# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 23:10:03 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: N-({4-[(6aR)-3-amino-1-hydroxy-9-oxo-5,6,6a,7-tetrahydroimidazo[1,5-f]pteridin-8(9H)-yl]phenyl}carbonyl)-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(O)c2N3[C@H](CNc2n1)CN(C3=O)c4ccc(cc4)C(=O)N[C@@H](CCC(O)=O)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
 L34  L34  'N-({4-[(6aR)-3-amino-1-hydroxy-9-oxo-5,6,6a,7-tetrahydroimidazo[1,5-f]pteridin-8(9H)-yl]phenyl}carbonyl)-L-glutamic acid'  ligand  55  34  .  2021-08-13  2021-08-13  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_L34
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
 L34  N2A   N  NH2   0  -0.819   0.6751   0.2050   9.3226
 L34  N1    N  N     0  -0.517  -0.7186  -0.1656   7.5482
 L34  C2    C  CR6   0   0.534   0.4706   0.2370   7.9860
 L34  N3    N  N     0  -0.499   1.4759   0.6908   7.2363
 L34  C4    C  CR6   0   0.465   1.2564   0.7961   5.9363
 L34  O4A   O  OH1   0  -0.626   2.2807   1.2527   5.2260
 L34  C4A   C  CR6   0  -0.015   0.0375   0.4448   5.3605
 L34  N5    N  NR5   0  -0.590  -0.3304   0.6502   4.0141
 L34  C6    C  CR15  0  -0.148  -1.7466   0.7322   3.7070
 L34  C7    C  CH2   0  -0.255  -2.4560  -0.4436   4.3642
 L34  N8    N  NH1   0  -0.670  -2.1398  -0.4383   5.7697
 L34  C8A   C  CR6   0   0.517  -0.9354  -0.0661   6.2385
 L34  CX    C  CR5   0   0.767   0.4014   0.2684   2.9384
 L34  OX    O  O     0  -0.533   1.6061   0.0389   2.9648
 L34  C9    C  CH2   0  -0.323  -1.7552   0.7000   2.1813
 L34  N10   N  NR5   0  -0.621  -0.4207   0.2235   1.8462
 L34  C1B   C  CR6   0   0.382  -0.0442  -0.0502   0.5333
 L34  C2B   C  CR16  0  -0.294   1.1208  -0.7585   0.2140
 L34  C3B   C  CR16  0  -0.258   1.4235  -1.0315  -1.1055
 L34  C4B   C  CR6   0  -0.057   0.5994  -0.6096  -2.1463
 L34  C5B   C  CR16  0  -0.274  -0.5660   0.0783  -1.8228
 L34  C6B   C  CR16  0  -0.331  -0.8865   0.3544  -0.5058
 L34  C7B   C  C     0   0.557   0.9758  -0.9557  -3.5417
 L34  O7B   O  O     0  -0.480   1.7271  -1.8860  -3.7975
 L34  N     N  NH1   0  -0.665   0.4330  -0.1984  -4.5199
 L34  CA    C  CH1   0  -0.176   0.7469  -0.4595  -5.8997
 L34  CB    C  CH2   0  -0.474  -0.1519   0.3677  -6.8217
 L34  CG    C  CH2   0  -0.577  -1.6132  -0.0257  -6.6754
 L34  CD    C  C     0   0.555  -2.5138   0.7158  -7.6244
 L34  OE1   O  O     0  -0.442  -2.1549   1.5662  -8.4000
 L34  OE2   O  OH1   0  -0.595  -3.7767   0.3204  -7.5105
 L34  C     C  C     0   0.541   2.2045  -0.1886  -6.2447
 L34  O     O  O     0  -0.440   2.7738  -0.7408  -7.1519
 L34  OXT   O  OH1   0  -0.583   2.7498   0.7470  -5.4866
 L34  HN21  H  HNH2  0   0.390   0.0382  -0.3324   9.8850
 L34  HN22  H  HNH2  0   0.391   1.6216   0.2653   9.6563
 L34  HO4   H  HOH1  0   0.486   2.2032   0.9360   4.2972
 L34  H6    H  HCR5  0   0.304  -2.1621   1.6676   4.0846
 L34  H71   H  HCH2  0   0.278  -3.5340  -0.3461   4.2415
 L34  H72   H  HCH2  0   0.247  -2.1488  -1.3782   3.8792
 L34  HN8   H  HNH1  0   0.401  -2.8121  -0.7858   6.4336
 L34  H91   H  HCH2  0   0.285  -2.5192   0.0296   1.7854
 L34  H92   H  HCH2  0   0.286  -1.9283   1.6972   1.7729
 L34  H2B   H  HCR6  0   0.284   1.7858  -1.1112   0.9850
 L34  H3B   H  HCR6  0   0.263   2.3234  -1.5897  -1.3270
 L34  H5B   H  HCR6  0   0.260  -1.2623   0.3930  -2.5898
 L34  H6B   H  HCR6  0   0.289  -1.8038   0.8875  -0.3002
 L34  HN    H  HNH1  0   0.410   0.0486   0.7035  -4.2850
 L34  HA    H  HCH1  0   0.294   0.5759  -1.5179  -6.1105
 L34  HB1   H  HCH2  0   0.262  -0.0149   1.4323  -6.6160
 L34  HB2   H  HCH2  0   0.273   0.1709   0.1987  -7.8497
 L34  HG1   H  HCH2  0   0.289  -1.7380  -1.0984  -6.8513
 L34  HG2   H  HCH2  0   0.285  -1.9786   0.1490  -5.6595
 L34  HE2   H  HOH1  0   0.481  -4.3349   0.8065  -8.1357
 L34  HXT   H  HOH1  0   0.486   3.6640   0.9100  -5.7649

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
 L34  N2A  C2    single    1.353  0.020  1.353
 L34  N2A  HN21  single    0.890  0.020  1.040
 L34  N2A  HN22  single    0.890  0.020  1.040
 L34  N1   C2    aromatic  1.330  0.020  1.330
 L34  N1   C8A   aromatic  1.331  0.020  1.331
 L34  C2   N3    aromatic  1.334  0.020  1.334
 L34  N3   C4    aromatic  1.323  0.020  1.323
 L34  C4   O4A   single    1.327  0.020  1.327
 L34  C4   C4A   aromatic  1.393  0.020  1.393
 L34  O4A  HO4   single    0.850  0.020  0.980
 L34  C4A  N5    single    1.411  0.020  1.411
 L34  C4A  C8A   aromatic  1.406  0.020  1.406
 L34  N5   C6    single    1.451  0.020  1.451
 L34  N5   CX    single    1.356  0.020  1.356
 L34  C6   C7    single    1.522  0.020  1.522
 L34  C6   C9    single    1.526  0.020  1.526
 L34  C6   H6    single    0.970  0.020  1.090
 L34  C7   N8    single    1.441  0.020  1.441
 L34  C7   H71   single    0.970  0.020  1.090
 L34  C7   H72   single    0.970  0.020  1.090
 L34  N8   C8A   single    1.345  0.020  1.345
 L34  N8   HN8   single    0.860  0.020  1.020
 L34  CX   OX    double    1.227  0.020  1.227
 L34  CX   N10   single    1.368  0.020  1.368
 L34  C9   N10   single    1.456  0.020  1.456
 L34  C9   H91   single    0.970  0.020  1.090
 L34  C9   H92   single    0.970  0.020  1.090
 L34  N10  C1B   single    1.393  0.020  1.393
 L34  C1B  C2B   aromatic  1.400  0.020  1.400
 L34  C1B  C6B   aromatic  1.397  0.020  1.397
 L34  C2B  C3B   aromatic  1.381  0.020  1.381
 L34  C2B  H2B   single    0.930  0.020  1.080
 L34  C3B  C4B   aromatic  1.393  0.020  1.393
 L34  C3B  H3B   single    0.930  0.020  1.080
 L34  C4B  C5B   aromatic  1.391  0.020  1.391
 L34  C4B  C7B   single    1.486  0.020  1.486
 L34  C5B  C6B   aromatic  1.383  0.020  1.383
 L34  C5B  H5B   single    0.930  0.020  1.080
 L34  C6B  H6B   single    0.930  0.020  1.080
 L34  C7B  O7B   double    1.223  0.020  1.223
 L34  C7B  N     single    1.351  0.020  1.351
 L34  N    CA    single    1.439  0.020  1.439
 L34  N    HN    single    0.860  0.020  1.020
 L34  CA   CB    single    1.530  0.020  1.530
 L34  CA   C     single    1.522  0.020  1.522
 L34  CA   HA    single    0.970  0.020  1.090
 L34  CB   CG    single    1.520  0.020  1.520
 L34  CB   HB1   single    0.970  0.020  1.090
 L34  CB   HB2   single    0.970  0.020  1.090
 L34  CG   CD    single    1.504  0.020  1.504
 L34  CG   HG1   single    0.970  0.020  1.090
 L34  CG   HG2   single    0.970  0.020  1.090
 L34  CD   OE1   double    1.206  0.020  1.206
 L34  CD   OE2   single    1.328  0.020  1.328
 L34  OE2  HE2   single    0.850  0.020  0.980
 L34  C    O     double    1.205  0.020  1.205
 L34  C    OXT   single    1.322  0.020  1.322
 L34  OXT  HXT   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
 L34  HN22  N2A  HN21  116.28  3.000
 L34  HN22  N2A  C2    117.97  3.000
 L34  HN21  N2A  C2    118.01  3.000
 L34  C8A   N1   C2    116.55  3.000
 L34  N3    C2   N1    126.31  3.000
 L34  N3    C2   N2A   116.71  3.000
 L34  N1    C2   N2A   116.97  3.000
 L34  C4    N3   C2    117.03  3.000
 L34  C4A   C4   O4A   122.74  3.000
 L34  C4A   C4   N3    122.10  3.000
 L34  O4A   C4   N3    115.17  3.000
 L34  HO4   O4A  C4    109.48  3.000
 L34  C8A   C4A  N5    117.92  3.000
 L34  C8A   C4A  C4    116.03  3.000
 L34  N5    C4A  C4    125.86  3.000
 L34  CX    N5   C6    112.00  3.000
 L34  CX    N5   C4A   125.13  3.000
 L34  C6    N5   C4A   117.69  3.000
 L34  H6    C6   C9    111.22  3.000
 L34  H6    C6   C7    109.59  3.000
 L34  C9    C6   C7    114.37  3.000
 L34  H6    C6   N5    110.29  3.000
 L34  C9    C6   N5    102.47  3.000
 L34  C7    C6   N5    108.65  3.000
 L34  H72   C7   H71   107.68  3.000
 L34  H72   C7   N8    111.90  3.000
 L34  H71   C7   N8    109.07  3.000
 L34  H72   C7   C6    109.67  3.000
 L34  H71   C7   C6    110.09  3.000
 L34  N8    C7   C6    108.42  3.000
 L34  HN8   N8   C8A   117.62  3.000
 L34  HN8   N8   C7    119.71  3.000
 L34  C8A   N8   C7    122.52  3.000
 L34  N8    C8A  C4A   120.16  3.000
 L34  N8    C8A  N1    117.91  3.000
 L34  C4A   C8A  N1    121.91  3.000
 L34  N10   CX   OX    126.96  3.000
 L34  N10   CX   N5    108.56  3.000
 L34  OX    CX   N5    124.45  3.000
 L34  H92   C9   H91   108.33  3.000
 L34  H92   C9   N10   110.99  3.000
 L34  H91   C9   N10   110.93  3.000
 L34  H92   C9   C6    110.84  3.000
 L34  H91   C9   C6    112.32  3.000
 L34  N10   C9   C6    103.40  3.000
 L34  C1B   N10  C9    121.93  3.000
 L34  C1B   N10  CX    126.63  3.000
 L34  C9    N10  CX    110.87  3.000
 L34  C6B   C1B  C2B   118.58  3.000
 L34  C6B   C1B  N10   118.75  3.000
 L34  C2B   C1B  N10   122.63  3.000
 L34  H2B   C2B  C3B   118.92  3.000
 L34  H2B   C2B  C1B   121.06  3.000
 L34  C3B   C2B  C1B   120.02  3.000
 L34  H3B   C3B  C4B   119.69  3.000
 L34  H3B   C3B  C2B   118.69  3.000
 L34  C4B   C3B  C2B   121.62  3.000
 L34  C7B   C4B  C5B   123.06  3.000
 L34  C7B   C4B  C3B   118.76  3.000
 L34  C5B   C4B  C3B   118.14  3.000
 L34  H5B   C5B  C6B   117.87  3.000
 L34  H5B   C5B  C4B   121.18  3.000
 L34  C6B   C5B  C4B   120.93  3.000
 L34  H6B   C6B  C5B   118.44  3.000
 L34  H6B   C6B  C1B   120.86  3.000
 L34  C5B   C6B  C1B   120.70  3.000
 L34  N     C7B  O7B   121.46  3.000
 L34  N     C7B  C4B   116.59  3.000
 L34  O7B   C7B  C4B   121.95  3.000
 L34  HN    N    CA    117.97  3.000
 L34  HN    N    C7B   119.08  3.000
 L34  CA    N    C7B   120.33  3.000
 L34  HA    CA   C     106.17  3.000
 L34  HA    CA   CB    108.38  3.000
 L34  C     CA   CB    109.25  3.000
 L34  HA    CA   N     109.06  3.000
 L34  C     CA   N     113.20  3.000
 L34  CB    CA   N     110.58  3.000
 L34  HB2   CB   HB1   106.93  3.000
 L34  HB2   CB   CG    109.58  3.000
 L34  HB1   CB   CG    110.75  3.000
 L34  HB2   CB   CA    108.08  3.000
 L34  HB1   CB   CA    109.84  3.000
 L34  CG    CB   CA    111.51  3.000
 L34  HG2   CG   HG1   105.54  3.000
 L34  HG2   CG   CD    107.90  3.000
 L34  HG1   CG   CD    108.28  3.000
 L34  HG2   CG   CB    111.66  3.000
 L34  HG1   CG   CB    110.35  3.000
 L34  CD    CG   CB    112.79  3.000
 L34  OE2   CD   OE1   123.25  3.000
 L34  OE2   CD   CG    111.62  3.000
 L34  OE1   CD   CG    125.13  3.000
 L34  HE2   OE2  CD    110.06  3.000
 L34  OXT   C    O     124.13  3.000
 L34  OXT   C    CA    113.02  3.000
 L34  O     C    CA    122.79  3.000
 L34  HXT   OXT  C     110.09  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
 L34  CONST_01  C4   N3   C2   N1      0.00   0.0  0
 L34  CONST_02  C4   C4A  C8A  N1      0.00   0.0  0
 L34  CONST_03  C4A  C8A  N1   C2      0.00   0.0  0
 L34  CONST_04  C4A  C4   N3   C2      0.00   0.0  0
 L34  CONST_05  C8A  N1   C2   N3      0.00   0.0  0
 L34  CONST_06  C8A  C4A  C4   N3      0.00   0.0  0
 L34  CONST_07  C4B  C3B  C2B  C1B     0.00   0.0  0
 L34  CONST_08  C4B  C5B  C6B  C1B     0.00   0.0  0
 L34  CONST_09  C5B  C6B  C1B  C2B     0.00   0.0  0
 L34  CONST_10  C5B  C4B  C3B  C2B     0.00   0.0  0
 L34  CONST_11  C6B  C1B  C2B  C3B     0.00   0.0  0
 L34  CONST_12  C6B  C5B  C4B  C3B     0.00   0.0  0
 L34  CONST_13  C3B  C2B  C1B  N10   180.00   0.0  0
 L34  CONST_14  C5B  C6B  C1B  N10   180.00   0.0  0
 L34  CONST_16  C9   N10  CX   N5      0.00   0.0  0
 L34  CONST_17  C1B  N10  CX   N5    180.00   0.0  0
 L34  CONST_18  N10  CX   N5   C6      0.00   0.0  0
 L34  CONST_19  CX   N10  C9   C6      0.00   0.0  0
 L34  CONST_20  C1B  N10  C9   C6    180.00   0.0  0
 L34  CONST_21  C8A  N1   C2   N2A   180.00   0.0  0
 L34  CONST_22  C4   N3   C2   N2A   180.00   0.0  0
 L34  CONST_23  O4A  C4   N3   C2    180.00   0.0  0
 L34  CONST_24  N5   C4A  C4   O4A     0.00   0.0  0
 L34  CONST_25  C8A  C4A  C4   O4A   180.00   0.0  0
 L34  CONST_26  C7B  C4B  C3B  C2B   180.00   0.0  0
 L34  CONST_27  C7B  C4B  C5B  C6B   180.00   0.0  0
 L34  CONST_29  OX   CX   N5   C6    180.00   0.0  0
 L34  CONST_30  C9   N10  CX   OX    180.00   0.0  0
 L34  CONST_31  C1B  N10  CX   OX      0.00   0.0  0
 L34  CONST_32  H2B  C2B  C1B  N10     0.00   0.0  0
 L34  CONST_33  H6B  C6B  C1B  N10     0.00   0.0  0
 L34  CONST_34  H3B  C3B  C2B  C1B   180.00   0.0  0
 L34  CONST_35  H5B  C5B  C6B  C1B   180.00   0.0  0
 L34  CONST_38  CA   N    C7B  C4B   180.00   0.0  0
 L34  CONST_40  CA   N    C7B  O7B     0.00   0.0  0
 L34  CONST_41  HXT  OXT  C    CA    180.00   0.0  0
 L34  CONST_42  HE2  OE2  CD   CG    180.00   0.0  0
 L34  Var_01    C7   N8   C8A  N1   -176.39  30.0  1
 L34  Var_02    C6   N5   C4A  C4   -155.84  30.0  1
 L34  Var_03    C8A  N8   C7   C6    -35.60  30.0  1
 L34  Var_04    C2B  C1B  N10  CX     22.81  30.0  2
 L34  Var_05    H91  C9   N10  CX   -133.77  30.0  1
 L34  Var_06    O7B  C7B  C4B  C3B    21.47  30.0  2
 L34  Var_07    CD   CG   CB   CA   -176.79  30.0  3
 L34  Var_08    OE1  CD   CG   CB     -2.24  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
 L34  chir_01  C6  N5  C7  C9  positiv
 L34  chir_02  CA  N   CB  C   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
 L34  plan-1  N10   0.020
 L34  plan-1  C1B   0.020
 L34  plan-1  C2B   0.020
 L34  plan-1  C3B   0.020
 L34  plan-1  C4B   0.020
 L34  plan-1  C5B   0.020
 L34  plan-1  C6B   0.020
 L34  plan-1  C7B   0.020
 L34  plan-1  H2B   0.020
 L34  plan-1  H3B   0.020
 L34  plan-1  H5B   0.020
 L34  plan-1  H6B   0.020
 L34  plan-2  CG    0.020
 L34  plan-2  CD    0.020
 L34  plan-2  OE1   0.020
 L34  plan-2  OE2   0.020
 L34  plan-2  HE2   0.020
 L34  plan-3  CA    0.020
 L34  plan-3  C     0.020
 L34  plan-3  O     0.020
 L34  plan-3  OXT   0.020
 L34  plan-3  HXT   0.020
 L34  plan-4  C4B   0.020
 L34  plan-4  C7B   0.020
 L34  plan-4  O7B   0.020
 L34  plan-4  N     0.020
 L34  plan-4  CA    0.020
 L34  plan-4  HN    0.020
 L34  plan-5  N2A   0.020
 L34  plan-5  C2    0.020
 L34  plan-5  HN21  0.020
 L34  plan-5  HN22  0.020
 L34  plan-6  N2A   0.020
 L34  plan-6  N1    0.020
 L34  plan-6  C2    0.020
 L34  plan-6  N3    0.020
 L34  plan-6  C4    0.020
 L34  plan-6  O4A   0.020
 L34  plan-6  C4A   0.020
 L34  plan-6  N5    0.020
 L34  plan-6  N8    0.020
 L34  plan-6  C8A   0.020
 L34  plan-7  C4A   0.020
 L34  plan-7  N5    0.020
 L34  plan-7  C6    0.020
 L34  plan-7  CX    0.020
 L34  plan-7  OX    0.020
 L34  plan-7  C9    0.020
 L34  plan-7  N10   0.020
 L34  plan-7  C1B   0.020

