# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 22:55:38 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: 5-(3,4,5-trimethoxybenzyl)pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(Cc2cnc(N)nc2N)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
 TOP  TOP  5-(3,4,5-trimethoxybenzyl)pyrimidine-2,4-diamine  ligand  39  21  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TOP
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
 TOP  C1    C  CR16  0  -0.076  -1.0852  -1.5328   3.0573
 TOP  N2    N  N     0  -0.485  -1.7120  -0.9458   4.0750
 TOP  C3    C  CR6   0   0.531  -1.2645   0.2684   4.3927
 TOP  N4    N  NH2   0  -0.822  -1.8389   0.8815   5.4566
 TOP  N5    N  N     0  -0.505  -0.2807   0.9268   3.7803
 TOP  C6    C  CR6   0   0.460   0.3265   0.3208   2.7655
 TOP  N7    N  NH2   0  -0.823   1.3411   0.9817   2.1720
 TOP  C8    C  CR6   0  -0.074  -0.0483  -0.9780   2.3456
 TOP  C9    C  CH2   0  -0.573   0.6388  -1.6941   1.2241
 TOP  C10   C  CR6   0   0.112   0.4670  -1.0519  -0.1362
 TOP  C11   C  CR16  0  -0.482   1.5256  -1.0627  -1.0364
 TOP  C12   C  CR6   0   0.345   1.3650  -0.5149  -2.3088
 TOP  O13   O  O2    0  -0.464   2.3265  -0.4816  -3.2475
 TOP  C14   C  CH3   0  -0.438   3.5856  -1.0472  -2.9415
 TOP  C15   C  CR6   0   0.160   0.1405   0.0457  -2.6777
 TOP  O16   O  O2    0  -0.482  -0.0258   0.5615  -3.9251
 TOP  C17   C  CH3   0  -0.408   0.2954   1.9422  -4.0295
 TOP  C18   C  CR6   0   0.348  -0.9149   0.0673  -1.7611
 TOP  O19   O  O2    0  -0.464  -2.0504   0.6373  -2.1997
 TOP  C20   C  CH3   0  -0.438  -3.1543   0.7042  -1.3191
 TOP  C21   C  CR16  0  -0.440  -0.7498  -0.4845  -0.4931
 TOP  H1    H  HCR6  0   0.254  -1.4368  -2.5262   2.7904
 TOP  HN41  H  HNH2  0   0.387  -2.7276   0.5301   5.7691
 TOP  HN42  H  HNH2  0   0.387  -1.6969   1.8716   5.5596
 TOP  HN71  H  HNH2  0   0.391   1.4618   1.9545   2.4006
 TOP  HN72  H  HNH2  0   0.404   1.6463   0.7118   1.2524
 TOP  H91   H  HCH2  0   0.277   0.2520  -2.7165   1.1774
 TOP  H92   H  HCH2  0   0.261   1.7081  -1.7965   1.4344
 TOP  H11   H  HCR6  0   0.276   2.4685  -1.4989  -0.7326
 TOP  H141  H  HCH3  0   0.261   4.2000  -0.9305  -3.8307
 TOP  H142  H  HCH3  0   0.229   4.0723  -0.5340  -2.1082
 TOP  H143  H  HCH3  0   0.229   3.5084  -2.1111  -2.7036
 TOP  H171  H  HCH3  0   0.236   0.1322   2.2333  -5.0656
 TOP  H172  H  HCH3  0   0.221  -0.3427   2.5561  -3.3894
 TOP  H173  H  HCH3  0   0.220   1.3398   2.1351  -3.7730
 TOP  H201  H  HCH3  0   0.261  -3.9569   1.1901  -1.8683
 TOP  H202  H  HCH3  0   0.229  -3.4915  -0.2878  -1.0083
 TOP  H203  H  HCH3  0   0.228  -2.9313   1.2968  -0.4283
 TOP  H21   H  HCR6  0   0.268  -1.5564  -0.4750   0.2274

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
 TOP  C1   N2    aromatic  1.332  0.020  1.332
 TOP  C1   C8    aromatic  1.375  0.020  1.375
 TOP  C1   H1    single    0.930  0.020  1.080
 TOP  N2   C3    aromatic  1.332  0.020  1.332
 TOP  C3   N4    single    1.356  0.020  1.356
 TOP  C3   N5    aromatic  1.333  0.020  1.333
 TOP  N4   HN41  single    0.890  0.020  1.040
 TOP  N4   HN42  single    0.890  0.020  1.040
 TOP  N5   C6    aromatic  1.329  0.020  1.329
 TOP  C6   N7    single    1.349  0.020  1.349
 TOP  C6   C8    aromatic  1.415  0.020  1.415
 TOP  N7   HN71  single    0.890  0.020  1.040
 TOP  N7   HN72  single    0.890  0.020  1.040
 TOP  C8   C9    single    1.498  0.020  1.498
 TOP  C9   C10   single    1.514  0.020  1.514
 TOP  C9   H91   single    0.970  0.020  1.090
 TOP  C9   H92   single    0.970  0.020  1.090
 TOP  C10  C11   aromatic  1.390  0.020  1.390
 TOP  C10  C21   aromatic  1.389  0.020  1.389
 TOP  C11  C12   aromatic  1.395  0.020  1.395
 TOP  C11  H11   single    0.930  0.020  1.080
 TOP  C12  O13   single    1.344  0.020  1.344
 TOP  C12  C15   aromatic  1.396  0.020  1.396
 TOP  O13  C14   single    1.414  0.020  1.414
 TOP  C14  H141  single    0.970  0.020  1.090
 TOP  C14  H142  single    0.970  0.020  1.090
 TOP  C14  H143  single    0.970  0.020  1.090
 TOP  C15  O16   single    1.360  0.020  1.360
 TOP  C15  C18   aromatic  1.398  0.020  1.398
 TOP  O16  C17   single    1.421  0.020  1.421
 TOP  C17  H171  single    0.970  0.020  1.090
 TOP  C17  H172  single    0.970  0.020  1.090
 TOP  C17  H173  single    0.970  0.020  1.090
 TOP  C18  O19   single    1.344  0.020  1.344
 TOP  C18  C21   aromatic  1.393  0.020  1.393
 TOP  O19  C20   single    1.414  0.020  1.414
 TOP  C20  H201  single    0.970  0.020  1.090
 TOP  C20  H202  single    0.970  0.020  1.090
 TOP  C20  H203  single    0.970  0.020  1.090
 TOP  C21  H21   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
 TOP  H1    C1   C8    119.06  3.000
 TOP  H1    C1   N2    115.99  3.000
 TOP  C8    C1   N2    124.95  3.000
 TOP  C3    N2   C1    115.21  3.000
 TOP  N5    C3   N4    116.74  3.000
 TOP  N5    C3   N2    126.05  3.000
 TOP  N4    C3   N2    117.19  3.000
 TOP  HN42  N4   HN41  115.92  3.000
 TOP  HN42  N4   C3    117.77  3.000
 TOP  HN41  N4   C3    117.41  3.000
 TOP  C6    N5   C3    117.57  3.000
 TOP  C8    C6   N7    121.22  3.000
 TOP  C8    C6   N5    121.61  3.000
 TOP  N7    C6   N5    117.15  3.000
 TOP  HN72  N7   HN71  115.50  3.000
 TOP  HN72  N7   C6    119.94  3.000
 TOP  HN71  N7   C6    117.65  3.000
 TOP  C9    C8   C6    122.65  3.000
 TOP  C9    C8   C1    122.74  3.000
 TOP  C6    C8   C1    114.61  3.000
 TOP  H92   C9   H91   105.43  3.000
 TOP  H92   C9   C10   108.85  3.000
 TOP  H91   C9   C10   108.54  3.000
 TOP  H92   C9   C8    110.43  3.000
 TOP  H91   C9   C8    108.46  3.000
 TOP  C10   C9   C8    114.71  3.000
 TOP  C21   C10  C11   120.27  3.000
 TOP  C21   C10  C9    120.23  3.000
 TOP  C11   C10  C9    119.49  3.000
 TOP  H11   C11  C12   120.97  3.000
 TOP  H11   C11  C10   119.01  3.000
 TOP  C12   C11  C10   120.02  3.000
 TOP  C15   C12  O13   115.65  3.000
 TOP  C15   C12  C11   119.98  3.000
 TOP  O13   C12  C11   124.37  3.000
 TOP  C14   O13  C12   118.42  3.000
 TOP  H143  C14  H142  108.82  3.000
 TOP  H143  C14  H141  108.81  3.000
 TOP  H142  C14  H141  108.76  3.000
 TOP  H143  C14  O13   111.94  3.000
 TOP  H142  C14  O13   111.95  3.000
 TOP  H141  C14  O13   106.46  3.000
 TOP  C18   C15  O16   120.21  3.000
 TOP  C18   C15  C12   119.67  3.000
 TOP  O16   C15  C12   120.12  3.000
 TOP  C17   O16  C15   114.09  3.000
 TOP  H173  C17  H172  108.76  3.000
 TOP  H173  C17  H171  108.63  3.000
 TOP  H172  C17  H171  108.65  3.000
 TOP  H173  C17  O16   111.73  3.000
 TOP  H172  C17  O16   111.77  3.000
 TOP  H171  C17  O16   107.21  3.000
 TOP  C21   C18  O19   124.42  3.000
 TOP  C21   C18  C15   120.09  3.000
 TOP  O19   C18  C15   115.49  3.000
 TOP  C20   O19  C18   118.46  3.000
 TOP  H203  C20  H202  108.87  3.000
 TOP  H203  C20  H201  108.66  3.000
 TOP  H202  C20  H201  108.76  3.000
 TOP  H203  C20  O19   111.96  3.000
 TOP  H202  C20  O19   112.03  3.000
 TOP  H201  C20  O19   106.44  3.000
 TOP  H21   C21  C18   120.98  3.000
 TOP  H21   C21  C10   119.06  3.000
 TOP  C18   C21  C10   119.97  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
 TOP  CONST_01  N5    C3   N2   C1      0.00   0.0  0
 TOP  CONST_02  N5    C6   C8   C1      0.00   0.0  0
 TOP  CONST_03  C6    C8   C1   N2      0.00   0.0  0
 TOP  CONST_04  C6    N5   C3   N2      0.00   0.0  0
 TOP  CONST_05  C8    C1   N2   C3      0.00   0.0  0
 TOP  CONST_06  C8    C6   N5   C3      0.00   0.0  0
 TOP  CONST_07  C15   C12  C11  C10     0.00   0.0  0
 TOP  CONST_08  C15   C18  C21  C10     0.00   0.0  0
 TOP  CONST_09  C18   C21  C10  C11     0.00   0.0  0
 TOP  CONST_10  C18   C15  C12  C11     0.00   0.0  0
 TOP  CONST_11  C21   C10  C11  C12     0.00   0.0  0
 TOP  CONST_12  C21   C18  C15  C12     0.00   0.0  0
 TOP  CONST_13  N4    C3   N2   C1    180.00   0.0  0
 TOP  CONST_14  N7    C6   C8   C1    180.00   0.0  0
 TOP  CONST_15  C9    C8   C1   N2    180.00   0.0  0
 TOP  CONST_16  N7    C6   N5   C3    180.00   0.0  0
 TOP  CONST_17  C6    N5   C3   N4    180.00   0.0  0
 TOP  CONST_18  C9    C8   C6   N5    180.00   0.0  0
 TOP  CONST_19  C12   C11  C10  C9    180.00   0.0  0
 TOP  CONST_20  C18   C21  C10  C9    180.00   0.0  0
 TOP  CONST_21  O13   C12  C11  C10   180.00   0.0  0
 TOP  CONST_22  O19   C18  C21  C10   180.00   0.0  0
 TOP  CONST_23  O16   C15  C12  C11   180.00   0.0  0
 TOP  CONST_24  O19   C18  C15  C12   180.00   0.0  0
 TOP  CONST_25  C18   C15  C12  O13   180.00   0.0  0
 TOP  CONST_26  C21   C18  C15  O16   180.00   0.0  0
 TOP  CONST_27  H1    C1   N2   C3    180.00   0.0  0
 TOP  CONST_28  H21   C21  C10  C11   180.00   0.0  0
 TOP  CONST_29  H11   C11  C12  C15   180.00   0.0  0
 TOP  CONST_32  HN71  N7   C6   N5      0.00   0.0  0
 TOP  Var_01    C10   C9   C8   C1    115.15  30.0  2
 TOP  Var_02    C11   C10  C9   C8    143.13  30.0  2
 TOP  Var_03    C15   C12  O13  C14  -179.29  30.0  3
 TOP  Var_04    C18   C15  O16  C17    89.88  30.0  2
 TOP  Var_05    C21   C18  O19  C20     0.88  30.0  3
 TOP  Var_06    H141  C14  O13  C12   179.05  30.0  3
 TOP  Var_07    H171  C17  O16  C15   179.51  30.0  3
 TOP  Var_08    H201  C20  O19  C18  -179.70  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
 TOP  plan-1  C1    0.020
 TOP  plan-1  N2    0.020
 TOP  plan-1  C3    0.020
 TOP  plan-1  N4    0.020
 TOP  plan-1  N5    0.020
 TOP  plan-1  C6    0.020
 TOP  plan-1  N7    0.020
 TOP  plan-1  C8    0.020
 TOP  plan-1  C9    0.020
 TOP  plan-1  H1    0.020
 TOP  plan-2  C9    0.020
 TOP  plan-2  C10   0.020
 TOP  plan-2  C11   0.020
 TOP  plan-2  C12   0.020
 TOP  plan-2  O13   0.020
 TOP  plan-2  C15   0.020
 TOP  plan-2  O16   0.020
 TOP  plan-2  C18   0.020
 TOP  plan-2  O19   0.020
 TOP  plan-2  C21   0.020
 TOP  plan-2  H11   0.020
 TOP  plan-2  H21   0.020
 TOP  plan-3  C3    0.020
 TOP  plan-3  N4    0.020
 TOP  plan-3  HN41  0.020
 TOP  plan-3  HN42  0.020
 TOP  plan-4  C6    0.020
 TOP  plan-4  N7    0.020
 TOP  plan-4  HN71  0.020
 TOP  plan-4  HN72  0.020

