# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 26 07:05:56 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: N-[(2-amino-4-oxo-1,4-dihydropteridin-7-yl)carbonyl]glycyl-L-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)c2ncc(nc2N1)C(=O)NCC(=O)N[C@@H](Cc3ccccc3)C(O)=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
 RS8  RS8  N-[(2-amino-4-oxo-1,4-dihydropteridin-7-yl)carbonyl]glycyl-L-phenylalanine  peptide  47  30  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RS8
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
 RS8  C1   C  CR6   0   0.697  -5.7082   1.5566   1.4287
 RS8  N1   N  NH2   0  -0.811  -5.8906   2.6263   2.1928
 RS8  O1   O  O     0  -0.458  -7.5395  -0.9847  -0.0038
 RS8  C2   C  CR6   0   0.437  -6.5950  -0.2815   0.3119
 RS8  N2   N  N     0  -0.524  -6.7371   0.8132   1.1002
 RS8  C3   C  CR66  0  -0.025  -5.2214  -0.5994  -0.1599
 RS8  N3   N  NR16  0  -0.736  -4.4322   1.3027   1.0262
 RS8  O2   O  O     0  -0.474  -1.0673  -2.2972  -2.0815
 RS8  C4   C  CR66  0   0.552  -4.1646   0.2276   0.2320
 RS8  N4   N  N     0  -0.428  -2.9191   0.0004  -0.1398
 RS8  C5   C  CR6   0   0.102  -2.7125  -1.0519  -0.9121
 RS8  N5   N  N     0  -0.348  -5.0004  -1.6475  -0.9339
 RS8  C6   C  CR16  0  -0.097  -3.7577  -1.8824  -1.3166
 RS8  C7   C  C     0   0.555  -1.3071  -1.3474  -1.3509
 RS8  N6   N  NH1   0  -0.654  -0.3877  -0.5079  -0.8781
 RS8  C8   C  CH2   0  -0.379   1.0062  -0.6536  -1.1824
 RS8  C9   C  C     0   0.536   1.8071   0.3826  -0.4155
 RS8  O3   O  O     0  -0.477   1.2898   1.1596   0.3692
 RS8  N7   N  NH1   0  -0.634   3.1256   0.3472  -0.6588
 RS8  C10  C  CH1   0  -0.181   4.0373   1.2797  -0.0594
 RS8  C18  C  C     0   0.549   3.9129   2.6492  -0.7140
 RS8  O5   O  O     0  -0.425   3.3253   2.8631  -1.7406
 RS8  C11  C  CH2   0  -0.566   5.4788   0.7542  -0.1657
 RS8  C12  C  CR6   0   0.152   5.6403  -0.5649   0.5385
 RS8  C13  C  CR16  0  -0.300   5.7029  -0.6176   1.9295
 RS8  C17  C  CR16  0  -0.323   5.7076  -1.7556  -0.1783
 RS8  C14  C  CR16  0  -0.239   5.8244  -1.8329   2.5877
 RS8  C16  C  CR16  0  -0.238   5.8296  -2.9749   0.4765
 RS8  C15  C  CR16  0  -0.269   5.8866  -3.0169   1.8625
 RS8  O4   O  OH1   0  -0.590   4.5500   3.5729  -0.0107
 RS8  H16  H  HNH2  0   0.422  -6.8142   2.8274   2.5359
 RS8  H17  H  HNH2  0   0.425  -5.1331   3.2127   2.4984
 RS8  H15  H  HNR6  0   0.435  -3.6659   1.9028   1.3028
 RS8  H14  H  HCR6  0   0.288  -3.5780  -2.7396  -1.9507
 RS8  H13  H  HNH1  0   0.411  -0.6686   0.2510  -0.2717
 RS8  H11  H  HCH2  0   0.287   1.1934  -0.5342  -2.2539
 RS8  H12  H  HCH2  0   0.289   1.3638  -1.6507  -0.9090
 RS8  H10  H  HNH1  0   0.411   3.4650  -0.2401  -1.4054
 RS8  H2   H  HCH1  0   0.303   3.7882   1.3916   0.9995
 RS8  H3   H  HCH2  0   0.276   5.7523   0.6556  -1.2195
 RS8  H4   H  HCH2  0   0.289   6.1517   1.4947   0.2675
 RS8  H9   H  HCR6  0   0.252   5.6607   0.2992   2.5066
 RS8  H5   H  HCR6  0   0.251   5.6742  -1.7321  -1.2615
 RS8  H8   H  HCR6  0   0.256   5.8744  -1.8558   3.6686
 RS8  H6   H  HCR6  0   0.257   5.8816  -3.8904  -0.0986
 RS8  H7   H  HCR6  0   0.256   5.9846  -3.9647   2.3758
 RS8  H1   H  HOH1  0   0.487   4.4916   4.4344  -0.4513

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
 RS8  C11  C12  single    1.504  0.020  1.504
 RS8  C11  C10  single    1.538  0.020  1.538
 RS8  C13  C12  aromatic  1.393  0.020  1.393
 RS8  C13  C14  aromatic  1.387  0.020  1.387
 RS8  C12  C17  aromatic  1.391  0.020  1.391
 RS8  O5   C18  double    1.202  0.020  1.202
 RS8  C14  C15  aromatic  1.390  0.020  1.390
 RS8  C10  C18  single    1.523  0.020  1.523
 RS8  C10  N7   single    1.435  0.020  1.435
 RS8  C17  C16  aromatic  1.389  0.020  1.389
 RS8  C18  O4   single    1.324  0.020  1.324
 RS8  C15  C16  aromatic  1.388  0.020  1.388
 RS8  N7   C9   single    1.341  0.020  1.341
 RS8  O3   C9   double    1.220  0.020  1.220
 RS8  C9   C8   single    1.518  0.020  1.518
 RS8  C8   N6   single    1.434  0.020  1.434
 RS8  N6   C7   single    1.332  0.020  1.332
 RS8  C6   N5   aromatic  1.321  0.020  1.321
 RS8  C6   C5   aromatic  1.395  0.020  1.395
 RS8  N5   C3   aromatic  1.322  0.020  1.322
 RS8  O1   C2   double    1.219  0.020  1.219
 RS8  C7   C5   single    1.502  0.020  1.502
 RS8  C7   O2   double    1.222  0.020  1.222
 RS8  C5   N4   aromatic  1.321  0.020  1.321
 RS8  C3   C2   single    1.487  0.020  1.487
 RS8  C3   C4   aromatic  1.398  0.020  1.398
 RS8  C2   N2   single    1.356  0.020  1.356
 RS8  N4   C4   aromatic  1.320  0.020  1.320
 RS8  C4   N3   single    1.363  0.020  1.363
 RS8  N2   C1   double    1.311  0.020  1.311
 RS8  N3   C1   single    1.362  0.020  1.362
 RS8  C1   N1   single    1.327  0.020  1.327
 RS8  O4   H1   single    0.850  0.020  0.980
 RS8  C10  H2   single    0.970  0.020  1.090
 RS8  C11  H3   single    0.970  0.020  1.090
 RS8  C11  H4   single    0.970  0.020  1.090
 RS8  C17  H5   single    0.930  0.020  1.080
 RS8  C16  H6   single    0.930  0.020  1.080
 RS8  C15  H7   single    0.930  0.020  1.080
 RS8  C14  H8   single    0.930  0.020  1.080
 RS8  C13  H9   single    0.930  0.020  1.080
 RS8  N7   H10  single    0.860  0.020  1.020
 RS8  C8   H11  single    0.970  0.020  1.090
 RS8  C8   H12  single    0.970  0.020  1.090
 RS8  N6   H13  single    0.860  0.020  1.020
 RS8  C6   H14  single    0.930  0.020  1.080
 RS8  N3   H15  single    0.860  0.020  1.020
 RS8  N1   H16  single    0.860  0.020  1.020
 RS8  N1   H17  single    0.860  0.020  1.020

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
 RS8  N3   C1   N2   123.75  3.000
 RS8  N3   C1   N1   116.69  3.000
 RS8  N2   C1   N1   119.56  3.000
 RS8  H17  N1   H16  118.14  3.000
 RS8  H17  N1   C1   122.79  3.000
 RS8  H16  N1   C1   118.94  3.000
 RS8  C3   C2   N2   116.99  3.000
 RS8  N2   C2   O1   122.33  3.000
 RS8  C3   C2   O1   120.68  3.000
 RS8  C2   N2   C1   121.39  3.000
 RS8  N5   C3   C4   120.46  3.000
 RS8  C4   C3   C2   118.88  3.000
 RS8  N5   C3   C2   120.66  3.000
 RS8  H15  N3   C4   118.57  3.000
 RS8  H15  N3   C1   121.22  3.000
 RS8  C4   N3   C1   120.21  3.000
 RS8  N4   C4   N3   119.03  3.000
 RS8  N3   C4   C3   118.78  3.000
 RS8  N4   C4   C3   122.18  3.000
 RS8  C5   N4   C4   116.70  3.000
 RS8  C7   C5   C6   119.96  3.000
 RS8  C7   C5   N4   118.28  3.000
 RS8  C6   C5   N4   121.76  3.000
 RS8  C6   N5   C3   117.90  3.000
 RS8  H14  C6   N5   117.85  3.000
 RS8  H14  C6   C5   121.16  3.000
 RS8  N5   C6   C5   120.99  3.000
 RS8  N6   C7   C5   114.73  3.000
 RS8  C5   C7   O2   120.75  3.000
 RS8  N6   C7   O2   124.52  3.000
 RS8  H13  N6   C8   118.26  3.000
 RS8  H13  N6   C7   119.62  3.000
 RS8  C8   N6   C7   122.11  3.000
 RS8  H12  C8   H11  106.75  3.000
 RS8  H12  C8   C9   108.87  3.000
 RS8  H11  C8   C9   109.27  3.000
 RS8  H12  C8   N6   110.93  3.000
 RS8  H11  C8   N6   111.28  3.000
 RS8  C9   C8   N6   109.66  3.000
 RS8  N7   C9   O3   123.40  3.000
 RS8  O3   C9   C8   122.43  3.000
 RS8  N7   C9   C8   114.15  3.000
 RS8  H10  N7   C10  118.27  3.000
 RS8  H10  N7   C9   118.71  3.000
 RS8  C10  N7   C9   122.11  3.000
 RS8  H2   C10  C11  108.39  3.000
 RS8  H2   C10  C18  107.79  3.000
 RS8  C11  C10  C18  110.74  3.000
 RS8  H2   C10  N7   109.04  3.000
 RS8  C18  C10  N7   110.66  3.000
 RS8  C11  C10  N7   110.15  3.000
 RS8  O4   C18  O5   124.38  3.000
 RS8  O4   C18  C10  111.08  3.000
 RS8  O5   C18  C10  124.54  3.000
 RS8  H4   C11  H3   106.85  3.000
 RS8  H4   C11  C12  110.08  3.000
 RS8  H3   C11  C12  110.20  3.000
 RS8  H4   C11  C10  108.60  3.000
 RS8  H3   C11  C10  109.39  3.000
 RS8  C12  C11  C10  111.59  3.000
 RS8  C17  C12  C13  118.66  3.000
 RS8  C17  C12  C11  120.97  3.000
 RS8  C13  C12  C11  120.36  3.000
 RS8  H9   C13  C14  119.45  3.000
 RS8  H9   C13  C12  119.84  3.000
 RS8  C14  C13  C12  120.71  3.000
 RS8  H5   C17  C16  119.52  3.000
 RS8  H5   C17  C12  119.65  3.000
 RS8  C16  C17  C12  120.83  3.000
 RS8  H8   C14  C15  120.07  3.000
 RS8  H8   C14  C13  119.76  3.000
 RS8  C15  C14  C13  120.17  3.000
 RS8  H6   C16  C15  120.21  3.000
 RS8  H6   C16  C17  119.74  3.000
 RS8  C15  C16  C17  120.05  3.000
 RS8  H7   C15  C16  120.25  3.000
 RS8  H7   C15  C14  120.17  3.000
 RS8  C16  C15  C14  119.57  3.000
 RS8  H1   O4   C18  110.46  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
 RS8  CONST_01  C5   C6   N5   C3      0.00   0.0  0
 RS8  CONST_02  C5   N4   C4   C3      0.00   0.0  0
 RS8  CONST_03  C6   N5   C3   C4      0.00   0.0  0
 RS8  CONST_04  C6   C5   N4   C4      0.00   0.0  0
 RS8  CONST_05  N5   C6   C5   N4      0.00   0.0  0
 RS8  CONST_06  N5   C3   C4   N4      0.00   0.0  0
 RS8  CONST_07  C15  C14  C13  C12     0.00   0.0  0
 RS8  CONST_08  C15  C16  C17  C12     0.00   0.0  0
 RS8  CONST_09  C16  C17  C12  C13     0.00   0.0  0
 RS8  CONST_10  C16  C15  C14  C13     0.00   0.0  0
 RS8  CONST_11  C14  C13  C12  C17     0.00   0.0  0
 RS8  CONST_12  C14  C15  C16  C17     0.00   0.0  0
 RS8  CONST_13  N3   C1   N2   C2      0.00   0.0  0
 RS8  CONST_14  C4   N3   C1   N2      0.00   0.0  0
 RS8  CONST_15  C7   C5   N4   C4    180.00   0.0  0
 RS8  CONST_16  C7   C5   C6   N5    180.00   0.0  0
 RS8  CONST_17  C14  C13  C12  C11   180.00   0.0  0
 RS8  CONST_18  C16  C17  C12  C11   180.00   0.0  0
 RS8  CONST_19  C2   N2   C1   N1    180.00   0.0  0
 RS8  CONST_20  C4   N3   C1   N1    180.00   0.0  0
 RS8  CONST_21  H14  C6   N5   C3    180.00   0.0  0
 RS8  CONST_22  H8   C14  C13  C12   180.00   0.0  0
 RS8  CONST_23  H6   C16  C17  C12   180.00   0.0  0
 RS8  CONST_24  H5   C17  C12  C13   180.00   0.0  0
 RS8  CONST_25  H7   C15  C14  C13   180.00   0.0  0
 RS8  CONST_26  H9   C13  C12  C17   180.00   0.0  0
 RS8  CONST_27  H15  N3   C1   N2    180.00   0.0  0
 RS8  CONST_28  H16  N1   C1   N2      0.00   0.0  0
 RS8  CONST_29  H17  N1   C1   N2    180.00   0.0  0
 RS8  CONST_30  C8   N6   C7   C5    180.00   0.0  0
 RS8  CONST_31  H13  N6   C7   C5      0.00   0.0  0
 RS8  CONST_32  C8   N6   C7   O2      0.00   0.0  0
 RS8  CONST_33  C10  N7   C9   C8    180.00   0.0  0
 RS8  CONST_34  C10  N7   C9   O3      0.00   0.0  0
 RS8  CONST_35  H10  N7   C9   C8      0.00   0.0  0
 RS8  CONST_36  H1   O4   C18  C10   180.00   0.0  0
 RS8  Var_01    C6   C5   C7   O2      1.33  30.0  2
 RS8  Var_02    C13  C12  C11  C10   -75.57  30.0  2
 RS8  Var_03    C9   C8   N6   C7   -175.61  30.0  2
 RS8  Var_04    N7   C9   C8   N6   -178.51  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
 RS8  chir_01  C10  C11  C18  N7  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
 RS8  plan-1  C11  0.020
 RS8  plan-1  C12  0.020
 RS8  plan-1  C13  0.020
 RS8  plan-1  C17  0.020
 RS8  plan-1  C14  0.020
 RS8  plan-1  C16  0.020
 RS8  plan-1  C15  0.020
 RS8  plan-1  H9   0.020
 RS8  plan-1  H5   0.020
 RS8  plan-1  H8   0.020
 RS8  plan-1  H6   0.020
 RS8  plan-1  H7   0.020
 RS8  plan-2  C10  0.020
 RS8  plan-2  C18  0.020
 RS8  plan-2  O5   0.020
 RS8  plan-2  O4   0.020
 RS8  plan-2  H1   0.020
 RS8  plan-3  C1   0.020
 RS8  plan-3  N1   0.020
 RS8  plan-3  O1   0.020
 RS8  plan-3  C2   0.020
 RS8  plan-3  N2   0.020
 RS8  plan-3  C3   0.020
 RS8  plan-3  N3   0.020
 RS8  plan-3  C4   0.020
 RS8  plan-3  N4   0.020
 RS8  plan-3  C5   0.020
 RS8  plan-3  N5   0.020
 RS8  plan-3  C6   0.020
 RS8  plan-3  C7   0.020
 RS8  plan-3  H16  0.020
 RS8  plan-3  H17  0.020
 RS8  plan-3  H15  0.020
 RS8  plan-3  H14  0.020
 RS8  plan-4  O2   0.020
 RS8  plan-4  C5   0.020
 RS8  plan-4  C7   0.020
 RS8  plan-4  N6   0.020
 RS8  plan-4  C8   0.020
 RS8  plan-4  H13  0.020
 RS8  plan-5  C8   0.020
 RS8  plan-5  C9   0.020
 RS8  plan-5  O3   0.020
 RS8  plan-5  N7   0.020
 RS8  plan-5  C10  0.020
 RS8  plan-5  H10  0.020

