# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 07:46:28 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: N~4~-(5-chloro-1,3-benzodioxol-4-yl)-N~2~-(3,4,5-trimethoxyphenyl)pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(Nc2nccc(Nc3c(Cl)ccc4OCOc34)n2)cc(OC)c1OC
#
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
 7X2  7X2  N~4~-(5-chloro-1,3-benzodioxol-4-yl)-N~2~-(3,4,5-trimethoxyphenyl)pyrimidine-2,4-diamine  ligand  49  30  .  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_7X2
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
 7X2  C1    C   CH3   0  -0.439  15.8009  11.6365  10.6186
 7X2  O2    O   O2    0  -0.465  14.5004  11.6086  10.0653
 7X2  C3    C   CR6   0   0.348  13.7535  10.5047  10.2350
 7X2  C4    C   CR16  0  -0.544  14.1746   9.3811  10.9350
 7X2  C5    C   CR6   0   0.420  13.3266   8.2766  11.0629
 7X2  N6    N   NH1   0  -0.779  13.8409   7.2016  11.7781
 7X2  C7    C   CR6   0   0.603  13.3161   5.9910  12.1173
 7X2  N8    N   N     0  -0.489  14.1516   5.2144  12.8139
 7X2  C9    C   CR16  0  -0.029  13.6756   4.0224  13.1478
 7X2  C10   C   CR16  0  -0.431  12.4106   3.5782  12.8299
 7X2  C11   C   CR6   0   0.549  11.6185   4.4826  12.1121
 7X2  N12   N   NH1   0  -0.731  10.3481   4.2143  11.7183
 7X2  C13   C   CR6   0   0.278   9.6422   3.0474  12.0133
 7X2  C14   C   CR56  0   0.294   9.3185   2.6967  13.3059
 7X2  O15   O   O     0  -0.468   9.6025   3.3686  14.4383
 7X2  C16   C   CH2   0   0.067   9.2259   2.5068  15.5099
 7X2  O17   O   O     0  -0.481   8.4251   1.4774  14.9452
 7X2  C18   C   CR56  0   0.317   8.6044   1.5482  13.6061
 7X2  C19   C   CR16  0  -0.352   8.1433   0.7033  12.6289
 7X2  C20   C   CR16  0  -0.250   8.4393   1.0430  11.3043
 7X2  C21   C   CR6   0  -0.125   9.1739   2.1759  11.0120
 7X2  CL1   CL  CL    0  -0.105   9.5409   2.5570   9.3655
 7X2  N23   N   N     0  -0.528  12.0802   5.6799  11.7566
 7X2  C24   C   CR16  0  -0.517  12.0582   8.2991  10.4879
 7X2  C25   C   CR6   0   0.381  11.6472   9.4332   9.7892
 7X2  O26   O   O2    0  -0.466  10.4402   9.5452   9.2072
 7X2  C27   C   CH3   0  -0.440   9.5373   8.4621   9.2994
 7X2  C28   C   CR6   0   0.149  12.4865  10.5371   9.6455
 7X2  O29   O   O2    0  -0.482  12.0904  11.6268   8.9324
 7X2  C30   C   CH3   0  -0.407  11.4019  12.6060   9.6971
 7X2  H1C1  H   HCH3  0   0.229  16.4393  10.8535  10.2014
 7X2  H1C2  H   HCH3  0   0.262  16.2230  12.6053  10.3634
 7X2  H1C3  H   HCH3  0   0.229  15.7847  11.5370  11.7071
 7X2  H4    H   HCR6  0   0.288  15.1565   9.3468  11.3892
 7X2  H6    H   HNH1  0   0.407  14.7813   7.3255  12.1213
 7X2  H24   H   HCR6  0   0.305  11.4124   7.4446  10.5913
 7X2  H9    H   HCR6  0   0.271  14.3472   3.3764  13.7027
 7X2  H10   H   HCR6  0   0.276  12.0802   2.5892  13.1070
 7X2  H12   H   HNH1  0   0.397   9.9247   4.8849  11.0940
 7X2  H161  H   HCH2  0   0.242  10.1216   2.0756  15.9679
 7X2  H162  H   HCH2  0   0.254   8.6478   3.0666  16.2435
 7X2  H19   H   HCR6  0   0.287   7.5728  -0.1853  12.8594
 7X2  H20   H   HCR6  0   0.287   8.0988   0.4033  10.5024
 7X2  H271  H   HCH3  0   0.227   9.9245   7.5630   8.8128
 7X2  H272  H   HCH3  0   0.227   9.2858   8.2229  10.3359
 7X2  H273  H   HCH3  0   0.263   8.6314   8.7726   8.7848
 7X2  H301  H   HCH3  0   0.218  12.0048  12.9652  10.5349
 7X2  H302  H   HCH3  0   0.234  11.1943  13.4456   9.0352
 7X2  H303  H   HCH3  0   0.220  10.4543  12.2253  10.0863

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
 7X2  C1   O2    single    1.414  0.020  1.414
 7X2  O2   C3    single    1.344  0.020  1.344
 7X2  C3   C4    aromatic  1.389  0.020  1.389
 7X2  C3   C28   aromatic  1.398  0.020  1.398
 7X2  C4   C5    aromatic  1.398  0.020  1.398
 7X2  C5   N6    single    1.390  0.020  1.390
 7X2  C5   C24   aromatic  1.393  0.020  1.393
 7X2  N6   C7    single    1.362  0.020  1.362
 7X2  C7   N8    aromatic  1.337  0.020  1.337
 7X2  C7   N23   aromatic  1.325  0.020  1.325
 7X2  N8   C9    aromatic  1.326  0.020  1.326
 7X2  C9   C10   aromatic  1.378  0.020  1.378
 7X2  C10  C11   aromatic  1.400  0.020  1.400
 7X2  C11  N12   single    1.357  0.020  1.357
 7X2  C11  N23   aromatic  1.332  0.020  1.332
 7X2  N12  C13   single    1.395  0.020  1.395
 7X2  C13  C14   aromatic  1.378  0.020  1.378
 7X2  C13  C21   aromatic  1.408  0.020  1.408
 7X2  C14  O15   single    1.347  0.020  1.347
 7X2  C14  C18   aromatic  1.385  0.020  1.385
 7X2  O15  C16   single    1.426  0.020  1.426
 7X2  C16  O17   single    1.421  0.020  1.421
 7X2  O17  C18   single    1.353  0.020  1.353
 7X2  C18  C19   aromatic  1.372  0.020  1.372
 7X2  C19  C20   aromatic  1.399  0.020  1.399
 7X2  C20  C21   aromatic  1.381  0.020  1.381
 7X2  C21  CL1   single    1.729  0.020  1.729
 7X2  C24  C25   aromatic  1.394  0.020  1.394
 7X2  C25  O26   single    1.345  0.020  1.345
 7X2  C25  C28   aromatic  1.394  0.020  1.394
 7X2  O26  C27   single    1.413  0.020  1.413
 7X2  C28  O29   single    1.361  0.020  1.361
 7X2  O29  C30   single    1.420  0.020  1.420
 7X2  C1   H1C1  single    0.970  0.020  1.090
 7X2  C1   H1C2  single    0.970  0.020  1.090
 7X2  C1   H1C3  single    0.970  0.020  1.090
 7X2  C4   H4    single    0.930  0.020  1.080
 7X2  N6   H6    single    0.860  0.020  1.020
 7X2  C24  H24   single    0.930  0.020  1.080
 7X2  C9   H9    single    0.930  0.020  1.080
 7X2  C10  H10   single    0.930  0.020  1.080
 7X2  N12  H12   single    0.860  0.020  1.020
 7X2  C16  H161  single    0.970  0.020  1.090
 7X2  C16  H162  single    0.970  0.020  1.090
 7X2  C19  H19   single    0.930  0.020  1.080
 7X2  C20  H20   single    0.930  0.020  1.080
 7X2  C27  H271  single    0.970  0.020  1.090
 7X2  C27  H272  single    0.970  0.020  1.090
 7X2  C27  H273  single    0.970  0.020  1.090
 7X2  C30  H301  single    0.970  0.020  1.090
 7X2  C30  H302  single    0.970  0.020  1.090
 7X2  C30  H303  single    0.970  0.020  1.090

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
 7X2  H1C3  C1   H1C2  108.70  3.000
 7X2  H1C3  C1   H1C1  108.87  3.000
 7X2  H1C2  C1   H1C1  108.78  3.000
 7X2  H1C3  C1   O2    111.99  3.000
 7X2  H1C2  C1   O2    106.43  3.000
 7X2  H1C1  C1   O2    111.95  3.000
 7X2  C3    O2   C1    118.57  3.000
 7X2  C28   C3   C4    120.40  3.000
 7X2  C28   C3   O2    115.57  3.000
 7X2  C4    C3   O2    124.03  3.000
 7X2  H4    C4   C5    119.12  3.000
 7X2  H4    C4   C3    120.80  3.000
 7X2  C5    C4   C3    120.07  3.000
 7X2  C24   C5   N6    124.19  3.000
 7X2  C24   C5   C4    120.11  3.000
 7X2  N6    C5   C4    115.70  3.000
 7X2  H6    N6   C7    112.55  3.000
 7X2  H6    N6   C5    115.16  3.000
 7X2  C7    N6   C5    132.30  3.000
 7X2  N23   C7   N8    126.07  3.000
 7X2  N23   C7   N6    120.02  3.000
 7X2  N8    C7   N6    113.91  3.000
 7X2  C9    N8   C7    115.41  3.000
 7X2  H9    C9   C10   119.64  3.000
 7X2  H9    C9   N8    116.22  3.000
 7X2  C10   C9   N8    124.14  3.000
 7X2  H10   C10  C11   123.40  3.000
 7X2  H10   C10  C9    121.16  3.000
 7X2  C11   C10  C9    115.43  3.000
 7X2  N23   C11  N12   115.15  3.000
 7X2  N23   C11  C10   121.43  3.000
 7X2  N12   C11  C10   123.41  3.000
 7X2  H12   N12  C13   118.30  3.000
 7X2  H12   N12  C11   116.16  3.000
 7X2  C13   N12  C11   125.29  3.000
 7X2  C21   C13  C14   115.57  3.000
 7X2  C21   C13  N12   122.39  3.000
 7X2  C14   C13  N12   122.01  3.000
 7X2  C18   C14  O15   109.88  3.000
 7X2  C18   C14  C13   122.38  3.000
 7X2  O15   C14  C13   127.74  3.000
 7X2  C16   O15  C14   105.94  3.000
 7X2  H162  C16  H161  110.80  3.000
 7X2  H162  C16  O17   109.93  3.000
 7X2  H161  C16  O17   110.00  3.000
 7X2  H162  C16  O15   109.62  3.000
 7X2  H161  C16  O15   109.67  3.000
 7X2  O17   C16  O15   106.74  3.000
 7X2  C18   O17  C16   106.31  3.000
 7X2  C19   C18  O17   128.93  3.000
 7X2  C19   C18  C14   121.97  3.000
 7X2  O17   C18  C14   109.04  3.000
 7X2  H19   C19  C20   120.87  3.000
 7X2  H19   C19  C18   122.14  3.000
 7X2  C20   C19  C18   116.99  3.000
 7X2  H20   C20  C21   119.73  3.000
 7X2  H20   C20  C19   119.47  3.000
 7X2  C21   C20  C19   120.79  3.000
 7X2  CL1   C21  C20   119.67  3.000
 7X2  CL1   C21  C13   118.05  3.000
 7X2  C20   C21  C13   122.28  3.000
 7X2  C11   N23  C7    117.52  3.000
 7X2  H24   C24  C25   121.14  3.000
 7X2  H24   C24  C5    119.61  3.000
 7X2  C25   C24  C5    119.25  3.000
 7X2  C28   C25  O26   115.46  3.000
 7X2  C28   C25  C24   121.22  3.000
 7X2  O26   C25  C24   123.33  3.000
 7X2  C27   O26  C25   118.78  3.000
 7X2  H273  C27  H272  108.64  3.000
 7X2  H273  C27  H271  108.63  3.000
 7X2  H272  C27  H271  108.88  3.000
 7X2  H273  C27  O26   106.42  3.000
 7X2  H272  C27  O26   112.12  3.000
 7X2  H271  C27  O26   112.02  3.000
 7X2  O29   C28  C25   120.84  3.000
 7X2  O29   C28  C3    120.21  3.000
 7X2  C25   C28  C3    118.94  3.000
 7X2  C30   O29  C28   114.26  3.000
 7X2  H303  C30  H302  108.64  3.000
 7X2  H303  C30  H301  108.65  3.000
 7X2  H302  C30  H301  108.53  3.000
 7X2  H303  C30  O29   111.83  3.000
 7X2  H302  C30  O29   107.26  3.000
 7X2  H301  C30  O29   111.83  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
 7X2  CONST_01  C24   C5   C4   C3     0.00   0.0  0
 7X2  CONST_02  C24   C25  C28  C3     0.00   0.0  0
 7X2  CONST_03  C25   C28  C3   C4     0.00   0.0  0
 7X2  CONST_04  C25   C24  C5   C4     0.00   0.0  0
 7X2  CONST_05  C28   C3   C4   C5     0.00   0.0  0
 7X2  CONST_06  C28   C25  C24  C5     0.00   0.0  0
 7X2  CONST_07  C10   C9   N8   C7     0.00   0.0  0
 7X2  CONST_08  C10   C11  N23  C7     0.00   0.0  0
 7X2  CONST_09  C11   N23  C7   N8     0.00   0.0  0
 7X2  CONST_10  C11   C10  C9   N8     0.00   0.0  0
 7X2  CONST_11  N23   C7   N8   C9     0.00   0.0  0
 7X2  CONST_12  N23   C11  C10  C9     0.00   0.0  0
 7X2  CONST_13  C19   C18  C14  C13    0.00   0.0  0
 7X2  CONST_14  C19   C20  C21  C13    0.00   0.0  0
 7X2  CONST_15  C20   C21  C13  C14    0.00   0.0  0
 7X2  CONST_16  C20   C19  C18  C14    0.00   0.0  0
 7X2  CONST_17  C21   C13  C14  C18    0.00   0.0  0
 7X2  CONST_18  C21   C20  C19  C18    0.00   0.0  0
 7X2  CONST_19  C5    C4   C3   O2   180.00   0.0  0
 7X2  CONST_20  C25   C28  C3   O2   180.00   0.0  0
 7X2  CONST_21  N6    C5   C4   C3   180.00   0.0  0
 7X2  CONST_22  O26   C25  C28  C3   180.00   0.0  0
 7X2  CONST_23  O29   C28  C3   C4   180.00   0.0  0
 7X2  CONST_24  O26   C25  C24  C5   180.00   0.0  0
 7X2  CONST_25  C25   C24  C5   N6   180.00   0.0  0
 7X2  CONST_26  C9    N8   C7   N6   180.00   0.0  0
 7X2  CONST_27  C11   N23  C7   N6   180.00   0.0  0
 7X2  CONST_28  N12   C11  N23  C7   180.00   0.0  0
 7X2  CONST_29  N12   C11  C10  C9   180.00   0.0  0
 7X2  CONST_30  O15   C14  C13  N12    0.00   0.0  0
 7X2  CONST_31  C18   C14  C13  N12  180.00   0.0  0
 7X2  CONST_32  C20   C21  C13  N12  180.00   0.0  0
 7X2  CONST_33  CL1   C21  C13  C14  180.00   0.0  0
 7X2  CONST_34  CL1   C21  C20  C19  180.00   0.0  0
 7X2  CONST_35  O29   C28  C25  C24  180.00   0.0  0
 7X2  CONST_36  H24   C24  C5   C4   180.00   0.0  0
 7X2  CONST_37  H9    C9   N8   C7   180.00   0.0  0
 7X2  CONST_38  H10   C10  C9   N8   180.00   0.0  0
 7X2  CONST_39  H20   C20  C21  C13  180.00   0.0  0
 7X2  CONST_40  H19   C19  C18  C14  180.00   0.0  0
 7X2  CONST_41  H4    C4   C5   C24  180.00   0.0  0
 7X2  Var_01    O17   C16  O15  C14  -14.06  30.0  1
 7X2  Var_02    C18   C14  O15  C16    8.83  30.0  1
 7X2  Var_03    C19   C18  O17  C16  173.80  30.0  1
 7X2  Var_04    C7    N6   C5   C4   179.01  30.0  2
 7X2  Var_05    N8    C7   N6   C5   179.36  30.0  2
 7X2  Var_06    C13   N12  C11  C10    2.82  30.0  2
 7X2  Var_07    C14   C13  N12  C11   63.56  30.0  2
 7X2  Var_08    C4    C3   O2   C1     0.56  30.0  2
 7X2  Var_09    C28   C25  O26  C27  179.46  30.0  3
 7X2  Var_10    H1C1  C1   O2   C3    61.04  30.0  3
 7X2  Var_11    H271  C27  O26  C25  -62.56  30.0  3
 7X2  Var_12    H301  C30  O29  C28   57.73  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
 7X2  plan-1  O2   0.020
 7X2  plan-1  C3   0.020
 7X2  plan-1  C4   0.020
 7X2  plan-1  C5   0.020
 7X2  plan-1  N6   0.020
 7X2  plan-1  C24  0.020
 7X2  plan-1  C25  0.020
 7X2  plan-1  O26  0.020
 7X2  plan-1  C28  0.020
 7X2  plan-1  O29  0.020
 7X2  plan-1  H4   0.020
 7X2  plan-1  H24  0.020
 7X2  plan-2  N6   0.020
 7X2  plan-2  C7   0.020
 7X2  plan-2  N8   0.020
 7X2  plan-2  C9   0.020
 7X2  plan-2  C10  0.020
 7X2  plan-2  C11  0.020
 7X2  plan-2  N12  0.020
 7X2  plan-2  N23  0.020
 7X2  plan-2  H9   0.020
 7X2  plan-2  H10  0.020
 7X2  plan-3  N12  0.020
 7X2  plan-3  C13  0.020
 7X2  plan-3  C14  0.020
 7X2  plan-3  O15  0.020
 7X2  plan-3  O17  0.020
 7X2  plan-3  C18  0.020
 7X2  plan-3  C19  0.020
 7X2  plan-3  C20  0.020
 7X2  plan-3  C21  0.020
 7X2  plan-3  CL1  0.020
 7X2  plan-3  H19  0.020
 7X2  plan-3  H20  0.020

