# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 05:47:20 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 3-({4-[(5-chloro-1,3-benzodioxol-4-yl)amino]pyrimidin-2-yl}amino)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1cccc(Nc2nccc(Nc3c(Cl)ccc4OCOc34)n2)c1
#
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
 7X8  7X8  3-({4-[(5-chloro-1,3-benzodioxol-4-yl)amino]pyrimidin-2-yl}amino)benzamide  ligand  41  27  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7X8
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
 7X8  N2    N   NH1   0  -0.774  13.5997   7.4280  11.5864
 7X8  C7    C   CR6   0   0.601  13.0888   6.2027  11.8989
 7X8  N3    N   N     0  -0.488  14.0026   5.3220  12.3147
 7X8  C8    C   CR16  0  -0.029  13.5331   4.1197  12.6229
 7X8  C9    C   CR16  0  -0.429  12.2038   3.7662  12.5455
 7X8  C10   C   CR6   0   0.546  11.3365   4.7753  12.1079
 7X8  N4    N   NH1   0  -0.732   9.9980   4.6027  11.9725
 7X8  C11   C   CR6   0   0.279   9.2973   3.4500  12.3287
 7X8  C12   C   CR56  0   0.294   9.2511   2.9991  13.6301
 7X8  O2    O   O     0  -0.468   9.8292   3.5529  14.7132
 7X8  C13   C   CH2   0   0.068   9.6407   2.6245  15.7788
 7X8  O3    O   O     0  -0.482   8.6809   1.6758  15.3317
 7X8  C14   C   CR56  0   0.318   8.5530   1.8610  13.9979
 7X8  C15   C   CR16  0  -0.353   7.8315   1.1283  13.0901
 7X8  C16   C   CR16  0  -0.251   7.8409   1.5731  11.7636
 7X8  C17   C   CR6   0  -0.126   8.5616   2.6935  11.3974
 7X8  CL1   CL  CL    0  -0.105   8.5745   3.2011   9.7447
 7X8  N5    N   N     0  -0.524  11.7887   5.9845  11.7814
 7X8  N1    N   NH2   0  -0.813   9.3646  10.9325   9.0388
 7X8  O1    O   O     0  -0.479   8.9218   9.1592  10.3535
 7X8  C2    C   CR6   0  -0.018  11.1692   9.9256  10.2837
 7X8  C3    C   CR16  0  -0.316  11.9948  11.0411  10.1979
 7X8  C4    C   CR16  0  -0.232  13.3263  10.9242  10.5735
 7X8  C5    C   CR16  0  -0.348  13.8276   9.7190  11.0249
 7X8  C6    C   CR6   0   0.387  13.0008   8.5925  11.1271
 7X8  C18   C   CR16  0  -0.346  11.6613   8.7127  10.7588
 7X8  H2    H   HNH1  0   0.408  14.5946   7.4878  11.7437
 7X8  H8    H   HCR6  0   0.271  14.2651   3.3889  12.9492
 7X8  H9    H   HCR6  0   0.277  11.8764   2.7676  12.7898
 7X8  H4    H   HNH1  0   0.402   9.4945   5.3551  11.5256
 7X8  H131  H   HCH2  0   0.243  10.5872   2.1229  16.0021
 7X8  H132  H   HCH2  0   0.253   9.2641   3.1474  16.6570
 7X8  H15   H   HCR6  0   0.287   7.2744   0.2467  13.3750
 7X8  H16   H   HCR6  0   0.287   7.2853   1.0248  11.0162
 7X8  H1N1  H   HNH2  0   0.404   8.4116  10.9799   8.7167
 7X8  H1N2  H   HNH2  0   0.412  10.0367  11.4945   8.5465
 7X8  H3    H   HCR6  0   0.257  11.6199  12.0015   9.8702
 7X8  H18   H   HCR6  0   0.292  11.0012   7.8649  10.8316
 7X8  HA    H   HCR6  0   0.265  13.9816  11.7835  10.5196
 7X8  H5    H   HCR6  0   0.274  14.8709   9.6445  11.3088
 7X8  C1    C   C     0   0.487   9.7211   9.9668   9.8999

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
 7X8  N2   C7    single    1.364  0.020  1.364
 7X8  N2   C6    single    1.388  0.020  1.388
 7X8  C7   N3    aromatic  1.336  0.020  1.336
 7X8  C7   N5    aromatic  1.324  0.020  1.324
 7X8  N3   C8    aromatic  1.327  0.020  1.327
 7X8  C8   C9    aromatic  1.378  0.020  1.378
 7X8  C9   C10   aromatic  1.401  0.020  1.401
 7X8  C10  N4    single    1.356  0.020  1.356
 7X8  C10  N5    aromatic  1.332  0.020  1.332
 7X8  N4   C11   single    1.395  0.020  1.395
 7X8  C11  C12   aromatic  1.378  0.020  1.378
 7X8  C11  C17   aromatic  1.407  0.020  1.407
 7X8  C12  O2    single    1.347  0.020  1.347
 7X8  C12  C14   aromatic  1.385  0.020  1.385
 7X8  O2   C13   single    1.426  0.020  1.426
 7X8  C13  O3    single    1.422  0.020  1.422
 7X8  O3   C14   single    1.353  0.020  1.353
 7X8  C14  C15   aromatic  1.372  0.020  1.372
 7X8  C15  C16   aromatic  1.399  0.020  1.399
 7X8  C16  C17   aromatic  1.382  0.020  1.382
 7X8  C17  CL1   single    1.729  0.020  1.729
 7X8  N1   C1    single    1.342  0.020  1.342
 7X8  C1   O1    double    1.223  0.020  1.223
 7X8  C1   C2    single    1.499  0.020  1.499
 7X8  C2   C3    aromatic  1.390  0.020  1.390
 7X8  C2   C18   aromatic  1.392  0.020  1.392
 7X8  C3   C4    aromatic  1.388  0.020  1.388
 7X8  C4   C5    aromatic  1.381  0.020  1.381
 7X8  C5   C6    aromatic  1.401  0.020  1.401
 7X8  C6   C18   aromatic  1.394  0.020  1.394
 7X8  N2   H2    single    0.860  0.020  1.020
 7X8  C8   H8    single    0.930  0.020  1.080
 7X8  C9   H9    single    0.930  0.020  1.080
 7X8  N4   H4    single    0.860  0.020  1.020
 7X8  C13  H131  single    0.970  0.020  1.090
 7X8  C13  H132  single    0.970  0.020  1.090
 7X8  C15  H15   single    0.930  0.020  1.080
 7X8  C16  H16   single    0.930  0.020  1.080
 7X8  N1   H1N1  single    0.860  0.020  1.020
 7X8  N1   H1N2  single    0.860  0.020  1.020
 7X8  C3   H3    single    0.930  0.020  1.080
 7X8  C18  H18   single    0.930  0.020  1.080
 7X8  C4   HA    single    0.930  0.020  1.080
 7X8  C5   H5    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
 7X8  H2    N2   C6    115.30  3.000
 7X8  H2    N2   C7    112.76  3.000
 7X8  C6    N2   C7    131.92  3.000
 7X8  N5    C7   N3    126.23  3.000
 7X8  N5    C7   N2    119.72  3.000
 7X8  N3    C7   N2    114.05  3.000
 7X8  C8    N3   C7    115.32  3.000
 7X8  H8    C8   C9    119.68  3.000
 7X8  H8    C8   N3    116.20  3.000
 7X8  C9    C8   N3    124.12  3.000
 7X8  H9    C9   C10   123.34  3.000
 7X8  H9    C9   C8    121.17  3.000
 7X8  C10   C9   C8    115.47  3.000
 7X8  N5    C10  N4    115.22  3.000
 7X8  N5    C10  C9    121.37  3.000
 7X8  N4    C10  C9    123.41  3.000
 7X8  H4    N4   C11   118.57  3.000
 7X8  H4    N4   C10   116.20  3.000
 7X8  C11   N4   C10   125.11  3.000
 7X8  C17   C11  C12   115.56  3.000
 7X8  C17   C11  N4    122.52  3.000
 7X8  C12   C11  N4    121.89  3.000
 7X8  C14   C12  O2    109.92  3.000
 7X8  C14   C12  C11   122.45  3.000
 7X8  O2    C12  C11   127.62  3.000
 7X8  C13   O2   C12   106.05  3.000
 7X8  H132  C13  H131  110.78  3.000
 7X8  H132  C13  O3    109.91  3.000
 7X8  H131  C13  O3    110.01  3.000
 7X8  H132  C13  O2    109.61  3.000
 7X8  H131  C13  O2    109.68  3.000
 7X8  O3    C13  O2    106.78  3.000
 7X8  C14   O3   C13   106.42  3.000
 7X8  C15   C14  O3    128.99  3.000
 7X8  C15   C14  C12   121.90  3.000
 7X8  O3    C14  C12   109.07  3.000
 7X8  H15   C15  C16   120.84  3.000
 7X8  H15   C15  C14   122.16  3.000
 7X8  C16   C15  C14   117.00  3.000
 7X8  H16   C16  C17   119.76  3.000
 7X8  H16   C16  C15   119.40  3.000
 7X8  C17   C16  C15   120.84  3.000
 7X8  CL1   C17  C16   119.69  3.000
 7X8  CL1   C17  C11   118.09  3.000
 7X8  C16   C17  C11   122.22  3.000
 7X8  C10   N5   C7    117.48  3.000
 7X8  H1N2  N1   H1N1  116.74  3.000
 7X8  H1N2  N1   C1    122.62  3.000
 7X8  H1N1  N1   C1    119.37  3.000
 7X8  C18   C2   C3    120.66  3.000
 7X8  C18   C2   C1    116.92  3.000
 7X8  C3    C2   C1    122.41  3.000
 7X8  H3    C3   C4    119.28  3.000
 7X8  H3    C3   C2    121.68  3.000
 7X8  C4    C3   C2    119.02  3.000
 7X8  HA    C4   C5    119.31  3.000
 7X8  HA    C4   C3    120.03  3.000
 7X8  C5    C4   C3    120.66  3.000
 7X8  H5    C5   C6    119.58  3.000
 7X8  H5    C5   C4    119.67  3.000
 7X8  C6    C5   C4    120.75  3.000
 7X8  C18   C6   C5    118.57  3.000
 7X8  C18   C6   N2    125.05  3.000
 7X8  C5    C6   N2    116.37  3.000
 7X8  H18   C18  C6    120.20  3.000
 7X8  H18   C18  C2    119.48  3.000
 7X8  C6    C18  C2    120.31  3.000
 7X8  C2    C1   O1    121.21  3.000
 7X8  C2    C1   N1    116.15  3.000
 7X8  O1    C1   N1    122.64  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
 7X8  CONST_01  C9    C8   N3   C7     0.00   0.0  0
 7X8  CONST_02  C9    C10  N5   C7     0.00   0.0  0
 7X8  CONST_03  C10   N5   C7   N3     0.00   0.0  0
 7X8  CONST_04  C10   C9   C8   N3     0.00   0.0  0
 7X8  CONST_05  N5    C7   N3   C8     0.00   0.0  0
 7X8  CONST_06  N5    C10  C9   C8     0.00   0.0  0
 7X8  CONST_07  C15   C14  C12  C11    0.00   0.0  0
 7X8  CONST_08  C15   C16  C17  C11    0.00   0.0  0
 7X8  CONST_09  C16   C17  C11  C12    0.00   0.0  0
 7X8  CONST_10  C16   C15  C14  C12    0.00   0.0  0
 7X8  CONST_11  C17   C11  C12  C14    0.00   0.0  0
 7X8  CONST_12  C17   C16  C15  C14    0.00   0.0  0
 7X8  CONST_13  C5    C4   C3   C2     0.00   0.0  0
 7X8  CONST_14  C5    C6   C18  C2     0.00   0.0  0
 7X8  CONST_15  C6    C18  C2   C3     0.00   0.0  0
 7X8  CONST_16  C6    C5   C4   C3     0.00   0.0  0
 7X8  CONST_17  C18   C2   C3   C4     0.00   0.0  0
 7X8  CONST_18  C18   C6   C5   C4     0.00   0.0  0
 7X8  CONST_19  C8    N3   C7   N2   180.00   0.0  0
 7X8  CONST_20  C10   N5   C7   N2   180.00   0.0  0
 7X8  CONST_21  C4    C5   C6   N2   180.00   0.0  0
 7X8  CONST_22  C2    C18  C6   N2   180.00   0.0  0
 7X8  CONST_23  N4    C10  N5   C7   180.00   0.0  0
 7X8  CONST_24  N4    C10  C9   C8   180.00   0.0  0
 7X8  CONST_25  O2    C12  C11  N4     0.00   0.0  0
 7X8  CONST_26  C14   C12  C11  N4   180.00   0.0  0
 7X8  CONST_27  C16   C17  C11  N4   180.00   0.0  0
 7X8  CONST_28  CL1   C17  C11  C12  180.00   0.0  0
 7X8  CONST_29  CL1   C17  C16  C15  180.00   0.0  0
 7X8  CONST_30  C4    C3   C2   C1   180.00   0.0  0
 7X8  CONST_31  C6    C18  C2   C1   180.00   0.0  0
 7X8  CONST_32  H8    C8   N3   C7   180.00   0.0  0
 7X8  CONST_33  H9    C9   C8   N3   180.00   0.0  0
 7X8  CONST_34  H16   C16  C17  C11  180.00   0.0  0
 7X8  CONST_35  H15   C15  C14  C12  180.00   0.0  0
 7X8  CONST_36  HA    C4   C3   C2   180.00   0.0  0
 7X8  CONST_37  H18   C18  C2   C3   180.00   0.0  0
 7X8  CONST_38  H5    C5   C4   C3   180.00   0.0  0
 7X8  CONST_39  H3    C3   C4   C5   180.00   0.0  0
 7X8  CONST_40  H1N1  N1   C1   C2   180.00   0.0  0
 7X8  CONST_41  H1N2  N1   C1   C2     0.00   0.0  0
 7X8  Var_01    O3    C13  O2   C12  -12.89  30.0  1
 7X8  Var_02    C14   C12  O2   C13    8.13  30.0  1
 7X8  Var_03    C15   C14  O3   C13  174.31  30.0  1
 7X8  Var_04    C5    C6   N2   C7   174.32  30.0  2
 7X8  Var_05    C6    N2   C7   N3   179.98  30.0  2
 7X8  Var_06    C11   N4   C10  C9     4.55  30.0  2
 7X8  Var_07    C12   C11  N4   C10   62.25  30.0  2
 7X8  Var_08    C3    C2   C1   N1    23.43  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
 7X8  plan-1  N2    0.020
 7X8  plan-1  C7    0.020
 7X8  plan-1  N3    0.020
 7X8  plan-1  C8    0.020
 7X8  plan-1  C9    0.020
 7X8  plan-1  C10   0.020
 7X8  plan-1  N4    0.020
 7X8  plan-1  N5    0.020
 7X8  plan-1  H8    0.020
 7X8  plan-1  H9    0.020
 7X8  plan-2  N2    0.020
 7X8  plan-2  C2    0.020
 7X8  plan-2  C3    0.020
 7X8  plan-2  C4    0.020
 7X8  plan-2  C5    0.020
 7X8  plan-2  C6    0.020
 7X8  plan-2  C18   0.020
 7X8  plan-2  H3    0.020
 7X8  plan-2  H18   0.020
 7X8  plan-2  HA    0.020
 7X8  plan-2  H5    0.020
 7X8  plan-2  C1    0.020
 7X8  plan-3  N4    0.020
 7X8  plan-3  C11   0.020
 7X8  plan-3  C12   0.020
 7X8  plan-3  O2    0.020
 7X8  plan-3  O3    0.020
 7X8  plan-3  C14   0.020
 7X8  plan-3  C15   0.020
 7X8  plan-3  C16   0.020
 7X8  plan-3  C17   0.020
 7X8  plan-3  CL1   0.020
 7X8  plan-3  H15   0.020
 7X8  plan-3  H16   0.020
 7X8  plan-4  N1    0.020
 7X8  plan-4  O1    0.020
 7X8  plan-4  C2    0.020
 7X8  plan-4  H1N1  0.020
 7X8  plan-4  H1N2  0.020
 7X8  plan-4  C1    0.020

