# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 12:51:08 2020
#   Inital geometry file: a 145 line input string
#   Ligand name: N-{[4-({[(6S)-2-amino-5-methyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1[C@@H](CNc2ccc(cc2)C(=O)N[C@@H](CCC(O)=O)C(O)=O)CNC3=C1C(=O)NC(=N3)N
#
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
 C2F  C2F  'N-{[4-({[(6S)-2-amino-5-methyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid'  ligand  58  33  .  2022-07-24  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_C2F
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
 C2F  N1    N  N     0  -0.529   1.8503   0.0439   5.6963
 C2F  C2    C  CR6   0   0.675   1.9051   1.3477   5.7172
 C2F  NA2   N  NH2   0  -0.829   3.0692   1.9624   5.9885
 C2F  N3    N  NR16  0  -0.717   0.8365   2.1277   5.4340
 C2F  C4    C  CR6   0   0.507  -0.4195   1.6232   5.0755
 C2F  O4    O  OC    0  -0.510  -1.3208   2.4085   4.7920
 C2F  C4A   C  CR6   0  -0.065  -0.4913   0.2099   5.1011
 C2F  N5    N  NT    0  -0.477  -1.6994  -0.4347   4.7428
 C2F  C6    C  CH1   0  -0.201  -1.4545  -1.7194   4.1114
 C2F  C7    C  CH2   0  -0.270  -0.5502  -2.5979   4.9795
 C2F  N8    N  NH1   0  -0.656   0.6387  -1.8605   5.3317
 C2F  C8A   C  CR6   0   0.512   0.6563  -0.5180   5.3910
 C2F  C9    C  CH2   0  -0.257  -0.8592  -1.5135   2.7177
 C2F  N10   N  NH1   0  -0.683  -1.6211  -0.5094   2.0218
 C2F  C11   C  CH3   0  -0.529  -2.7001  -0.4617   5.7944
 C2F  C12   C  CR6   0  -0.082  -0.8508   0.7616  -1.8893
 C2F  C13   C  CR16  0  -0.256  -1.6932   1.4844  -1.0373
 C2F  C14   C  CR16  0  -0.342  -1.9436   1.0627   0.2473
 C2F  C15   C  CR6   0   0.391  -1.3422  -0.1054   0.7578
 C2F  C16   C  CR16  0  -0.346  -0.4763  -0.8188  -0.0885
 C2F  C17   C  CR16  0  -0.276  -0.2480  -0.3898  -1.3824
 C2F  O     O  O     0  -0.492  -0.8239   2.4338  -3.5709
 C2F  N     N  NH1   0  -0.670  -0.1323   0.3825  -4.1629
 C2F  CA    C  CH1   0  -0.169   0.1126   0.7933  -5.5193
 C2F  CB    C  CH2   0  -0.477   0.7967  -0.3298  -6.3028
 C2F  CG    C  CH2   0  -0.577   2.1678  -0.6521  -5.7303
 C2F  CD    C  C     0   0.555   2.8889  -1.7202  -6.5049
 C2F  OE1   O  O     0  -0.442   2.4674  -2.2629  -7.4954
 C2F  OE2   O  OH1   0  -0.595   4.0688  -2.0032  -5.9646
 C2F  CT    C  C     0   0.539  -1.1491   1.2195  -6.2562
 C2F  O1    O  O     0  -0.442  -1.1394   2.0081  -7.1679
 C2F  O2    O  OH1   0  -0.584  -2.2332   0.5922  -5.8322
 C2F  HN21  H  HNH2  0   0.407   3.8108   1.3982   6.3668
 C2F  HN22  H  HNH2  0   0.410   3.0898   2.9394   6.2259
 C2F  HN3   H  HNR6  0   0.415   0.9345   3.1342   5.4386
 C2F  H6    H  HCH1  0   0.269  -2.4170  -2.2248   4.0027
 C2F  H71   H  HCH2  0   0.247  -1.1017  -2.9103   5.8722
 C2F  H72   H  HCH2  0   0.257  -0.2628  -3.5067   4.4489
 C2F  HN8   H  HNH1  0   0.392   1.4979  -2.3522   5.5117
 C2F  H91   H  HCH2  0   0.232   0.2009  -1.2358   2.7854
 C2F  H92   H  HCH2  0   0.249  -0.9027  -2.4659   2.1828
 C2F  HN1   H  HNH1  0   0.383  -2.0449   0.1690   2.6418
 C2F  H111  H  HCH3  0   0.245  -2.9131   0.5557   6.1186
 C2F  H112  H  HCH3  0   0.232  -3.6266  -0.8883   5.4074
 C2F  H113  H  HCH3  0   0.204  -2.3994  -1.0410   6.6771
 C2F  H13   H  HCR6  0   0.253  -2.1663   2.3904  -1.3933
 C2F  H14   H  HCR6  0   0.259  -2.6117   1.6339   0.8809
 C2F  H16   H  HCR6  0   0.269   0.0273  -1.7091   0.2633
 C2F  H17   H  HCR6  0   0.248   0.4469  -0.9617  -1.9854
 C2F  HN    H  HNH1  0   0.406  -0.2344  -0.6038  -3.9822
 C2F  HA    H  HCH1  0   0.289   0.7722   1.6649  -5.5177
 C2F  HB1   H  HCH2  0   0.261   0.1607  -1.2185  -6.3043
 C2F  HB2   H  HCH2  0   0.273   0.8981  -0.0115  -7.3409
 C2F  HG1   H  HCH2  0   0.290   2.7954   0.2445  -5.7211
 C2F  HG2   H  HCH2  0   0.283   2.1024  -0.9748  -4.6879
 C2F  HOE2  H  HOH1  0   0.481   4.5139  -2.6918  -6.4808
 C2F  HO2   H  HOH1  0   0.485  -3.0019   0.8694  -6.3535
 C2F  C     C  C     0   0.550  -0.6124   1.2683  -3.2568

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
 C2F  N1   C2    aromatic  1.305  0.020  1.305
 C2F  N1   C8A   aromatic  1.354  0.020  1.354
 C2F  C2   NA2   single    1.344  0.020  1.344
 C2F  C2   N3    aromatic  1.353  0.020  1.353
 C2F  NA2  HN21  single    0.890  0.020  1.040
 C2F  NA2  HN22  single    0.890  0.020  1.040
 C2F  N3   C4    aromatic  1.400  0.020  1.400
 C2F  N3   HN3   single    0.860  0.020  1.020
 C2F  C4   O4    double    1.229  0.020  1.229
 C2F  C4   C4A   aromatic  1.415  0.020  1.415
 C2F  C4A  N5    single    1.415  0.020  1.415
 C2F  C4A  C8A   aromatic  1.390  0.020  1.390
 C2F  N5   C6    single    1.452  0.020  1.452
 C2F  N5   C11   single    1.452  0.020  1.452
 C2F  C6   C7    single    1.531  0.020  1.531
 C2F  C6   C9    single    1.529  0.020  1.529
 C2F  C6   H6    single    0.970  0.020  1.090
 C2F  C7   N8    single    1.443  0.020  1.443
 C2F  C7   H71   single    0.970  0.020  1.090
 C2F  C7   H72   single    0.970  0.020  1.090
 C2F  N8   C8A   single    1.344  0.020  1.344
 C2F  N8   HN8   single    0.860  0.020  1.020
 C2F  C9   N10   single    1.440  0.020  1.440
 C2F  C9   H91   single    0.970  0.020  1.090
 C2F  C9   H92   single    0.970  0.020  1.090
 C2F  N10  C15   single    1.356  0.020  1.356
 C2F  N10  HN1   single    0.890  0.020  1.040
 C2F  C11  H111  single    0.970  0.020  1.090
 C2F  C11  H112  single    0.970  0.020  1.090
 C2F  C11  H113  single    0.970  0.020  1.090
 C2F  C12  C13   aromatic  1.399  0.020  1.399
 C2F  C12  C17   aromatic  1.395  0.020  1.395
 C2F  C12  C     single    1.478  0.020  1.478
 C2F  C13  C14   aromatic  1.375  0.020  1.375
 C2F  C13  H13   single    0.930  0.020  1.080
 C2F  C14  C15   aromatic  1.410  0.020  1.410
 C2F  C14  H14   single    0.930  0.020  1.080
 C2F  C15  C16   aromatic  1.405  0.020  1.405
 C2F  C16  C17   aromatic  1.382  0.020  1.382
 C2F  C16  H16   single    0.930  0.020  1.080
 C2F  C17  H17   single    0.930  0.020  1.080
 C2F  C    O     double    1.225  0.020  1.225
 C2F  C    N     single    1.355  0.020  1.355
 C2F  N    CA    single    1.438  0.020  1.438
 C2F  N    HN    single    0.890  0.020  1.040
 C2F  CA   CB    single    1.531  0.020  1.531
 C2F  CA   CT    single    1.522  0.020  1.522
 C2F  CA   HA    single    0.970  0.020  1.090
 C2F  CB   CG    single    1.520  0.020  1.520
 C2F  CB   HB1   single    0.970  0.020  1.090
 C2F  CB   HB2   single    0.970  0.020  1.090
 C2F  CG   CD    single    1.504  0.020  1.504
 C2F  CG   HG1   single    0.970  0.020  1.090
 C2F  CG   HG2   single    0.970  0.020  1.090
 C2F  CD   OE1   double    1.205  0.020  1.205
 C2F  CD   OE2   single    1.328  0.020  1.328
 C2F  OE2  HOE2  single    0.850  0.020  0.980
 C2F  CT   O1    double    1.205  0.020  1.205
 C2F  CT   O2    single    1.322  0.020  1.322
 C2F  O2   HO2   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
 C2F  C8A   N1   C2    117.06  3.000
 C2F  N3    C2   NA2   117.56  3.000
 C2F  N3    C2   N1    122.64  3.000
 C2F  NA2   C2   N1    119.77  3.000
 C2F  HN22  NA2  HN21  116.18  3.000
 C2F  HN22  NA2  C2    120.64  3.000
 C2F  HN21  NA2  C2    117.26  3.000
 C2F  HN3   N3   C4    116.53  3.000
 C2F  HN3   N3   C2    119.76  3.000
 C2F  C4    N3   C2    123.67  3.000
 C2F  C4A   C4   O4    127.24  3.000
 C2F  C4A   C4   N3    113.62  3.000
 C2F  O4    C4   N3    119.13  3.000
 C2F  C8A   C4A  N5    121.28  3.000
 C2F  C8A   C4A  C4    119.01  3.000
 C2F  N5    C4A  C4    119.57  3.000
 C2F  C11   N5   C6    114.49  3.000
 C2F  C11   N5   C4A   114.42  3.000
 C2F  C6    N5   C4A   111.65  3.000
 C2F  H6    C6   C9    108.33  3.000
 C2F  H6    C6   C7    108.15  3.000
 C2F  C9    C6   C7    111.35  3.000
 C2F  H6    C6   N5    107.69  3.000
 C2F  C9    C6   N5    110.04  3.000
 C2F  C7    C6   N5    111.15  3.000
 C2F  H72   C7   H71   106.95  3.000
 C2F  H72   C7   N8    109.11  3.000
 C2F  H71   C7   N8    111.22  3.000
 C2F  H72   C7   C6    110.97  3.000
 C2F  H71   C7   C6    109.18  3.000
 C2F  N8    C7   C6    109.39  3.000
 C2F  HN8   N8   C8A   117.97  3.000
 C2F  HN8   N8   C7    119.85  3.000
 C2F  C8A   N8   C7    122.15  3.000
 C2F  N8    C8A  C4A   120.22  3.000
 C2F  N8    C8A  N1    115.84  3.000
 C2F  C4A   C8A  N1    123.90  3.000
 C2F  H92   C9   H91   106.80  3.000
 C2F  H92   C9   N10   110.49  3.000
 C2F  H91   C9   N10   111.37  3.000
 C2F  H92   C9   C6    108.24  3.000
 C2F  H91   C9   C6    110.71  3.000
 C2F  N10   C9   C6    109.17  3.000
 C2F  HN1   N10  C15   117.23  3.000
 C2F  HN1   N10  C9    113.14  3.000
 C2F  C15   N10  C9    123.33  3.000
 C2F  H113  C11  H112  108.15  3.000
 C2F  H113  C11  H111  107.89  3.000
 C2F  H112  C11  H111  107.75  3.000
 C2F  H113  C11  N5    113.79  3.000
 C2F  H112  C11  N5    109.62  3.000
 C2F  H111  C11  N5    109.46  3.000
 C2F  C     C12  C17   123.33  3.000
 C2F  C     C12  C13   118.91  3.000
 C2F  C17   C12  C13   117.73  3.000
 C2F  H13   C13  C14   118.97  3.000
 C2F  H13   C13  C12   119.69  3.000
 C2F  C14   C13  C12   121.34  3.000
 C2F  H14   C14  C15   119.22  3.000
 C2F  H14   C14  C13   119.80  3.000
 C2F  C15   C14  C13   120.98  3.000
 C2F  C16   C15  C14   117.75  3.000
 C2F  C16   C15  N10   122.47  3.000
 C2F  C14   C15  N10   119.78  3.000
 C2F  H16   C16  C17   118.89  3.000
 C2F  H16   C16  C15   120.59  3.000
 C2F  C17   C16  C15   120.52  3.000
 C2F  H17   C17  C16   117.59  3.000
 C2F  H17   C17  C12   120.71  3.000
 C2F  C16   C17  C12   121.67  3.000
 C2F  HN    N    CA    117.76  3.000
 C2F  HN    N    C     118.94  3.000
 C2F  CA    N    C     120.28  3.000
 C2F  HA    CA   CT    106.12  3.000
 C2F  HA    CA   CB    108.43  3.000
 C2F  CT    CA   CB    109.15  3.000
 C2F  HA    CA   N     109.22  3.000
 C2F  CT    CA   N     113.29  3.000
 C2F  CB    CA   N     110.44  3.000
 C2F  HB2   CB   HB1   106.86  3.000
 C2F  HB2   CB   CG    109.66  3.000
 C2F  HB1   CB   CG    110.67  3.000
 C2F  HB2   CB   CA    108.34  3.000
 C2F  HB1   CB   CA    109.71  3.000
 C2F  CG    CB   CA    111.46  3.000
 C2F  HG2   CG   HG1   105.56  3.000
 C2F  HG2   CG   CD    108.08  3.000
 C2F  HG1   CG   CD    108.14  3.000
 C2F  HG2   CG   CB    111.57  3.000
 C2F  HG1   CG   CB    110.28  3.000
 C2F  CD    CG   CB    112.90  3.000
 C2F  OE2   CD   OE1   123.29  3.000
 C2F  OE2   CD   CG    111.58  3.000
 C2F  OE1   CD   CG    125.13  3.000
 C2F  HOE2  OE2  CD    110.05  3.000
 C2F  O2    CT   O1    124.02  3.000
 C2F  O2    CT   CA    113.05  3.000
 C2F  O1    CT   CA    122.87  3.000
 C2F  HO2   O2   CT    110.00  3.000
 C2F  N     C    O     120.76  3.000
 C2F  N     C    C12   116.86  3.000
 C2F  O     C    C12   122.37  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
 C2F  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 C2F  CONST_02  C4    C4A  C8A  N1      0.00   0.0  0
 C2F  CONST_03  C4A   C8A  N1   C2      0.00   0.0  0
 C2F  CONST_04  C4A   C4   N3   C2      0.00   0.0  0
 C2F  CONST_05  C8A   N1   C2   N3      0.00   0.0  0
 C2F  CONST_06  C8A   C4A  C4   N3      0.00   0.0  0
 C2F  CONST_07  C15   C14  C13  C12     0.00   0.0  0
 C2F  CONST_08  C15   C16  C17  C12     0.00   0.0  0
 C2F  CONST_09  C16   C17  C12  C13     0.00   0.0  0
 C2F  CONST_10  C16   C15  C14  C13     0.00   0.0  0
 C2F  CONST_11  C17   C12  C13  C14     0.00   0.0  0
 C2F  CONST_12  C17   C16  C15  C14     0.00   0.0  0
 C2F  CONST_13  O4    C4   N3   C2    180.00   0.0  0
 C2F  CONST_14  C8A   N1   C2   NA2   180.00   0.0  0
 C2F  CONST_15  C4    N3   C2   NA2   180.00   0.0  0
 C2F  CONST_16  N5    C4A  C4   O4      0.00   0.0  0
 C2F  CONST_17  C8A   C4A  C4   O4    180.00   0.0  0
 C2F  CONST_18  C13   C14  C15  N10   180.00   0.0  0
 C2F  CONST_19  C17   C16  C15  N10   180.00   0.0  0
 C2F  CONST_20  C     C12  C13  C14   180.00   0.0  0
 C2F  CONST_21  C     C12  C17  C16   180.00   0.0  0
 C2F  CONST_22  HN3   N3   C2   N1    180.00   0.0  0
 C2F  CONST_23  H14   C14  C13  C12   180.00   0.0  0
 C2F  CONST_24  H16   C16  C17  C12   180.00   0.0  0
 C2F  CONST_25  H17   C17  C12  C13   180.00   0.0  0
 C2F  CONST_26  H13   C13  C14  C15   180.00   0.0  0
 C2F  CONST_27  C14   C15  N10  C9    180.00   0.0  0
 C2F  CONST_28  C16   C15  N10  C9      0.00   0.0  0
 C2F  CONST_29  HN21  NA2  C2   N1      0.00   0.0  0
 C2F  CONST_30  HN22  NA2  C2   N1    180.00   0.0  0
 C2F  CONST_32  CA    N    C    C12   180.00   0.0  0
 C2F  CONST_34  CA    N    C    O       0.00   0.0  0
 C2F  CONST_35  HO2   O2   CT   CA    180.00   0.0  0
 C2F  CONST_36  HOE2  OE2  CD   CG    180.00   0.0  0
 C2F  Var_01    C7    N8   C8A  N1   -178.13  30.0  1
 C2F  Var_02    C6    N5   C4A  C4    147.90  30.0  1
 C2F  Var_03    C8A   N8   C7   C6     26.10  30.0  1
 C2F  Var_04    C15   N10  C9   C6   -179.83  30.0  3
 C2F  Var_05    O     C    C12  C13    19.24  30.0  2
 C2F  Var_06    H111  C11  N5   C4A    56.68  30.0  3
 C2F  Var_07    CD    CG   CB   CA   -178.05  30.0  3
 C2F  Var_08    OE1   CD   CG   CB      1.57  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
 C2F  chir_01  C6  N5  C7  C9  positiv
 C2F  chir_02  CA  N   CB  CT  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
 C2F  plan-1  N10   0.020
 C2F  plan-1  C12   0.020
 C2F  plan-1  C13   0.020
 C2F  plan-1  C14   0.020
 C2F  plan-1  C15   0.020
 C2F  plan-1  C16   0.020
 C2F  plan-1  C17   0.020
 C2F  plan-1  H13   0.020
 C2F  plan-1  H14   0.020
 C2F  plan-1  H16   0.020
 C2F  plan-1  H17   0.020
 C2F  plan-1  C     0.020
 C2F  plan-2  CG    0.020
 C2F  plan-2  CD    0.020
 C2F  plan-2  OE1   0.020
 C2F  plan-2  OE2   0.020
 C2F  plan-2  HOE2  0.020
 C2F  plan-3  CA    0.020
 C2F  plan-3  CT    0.020
 C2F  plan-3  O1    0.020
 C2F  plan-3  O2    0.020
 C2F  plan-3  HO2   0.020
 C2F  plan-4  C12   0.020
 C2F  plan-4  O     0.020
 C2F  plan-4  N     0.020
 C2F  plan-4  CA    0.020
 C2F  plan-4  HN    0.020
 C2F  plan-4  C     0.020
 C2F  plan-5  C2    0.020
 C2F  plan-5  NA2   0.020
 C2F  plan-5  HN21  0.020
 C2F  plan-5  HN22  0.020
 C2F  plan-6  N1    0.020
 C2F  plan-6  C2    0.020
 C2F  plan-6  NA2   0.020
 C2F  plan-6  N3    0.020
 C2F  plan-6  C4    0.020
 C2F  plan-6  O4    0.020
 C2F  plan-6  C4A   0.020
 C2F  plan-6  N5    0.020
 C2F  plan-6  N8    0.020
 C2F  plan-6  C8A   0.020
 C2F  plan-6  HN3   0.020
 C2F  plan-7  C9    0.020
 C2F  plan-7  N10   0.020
 C2F  plan-7  C15   0.020
 C2F  plan-7  HN1   0.020

