# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 07:27:45 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: 5-{3-methoxy-4-[(4-methoxybenzyl)oxy]benzyl}pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(COc2ccc(Cc3cnc(N)nc3N)cc2OC)cc1
#
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
 MUJ  MUJ  5-{3-methoxy-4-[(4-methoxybenzyl)oxy]benzyl}pyrimidine-2,4-diamine  ligand  49  27  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MUJ
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
 MUJ  N1    N  N     0  -0.509   5.5989   1.2726   1.1695
 MUJ  C2    C  CR6   0  -0.059   4.6827  -0.0258  -0.6258
 MUJ  C3    C  CR6   0   0.474   4.8250   0.2741   0.7518
 MUJ  C4    C  CR16  0  -0.082   5.3998   0.7906  -1.4662
 MUJ  C5    C  CR6   0   0.527   6.2352   1.9888   0.2438
 MUJ  N6    N  N     0  -0.488   6.1783   1.7987  -1.0734
 MUJ  C7    C  CH2   0  -0.603   3.8198  -1.1451  -1.1227
 MUJ  C8    C  CR6   0   0.123   2.3388  -0.9220  -0.9040
 MUJ  C9    C  CR16  0  -0.369   0.3733   0.4744  -1.0067
 MUJ  C10   C  CR16  0  -0.298   1.7425   0.2917  -1.1914
 MUJ  C11   C  CR6   0   0.300  -0.4193  -0.5543  -0.5246
 MUJ  C12   C  CR16  0  -0.465   1.5400  -1.9621  -0.4212
 MUJ  C13   C  CR6   0   0.318   0.1777  -1.7951  -0.2275
 MUJ  O14   O  O2    0  -0.465  -0.6546  -2.7447   0.2402
 MUJ  C15   C  CH3   0  -0.437  -0.1103  -4.0052   0.5728
 MUJ  O16   O  O2    0  -0.463  -1.7480  -0.4761  -0.3035
 MUJ  C17   C  CH2   0  -0.268  -2.3813   0.7813  -0.4985
 MUJ  C18   C  CR6   0   0.076  -3.8215   0.6353  -0.1205
 MUJ  C19   C  CR16  0  -0.329  -5.5178   0.3483   1.5788
 MUJ  C20   C  CR16  0  -0.270  -4.1937   0.4948   1.2176
 MUJ  C21   C  CR6   0   0.374  -6.5169   0.3394   0.5997
 MUJ  C22   C  CR16  0  -0.288  -4.8201   0.6209  -1.0815
 MUJ  C23   C  CR16  0  -0.372  -6.1609   0.4795  -0.7384
 MUJ  O24   O  O2    0  -0.469  -7.7798   0.1953   1.0406
 MUJ  C25   C  CH3   0  -0.437  -8.8297   0.1879   0.0930
 MUJ  N26   N  NH2   0  -0.828   4.1865  -0.4376   1.6922
 MUJ  N27   N  NH2   0  -0.823   6.9831   3.0303   0.6889
 MUJ  H4    H  HCR6  0   0.252   5.3465   0.6198  -2.5388
 MUJ  H71C  H  HCH2  0   0.275   4.0112  -1.2812  -2.1914
 MUJ  H72C  H  HCH2  0   0.258   4.1122  -2.0906  -0.6535
 MUJ  H261  H  HNH2  0   0.396   4.3353  -0.2290   2.6642
 MUJ  H262  H  HNH2  0   0.408   3.5964  -1.2179   1.4676
 MUJ  H271  H  HNH2  0   0.386   7.2489   3.0285   1.6589
 MUJ  H272  H  HNH2  0   0.386   7.6620   3.4144   0.0541
 MUJ  H10   H  HCR6  0   0.245   2.3345   1.1194  -1.5620
 MUJ  H12   H  HCR6  0   0.279   2.0083  -2.9118  -0.1927
 MUJ  H9    H  HCR6  0   0.282  -0.0585   1.4363  -1.2487
 MUJ  H151  H  HCH3  0   0.227   0.6503  -3.9293   1.3543
 MUJ  H152  H  HCH3  0   0.260  -0.9347  -4.6090   0.9442
 MUJ  H153  H  HCH3  0   0.228   0.3277  -4.5049  -0.2955
 MUJ  H171  H  HCH2  0   0.236  -1.8939   1.5429   0.1210
 MUJ  H172  H  HCH2  0   0.240  -2.2925   1.0985  -1.5430
 MUJ  H20   H  HCR6  0   0.255  -3.4360   0.5068   1.9920
 MUJ  H22   H  HCR6  0   0.257  -4.5605   0.7269  -2.1283
 MUJ  H19   H  HCR6  0   0.263  -5.7926   0.2436   2.6212
 MUJ  H23   H  HCR6  0   0.280  -6.9021   0.4808  -1.5252
 MUJ  H251  H  HCH3  0   0.229  -8.8838   1.1275  -0.4626
 MUJ  H252  H  HCH3  0   0.229  -8.7330  -0.6369  -0.6176
 MUJ  H253  H  HCH3  0   0.260  -9.7522   0.0609   0.6540

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
 MUJ  N1   C3    aromatic  1.331  0.020  1.331
 MUJ  N1   C5    aromatic  1.332  0.020  1.332
 MUJ  C2   C3    aromatic  1.417  0.020  1.417
 MUJ  C2   C4    aromatic  1.374  0.020  1.374
 MUJ  C2   C7    single    1.498  0.020  1.498
 MUJ  C3   N26   single    1.341  0.020  1.341
 MUJ  C4   N6    aromatic  1.333  0.020  1.333
 MUJ  C5   N6    aromatic  1.332  0.020  1.332
 MUJ  C5   N27   single    1.357  0.020  1.357
 MUJ  C7   C8    single    1.514  0.020  1.514
 MUJ  C8   C10   aromatic  1.383  0.020  1.383
 MUJ  C8   C12   aromatic  1.397  0.020  1.397
 MUJ  C9   C10   aromatic  1.394  0.020  1.394
 MUJ  C9   C11   aromatic  1.385  0.020  1.385
 MUJ  C11  C13   aromatic  1.409  0.020  1.409
 MUJ  C11  O16   single    1.349  0.020  1.349
 MUJ  C12  C13   aromatic  1.386  0.020  1.386
 MUJ  C13  O14   single    1.347  0.020  1.347
 MUJ  O14  C15   single    1.413  0.020  1.413
 MUJ  O16  C17   single    1.421  0.020  1.421
 MUJ  C17  C18   single    1.496  0.020  1.496
 MUJ  C18  C20   aromatic  1.396  0.020  1.396
 MUJ  C18  C22   aromatic  1.386  0.020  1.386
 MUJ  C19  C20   aromatic  1.380  0.020  1.380
 MUJ  C19  C21   aromatic  1.399  0.020  1.399
 MUJ  C21  C23   aromatic  1.392  0.020  1.392
 MUJ  C21  O24   single    1.345  0.020  1.345
 MUJ  C22  C23   aromatic  1.391  0.020  1.391
 MUJ  O24  C25   single    1.414  0.020  1.414
 MUJ  C4   H4    single    0.930  0.020  1.080
 MUJ  C7   H71C  single    0.970  0.020  1.090
 MUJ  C7   H72C  single    0.970  0.020  1.090
 MUJ  N26  H261  single    0.860  0.020  1.020
 MUJ  N26  H262  single    0.860  0.020  1.020
 MUJ  N27  H271  single    0.890  0.020  1.040
 MUJ  N27  H272  single    0.890  0.020  1.040
 MUJ  C10  H10   single    0.930  0.020  1.080
 MUJ  C12  H12   single    0.930  0.020  1.080
 MUJ  C9   H9    single    0.930  0.020  1.080
 MUJ  C15  H151  single    0.970  0.020  1.090
 MUJ  C15  H152  single    0.970  0.020  1.090
 MUJ  C15  H153  single    0.970  0.020  1.090
 MUJ  C17  H171  single    0.970  0.020  1.090
 MUJ  C17  H172  single    0.970  0.020  1.090
 MUJ  C20  H20   single    0.930  0.020  1.080
 MUJ  C22  H22   single    0.930  0.020  1.080
 MUJ  C19  H19   single    0.930  0.020  1.080
 MUJ  C23  H23   single    0.930  0.020  1.080
 MUJ  C25  H251  single    0.970  0.020  1.090
 MUJ  C25  H252  single    0.970  0.020  1.090
 MUJ  C25  H253  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
 MUJ  C5    N1   C3    117.59  3.000
 MUJ  C7    C2   C4    122.80  3.000
 MUJ  C7    C2   C3    122.57  3.000
 MUJ  C4    C2   C3    114.63  3.000
 MUJ  N26   C3   C2    121.44  3.000
 MUJ  N26   C3   N1    117.07  3.000
 MUJ  C2    C3   N1    121.49  3.000
 MUJ  H4    C4   N6    115.98  3.000
 MUJ  H4    C4   C2    118.99  3.000
 MUJ  N6    C4   C2    125.03  3.000
 MUJ  N27   C5   N6    117.21  3.000
 MUJ  N27   C5   N1    116.61  3.000
 MUJ  N6    C5   N1    126.16  3.000
 MUJ  C5    N6   C4    115.10  3.000
 MUJ  H72C  C7   H71C  105.33  3.000
 MUJ  H72C  C7   C8    109.06  3.000
 MUJ  H71C  C7   C8    109.31  3.000
 MUJ  H72C  C7   C2    110.43  3.000
 MUJ  H71C  C7   C2    108.43  3.000
 MUJ  C8    C7   C2    113.93  3.000
 MUJ  C12   C8   C10   118.60  3.000
 MUJ  C12   C8   C7    119.97  3.000
 MUJ  C10   C8   C7    121.42  3.000
 MUJ  H9    C9   C11   120.65  3.000
 MUJ  H9    C9   C10   118.63  3.000
 MUJ  C11   C9   C10   120.73  3.000
 MUJ  H10   C10  C9    118.83  3.000
 MUJ  H10   C10  C8    120.42  3.000
 MUJ  C9    C10  C8    120.75  3.000
 MUJ  O16   C11  C13   115.71  3.000
 MUJ  O16   C11  C9    125.28  3.000
 MUJ  C13   C11  C9    119.01  3.000
 MUJ  H12   C12  C13   120.07  3.000
 MUJ  H12   C12  C8    118.57  3.000
 MUJ  C13   C12  C8    121.36  3.000
 MUJ  O14   C13  C12   124.82  3.000
 MUJ  O14   C13  C11   115.62  3.000
 MUJ  C12   C13  C11   119.56  3.000
 MUJ  C15   O14  C13   118.22  3.000
 MUJ  H153  C15  H152  108.74  3.000
 MUJ  H153  C15  H151  108.71  3.000
 MUJ  H152  C15  H151  108.78  3.000
 MUJ  H153  C15  O14   112.03  3.000
 MUJ  H152  C15  O14   106.49  3.000
 MUJ  H151  C15  O14   111.98  3.000
 MUJ  C17   O16  C11   117.88  3.000
 MUJ  H172  C17  H171  107.57  3.000
 MUJ  H172  C17  C18   110.32  3.000
 MUJ  H171  C17  C18   110.67  3.000
 MUJ  H172  C17  O16   110.54  3.000
 MUJ  H171  C17  O16   109.81  3.000
 MUJ  C18   C17  O16   107.93  3.000
 MUJ  C22   C18  C20   118.13  3.000
 MUJ  C22   C18  C17   121.29  3.000
 MUJ  C20   C18  C17   120.58  3.000
 MUJ  H19   C19  C21   119.45  3.000
 MUJ  H19   C19  C20   120.37  3.000
 MUJ  C21   C19  C20   120.18  3.000
 MUJ  H20   C20  C19   119.02  3.000
 MUJ  H20   C20  C18   119.83  3.000
 MUJ  C19   C20  C18   121.15  3.000
 MUJ  O24   C21  C23   124.47  3.000
 MUJ  O24   C21  C19   116.22  3.000
 MUJ  C23   C21  C19   119.31  3.000
 MUJ  H22   C22  C23   118.62  3.000
 MUJ  H22   C22  C18   119.75  3.000
 MUJ  C23   C22  C18   121.63  3.000
 MUJ  H23   C23  C22   118.76  3.000
 MUJ  H23   C23  C21   121.64  3.000
 MUJ  C22   C23  C21   119.60  3.000
 MUJ  C25   O24  C21   118.54  3.000
 MUJ  H253  C25  H252  108.81  3.000
 MUJ  H253  C25  H251  108.71  3.000
 MUJ  H252  C25  H251  108.82  3.000
 MUJ  H253  C25  O24   106.54  3.000
 MUJ  H252  C25  O24   111.95  3.000
 MUJ  H251  C25  O24   111.89  3.000
 MUJ  H262  N26  H261  117.69  3.000
 MUJ  H262  N26  C3    122.38  3.000
 MUJ  H261  N26  C3    119.83  3.000
 MUJ  H272  N27  H271  115.53  3.000
 MUJ  H272  N27  C5    117.26  3.000
 MUJ  H271  N27  C5    117.42  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
 MUJ  CONST_01  C4    C2   C3   N1      0.00   0.0  0
 MUJ  CONST_02  C4    N6   C5   N1      0.00   0.0  0
 MUJ  CONST_03  C5    N1   C3   C2      0.00   0.0  0
 MUJ  CONST_04  C5    N6   C4   C2      0.00   0.0  0
 MUJ  CONST_05  N6    C5   N1   C3      0.00   0.0  0
 MUJ  CONST_06  N6    C4   C2   C3      0.00   0.0  0
 MUJ  CONST_07  C11   C9   C10  C8      0.00   0.0  0
 MUJ  CONST_08  C11   C13  C12  C8      0.00   0.0  0
 MUJ  CONST_09  C12   C8   C10  C9      0.00   0.0  0
 MUJ  CONST_10  C12   C13  C11  C9      0.00   0.0  0
 MUJ  CONST_11  C13   C12  C8   C10     0.00   0.0  0
 MUJ  CONST_12  C13   C11  C9   C10     0.00   0.0  0
 MUJ  CONST_13  C21   C19  C20  C18     0.00   0.0  0
 MUJ  CONST_14  C21   C23  C22  C18     0.00   0.0  0
 MUJ  CONST_15  C22   C18  C20  C19     0.00   0.0  0
 MUJ  CONST_16  C22   C23  C21  C19     0.00   0.0  0
 MUJ  CONST_17  C23   C22  C18  C20     0.00   0.0  0
 MUJ  CONST_18  C23   C21  C19  C20     0.00   0.0  0
 MUJ  CONST_19  C7    C2   C3   N1    180.00   0.0  0
 MUJ  CONST_20  N27   C5   N1   C3    180.00   0.0  0
 MUJ  CONST_21  N26   C3   C2   C4    180.00   0.0  0
 MUJ  CONST_22  N27   C5   N6   C4    180.00   0.0  0
 MUJ  CONST_23  N26   C3   N1   C5    180.00   0.0  0
 MUJ  CONST_24  C7    C2   C4   N6    180.00   0.0  0
 MUJ  CONST_25  C9    C10  C8   C7    180.00   0.0  0
 MUJ  CONST_26  C13   C12  C8   C7    180.00   0.0  0
 MUJ  CONST_27  O14   C13  C12  C8    180.00   0.0  0
 MUJ  CONST_28  O14   C13  C11  C9    180.00   0.0  0
 MUJ  CONST_29  O16   C11  C9   C10   180.00   0.0  0
 MUJ  CONST_30  O16   C11  C13  C12   180.00   0.0  0
 MUJ  CONST_31  C19   C20  C18  C17   180.00   0.0  0
 MUJ  CONST_32  C23   C22  C18  C17   180.00   0.0  0
 MUJ  CONST_33  O24   C21  C19  C20   180.00   0.0  0
 MUJ  CONST_34  O24   C21  C23  C22   180.00   0.0  0
 MUJ  CONST_35  H4    C4   C2   C3    180.00   0.0  0
 MUJ  CONST_36  H9    C9   C10  C8    180.00   0.0  0
 MUJ  CONST_37  H12   C12  C8   C10   180.00   0.0  0
 MUJ  CONST_38  H10   C10  C9   C11   180.00   0.0  0
 MUJ  CONST_39  H19   C19  C20  C18   180.00   0.0  0
 MUJ  CONST_40  H23   C23  C22  C18   180.00   0.0  0
 MUJ  CONST_41  H22   C22  C18  C20   180.00   0.0  0
 MUJ  CONST_42  H20   C20  C19  C21   180.00   0.0  0
 MUJ  CONST_43  H261  N26  C3   N1      0.00   0.0  0
 MUJ  CONST_44  H262  N26  C3   N1    180.00   0.0  0
 MUJ  Var_01    C10   C8   C7   C2     45.16  30.0  2
 MUJ  Var_02    C8    C7   C2   C3     67.74  30.0  2
 MUJ  Var_03    C18   C17  O16  C11  -176.85  30.0  3
 MUJ  Var_04    C20   C18  C17  O16    71.61  30.0  2
 MUJ  Var_05    H151  C15  O14  C13    60.06  30.0  3
 MUJ  Var_06    H251  C25  O24  C21   -61.39  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
 MUJ  plan-1  N1    0.020
 MUJ  plan-1  C2    0.020
 MUJ  plan-1  C3    0.020
 MUJ  plan-1  C4    0.020
 MUJ  plan-1  C5    0.020
 MUJ  plan-1  N6    0.020
 MUJ  plan-1  C7    0.020
 MUJ  plan-1  N26   0.020
 MUJ  plan-1  N27   0.020
 MUJ  plan-1  H4    0.020
 MUJ  plan-2  C7    0.020
 MUJ  plan-2  C8    0.020
 MUJ  plan-2  C9    0.020
 MUJ  plan-2  C10   0.020
 MUJ  plan-2  C11   0.020
 MUJ  plan-2  C12   0.020
 MUJ  plan-2  C13   0.020
 MUJ  plan-2  O14   0.020
 MUJ  plan-2  O16   0.020
 MUJ  plan-2  H10   0.020
 MUJ  plan-2  H12   0.020
 MUJ  plan-2  H9    0.020
 MUJ  plan-3  C17   0.020
 MUJ  plan-3  C18   0.020
 MUJ  plan-3  C19   0.020
 MUJ  plan-3  C20   0.020
 MUJ  plan-3  C21   0.020
 MUJ  plan-3  C22   0.020
 MUJ  plan-3  C23   0.020
 MUJ  plan-3  O24   0.020
 MUJ  plan-3  H20   0.020
 MUJ  plan-3  H22   0.020
 MUJ  plan-3  H19   0.020
 MUJ  plan-3  H23   0.020
 MUJ  plan-4  C3    0.020
 MUJ  plan-4  N26   0.020
 MUJ  plan-4  H261  0.020
 MUJ  plan-4  H262  0.020
 MUJ  plan-5  C5    0.020
 MUJ  plan-5  N27   0.020
 MUJ  plan-5  H271  0.020
 MUJ  plan-5  H272  0.020

