# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 23 15:51:52 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 2-amino-4-oxo-N-{2-[(phenylcarbamoyl)amino]ethyl}-3,4-dihydropteridine-7-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2nc(cnc2C(=O)N1)C(=O)NCCNC(=O)Nc3ccccc3
#
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
 1MX  1MX  2-amino-4-oxo-N-{2-[(phenylcarbamoyl)amino]ethyl}-3,4-dihydropteridine-7-carboxamide  ligand  43  27  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_1MX
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
 1MX  C    C  CR6   0   0.706    5.7861  -1.9887  -0.5387
 1MX  N    N  NH2   0  -0.820    6.1468  -3.1505  -1.0724
 1MX  O    O  O     0  -0.429    7.5182   0.6485   1.0409
 1MX  C1   C  CR6   0   0.547    6.5969   0.0089   0.5840
 1MX  N1   N  NR16  0  -0.715    6.7875  -1.2169  -0.0145
 1MX  O1   O  O     0  -0.476    0.8606   2.5934   1.0394
 1MX  C2   C  CR66  0  -0.029    5.1894   0.4188   0.5922
 1MX  N2   N  N     0  -0.506    4.5290  -1.6307  -0.5347
 1MX  O2   O  O     0  -0.519   -3.7933  -0.9186   0.5858
 1MX  C3   C  CR66  0   0.404    4.2298  -0.4394   0.0187
 1MX  N3   N  N     0  -0.427    2.9452  -0.0616   0.0162
 1MX  C4   C  CR6   0   0.092    2.6402   1.0967   0.5563
 1MX  N4   N  N     0  -0.348    4.8739   1.5841   1.1371
 1MX  C5   C  CR16  0  -0.105    3.6056   1.9352   1.1286
 1MX  N5   N  NH1   0  -0.653    0.3643   0.6665  -0.0366
 1MX  C6   C  C     0   0.544    1.1978   1.5269   0.5458
 1MX  N6   N  NH1   0  -0.682   -3.0817   0.1070  -1.3032
 1MX  C7   C  CH2   0  -0.250   -1.0545   0.9155  -0.1603
 1MX  N7   N  NH1   0  -0.789   -5.3053   0.1009  -0.8016
 1MX  C8   C  CH2   0  -0.328   -1.6831  -0.1361  -1.0688
 1MX  C9   C  C     0   0.744   -4.0417  -0.2807  -0.4269
 1MX  C10  C  CR6   0   0.375   -6.5171  -0.1453  -0.1590
 1MX  C11  C  CR16  0  -0.320   -6.6459  -0.6954   1.1191
 1MX  C12  C  CR16  0  -0.245   -7.9099  -0.8818   1.6643
 1MX  C13  C  CR16  0  -0.279   -9.0580  -0.5294   0.9706
 1MX  C14  C  CR16  0  -0.244   -8.9289   0.0218  -0.2980
 1MX  C15  C  CR16  0  -0.353   -7.6770   0.2108  -0.8567
 1MX  HN   H  HNH2  0   0.425    7.0989  -3.4739  -1.0823
 1MX  HNA  H  HNH2  0   0.422    5.4376  -3.7567  -1.4481
 1MX  HN1  H  HNR6  0   0.435    7.7413  -1.5545  -0.0586
 1MX  H5   H  HCR6  0   0.283    3.3370   2.8845   1.5715
 1MX  HN5  H  HNH1  0   0.412    0.7561  -0.1919  -0.3970
 1MX  HN6  H  HNH1  0   0.403   -3.3196   0.7016  -2.0799
 1MX  H7   H  HCH2  0   0.246   -1.5336   0.8934   0.8217
 1MX  H7A  H  HCH2  0   0.245   -1.2194   1.9097  -0.5818
 1MX  HN7  H  HNH1  0   0.408   -5.3923   0.5736  -1.6886
 1MX  H8   H  HCH2  0   0.257   -1.5492  -1.1314  -0.6421
 1MX  H8A  H  HCH2  0   0.266   -1.1798  -0.1333  -2.0365
 1MX  H11  H  HCR6  0   0.276   -5.7757  -0.9766   1.6884
 1MX  H12  H  HCR6  0   0.255   -7.9892  -1.3117   2.6549
 1MX  H13  H  HCR6  0   0.252  -10.0353  -0.6808   1.4088
 1MX  H14  H  HCR6  0   0.257   -9.8082   0.3049  -0.8622
 1MX  H15  H  HCR6  0   0.265   -7.5939   0.6407  -1.8486

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
 1MX  C    N    single    1.328  0.020  1.328
 1MX  C    N1   single    1.369  0.020  1.369
 1MX  C    N2   double    1.307  0.020  1.307
 1MX  O    C1   double    1.211  0.020  1.211
 1MX  C1   N1   single    1.377  0.020  1.377
 1MX  C1   C2   single    1.466  0.020  1.466
 1MX  O1   C6   double    1.223  0.020  1.223
 1MX  C2   C3   aromatic  1.409  0.020  1.409
 1MX  C2   N4   aromatic  1.325  0.020  1.325
 1MX  N2   C3   single    1.347  0.020  1.347
 1MX  O2   C9   double    1.222  0.020  1.222
 1MX  C3   N3   aromatic  1.339  0.020  1.339
 1MX  N3   C4   aromatic  1.314  0.020  1.314
 1MX  C4   C5   aromatic  1.401  0.020  1.401
 1MX  C4   C6   single    1.505  0.020  1.505
 1MX  N4   C5   aromatic  1.316  0.020  1.316
 1MX  N5   C6   single    1.332  0.020  1.332
 1MX  N5   C7   single    1.446  0.020  1.446
 1MX  N6   C8   single    1.439  0.020  1.439
 1MX  N6   C9   single    1.356  0.020  1.356
 1MX  C7   C8   single    1.525  0.020  1.525
 1MX  N7   C9   single    1.372  0.020  1.372
 1MX  N7   C10  single    1.394  0.020  1.394
 1MX  C10  C11  aromatic  1.397  0.020  1.397
 1MX  C10  C15  aromatic  1.400  0.020  1.400
 1MX  C11  C12  aromatic  1.389  0.020  1.389
 1MX  C12  C13  aromatic  1.387  0.020  1.387
 1MX  C13  C14  aromatic  1.389  0.020  1.389
 1MX  C14  C15  aromatic  1.384  0.020  1.384
 1MX  N    HN   single    0.860  0.020  1.020
 1MX  N    HNA  single    0.860  0.020  1.020
 1MX  N1   HN1  single    0.860  0.020  1.020
 1MX  C5   H5   single    0.930  0.020  1.080
 1MX  N5   HN5  single    0.860  0.020  1.020
 1MX  N6   HN6  single    0.860  0.020  1.020
 1MX  C7   H7   single    0.970  0.020  1.090
 1MX  C7   H7A  single    0.970  0.020  1.090
 1MX  N7   HN7  single    0.860  0.020  1.020
 1MX  C8   H8   single    0.970  0.020  1.090
 1MX  C8   H8A  single    0.970  0.020  1.090
 1MX  C11  H11  single    0.930  0.020  1.080
 1MX  C12  H12  single    0.930  0.020  1.080
 1MX  C13  H13  single    0.930  0.020  1.080
 1MX  C14  H14  single    0.930  0.020  1.080
 1MX  C15  H15  single    0.930  0.020  1.080

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
 1MX  N2   C    N1   123.24  3.000
 1MX  N2   C    N    120.13  3.000
 1MX  N1   C    N    116.63  3.000
 1MX  HNA  N    HN   118.04  3.000
 1MX  HNA  N    C    119.06  3.000
 1MX  HN   N    C    122.84  3.000
 1MX  C2   C1   N1   112.59  3.000
 1MX  C2   C1   O    125.50  3.000
 1MX  N1   C1   O    121.92  3.000
 1MX  HN1  N1   C1   116.48  3.000
 1MX  HN1  N1   C    118.98  3.000
 1MX  C1   N1   C    124.54  3.000
 1MX  N4   C2   C3   122.75  3.000
 1MX  N4   C2   C1   118.49  3.000
 1MX  C3   C2   C1   118.76  3.000
 1MX  C3   N2   C    117.19  3.000
 1MX  N3   C3   N2   117.50  3.000
 1MX  N3   C3   C2   118.83  3.000
 1MX  N2   C3   C2   123.67  3.000
 1MX  C4   N3   C3   118.08  3.000
 1MX  C6   C4   C5   119.48  3.000
 1MX  C6   C4   N3   118.14  3.000
 1MX  C5   C4   N3   122.38  3.000
 1MX  C5   N4   C2   117.49  3.000
 1MX  H5   C5   N4   118.09  3.000
 1MX  H5   C5   C4   121.44  3.000
 1MX  N4   C5   C4   120.47  3.000
 1MX  HN5  N5   C7   119.77  3.000
 1MX  HN5  N5   C6   117.53  3.000
 1MX  C7   N5   C6   122.70  3.000
 1MX  N5   C6   C4   114.71  3.000
 1MX  N5   C6   O1   124.56  3.000
 1MX  C4   C6   O1   120.72  3.000
 1MX  HN6  N6   C9   120.00  3.000
 1MX  HN6  N6   C8   117.08  3.000
 1MX  C9   N6   C8   122.31  3.000
 1MX  H7A  C7   H7   107.39  3.000
 1MX  H7A  C7   C8   109.60  3.000
 1MX  H7   C7   C8   109.91  3.000
 1MX  H7A  C7   N5   109.75  3.000
 1MX  H7   C7   N5   110.48  3.000
 1MX  C8   C7   N5   109.67  3.000
 1MX  HN7  N7   C10  114.40  3.000
 1MX  HN7  N7   C9   116.73  3.000
 1MX  C10  N7   C9   128.74  3.000
 1MX  H8A  C8   H8   107.02  3.000
 1MX  H8A  C8   C7   109.66  3.000
 1MX  H8   C8   C7   110.21  3.000
 1MX  H8A  C8   N6   107.67  3.000
 1MX  H8   C8   N6   109.70  3.000
 1MX  C7   C8   N6   112.40  3.000
 1MX  N7   C9   N6   113.33  3.000
 1MX  N7   C9   O2   123.95  3.000
 1MX  N6   C9   O2   122.72  3.000
 1MX  C15  C10  C11  118.67  3.000
 1MX  C15  C10  N7   116.48  3.000
 1MX  C11  C10  N7   124.84  3.000
 1MX  H11  C11  C12  119.52  3.000
 1MX  H11  C11  C10  120.78  3.000
 1MX  C12  C11  C10  119.71  3.000
 1MX  H12  C12  C13  119.86  3.000
 1MX  H12  C12  C11  118.62  3.000
 1MX  C13  C12  C11  121.53  3.000
 1MX  H13  C13  C14  120.63  3.000
 1MX  H13  C13  C12  120.64  3.000
 1MX  C14  C13  C12  118.73  3.000
 1MX  H14  C14  C15  119.26  3.000
 1MX  H14  C14  C13  120.28  3.000
 1MX  C15  C14  C13  120.46  3.000
 1MX  H15  C15  C14  119.53  3.000
 1MX  H15  C15  C10  119.56  3.000
 1MX  C14  C15  C10  120.91  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
 1MX  CONST_01  C4   N3   C3   C2      0.00   0.0  0
 1MX  CONST_02  C4   C5   N4   C2      0.00   0.0  0
 1MX  CONST_03  C5   N4   C2   C3      0.00   0.0  0
 1MX  CONST_04  C5   C4   N3   C3      0.00   0.0  0
 1MX  CONST_05  N4   C2   C3   N3      0.00   0.0  0
 1MX  CONST_06  N4   C5   C4   N3      0.00   0.0  0
 1MX  CONST_07  C13  C12  C11  C10     0.00   0.0  0
 1MX  CONST_08  C13  C14  C15  C10     0.00   0.0  0
 1MX  CONST_09  C14  C15  C10  C11     0.00   0.0  0
 1MX  CONST_10  C14  C13  C12  C11     0.00   0.0  0
 1MX  CONST_11  C15  C10  C11  C12     0.00   0.0  0
 1MX  CONST_12  C15  C14  C13  C12     0.00   0.0  0
 1MX  CONST_13  C2   C1   N1   C       0.00   0.0  0
 1MX  CONST_14  N2   C    N1   C1      0.00   0.0  0
 1MX  CONST_15  C3   N2   C    N1      0.00   0.0  0
 1MX  CONST_16  C6   C4   N3   C3    180.00   0.0  0
 1MX  CONST_17  C6   C4   C5   N4    180.00   0.0  0
 1MX  CONST_18  C12  C11  C10  N7    180.00   0.0  0
 1MX  CONST_19  C14  C15  C10  N7    180.00   0.0  0
 1MX  CONST_20  O    C1   N1   C     180.00   0.0  0
 1MX  CONST_21  C1   N1   C    N     180.00   0.0  0
 1MX  CONST_22  C3   N2   C    N     180.00   0.0  0
 1MX  CONST_23  H5   C5   N4   C2    180.00   0.0  0
 1MX  CONST_24  H12  C12  C11  C10   180.00   0.0  0
 1MX  CONST_25  H14  C14  C15  C10   180.00   0.0  0
 1MX  CONST_26  H15  C15  C10  C11   180.00   0.0  0
 1MX  CONST_27  H13  C13  C12  C11   180.00   0.0  0
 1MX  CONST_28  H11  C11  C12  C13   180.00   0.0  0
 1MX  CONST_29  HN1  N1   C1   C2    180.00   0.0  0
 1MX  CONST_30  C11  C10  N7   C9      0.00   0.0  0
 1MX  CONST_31  C15  C10  N7   C9    180.00   0.0  0
 1MX  CONST_32  HN7  N7   C10  C11   180.00   0.0  0
 1MX  CONST_33  HN   N    C    N1      0.00   0.0  0
 1MX  CONST_34  HNA  N    C    N1    180.00   0.0  0
 1MX  CONST_35  C10  N7   C9   O2      0.00   0.0  0
 1MX  CONST_36  C7   N5   C6   C4    180.00   0.0  0
 1MX  CONST_37  C10  N7   C9   N6    180.00   0.0  0
 1MX  CONST_38  HN5  N5   C6   C4      0.00   0.0  0
 1MX  CONST_39  C7   N5   C6   O1      0.00   0.0  0
 1MX  CONST_40  C8   N6   C9   O2      0.00   0.0  0
 1MX  CONST_41  C8   N6   C9   N7    180.00   0.0  0
 1MX  CONST_42  HN6  N6   C9   O2    180.00   0.0  0
 1MX  Var_01    N3   C4   C6   O1    179.75  30.0  2
 1MX  Var_02    N6   C8   C7   N5   -176.21  30.0  3
 1MX  Var_03    C8   C7   N5   C6    170.63  30.0  3
 1MX  Var_04    C9   N6   C8   C7    -82.67  30.0  2

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
 1MX  plan-1  N7   0.020
 1MX  plan-1  C10  0.020
 1MX  plan-1  C11  0.020
 1MX  plan-1  C12  0.020
 1MX  plan-1  C13  0.020
 1MX  plan-1  C14  0.020
 1MX  plan-1  C15  0.020
 1MX  plan-1  H11  0.020
 1MX  plan-1  H12  0.020
 1MX  plan-1  H13  0.020
 1MX  plan-1  H14  0.020
 1MX  plan-1  H15  0.020
 1MX  plan-2  C    0.020
 1MX  plan-2  N    0.020
 1MX  plan-2  O    0.020
 1MX  plan-2  C1   0.020
 1MX  plan-2  N1   0.020
 1MX  plan-2  C2   0.020
 1MX  plan-2  N2   0.020
 1MX  plan-2  C3   0.020
 1MX  plan-2  N3   0.020
 1MX  plan-2  C4   0.020
 1MX  plan-2  N4   0.020
 1MX  plan-2  C5   0.020
 1MX  plan-2  C6   0.020
 1MX  plan-2  HN   0.020
 1MX  plan-2  HNA  0.020
 1MX  plan-2  HN1  0.020
 1MX  plan-2  H5   0.020
 1MX  plan-3  O1   0.020
 1MX  plan-3  C4   0.020
 1MX  plan-3  N5   0.020
 1MX  plan-3  C6   0.020
 1MX  plan-3  C7   0.020
 1MX  plan-3  HN5  0.020
 1MX  plan-4  O2   0.020
 1MX  plan-4  N6   0.020
 1MX  plan-4  N7   0.020
 1MX  plan-4  C8   0.020
 1MX  plan-4  C9   0.020
 1MX  plan-4  C10  0.020
 1MX  plan-4  HN6  0.020
 1MX  plan-4  HN7  0.020

