# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 15 18:56:56 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: 4-(1,3-dimethyl-2,6-dioxo-1,2,3,6-tetrahydro-7H-purin-7-yl)butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)N(C)c2ncn(CCCC(O)=O)c2C1=O
#
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
 M1D  M1D  '4-(1,3-dimethyl-2,6-dioxo-1,2,3,6-tetrahydro-7H-purin-7-yl)butanoic acid'  ligand  33  19  .  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_M1D
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
 M1D  O3   O  O     0  -0.492  -4.2973   1.1994   0.6541
 M1D  C9   C  CR6   0   0.738  -3.2293   0.7123   0.3347
 M1D  N3   N  NR6   0  -0.586  -3.0357  -0.6436   0.3825
 M1D  C10  C  CH3   0  -0.531  -4.1365  -1.4911   0.8103
 M1D  C5   C  CR56  0   0.435  -1.8328  -1.1713   0.0107
 M1D  N1   N  N     0  -0.474  -1.5001  -2.4728  -0.0100
 M1D  C4   C  CR15  0   0.135  -0.2514  -2.4756  -0.4418
 M1D  N2   N  NR6   0  -0.605  -2.1588   1.4958  -0.0911
 M1D  C8   C  CH3   0  -0.532  -2.3451   2.9421  -0.1376
 M1D  C7   C  CR6   0   0.579  -0.9021   1.0374  -0.4941
 M1D  O2   O  O     0  -0.469  -0.0384   1.8132  -0.8661
 M1D  C6   C  CR56  0   0.126  -0.7947  -0.3786  -0.4063
 M1D  N    N  NR5   0  -0.481   0.2261  -1.2538  -0.7017
 M1D  C3   C  CH2   0  -0.295   1.5750  -0.9376  -1.1360
 M1D  C2   C  CH2   0  -0.443   2.4260  -0.3691  -0.0098
 M1D  C1   C  CH2   0  -0.590   3.8351  -0.0969  -0.5096
 M1D  C    C  C     0   0.555   4.7408   0.4727   0.5468
 M1D  O1   O  OH1   0  -0.596   5.9826   0.6255   0.0984
 M1D  O    O  O     0  -0.442   4.4042   0.7653   1.6668
 M1D  H1   H  HCH3  0   0.259  -4.4858  -1.1983   1.7977
 M1D  H2   H  HCH3  0   0.258  -4.9652  -1.4351   0.1069
 M1D  H3   H  HCH3  0   0.268  -3.7816  -2.5152   0.8529
 M1D  H4   H  HCR5  0   0.302   0.3479  -3.3622  -0.5844
 M1D  H5   H  HCH3  0   0.270  -3.3512   3.1851   0.1774
 M1D  H6   H  HCH3  0   0.255  -1.6403   3.4357   0.5284
 M1D  H7   H  HCH3  0   0.255  -2.1922   3.3117  -1.1492
 M1D  H8   H  HCH2  0   0.273   2.0087  -1.8633  -1.5144
 M1D  H9   H  HCH2  0   0.273   1.5161  -0.2412  -1.9719
 M1D  H10  H  HCH2  0   0.254   1.9742   0.5523   0.3592
 M1D  H11  H  HCH2  0   0.249   2.4483  -1.0794   0.8190
 M1D  H12  H  HCH2  0   0.284   4.2938  -1.0114  -0.8976
 M1D  H13  H  HCH2  0   0.287   3.8176   0.6032  -1.3512
 M1D  H14  H  HOH1  0   0.480   6.5428   0.9960   0.7965

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
 M1D  O    C    double    1.206  0.020  1.206
 M1D  C    O1   single    1.329  0.020  1.329
 M1D  C    C1   single    1.504  0.020  1.504
 M1D  C1   C2   single    1.520  0.020  1.520
 M1D  C10  N3   single    1.454  0.020  1.454
 M1D  N1   C4   aromatic  1.321  0.020  1.321
 M1D  N1   C5   aromatic  1.343  0.020  1.343
 M1D  N3   C5   single    1.365  0.020  1.365
 M1D  N3   C9   single    1.371  0.020  1.371
 M1D  C2   C3   single    1.522  0.020  1.522
 M1D  C4   N    aromatic  1.337  0.020  1.337
 M1D  C5   C6   aromatic  1.371  0.020  1.371
 M1D  O3   C9   double    1.217  0.020  1.217
 M1D  C9   N2   single    1.393  0.020  1.393
 M1D  N    C6   aromatic  1.377  0.020  1.377
 M1D  N    C3   single    1.452  0.020  1.452
 M1D  C6   C7   single    1.423  0.020  1.423
 M1D  N2   C7   single    1.397  0.020  1.397
 M1D  N2   C8   single    1.459  0.020  1.459
 M1D  C7   O2   double    1.219  0.020  1.219
 M1D  C10  H1   single    0.970  0.020  1.090
 M1D  C10  H2   single    0.970  0.020  1.090
 M1D  C10  H3   single    0.970  0.020  1.090
 M1D  C4   H4   single    0.930  0.020  1.080
 M1D  C8   H5   single    0.970  0.020  1.090
 M1D  C8   H6   single    0.970  0.020  1.090
 M1D  C8   H7   single    0.970  0.020  1.090
 M1D  C3   H8   single    0.970  0.020  1.090
 M1D  C3   H9   single    0.970  0.020  1.090
 M1D  C2   H10  single    0.970  0.020  1.090
 M1D  C2   H11  single    0.970  0.020  1.090
 M1D  C1   H12  single    0.970  0.020  1.090
 M1D  C1   H13  single    0.970  0.020  1.090
 M1D  O1   H14  single    0.850  0.020  0.980

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
 M1D  N2   C9   N3   117.28  3.000
 M1D  N2   C9   O3   121.98  3.000
 M1D  N3   C9   O3   120.73  3.000
 M1D  C5   N3   C10  121.47  3.000
 M1D  C5   N3   C9   119.83  3.000
 M1D  C10  N3   C9   118.69  3.000
 M1D  H3   C10  H2   108.86  3.000
 M1D  H3   C10  H1   108.88  3.000
 M1D  H2   C10  H1   109.17  3.000
 M1D  H3   C10  N3   108.31  3.000
 M1D  H2   C10  N3   110.88  3.000
 M1D  H1   C10  N3   110.70  3.000
 M1D  C6   C5   N1   111.59  3.000
 M1D  C6   C5   N3   121.76  3.000
 M1D  N1   C5   N3   126.65  3.000
 M1D  C4   N1   C5   103.96  3.000
 M1D  H4   C4   N    121.76  3.000
 M1D  H4   C4   N1   124.72  3.000
 M1D  N    C4   N1   113.51  3.000
 M1D  C7   N2   C8   115.53  3.000
 M1D  C8   N2   C9   117.97  3.000
 M1D  C7   N2   C9   126.50  3.000
 M1D  H7   C8   H6   108.90  3.000
 M1D  H7   C8   H5   108.98  3.000
 M1D  H6   C8   H5   108.80  3.000
 M1D  H7   C8   N2   110.40  3.000
 M1D  H6   C8   N2   110.33  3.000
 M1D  H5   C8   N2   109.40  3.000
 M1D  C6   C7   O2   126.78  3.000
 M1D  O2   C7   N2   121.10  3.000
 M1D  C6   C7   N2   112.13  3.000
 M1D  N    C6   C7   132.49  3.000
 M1D  C7   C6   C5   122.48  3.000
 M1D  N    C6   C5   105.02  3.000
 M1D  C3   N    C6   127.92  3.000
 M1D  C3   N    C4   126.07  3.000
 M1D  C6   N    C4   105.92  3.000
 M1D  H9   C3   H8   107.33  3.000
 M1D  H9   C3   C2   111.05  3.000
 M1D  H8   C3   C2   110.59  3.000
 M1D  H9   C3   N    108.57  3.000
 M1D  H8   C3   N    106.77  3.000
 M1D  C2   C3   N    112.30  3.000
 M1D  H11  C2   H10  107.53  3.000
 M1D  H11  C2   C1   110.32  3.000
 M1D  H10  C2   C1   110.13  3.000
 M1D  H11  C2   C3   109.28  3.000
 M1D  H10  C2   C3   109.54  3.000
 M1D  C1   C2   C3   110.00  3.000
 M1D  H13  C1   H12  105.58  3.000
 M1D  H13  C1   C    107.90  3.000
 M1D  H12  C1   C    108.25  3.000
 M1D  H13  C1   C2   110.64  3.000
 M1D  H12  C1   C2   110.84  3.000
 M1D  C    C1   C2   113.29  3.000
 M1D  O    C    O1   123.12  3.000
 M1D  O1   C    C1   111.68  3.000
 M1D  O    C    C1   125.20  3.000
 M1D  H14  O1   C    109.95  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
 M1D  CONST_01  N    C4   N1  C5      0.00   0.0  0
 M1D  CONST_02  C4   N    C6  C5      0.00   0.0  0
 M1D  CONST_03  C6   N    C4  N1      0.00   0.0  0
 M1D  CONST_04  N    C6   C5  N1      0.00   0.0  0
 M1D  CONST_05  C6   C5   N1  C4      0.00   0.0  0
 M1D  CONST_06  C6   C7   N2  C9      0.00   0.0  0
 M1D  CONST_07  C7   N2   C9  N3      0.00   0.0  0
 M1D  CONST_08  N2   C9   N3  C5      0.00   0.0  0
 M1D  CONST_09  C3   N    C6  C5    180.00   0.0  0
 M1D  CONST_10  C3   N    C4  N1    180.00   0.0  0
 M1D  CONST_11  C3   N    C6  C7      0.00   0.0  0
 M1D  CONST_12  C5   N3   C9  O3    180.00   0.0  0
 M1D  CONST_13  C7   N2   C9  O3    180.00   0.0  0
 M1D  CONST_14  O2   C7   N2  C9    180.00   0.0  0
 M1D  CONST_15  C8   N2   C9  N3    180.00   0.0  0
 M1D  CONST_16  N2   C9   N3  C10   180.00   0.0  0
 M1D  CONST_17  C6   C7   N2  C8    180.00   0.0  0
 M1D  CONST_18  H4   C4   N1  C5    180.00   0.0  0
 M1D  CONST_19  C10  N3   C9  O3      0.00   0.0  0
 M1D  CONST_20  C8   N2   C9  O3      0.00   0.0  0
 M1D  CONST_21  O2   C7   N2  C8      0.00   0.0  0
 M1D  CONST_22  H14  O1   C   C1    180.00   0.0  0
 M1D  Var_01    C2   C3   N   C4   -103.43  30.0  2
 M1D  Var_02    H1   C10  N3  C9    -56.76  30.0  3
 M1D  Var_03    H5   C8   N2  C9     -0.56  30.0  3
 M1D  Var_04    C1   C2   C3  N     178.29  30.0  2
 M1D  Var_05    C    C1   C2  C3    179.81  30.0  1
 M1D  Var_06    O    C    C1  C2     -3.81  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
 M1D  plan-1  O3   0.020
 M1D  plan-1  C9   0.020
 M1D  plan-1  N3   0.020
 M1D  plan-1  C10  0.020
 M1D  plan-1  C5   0.020
 M1D  plan-1  N1   0.020
 M1D  plan-1  C4   0.020
 M1D  plan-1  N2   0.020
 M1D  plan-1  C8   0.020
 M1D  plan-1  C7   0.020
 M1D  plan-1  O2   0.020
 M1D  plan-1  C6   0.020
 M1D  plan-1  N    0.020
 M1D  plan-1  C3   0.020
 M1D  plan-1  H4   0.020
 M1D  plan-2  C1   0.020
 M1D  plan-2  C    0.020
 M1D  plan-2  O1   0.020
 M1D  plan-2  O    0.020
 M1D  plan-2  H14  0.020

