# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 17:29:46 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: N-{4-[(2-amino-4-hydroxy-7H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl]benzoyl}-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(O)c2c(Cc3ccc(cc3)C(=O)N[C@@H](CCC(O)=O)C(O)=O)c[nH]c2n1
#
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
 2XB  2XB  'N-{4-[(2-amino-4-hydroxy-7H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl]benzoyl}-L-glutamic acid'  ligand  49  30  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2XB
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
 2XB  OE1  O  OH1   0  -0.595   4.6011  -4.2093   1.1711
 2XB  CT4  C  C     0   0.554   5.2087  -3.1914   0.5711
 2XB  OE2  O  O     0  -0.442   6.1853  -3.3227  -0.1235
 2XB  CT3  C  CH2   0  -0.577   4.5284  -1.8848   0.8716
 2XB  CT2  C  CH2   0  -0.462   5.2036  -0.6986   0.2029
 2XB  CT1  C  CH1   0  -0.199   4.4905   0.6127   0.5467
 2XB  CT5  C  C     0   0.550   5.2830   1.8043   0.0250
 2XB  OT1  O  O     0  -0.430   4.9633   2.4754  -0.9201
 2XB  OXT  O  OH1   0  -0.590   6.3860   1.9953   0.7335
 2XB  NT1  N  NH1   0  -0.653   3.1589   0.6148   0.0086
 2XB  CAV  C  C     0   0.550   2.2341   1.5015   0.4378
 2XB  OAD  O  O     0  -0.481   2.4694   2.2957   1.3367
 2XB  CAY  C  CR6   0  -0.061   0.9054   1.4429  -0.2326
 2XB  CAJ  C  CR16  0  -0.276   0.4339   0.2983  -0.8748
 2XB  CAH  C  CR16  0  -0.271  -0.8185   0.2903  -1.4659
 2XB  CAK  C  CR16  0  -0.255   0.0890   2.5697  -0.1871
 2XB  CAI  C  CR16  0  -0.305  -1.1588   2.5572  -0.7876
 2XB  CAX  C  CR6   0   0.149  -1.6303   1.4209  -1.4378
 2XB  CAO  C  CH2   0  -0.605  -2.9809   1.4226  -2.1124
 2XB  CAZ  C  CR5   0   0.020  -3.8130   0.2270  -1.7863
 2XB  CBC  C  CR56  0  -0.165  -4.3725  -0.1302  -0.5150
 2XB  CBA  C  CR6   0   0.427  -4.4218   0.3813   0.7828
 2XB  OAE  O  OH1   0  -0.588  -3.8143   1.5260   1.0567
 2XB  NAS  N  N     0  -0.523  -5.0601  -0.2448   1.7471
 2XB  CAW  C  CR6   0   0.533  -5.6812  -1.4058   1.4580
 2XB  NAA  N  NH2   0  -0.823  -6.3616  -1.9813   2.4781
 2XB  NAP  N  N     0  -0.502  -5.7176  -2.0049   0.2756
 2XB  CBB  C  CR56  0   0.510  -5.0603  -1.3429  -0.6743
 2XB  NAR  N  NR15  0  -0.673  -4.9323  -1.7123  -1.9664
 2XB  CAL  C  CR15  0  -0.083  -4.1807  -0.7690  -2.6388
 2XB  H1   H  HOH1  0   0.480   5.0612  -5.0367   0.9659
 2XB  H2   H  HCH2  0   0.287   3.4803  -1.9706   0.5722
 2XB  H3   H  HCH2  0   0.273   6.2403  -0.6313   0.5322
 2XB  H4   H  HCH1  0   0.295   4.4328   0.7045   1.6348
 2XB  H5   H  HOH1  0   0.486   6.8987   2.7303   0.3643
 2XB  H6   H  HNH1  0   0.408   3.0236   0.1686  -0.8854
 2XB  H7   H  HCR6  0   0.254   1.0238  -0.6099  -0.8970
 2XB  H8   H  HCR6  0   0.252  -1.1730  -0.6137  -1.9466
 2XB  H9   H  HCR6  0   0.256   0.4321   3.4635   0.3170
 2XB  H10  H  HCR6  0   0.251  -1.7791   3.4444  -0.7471
 2XB  H11  H  HCH2  0   0.258  -3.5092   2.3391  -1.8410
 2XB  H12  H  HCH2  0   0.269  -2.8345   1.4655  -3.1955
 2XB  H14  H  HNH2  0   0.390  -6.1492  -1.6818   3.4139
 2XB  H15  H  HNH2  0   0.390  -6.6432  -2.9409   2.3737
 2XB  H16  H  HNR5  0   0.408  -5.3310  -2.5408  -2.3764
 2XB  H17  H  HCR5  0   0.286  -3.9643  -0.8876  -3.6884
 2XB  H18  H  HCH2  0   0.289   4.5131  -1.7506   1.9575
 2XB  H19  H  HCH2  0   0.259   5.2252  -0.8276  -0.8823
 2XB  H20  H  HOH1  0   0.475  -3.9346   1.7317   1.9945

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
 2XB  OT1  CT5  double    1.202  0.020  1.202
 2XB  CT5  CT1  single    1.523  0.020  1.523
 2XB  CT5  OXT  single    1.325  0.020  1.325
 2XB  NAA  CAW  single    1.355  0.020  1.355
 2XB  CT1  CT2  single    1.532  0.020  1.532
 2XB  CT1  NT1  single    1.436  0.020  1.436
 2XB  CT2  CT3  single    1.520  0.020  1.520
 2XB  CAW  NAS  aromatic  1.348  0.020  1.348
 2XB  CAW  NAP  aromatic  1.326  0.020  1.326
 2XB  OAD  CAV  double    1.222  0.020  1.222
 2XB  NAS  CBA  aromatic  1.315  0.020  1.315
 2XB  OE2  CT4  double    1.206  0.020  1.206
 2XB  NT1  CAV  single    1.351  0.020  1.351
 2XB  CAV  CAY  single    1.489  0.020  1.489
 2XB  CT3  CT4  single    1.503  0.020  1.503
 2XB  NAP  CBB  aromatic  1.331  0.020  1.331
 2XB  CT4  OE1  single    1.329  0.020  1.329
 2XB  CAJ  CAY  aromatic  1.395  0.020  1.395
 2XB  CAJ  CAH  aromatic  1.385  0.020  1.385
 2XB  CBA  OAE  single    1.324  0.020  1.324
 2XB  CBA  CBC  aromatic  1.396  0.020  1.396
 2XB  CAY  CAK  aromatic  1.392  0.020  1.392
 2XB  CBB  CBC  aromatic  1.403  0.020  1.403
 2XB  CBB  NAR  aromatic  1.350  0.020  1.350
 2XB  CAH  CAX  aromatic  1.392  0.020  1.392
 2XB  CBC  CAZ  aromatic  1.434  0.020  1.434
 2XB  CAK  CAI  aromatic  1.385  0.020  1.385
 2XB  NAR  CAL  aromatic  1.381  0.020  1.381
 2XB  CAX  CAI  aromatic  1.391  0.020  1.391
 2XB  CAX  CAO  single    1.510  0.020  1.510
 2XB  CAZ  CAL  aromatic  1.362  0.020  1.362
 2XB  CAZ  CAO  single    1.493  0.020  1.493
 2XB  OE1  H1   single    0.850  0.020  0.980
 2XB  CT3  H2   single    0.970  0.020  1.090
 2XB  CT2  H3   single    0.970  0.020  1.090
 2XB  CT1  H4   single    0.970  0.020  1.090
 2XB  OXT  H5   single    0.850  0.020  0.980
 2XB  NT1  H6   single    0.890  0.020  1.040
 2XB  CAJ  H7   single    0.930  0.020  1.080
 2XB  CAH  H8   single    0.930  0.020  1.080
 2XB  CAK  H9   single    0.930  0.020  1.080
 2XB  CAI  H10  single    0.930  0.020  1.080
 2XB  CAO  H11  single    0.970  0.020  1.090
 2XB  CAO  H12  single    0.970  0.020  1.090
 2XB  NAA  H14  single    0.890  0.020  1.040
 2XB  NAA  H15  single    0.890  0.020  1.040
 2XB  NAR  H16  single    0.860  0.020  1.020
 2XB  CAL  H17  single    0.930  0.020  1.080
 2XB  CT3  H18  single    0.970  0.020  1.090
 2XB  CT2  H19  single    0.970  0.020  1.090
 2XB  OAE  H20  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
 2XB  H1   OE1  CT4  109.97  3.000
 2XB  CT3  CT4  OE2  125.19  3.000
 2XB  CT3  CT4  OE1  111.63  3.000
 2XB  OE2  CT4  OE1  123.17  3.000
 2XB  H18  CT3  H2   105.54  3.000
 2XB  H18  CT3  CT2  110.31  3.000
 2XB  H2   CT3  CT2  111.51  3.000
 2XB  H18  CT3  CT4  108.14  3.000
 2XB  H2   CT3  CT4  108.11  3.000
 2XB  CT2  CT3  CT4  112.91  3.000
 2XB  H19  CT2  H3   106.77  3.000
 2XB  H19  CT2  CT1  109.45  3.000
 2XB  H3   CT2  CT1  108.79  3.000
 2XB  H19  CT2  CT3  110.70  3.000
 2XB  H3   CT2  CT3  109.75  3.000
 2XB  CT1  CT2  CT3  111.26  3.000
 2XB  H4   CT1  NT1  108.89  3.000
 2XB  H4   CT1  CT5  107.61  3.000
 2XB  NT1  CT1  CT5  110.67  3.000
 2XB  H4   CT1  CT2  108.65  3.000
 2XB  NT1  CT1  CT2  110.42  3.000
 2XB  CT5  CT1  CT2  110.53  3.000
 2XB  OXT  CT5  OT1  124.14  3.000
 2XB  OXT  CT5  CT1  111.27  3.000
 2XB  OT1  CT5  CT1  124.58  3.000
 2XB  H5   OXT  CT5  110.24  3.000
 2XB  H6   NT1  CAV  118.70  3.000
 2XB  H6   NT1  CT1  117.12  3.000
 2XB  CAV  NT1  CT1  121.10  3.000
 2XB  CAY  CAV  OAD  121.89  3.000
 2XB  CAY  CAV  NT1  116.22  3.000
 2XB  OAD  CAV  NT1  121.88  3.000
 2XB  CAK  CAY  CAJ  118.75  3.000
 2XB  CAK  CAY  CAV  118.46  3.000
 2XB  CAJ  CAY  CAV  122.76  3.000
 2XB  H7   CAJ  CAH  118.61  3.000
 2XB  H7   CAJ  CAY  120.90  3.000
 2XB  CAH  CAJ  CAY  120.47  3.000
 2XB  H8   CAH  CAX  119.72  3.000
 2XB  H8   CAH  CAJ  119.35  3.000
 2XB  CAX  CAH  CAJ  120.93  3.000
 2XB  H9   CAK  CAI  119.68  3.000
 2XB  H9   CAK  CAY  119.86  3.000
 2XB  CAI  CAK  CAY  120.46  3.000
 2XB  H10  CAI  CAX  119.49  3.000
 2XB  H10  CAI  CAK  119.50  3.000
 2XB  CAX  CAI  CAK  121.02  3.000
 2XB  CAO  CAX  CAI  120.73  3.000
 2XB  CAO  CAX  CAH  120.90  3.000
 2XB  CAI  CAX  CAH  118.36  3.000
 2XB  H12  CAO  H11  106.14  3.000
 2XB  H12  CAO  CAZ  108.81  3.000
 2XB  H11  CAO  CAZ  110.38  3.000
 2XB  H12  CAO  CAX  108.83  3.000
 2XB  H11  CAO  CAX  108.82  3.000
 2XB  CAZ  CAO  CAX  113.59  3.000
 2XB  CAL  CAZ  CBC  105.52  3.000
 2XB  CAL  CAZ  CAO  126.84  3.000
 2XB  CBC  CAZ  CAO  127.63  3.000
 2XB  CBB  CBC  CBA  113.89  3.000
 2XB  CBB  CBC  CAZ  107.81  3.000
 2XB  CBA  CBC  CAZ  138.30  3.000
 2XB  NAS  CBA  OAE  118.84  3.000
 2XB  OAE  CBA  CBC  119.53  3.000
 2XB  NAS  CBA  CBC  121.63  3.000
 2XB  H20  OAE  CBA  109.10  3.000
 2XB  CAW  NAS  CBA  118.45  3.000
 2XB  NAP  CAW  NAA  117.76  3.000
 2XB  NAP  CAW  NAS  126.37  3.000
 2XB  NAA  CAW  NAS  115.84  3.000
 2XB  H15  NAA  H14  116.12  3.000
 2XB  H15  NAA  CAW  117.90  3.000
 2XB  H14  NAA  CAW  117.92  3.000
 2XB  CBB  NAP  CAW  113.45  3.000
 2XB  NAR  CBB  NAP  126.41  3.000
 2XB  NAR  CBB  CBC  107.38  3.000
 2XB  NAP  CBB  CBC  126.21  3.000
 2XB  H16  NAR  CAL  125.41  3.000
 2XB  H16  NAR  CBB  125.28  3.000
 2XB  CAL  NAR  CBB  109.31  3.000
 2XB  H17  CAL  NAR  120.54  3.000
 2XB  H17  CAL  CAZ  129.48  3.000
 2XB  NAR  CAL  CAZ  109.98  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
 2XB  CONST_01  CAX  CAH  CAJ  CAY     0.00   0.0  0
 2XB  CONST_02  CAX  CAI  CAK  CAY     0.00   0.0  0
 2XB  CONST_03  CAI  CAK  CAY  CAJ     0.00   0.0  0
 2XB  CONST_04  CAI  CAX  CAH  CAJ     0.00   0.0  0
 2XB  CONST_05  CAK  CAY  CAJ  CAH     0.00   0.0  0
 2XB  CONST_06  CAK  CAI  CAX  CAH     0.00   0.0  0
 2XB  CONST_07  NAS  CBA  CBC  CAZ   180.00   0.0  0
 2XB  CONST_08  NAP  CBB  CBC  CAZ   180.00   0.0  0
 2XB  CONST_09  NAR  CBB  CBC  CAZ     0.00   0.0  0
 2XB  CONST_10  CBB  NAR  CAL  CAZ     0.00   0.0  0
 2XB  CONST_11  CAW  NAS  CBA  CBC     0.00   0.0  0
 2XB  CONST_12  CAW  NAP  CBB  CBC     0.00   0.0  0
 2XB  CONST_13  CAL  NAR  CBB  CBC     0.00   0.0  0
 2XB  CONST_14  NAR  CAL  CAZ  CBC     0.00   0.0  0
 2XB  CONST_15  NAP  CAW  NAS  CBA     0.00   0.0  0
 2XB  CONST_16  NAP  CBB  CBC  CBA     0.00   0.0  0
 2XB  CONST_17  NAR  CBB  CBC  CBA   180.00   0.0  0
 2XB  CONST_18  CAL  CAZ  CBC  CBA   180.00   0.0  0
 2XB  CONST_19  CBB  NAP  CAW  NAS     0.00   0.0  0
 2XB  CONST_20  CBB  CBC  CBA  NAS     0.00   0.0  0
 2XB  CONST_21  NAR  CBB  NAP  CAW   180.00   0.0  0
 2XB  CONST_22  CAL  NAR  CBB  NAP   180.00   0.0  0
 2XB  CONST_23  CAL  CAZ  CBC  CBB     0.00   0.0  0
 2XB  CONST_24  CAH  CAJ  CAY  CAV   180.00   0.0  0
 2XB  CONST_25  CAI  CAK  CAY  CAV   180.00   0.0  0
 2XB  CONST_26  CAO  CAX  CAH  CAJ   180.00   0.0  0
 2XB  CONST_27  CAO  CAX  CAI  CAK   180.00   0.0  0
 2XB  CONST_28  CBA  CBC  CAZ  CAO     0.00   0.0  0
 2XB  CONST_29  CBB  CBC  CAZ  CAO   180.00   0.0  0
 2XB  CONST_30  NAR  CAL  CAZ  CAO   180.00   0.0  0
 2XB  CONST_31  OAE  CBA  CBC  CAZ     0.00   0.0  0
 2XB  CONST_32  NAA  CAW  NAS  CBA   180.00   0.0  0
 2XB  CONST_33  CAW  NAS  CBA  OAE   180.00   0.0  0
 2XB  CONST_34  CBB  CBC  CBA  OAE   180.00   0.0  0
 2XB  CONST_35  CBB  NAP  CAW  NAA   180.00   0.0  0
 2XB  CONST_36  H8   CAH  CAJ  CAY   180.00   0.0  0
 2XB  CONST_37  H10  CAI  CAK  CAY   180.00   0.0  0
 2XB  CONST_38  H9   CAK  CAY  CAJ   180.00   0.0  0
 2XB  CONST_39  H7   CAJ  CAY  CAK   180.00   0.0  0
 2XB  CONST_40  H16  NAR  CAL  CAZ   180.00   0.0  0
 2XB  CONST_41  H17  CAL  CAZ  CBC   180.00   0.0  0
 2XB  CONST_43  H15  NAA  CAW  NAS   180.00   0.0  0
 2XB  CONST_44  CAY  CAV  NT1  CT1   180.00   0.0  0
 2XB  CONST_46  OAD  CAV  NT1  CT1     0.00   0.0  0
 2XB  CONST_47  H1   OE1  CT4  OE2     0.00   0.0  0
 2XB  CONST_48  H5   OXT  CT5  CT1   180.00   0.0  0
 2XB  Var_01    CAZ  CAO  CAX  CAH    47.96  30.0  2
 2XB  Var_02    CBC  CAZ  CAO  CAX    66.31  30.0  3
 2XB  Var_03    CAJ  CAY  CAV  NT1    23.36  30.0  2
 2XB  Var_04    CT2  CT3  CT4  OE1   179.79  30.0  2
 2XB  Var_05    CT1  CT2  CT3  CT4  -179.36  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
 2XB  chir_01  CT1  CT5  CT2  NT1  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
 2XB  plan-1  CAV  0.020
 2XB  plan-1  CAY  0.020
 2XB  plan-1  CAJ  0.020
 2XB  plan-1  CAH  0.020
 2XB  plan-1  CAK  0.020
 2XB  plan-1  CAI  0.020
 2XB  plan-1  CAX  0.020
 2XB  plan-1  CAO  0.020
 2XB  plan-1  H7   0.020
 2XB  plan-1  H8   0.020
 2XB  plan-1  H9   0.020
 2XB  plan-1  H10  0.020
 2XB  plan-2  CAO  0.020
 2XB  plan-2  CAZ  0.020
 2XB  plan-2  CBC  0.020
 2XB  plan-2  CBA  0.020
 2XB  plan-2  OAE  0.020
 2XB  plan-2  NAS  0.020
 2XB  plan-2  CAW  0.020
 2XB  plan-2  NAA  0.020
 2XB  plan-2  NAP  0.020
 2XB  plan-2  CBB  0.020
 2XB  plan-2  NAR  0.020
 2XB  plan-2  CAL  0.020
 2XB  plan-2  H16  0.020
 2XB  plan-2  H17  0.020
 2XB  plan-3  CT1  0.020
 2XB  plan-3  NT1  0.020
 2XB  plan-3  CAV  0.020
 2XB  plan-3  OAD  0.020
 2XB  plan-3  CAY  0.020
 2XB  plan-3  H6   0.020
 2XB  plan-4  CAW  0.020
 2XB  plan-4  NAA  0.020
 2XB  plan-4  H14  0.020
 2XB  plan-4  H15  0.020
 2XB  plan-5  OE1  0.020
 2XB  plan-5  CT4  0.020
 2XB  plan-5  OE2  0.020
 2XB  plan-5  CT3  0.020
 2XB  plan-5  H1   0.020
 2XB  plan-6  CT1  0.020
 2XB  plan-6  CT5  0.020
 2XB  plan-6  OT1  0.020
 2XB  plan-6  OXT  0.020
 2XB  plan-6  H5   0.020

