# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 14:47:48 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 4-{[(2-amino-4-oxo-3,4-dihydropteridin-6-yl)methyl]amino}benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2ncc(CNc3ccc(cc3)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
 22D  22D  '4-{[(2-amino-4-oxo-3,4-dihydropteridin-6-yl)methyl]amino}benzoic acid'  ligand  35  23  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_22D
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
 22D  C7   C  CR16  0  -0.093  -1.8444   2.0243  -0.4558
 22D  N8   N  N     0  -0.384  -3.1118   2.1067  -0.1268
 22D  C8A  C  CR66  0   0.399  -3.7925   0.9574   0.0029
 22D  N1   N  N     0  -0.505  -5.0937   1.0438   0.3489
 22D  C2   C  CR6   0   0.702  -5.7546  -0.0751   0.4774
 22D  N2   N  NH2   0  -0.820  -7.0418  -0.0558   0.8128
 22D  N3   N  NR16  0  -0.715  -5.1937  -1.3063   0.2718
 22D  C4   C  CR6   0   0.540  -3.8782  -1.5139  -0.0806
 22D  O4   O  O     0  -0.433  -3.4292  -2.6273  -0.2468
 22D  C4A  C  CR66  0  -0.043  -3.1294  -0.2634  -0.2211
 22D  N5   N  N     0  -0.354  -1.8486  -0.3294  -0.5565
 22D  C6   C  CR6   0   0.139  -1.1886   0.8029  -0.6798
 22D  C9   C  CH2   0  -0.329   0.2680   0.7382  -1.0300
 22D  N10  N  NH1   0  -0.684   1.0278   0.2995   0.1193
 22D  CBX  C  CR6   0   0.399   2.3777   0.1548   0.0977
 22D  CAR  C  CR16  0  -0.334   3.0281  -0.4849   1.1709
 22D  CAT  C  CR16  0  -0.248   4.3965  -0.6202   1.1896
 22D  CAQ  C  CR16  0  -0.343   3.1679   0.6419  -0.9576
 22D  CAS  C  CR16  0  -0.245   4.5403   0.5021  -0.9231
 22D  CBY  C  CR6   0  -0.119   5.1846  -0.1269   0.1423
 22D  CBV  C  C     0   0.518   6.6483  -0.2468   0.1179
 22D  OAJ  O  O     0  -0.458   7.3544   0.1697  -0.7746
 22D  H1   H  HCR6  0   0.281  -1.2990   2.9567  -0.5582
 22D  H2   H  HNH2  0   0.420  -7.4760   0.8266   1.0226
 22D  H3   H  HNH2  0   0.423  -7.5633  -0.8935   1.0050
 22D  H4   H  HNR6  0   0.434  -5.7669  -2.1335   0.3876
 22D  H5   H  HCH2  0   0.256   0.4030   0.0637  -1.8842
 22D  H6   H  HCH2  0   0.259   0.6078   1.7278  -1.3442
 22D  H7   H  HNH1  0   0.395   0.5291  -0.2547   0.7977
 22D  H8   H  HCR6  0   0.265   2.4402  -0.8758   1.9925
 22D  H9   H  HCR6  0   0.262   4.8513  -1.1199   2.0339
 22D  H10  H  HCR6  0   0.274   2.7132   1.1293  -1.8089
 22D  H11  H  HCR6  0   0.261   5.1218   0.8893  -1.7496
 22D  OXT  O  OH1   0  -0.603   7.1437  -0.8667   1.1869
 22D  HXT  H  HOH1  0   0.482   8.1081  -0.9137   1.1164

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
 22D  CBV  OAJ  double    1.212  0.020  1.212
 22D  CBV  CBY  single    1.469  0.020  1.469
 22D  N2   C2   single    1.330  0.020  1.330
 22D  CAS  CBY  aromatic  1.395  0.020  1.395
 22D  CAS  CAQ  aromatic  1.380  0.020  1.380
 22D  CBY  CAT  aromatic  1.400  0.020  1.400
 22D  N1   C2   double    1.306  0.020  1.306
 22D  N1   C8A  single    1.349  0.020  1.349
 22D  C2   N3   single    1.368  0.020  1.368
 22D  CAQ  CBX  aromatic  1.405  0.020  1.405
 22D  N8   C8A  aromatic  1.342  0.020  1.342
 22D  N8   C7   aromatic  1.312  0.020  1.312
 22D  C8A  C4A  aromatic  1.407  0.020  1.407
 22D  N3   C4   single    1.378  0.020  1.378
 22D  CAT  CAR  aromatic  1.375  0.020  1.375
 22D  C7   C6   aromatic  1.404  0.020  1.404
 22D  C4A  C4   single    1.464  0.020  1.464
 22D  C4A  N5   aromatic  1.326  0.020  1.326
 22D  C4   O4   double    1.212  0.020  1.212
 22D  CBX  CAR  aromatic  1.409  0.020  1.409
 22D  CBX  N10  single    1.358  0.020  1.358
 22D  C6   N5   aromatic  1.316  0.020  1.316
 22D  C6   C9   single    1.500  0.020  1.500
 22D  N10  C9   single    1.446  0.020  1.446
 22D  C7   H1   single    0.930  0.020  1.080
 22D  N2   H2   single    0.860  0.020  1.020
 22D  N2   H3   single    0.860  0.020  1.020
 22D  N3   H4   single    0.860  0.020  1.020
 22D  C9   H5   single    0.970  0.020  1.090
 22D  C9   H6   single    0.970  0.020  1.090
 22D  N10  H7   single    0.890  0.020  1.040
 22D  CAR  H8   single    0.930  0.020  1.080
 22D  CAT  H9   single    0.930  0.020  1.080
 22D  CAQ  H10  single    0.930  0.020  1.080
 22D  CAS  H11  single    0.930  0.020  1.080
 22D  CBV  OXT  single    1.331  0.020  1.331
 22D  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
 22D  H1   C7   C6   119.84  3.000
 22D  H1   C7   N8   117.08  3.000
 22D  C6   C7   N8   123.08  3.000
 22D  C8A  N8   C7   117.42  3.000
 22D  C4A  C8A  N1   123.43  3.000
 22D  C4A  C8A  N8   119.24  3.000
 22D  N1   C8A  N8   117.33  3.000
 22D  C2   N1   C8A  117.28  3.000
 22D  N3   C2   N2   116.59  3.000
 22D  N3   C2   N1   123.28  3.000
 22D  N2   C2   N1   120.13  3.000
 22D  H3   N2   H2   117.86  3.000
 22D  H3   N2   C2   122.55  3.000
 22D  H2   N2   C2   118.89  3.000
 22D  H4   N3   C4   116.52  3.000
 22D  H4   N3   C2   119.05  3.000
 22D  C4   N3   C2   124.43  3.000
 22D  C4A  C4   O4   125.59  3.000
 22D  O4   C4   N3   121.82  3.000
 22D  C4A  C4   N3   112.59  3.000
 22D  N5   C4A  C4   118.41  3.000
 22D  N5   C4A  C8A  122.60  3.000
 22D  C4   C4A  C8A  118.99  3.000
 22D  C6   N5   C4A  117.73  3.000
 22D  C9   C6   N5   118.15  3.000
 22D  C9   C6   C7   121.90  3.000
 22D  N5   C6   C7   119.94  3.000
 22D  H6   C9   H5   107.15  3.000
 22D  H6   C9   N10  109.88  3.000
 22D  H5   C9   N10  111.58  3.000
 22D  H6   C9   C6   109.28  3.000
 22D  H5   C9   C6   109.15  3.000
 22D  N10  C9   C6   109.75  3.000
 22D  H7   N10  CBX  116.36  3.000
 22D  H7   N10  C9   116.22  3.000
 22D  CBX  N10  C9   122.83  3.000
 22D  CAQ  CBX  CAR  118.03  3.000
 22D  CAR  CBX  N10  119.69  3.000
 22D  CAQ  CBX  N10  122.27  3.000
 22D  H8   CAR  CAT  119.62  3.000
 22D  H8   CAR  CBX  119.42  3.000
 22D  CAT  CAR  CBX  120.96  3.000
 22D  H9   CAT  CBY  120.66  3.000
 22D  H9   CAT  CAR  118.33  3.000
 22D  CBY  CAT  CAR  121.01  3.000
 22D  H10  CAQ  CAS  118.92  3.000
 22D  H10  CAQ  CBX  120.73  3.000
 22D  CAS  CAQ  CBX  120.35  3.000
 22D  H11  CAS  CBY  119.77  3.000
 22D  H11  CAS  CAQ  118.62  3.000
 22D  CBY  CAS  CAQ  121.61  3.000
 22D  CBV  CBY  CAS  118.97  3.000
 22D  CAS  CBY  CAT  118.04  3.000
 22D  CBV  CBY  CAT  122.98  3.000
 22D  OXT  CBV  OAJ  122.31  3.000
 22D  OXT  CBV  CBY  113.30  3.000
 22D  OAJ  CBV  CBY  124.39  3.000
 22D  HXT  OXT  CBV  109.56  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
 22D  CONST_01  C4A  C8A  N8   C7      0.00   0.0  0
 22D  CONST_02  C4A  N5   C6   C7      0.00   0.0  0
 22D  CONST_03  N5   C4A  C8A  N8      0.00   0.0  0
 22D  CONST_04  N5   C6   C7   N8      0.00   0.0  0
 22D  CONST_05  C6   C7   N8   C8A     0.00   0.0  0
 22D  CONST_06  C6   N5   C4A  C8A     0.00   0.0  0
 22D  CONST_07  CBY  CAS  CAQ  CBX     0.00   0.0  0
 22D  CONST_08  CBY  CAT  CAR  CBX     0.00   0.0  0
 22D  CONST_09  CAS  CBY  CAT  CAR     0.00   0.0  0
 22D  CONST_10  CAS  CAQ  CBX  CAR     0.00   0.0  0
 22D  CONST_11  CAQ  CAS  CBY  CAT     0.00   0.0  0
 22D  CONST_12  CAQ  CBX  CAR  CAT     0.00   0.0  0
 22D  CONST_13  N3   C2   N1   C8A     0.00   0.0  0
 22D  CONST_14  C4   N3   C2   N1      0.00   0.0  0
 22D  CONST_15  C4A  C4   N3   C2      0.00   0.0  0
 22D  CONST_16  C9   C6   C7   N8    180.00   0.0  0
 22D  CONST_17  C9   C6   N5   C4A   180.00   0.0  0
 22D  CONST_18  CAS  CAQ  CBX  N10   180.00   0.0  0
 22D  CONST_19  CAT  CAR  CBX  N10   180.00   0.0  0
 22D  CONST_20  CBV  CBY  CAT  CAR   180.00   0.0  0
 22D  CONST_21  CBV  CBY  CAS  CAQ   180.00   0.0  0
 22D  CONST_22  N2   C2   N1   C8A   180.00   0.0  0
 22D  CONST_23  O4   C4   N3   C2    180.00   0.0  0
 22D  CONST_24  C4   N3   C2   N2    180.00   0.0  0
 22D  CONST_25  H1   C7   N8   C8A   180.00   0.0  0
 22D  CONST_26  H11  CAS  CAQ  CBX   180.00   0.0  0
 22D  CONST_27  H9   CAT  CAR  CBX   180.00   0.0  0
 22D  CONST_28  H10  CAQ  CBX  CAR   180.00   0.0  0
 22D  CONST_29  H8   CAR  CBX  CAQ   180.00   0.0  0
 22D  CONST_30  H4   N3   C2   N1    180.00   0.0  0
 22D  CONST_31  CAQ  CBX  N10  C9      0.00   0.0  0
 22D  CONST_32  CAR  CBX  N10  C9    180.00   0.0  0
 22D  CONST_33  H7   N10  CBX  CAR     0.00   0.0  0
 22D  CONST_34  H2   N2   C2   N1      0.00   0.0  0
 22D  CONST_35  H3   N2   C2   N1    180.00   0.0  0
 22D  CONST_36  HXT  OXT  CBV  CBY   180.00   0.0  0
 22D  Var_01    N10  C9   C6   C7    104.79  30.0  2
 22D  Var_02    CBX  N10  C9   C6   -179.65  30.0  2
 22D  Var_03    OAJ  CBV  CBY  CAT   179.95  30.0  3

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
 22D  plan-1  N10  0.020
 22D  plan-1  CBX  0.020
 22D  plan-1  CAR  0.020
 22D  plan-1  CAT  0.020
 22D  plan-1  CAQ  0.020
 22D  plan-1  CAS  0.020
 22D  plan-1  CBY  0.020
 22D  plan-1  CBV  0.020
 22D  plan-1  H8   0.020
 22D  plan-1  H9   0.020
 22D  plan-1  H10  0.020
 22D  plan-1  H11  0.020
 22D  plan-2  C7   0.020
 22D  plan-2  N8   0.020
 22D  plan-2  C8A  0.020
 22D  plan-2  N1   0.020
 22D  plan-2  C2   0.020
 22D  plan-2  N2   0.020
 22D  plan-2  N3   0.020
 22D  plan-2  C4   0.020
 22D  plan-2  O4   0.020
 22D  plan-2  C4A  0.020
 22D  plan-2  N5   0.020
 22D  plan-2  C6   0.020
 22D  plan-2  C9   0.020
 22D  plan-2  H1   0.020
 22D  plan-2  H2   0.020
 22D  plan-2  H3   0.020
 22D  plan-2  H4   0.020
 22D  plan-3  C9   0.020
 22D  plan-3  N10  0.020
 22D  plan-3  CBX  0.020
 22D  plan-3  H7   0.020
 22D  plan-4  CBY  0.020
 22D  plan-4  CBV  0.020
 22D  plan-4  OAJ  0.020
 22D  plan-4  OXT  0.020
 22D  plan-4  HXT  0.020

