  C18  C16  C01  N02   180.00   0.0  0
 Y49  CONST_09  C04  C06  C05  N03     0.00   0.0  0
 Y49  CONST_10  C04  N02  C01  N03     0.00   0.0  0
 Y49  CONST_11  C17  C16  C01  N03   180.00   0.0  0
 Y49  CONST_12  C18  C16  C01  N03     0.00   0.0  0
 Y49  CONST_13  C16  C01  N02  C04   180.00   0.0  0
 Y49  CONST_14  C16  C01  N03  C05   180.00   0.0  0
 Y49  CONST_15  C15  C14  C12  C10     0.00   0.0  0
 Y49  CONST_16  C15  C13  C11  C10     0.00   0.0  0
 Y49  CONST_17  C14  C12  C10  C11     0.00   0.0  0
 Y49  CONST_18  C14  C15  C13  C11     0.00   0.0  0
 Y49  CONST_19  C13  C11  C10  C12     0.00   0.0  0
 Y49  CONST_20  C13  C15  C14  C12     0.00   0.0  0
 Y49  CONST_21  C21  C19  C17  C16     0.00   0.0  0
 Y49  CONST_22  C21  C20  C18  C16     0.00   0.0  0
 Y49  CONST_23  C20  C18  C16  C17     0.00   0.0  0
 Y49  CONST_24  C20  C21  C19  C17     0.00   0.0  0
 Y49  CONST_25  C19  C17  C16  C18     0.00   0.0  0
 Y49  CONST_26  C19  C21  C20  C18     0.00   0.0  0
 Y49  CONST_27  C14  C12  C10  N07   180.00   0.0  0
 Y49  CONST_28  C13  C11  C10  N07   180.00   0.0  0
 Y49  CONST_29  C08  N09  C06  C05     0.00   0.0  0
 Y49  CONST_30  N09  C08  N07  C05     0.00   0.0  0
 Y49  CONST_31  N07  C08  N09  C06     0.00   0.0  0
 Y49  CONST_32  C08  N07  C05  C06     0.00   0.0  0
 Y49  CONST_33  C10  N07  C05  C06   180.00   0.0  0
 Y49  CONST_34  N09  C06  C05  N07     0.00   0.0  0
 Y49  CONST_35  C10  N07  C08  N09   180.00   0.0  0
 Y49  CONST_36  C23  C04  N02  C01   180.00   0.0  0
 Y49  CONST_37  C23  C04  C06  C05   180.00   0.0  0
 Y49  CONST_38  C23  C04  C06  N09     0.00   0.0  0
 Y49  CONST_39  C26  C21  C19  C17   180.00   0.0  0
 Y49  CONST_40  C26  C21  C20  C18   180.00   0.0  0
 Y49  CONST_41  O22  C08  N07  C05   180.00   0.0  0
 Y49  CONST_42  O22  C08  N09  C06   180.00   0.0  0
 Y49  CONST_43  O22  C08  N07  C10     0.00   0.0  0
 Y49  CONST_44  H7   C17  C16  C01     0.00   0.0  0
 Y49  CONST_45  H8   C18  C16  C01     0.00   0.0  0
 Y49  CONST_46  H3   C12  C10  N07     0.00   0.0  0
 Y49  CONST_47  H2   C11  C10  N07     0.00   0.0  0
 Y49  CONST_48  H5   C14  C12  C10   180.00   0.0  0
 Y49  CONST_49  H4   C13  C11  C10   180.00   0.0  0
 Y49  CONST_50  H6   C15  C13  C11   180.00   0.0  0
 Y49  CONST_51  H9   C19  C17  C16   180.00   0.0  0
 Y49  CONST_52  H10  C20  C18  C16   180.00   0.0  0
 Y49  CONST_53  H1   N09  C06  C05   180.00   0.0  0
 Y49  CONST_54  H11  N25  C23  C04   180.00   0.0  0
 Y49  CONST_55  H12  N25  C23  C04     0.00   0.0  0
 Y49  Var_01    C12  C10  N07  C05  -121.16  30.0  2
 Y49  Var_02    O24  C23  C04  N02   179.61  30.0  2
 Y49  Var_03    O28  C26  C21  C19    -1.07  30.0  2

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
 Y49  plan-1  N07  0.020
 Y49  plan-1  C10  0.020
 Y49  plan-1  C11  0.020
 Y49  plan-1  C12  0.020
 Y49  plan-1  C13  0.020
 Y49  plan-1  C14  0.020
 Y49  plan-1  C15  0.020
 Y49  plan-1  H2   0.020
 Y49  plan-1  H3   0.020
 Y49  plan-1  H4   0.020
 Y49  plan-1  H5   0.020
 Y49  plan-1  H6   0.020
 Y49  plan-2  C01  0.020
 Y49  plan-2  C16  0.020
 Y49  plan-2  C17  0.020
 Y49  plan-2  C18  0.020
 Y49  plan-2  C19  0.020
 Y49  plan-2  C20  0.020
 Y49  plan-2  C21  0.020
 Y49  plan-2  C26  0.020
 Y49  plan-2  H7   0.020
 Y49  plan-2  H8   0.020
 Y49  plan-2  H9   0.020
 Y49  plan-2  H10  0.020
 Y49  plan-3  C01  0.020
 Y49  plan-3  N02  0.020
 Y49  plan-3  N03  0.020
 Y49  plan-3  C04  0.020
 Y49  plan-3  C05  0.020
 Y49  plan-3  C06  0.020
 Y49  plan-3  N07  0.020
 Y49  plan-3  C08  0.020
 Y49  plan-3  N09  0.020
 Y49  plan-3  C10  0.020
 Y49  plan-3  C16  0.020
 Y49  plan-3  O22  0.020
 Y49  plan-3  C23  0.020
 Y49  plan-3  H1   0.020
 Y49  plan-4  C04  0.020
 Y49  plan-4  C23  0.020
 Y49  plan-4  O24  0.020
 Y49  plan-4  N25  0.020
 Y49  plan-4  H11  0.020
 Y49  plan-4  H12  0.020
 Y49  plan-5  C21  0.020
 Y49  plan-5  C26  0.020
 Y49  plan-5  O27  0.020
 Y49  plan-5  O28  0.020

