# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 17:07:48 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 6-{5-[(2,4-diaminopyrimidin-5-yl)methyl]-2,3-dimethoxyphenyl}hex-5-ynoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(Cc2cnc(N)nc2N)cc(C#CCCCC(O)=O)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
 DH3  DH3  '6-{5-[(2,4-diaminopyrimidin-5-yl)methyl]-2,3-dimethoxyphenyl}hex-5-ynoic acid'  ligand  49  27  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DH3
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
 DH3  N4    N  NH2   0  -0.834  47.3311   0.7467  15.3992
 DH3  C4    C  CR6   0   0.474  47.6233   0.0834  14.2657
 DH3  N3    N  N     0  -0.506  46.8440  -0.9469  13.9535
 DH3  C2    C  CR6   0   0.524  47.1019  -1.5911  12.8163
 DH3  N2    N  NH2   0  -0.823  46.3253  -2.6674  12.5349
 DH3  N1    N  N     0  -0.488  48.0730  -1.2974  11.9547
 DH3  C6    C  CR16  0  -0.061  48.8442  -0.2625  12.2913
 DH3  C5    C  CR6   0  -0.073  48.6961   0.4884  13.4328
 DH3  C51   C  CH2   0  -0.582  49.5630   1.6629  13.8067
 DH3  C1'   C  CR6   0   0.097  50.7038   1.9036  12.8581
 DH3  C6'   C  CR16  0  -0.357  50.5783   2.8011  11.8089
 DH3  C52   C  CR6   0  -0.188  51.6259   3.0045  10.9063
 DH3  C53   C  CSP   0   0.181  51.4946   3.9305   9.8316
 DH3  C54   C  CSP   0   0.034  51.3742   4.7058   8.9161
 DH3  C1    C  CH2   0  -0.619  51.2266   5.6182   7.7905
 DH3  C3    C  CH2   0  -0.435  50.4662   5.0011   6.6127
 DH3  C7    C  CH2   0  -0.583  51.1687   3.7760   6.0535
 DH3  C8    C  C     0   0.555  50.4605   3.1741   4.8721
 DH3  O10   O  O     0  -0.445  49.4208   3.5733   4.4094
 DH3  O9    O  OH1   0  -0.596  51.1169   2.1277   4.3800
 DH3  C4'   C  CR6   0   0.238  52.8231   2.2999  11.0679
 DH3  O5    O  O2    0  -0.475  53.8608   2.5218  10.2268
 DH3  C5'   C  CH3   0  -0.411  53.9242   1.6315   9.1188
 DH3  C3'   C  CR6   0   0.304  52.9495   1.3924  12.1209
 DH3  O4    O  O2    0  -0.492  54.0981   0.6811  12.2662
 DH3  C4B   C  CH3   0  -0.410  55.1129   1.3521  13.0034
 DH3  C2'   C  CR16  0  -0.372  51.8992   1.2058  13.0069
 DH3  HN41  H  HNH2  0   0.413  47.9665   1.4191  15.7903
 DH3  HN42  H  HNH2  0   0.395  46.6584   0.3462  16.0307
 DH3  HN21  H  HNH2  0   0.386  46.3348  -3.0090  11.5891
 DH3  HN22  H  HNH2  0   0.386  45.4480  -2.7489  13.0196
 DH3  H6    H  HCR6  0   0.250  49.6356  -0.0238  11.5876
 DH3  H511  H  HCH2  0   0.263  49.9704   1.5098  14.8119
 DH3  H512  H  HCH2  0   0.267  48.9499   2.5681  13.8674
 DH3  H6'   H  HCR6  0   0.256  49.6573   3.3558  11.6787
 DH3  H11   H  HCH2  0   0.270  52.2180   5.9438   7.4631
 DH3  H12   H  HCH2  0   0.282  50.7032   6.5181   8.1221
 DH3  H31   H  HCH2  0   0.251  50.3703   5.7651   5.8396
 DH3  H32   H  HCH2  0   0.243  49.4554   4.7433   6.9328
 DH3  H71   H  HCH2  0   0.282  51.2608   3.0010   6.8217
 DH3  H72   H  HCH2  0   0.279  52.1935   4.0186   5.7551
 DH3  HO9   H  HOH1  0   0.479  50.6323   1.7605   3.6257
 DH3  H5'1  H  HCH3  0   0.228  54.0287   0.5936   9.4415
 DH3  H5'2  H  HCH3  0   0.241  54.7992   1.9094   8.5351
 DH3  H5'3  H  HCH3  0   0.222  53.0370   1.7180   8.4861
 DH3  H4'1  H  HCH3  0   0.225  55.4195   2.2811  12.5182
 DH3  H4'2  H  HCH3  0   0.241  55.9691   0.6828  13.0539
 DH3  H4'3  H  HCH3  0   0.223  54.7812   1.5783  14.0202
 DH3  H2'   H  HCR6  0   0.264  52.0159   0.4935  13.8160

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
 DH3  N4   C4    single    1.345  0.020  1.345
 DH3  N4   HN41  single    0.890  0.020  1.040
 DH3  N4   HN42  single    0.890  0.020  1.040
 DH3  C4   N3    aromatic  1.329  0.020  1.329
 DH3  C4   C5    aromatic  1.417  0.020  1.417
 DH3  N3   C2    aromatic  1.332  0.020  1.332
 DH3  C2   N2    single    1.357  0.020  1.357
 DH3  C2   N1    aromatic  1.331  0.020  1.331
 DH3  N2   HN21  single    0.890  0.020  1.040
 DH3  N2   HN22  single    0.890  0.020  1.040
 DH3  N1   C6    aromatic  1.334  0.020  1.334
 DH3  C6   C5    aromatic  1.374  0.020  1.374
 DH3  C6   H6    single    0.930  0.020  1.080
 DH3  C5   C51   single    1.507  0.020  1.507
 DH3  C51  C1'   single    1.503  0.020  1.503
 DH3  C51  H511  single    0.970  0.020  1.090
 DH3  C51  H512  single    0.970  0.020  1.090
 DH3  C1'  C6'   aromatic  1.386  0.020  1.386
 DH3  C1'  C2'   aromatic  1.392  0.020  1.392
 DH3  C6'  C52   aromatic  1.398  0.020  1.398
 DH3  C6'  H6'   single    0.930  0.020  1.080
 DH3  C52  C53   single    1.425  0.020  1.425
 DH3  C52  C4'   aromatic  1.399  0.020  1.399
 DH3  C53  C54   triple    1.206  0.020  1.206
 DH3  C54  C1    single    1.456  0.020  1.456
 DH3  C1   C3    single    1.532  0.020  1.532
 DH3  C1   H11   single    0.970  0.020  1.090
 DH3  C1   H12   single    0.970  0.020  1.090
 DH3  C3   C7    single    1.519  0.020  1.519
 DH3  C3   H31   single    0.970  0.020  1.090
 DH3  C3   H32   single    0.970  0.020  1.090
 DH3  C7   C8    single    1.503  0.020  1.503
 DH3  C7   H71   single    0.970  0.020  1.090
 DH3  C7   H72   single    0.970  0.020  1.090
 DH3  C8   O10   double    1.206  0.020  1.206
 DH3  C8   O9    single    1.330  0.020  1.330
 DH3  O9   HO9   single    0.850  0.020  0.980
 DH3  C4'  O5    single    1.354  0.020  1.354
 DH3  C4'  C3'   aromatic  1.396  0.020  1.396
 DH3  O5   C5'   single    1.423  0.020  1.423
 DH3  C5'  H5'1  single    0.970  0.020  1.090
 DH3  C5'  H5'2  single    0.970  0.020  1.090
 DH3  C5'  H5'3  single    0.970  0.020  1.090
 DH3  C3'  O4    single    1.359  0.020  1.359
 DH3  C3'  C2'   aromatic  1.387  0.020  1.387
 DH3  O4   C4B   single    1.423  0.020  1.423
 DH3  C4B  H4'1  single    0.970  0.020  1.090
 DH3  C4B  H4'2  single    0.970  0.020  1.090
 DH3  C4B  H4'3  single    0.970  0.020  1.090
 DH3  C2'  H2'   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
 DH3  HN42  N4   HN41  116.44  3.000
 DH3  HN42  N4   C4    118.55  3.000
 DH3  HN41  N4   C4    121.37  3.000
 DH3  C5    C4   N3    121.83  3.000
 DH3  C5    C4   N4    121.24  3.000
 DH3  N3    C4   N4    116.92  3.000
 DH3  C2    N3   C4    117.51  3.000
 DH3  N1    C2   N2    117.28  3.000
 DH3  N1    C2   N3    125.96  3.000
 DH3  N2    C2   N3    116.73  3.000
 DH3  HN22  N2   HN21  115.73  3.000
 DH3  HN22  N2   C2    117.63  3.000
 DH3  HN21  N2   C2    117.33  3.000
 DH3  C6    N1   C2    115.45  3.000
 DH3  H6    C6   C5    119.79  3.000
 DH3  H6    C6   N1    115.38  3.000
 DH3  C5    C6   N1    124.83  3.000
 DH3  C51   C5   C6    124.74  3.000
 DH3  C51   C5   C4    120.82  3.000
 DH3  C6    C5   C4    114.43  3.000
 DH3  H512  C51  H511  105.84  3.000
 DH3  H512  C51  C1'   109.12  3.000
 DH3  H511  C51  C1'   108.62  3.000
 DH3  H512  C51  C5    109.63  3.000
 DH3  H511  C51  C5    109.43  3.000
 DH3  C1'   C51  C5    113.88  3.000
 DH3  C2'   C1'  C6'   118.89  3.000
 DH3  C2'   C1'  C51   120.26  3.000
 DH3  C6'   C1'  C51   120.84  3.000
 DH3  H6'   C6'  C52   119.02  3.000
 DH3  H6'   C6'  C1'   119.97  3.000
 DH3  C52   C6'  C1'   121.01  3.000
 DH3  C4'   C52  C53   119.57  3.000
 DH3  C4'   C52  C6'   119.58  3.000
 DH3  C53   C52  C6'   120.84  3.000
 DH3  C54   C53  C52   180.00  3.000
 DH3  C1    C54  C53   180.00  3.000
 DH3  H12   C1   H11   106.25  3.000
 DH3  H12   C1   C3    109.11  3.000
 DH3  H11   C1   C3    109.87  3.000
 DH3  H12   C1   C54   109.27  3.000
 DH3  H11   C1   C54   109.02  3.000
 DH3  C3    C1   C54   113.09  3.000
 DH3  H32   C3   H31   106.97  3.000
 DH3  H32   C3   C7    110.24  3.000
 DH3  H31   C3   C7    110.15  3.000
 DH3  H32   C3   C1    109.24  3.000
 DH3  H31   C3   C1    107.84  3.000
 DH3  C7    C3   C1    112.24  3.000
 DH3  H72   C7   H71   105.63  3.000
 DH3  H72   C7   C8    108.40  3.000
 DH3  H71   C7   C8    107.91  3.000
 DH3  H72   C7   C3    110.77  3.000
 DH3  H71   C7   C3    110.58  3.000
 DH3  C8    C7   C3    113.23  3.000
 DH3  O9    C8   O10   122.96  3.000
 DH3  O9    C8   C7    111.93  3.000
 DH3  O10   C8   C7    125.12  3.000
 DH3  HO9   O9   C8    109.85  3.000
 DH3  C3'   C4'  O5    120.38  3.000
 DH3  C3'   C4'  C52   119.49  3.000
 DH3  O5    C4'  C52   120.12  3.000
 DH3  C5'   O5   C4'   114.54  3.000
 DH3  H5'3  C5'  H5'2  108.78  3.000
 DH3  H5'3  C5'  H5'1  108.90  3.000
 DH3  H5'2  C5'  H5'1  108.93  3.000
 DH3  H5'3  C5'  O5    111.41  3.000
 DH3  H5'2  C5'  O5    107.08  3.000
 DH3  H5'1  C5'  O5    111.65  3.000
 DH3  C2'   C3'  O4    120.10  3.000
 DH3  C2'   C3'  C4'   120.06  3.000
 DH3  O4    C3'  C4'   119.84  3.000
 DH3  C4B   O4   C3'   114.30  3.000
 DH3  H4'3  C4B  H4'2  108.84  3.000
 DH3  H4'3  C4B  H4'1  108.82  3.000
 DH3  H4'2  C4B  H4'1  108.85  3.000
 DH3  H4'3  C4B  O4    111.29  3.000
 DH3  H4'2  C4B  O4    107.17  3.000
 DH3  H4'1  C4B  O4    111.80  3.000
 DH3  H2'   C2'  C3'   118.93  3.000
 DH3  H2'   C2'  C1'   120.09  3.000
 DH3  C3'   C2'  C1'   120.97  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
 DH3  CONST_01  N1    C2   N3   C4      0.00   0.0  0
 DH3  CONST_02  N1    C6   C5   C4      0.00   0.0  0
 DH3  CONST_03  C6    C5   C4   N3      0.00   0.0  0
 DH3  CONST_04  C6    N1   C2   N3      0.00   0.0  0
 DH3  CONST_05  C5    C4   N3   C2      0.00   0.0  0
 DH3  CONST_06  C5    C6   N1   C2      0.00   0.0  0
 DH3  CONST_07  C4'   C52  C6'  C1'     0.00   0.0  0
 DH3  CONST_08  C4'   C3'  C2'  C1'     0.00   0.0  0
 DH3  CONST_09  C3'   C2'  C1'  C6'     0.00   0.0  0
 DH3  CONST_10  C3'   C4'  C52  C6'     0.00   0.0  0
 DH3  CONST_11  C2'   C1'  C6'  C52     0.00   0.0  0
 DH3  CONST_12  C2'   C3'  C4'  C52     0.00   0.0  0
 DH3  CONST_13  C2    N3   C4   N4    180.00   0.0  0
 DH3  CONST_14  C6    C5   C4   N4    180.00   0.0  0
 DH3  CONST_15  N2    C2   N3   C4    180.00   0.0  0
 DH3  CONST_16  C51   C5   C4   N3    180.00   0.0  0
 DH3  CONST_17  C6    N1   C2   N2    180.00   0.0  0
 DH3  CONST_18  C51   C5   C6   N1    180.00   0.0  0
 DH3  CONST_19  C52   C6'  C1'  C51   180.00   0.0  0
 DH3  CONST_20  C3'   C2'  C1'  C51   180.00   0.0  0
 DH3  CONST_21  C53   C52  C6'  C1'   180.00   0.0  0
 DH3  CONST_22  O4    C3'  C2'  C1'   180.00   0.0  0
 DH3  CONST_23  O5    C4'  C52  C6'   180.00   0.0  0
 DH3  CONST_24  O4    C3'  C4'  C52   180.00   0.0  0
 DH3  CONST_25  C3'   C4'  C52  C53   180.00   0.0  0
 DH3  CONST_26  C2'   C3'  C4'  O5    180.00   0.0  0
 DH3  CONST_27  H6    C6   C5   C4    180.00   0.0  0
 DH3  CONST_28  H2'   C2'  C1'  C6'   180.00   0.0  0
 DH3  CONST_29  H6'   C6'  C52  C4'   180.00   0.0  0
 DH3  CONST_30  HN41  N4   C4   N3    180.00   0.0  0
 DH3  CONST_31  HN42  N4   C4   N3      0.00   0.0  0
 DH3  CONST_34  HO9   O9   C8   C7    180.00   0.0  0
 DH3  Var_01    C1'   C51  C5   C4    176.45  30.0  2
 DH3  Var_02    C6'   C1'  C51  C5     94.18  30.0  2
 DH3  Var_03    C3'   C4'  O5   C5'    87.56  30.0  2
 DH3  Var_04    C2'   C3'  O4   C4B   -94.83  30.0  2
 DH3  Var_05    H5'1  C5'  O5   C4'   -60.28  30.0  3
 DH3  Var_06    H4'1  C4B  O4   C3'   -61.15  30.0  3
 DH3  Var_07    C3    C1   C54  C53    25.86  30.0  3
 DH3  Var_08    C7    C3   C1   C54   -60.75  30.0  3
 DH3  Var_09    C8    C7   C3   C1   -178.43  30.0  3
 DH3  Var_10    O10   C8   C7   C3     -1.90  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
 DH3  plan-1  N4    0.020
 DH3  plan-1  C4    0.020
 DH3  plan-1  N3    0.020
 DH3  plan-1  C2    0.020
 DH3  plan-1  N2    0.020
 DH3  plan-1  N1    0.020
 DH3  plan-1  C6    0.020
 DH3  plan-1  C5    0.020
 DH3  plan-1  C51   0.020
 DH3  plan-1  H6    0.020
 DH3  plan-2  C51   0.020
 DH3  plan-2  C1'   0.020
 DH3  plan-2  C6'   0.020
 DH3  plan-2  C52   0.020
 DH3  plan-2  C53   0.020
 DH3  plan-2  C54   0.020
 DH3  plan-2  C4'   0.020
 DH3  plan-2  O5    0.020
 DH3  plan-2  C3'   0.020
 DH3  plan-2  O4    0.020
 DH3  plan-2  C2'   0.020
 DH3  plan-2  H6'   0.020
 DH3  plan-2  H2'   0.020
 DH3  plan-3  N4    0.020
 DH3  plan-3  C4    0.020
 DH3  plan-3  HN41  0.020
 DH3  plan-3  HN42  0.020
 DH3  plan-4  C2    0.020
 DH3  plan-4  N2    0.020
 DH3  plan-4  HN21  0.020
 DH3  plan-4  HN22  0.020
 DH3  plan-5  C7    0.020
 DH3  plan-5  C8    0.020
 DH3  plan-5  O10   0.020
 DH3  plan-5  O9    0.020
 DH3  plan-5  HO9   0.020

