# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 03:18:11 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: 2,4-diamino-5-(3,4,5-trimethoxybenzyl)pyrimidin-1-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(Cc2c[nH+]c(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
 TRR  TRR  2,4-diamino-5-(3,4,5-trimethoxybenzyl)pyrimidin-1-ium  ligand  40  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_TRR
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
 TRR  N1    N  NR16  1  -0.659   4.0483   1.5751  -0.5078
 TRR  C2    C  CR6   0   0.736   4.3300   0.9066   0.6338
 TRR  N2    N  NH2   0  -0.815   5.3493   1.3144   1.3739
 TRR  N3    N  N     0  -0.499   3.6110  -0.1291   1.0150
 TRR  C4    C  CR6   0   0.531   2.5901  -0.5309   0.2609
 TRR  N4    N  NH2   0  -0.795   1.9047  -1.5785   0.6867
 TRR  C5    C  CR6   0  -0.052   2.2443   0.1258  -0.9710
 TRR  C6    C  CR16  0   0.043   3.0198   1.1813  -1.2980
 TRR  C7    C  CH2   0  -0.606   1.1175  -0.3345  -1.8472
 TRR  C11   C  CR6   0   0.135  -0.2355  -0.2446  -1.1780
 TRR  C12   C  CR16  0  -0.433  -0.6519   0.9624  -0.6312
 TRR  C13   C  CR6   0   0.347  -1.8960   1.0494  -0.0119
 TRR  C14   C  CR6   0   0.165  -2.7210  -0.0780   0.0655
 TRR  C15   C  CR6   0   0.349  -2.2920  -1.2896  -0.4777
 TRR  C16   C  CR16  0  -0.510  -1.0494  -1.3679  -1.1097
 TRR  O13   O  O2    0  -0.460  -2.3944   2.1677   0.5380
 TRR  O14   O  O2    0  -0.480  -3.9406   0.0097   0.6578
 TRR  O15   O  O2    0  -0.459  -3.1425  -2.3199  -0.3479
 TRR  C17   C  CH3   0  -0.439  -1.6348   3.3578   0.4551
 TRR  C18   C  CH3   0  -0.407  -3.9305  -0.2685   2.0523
 TRR  C19   C  CH3   0  -0.439  -2.7398  -3.5916  -0.8179
 TRR  H1    H  HNR6  0   0.451   4.6075   2.3678  -0.7914
 TRR  H21   H  HNH2  0   0.430   5.9324   2.0898   1.1086
 TRR  H22   H  HNH2  0   0.428   5.5770   0.8168   2.2179
 TRR  H41   H  HNH2  0   0.419   2.1498  -2.0138   1.5614
 TRR  H42   H  HNH2  0   0.429   1.0727  -1.9050   0.2242
 TRR  H6    H  HCR6  0   0.333   2.8730   1.7630  -2.1965
 TRR  H71   H  HCH2  0   0.285   1.2989  -1.3619  -2.1745
 TRR  H72   H  HCH2  0   0.294   1.1177   0.2751  -2.7536
 TRR  H12   H  HCR6  0   0.271   0.0006   1.8236  -0.6902
 TRR  H16   H  HCR6  0   0.285  -0.7098  -2.2953  -1.5541
 TRR  H171  H  HCH3  0   0.228  -0.6876   3.2776   0.9946
 TRR  H172  H  HCH3  0   0.230  -1.4300   3.6401  -0.5806
 TRR  H173  H  HCH3  0   0.263  -2.2344   4.1372   0.9186
 TRR  H181  H  HCH3  0   0.236  -4.9550  -0.1701   2.4069
 TRR  H182  H  HCH3  0   0.222  -3.5845  -1.2839   2.2589
 TRR  H183  H  HCH3  0   0.222  -3.3015   0.4365   2.6010
 TRR  H191  H  HCH3  0   0.264  -3.5479  -4.2778  -0.5777
 TRR  H192  H  HCH3  0   0.230  -2.5838  -3.5986  -1.8995
 TRR  H193  H  HCH3  0   0.228  -1.8274  -3.9373  -0.3254

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
 TRR  N1   C2    aromatic  1.353  0.020  1.353
 TRR  N1   C6    aromatic  1.355  0.020  1.355
 TRR  N1   H1    single    0.860  0.020  1.020
 TRR  C2   N2    single    1.324  0.020  1.324
 TRR  C2   N3    aromatic  1.317  0.020  1.317
 TRR  N2   H21   single    0.860  0.020  1.020
 TRR  N2   H22   single    0.860  0.020  1.020
 TRR  N3   C4    aromatic  1.331  0.020  1.331
 TRR  C4   N4    single    1.322  0.020  1.322
 TRR  C4   C5    aromatic  1.438  0.020  1.438
 TRR  N4   H41   single    0.860  0.020  1.020
 TRR  N4   H42   single    0.860  0.020  1.020
 TRR  C5   C6    aromatic  1.350  0.020  1.350
 TRR  C5   C7    single    1.500  0.020  1.500
 TRR  C6   H6    single    0.930  0.020  1.080
 TRR  C7   C11   single    1.512  0.020  1.512
 TRR  C7   H71   single    0.970  0.020  1.090
 TRR  C7   H72   single    0.970  0.020  1.090
 TRR  C11  C12   aromatic  1.389  0.020  1.389
 TRR  C11  C16   aromatic  1.389  0.020  1.389
 TRR  C12  C13   aromatic  1.392  0.020  1.392
 TRR  C12  H12   single    0.930  0.020  1.080
 TRR  C13  C14   aromatic  1.399  0.020  1.399
 TRR  C13  O13   single    1.342  0.020  1.342
 TRR  C14  C15   aromatic  1.395  0.020  1.395
 TRR  C14  O14   single    1.359  0.020  1.359
 TRR  C15  C16   aromatic  1.396  0.020  1.396
 TRR  C15  O15   single    1.342  0.020  1.342
 TRR  C16  H16   single    0.930  0.020  1.080
 TRR  O13  C17   single    1.414  0.020  1.414
 TRR  O14  C18   single    1.422  0.020  1.422
 TRR  O15  C19   single    1.414  0.020  1.414
 TRR  C17  H171  single    0.970  0.020  1.090
 TRR  C17  H172  single    0.970  0.020  1.090
 TRR  C17  H173  single    0.970  0.020  1.090
 TRR  C18  H181  single    0.970  0.020  1.090
 TRR  C18  H182  single    0.970  0.020  1.090
 TRR  C18  H183  single    0.970  0.020  1.090
 TRR  C19  H191  single    0.970  0.020  1.090
 TRR  C19  H192  single    0.970  0.020  1.090
 TRR  C19  H193  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
 TRR  H1    N1   C6    118.96  3.000
 TRR  H1    N1   C2    120.61  3.000
 TRR  C6    N1   C2    120.43  3.000
 TRR  N3    C2   N2    120.04  3.000
 TRR  N3    C2   N1    121.27  3.000
 TRR  N2    C2   N1    118.68  3.000
 TRR  H22   N2   H21   118.13  3.000
 TRR  H22   N2   C2    119.40  3.000
 TRR  H21   N2   C2    122.44  3.000
 TRR  C4    N3   C2    119.47  3.000
 TRR  C5    C4   N4    120.86  3.000
 TRR  C5    C4   N3    122.12  3.000
 TRR  N4    C4   N3    117.01  3.000
 TRR  H42   N4   H41   117.39  3.000
 TRR  H42   N4   C4    122.52  3.000
 TRR  H41   N4   C4    119.73  3.000
 TRR  C7    C5   C6    122.01  3.000
 TRR  C7    C5   C4    122.74  3.000
 TRR  C6    C5   C4    115.24  3.000
 TRR  H6    C6   C5    122.98  3.000
 TRR  H6    C6   N1    115.57  3.000
 TRR  C5    C6   N1    121.46  3.000
 TRR  H72   C7   H71   106.02  3.000
 TRR  H72   C7   C11   109.52  3.000
 TRR  H71   C7   C11   109.68  3.000
 TRR  H72   C7   C5    108.26  3.000
 TRR  H71   C7   C5    109.80  3.000
 TRR  C11   C7   C5    113.29  3.000
 TRR  C16   C11  C12   120.52  3.000
 TRR  C16   C11  C7    119.87  3.000
 TRR  C12   C11  C7    119.61  3.000
 TRR  H12   C12  C13   120.89  3.000
 TRR  H12   C12  C11   119.30  3.000
 TRR  C13   C12  C11   119.82  3.000
 TRR  O13   C13  C14   115.45  3.000
 TRR  O13   C13  C12   124.48  3.000
 TRR  C14   C13  C12   120.07  3.000
 TRR  O14   C14  C15   120.12  3.000
 TRR  O14   C14  C13   120.09  3.000
 TRR  C15   C14  C13   119.79  3.000
 TRR  O15   C15  C16   124.37  3.000
 TRR  O15   C15  C14   115.72  3.000
 TRR  C16   C15  C14   119.90  3.000
 TRR  H16   C16  C15   120.85  3.000
 TRR  H16   C16  C11   119.26  3.000
 TRR  C15   C16  C11   119.89  3.000
 TRR  C17   O13  C13   118.53  3.000
 TRR  C18   O14  C14   114.11  3.000
 TRR  C19   O15  C15   118.53  3.000
 TRR  H173  C17  H172  108.79  3.000
 TRR  H173  C17  H171  108.67  3.000
 TRR  H172  C17  H171  108.92  3.000
 TRR  H173  C17  O13   106.39  3.000
 TRR  H172  C17  O13   111.93  3.000
 TRR  H171  C17  O13   112.02  3.000
 TRR  H183  C18  H182  108.81  3.000
 TRR  H183  C18  H181  108.66  3.000
 TRR  H182  C18  H181  108.69  3.000
 TRR  H183  C18  O14   111.73  3.000
 TRR  H182  C18  O14   111.69  3.000
 TRR  H181  C18  O14   107.16  3.000
 TRR  H193  C19  H192  108.95  3.000
 TRR  H193  C19  H191  108.74  3.000
 TRR  H192  C19  H191  108.71  3.000
 TRR  H193  C19  O15   111.86  3.000
 TRR  H192  C19  O15   112.05  3.000
 TRR  H191  C19  O15   106.41  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
 TRR  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 TRR  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 TRR  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 TRR  CONST_04  C5    C4   N3   C2      0.00   0.0  0
 TRR  CONST_05  C6    N1   C2   N3      0.00   0.0  0
 TRR  CONST_06  C6    C5   C4   N3      0.00   0.0  0
 TRR  CONST_07  C14   C13  C12  C11     0.00   0.0  0
 TRR  CONST_08  C14   C15  C16  C11     0.00   0.0  0
 TRR  CONST_09  C15   C16  C11  C12     0.00   0.0  0
 TRR  CONST_10  C15   C14  C13  C12     0.00   0.0  0
 TRR  CONST_11  C16   C11  C12  C13     0.00   0.0  0
 TRR  CONST_12  C16   C15  C14  C13     0.00   0.0  0
 TRR  CONST_13  C7    C5   C6   N1    180.00   0.0  0
 TRR  CONST_14  N4    C4   N3   C2    180.00   0.0  0
 TRR  CONST_15  C6    N1   C2   N2    180.00   0.0  0
 TRR  CONST_16  C4    N3   C2   N2    180.00   0.0  0
 TRR  CONST_17  C7    C5   C4   N3    180.00   0.0  0
 TRR  CONST_18  C6    C5   C4   N4    180.00   0.0  0
 TRR  CONST_19  C13   C12  C11  C7    180.00   0.0  0
 TRR  CONST_20  C15   C16  C11  C7    180.00   0.0  0
 TRR  CONST_21  O13   C13  C12  C11   180.00   0.0  0
 TRR  CONST_22  O15   C15  C16  C11   180.00   0.0  0
 TRR  CONST_23  O14   C14  C13  C12   180.00   0.0  0
 TRR  CONST_24  O15   C15  C14  C13   180.00   0.0  0
 TRR  CONST_25  O13   C13  C14  C15   180.00   0.0  0
 TRR  CONST_26  O14   C14  C15  C16   180.00   0.0  0
 TRR  CONST_27  H6    C6   N1   C2    180.00   0.0  0
 TRR  CONST_28  H1    N1   C2   N3    180.00   0.0  0
 TRR  CONST_29  H16   C16  C11  C12   180.00   0.0  0
 TRR  CONST_30  H12   C12  C13  C14   180.00   0.0  0
 TRR  CONST_31  H21   N2   C2   N1      0.00   0.0  0
 TRR  CONST_32  H22   N2   C2   N1    180.00   0.0  0
 TRR  CONST_33  H41   N4   C4   N3      0.00   0.0  0
 TRR  CONST_34  H42   N4   C4   N3    180.00   0.0  0
 TRR  Var_01    C11   C7   C5   C4     63.00  30.0  2
 TRR  Var_02    C12   C11  C7   C5     54.22  30.0  2
 TRR  Var_03    H171  C17  O13  C13   -63.79  30.0  3
 TRR  Var_04    H181  C18  O14  C14  -179.81  30.0  3
 TRR  Var_05    H191  C19  O15  C15   177.59  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
 TRR  plan-1  N1   0.020
 TRR  plan-1  C2   0.020
 TRR  plan-1  N2   0.020
 TRR  plan-1  N3   0.020
 TRR  plan-1  C4   0.020
 TRR  plan-1  N4   0.020
 TRR  plan-1  C5   0.020
 TRR  plan-1  C6   0.020
 TRR  plan-1  C7   0.020
 TRR  plan-1  H1   0.020
 TRR  plan-1  H6   0.020
 TRR  plan-2  C7   0.020
 TRR  plan-2  C11  0.020
 TRR  plan-2  C12  0.020
 TRR  plan-2  C13  0.020
 TRR  plan-2  C14  0.020
 TRR  plan-2  C15  0.020
 TRR  plan-2  C16  0.020
 TRR  plan-2  O13  0.020
 TRR  plan-2  O14  0.020
 TRR  plan-2  O15  0.020
 TRR  plan-2  H12  0.020
 TRR  plan-2  H16  0.020
 TRR  plan-3  C2   0.020
 TRR  plan-3  N2   0.020
 TRR  plan-3  H21  0.020
 TRR  plan-3  H22  0.020
 TRR  plan-4  C4   0.020
 TRR  plan-4  N4   0.020
 TRR  plan-4  H41  0.020
 TRR  plan-4  H42  0.020

