# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 06:13:09 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: (6R)-6-phenyl-5,6,7,8-tetrahydropteridine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(N)c2N[C@@H](CNc2n1)c3ccccc3
#
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
 AP6  AP6  (6R)-6-phenyl-5,6,7,8-tetrahydropteridine-2,4-diamine  ligand  32  18  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AP6
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
 AP6  N1    N  N     0  -0.521  -1.2214  -0.1598   2.9850
 AP6  C2    C  CR6   0   0.504  -0.1979  -0.0403   3.8223
 AP6  N2    N  NH2   0  -0.828  -0.4808  -0.1111   5.1573
 AP6  N3    N  N     0  -0.512   1.0785   0.1137   3.4876
 AP6  C4    C  CR6   0   0.382   1.3625   0.1094   2.1822
 AP6  N4    N  NH2   0  -0.836   2.6750   0.2451   1.8256
 AP6  C9    C  CR6   0   0.063   0.3833  -0.0709   1.2083
 AP6  C10   C  CR6   0   0.485  -0.9244  -0.1733   1.6834
 AP6  N5    N  NH1   0  -0.687   0.6862  -0.0886  -0.1726
 AP6  C6    C  CH1   0  -0.159  -0.3705  -0.6137  -1.0219
 AP6  C7    C  CH2   0  -0.258  -1.6996   0.0079  -0.5923
 AP6  N8    N  NH1   0  -0.667  -1.9416  -0.2971   0.7956
 AP6  C11   C  CR6   0   0.107  -0.0991  -0.3102  -2.4738
 AP6  C12   C  CR16  0  -0.310  -0.4863  -1.2212  -3.4524
 AP6  C16   C  CR16  0  -0.299   0.4876   0.8902  -2.8652
 AP6  C13   C  CR16  0  -0.241  -0.2961  -0.9406  -4.7987
 AP6  C15   C  CR16  0  -0.240   0.6805   1.1726  -4.2110
 AP6  C14   C  CR16  0  -0.268   0.2884   0.2595  -5.1816
 AP6  HN21  H  HNH2  0   0.379   0.2114   0.2744   5.7779
 AP6  HN22  H  HNH2  0   0.379  -1.4308   0.0910   5.4203
 AP6  HN41  H  HNH2  0   0.383   3.2816   0.5734   2.5601
 AP6  HN42  H  HNH2  0   0.385   2.8615   0.6859   0.9384
 AP6  HN5   H  HNH1  0   0.366   1.5445  -0.5959  -0.3518
 AP6  H6    H  HCH1  0   0.249  -0.4755  -1.7026  -0.9096
 AP6  H71   H  HCH2  0   0.234  -1.6724   1.0885  -0.7803
 AP6  H72   H  HCH2  0   0.261  -2.5060  -0.4118  -1.1927
 AP6  HN8   H  HNH1  0   0.386  -2.8776  -0.1994   1.1550
 AP6  H12   H  HCR6  0   0.250  -0.9390  -2.1610  -3.1570
 AP6  H16   H  HCR6  0   0.249   0.8015   1.6003  -2.1107
 AP6  H13   H  HCR6  0   0.254  -0.5995  -1.6611  -5.5475
 AP6  H15   H  HCR6  0   0.254   1.1397   2.1084  -4.5030
 AP6  H14   H  HCR6  0   0.255   0.4394   0.4818  -6.2301

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
 AP6  N1   C2    aromatic  1.328  0.020  1.328
 AP6  N1   C10   aromatic  1.335  0.020  1.335
 AP6  C2   N2    single    1.366  0.020  1.366
 AP6  C2   N3    aromatic  1.329  0.020  1.329
 AP6  N2   HN21  single    0.890  0.020  1.040
 AP6  N2   HN22  single    0.890  0.020  1.040
 AP6  N3   C4    aromatic  1.336  0.020  1.336
 AP6  C4   N4    single    1.367  0.020  1.367
 AP6  C4   C9    aromatic  1.393  0.020  1.393
 AP6  N4   HN41  single    0.890  0.020  1.040
 AP6  N4   HN42  single    0.890  0.020  1.040
 AP6  C9   C10   aromatic  1.395  0.020  1.395
 AP6  C9   N5    single    1.414  0.020  1.414
 AP6  C10  N8    single    1.356  0.020  1.356
 AP6  N5   C6    single    1.454  0.020  1.454
 AP6  N5   HN5   single    0.890  0.020  1.040
 AP6  C6   C7    single    1.529  0.020  1.529
 AP6  C6   C11   single    1.508  0.020  1.508
 AP6  C6   H6    single    0.970  0.020  1.090
 AP6  C7   N8    single    1.441  0.020  1.441
 AP6  C7   H71   single    0.970  0.020  1.090
 AP6  C7   H72   single    0.970  0.020  1.090
 AP6  N8   HN8   single    0.890  0.020  1.040
 AP6  C11  C12   aromatic  1.392  0.020  1.392
 AP6  C11  C16   aromatic  1.392  0.020  1.392
 AP6  C12  C13   aromatic  1.388  0.020  1.388
 AP6  C12  H12   single    0.930  0.020  1.080
 AP6  C16  C15   aromatic  1.389  0.020  1.389
 AP6  C16  H16   single    0.930  0.020  1.080
 AP6  C13  C14   aromatic  1.389  0.020  1.389
 AP6  C13  H13   single    0.930  0.020  1.080
 AP6  C15  C14   aromatic  1.389  0.020  1.389
 AP6  C15  H15   single    0.930  0.020  1.080
 AP6  C14  H14   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
 AP6  C10   N1   C2    116.38  3.000
 AP6  N3    C2   N2    116.81  3.000
 AP6  N3    C2   N1    126.31  3.000
 AP6  N2    C2   N1    116.87  3.000
 AP6  HN22  N2   HN21  114.29  3.000
 AP6  HN22  N2   C2    116.13  3.000
 AP6  HN21  N2   C2    116.11  3.000
 AP6  C4    N3   C2    116.75  3.000
 AP6  C9    C4   N4    120.37  3.000
 AP6  C9    C4   N3    122.29  3.000
 AP6  N4    C4   N3    117.31  3.000
 AP6  HN42  N4   HN41  112.81  3.000
 AP6  HN42  N4   C4    116.79  3.000
 AP6  HN41  N4   C4    114.86  3.000
 AP6  N5    C9   C10   122.17  3.000
 AP6  N5    C9   C4    122.27  3.000
 AP6  C10   C9   C4    115.50  3.000
 AP6  N8    C10  C9    119.15  3.000
 AP6  N8    C10  N1    118.19  3.000
 AP6  C9    C10  N1    122.67  3.000
 AP6  HN5   N5   C6    109.37  3.000
 AP6  HN5   N5   C9    111.14  3.000
 AP6  C6    N5   C9    114.80  3.000
 AP6  H6    C6   C11   108.35  3.000
 AP6  H6    C6   C7    106.91  3.000
 AP6  C11   C6   C7    110.19  3.000
 AP6  H6    C6   N5    111.55  3.000
 AP6  C11   C6   N5    111.04  3.000
 AP6  C7    C6   N5    108.72  3.000
 AP6  H72   C7   H71   107.66  3.000
 AP6  H72   C7   N8    108.96  3.000
 AP6  H71   C7   N8    112.18  3.000
 AP6  H72   C7   C6    109.39  3.000
 AP6  H71   C7   C6    109.31  3.000
 AP6  N8    C7   C6    109.29  3.000
 AP6  HN8   N8   C7    118.62  3.000
 AP6  HN8   N8   C10   117.04  3.000
 AP6  C7    N8   C10   119.02  3.000
 AP6  C16   C11  C12   118.94  3.000
 AP6  C16   C11  C6    121.34  3.000
 AP6  C12   C11  C6    119.68  3.000
 AP6  H12   C12  C13   119.78  3.000
 AP6  H12   C12  C11   119.47  3.000
 AP6  C13   C12  C11   120.75  3.000
 AP6  H16   C16  C15   120.12  3.000
 AP6  H16   C16  C11   119.46  3.000
 AP6  C15   C16  C11   120.42  3.000
 AP6  H13   C13  C14   120.16  3.000
 AP6  H13   C13  C12   119.86  3.000
 AP6  C14   C13  C12   119.98  3.000
 AP6  H15   C15  C14   119.96  3.000
 AP6  H15   C15  C16   119.75  3.000
 AP6  C14   C15  C16   120.29  3.000
 AP6  H14   C14  C15   120.17  3.000
 AP6  H14   C14  C13   120.22  3.000
 AP6  C15   C14  C13   119.61  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
 AP6  CONST_01  C4   N3   C2   N1     0.00   0.0  0
 AP6  CONST_02  C4   C9   C10  N1     0.00   0.0  0
 AP6  CONST_03  C9   C10  N1   C2     0.00   0.0  0
 AP6  CONST_04  C9   C4   N3   C2     0.00   0.0  0
 AP6  CONST_05  C10  N1   C2   N3     0.00   0.0  0
 AP6  CONST_06  C10  C9   C4   N3     0.00   0.0  0
 AP6  CONST_07  C14  C13  C12  C11    0.00   0.0  0
 AP6  CONST_08  C14  C15  C16  C11    0.00   0.0  0
 AP6  CONST_09  C15  C16  C11  C12    0.00   0.0  0
 AP6  CONST_10  C15  C14  C13  C12    0.00   0.0  0
 AP6  CONST_11  C13  C12  C11  C16    0.00   0.0  0
 AP6  CONST_12  C13  C14  C15  C16    0.00   0.0  0
 AP6  CONST_13  C13  C12  C11  C6   180.00   0.0  0
 AP6  CONST_14  C15  C16  C11  C6   180.00   0.0  0
 AP6  CONST_15  N4   C4   N3   C2   180.00   0.0  0
 AP6  CONST_16  C10  N1   C2   N2   180.00   0.0  0
 AP6  CONST_17  C4   N3   C2   N2   180.00   0.0  0
 AP6  CONST_18  C10  C9   C4   N4   180.00   0.0  0
 AP6  CONST_19  N5   C9   C4   N4     0.00   0.0  0
 AP6  CONST_20  H12  C12  C11  C6     0.00   0.0  0
 AP6  CONST_21  H16  C16  C11  C6     0.00   0.0  0
 AP6  CONST_22  H13  C13  C12  C11  180.00   0.0  0
 AP6  CONST_23  H15  C15  C16  C11  180.00   0.0  0
 AP6  CONST_24  H14  C14  C13  C12  180.00   0.0  0
 AP6  Var_01    C7   N8   C10  N1   165.07  30.0  1
 AP6  Var_02    C6   N5   C9   C4   165.26  30.0  1
 AP6  Var_03    C6   C7   N8   C10   44.22  30.0  1

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
 AP6  chir_01  C6  N5  C7  C11  negativ

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
 AP6  plan-1  C6    0.020
 AP6  plan-1  C11   0.020
 AP6  plan-1  C12   0.020
 AP6  plan-1  C16   0.020
 AP6  plan-1  C13   0.020
 AP6  plan-1  C15   0.020
 AP6  plan-1  C14   0.020
 AP6  plan-1  H12   0.020
 AP6  plan-1  H16   0.020
 AP6  plan-1  H13   0.020
 AP6  plan-1  H15   0.020
 AP6  plan-1  H14   0.020
 AP6  plan-2  C2    0.020
 AP6  plan-2  N2    0.020
 AP6  plan-2  HN21  0.020
 AP6  plan-2  HN22  0.020
 AP6  plan-3  N1    0.020
 AP6  plan-3  C2    0.020
 AP6  plan-3  N2    0.020
 AP6  plan-3  N3    0.020
 AP6  plan-3  C4    0.020
 AP6  plan-3  N4    0.020
 AP6  plan-3  C9    0.020
 AP6  plan-3  C10   0.020
 AP6  plan-3  N5    0.020
 AP6  plan-3  N8    0.020
 AP6  plan-4  C4    0.020
 AP6  plan-4  N4    0.020
 AP6  plan-4  HN41  0.020
 AP6  plan-4  HN42  0.020

