# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:11:57 2022
#   Inital geometry file: a 147 line input string
#   Ligand name: N-(4-{2-[(6S)-2-amino-4-oxo-1,4,5,6,7,8-hexahydropyrido[2,3-d]pyrimidin-6-yl]ethyl}benzoyl)-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)C2=C(NC[C@@H](CCc3ccc(cc3)C(=O)N[C@@H](CCC(O)=O)C(O)=O)C2)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
 21V  21V  'N-(4-{2-[(6S)-2-amino-4-oxo-1,4,5,6,7,8-hexahydropyrido[2,3-d]pyrimidin-6-yl]ethyl}benzoyl)-L-glutamic acid'  ligand  55  32  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_21V
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
 21V  OE2  O  OC    -1  -0.633  -7.0302   4.2964  -0.4646
 21V  CD   C  C      0   0.412  -7.3252   3.1144  -0.7423
 21V  OE1  O  O      0  -0.609  -8.1923   2.7438  -1.5581
 21V  CG   C  CH2    0  -0.577  -6.5243   2.0302   0.0007
 21V  CB   C  CH2    0  -0.449  -6.9583   0.5976  -0.2645
 21V  CA   C  CH1    0  -0.186  -6.1958  -0.4360   0.5644
 21V  CT   C  C      0   0.410  -6.8196  -1.8449   0.3874
 21V  O1   O  O      0  -0.600  -6.1861  -2.6813  -0.2783
 21V  O2   O  OC    -1  -0.619  -7.9367  -1.9943   0.9226
 21V  N    N  NH1    0  -0.633  -4.7929  -0.4001   0.2176
 21V  C    C  C      0   0.535  -3.8599  -0.9920   0.9746
 21V  O    O  O      0  -0.506  -4.1066  -1.4967   2.0650
 21V  C11  C  CR6    0  -0.058  -2.4650  -0.9843   0.4367
 21V  C12  C  CR16   0  -0.278  -2.0017  -0.0237  -0.4597
 21V  C13  C  CR16   0  -0.299  -0.6908  -0.0553  -0.9121
 21V  C16  C  CR16   0  -0.256  -1.5802  -1.9658   0.8779
 21V  C15  C  CR16   0  -0.297  -0.2766  -1.9999   0.4134
 21V  C14  C  CR6    0   0.141   0.1904  -1.0470  -0.4902
 21V  C10  C  CH2    0  -0.522   1.6205  -1.0637  -0.9468
 21V  C9   C  CH2    0  -0.418   2.5239  -0.2892   0.0166
 21V  C6   C  CH1    0  -0.282   4.0002  -0.2916  -0.3651
 21V  C7   C  CH2    0  -0.255   4.6192  -1.6781  -0.2158
 21V  N8   N  NH1    0  -0.685   6.0163  -1.6433  -0.5914
 21V  C5   C  CH2    0  -0.437   4.7793   0.7095   0.4901
 21V  C4A  C  CR6    0  -0.279   6.2616   0.5530   0.3257
 21V  C4   C  CR6    0   0.403   7.1704   1.6017   0.7060
 21V  O4   O  O      0  -0.526   6.7735   2.6555   1.2138
 21V  C8A  C  CR6    0   0.657   6.7739  -0.5989  -0.2009
 21V  N1   N  NR16   0  -0.738   8.1276  -0.7107  -0.3763
 21V  C2   C  CR6    0   0.657   8.9510   0.3141  -0.0249
 21V  N3   N  N      0  -0.531   8.5223   1.4206   0.5003
 21V  NA2  N  NH2    0  -0.829  10.2599   0.1420  -0.2853
 21V  H2   H  HCH2   0   0.222  -5.4660   2.1620  -0.2512
 21V  H3   H  HCH2   0   0.217  -6.5836   2.2338   1.0764
 21V  H4   H  HCH2   0   0.228  -8.0176   0.4870  -0.0327
 21V  H5   H  HCH2   0   0.211  -6.8532   0.3594  -1.3284
 21V  H6   H  HCH1   0   0.226  -6.2888  -0.1597   1.6189
 21V  H8   H  HNH1   0   0.391  -4.5669  -0.2003  -0.7439
 21V  H9   H  HCR6   0   0.252  -2.6475   0.7760  -0.8013
 21V  H10  H  HCR6   0   0.251  -0.3498   0.7068  -1.6031
 21V  H11  H  HCR6   0   0.253  -1.9170  -2.7157   1.5816
 21V  H12  H  HCR6   0   0.248   0.3913  -2.7801   0.7601
 21V  H13  H  HCH2   0   0.248   1.9557  -2.0999  -1.0327
 21V  H14  H  HCH2   0   0.245   1.6981  -0.6256  -1.9451
 21V  H15  H  HCH2   0   0.240   2.1757   0.7471   0.0654
 21V  H16  H  HCH2   0   0.228   2.4115  -0.6938   1.0286
 21V  H17  H  HCH1   0   0.239   4.0945   0.0041  -1.4168
 21V  H18  H  HCH2   0   0.227   4.4955  -2.0210   0.8199
 21V  H19  H  HCH2   0   0.256   4.1259  -2.4069  -0.8578
 21V  H20  H  HCH2   0   0.240   4.4811   1.7235   0.2124
 21V  H21  H  HCH2   0   0.226   4.4873   0.5897   1.5409
 21V  H24  H  HNH2   0   0.408  10.6344  -0.7720  -0.4749
 21V  H25  H  HNH2   0   0.406  10.8982   0.8117   0.1087
 21V  H26  H  HNH1   0   0.400   6.4675  -2.5227  -0.7841
 21V  H22  H  HNR6   0   0.426   8.5111  -1.5500  -0.7863

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
 21V  NA2  C2   single    1.346  0.020  1.346
 21V  N3   C2   double    1.298  0.020  1.298
 21V  N3   C4   single    1.379  0.020  1.379
 21V  O4   C4   double    1.235  0.020  1.235
 21V  C2   N1   single    1.361  0.020  1.361
 21V  C4   C4A  single    1.439  0.020  1.439
 21V  N1   C8A  single    1.370  0.020  1.370
 21V  C4A  C8A  double    1.366  0.020  1.366
 21V  C4A  C5   single    1.500  0.020  1.500
 21V  C8A  N8   single    1.348  0.020  1.348
 21V  C5   C6   single    1.530  0.020  1.530
 21V  N8   C7   single    1.447  0.020  1.447
 21V  OE1  CD   deloc     1.247  0.020  1.247
 21V  OE2  CD   deloc     1.250  0.020  1.250
 21V  CD   CG   single    1.539  0.020  1.539
 21V  C6   C7   single    1.526  0.020  1.526
 21V  C6   C9   single    1.525  0.020  1.525
 21V  C9   C10  single    1.531  0.020  1.531
 21V  CG   CB   single    1.520  0.020  1.520
 21V  C13  C12  aromatic  1.387  0.020  1.387
 21V  C13  C14  aromatic  1.392  0.020  1.392
 21V  CB   CA   single    1.529  0.020  1.529
 21V  C12  C11  aromatic  1.393  0.020  1.393
 21V  C10  C14  single    1.501  0.020  1.501
 21V  C14  C15  aromatic  1.394  0.020  1.394
 21V  C11  C    single    1.495  0.020  1.495
 21V  C11  C16  aromatic  1.393  0.020  1.393
 21V  C    O    double    1.227  0.020  1.227
 21V  C    N    single    1.339  0.020  1.339
 21V  C15  C16  aromatic  1.384  0.020  1.384
 21V  N    CA   single    1.446  0.020  1.446
 21V  CA   CT   single    1.551  0.020  1.551
 21V  O1   CT   deloc     1.243  0.020  1.243
 21V  CT   O2   deloc     1.248  0.020  1.248
 21V  CG   H2   single    0.970  0.020  1.090
 21V  CG   H3   single    0.970  0.020  1.090
 21V  CB   H4   single    0.970  0.020  1.090
 21V  CB   H5   single    0.970  0.020  1.090
 21V  CA   H6   single    0.970  0.020  1.090
 21V  N    H8   single    0.890  0.020  1.040
 21V  C12  H9   single    0.930  0.020  1.080
 21V  C13  H10  single    0.930  0.020  1.080
 21V  C16  H11  single    0.930  0.020  1.080
 21V  C15  H12  single    0.930  0.020  1.080
 21V  C10  H13  single    0.970  0.020  1.090
 21V  C10  H14  single    0.970  0.020  1.090
 21V  C9   H15  single    0.970  0.020  1.090
 21V  C9   H16  single    0.970  0.020  1.090
 21V  C6   H17  single    0.970  0.020  1.090
 21V  C7   H18  single    0.970  0.020  1.090
 21V  C7   H19  single    0.970  0.020  1.090
 21V  C5   H20  single    0.970  0.020  1.090
 21V  C5   H21  single    0.970  0.020  1.090
 21V  NA2  H24  single    0.890  0.020  1.040
 21V  NA2  H25  single    0.890  0.020  1.040
 21V  N8   H26  single    0.890  0.020  1.040
 21V  N1   H22  single    0.860  0.020  1.020

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
 21V  CG   CD   OE1  117.93  3.000
 21V  CG   CD   OE2  115.86  3.000
 21V  OE1  CD   OE2  126.21  3.000
 21V  H3   CG   H2   104.80  3.000
 21V  H3   CG   CB   109.31  3.000
 21V  H2   CG   CB   110.42  3.000
 21V  H3   CG   CD   108.34  3.000
 21V  H2   CG   CD   107.87  3.000
 21V  CB   CG   CD   115.53  3.000
 21V  H5   CB   H4   106.13  3.000
 21V  H5   CB   CA   109.38  3.000
 21V  H4   CB   CA   107.51  3.000
 21V  H5   CB   CG   110.30  3.000
 21V  H4   CB   CG   109.63  3.000
 21V  CA   CB   CG   113.59  3.000
 21V  H6   CA   N    107.91  3.000
 21V  H6   CA   CT   107.77  3.000
 21V  N    CA   CT   112.67  3.000
 21V  H6   CA   CB   108.03  3.000
 21V  CT   CA   CB   110.59  3.000
 21V  N    CA   CB   109.71  3.000
 21V  O2   CT   O1   127.27  3.000
 21V  O2   CT   CA   114.83  3.000
 21V  O1   CT   CA   117.88  3.000
 21V  H8   N    C    118.07  3.000
 21V  H8   N    CA   116.84  3.000
 21V  C    N    CA   121.98  3.000
 21V  C11  C    O    120.64  3.000
 21V  O    C    N    122.96  3.000
 21V  C11  C    N    116.38  3.000
 21V  C16  C11  C12  118.58  3.000
 21V  C16  C11  C    118.36  3.000
 21V  C12  C11  C    123.05  3.000
 21V  H9   C12  C13  118.52  3.000
 21V  H9   C12  C11  120.91  3.000
 21V  C13  C12  C11  120.56  3.000
 21V  H10  C13  C14  119.67  3.000
 21V  H10  C13  C12  119.29  3.000
 21V  C14  C13  C12  121.04  3.000
 21V  H11  C16  C15  119.62  3.000
 21V  H11  C16  C11  119.77  3.000
 21V  C15  C16  C11  120.61  3.000
 21V  H12  C15  C14  119.54  3.000
 21V  H12  C15  C16  119.38  3.000
 21V  C14  C15  C16  121.08  3.000
 21V  C10  C14  C15  120.58  3.000
 21V  C15  C14  C13  118.13  3.000
 21V  C10  C14  C13  121.25  3.000
 21V  H14  C10  H13  106.65  3.000
 21V  H14  C10  C9   109.28  3.000
 21V  H13  C10  C9   110.38  3.000
 21V  H14  C10  C14  109.94  3.000
 21V  H13  C10  C14  109.08  3.000
 21V  C9   C10  C14  111.41  3.000
 21V  H16  C9   H15  106.01  3.000
 21V  H16  C9   C6   109.26  3.000
 21V  H15  C9   C6   108.70  3.000
 21V  H16  C9   C10  109.51  3.000
 21V  H15  C9   C10  108.62  3.000
 21V  C6   C9   C10  114.39  3.000
 21V  H17  C6   C5   108.41  3.000
 21V  H17  C6   C7   107.70  3.000
 21V  C5   C6   C7   109.47  3.000
 21V  H17  C6   C9   108.84  3.000
 21V  C7   C6   C9   111.70  3.000
 21V  C5   C6   C9   110.61  3.000
 21V  H19  C7   H18  107.21  3.000
 21V  H19  C7   N8   107.48  3.000
 21V  H18  C7   N8   111.17  3.000
 21V  H19  C7   C6   111.50  3.000
 21V  H18  C7   C6   109.29  3.000
 21V  N8   C7   C6   110.15  3.000
 21V  H26  N8   C8A  118.70  3.000
 21V  H26  N8   C7   117.46  3.000
 21V  C8A  N8   C7   119.08  3.000
 21V  H21  C5   H20  105.79  3.000
 21V  H21  C5   C4A  110.90  3.000
 21V  H20  C5   C4A  109.80  3.000
 21V  H21  C5   C6   109.17  3.000
 21V  H20  C5   C6   109.04  3.000
 21V  C4A  C5   C6   111.95  3.000
 21V  C8A  C4A  C4   118.65  3.000
 21V  C8A  C4A  C5   120.06  3.000
 21V  C4   C4A  C5   121.29  3.000
 21V  N3   C4   O4   119.22  3.000
 21V  O4   C4   C4A  121.84  3.000
 21V  N3   C4   C4A  118.94  3.000
 21V  N1   C8A  C4A  119.26  3.000
 21V  C4A  C8A  N8   123.65  3.000
 21V  N1   C8A  N8   117.08  3.000
 21V  H22  N1   C2   120.06  3.000
 21V  H22  N1   C8A  119.69  3.000
 21V  C2   N1   C8A  120.24  3.000
 21V  NA2  C2   N3   120.58  3.000
 21V  N3   C2   N1   123.15  3.000
 21V  NA2  C2   N1   116.26  3.000
 21V  C2   N3   C4   119.74  3.000
 21V  H25  NA2  H24  116.28  3.000
 21V  H25  NA2  C2   117.16  3.000
 21V  H24  NA2  C2   120.98  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
 21V  CONST_01  C14  C13  C12  C11     0.00   0.0  0
 21V  CONST_02  C14  C15  C16  C11     0.00   0.0  0
 21V  CONST_03  C15  C14  C13  C12     0.00   0.0  0
 21V  CONST_04  C15  C16  C11  C12     0.00   0.0  0
 21V  CONST_05  C16  C11  C12  C13     0.00   0.0  0
 21V  CONST_06  C16  C15  C14  C13     0.00   0.0  0
 21V  CONST_07  N1   C8A  N8   C7    180.00   0.0  0
 21V  CONST_08  C4A  C8A  N8   C7      0.00   0.0  0
 21V  CONST_09  C2   N1   C8A  N8    180.00   0.0  0
 21V  CONST_10  C2   N1   C8A  C4A     0.00   0.0  0
 21V  CONST_11  N1   C2   N3   C4      0.00   0.0  0
 21V  CONST_12  N3   C2   N1   C8A     0.00   0.0  0
 21V  CONST_13  C13  C12  C11  C     180.00   0.0  0
 21V  CONST_14  C15  C16  C11  C     180.00   0.0  0
 21V  CONST_15  C10  C14  C13  C12   180.00   0.0  0
 21V  CONST_16  C10  C14  C15  C16   180.00   0.0  0
 21V  CONST_17  NA2  C2   N3   C4    180.00   0.0  0
 21V  CONST_18  NA2  C2   N1   C8A   180.00   0.0  0
 21V  CONST_19  H10  C13  C12  C11   180.00   0.0  0
 21V  CONST_20  H12  C15  C16  C11   180.00   0.0  0
 21V  CONST_21  H11  C16  C11  C12   180.00   0.0  0
 21V  CONST_22  H9   C12  C11  C16   180.00   0.0  0
 21V  CONST_23  H22  N1   C8A  N8      0.00   0.0  0
 21V  CONST_24  H26  N8   C8A  C4A   180.00   0.0  0
 21V  CONST_26  H25  NA2  C2   N1    180.00   0.0  0
 21V  CONST_27  C11  C    N    CA    180.00   0.0  0
 21V  CONST_29  O    C    N    CA      0.00   0.0  0
 21V  Var_01    C4   C4A  C5   C6    161.62  30.0  1
 21V  Var_02    C8A  N8   C7   C6     41.43  30.0  1
 21V  Var_03    C12  C11  C    N      25.28  30.0  2
 21V  Var_04    C9   C10  C14  C13    91.04  30.0  2
 21V  Var_05    C6   C9   C10  C14   178.57  30.0  1
 21V  Var_06    CB   CG   CD   OE2   175.64  30.0  3
 21V  Var_07    CA   CB   CG   CD   -176.19  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
 21V  chir_01  CA  CB  N   CT  positiv
 21V  chir_02  C6  C5  C7  C9  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
 21V  plan-1  C    0.020
 21V  plan-1  C11  0.020
 21V  plan-1  C12  0.020
 21V  plan-1  C13  0.020
 21V  plan-1  C16  0.020
 21V  plan-1  C15  0.020
 21V  plan-1  C14  0.020
 21V  plan-1  C10  0.020
 21V  plan-1  H9   0.020
 21V  plan-1  H10  0.020
 21V  plan-1  H11  0.020
 21V  plan-1  H12  0.020
 21V  plan-2  OE2  0.020
 21V  plan-2  CD   0.020
 21V  plan-2  OE1  0.020
 21V  plan-2  CG   0.020
 21V  plan-3  CA   0.020
 21V  plan-3  CT   0.020
 21V  plan-3  O1   0.020
 21V  plan-3  O2   0.020
 21V  plan-4  CA   0.020
 21V  plan-4  N    0.020
 21V  plan-4  C    0.020
 21V  plan-4  O    0.020
 21V  plan-4  C11  0.020
 21V  plan-4  H8   0.020
 21V  plan-5  C7   0.020
 21V  plan-5  N8   0.020
 21V  plan-5  C5   0.020
 21V  plan-5  C4A  0.020
 21V  plan-5  C4   0.020
 21V  plan-5  O4   0.020
 21V  plan-5  C8A  0.020
 21V  plan-5  N1   0.020
 21V  plan-5  C2   0.020
 21V  plan-5  N3   0.020
 21V  plan-5  NA2  0.020
 21V  plan-5  H24  0.020
 21V  plan-5  H25  0.020
 21V  plan-5  H26  0.020
 21V  plan-5  H22  0.020

