# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 15:12:50 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: (7R)-5-butyl-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-7,8-dimethyl-7,8-dihydropteridin-6(5H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCN1C(=O)[C@@H](C)N(C)c2nc(Nc3cc(F)c(O)c(F)c3)ncc12
#
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
 FBY  FBY  (7R)-5-butyl-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-7,8-dimethyl-7,8-dihydropteridin-6(5H)-one  ligand  48  27  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_FBY
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
 FBY  C4   C  CR6   0   0.519  -4.3916  -1.2341   0.4386
 FBY  C14  C  CH2   0  -0.423   3.5988  -2.4065  -0.5990
 FBY  C5   C  CR16  0  -0.514  -3.1139  -0.7212   0.3515
 FBY  C6   C  CR6   0   0.387  -2.9306   0.5623  -0.1660
 FBY  C11  C  C     0   0.571   4.4162   0.6604   0.5944
 FBY  C7   C  CR6   0   0.596  -0.4401   0.7804   0.0214
 FBY  C8   C  CR16  0  -0.060   1.0304  -0.7274   0.8243
 FBY  C9   C  CR6   0   0.181   2.0912   0.0955   0.5400
 FBY  C10  C  CR6   0   0.535   1.7585   1.3597  -0.0059
 FBY  C12  C  CH1   0  -0.212   3.9385   2.1116   0.5896
 FBY  N1   N  NH1   0  -0.777  -1.7028   1.1885  -0.3070
 FBY  N2   N  N     0  -0.487  -0.2422  -0.3979   0.5802
 FBY  C3   C  CR6   0   0.042  -5.5299  -0.5505   0.0386
 FBY  N3   N  N     0  -0.520   0.5054   1.6770  -0.2682
 FBY  C1   C  CR16  0  -0.533  -4.0546   1.2840  -0.5814
 FBY  C2   C  CR6   0   0.478  -5.3046   0.7210  -0.4724
 FBY  F1   F  F     0  -0.314  -4.5565  -2.4673   0.9377
 FBY  O1   O  OH1   0  -0.622  -6.7382  -1.1324   0.1596
 FBY  F2   F  F     0  -0.319  -6.3782   1.4240  -0.8727
 FBY  N4   N  NT    0  -0.571   3.4362  -0.2747   0.6647
 FBY  N5   N  NT    0  -0.494   2.7573   2.2346  -0.2685
 FBY  C15  C  CH2   0  -0.426   3.9032  -3.8943  -0.4842
 FBY  C16  C  CH3   0  -0.661   3.7135  -4.6304  -1.8026
 FBY  C17  C  CH3   0  -0.541   2.4222   3.5397  -0.8039
 FBY  C18  C  CH3   0  -0.697   5.0635   3.0443   0.1838
 FBY  O2   O  O     0  -0.468   5.5988   0.3745   0.5850
 FBY  H1   H  HCH2  0   0.227   2.5743  -2.2730  -0.9597
 FBY  H2   H  HCH2  0   0.231   4.2525  -1.9477  -1.3464
 FBY  H3   H  HCR6  0   0.311  -2.2769  -1.3142   0.6842
 FBY  H4   H  HCR6  0   0.278   1.1823  -1.7125   1.2489
 FBY  H5   H  HCH1  0   0.280   3.6566   2.3552   1.6265
 FBY  H6   H  HCH2  0   0.256   3.1794  -2.1626   1.5105
 FBY  H7   H  HCH2  0   0.274   4.8151  -1.7646   1.0618
 FBY  H8   H  HNH1  0   0.411  -1.7289   2.1074  -0.7213
 FBY  H9   H  HCR6  0   0.296  -3.9595   2.2824  -0.9906
 FBY  H10  H  HOH1  0   0.479  -7.4371  -0.5230  -0.1042
 FBY  H11  H  HCH2  0   0.220   4.9301  -4.0306  -0.1321
 FBY  H12  H  HCH2  0   0.219   3.2583  -4.3375   0.2806
 FBY  H13  H  HCH3  0   0.219   2.6846  -4.5456  -2.1572
 FBY  H14  H  HCH3  0   0.219   4.3634  -4.2228  -2.5790
 FBY  H15  H  HCH3  0   0.229   3.9432  -5.6915  -1.7025
 FBY  H16  H  HCH3  0   0.235   2.1641   4.2548  -0.0174
 FBY  H17  H  HCH3  0   0.260   3.2601   3.9333  -1.3718
 FBY  H18  H  HCH3  0   0.267   1.5751   3.4464  -1.4750
 FBY  H19  H  HCH3  0   0.242   5.3828   2.8783  -0.8451
 FBY  H20  H  HCH3  0   0.254   4.7649   4.0848   0.2950
 FBY  H21  H  HCH3  0   0.261   5.9174   2.8839   0.8372
 FBY  C13  C  CH2   0  -0.338   3.7817  -1.6904   0.7322

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
 FBY  F2   C2   single    1.344  0.020  1.344
 FBY  N2   C8   aromatic  1.337  0.020  1.337
 FBY  N2   C7   aromatic  1.319  0.020  1.319
 FBY  C1   C2   aromatic  1.375  0.020  1.375
 FBY  C1   C6   aromatic  1.399  0.020  1.399
 FBY  N1   C7   single    1.367  0.020  1.367
 FBY  N1   C6   single    1.385  0.020  1.385
 FBY  C8   C9   aromatic  1.372  0.020  1.372
 FBY  C2   C3   aromatic  1.389  0.020  1.389
 FBY  C14  C13  single    1.523  0.020  1.523
 FBY  C14  C15  single    1.523  0.020  1.523
 FBY  C16  C15  single    1.522  0.020  1.522
 FBY  C7   N3   aromatic  1.335  0.020  1.335
 FBY  C6   C5   aromatic  1.396  0.020  1.396
 FBY  C13  N4   single    1.459  0.020  1.459
 FBY  C9   N4   single    1.401  0.020  1.401
 FBY  C9   C10  aromatic  1.417  0.020  1.417
 FBY  C3   O1   single    1.347  0.020  1.347
 FBY  C3   C4   aromatic  1.387  0.020  1.387
 FBY  N3   C10  aromatic  1.319  0.020  1.319
 FBY  N4   C11  single    1.356  0.020  1.356
 FBY  C5   C4   aromatic  1.380  0.020  1.380
 FBY  C10  N5   single    1.354  0.020  1.354
 FBY  C4   F1   single    1.341  0.020  1.341
 FBY  C11  O2   double    1.217  0.020  1.217
 FBY  C11  C12  single    1.528  0.020  1.528
 FBY  N5   C12  single    1.465  0.020  1.465
 FBY  N5   C17  single    1.450  0.020  1.450
 FBY  C12  C18  single    1.517  0.020  1.517
 FBY  C14  H1   single    0.970  0.020  1.090
 FBY  C14  H2   single    0.970  0.020  1.090
 FBY  C5   H3   single    0.930  0.020  1.080
 FBY  C8   H4   single    0.930  0.020  1.080
 FBY  C12  H5   single    0.970  0.020  1.090
 FBY  C13  H6   single    0.970  0.020  1.090
 FBY  C13  H7   single    0.970  0.020  1.090
 FBY  N1   H8   single    0.860  0.020  1.020
 FBY  C1   H9   single    0.930  0.020  1.080
 FBY  O1   H10  single    0.850  0.020  0.980
 FBY  C15  H11  single    0.970  0.020  1.090
 FBY  C15  H12  single    0.970  0.020  1.090
 FBY  C16  H13  single    0.970  0.020  1.090
 FBY  C16  H14  single    0.970  0.020  1.090
 FBY  C16  H15  single    0.970  0.020  1.090
 FBY  C17  H16  single    0.970  0.020  1.090
 FBY  C17  H17  single    0.970  0.020  1.090
 FBY  C17  H18  single    0.970  0.020  1.090
 FBY  C18  H19  single    0.970  0.020  1.090
 FBY  C18  H20  single    0.970  0.020  1.090
 FBY  C18  H21  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
 FBY  F1   C4   C3   117.38  3.000
 FBY  F1   C4   C5   118.65  3.000
 FBY  C3   C4   C5   123.97  3.000
 FBY  H2   C14  H1   106.44  3.000
 FBY  H2   C14  C15  109.99  3.000
 FBY  H1   C14  C15  109.34  3.000
 FBY  H2   C14  C13  109.17  3.000
 FBY  H1   C14  C13  110.08  3.000
 FBY  C15  C14  C13  111.69  3.000
 FBY  H3   C5   C6   121.20  3.000
 FBY  H3   C5   C4   119.66  3.000
 FBY  C6   C5   C4   119.13  3.000
 FBY  C1   C6   N1   116.66  3.000
 FBY  N1   C6   C5   124.73  3.000
 FBY  C1   C6   C5   118.61  3.000
 FBY  O2   C11  N4   122.73  3.000
 FBY  O2   C11  C12  121.81  3.000
 FBY  N4   C11  C12  115.41  3.000
 FBY  N3   C7   N2   125.85  3.000
 FBY  N3   C7   N1   113.68  3.000
 FBY  N2   C7   N1   120.47  3.000
 FBY  H4   C8   N2   115.41  3.000
 FBY  H4   C8   C9   121.20  3.000
 FBY  N2   C8   C9   123.38  3.000
 FBY  N4   C9   C10  119.71  3.000
 FBY  C10  C9   C8   115.69  3.000
 FBY  N4   C9   C8   124.43  3.000
 FBY  N5   C10  N3   120.47  3.000
 FBY  N5   C10  C9   118.58  3.000
 FBY  N3   C10  C9   120.95  3.000
 FBY  H5   C12  C18  107.79  3.000
 FBY  H5   C12  N5   109.05  3.000
 FBY  C18  C12  N5   112.93  3.000
 FBY  H5   C12  C11  106.68  3.000
 FBY  C18  C12  C11  110.68  3.000
 FBY  N5   C12  C11  109.49  3.000
 FBY  H8   N1   C7   113.24  3.000
 FBY  H8   N1   C6   115.52  3.000
 FBY  C7   N1   C6   131.24  3.000
 FBY  C8   N2   C7   116.13  3.000
 FBY  O1   C3   C2   125.04  3.000
 FBY  O1   C3   C4   119.85  3.000
 FBY  C2   C3   C4   115.11  3.000
 FBY  C10  N3   C7   117.92  3.000
 FBY  H9   C1   C2   119.15  3.000
 FBY  H9   C1   C6   121.14  3.000
 FBY  C2   C1   C6   119.71  3.000
 FBY  F2   C2   C1   119.23  3.000
 FBY  C1   C2   C3   123.46  3.000
 FBY  F2   C2   C3   117.31  3.000
 FBY  H10  O1   C3   110.66  3.000
 FBY  C13  N4   C9   119.21  3.000
 FBY  C9   N4   C11  120.47  3.000
 FBY  C13  N4   C11  120.02  3.000
 FBY  C17  N5   C12  118.57  3.000
 FBY  C17  N5   C10  118.88  3.000
 FBY  C12  N5   C10  115.28  3.000
 FBY  H12  C15  H11  106.12  3.000
 FBY  H12  C15  C16  109.64  3.000
 FBY  H11  C15  C16  109.60  3.000
 FBY  H12  C15  C14  109.31  3.000
 FBY  H11  C15  C14  109.49  3.000
 FBY  C16  C15  C14  112.48  3.000
 FBY  H15  C16  H14  107.66  3.000
 FBY  H15  C16  H13  107.71  3.000
 FBY  H14  C16  H13  107.53  3.000
 FBY  H15  C16  C15  111.40  3.000
 FBY  H14  C16  C15  111.18  3.000
 FBY  H13  C16  C15  111.18  3.000
 FBY  H18  C17  H17  108.07  3.000
 FBY  H18  C17  H16  108.46  3.000
 FBY  H17  C17  H16  108.73  3.000
 FBY  H18  C17  N5   109.36  3.000
 FBY  H17  C17  N5   109.94  3.000
 FBY  H16  C17  N5   112.18  3.000
 FBY  H21  C18  H20  107.17  3.000
 FBY  H21  C18  H19  108.34  3.000
 FBY  H20  C18  H19  108.81  3.000
 FBY  H21  C18  C12  109.33  3.000
 FBY  H20  C18  C12  110.93  3.000
 FBY  H19  C18  C12  112.10  3.000
 FBY  H7   C13  H6   106.19  3.000
 FBY  H7   C13  N4   107.78  3.000
 FBY  H6   C13  N4   108.79  3.000
 FBY  H7   C13  C14  110.31  3.000
 FBY  H6   C13  C14  110.71  3.000
 FBY  N4   C13  C14  112.80  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
 FBY  CONST_01  C1   C2   C3   C4      0.00   0.0  0
 FBY  CONST_02  C1   C6   C5   C4      0.00   0.0  0
 FBY  CONST_03  C2   C1   C6   C5      0.00   0.0  0
 FBY  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 FBY  CONST_05  C3   C2   C1   C6      0.00   0.0  0
 FBY  CONST_06  C3   C4   C5   C6      0.00   0.0  0
 FBY  CONST_07  C9   C8   N2   C7      0.00   0.0  0
 FBY  CONST_08  C9   C10  N3   C7      0.00   0.0  0
 FBY  CONST_09  N3   C7   N2   C8      0.00   0.0  0
 FBY  CONST_10  N3   C10  C9   C8      0.00   0.0  0
 FBY  CONST_11  N2   C8   C9   C10     0.00   0.0  0
 FBY  CONST_12  N2   C7   N3   C10     0.00   0.0  0
 FBY  CONST_13  C12  C11  N4   C9      0.00   0.0  0
 FBY  CONST_14  F2   C2   C3   C4    180.00   0.0  0
 FBY  CONST_15  N1   C6   C5   C4    180.00   0.0  0
 FBY  CONST_16  O1   C3   C4   C5    180.00   0.0  0
 FBY  CONST_17  F2   C2   C1   C6    180.00   0.0  0
 FBY  CONST_18  F1   C4   C5   C6    180.00   0.0  0
 FBY  CONST_19  N1   C7   N2   C8    180.00   0.0  0
 FBY  CONST_20  N1   C7   N3   C10   180.00   0.0  0
 FBY  CONST_21  C2   C1   C6   N1    180.00   0.0  0
 FBY  CONST_22  O1   C3   C2   C1    180.00   0.0  0
 FBY  CONST_23  F1   C4   C3   C2    180.00   0.0  0
 FBY  CONST_24  O2   C11  N4   C9    180.00   0.0  0
 FBY  CONST_25  C13  N4   C11  C12   180.00   0.0  0
 FBY  CONST_26  H9   C1   C6   C5    180.00   0.0  0
 FBY  CONST_27  H4   C8   N2   C7    180.00   0.0  0
 FBY  CONST_28  H3   C5   C4   C3    180.00   0.0  0
 FBY  CONST_29  O2   C11  N4   C13     0.00   0.0  0
 FBY  Var_01    C8   C9   N4   C11  -168.22  30.0  1
 FBY  Var_02    C12  N5   C10  C9    -29.05  30.0  1
 FBY  Var_03    C7   N1   C6   C5     -1.77  30.0  2
 FBY  Var_04    N2   C7   N1   C6     -0.27  30.0  2
 FBY  Var_05    C9   N4   C13  C14    71.30  30.0  3
 FBY  Var_06    H16  C17  N5   C10    84.81  30.0  3
 FBY  Var_07    C15  C14  C13  N4   -177.32  30.0  1
 FBY  Var_08    C16  C15  C14  C13   179.47  30.0  3
 FBY  Var_09    H13  C16  C15  C14   -60.30  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
 FBY  chir_01  C12  C11  N5  C18  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
 FBY  plan-1  C4   0.020
 FBY  plan-1  C5   0.020
 FBY  plan-1  C6   0.020
 FBY  plan-1  N1   0.020
 FBY  plan-1  C3   0.020
 FBY  plan-1  C1   0.020
 FBY  plan-1  C2   0.020
 FBY  plan-1  F1   0.020
 FBY  plan-1  O1   0.020
 FBY  plan-1  F2   0.020
 FBY  plan-1  H3   0.020
 FBY  plan-1  H9   0.020
 FBY  plan-2  C7   0.020
 FBY  plan-2  C8   0.020
 FBY  plan-2  C9   0.020
 FBY  plan-2  C10  0.020
 FBY  plan-2  N1   0.020
 FBY  plan-2  N2   0.020
 FBY  plan-2  N3   0.020
 FBY  plan-2  N4   0.020
 FBY  plan-2  N5   0.020
 FBY  plan-2  H4   0.020
 FBY  plan-3  C11  0.020
 FBY  plan-3  C9   0.020
 FBY  plan-3  C12  0.020
 FBY  plan-3  N4   0.020
 FBY  plan-3  O2   0.020
 FBY  plan-3  C13  0.020

