# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 19:16:40 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: (2-amino-4-oxo-3,4,7,8-tetrahydropteridin-6-yl)methyl trihydrogen diphosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC2=C(N=C(CN2)CO[P@](O)(=O)O[P](O)(O)=O)C(=O)N1
#
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
 2PH  2PH  '(2-amino-4-oxo-3,4,7,8-tetrahydropteridin-6-yl)methyl trihydrogen diphosphate'  ligand  33  22  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2PH
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
 2PH  N1    N  N     0  -0.341   0.2144  -0.1889   1.5809
 2PH  C2    C  CR6   0   0.075   1.4492  -0.2118   1.3025
 2PH  C3    C  C     0  -0.315   2.5384  -0.2946   2.3435
 2PH  N4    N  NR16  0  -0.634   2.0478   0.2693   3.5786
 2PH  N5    N  N     0  -0.446   0.4354   0.3705   5.2067
 2PH  C6    C  CR6   0   0.617  -0.8358   0.2714   5.5211
 2PH  N6    N  NH2   0  -0.788  -1.2179   0.4844   6.7800
 2PH  N7    N  NR16  0  -0.654  -1.7909  -0.0360   4.6135
 2PH  C8    C  CR6   0   0.463  -1.5428  -0.2309   3.2482
 2PH  O8    O  OC    0  -0.390  -2.4845  -0.4527   2.4968
 2PH  C9    C  CR66  0  -0.151  -0.1662  -0.1420   2.9139
 2PH  C10   C  CR66  0   0.423   0.7553   0.1487   3.9212
 2PH  C11   C  CH2   0  -0.235   1.9376  -0.2096  -0.1095
 2PH  O4    O  O2    0  -0.561   0.8307  -0.2154  -1.0027
 2PH  P1    P  P     0   1.442   1.0696  -0.5240  -2.5429
 2PH  O1P   O  O     0  -0.619   2.1771   0.1708  -3.2124
 2PH  O2P   O  OH1   0  -0.669   1.1879  -2.0971  -2.7058
 2PH  O3P   O  O2    0  -0.700  -0.4171  -0.1360  -3.0437
 2PH  P2    P  P     0   1.408  -0.8242   0.3395  -4.5416
 2PH  O4P   O  O     0  -0.676  -0.1119  -0.3456  -5.6280
 2PH  O5P   O  OH1   0  -0.695  -2.3835   0.0945  -4.3742
 2PH  O6P   O  OH1   0  -0.662  -0.5673   1.9045  -4.5770
 2PH  H31   H  H     0   0.273   2.8452  -1.3442   2.4620
 2PH  H32   H  H     0   0.255   3.4247   0.2563   2.0234
 2PH  HN4   H  HNR6  0   0.367   2.7103   0.4497   4.3164
 2PH  HN61  H  HNH2  0   0.412  -0.5174   0.6640   7.4781
 2PH  HN62  H  HNH2  0   0.425  -2.1661   0.3527   7.0867
 2PH  HN7   H  HNR6  0   0.409  -2.7579  -0.0859   4.9056
 2PH  H111  H  HCH2  0   0.253   2.5580   0.6764  -0.2788
 2PH  H112  H  HCH2  0   0.181   2.5831  -1.0836  -0.2641
 2PH  HOP2  H  HOH1  0   0.510   0.4887  -2.6284  -2.2988
 2PH  HOP5  H  HOH1  0   0.507  -2.9005   0.2653  -5.1743
 2PH  HOP6  H  HOH1  0   0.514  -1.0679   2.4372  -3.9437

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
 2PH  N1   C2    double    1.266  0.020  1.266
 2PH  N1   C9    single    1.387  0.020  1.387
 2PH  C2   C3    single    1.509  0.020  1.509
 2PH  C2   C11   single    1.494  0.020  1.494
 2PH  C3   N4    single    1.444  0.020  1.444
 2PH  C3   H31   single    0.970  0.020  1.090
 2PH  C3   H32   single    0.970  0.020  1.090
 2PH  N4   C10   single    1.343  0.020  1.343
 2PH  N4   HN4   single    0.890  0.020  1.040
 2PH  N5   C6    aromatic  1.313  0.020  1.313
 2PH  N5   C10   aromatic  1.343  0.020  1.343
 2PH  C6   N6    single    1.333  0.020  1.333
 2PH  C6   N7    aromatic  1.353  0.020  1.353
 2PH  N6   HN61  single    0.860  0.020  1.020
 2PH  N6   HN62  single    0.860  0.020  1.020
 2PH  N7   C8    aromatic  1.401  0.020  1.401
 2PH  N7   HN7   single    0.860  0.020  1.020
 2PH  C8   O8    double    1.225  0.020  1.225
 2PH  C8   C9    aromatic  1.419  0.020  1.419
 2PH  C9   C10   aromatic  1.396  0.020  1.396
 2PH  C11  O4    single    1.422  0.020  1.422
 2PH  C11  H111  single    0.970  0.020  1.090
 2PH  C11  H112  single    0.970  0.020  1.090
 2PH  O4   P1    single    1.589  0.020  1.589
 2PH  P1   O1P   double    1.469  0.020  1.469
 2PH  P1   O2P   single    1.586  0.020  1.586
 2PH  P1   O3P   single    1.616  0.020  1.616
 2PH  O2P  HOP2  single    0.850  0.020  0.980
 2PH  O3P  P2    single    1.623  0.020  1.623
 2PH  P2   O4P   double    1.469  0.020  1.469
 2PH  P2   O5P   single    1.587  0.020  1.587
 2PH  P2   O6P   single    1.586  0.020  1.586
 2PH  O5P  HOP5  single    0.850  0.020  0.980
 2PH  O6P  HOP6  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
 2PH  C9    N1   C2    118.66  3.000
 2PH  C11   C2   C3    114.59  3.000
 2PH  C11   C2   N1    121.78  3.000
 2PH  C3    C2   N1    123.60  3.000
 2PH  H32   C3   H31   106.67  3.000
 2PH  H32   C3   N4    109.25  3.000
 2PH  H31   C3   N4    112.05  3.000
 2PH  H32   C3   C2    110.86  3.000
 2PH  H31   C3   C2    109.15  3.000
 2PH  N4    C3   C2    108.87  3.000
 2PH  HN4   N4   C10   117.52  3.000
 2PH  HN4   N4   C3    118.21  3.000
 2PH  C10   N4   C3    120.69  3.000
 2PH  C10   N5   C6    116.57  3.000
 2PH  N7    C6   N6    117.88  3.000
 2PH  N7    C6   N5    122.67  3.000
 2PH  N6    C6   N5    119.45  3.000
 2PH  HN62  N6   HN61  117.96  3.000
 2PH  HN62  N6   C6    122.52  3.000
 2PH  HN61  N6   C6    119.00  3.000
 2PH  HN7   N7   C8    116.34  3.000
 2PH  HN7   N7   C6    119.50  3.000
 2PH  C8    N7   C6    124.07  3.000
 2PH  C9    C8   O8    127.76  3.000
 2PH  C9    C8   N7    113.11  3.000
 2PH  O8    C8   N7    119.13  3.000
 2PH  C10   C9   C8    118.90  3.000
 2PH  C10   C9   N1    121.29  3.000
 2PH  C8    C9   N1    119.36  3.000
 2PH  C9    C10  N5    124.60  3.000
 2PH  C9    C10  N4    118.04  3.000
 2PH  N5    C10  N4    117.30  3.000
 2PH  H112  C11  H111  106.83  3.000
 2PH  H112  C11  O4    111.48  3.000
 2PH  H111  C11  O4    110.31  3.000
 2PH  H112  C11  C2    108.92  3.000
 2PH  H111  C11  C2    109.42  3.000
 2PH  O4    C11  C2    109.82  3.000
 2PH  P1    O4   C11   119.51  3.000
 2PH  O3P   P1   O2P   105.96  3.000
 2PH  O3P   P1   O1P   116.03  3.000
 2PH  O2P   P1   O1P   111.47  3.000
 2PH  O3P   P1   O4     96.63  3.000
 2PH  O2P   P1   O4    107.66  3.000
 2PH  O1P   P1   O4    117.60  3.000
 2PH  HOP2  O2P  P1    116.57  3.000
 2PH  P2    O3P  P1    125.94  3.000
 2PH  O6P   P2   O5P   108.28  3.000
 2PH  O6P   P2   O4P   111.42  3.000
 2PH  O5P   P2   O4P   118.85  3.000
 2PH  O6P   P2   O3P   105.60  3.000
 2PH  O5P   P2   O3P    95.96  3.000
 2PH  O4P   P2   O3P   115.11  3.000
 2PH  HOP5  O5P  P2    114.23  3.000
 2PH  HOP6  O6P  P2    116.42  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
 2PH  CONST_01  C8    N7   C6   N5      0.00   0.0  0
 2PH  CONST_02  C8    C9   C10  N5      0.00   0.0  0
 2PH  CONST_03  C9    C10  N5   C6      0.00   0.0  0
 2PH  CONST_04  C9    C8   N7   C6      0.00   0.0  0
 2PH  CONST_05  C10   N5   C6   N7      0.00   0.0  0
 2PH  CONST_06  C10   C9   C8   N7      0.00   0.0  0
 2PH  CONST_07  O8    C8   C9   N1      0.00   0.0  0
 2PH  CONST_08  O8    C8   N7   C6    180.00   0.0  0
 2PH  CONST_09  C10   N5   C6   N6    180.00   0.0  0
 2PH  CONST_10  C8    N7   C6   N6    180.00   0.0  0
 2PH  CONST_11  C10   C9   C8   O8    180.00   0.0  0
 2PH  CONST_12  HN7   N7   C6   N5    180.00   0.0  0
 2PH  CONST_13  HN61  N6   C6   N5      0.00   0.0  0
 2PH  CONST_14  HN62  N6   C6   N5    180.00   0.0  0
 2PH  Var_01    N4    C3   C2   N1    -26.45  30.0  1
 2PH  Var_02    C8    C9   N1   C2   -174.66  30.0  1
 2PH  Var_03    C10   N4   C3   C2     33.44  30.0  1
 2PH  Var_04    N5    C10  N4   C3    162.84  30.0  1
 2PH  Var_05    O4    C11  C2   N1     -1.55  30.0  3
 2PH  Var_06    O1P   P1   O4   C11   -46.52  30.0  3
 2PH  Var_07    O4P   P2   O3P  P1     37.97  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 2PH  chir_01  P1  O1P  O2P  O3P  both

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
 2PH  plan-1  C6    0.020
 2PH  plan-1  N6    0.020
 2PH  plan-1  HN61  0.020
 2PH  plan-1  HN62  0.020
 2PH  plan-2  N1    0.020
 2PH  plan-2  N4    0.020
 2PH  plan-2  N5    0.020
 2PH  plan-2  C6    0.020
 2PH  plan-2  N6    0.020
 2PH  plan-2  N7    0.020
 2PH  plan-2  C8    0.020
 2PH  plan-2  O8    0.020
 2PH  plan-2  C9    0.020
 2PH  plan-2  C10   0.020
 2PH  plan-2  HN7   0.020

