# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 08:01:43 2020
#   Inital geometry file: a 147 line input string
#   Ligand name: (2~{S})-2-[[4-[(6~{a}~{R})-3-azanyl-1-oxidanylidene-5,6,6~{a},7-tetrahydro-4~{H}-imidazo[1,5-f]pteridin-10-ium-8-yl]phenyl]carbonylamino]pentanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)C2=C(NC[C@@H]3CN(C=[N+]23)c4ccc(cc4)C(=O)N[C@@H](CCC(O)=O)C(O)=O)N1
#
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
 GUE  GUE  '(2~{S})-2-[[4-[(6~{a}~{R})-3-azanyl-1-oxidanylidene-5,6,6~{a},7-tetrahydro-4~{H}-imidazo[1,5-f]pteridin-10-ium-8-yl]phenyl]carbonylamino]pentanedioic acid'  ligand  53  33  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_GUE
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
 GUE  N1   N  NR16   0  -0.731  -7.4577   0.5760   0.4292
 GUE  C2   C  CR6    0   0.717  -7.3324   1.9079   0.7106
 GUE  N3   N  N      0  -0.517  -6.1876   2.5269   0.7372
 GUE  C4   C  CR6    0   0.463  -5.0307   1.8514   0.4680
 GUE  C6   C  CR15   0  -0.156  -4.2707  -1.5580  -0.9639
 GUE  C1'  C  CR6    0  -0.050   2.1590  -1.3904  -0.4331
 GUE  C2'  C  CR16   0  -0.273   1.5189  -0.1550  -0.3510
 GUE  C3'  C  CR16   0  -0.281   0.1392  -0.0632  -0.3640
 GUE  C4'  C  CR6    0   0.420  -0.6299  -1.2220  -0.4366
 GUE  C5'  C  CR16   0  -0.290  -0.0046  -2.4621  -0.5284
 GUE  O4   O  O      0  -0.500  -3.9408   2.4255   0.4768
 GUE  C4A  C  CR6    0   0.028  -5.1374   0.4469   0.1751
 GUE  N5   N  NR5    1  -0.535  -4.0334  -0.3282  -0.1945
 GUE  C7   C  CH2    0  -0.232  -5.3750  -2.3421  -0.2784
 GUE  N8   N  NH1    0  -0.674  -6.5222  -1.4788  -0.1163
 GUE  C8A  C  CR6    0   0.702  -6.3606  -0.1820   0.1619
 GUE  N2   N  NH2    0  -0.795  -8.4623   2.5615   0.9850
 GUE  C9   C  CH2    0  -0.281  -2.8923  -2.2206  -0.9653
 GUE  N10  N  NR5    0  -0.589  -2.0270  -1.1532  -0.4498
 GUE  C6'  C  CR16   0  -0.242   1.3767  -2.5360  -0.5372
 GUE  O11  O  O      0  -0.488   4.1585  -2.5223  -0.9985
 GUE  N    N  NH1    0  -0.629   4.3580  -0.5300   0.0421
 GUE  CA   C  CH1    0  -0.206   5.7997  -0.5724   0.1419
 GUE  C    C  C      0   0.319   6.2897  -1.5215   1.2654
 GUE  OX1  O  OC    -1  -0.648   7.5089  -1.7835   1.2365
 GUE  OX2  O  O      0  -0.533   5.4543  -1.9145   2.0976
 GUE  CB   C  CH2    0  -0.453   6.3415   0.8427   0.3496
 GUE  CG   C  CH2    0  -0.559   6.0109   1.7880  -0.7945
 GUE  CD   C  C      0   0.445   6.5934   3.2081  -0.6817
 GUE  OE1  O  OC    -1  -0.585   6.2406   4.0121  -1.5710
 GUE  OE2  O  O      0  -0.569   7.3665   3.4502   0.2658
 GUE  C1   C  CR15   0   0.365  -2.7622  -0.1593   0.0267
 GUE  H1   H  HCR5   0   0.328  -4.5851  -1.2714  -1.9699
 GUE  H2   H  HCR6   0   0.260   2.0869   0.7658  -0.3217
 GUE  H3   H  HCR6   0   0.261  -0.3210   0.9161  -0.3484
 GUE  H4   H  HCR6   0   0.266  -0.5833  -3.3739  -0.5894
 GUE  H7   H  HCH2   0   0.289  -5.6600  -3.1946  -0.8912
 GUE  H8   H  HCH2   0   0.254  -5.0232  -2.7185   0.6865
 GUE  H9   H  HNH1   0   0.390  -7.4438  -1.8845  -0.1274
 GUE  H10  H  HNH2   0   0.384  -9.3699   2.1417   0.8790
 GUE  H11  H  HNH2   0   0.401  -8.4210   3.5585   1.1065
 GUE  H12  H  HCH2   0   0.272  -2.8506  -3.0889  -0.3048
 GUE  H13  H  HCH2   0   0.303  -2.5783  -2.5173  -1.9633
 GUE  H14  H  HCR6   0   0.261   1.8491  -3.5054  -0.6190
 GUE  H15  H  HNH1   0   0.374   3.8843   0.1288   0.6394
 GUE  H16  H  HCH1   0   0.200   6.1885  -0.9485  -0.8090
 GUE  H18  H  HCH2   0   0.209   5.9583   1.2436   1.2949
 GUE  H19  H  HCH2   0   0.242   7.4220   0.7694   0.4689
 GUE  H20  H  HCH2   0   0.192   6.3647   1.3518  -1.7370
 GUE  H21  H  HCH2   0   0.189   4.9268   1.8755  -0.9173
 GUE  H23  H  HCR5   0   0.340  -2.3593   0.6899   0.5541
 GUE  H25  H  HNR6   0   0.391  -8.3718   0.1445   0.4199
 GUE  C11  C  C      0   0.550   3.6472  -1.5374  -0.4775

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
 GUE  OX2  C    deloc     1.243  0.020  1.243
 GUE  C    OX1  deloc     1.247  0.020  1.247
 GUE  C    CA   single    1.550  0.020  1.550
 GUE  CA   CB   single    1.529  0.020  1.529
 GUE  CA   N    single    1.446  0.020  1.446
 GUE  O11  C11  double    1.226  0.020  1.226
 GUE  CB   CG   single    1.521  0.020  1.521
 GUE  C11  N    single    1.338  0.020  1.338
 GUE  C11  C1'  single    1.496  0.020  1.496
 GUE  C2'  C1'  aromatic  1.394  0.020  1.394
 GUE  C2'  C3'  aromatic  1.383  0.020  1.383
 GUE  C1'  C6'  aromatic  1.391  0.020  1.391
 GUE  O4   C4   double    1.232  0.020  1.232
 GUE  CG   CD   single    1.539  0.020  1.539
 GUE  C3'  C4'  aromatic  1.393  0.020  1.393
 GUE  OE2  CD   deloc     1.247  0.020  1.247
 GUE  C6'  C5'  aromatic  1.383  0.020  1.383
 GUE  CD   OE1  deloc     1.250  0.020  1.250
 GUE  C4   N3   single    1.366  0.020  1.366
 GUE  C4   C4A  single    1.439  0.020  1.439
 GUE  C4'  C5'  aromatic  1.392  0.020  1.392
 GUE  C4'  N10  single    1.399  0.020  1.399
 GUE  N3   C2   double    1.302  0.020  1.302
 GUE  C1   N10  single    1.325  0.020  1.325
 GUE  C1   N5   double    1.301  0.020  1.301
 GUE  N10  C9   single    1.468  0.020  1.468
 GUE  C4A  N5   single    1.399  0.020  1.399
 GUE  C4A  C8A  double    1.375  0.020  1.375
 GUE  N5   C6   single    1.470  0.020  1.470
 GUE  C2   N2   single    1.334  0.020  1.334
 GUE  C2   N1   single    1.367  0.020  1.367
 GUE  C9   C6   single    1.529  0.020  1.529
 GUE  C6   C7   single    1.518  0.020  1.518
 GUE  C8A  N1   single    1.360  0.020  1.360
 GUE  C8A  N8   single    1.336  0.020  1.336
 GUE  C7   N8   single    1.445  0.020  1.445
 GUE  C6   H1   single    0.970  0.020  1.090
 GUE  C2'  H2   single    0.930  0.020  1.080
 GUE  C3'  H3   single    0.930  0.020  1.080
 GUE  C5'  H4   single    0.930  0.020  1.080
 GUE  C7   H7   single    0.970  0.020  1.090
 GUE  C7   H8   single    0.970  0.020  1.090
 GUE  N8   H9   single    0.860  0.020  1.020
 GUE  N2   H10  single    0.860  0.020  1.020
 GUE  N2   H11  single    0.860  0.020  1.020
 GUE  C9   H12  single    0.970  0.020  1.090
 GUE  C9   H13  single    0.970  0.020  1.090
 GUE  C6'  H14  single    0.930  0.020  1.080
 GUE  N    H15  single    0.890  0.020  1.040
 GUE  CA   H16  single    0.970  0.020  1.090
 GUE  CB   H18  single    0.970  0.020  1.090
 GUE  CB   H19  single    0.970  0.020  1.090
 GUE  CG   H20  single    0.970  0.020  1.090
 GUE  CG   H21  single    0.970  0.020  1.090
 GUE  C1   H23  single    0.930  0.020  1.080
 GUE  N1   H25  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
 GUE  H25  N1   C8A  119.33  3.000
 GUE  H25  N1   C2   120.04  3.000
 GUE  C8A  N1   C2   120.63  3.000
 GUE  N2   C2   N3   120.52  3.000
 GUE  N2   C2   N1   116.24  3.000
 GUE  N3   C2   N1   123.24  3.000
 GUE  C4   N3   C2   120.37  3.000
 GUE  C4A  C4   O4   121.47  3.000
 GUE  C4A  C4   N3   117.38  3.000
 GUE  O4   C4   N3   121.15  3.000
 GUE  H1   C6   C9   111.85  3.000
 GUE  H1   C6   C7   110.00  3.000
 GUE  C9   C6   C7   115.61  3.000
 GUE  H1   C6   N5   108.00  3.000
 GUE  C7   C6   N5   108.26  3.000
 GUE  C9   C6   N5   102.56  3.000
 GUE  C11  C1'  C6'  118.44  3.000
 GUE  C6'  C1'  C2'  118.43  3.000
 GUE  C11  C1'  C2'  123.08  3.000
 GUE  H2   C2'  C3'  117.86  3.000
 GUE  H2   C2'  C1'  120.97  3.000
 GUE  C3'  C2'  C1'  121.10  3.000
 GUE  H3   C3'  C4'  121.26  3.000
 GUE  H3   C3'  C2'  118.96  3.000
 GUE  C4'  C3'  C2'  119.75  3.000
 GUE  N10  C4'  C5'  119.46  3.000
 GUE  N10  C4'  C3'  120.74  3.000
 GUE  C5'  C4'  C3'  119.78  3.000
 GUE  H4   C5'  C6'  119.27  3.000
 GUE  H4   C5'  C4'  120.95  3.000
 GUE  C6'  C5'  C4'  119.77  3.000
 GUE  C8A  C4A  N5   116.49  3.000
 GUE  C8A  C4A  C4   120.94  3.000
 GUE  N5   C4A  C4   122.43  3.000
 GUE  C1   N5   C4A  130.86  3.000
 GUE  C4A  N5   C6   118.33  3.000
 GUE  C1   N5   C6   110.81  3.000
 GUE  H8   C7   H7   108.15  3.000
 GUE  H8   C7   N8   111.22  3.000
 GUE  H7   C7   N8   108.87  3.000
 GUE  H8   C7   C6   110.01  3.000
 GUE  H7   C7   C6   109.94  3.000
 GUE  N8   C7   C6   108.64  3.000
 GUE  H9   N8   C8A  120.26  3.000
 GUE  H9   N8   C7   118.99  3.000
 GUE  C8A  N8   C7   120.48  3.000
 GUE  N8   C8A  C4A  123.59  3.000
 GUE  N8   C8A  N1   118.97  3.000
 GUE  C4A  C8A  N1   117.44  3.000
 GUE  H11  N2   H10  117.64  3.000
 GUE  H11  N2   C2   118.43  3.000
 GUE  H10  N2   C2   122.57  3.000
 GUE  H13  C9   H12  109.10  3.000
 GUE  H13  C9   N10  110.52  3.000
 GUE  H12  C9   N10  110.08  3.000
 GUE  H13  C9   C6   112.29  3.000
 GUE  H12  C9   C6   112.23  3.000
 GUE  N10  C9   C6   102.47  3.000
 GUE  C1   N10  C9   110.17  3.000
 GUE  C9   N10  C4'  123.81  3.000
 GUE  C1   N10  C4'  126.00  3.000
 GUE  H14  C6'  C5'  118.98  3.000
 GUE  H14  C6'  C1'  119.88  3.000
 GUE  C5'  C6'  C1'  121.14  3.000
 GUE  H15  N    CA   116.56  3.000
 GUE  H15  N    C11  118.21  3.000
 GUE  CA   N    C11  122.31  3.000
 GUE  H16  CA   CB   108.08  3.000
 GUE  H16  CA   C    107.88  3.000
 GUE  CB   CA   C    110.86  3.000
 GUE  H16  CA   N    107.73  3.000
 GUE  CB   CA   N    109.60  3.000
 GUE  C    CA   N    112.53  3.000
 GUE  OX2  C    OX1  127.31  3.000
 GUE  OX1  C    CA   114.88  3.000
 GUE  OX2  C    CA   117.80  3.000
 GUE  H19  CB   H18  106.07  3.000
 GUE  H19  CB   CG   109.87  3.000
 GUE  H18  CB   CG   110.22  3.000
 GUE  H19  CB   CA   107.69  3.000
 GUE  H18  CB   CA   109.37  3.000
 GUE  CG   CB   CA   113.33  3.000
 GUE  H21  CG   H20  104.76  3.000
 GUE  H21  CG   CD   108.02  3.000
 GUE  H20  CG   CD   107.93  3.000
 GUE  H21  CG   CB   110.45  3.000
 GUE  H20  CG   CB   109.22  3.000
 GUE  CD   CG   CB   115.87  3.000
 GUE  OE2  CD   OE1  126.23  3.000
 GUE  OE1  CD   CG   115.76  3.000
 GUE  OE2  CD   CG   118.01  3.000
 GUE  H23  C1   N10  124.03  3.000
 GUE  H23  C1   N5   123.40  3.000
 GUE  N10  C1   N5   112.56  3.000
 GUE  N    C11  O11  123.25  3.000
 GUE  N    C11  C1'  116.29  3.000
 GUE  O11  C11  C1'  120.43  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
 GUE  CONST_01  C4'  C3'  C2'  C1'     0.00   0.0  0
 GUE  CONST_02  C4'  C5'  C6'  C1'     0.00   0.0  0
 GUE  CONST_03  C5'  C6'  C1'  C2'     0.00   0.0  0
 GUE  CONST_04  C5'  C4'  C3'  C2'     0.00   0.0  0
 GUE  CONST_05  C6'  C1'  C2'  C3'     0.00   0.0  0
 GUE  CONST_06  C6'  C5'  C4'  C3'     0.00   0.0  0
 GUE  CONST_07  N10  C4'  C3'  C2'   180.00   0.0  0
 GUE  CONST_08  C6'  C5'  C4'  N10   180.00   0.0  0
 GUE  CONST_09  C4   N3   C2   N1      0.00   0.0  0
 GUE  CONST_10  C7   N8   C8A  N1    180.00   0.0  0
 GUE  CONST_11  C4A  C8A  N1   C2      0.00   0.0  0
 GUE  CONST_12  N8   C8A  N1   C2    180.00   0.0  0
 GUE  CONST_13  C8A  N1   C2   N3      0.00   0.0  0
 GUE  CONST_14  N10  C1   N5   C6      0.00   0.0  0
 GUE  CONST_15  C4'  N10  C9   C6    180.00   0.0  0
 GUE  CONST_16  C1   N10  C9   C6      0.00   0.0  0
 GUE  CONST_17  N5   C1   N10  C4'   180.00   0.0  0
 GUE  CONST_18  N10  C1   N5   C4A   180.00   0.0  0
 GUE  CONST_19  C7   N8   C8A  C4A     0.00   0.0  0
 GUE  CONST_20  C9   N10  C1   N5      0.00   0.0  0
 GUE  CONST_21  C11  C1'  C2'  C3'   180.00   0.0  0
 GUE  CONST_22  C11  C1'  C6'  C5'   180.00   0.0  0
 GUE  CONST_23  N2   C2   N3   C4    180.00   0.0  0
 GUE  CONST_24  N2   C2   N1   C8A   180.00   0.0  0
 GUE  CONST_25  H3   C3'  C2'  C1'   180.00   0.0  0
 GUE  CONST_26  H4   C5'  C6'  C1'   180.00   0.0  0
 GUE  CONST_27  H14  C6'  C1'  C2'   180.00   0.0  0
 GUE  CONST_28  H2   C2'  C3'  C4'   180.00   0.0  0
 GUE  CONST_29  H9   N8   C8A  N1      0.00   0.0  0
 GUE  CONST_30  H25  N1   C2   N3    180.00   0.0  0
 GUE  CONST_31  H23  C1   N5   C6    180.00   0.0  0
 GUE  CONST_32  H10  N2   C2   N1      0.00   0.0  0
 GUE  CONST_33  H11  N2   C2   N1    180.00   0.0  0
 GUE  CONST_34  CA   N    C11  C1'   180.00   0.0  0
 GUE  CONST_36  CA   N    C11  O11     0.00   0.0  0
 GUE  Var_01    C1   N5   C4A  C4     23.68  30.0  1
 GUE  Var_02    C8A  N8   C7   C6    -36.38  30.0  1
 GUE  Var_03    C1   N10  C4'  C3'   -23.67  30.0  2
 GUE  Var_04    H12  C9   N10  C4'    69.45  30.0  1
 GUE  Var_05    O11  C11  C1'  C2'  -154.52  30.0  2
 GUE  Var_06    CD   CG   CB   CA   -176.82  30.0  3
 GUE  Var_07    OE2  CD   CG   CB      5.44  30.0  3

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
 GUE  chir_01  C6  N5  C9  C7  negativ
 GUE  chir_02  CA  C   CB  N   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
 GUE  plan-1  C1'  0.020
 GUE  plan-1  C2'  0.020
 GUE  plan-1  C3'  0.020
 GUE  plan-1  C4'  0.020
 GUE  plan-1  C5'  0.020
 GUE  plan-1  N10  0.020
 GUE  plan-1  C6'  0.020
 GUE  plan-1  H2   0.020
 GUE  plan-1  H3   0.020
 GUE  plan-1  H4   0.020
 GUE  plan-1  H14  0.020
 GUE  plan-1  C11  0.020
 GUE  plan-2  CA   0.020
 GUE  plan-2  C    0.020
 GUE  plan-2  OX1  0.020
 GUE  plan-2  OX2  0.020
 GUE  plan-3  CG   0.020
 GUE  plan-3  CD   0.020
 GUE  plan-3  OE1  0.020
 GUE  plan-3  OE2  0.020
 GUE  plan-4  C1'  0.020
 GUE  plan-4  O11  0.020
 GUE  plan-4  N    0.020
 GUE  plan-4  CA   0.020
 GUE  plan-4  H15  0.020
 GUE  plan-4  C11  0.020
 GUE  plan-5  N1   0.020
 GUE  plan-5  C2   0.020
 GUE  plan-5  N3   0.020
 GUE  plan-5  C4   0.020
 GUE  plan-5  O4   0.020
 GUE  plan-5  C4A  0.020
 GUE  plan-5  N5   0.020
 GUE  plan-5  C7   0.020
 GUE  plan-5  N8   0.020
 GUE  plan-5  C8A  0.020
 GUE  plan-5  N2   0.020
 GUE  plan-5  H9   0.020
 GUE  plan-5  H10  0.020
 GUE  plan-5  H11  0.020
 GUE  plan-5  H25  0.020
 GUE  plan-6  C6   0.020
 GUE  plan-6  C4'  0.020
 GUE  plan-6  C4A  0.020
 GUE  plan-6  N5   0.020
 GUE  plan-6  C9   0.020
 GUE  plan-6  N10  0.020
 GUE  plan-6  C1   0.020
 GUE  plan-6  H23  0.020

