# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 03:22:52 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: (7S)-2-amino-6-(hydroxymethyl)-7-methyl-7-(2-phenylethyl)-7,8-dihydropteridin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@]1(CCc2ccccc2)NC3=C(N=C1CO)C(=O)NC(=N3)N
#
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
 87Y  87Y  (7S)-2-amino-6-(hydroxymethyl)-7-methyl-7-(2-phenylethyl)-7,8-dihydropteridin-4(3H)-one  ligand  42  23  .  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_87Y
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
 87Y  N2    N  NR16  0  -0.715  -2.1113   0.5754   3.1701
 87Y  C3    C  CR6   0   0.486  -0.8397   1.1232   2.9568
 87Y  O8    O  OC    0  -0.497  -0.5462   2.1800   3.5020
 87Y  C7    C  CR6   0  -0.114  -0.0314   0.3344   2.0943
 87Y  N10   N  N     0  -0.379   1.3016   0.6626   1.9125
 87Y  C12   C  C     0   0.196   1.9877   0.0207   1.0578
 87Y  C15   C  CH2   0  -0.212   3.4511   0.3099   0.8972
 87Y  O16   O  OH1   0  -0.659   3.8167   1.4162   1.6695
 87Y  C11   C  CT    0   0.004   1.3686  -1.0006   0.1057
 87Y  C14   C  CH2   0  -0.400   0.8951  -0.2241  -1.1446
 87Y  C13   C  CH3   0  -0.687   2.3374  -2.1170  -0.2733
 87Y  N9    N  NH1   0  -0.649   0.2507  -1.6023   0.8161
 87Y  C6    C  CR6   0   0.507  -0.5494  -0.8596   1.5984
 87Y  N4    N  N     0  -0.525  -1.7650  -1.3523   1.8933
 87Y  C1    C  CR6   0   0.697  -2.5184  -0.6166   2.6750
 87Y  N5    N  NH2   0  -0.825  -3.7517  -1.0297   2.9792
 87Y  C17   C  CH2   0  -0.528   0.0637  -1.0480  -2.1297
 87Y  C18   C  CR6   0   0.146  -0.3410  -0.2230  -3.3196
 87Y  C19   C  CR16  0  -0.316   0.4207  -0.2288  -4.4858
 87Y  C20   C  CR16  0  -0.239   0.0644   0.5574  -5.5739
 87Y  C21   C  CR16  0  -0.273  -1.0623   1.3667  -5.5104
 87Y  C22   C  CR16  0  -0.240  -1.8298   1.3812  -4.3525
 87Y  C23   C  CR16  0  -0.309  -1.4695   0.5932  -3.2678
 87Y  H2    H  HNR6  0   0.419  -2.7318   1.1017   3.7707
 87Y  H152  H  HCH2  0   0.225   4.0148  -0.5912   1.1817
 87Y  H151  H  HCH2  0   0.217   3.6652   0.4656  -0.1712
 87Y  H16   H  HOH1  0   0.459   4.7584   1.5603   1.5395
 87Y  H142  H  HCH2  0   0.248   0.3056   0.6407  -0.8237
 87Y  H141  H  HCH2  0   0.245   1.7750   0.1764  -1.6565
 87Y  H133  H  HCH3  0   0.254   2.7446  -2.6049   0.6121
 87Y  H132  H  HCH3  0   0.253   1.8320  -2.8794  -0.8666
 87Y  H131  H  HCH3  0   0.245   3.1630  -1.7393  -0.8751
 87Y  H9    H  HNH1  0   0.391  -0.1210  -2.4757   0.4736
 87Y  H52   H  HNH2  0   0.414  -4.0242  -1.9581   2.7057
 87Y  H51   H  HNH2  0   0.417  -4.3037  -0.5762   3.6864
 87Y  H172  H  HCH2  0   0.252   0.6271  -1.9205  -2.4674
 87Y  H171  H  HCH2  0   0.245  -0.8310  -1.4226  -1.6268
 87Y  H19   H  HCR6  0   0.246   1.2996  -0.8605  -4.5453
 87Y  H20   H  HCR6  0   0.253   0.6667   0.5342  -6.4733
 87Y  H21   H  HCR6  0   0.253  -1.3429   1.9789  -6.3579
 87Y  H22   H  HCR6  0   0.253  -2.7134   2.0042  -4.2953
 87Y  H23   H  HCR6  0   0.244  -2.0770   0.6062  -2.3700

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
 87Y  N2   C3    aromatic  1.401  0.020  1.401
 87Y  N2   C1    aromatic  1.353  0.020  1.353
 87Y  N2   H2    single    0.860  0.020  1.020
 87Y  C3   O8    double    1.225  0.020  1.225
 87Y  C3   C7    aromatic  1.421  0.020  1.421
 87Y  C7   N10   single    1.385  0.020  1.385
 87Y  C7   C6    aromatic  1.393  0.020  1.393
 87Y  N10  C12   double    1.270  0.020  1.270
 87Y  C12  C15   single    1.500  0.020  1.500
 87Y  C12  C11   single    1.527  0.020  1.527
 87Y  C15  O16   single    1.398  0.020  1.398
 87Y  C15  H152  single    0.970  0.020  1.090
 87Y  C15  H151  single    0.970  0.020  1.090
 87Y  O16  H16   single    0.850  0.020  0.980
 87Y  C11  C14   single    1.546  0.020  1.546
 87Y  C11  C13   single    1.526  0.020  1.526
 87Y  C11  N9    single    1.455  0.020  1.455
 87Y  C14  C17   single    1.530  0.020  1.530
 87Y  C14  H142  single    0.970  0.020  1.090
 87Y  C14  H141  single    0.970  0.020  1.090
 87Y  C13  H133  single    0.970  0.020  1.090
 87Y  C13  H132  single    0.970  0.020  1.090
 87Y  C13  H131  single    0.970  0.020  1.090
 87Y  N9   C6    single    1.343  0.020  1.343
 87Y  N9   H9    single    0.890  0.020  1.040
 87Y  C6   N4    aromatic  1.344  0.020  1.344
 87Y  N4   C1    aromatic  1.311  0.020  1.311
 87Y  C1   N5    single    1.336  0.020  1.336
 87Y  N5   H52   single    0.860  0.020  1.020
 87Y  N5   H51   single    0.860  0.020  1.020
 87Y  C17  C18   single    1.503  0.020  1.503
 87Y  C17  H172  single    0.970  0.020  1.090
 87Y  C17  H171  single    0.970  0.020  1.090
 87Y  C18  C19   aromatic  1.393  0.020  1.393
 87Y  C18  C23   aromatic  1.394  0.020  1.394
 87Y  C19  C20   aromatic  1.389  0.020  1.389
 87Y  C19  H19   single    0.930  0.020  1.080
 87Y  C20  C21   aromatic  1.389  0.020  1.389
 87Y  C20  H20   single    0.930  0.020  1.080
 87Y  C21  C22   aromatic  1.389  0.020  1.389
 87Y  C21  H21   single    0.930  0.020  1.080
 87Y  C22  C23   aromatic  1.388  0.020  1.388
 87Y  C22  H22   single    0.930  0.020  1.080
 87Y  C23  H23   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
 87Y  H2    N2   C1    119.40  3.000
 87Y  H2    N2   C3    116.35  3.000
 87Y  C1    N2   C3    124.18  3.000
 87Y  C7    C3   O8    127.79  3.000
 87Y  C7    C3   N2    113.06  3.000
 87Y  O8    C3   N2    119.15  3.000
 87Y  C6    C7   N10   120.96  3.000
 87Y  C6    C7   C3    118.71  3.000
 87Y  N10   C7   C3    119.71  3.000
 87Y  C12   N10  C7    119.24  3.000
 87Y  C11   C12  C15   117.23  3.000
 87Y  C11   C12  N10   122.58  3.000
 87Y  C15   C12  N10   120.10  3.000
 87Y  H151  C15  H152  105.50  3.000
 87Y  H151  C15  O16   111.93  3.000
 87Y  H152  C15  O16   111.80  3.000
 87Y  H151  C15  C12   108.72  3.000
 87Y  H152  C15  C12   108.31  3.000
 87Y  O16   C15  C12   110.40  3.000
 87Y  H16   O16  C15   107.46  3.000
 87Y  N9    C11  C13   107.85  3.000
 87Y  N9    C11  C14   111.55  3.000
 87Y  C13   C11  C14   111.16  3.000
 87Y  N9    C11  C12   106.48  3.000
 87Y  C13   C11  C12   112.75  3.000
 87Y  C14   C11  C12   107.00  3.000
 87Y  H141  C14  H142  106.33  3.000
 87Y  H141  C14  C17   109.45  3.000
 87Y  H142  C14  C17   108.76  3.000
 87Y  H141  C14  C11   108.42  3.000
 87Y  H142  C14  C11   108.94  3.000
 87Y  C17   C14  C11   114.63  3.000
 87Y  H131  C13  H132  107.05  3.000
 87Y  H131  C13  H133  108.72  3.000
 87Y  H132  C13  H133  107.59  3.000
 87Y  H131  C13  C11   111.39  3.000
 87Y  H132  C13  C11   110.63  3.000
 87Y  H133  C13  C11   111.29  3.000
 87Y  H9    N9   C6    117.19  3.000
 87Y  H9    N9   C11   118.38  3.000
 87Y  C6    N9   C11   120.90  3.000
 87Y  N4    C6   N9    117.63  3.000
 87Y  N4    C6   C7    124.91  3.000
 87Y  N9    C6   C7    117.38  3.000
 87Y  C1    N4   C6    116.40  3.000
 87Y  N5    C1   N4    119.52  3.000
 87Y  N5    C1   N2    117.83  3.000
 87Y  N4    C1   N2    122.63  3.000
 87Y  H51   N5   H52   117.33  3.000
 87Y  H51   N5   C1    121.84  3.000
 87Y  H52   N5   C1    118.29  3.000
 87Y  H171  C17  H172  106.91  3.000
 87Y  H171  C17  C18   109.39  3.000
 87Y  H172  C17  C18   109.43  3.000
 87Y  H171  C17  C14   109.46  3.000
 87Y  H172  C17  C14   110.43  3.000
 87Y  C18   C17  C14   111.12  3.000
 87Y  C23   C18  C19   118.45  3.000
 87Y  C23   C18  C17   120.66  3.000
 87Y  C19   C18  C17   120.87  3.000
 87Y  H19   C19  C20   119.66  3.000
 87Y  H19   C19  C18   119.46  3.000
 87Y  C20   C19  C18   120.88  3.000
 87Y  H20   C20  C21   120.12  3.000
 87Y  H20   C20  C19   119.73  3.000
 87Y  C21   C20  C19   120.14  3.000
 87Y  H21   C21  C22   120.23  3.000
 87Y  H21   C21  C20   120.27  3.000
 87Y  C22   C21  C20   119.50  3.000
 87Y  H22   C22  C23   119.81  3.000
 87Y  H22   C22  C21   120.06  3.000
 87Y  C23   C22  C21   120.13  3.000
 87Y  H23   C23  C22   119.65  3.000
 87Y  H23   C23  C18   119.44  3.000
 87Y  C22   C23  C18   120.90  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
 87Y  CONST_01  C6   C7   C3   N2      0.00   0.0  0
 87Y  CONST_02  C6   N4   C1   N2      0.00   0.0  0
 87Y  CONST_03  N4   C1   N2   C3      0.00   0.0  0
 87Y  CONST_04  N4   C6   C7   C3      0.00   0.0  0
 87Y  CONST_05  C1   N2   C3   C7      0.00   0.0  0
 87Y  CONST_06  C1   N4   C6   C7      0.00   0.0  0
 87Y  CONST_07  C21  C20  C19  C18     0.00   0.0  0
 87Y  CONST_08  C21  C22  C23  C18     0.00   0.0  0
 87Y  CONST_09  C22  C23  C18  C19     0.00   0.0  0
 87Y  CONST_10  C22  C21  C20  C19     0.00   0.0  0
 87Y  CONST_11  C23  C18  C19  C20     0.00   0.0  0
 87Y  CONST_12  C23  C22  C21  C20     0.00   0.0  0
 87Y  CONST_13  N5   C1   N2   C3    180.00   0.0  0
 87Y  CONST_14  C1   N2   C3   O8    180.00   0.0  0
 87Y  CONST_15  N10  C7   C3   O8      0.00   0.0  0
 87Y  CONST_16  C6   C7   C3   O8    180.00   0.0  0
 87Y  CONST_17  N5   C1   N4   C6    180.00   0.0  0
 87Y  CONST_18  C20  C19  C18  C17   180.00   0.0  0
 87Y  CONST_19  C22  C23  C18  C17   180.00   0.0  0
 87Y  CONST_20  H2   N2   C3   C7    180.00   0.0  0
 87Y  CONST_21  H20  C20  C19  C18   180.00   0.0  0
 87Y  CONST_22  H22  C22  C23  C18   180.00   0.0  0
 87Y  CONST_23  H23  C23  C18  C19   180.00   0.0  0
 87Y  CONST_24  H21  C21  C20  C19   180.00   0.0  0
 87Y  CONST_25  H19  C19  C20  C21   180.00   0.0  0
 87Y  CONST_26  H52  N5   C1   N2    180.00   0.0  0
 87Y  CONST_27  H51  N5   C1   N2      0.00   0.0  0
 87Y  Var_01    C11  C12  N10  C7      6.94  30.0  1
 87Y  Var_02    C11  N9   C6   C7    -22.75  30.0  1
 87Y  Var_03    C6   C7   N10  C12    14.85  30.0  1
 87Y  Var_04    O16  C15  C12  N10    -6.78  30.0  3
 87Y  Var_05    C18  C17  C14  C11  -179.37  30.0  3
 87Y  Var_06    C19  C18  C17  C14    94.25  30.0  2

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
 87Y  chir_01  C11  C12  C13  N9  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
 87Y  plan-1  C17  0.020
 87Y  plan-1  C18  0.020
 87Y  plan-1  C19  0.020
 87Y  plan-1  C20  0.020
 87Y  plan-1  C21  0.020
 87Y  plan-1  C22  0.020
 87Y  plan-1  C23  0.020
 87Y  plan-1  H19  0.020
 87Y  plan-1  H20  0.020
 87Y  plan-1  H21  0.020
 87Y  plan-1  H22  0.020
 87Y  plan-1  H23  0.020
 87Y  plan-2  C1   0.020
 87Y  plan-2  N5   0.020
 87Y  plan-2  H52  0.020
 87Y  plan-2  H51  0.020
 87Y  plan-3  N2   0.020
 87Y  plan-3  C3   0.020
 87Y  plan-3  O8   0.020
 87Y  plan-3  C7   0.020
 87Y  plan-3  N10  0.020
 87Y  plan-3  N9   0.020
 87Y  plan-3  C6   0.020
 87Y  plan-3  N4   0.020
 87Y  plan-3  C1   0.020
 87Y  plan-3  N5   0.020
 87Y  plan-3  H2   0.020

