# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 04:49:45 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: N-(4-{[(2-amino-4-oxo-3,4-dihydropteridin-6-yl)methyl]amino}-2-hydroxybenzene-1-carbonyl)-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2ncc(CNc3ccc(c(O)c3)C(=O)N[C@@H](CCC(O)=O)C(O)=O)nc2C(=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
 G7D  G7D  'N-(4-{[(2-amino-4-oxo-3,4-dihydropteridin-6-yl)methyl]amino}-2-hydroxybenzene-1-carbonyl)-L-glutamic acid'  ligand  50  33  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_G7D
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
 G7D  C4   C  CR6    0   0.537   -7.2187   1.2382  -0.8555
 G7D  C6   C  CR6    0   0.149   -4.0143   0.3609   0.5233
 G7D  C7   C  CR16   0  -0.073   -4.4022  -0.5761   1.5007
 G7D  C9   C  CH2    0  -0.351   -2.5659   0.6849   0.3033
 G7D  N1   N  N      0  -0.504   -7.8718  -0.6657   1.1805
 G7D  N3   N  NR16   0  -0.714   -8.4904   0.8013  -0.5514
 G7D  OE1  O  O      0  -0.609    7.9598   2.8742   1.5044
 G7D  CD   C  C      0   0.412    7.2781   3.0372   0.4733
 G7D  OE2  O  OC    -1  -0.633    7.1440   4.1048  -0.1619
 G7D  CB   C  CH2    0  -0.450    6.6887   0.5244   0.6842
 G7D  CA   C  CH1    0  -0.191    5.9724  -0.6649   0.0443
 G7D  C    C  C      0   0.414    6.3189  -1.9810   0.7883
 G7D  OXT  O  OC    -1  -0.618    7.4973  -2.3652   0.6487
 G7D  O    O  O      0  -0.598    5.4256  -2.5177   1.4647
 G7D  N    N  NH1    0  -0.643    4.5481  -0.4074   0.0095
 G7D  OAU  O  O      0  -0.566    4.1363  -1.9504  -1.5681
 G7D  CAR  C  CR6    0  -0.232    2.2576  -0.8958  -0.6072
 G7D  CAN  C  CR6    0   0.373    1.3683  -1.7238  -1.3329
 G7D  CAO  C  CR16   0  -0.455   -0.0039  -1.5550  -1.2136
 G7D  OAS  O  OH1    0  -0.645    1.8130  -2.6820  -2.1460
 G7D  CAQ  C  CR16   0  -0.283    1.6930   0.1072   0.1845
 G7D  CAP  C  CR16   0  -0.363    0.3332   0.2930   0.2984
 G7D  CAM  C  CR6    0   0.409   -0.5460  -0.5590  -0.3963
 G7D  N10  N  NH1    0  -0.696   -1.9041  -0.4573  -0.2860
 G7D  N5   N  N      0  -0.361   -4.9224   0.9410  -0.2267
 G7D  C4A  C  CR66   0  -0.045   -6.1945   0.6125  -0.0204
 G7D  O4   O  O      0  -0.436   -7.0173   2.0513  -1.7324
 G7D  C2   C  CR6    0   0.700   -8.7826  -0.1051   0.4307
 G7D  C8A  C  CR66   0   0.396   -6.5879  -0.3177   0.9559
 G7D  N8   N  N      0  -0.385   -5.6501  -0.9069   1.7191
 G7D  H1   H  HCR6   0   0.281   -3.6492  -1.0561   2.1175
 G7D  H2   H  HCH2   0   0.255   -2.4920   1.5851  -0.3169
 G7D  H3   H  HCH2   0   0.264   -2.1030   0.9124   1.2655
 G7D  H4   H  HNH2   0   0.420  -10.3164  -1.1046   1.2805
 G7D  H5   H  HNH2   0   0.423  -10.7901  -0.0558  -0.0005
 G7D  H6   H  HNR6   0   0.433   -9.2464   1.1864  -1.1049
 G7D  H8   H  HCH2   0   0.220    5.4594   2.0906  -0.1590
 G7D  H9   H  HCH2   0   0.220    6.8370   1.6693  -1.1277
 G7D  H10  H  HCH2   0   0.229    7.7468   0.2727   0.7549
 G7D  H11  H  HCH2   0   0.212    6.3364   0.6494   1.7138
 G7D  H12  H  HCH1   0   0.231    6.3234  -0.7593  -0.9869
 G7D  H14  H  HNH1   0   0.396    4.1716   0.1156   0.7831
 G7D  H15  H  HCR6   0   0.261   -0.6608  -2.2117  -1.7728
 G7D  H16  H  HOH1   0   0.472    2.8081  -2.6138  -2.1229
 G7D  H17  H  HCR6   0   0.247    2.3264   0.7973   0.7280
 G7D  H18  H  HCR6   0   0.268   -0.0360   1.1017   0.9122
 G7D  H19  H  HNH1   0   0.392   -2.4258  -0.9153  -1.0177
 G7D  N2   N  NH2    0  -0.820  -10.0683  -0.3965   0.6108
 G7D  CAT  C  C      0   0.632    3.7090  -1.1211  -0.7401
 G7D  CG   C  CH2    0  -0.577    6.5190   1.8222  -0.0894

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
 G7D  N2   C2   single    1.331  0.020  1.331
 G7D  C2   N1   double    1.306  0.020  1.306
 G7D  C2   N3   single    1.368  0.020  1.368
 G7D  N1   C8A  single    1.349  0.020  1.349
 G7D  N3   C4   single    1.379  0.020  1.379
 G7D  OE1  CD   deloc     1.247  0.020  1.247
 G7D  C8A  N8   aromatic  1.345  0.020  1.345
 G7D  C8A  C4A  aromatic  1.405  0.020  1.405
 G7D  C4   C4A  single    1.462  0.020  1.462
 G7D  C4   O4   double    1.213  0.020  1.213
 G7D  N8   C7   aromatic  1.309  0.020  1.309
 G7D  CD   CG   single    1.539  0.020  1.539
 G7D  CD   OE2  deloc     1.250  0.020  1.250
 G7D  C4A  N5   aromatic  1.330  0.020  1.330
 G7D  CG   CB   single    1.520  0.020  1.520
 G7D  O    C    deloc     1.242  0.020  1.242
 G7D  C7   C6   aromatic  1.408  0.020  1.408
 G7D  N5   C6   aromatic  1.313  0.020  1.313
 G7D  C    OXT  deloc     1.247  0.020  1.247
 G7D  C    CA   single    1.551  0.020  1.551
 G7D  C6   C9   single    1.500  0.020  1.500
 G7D  CB   CA   single    1.529  0.020  1.529
 G7D  CA   N    single    1.448  0.020  1.448
 G7D  N    CAT  single    1.332  0.020  1.332
 G7D  CAQ  CAP  aromatic  1.377  0.020  1.377
 G7D  CAQ  CAR  aromatic  1.397  0.020  1.397
 G7D  CAP  CAM  aromatic  1.408  0.020  1.408
 G7D  C9   N10  single    1.446  0.020  1.446
 G7D  CAT  CAR  single    1.475  0.020  1.475
 G7D  CAT  OAU  double    1.247  0.020  1.247
 G7D  CAR  CAN  aromatic  1.415  0.020  1.415
 G7D  CAM  N10  single    1.366  0.020  1.366
 G7D  CAM  CAO  aromatic  1.398  0.020  1.398
 G7D  CAN  CAO  aromatic  1.388  0.020  1.388
 G7D  CAN  OAS  single    1.333  0.020  1.333
 G7D  C7   H1   single    0.930  0.020  1.080
 G7D  C9   H2   single    0.970  0.020  1.090
 G7D  C9   H3   single    0.970  0.020  1.090
 G7D  N2   H4   single    0.860  0.020  1.020
 G7D  N2   H5   single    0.860  0.020  1.020
 G7D  N3   H6   single    0.860  0.020  1.020
 G7D  CG   H8   single    0.970  0.020  1.090
 G7D  CG   H9   single    0.970  0.020  1.090
 G7D  CB   H10  single    0.970  0.020  1.090
 G7D  CB   H11  single    0.970  0.020  1.090
 G7D  CA   H12  single    0.970  0.020  1.090
 G7D  N    H14  single    0.890  0.020  1.040
 G7D  CAO  H15  single    0.930  0.020  1.080
 G7D  OAS  H16  single    0.850  0.020  0.980
 G7D  CAQ  H17  single    0.930  0.020  1.080
 G7D  CAP  H18  single    0.930  0.020  1.080
 G7D  N10  H19  single    0.890  0.020  1.040

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
 G7D  O4   C4   C4A  125.71  3.000
 G7D  O4   C4   N3   121.68  3.000
 G7D  C4A  C4   N3   112.61  3.000
 G7D  N5   C6   C9   119.24  3.000
 G7D  C9   C6   C7   120.75  3.000
 G7D  N5   C6   C7   119.99  3.000
 G7D  H1   C7   N8   117.04  3.000
 G7D  H1   C7   C6   119.84  3.000
 G7D  N8   C7   C6   123.11  3.000
 G7D  H3   C9   H2   107.40  3.000
 G7D  H3   C9   N10  109.26  3.000
 G7D  H2   C9   N10  112.80  3.000
 G7D  H3   C9   C6   108.97  3.000
 G7D  H2   C9   C6   109.00  3.000
 G7D  N10  C9   C6   109.33  3.000
 G7D  C8A  N1   C2   117.21  3.000
 G7D  H6   N3   C2   118.99  3.000
 G7D  H6   N3   C4   116.58  3.000
 G7D  C2   N3   C4   124.43  3.000
 G7D  CG   CD   OE2  115.82  3.000
 G7D  OE2  CD   OE1  126.22  3.000
 G7D  CG   CD   OE1  117.96  3.000
 G7D  H11  CB   H10  106.11  3.000
 G7D  H11  CB   CA   109.36  3.000
 G7D  H10  CB   CA   107.60  3.000
 G7D  H11  CB   CG   110.18  3.000
 G7D  H10  CB   CG   109.79  3.000
 G7D  CA   CB   CG   113.50  3.000
 G7D  H12  CA   N    107.97  3.000
 G7D  H12  CA   C    107.90  3.000
 G7D  N    CA   C    112.47  3.000
 G7D  H12  CA   CB   108.15  3.000
 G7D  N    CA   CB   109.43  3.000
 G7D  C    CA   CB   110.77  3.000
 G7D  O    C    OXT  127.39  3.000
 G7D  OXT  C    CA   114.75  3.000
 G7D  O    C    CA   117.84  3.000
 G7D  H14  N    CAT  118.36  3.000
 G7D  H14  N    CA   116.22  3.000
 G7D  CAT  N    CA   122.53  3.000
 G7D  CAQ  CAR  CAN  117.17  3.000
 G7D  CAN  CAR  CAT  118.87  3.000
 G7D  CAQ  CAR  CAT  123.96  3.000
 G7D  OAS  CAN  CAO  118.02  3.000
 G7D  OAS  CAN  CAR  121.57  3.000
 G7D  CAO  CAN  CAR  120.40  3.000
 G7D  H15  CAO  CAM  119.88  3.000
 G7D  H15  CAO  CAN  118.76  3.000
 G7D  CAM  CAO  CAN  121.36  3.000
 G7D  H16  OAS  CAN  105.63  3.000
 G7D  H17  CAQ  CAP  116.75  3.000
 G7D  H17  CAQ  CAR  120.37  3.000
 G7D  CAP  CAQ  CAR  122.88  3.000
 G7D  H18  CAP  CAM  121.34  3.000
 G7D  H18  CAP  CAQ  119.04  3.000
 G7D  CAM  CAP  CAQ  119.62  3.000
 G7D  N10  CAM  CAP  122.41  3.000
 G7D  N10  CAM  CAO  119.06  3.000
 G7D  CAP  CAM  CAO  118.53  3.000
 G7D  H19  N10  CAM  114.95  3.000
 G7D  H19  N10  C9   114.69  3.000
 G7D  CAM  N10  C9   123.14  3.000
 G7D  C4A  N5   C6   117.63  3.000
 G7D  C8A  C4A  N5   122.64  3.000
 G7D  N5   C4A  C4   118.40  3.000
 G7D  C8A  C4A  C4   118.96  3.000
 G7D  N3   C2   N2   116.66  3.000
 G7D  N3   C2   N1   123.20  3.000
 G7D  N2   C2   N1   120.14  3.000
 G7D  N8   C8A  C4A  119.28  3.000
 G7D  C4A  C8A  N1   123.58  3.000
 G7D  N8   C8A  N1   117.14  3.000
 G7D  C8A  N8   C7   117.34  3.000
 G7D  H5   N2   H4   117.79  3.000
 G7D  H5   N2   C2   122.50  3.000
 G7D  H4   N2   C2   118.86  3.000
 G7D  CAR  CAT  OAU  119.90  3.000
 G7D  OAU  CAT  N    120.92  3.000
 G7D  CAR  CAT  N    119.16  3.000
 G7D  H9   CG   H8   104.75  3.000
 G7D  H9   CG   CB   109.29  3.000
 G7D  H8   CG   CB   110.45  3.000
 G7D  H9   CG   CD   108.25  3.000
 G7D  H8   CG   CD   107.88  3.000
 G7D  CB   CG   CD   115.64  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
 G7D  CONST_01  C8A  N8   C7   C6      0.00   0.0  0
 G7D  CONST_02  C8A  C4A  N5   C6      0.00   0.0  0
 G7D  CONST_03  C4A  C8A  N8   C7      0.00   0.0  0
 G7D  CONST_04  C4A  N5   C6   C7      0.00   0.0  0
 G7D  CONST_05  CAM  CAP  CAQ  CAR     0.00   0.0  0
 G7D  CONST_06  CAM  CAO  CAN  CAR     0.00   0.0  0
 G7D  CONST_07  CAP  CAQ  CAR  CAN     0.00   0.0  0
 G7D  CONST_08  CAP  CAM  CAO  CAN     0.00   0.0  0
 G7D  CONST_09  CAQ  CAP  CAM  CAO     0.00   0.0  0
 G7D  CONST_10  CAQ  CAR  CAN  CAO     0.00   0.0  0
 G7D  CONST_11  N8   C8A  C4A  N5      0.00   0.0  0
 G7D  CONST_12  N8   C7   C6   N5      0.00   0.0  0
 G7D  CONST_13  N1   C2   N3   C4      0.00   0.0  0
 G7D  CONST_14  C8A  N1   C2   N3      0.00   0.0  0
 G7D  CONST_15  C2   N3   C4   C4A     0.00   0.0  0
 G7D  CONST_16  N8   C7   C6   C9    180.00   0.0  0
 G7D  CONST_17  C4A  N5   C6   C9    180.00   0.0  0
 G7D  CONST_18  CAP  CAQ  CAR  CAT   180.00   0.0  0
 G7D  CONST_19  CAO  CAN  CAR  CAT   180.00   0.0  0
 G7D  CONST_20  N10  CAM  CAO  CAN   180.00   0.0  0
 G7D  CONST_21  CAQ  CAR  CAN  OAS   180.00   0.0  0
 G7D  CONST_22  CAM  CAO  CAN  OAS   180.00   0.0  0
 G7D  CONST_23  N10  CAM  CAP  CAQ   180.00   0.0  0
 G7D  CONST_24  N2   C2   N3   C4    180.00   0.0  0
 G7D  CONST_25  C8A  N1   C2   N2    180.00   0.0  0
 G7D  CONST_26  C2   N3   C4   O4    180.00   0.0  0
 G7D  CONST_27  H18  CAP  CAQ  CAR   180.00   0.0  0
 G7D  CONST_28  H15  CAO  CAN  CAR   180.00   0.0  0
 G7D  CONST_29  H17  CAQ  CAR  CAN   180.00   0.0  0
 G7D  CONST_30  H1   C7   C6   N5    180.00   0.0  0
 G7D  CONST_31  H6   N3   C2   N1    180.00   0.0  0
 G7D  CONST_32  CAP  CAM  N10  C9      0.00   0.0  0
 G7D  CONST_33  CAO  CAM  N10  C9    180.00   0.0  0
 G7D  CONST_35  H4   N2   C2   N1      0.00   0.0  0
 G7D  CONST_36  H5   N2   C2   N1    180.00   0.0  0
 G7D  CONST_37  CAR  CAT  N    CA    180.00   0.0  0
 G7D  CONST_38  H14  N    CAT  CAR     0.00   0.0  0
 G7D  CONST_39  OAU  CAT  N    CA      0.00   0.0  0
 G7D  Var_01    CAM  N10  C9   C6   -168.51  30.0  3
 G7D  Var_02    N10  C9   C6   C7     69.35  30.0  2
 G7D  Var_03    CAQ  CAR  CAT  N       5.53  30.0  2
 G7D  Var_04    CB   CG   CD   OE1    -0.24  30.0  3
 G7D  Var_05    CA   CB   CG   CD   -177.08  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
 G7D  chir_01  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
 G7D  plan-1  CAR  0.020
 G7D  plan-1  CAN  0.020
 G7D  plan-1  CAO  0.020
 G7D  plan-1  OAS  0.020
 G7D  plan-1  CAQ  0.020
 G7D  plan-1  CAP  0.020
 G7D  plan-1  CAM  0.020
 G7D  plan-1  N10  0.020
 G7D  plan-1  H15  0.020
 G7D  plan-1  H17  0.020
 G7D  plan-1  H18  0.020
 G7D  plan-1  CAT  0.020
 G7D  plan-2  C4   0.020
 G7D  plan-2  C6   0.020
 G7D  plan-2  C7   0.020
 G7D  plan-2  C9   0.020
 G7D  plan-2  N1   0.020
 G7D  plan-2  N3   0.020
 G7D  plan-2  N5   0.020
 G7D  plan-2  C4A  0.020
 G7D  plan-2  O4   0.020
 G7D  plan-2  C2   0.020
 G7D  plan-2  C8A  0.020
 G7D  plan-2  N8   0.020
 G7D  plan-2  H1   0.020
 G7D  plan-2  H4   0.020
 G7D  plan-2  H5   0.020
 G7D  plan-2  H6   0.020
 G7D  plan-2  N2   0.020
 G7D  plan-3  CA   0.020
 G7D  plan-3  N    0.020
 G7D  plan-3  OAU  0.020
 G7D  plan-3  CAR  0.020
 G7D  plan-3  H14  0.020
 G7D  plan-3  CAT  0.020
 G7D  plan-4  C9   0.020
 G7D  plan-4  CAM  0.020
 G7D  plan-4  N10  0.020
 G7D  plan-4  H19  0.020
 G7D  plan-5  OE1  0.020
 G7D  plan-5  CD   0.020
 G7D  plan-5  OE2  0.020
 G7D  plan-5  CG   0.020
 G7D  plan-6  CA   0.020
 G7D  plan-6  C    0.020
 G7D  plan-6  OXT  0.020
 G7D  plan-6  O    0.020

