# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 03:08:19 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: 6,7,7-trimethyl-7,8-dihydropteridine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=Nc2c(N)nc(N)nc2NC1(C)C
#
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
 DX3  DX3  6,7,7-trimethyl-7,8-dihydropteridine-2,4-diamine  ligand  29  15  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_DX3
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
 DX3  C4    C  CR66  0   0.495   0.3470   0.7150   0.2200
 DX3  C5    C  CR66  0  -0.041   0.3295  -0.6750   0.0906
 DX3  C6    C  CR6   0   0.429   1.5815  -1.2998   0.0027
 DX3  N1    N  N     0  -0.522   2.7145  -0.5924   0.0222
 DX3  N3    N  N     0  -0.526   1.4682   1.4305   0.2710
 DX3  NAI   N  NR16  0  -0.649  -0.8432   1.3352   0.3543
 DX3  CAO   C  CR6   0  -0.005  -2.0656   0.7086  -0.1366
 DX3  CAB   C  CH3   0  -0.630  -2.2118   0.9062  -1.6530
 DX3  CAC   C  CH3   0  -0.663  -3.2404   1.3539   0.5910
 DX3  CAJ   C  CR6   0   0.245  -1.9626  -0.7909   0.1365
 DX3  CAA   C  CH3   0  -0.749  -3.2291  -1.5705   0.2786
 DX3  NAF   N  N     0  -0.410  -0.8458  -1.4037   0.1745
 DX3  C2    C  CR6   0   0.531   2.5986   0.7271   0.1687
 DX3  NAD   N  NH2   0  -0.822   3.7525   1.4286   0.2525
 DX3  NAE   N  NH2   0  -0.823   1.6791  -2.6390  -0.0794
 DX3  HNAI  H  HNR6  0   0.382  -0.8252   2.3449   0.3612
 DX3  HAB   H  HCH3  0   0.238  -1.3560   0.4912  -2.1881
 DX3  HABA  H  HCH3  0   0.234  -3.1155   0.4250  -2.0308
 DX3  HABB  H  HCH3  0   0.240  -2.2770   1.9704  -1.8892
 DX3  HAC   H  HCH3  0   0.245  -3.2352   2.4320   0.4181
 DX3  HACA  H  HCH3  0   0.242  -4.1933   0.9729   0.2278
 DX3  HACB  H  HCH3  0   0.245  -3.1851   1.1844   1.6664
 DX3  HAA   H  HCH3  0   0.246  -3.9200  -1.3771  -0.5449
 DX3  HAAA  H  HCH3  0   0.256  -3.0121  -2.6363   0.3051
 DX3  HAAB  H  HCH3  0   0.253  -3.7572  -1.3052   1.1969
 DX3  HNAD  H  HNH2  0   0.388   4.6042   0.9788  -0.0342
 DX3  HNAA  H  HNH2  0   0.388   3.7110   2.4263   0.1386
 DX3  HNAE  H  HNH2  0   0.395   0.8528  -3.1775  -0.2719
 DX3  HNAB  H  HNH2  0   0.390   2.5647  -3.0479  -0.3218

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
 DX3  C4   C5    aromatic  1.396  0.020  1.396
 DX3  C4   N3    aromatic  1.331  0.020  1.331
 DX3  C4   NAI   single    1.349  0.020  1.349
 DX3  C5   C6    aromatic  1.402  0.020  1.402
 DX3  C5   NAF   single    1.385  0.020  1.385
 DX3  C6   N1    aromatic  1.336  0.020  1.336
 DX3  C6   NAE   single    1.345  0.020  1.345
 DX3  N1   C2    aromatic  1.333  0.020  1.333
 DX3  N3   C2    aromatic  1.335  0.020  1.335
 DX3  NAI  CAO   single    1.459  0.020  1.459
 DX3  CAO  CAB   single    1.536  0.020  1.536
 DX3  CAO  CAC   single    1.525  0.020  1.525
 DX3  CAO  CAJ   single    1.528  0.020  1.528
 DX3  CAJ  CAA   single    1.494  0.020  1.494
 DX3  CAJ  NAF   double    1.274  0.020  1.274
 DX3  C2   NAD   single    1.353  0.020  1.353
 DX3  NAI  HNAI  single    0.890  0.020  1.040
 DX3  CAB  HAB   single    0.970  0.020  1.090
 DX3  CAB  HABA  single    0.970  0.020  1.090
 DX3  CAB  HABB  single    0.970  0.020  1.090
 DX3  CAC  HAC   single    0.970  0.020  1.090
 DX3  CAC  HACA  single    0.970  0.020  1.090
 DX3  CAC  HACB  single    0.970  0.020  1.090
 DX3  CAA  HAA   single    0.970  0.020  1.090
 DX3  CAA  HAAA  single    0.970  0.020  1.090
 DX3  CAA  HAAB  single    0.970  0.020  1.090
 DX3  NAD  HNAD  single    0.890  0.020  1.040
 DX3  NAD  HNAA  single    0.890  0.020  1.040
 DX3  NAE  HNAE  single    0.890  0.020  1.040
 DX3  NAE  HNAB  single    0.890  0.020  1.040

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
 DX3  NAI   C4   N3    119.49  3.000
 DX3  NAI   C4   C5    117.13  3.000
 DX3  N3    C4   C5    123.32  3.000
 DX3  NAF   C5   C6    121.80  3.000
 DX3  NAF   C5   C4    121.92  3.000
 DX3  C6    C5   C4    116.00  3.000
 DX3  NAE   C6   N1    117.81  3.000
 DX3  NAE   C6   C5    120.81  3.000
 DX3  N1    C6   C5    121.36  3.000
 DX3  C2    N1   C6    116.89  3.000
 DX3  C2    N3   C4    115.28  3.000
 DX3  HNAI  NAI  CAO   116.53  3.000
 DX3  HNAI  NAI  C4    116.40  3.000
 DX3  CAO   NAI  C4    120.56  3.000
 DX3  CAJ   CAO  CAC   112.46  3.000
 DX3  CAJ   CAO  CAB   108.01  3.000
 DX3  CAC   CAO  CAB   110.07  3.000
 DX3  CAJ   CAO  NAI   107.75  3.000
 DX3  CAC   CAO  NAI   107.65  3.000
 DX3  CAB   CAO  NAI   110.90  3.000
 DX3  HABB  CAB  HABA  107.78  3.000
 DX3  HABB  CAB  HAB   108.14  3.000
 DX3  HABA  CAB  HAB   108.18  3.000
 DX3  HABB  CAB  CAO   110.15  3.000
 DX3  HABA  CAB  CAO   111.34  3.000
 DX3  HAB   CAB  CAO   111.13  3.000
 DX3  HACB  CAC  HACA  108.61  3.000
 DX3  HACB  CAC  HAC   108.03  3.000
 DX3  HACA  CAC  HAC   107.27  3.000
 DX3  HACB  CAC  CAO   111.46  3.000
 DX3  HACA  CAC  CAO   111.53  3.000
 DX3  HAC   CAC  CAO   109.79  3.000
 DX3  NAF   CAJ  CAA   119.28  3.000
 DX3  NAF   CAJ  CAO   122.44  3.000
 DX3  CAA   CAJ  CAO   118.17  3.000
 DX3  HAAB  CAA  HAAA  108.30  3.000
 DX3  HAAB  CAA  HAA   106.57  3.000
 DX3  HAAA  CAA  HAA   108.54  3.000
 DX3  HAAB  CAA  CAJ   111.29  3.000
 DX3  HAAA  CAA  CAJ   110.15  3.000
 DX3  HAA   CAA  CAJ   111.85  3.000
 DX3  CAJ   NAF  C5    119.26  3.000
 DX3  NAD   C2   N3    116.37  3.000
 DX3  NAD   C2   N1    116.49  3.000
 DX3  N3    C2   N1    127.12  3.000
 DX3  HNAA  NAD  HNAD  116.55  3.000
 DX3  HNAA  NAD  C2    118.19  3.000
 DX3  HNAD  NAD  C2    118.24  3.000
 DX3  HNAB  NAE  HNAE  117.40  3.000
 DX3  HNAB  NAE  C6    118.92  3.000
 DX3  HNAE  NAE  C6    119.05  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
 DX3  CONST_01  N1    C6   C5   C4     0.00   0.0  0
 DX3  CONST_02  N1    C2   N3   C4     0.00   0.0  0
 DX3  CONST_03  C2    N3   C4   C5     0.00   0.0  0
 DX3  CONST_04  C2    N1   C6   C5     0.00   0.0  0
 DX3  CONST_05  N3    C4   C5   C6     0.00   0.0  0
 DX3  CONST_06  N3    C2   N1   C6     0.00   0.0  0
 DX3  CONST_07  NAE   C6   C5   C4   180.00   0.0  0
 DX3  CONST_08  NAD   C2   N3   C4   180.00   0.0  0
 DX3  CONST_09  NAD   C2   N1   C6   180.00   0.0  0
 DX3  CONST_10  NAE   C6   C5   NAF    0.00   0.0  0
 DX3  CONST_11  NAE   C6   N1   C2   180.00   0.0  0
 DX3  CONST_12  HNAE  NAE  C6   C5     0.00   0.0  0
 DX3  CONST_13  HNAB  NAE  C6   C5   180.00   0.0  0
 DX3  CONST_15  HNAA  NAD  C2   N1   180.00   0.0  0
 DX3  Var_01    CAJ   CAO  NAI  C4    37.79  30.0  1
 DX3  Var_02    CAO   NAI  C4   C5   -23.80  30.0  1
 DX3  Var_03    CAO   CAJ  NAF  C5     6.18  30.0  1
 DX3  Var_04    NAF   CAJ  CAO  NAI  -29.23  30.0  1
 DX3  Var_05    HAB   CAB  CAO  NAI   58.34  30.0  3
 DX3  Var_06    HAC   CAC  CAO  NAI   57.83  30.0  3
 DX3  Var_07    HAA   CAA  CAJ  CAO   49.91  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
 DX3  plan-1  C2    0.020
 DX3  plan-1  NAD   0.020
 DX3  plan-1  HNAD  0.020
 DX3  plan-1  HNAA  0.020
 DX3  plan-2  C4    0.020
 DX3  plan-2  C5    0.020
 DX3  plan-2  C6    0.020
 DX3  plan-2  N1    0.020
 DX3  plan-2  N3    0.020
 DX3  plan-2  NAI   0.020
 DX3  plan-2  NAF   0.020
 DX3  plan-2  C2    0.020
 DX3  plan-2  NAD   0.020
 DX3  plan-2  NAE   0.020
 DX3  plan-3  C6    0.020
 DX3  plan-3  NAE   0.020
 DX3  plan-3  HNAE  0.020
 DX3  plan-3  HNAB  0.020

