# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 19:34:48 2022
#   Inital geometry file: a 119 line input string
#   Ligand name: (2~{R},4~{S})-2-(2-hydroxyethyl)-2,6-dimethyl-4-(2-methylprop-1-enyl)-3,4-dihydropyrano[3,2-c][1,8]naphthyridin-5-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)C2=C(O[C@@](C)(CCO)C[C@H]2C=C(C)C)c3cccnc13
#
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
 8G7  8G7  "(2R,4S)-2-(2-hydroxyethyl)-2,6-dimethyl-4-(2-methylprop-1-enyl)-3,4-dihydropyrano[3,2-c][1,8]naphthyridin-5-one"
  ligand  48  24  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_8G7
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
 8G7  C1   C  CR6   0  -0.196  24.5552   3.1634  -25.9860
 8G7  C2   C  CR6   0   0.472  23.6344   2.4942  -25.2472
 8G7  C3   C  CT    0   0.174  22.8713   1.2149  -27.1068
 8G7  C7   C  CH1   0  -0.360  24.5557   3.1029  -27.4915
 8G7  C10  C  CH3   0  -0.705  25.1151   6.2701  -29.7140
 8G7  C12  C  CH3   0  -0.661  23.9244   0.1149  -27.1113
 8G7  C13  C  CR66  0  -0.173  23.6082   2.6196  -23.8132
 8G7  C14  C  CR66  0   0.506  24.5705   3.4311  -23.1864
 8G7  C15  C  CR16  0  -0.047  23.6990   2.9965  -21.1248
 8G7  C16  C  CR16  0  -0.343  22.7127   2.1625  -21.6372
 8G7  C6   C  CH2   0  -0.436  23.2850   2.3934  -27.9780
 8G7  C4   C  CH2   0  -0.454  21.4848   0.7361  -27.5358
 8G7  C    C  CR6   0   0.549  25.6051   3.9122  -25.3227
 8G7  N1   N  NR6   0  -0.590  25.5310   4.0556  -23.9445
 8G7  C18  C  CH3   0  -0.536  26.5700   4.8624  -23.3195
 8G7  N    N  N     0  -0.448  24.6012   3.6082  -21.8706
 8G7  C17  C  CR16  0  -0.175  22.6740   1.9754  -23.0036
 8G7  O1   O  O2    0  -0.479  22.7040   1.6891  -25.7499
 8G7  O2   O  OH1   0  -0.665  21.3938  -1.6405  -27.1741
 8G7  C8   C  C1    0  -0.195  24.5748   4.4732  -28.1144
 8G7  C11  C  CH3   0  -0.720  26.3063   4.0552  -29.8883
 8G7  H1   H  HCH1  0   0.268  25.4329   2.5372  -27.8175
 8G7  H2   H  HCH3  0   0.235  24.3741   6.8440  -29.1581
 8G7  H3   H  HCH3  0   0.229  26.0586   6.8220  -29.6891
 8G7  H4   H  HCH3  0   0.229  24.8031   6.2397  -30.7612
 8G7  H5   H  HCH3  0   0.249  23.6690  -0.6888  -26.4241
 8G7  H6   H  HCH3  0   0.237  24.0047  -0.3116  -28.1111
 8G7  H7   H  HCH3  0   0.238  24.9084   0.4959  -26.8356
 8G7  H8   H  HCR6  0   0.270  23.7634   3.1749  -20.0573
 8G7  H9   H  HCR6  0   0.272  22.0035   1.6798  -20.9804
 8G7  H10  H  HCH2  0   0.246  22.4602   3.1130  -28.0063
 8G7  H11  H  HCH2  0   0.258  23.4320   2.0511  -29.0040
 8G7  H12  H  HCH2  0   0.206  19.7719  -0.3726  -26.9389
 8G7  H13  H  HCH2  0   0.204  20.9873  -0.2494  -25.6781
 8G7  H14  H  HCH2  0   0.243  20.8079   1.5932  -27.4789
 8G7  H15  H  HCH2  0   0.241  21.5305   0.4597  -28.5930
 8G7  H16  H  HCH3  0   0.270  26.3452   4.9760  -22.2671
 8G7  H17  H  HCH3  0   0.248  27.5440   4.3869  -23.4243
 8G7  H18  H  HCH3  0   0.249  26.6103   5.8453  -23.7832
 8G7  H19  H  HCR6  0   0.279  21.9240   1.3342  -23.4460
 8G7  H20  H  HOH1  0   0.451  21.0451  -2.3289  -26.6008
 8G7  H21  H  H     0   0.225  23.8597   5.1692  -27.6803
 8G7  H22  H  HCH3  0   0.239  26.4272   3.0523  -29.4840
 8G7  H23  H  HCH3  0   0.234  26.0406   3.9570  -30.9438
 8G7  H24  H  HCH3  0   0.234  27.2833   4.5445  -29.8614
 8G7  C9   C  C     0   0.070  25.2870   4.8834  -29.1642
 8G7  C5   C  CH2   0  -0.170  20.8535  -0.4050  -26.7554
 8G7  O    O  O     0  -0.474  26.5414   4.4168  -25.9270

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
 8G7  C11  C9   single    1.500  0.020  1.500
 8G7  C10  C9   single    1.502  0.020  1.502
 8G7  C9   C8   double    1.333  0.020  1.333
 8G7  C8   C7   single    1.505  0.020  1.505
 8G7  O2   C5   single    1.412  0.020  1.412
 8G7  C6   C7   single    1.535  0.020  1.535
 8G7  C6   C3   single    1.523  0.020  1.523
 8G7  C7   C1   single    1.507  0.020  1.507
 8G7  C12  C3   single    1.523  0.020  1.523
 8G7  C4   C3   single    1.528  0.020  1.528
 8G7  C4   C5   single    1.520  0.020  1.520
 8G7  C3   O1   single    1.447  0.020  1.447
 8G7  O    C    double    1.223  0.020  1.223
 8G7  C1   C    single    1.450  0.020  1.450
 8G7  C1   C2   double    1.357  0.020  1.357
 8G7  O1   C2   single    1.329  0.020  1.329
 8G7  C    N1   single    1.388  0.020  1.388
 8G7  C2   C13  single    1.440  0.020  1.440
 8G7  N1   C18  single    1.456  0.020  1.456
 8G7  N1   C14  single    1.374  0.020  1.374
 8G7  C13  C14  aromatic  1.406  0.020  1.406
 8G7  C13  C17  aromatic  1.394  0.020  1.394
 8G7  C14  N    aromatic  1.328  0.020  1.328
 8G7  C17  C16  aromatic  1.380  0.020  1.380
 8G7  N    C15  aromatic  1.321  0.020  1.321
 8G7  C16  C15  aromatic  1.390  0.020  1.390
 8G7  C7   H1   single    0.970  0.020  1.090
 8G7  C10  H2   single    0.970  0.020  1.090
 8G7  C10  H3   single    0.970  0.020  1.090
 8G7  C10  H4   single    0.970  0.020  1.090
 8G7  C12  H5   single    0.970  0.020  1.090
 8G7  C12  H6   single    0.970  0.020  1.090
 8G7  C12  H7   single    0.970  0.020  1.090
 8G7  C15  H8   single    0.930  0.020  1.080
 8G7  C16  H9   single    0.930  0.020  1.080
 8G7  C6   H10  single    0.970  0.020  1.090
 8G7  C6   H11  single    0.970  0.020  1.090
 8G7  C5   H12  single    0.970  0.020  1.090
 8G7  C5   H13  single    0.970  0.020  1.090
 8G7  C4   H14  single    0.970  0.020  1.090
 8G7  C4   H15  single    0.970  0.020  1.090
 8G7  C18  H16  single    0.970  0.020  1.090
 8G7  C18  H17  single    0.970  0.020  1.090
 8G7  C18  H18  single    0.970  0.020  1.090
 8G7  C17  H19  single    0.930  0.020  1.080
 8G7  O2   H20  single    0.850  0.020  0.980
 8G7  C8   H21  single    0.930  0.020  1.080
 8G7  C11  H22  single    0.970  0.020  1.090
 8G7  C11  H23  single    0.970  0.020  1.090
 8G7  C11  H24  single    0.970  0.020  1.090

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
 8G7  C    C1   C7   118.52  3.000
 8G7  C    C1   C2   119.79  3.000
 8G7  C7   C1   C2   121.63  3.000
 8G7  O1   C2   C13  114.63  3.000
 8G7  C13  C2   C1   120.78  3.000
 8G7  O1   C2   C1   124.60  3.000
 8G7  O1   C3   C4   105.13  3.000
 8G7  O1   C3   C6   108.32  3.000
 8G7  C4   C3   C6   109.17  3.000
 8G7  O1   C3   C12  108.63  3.000
 8G7  C4   C3   C12  113.59  3.000
 8G7  C6   C3   C12  111.68  3.000
 8G7  H1   C7   C8   109.72  3.000
 8G7  H1   C7   C6   109.31  3.000
 8G7  C8   C7   C6   107.47  3.000
 8G7  H1   C7   C1   108.60  3.000
 8G7  C6   C7   C1   109.57  3.000
 8G7  C8   C7   C1   112.14  3.000
 8G7  H4   C10  H3   106.39  3.000
 8G7  H4   C10  H2   108.02  3.000
 8G7  H3   C10  H2   108.02  3.000
 8G7  H4   C10  C9   110.97  3.000
 8G7  H3   C10  C9   111.04  3.000
 8G7  H2   C10  C9   112.17  3.000
 8G7  H7   C12  H6   107.59  3.000
 8G7  H7   C12  H5   108.07  3.000
 8G7  H6   C12  H5   107.92  3.000
 8G7  H7   C12  C3   111.77  3.000
 8G7  H6   C12  C3   109.65  3.000
 8G7  H5   C12  C3   111.68  3.000
 8G7  C17  C13  C14  117.80  3.000
 8G7  C17  C13  C2   123.40  3.000
 8G7  C14  C13  C2   118.81  3.000
 8G7  N    C14  N1   118.03  3.000
 8G7  N    C14  C13  122.31  3.000
 8G7  N1   C14  C13  119.65  3.000
 8G7  H8   C15  N    116.05  3.000
 8G7  H8   C15  C16  120.26  3.000
 8G7  N    C15  C16  123.68  3.000
 8G7  H9   C16  C17  121.54  3.000
 8G7  H9   C16  C15  120.65  3.000
 8G7  C17  C16  C15  117.81  3.000
 8G7  H11  C6   H10  106.46  3.000
 8G7  H11  C6   C7   109.36  3.000
 8G7  H10  C6   C7   109.16  3.000
 8G7  H11  C6   C3   109.37  3.000
 8G7  H10  C6   C3   108.58  3.000
 8G7  C7   C6   C3   113.66  3.000
 8G7  H15  C4   H14  105.91  3.000
 8G7  H15  C4   C5   108.90  3.000
 8G7  H14  C4   C5   107.74  3.000
 8G7  H15  C4   C3   108.22  3.000
 8G7  H14  C4   C3   107.54  3.000
 8G7  C5   C4   C3   117.90  3.000
 8G7  N1   C    O    119.27  3.000
 8G7  N1   C    C1   117.97  3.000
 8G7  O    C    C1   122.76  3.000
 8G7  C18  N1   C    116.45  3.000
 8G7  C18  N1   C14  120.91  3.000
 8G7  C    N1   C14  122.58  3.000
 8G7  H18  C18  H17  108.69  3.000
 8G7  H18  C18  H16  109.12  3.000
 8G7  H17  C18  H16  108.98  3.000
 8G7  H18  C18  N1   110.13  3.000
 8G7  H17  C18  N1   110.78  3.000
 8G7  H16  C18  N1   109.11  3.000
 8G7  C15  N    C14  118.81  3.000
 8G7  H19  C17  C16  120.34  3.000
 8G7  H19  C17  C13  120.08  3.000
 8G7  C16  C17  C13  119.59  3.000
 8G7  C3   O1   C2   118.18  3.000
 8G7  H20  O2   C5   108.12  3.000
 8G7  H21  C8   C9   117.92  3.000
 8G7  H21  C8   C7   114.14  3.000
 8G7  C9   C8   C7   127.78  3.000
 8G7  H24  C11  H23  106.34  3.000
 8G7  H24  C11  H22  107.71  3.000
 8G7  H23  C11  H22  107.64  3.000
 8G7  H24  C11  C9   110.39  3.000
 8G7  H23  C11  C9   110.53  3.000
 8G7  H22  C11  C9   113.90  3.000
 8G7  C11  C9   C8   124.98  3.000
 8G7  C8   C9   C10  120.75  3.000
 8G7  C11  C9   C10  114.27  3.000
 8G7  H13  C5   H12  106.27  3.000
 8G7  H13  C5   O2   111.64  3.000
 8G7  H12  C5   O2   110.70  3.000
 8G7  H13  C5   C4   110.31  3.000
 8G7  H12  C5   C4   107.54  3.000
 8G7  O2   C5   C4   110.23  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
 8G7  CONST_01  C15  N    C14  C13     0.00   0.0  0
 8G7  CONST_02  C15  C16  C17  C13     0.00   0.0  0
 8G7  CONST_03  C16  C17  C13  C14     0.00   0.0  0
 8G7  CONST_04  C16  C15  N    C14     0.00   0.0  0
 8G7  CONST_05  C17  C13  C14  N       0.00   0.0  0
 8G7  CONST_06  C17  C16  C15  N       0.00   0.0  0
 8G7  CONST_07  C14  N1   C    C1      0.00   0.0  0
 8G7  CONST_08  C18  N1   C    C1    180.00   0.0  0
 8G7  CONST_09  O    C    N1   C14   180.00   0.0  0
 8G7  CONST_10  H19  C17  C13  C2      0.00   0.0  0
 8G7  CONST_11  H9   C16  C17  C13   180.00   0.0  0
 8G7  CONST_12  H19  C17  C13  C14   180.00   0.0  0
 8G7  CONST_13  H8   C15  N    C14   180.00   0.0  0
 8G7  CONST_14  H19  C17  C16  C15   180.00   0.0  0
 8G7  CONST_15  H9   C16  C15  N     180.00   0.0  0
 8G7  CONST_16  H8   C15  C16  C17   180.00   0.0  0
 8G7  CONST_17  C18  N1   C    O       0.00   0.0  0
 8G7  CONST_18  C11  C9   C8   C7      0.00   0.0  0
 8G7  CONST_19  C10  C9   C8   C7    180.00   0.0  0
 8G7  CONST_20  H21  C8   C9   C10     0.00   0.0  0
 8G7  CONST_21  H21  C8   C9   C11   180.00   0.0  0
 8G7  Var_01    C3   O1   C2   C1     16.57  30.0  1
 8G7  Var_02    C14  C13  C2   C1     -1.11  30.0  1
 8G7  Var_03    C17  C13  C2   C1    178.91  30.0  1
 8G7  Var_04    N1   C    C1   C2     -7.99  30.0  1
 8G7  Var_05    C13  C2   O1   C3   -163.38  30.0  1
 8G7  Var_06    N1   C    C1   C7    174.65  30.0  1
 8G7  Var_07    O1   C2   C1   C7      3.27  30.0  1
 8G7  Var_08    C13  C2   C1   C7   -176.78  30.0  1
 8G7  Var_09    C    C1   C2   C13     5.94  30.0  1
 8G7  Var_10    C    N1   C14  C13    -0.57  30.0  1
 8G7  Var_11    O1   C2   C13  C14   178.84  30.0  1
 8G7  Var_12    O1   C2   C1   C    -174.00  30.0  1
 8G7  Var_13    N    C14  N1   C     178.55  30.0  1
 8G7  Var_14    O1   C2   C13  C17    -1.14  30.0  1
 8G7  Var_15    O    C    C1   C2    172.09  30.0  1
 8G7  Var_16    O    C    C1   C7     -5.27  30.0  1
 8G7  Var_17    C18  N1   C14  C13  -177.73  30.0  1
 8G7  Var_18    N    C14  N1   C18     1.40  30.0  1
 8G7  Var_19    H16  C18  N1   C14    -8.20  30.0  3
 8G7  Var_20    H17  C18  N1   C14   111.79  30.0  3
 8G7  Var_21    H18  C18  N1   C14  -127.94  30.0  3
 8G7  Var_22    H16  C18  N1   C     174.48  30.0  3
 8G7  Var_23    H17  C18  N1   C     -65.54  30.0  3
 8G7  Var_24    H18  C18  N1   C      54.73  30.0  3
 8G7  Var_25    O2   C5   C4   C3    -79.46  30.0  3
 8G7  Var_26    H12  C5   C4   C3    159.77  30.0  3
 8G7  Var_27    H13  C5   C4   C3     44.28  30.0  3
 8G7  Var_28    H22  C11  C9   C10   179.91  30.0  3
 8G7  Var_29    H23  C11  C9   C10   -58.77  30.0  3
 8G7  Var_30    H24  C11  C9   C10    58.60  30.0  3
 8G7  Var_31    H14  C4   C5   O2    158.70  30.0  2
 8G7  Var_32    H15  C4   C5   O2     44.26  30.0  2
 8G7  Var_33    H22  C11  C9   C8      0.25  30.0  3
 8G7  Var_34    H23  C11  C9   C8    121.58  30.0  3
 8G7  Var_35    H24  C11  C9   C8   -121.06  30.0  3
 8G7  Var_36    H2   C10  C9   C8      0.17  30.0  3
 8G7  Var_37    H3   C10  C9   C8    121.14  30.0  3
 8G7  Var_38    H4   C10  C9   C8   -120.75  30.0  3
 8G7  Var_39    H2   C10  C9   C11  -179.50  30.0  3
 8G7  Var_40    H3   C10  C9   C11   -58.53  30.0  3
 8G7  Var_41    H4   C10  C9   C11    59.58  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
 8G7  chir_01  C3  C6  C4  O1  positiv
 8G7  chir_02  C7  C8  C6  C1  positiv

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
 8G7  plan-1  C1   0.020
 8G7  plan-1  C14  0.020
 8G7  plan-1  C    0.020
 8G7  plan-1  N1   0.020
 8G7  plan-1  C18  0.020
 8G7  plan-1  O    0.020
 8G7  plan-2  C2   0.020
 8G7  plan-2  C13  0.020
 8G7  plan-2  C14  0.020
 8G7  plan-2  C15  0.020
 8G7  plan-2  C16  0.020
 8G7  plan-2  N1   0.020
 8G7  plan-2  N    0.020
 8G7  plan-2  C17  0.020
 8G7  plan-2  H8   0.020
 8G7  plan-2  H9   0.020
 8G7  plan-2  H19  0.020
 8G7  plan-3  C7   0.020
 8G7  plan-3  C10  0.020
 8G7  plan-3  C8   0.020
 8G7  plan-3  C11  0.020
 8G7  plan-3  H21  0.020
 8G7  plan-3  C9   0.020

