# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 22:31:27 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  48  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 OK
;

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  -0.835  46.7498   0.4340  14.0112
 DH3  C4    C  CR6    0   0.476  47.5580  -0.4152  13.3523
 DH3  N3    N  N      0  -0.507  47.1270  -1.6628  13.1978
 DH3  C2    C  CR6    0   0.523  47.9053  -2.5019  12.5157
 DH3  N2    N  NH2    0  -0.823  47.4684  -3.7825  12.4045
 DH3  N1    N  N      0  -0.488  49.0824  -2.2084  11.9691
 DH3  C6    C  CR16   0  -0.064  49.4952  -0.9510  12.1393
 DH3  C5    C  CR6    0  -0.071  48.7988   0.0179  12.8211
 DH3  C51   C  CH2    0  -0.586  49.2578   1.4416  13.0027
 DH3  C1'   C  CR6    0   0.099  50.5980   1.7319  12.3880
 DH3  C6'   C  CR16   0  -0.361  50.6923   2.1909  11.0832
 DH3  C52   C  CR6    0  -0.185  51.9372   2.4303  10.4967
 DH3  C53   C  CSP    0   0.168  52.0218   2.8918   9.1512
 DH3  C54   C  CSP    0   0.040  52.0466   3.2743   8.0076
 DH3  C1    C  CH2    0  -0.615  52.0493   3.7489   6.6304
 DH3  C3    C  CH2    0  -0.421  51.1563   4.9761   6.4107
 DH3  C7    C  CH2    0  -0.582  49.6947   4.7182   6.7305
 DH3  C8    C  C      0   0.413  48.7447   5.8990   6.4603
 DH3  O10   O  O      0  -0.609  49.1778   6.8456   5.7740
 DH3  O9    O  OC    -1  -0.631  47.5973   5.8007   6.9437
 DH3  C4'   C  CR6    0   0.233  53.1054   2.2129  11.2352
 DH3  O5    O  O2     0  -0.476  54.3123   2.4636  10.6706
 DH3  C5'   C  CH3    0  -0.413  54.9356   1.3249  10.0860
 DH3  C3'   C  CR6    0   0.321  53.0140   1.7600  12.5536
 DH3  O4    O  O2     0  -0.498  54.1122   1.5048  13.3052
 DH3  C4B   C  CH3    0  -0.412  54.9964   2.5892  13.5696
 DH3  C2'   C  CR16   0  -0.387  51.7653   1.5256  13.1152
 DH3  HN41  H  HNH2   0   0.414  47.0714   1.3373  14.3099
 DH3  HN42  H  HNH2   0   0.395  45.9364   0.0679  14.4756
 DH3  HN21  H  HNH2   0   0.386  47.8938  -4.3531  11.6941
 DH3  HN22  H  HNH2   0   0.386  46.4915  -3.9533  12.5714
 DH3  H6    H  HCR6   0   0.251  50.4540  -0.7102  11.6914
 DH3  H511  H  HCH2   0   0.264  49.2995   1.6789  14.0718
 DH3  H512  H  HCH2   0   0.266  48.5137   2.1216  12.5738
 DH3  H6'   H  HCR6   0   0.254  49.7938   2.3624  10.5031
 DH3  H11   H  HCH2   0   0.259  51.7220   2.9339   5.9767
 DH3  H12   H  HCH2   0   0.270  53.0763   3.9814   6.3367
 DH3  H31   H  HCH2   0   0.228  51.2616   5.2807   5.3685
 DH3  H32   H  HCH2   0   0.217  51.5353   5.8045   7.0141
 DH3  H71   H  HCH2   0   0.221  49.5848   4.4126   7.7756
 DH3  H72   H  HCH2   0   0.223  49.3408   3.8606   6.1440
 DH3  H5'1  H  HCH3   0   0.227  55.0853   0.5266  10.8163
 DH3  H5'2  H  HCH3   0   0.242  55.9051   1.6477   9.7126
 DH3  H5'3  H  HCH3   0   0.228  54.3472   0.9373   9.2509
 DH3  H4'1  H  HCH3   0   0.223  54.4548   3.5311  13.6786
 DH3  H4'2  H  HCH3   0   0.230  55.7512   2.7042  12.7919
 DH3  H4'3  H  HCH3   0   0.243  55.4957   2.3661  14.5111
 DH3  H2'   H  HCR6   0   0.263  51.7117   1.1733  14.1389

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  1.418  0.020  1.418
 DH3  N3   C2    aromatic  1.332  0.020  1.332
 DH3  C2   N2    single    1.358  0.020  1.358
 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  1.391  0.020  1.391
 DH3  C6'  C52   aromatic  1.397  0.020  1.397
 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    1.457  0.020  1.457
 DH3  C1   C3    single    1.534  0.020  1.534
 DH3  C1   H11   single    0.970  0.020  1.090
 DH3  C1   H12   single    0.970  0.020  1.090
 DH3  C3   C7    single    1.518  0.020  1.518
 DH3  C3   H31   single    0.970  0.020  1.090
 DH3  C3   H32   single    0.970  0.020  1.090
 DH3  C7   C8    single    1.539  0.020  1.539
 DH3  C7   H71   single    0.970  0.020  1.090
 DH3  C7   H72   single    0.970  0.020  1.090
 DH3  C8   O10   deloc     1.247  0.020  1.247
 DH3  C8   O9    deloc     1.249  0.020  1.249
 DH3  C4'  O5    single    1.356  0.020  1.356
 DH3  C4'  C3'   aromatic  1.397  0.020  1.397
 DH3  O5   C5'   single    1.424  0.020  1.424
 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    1.355  0.020  1.355
 DH3  C3'  C2'   aromatic  1.389  0.020  1.389
 DH3  O4   C4B   single    1.424  0.020  1.424
 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  116.69  3.000
 DH3  HN42  N4   C4    118.84  3.000
 DH3  HN41  N4   C4    121.41  3.000
 DH3  C5    C4   N3    121.81  3.000
 DH3  C5    C4   N4    121.11  3.000
 DH3  N3    C4   N4    117.06  3.000
 DH3  C2    N3   C4    117.48  3.000
 DH3  N1    C2   N2    117.33  3.000
 DH3  N1    C2   N3    126.02  3.000
 DH3  N2    C2   N3    116.62  3.000
 DH3  HN22  N2   HN21  115.58  3.000
 DH3  HN22  N2   C2    117.34  3.000
 DH3  HN21  N2   C2    117.20  3.000
 DH3  C6    N1   C2    115.41  3.000
 DH3  H6    C6   C5    119.73  3.000
 DH3  H6    C6   N1    115.45  3.000
 DH3  C5    C6   N1    124.82  3.000
 DH3  C51   C5   C6    124.87  3.000
 DH3  C51   C5   C4    120.67  3.000
 DH3  C6    C5   C4    114.46  3.000
 DH3  H512  C51  H511  105.87  3.000
 DH3  H512  C51  C1'   109.00  3.000
 DH3  H511  C51  C1'   108.86  3.000
 DH3  H512  C51  C5    109.42  3.000
 DH3  H511  C51  C5    109.50  3.000
 DH3  C1'   C51  C5    113.88  3.000
 DH3  C2'   C1'  C6'   118.96  3.000
 DH3  C2'   C1'  C51   120.40  3.000
 DH3  C6'   C1'  C51   120.64  3.000
 DH3  H6'   C6'  C52   119.16  3.000
 DH3  H6'   C6'  C1'   120.00  3.000
 DH3  C52   C6'  C1'   120.83  3.000
 DH3  C4'   C52  C53   119.94  3.000
 DH3  C4'   C52  C6'   119.73  3.000
 DH3  C53   C52  C6'   120.33  3.000
 DH3  C54   C53  C52   180.00  3.000
 DH3  C1    C54  C53   180.00  3.000
 DH3  H12   C1   H11   106.19  3.000
 DH3  H12   C1   C3    109.78  3.000
 DH3  H11   C1   C3    109.64  3.000
 DH3  H12   C1   C54   108.97  3.000
 DH3  H11   C1   C54   108.75  3.000
 DH3  C3    C1   C54   113.27  3.000
 DH3  H32   C3   H31   106.40  3.000
 DH3  H32   C3   C7    110.27  3.000
 DH3  H31   C3   C7    109.97  3.000
 DH3  H32   C3   C1    109.00  3.000
 DH3  H31   C3   C1    107.70  3.000
 DH3  C7    C3   C1    113.24  3.000
 DH3  H72   C7   H71   105.05  3.000
 DH3  H72   C7   C8    107.85  3.000
 DH3  H71   C7   C8    108.65  3.000
 DH3  H72   C7   C3    109.30  3.000
 DH3  H71   C7   C3    110.20  3.000
 DH3  C8    C7   C3    115.27  3.000
 DH3  O9    C8   O10   126.30  3.000
 DH3  O9    C8   C7    116.02  3.000
 DH3  O10   C8   C7    117.68  3.000
 DH3  C3'   C4'  O5    120.74  3.000
 DH3  C3'   C4'  C52   119.60  3.000
 DH3  O5    C4'  C52   119.65  3.000
 DH3  C5'   O5   C4'   114.38  3.000
 DH3  H5'3  C5'  H5'2  108.83  3.000
 DH3  H5'3  C5'  H5'1  109.00  3.000
 DH3  H5'2  C5'  H5'1  108.92  3.000
 DH3  H5'3  C5'  O5    111.21  3.000
 DH3  H5'2  C5'  O5    107.09  3.000
 DH3  H5'1  C5'  O5    111.72  3.000
 DH3  C2'   C3'  O4    118.19  3.000
 DH3  C2'   C3'  C4'   119.67  3.000
 DH3  O4    C3'  C4'   122.11  3.000
 DH3  C4B   O4   C3'   117.57  3.000
 DH3  H4'3  C4B  H4'2  108.73  3.000
 DH3  H4'3  C4B  H4'1  108.53  3.000
 DH3  H4'2  C4B  H4'1  108.89  3.000
 DH3  H4'3  C4B  O4    106.82  3.000
 DH3  H4'2  C4B  O4    112.20  3.000
 DH3  H4'1  C4B  O4    111.56  3.000
 DH3  H2'   C2'  C3'   118.76  3.000
 DH3  H2'   C2'  C1'   120.03  3.000
 DH3  C3'   C2'  C1'   121.20  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  Var_01    C1'   C51  C5   C4    179.57  30.0  2
 DH3  Var_02    C6'   C1'  C51  C5     91.00  30.0  2
 DH3  Var_03    C3'   C4'  O5   C5'    86.03  30.0  2
 DH3  Var_04    C2'   C3'  O4   C4B  -120.20  30.0  1
 DH3  Var_05    H5'1  C5'  O5   C4'   -58.33  30.0  3
 DH3  Var_06    H4'1  C4B  O4   C3'    34.54  30.0  3
 DH3  Var_07    C3    C1   C54  C53    24.62  30.0  3
 DH3  Var_08    C7    C3   C1   C54   -60.78  30.0  3
 DH3  Var_09    C8    C7   C3   C1   -177.12  30.0  3
 DH3  Var_10    O10   C8   C7   C3     13.83  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

