# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 10:31:34 2022
#   Inital geometry file: a 122 line input string
#   Ligand name: (7S)-8-(cyclopropylmethyl)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-7-methyl-5-(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1N(CC2CC2)c3nc(Nc4cc(F)c(O)c(F)c4)ncc3N(CC#C)C1=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
 VBD  VBD  (7S)-8-(cyclopropylmethyl)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-7-methyl-5-(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one  ligand  48  29  .  2022-08-11  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_VBD
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
 VBD  C4   C  CR6   0   0.514  -22.5325  -54.2792  33.5080
 VBD  C14  C  CH2   0  -0.489  -30.1219  -58.9010  35.2604
 VBD  C5   C  CR6   0   0.042  -21.7168  -53.4209  34.2306
 VBD  C6   C  CR6   0   0.480  -22.1933  -53.0768  35.4892
 VBD  C11  C  C     0   0.548  -28.6708  -59.5754  33.4405
 VBD  C7   C  CR6   0   0.585  -26.2202  -55.8430  35.4716
 VBD  C8   C  CR16  0  -0.093  -28.0110  -57.0815  36.0686
 VBD  C9   C  CR6   0   0.189  -27.9505  -57.7941  34.8940
 VBD  C10  C  CR6   0   0.582  -26.8979  -57.4505  34.0181
 VBD  C12  C  CH1   0  -0.254  -27.3194  -59.4575  32.7636
 VBD  C13  C  CH3   0  -0.651  -26.3766  -60.5213  33.3309
 VBD  N2   N  N     0  -0.481  -27.1525  -56.1111  36.3777
 VBD  C3   C  CR16  0  -0.522  -23.7365  -54.7694  33.9690
 VBD  N3   N  N     0  -0.525  -26.0643  -56.4617  34.3090
 VBD  C1   C  CR16  0  -0.528  -23.3849  -53.5378  35.9996
 VBD  C2   C  CR6   0   0.384  -24.1794  -54.4029  35.2408
 VBD  N4   N  NT    0  -0.567  -28.8963  -58.7503  34.4959
 VBD  N5   N  NT    0  -0.483  -26.7574  -58.1234  32.8628
 VBD  F1   F  F     0  -0.318  -21.4333  -52.2619  36.2404
 VBD  F2   F  F     0  -0.312  -22.1136  -54.6515  32.2908
 VBD  O2   O  OH1   0  -0.619  -20.5558  -52.9971  33.6962
 VBD  C15  C  CSP   0   0.265  -29.9252  -59.7120  36.4589
 VBD  C16  C  CSP1  0  -0.501  -29.7544  -60.3753  37.4454
 VBD  C17  C  CH2   0  -0.336  -25.7430  -57.7346  31.8910
 VBD  C18  C  CH1   0  -0.241  -26.1596  -56.5438  31.0709
 VBD  C19  C  CH2   0  -0.481  -27.1061  -56.7354  29.9271
 VBD  C20  C  CH2   0  -0.488  -25.6631  -56.4210  29.6642
 VBD  H1   H  HCH2  0   0.307  -30.5028  -57.9135  35.5296
 VBD  H2   H  HCH2  0   0.319  -30.8750  -59.3604  34.6221
 VBD  H3   H  HCR6  0   0.279  -28.7804  -57.2783  36.8064
 VBD  H4   H  HCH1  0   0.300  -27.4959  -59.6640  31.7070
 VBD  H5   H  HCH3  0   0.252  -26.7843  -61.5197  33.1787
 VBD  H6   H  HCH3  0   0.257  -25.4128  -60.4724  32.8244
 VBD  H7   H  HCH3  0   0.241  -26.2103  -60.3728  34.3987
 VBD  H8   H  HNH1  0   0.410  -25.5695  -54.4474  36.7278
 VBD  H9   H  HCR6  0   0.329  -24.3118  -55.4308  33.3417
 VBD  H10  H  HCR6  0   0.295  -23.6840  -53.2302  36.9943
 VBD  H11  H  HOH1  0   0.477  -20.1236  -52.3585  34.2749
 VBD  H12  H  H     0   0.283  -29.6026  -60.9707  38.3169
 VBD  H13  H  HCH2  0   0.264  -25.5782  -58.5900  31.2332
 VBD  H14  H  HCH2  0   0.263  -24.7946  -57.5422  32.3965
 VBD  H15  H  HCH1  0   0.261  -26.2580  -55.6194  31.6295
 VBD  H16  H  HCH2  0   0.250  -27.8435  -55.9663  29.7367
 VBD  H17  H  HCH2  0   0.246  -27.4502  -57.7413  29.7168
 VBD  H18  H  HCH2  0   0.245  -25.0349  -57.2138  29.2761
 VBD  H19  H  HCH2  0   0.252  -25.4083  -55.4354  29.2973
 VBD  N1   N  NH1   0  -0.776  -25.3647  -54.8337  35.8186
 VBD  O1   O  O     0  -0.453  -29.4728  -60.4119  33.0740

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
 VBD  C19  C20  single    1.500  0.020  1.500
 VBD  C19  C18  single    1.497  0.020  1.497
 VBD  C20  C18  single    1.497  0.020  1.497
 VBD  C18  C17  single    1.505  0.020  1.505
 VBD  F2   C4   single    1.340  0.020  1.340
 VBD  C17  N5   single    1.458  0.020  1.458
 VBD  C12  C13  single    1.531  0.020  1.531
 VBD  C12  N5   single    1.451  0.020  1.451
 VBD  C12  C11  single    1.516  0.020  1.516
 VBD  N5   C10  single    1.344  0.020  1.344
 VBD  O2   C5   single    1.347  0.020  1.347
 VBD  C4   C5   aromatic  1.387  0.020  1.387
 VBD  C4   C3   aromatic  1.379  0.020  1.379
 VBD  O1   C11  double    1.215  0.020  1.215
 VBD  C11  N4   single    1.358  0.020  1.358
 VBD  C5   C6   aromatic  1.389  0.020  1.389
 VBD  C3   C2   aromatic  1.396  0.020  1.396
 VBD  C10  N3   aromatic  1.326  0.020  1.326
 VBD  C10  C9   aromatic  1.412  0.020  1.412
 VBD  N3   C7   aromatic  1.326  0.020  1.326
 VBD  N4   C9   single    1.403  0.020  1.403
 VBD  N4   C14  single    1.452  0.020  1.452
 VBD  C9   C8   aromatic  1.375  0.020  1.375
 VBD  C6   F1   single    1.344  0.020  1.344
 VBD  C6   C1   aromatic  1.376  0.020  1.376
 VBD  C2   C1   aromatic  1.398  0.020  1.398
 VBD  C2   N1   single    1.387  0.020  1.387
 VBD  C14  C15  single    1.460  0.020  1.460
 VBD  C7   N1   single    1.368  0.020  1.368
 VBD  C7   N2   aromatic  1.327  0.020  1.327
 VBD  C8   N2   aromatic  1.332  0.020  1.332
 VBD  C15  C16  triple    1.201  0.020  1.201
 VBD  C14  H1   single    0.939  0.020  1.096
 VBD  C14  H2   single    0.939  0.020  1.096
 VBD  C8   H3   single    0.929  0.020  1.085
 VBD  C12  H4   single    0.939  0.020  1.096
 VBD  C13  H5   single    0.939  0.020  1.096
 VBD  C13  H6   single    0.939  0.020  1.096
 VBD  C13  H7   single    0.939  0.020  1.096
 VBD  N1   H8   single    0.868  0.020  1.013
 VBD  C3   H9   single    0.929  0.020  1.085
 VBD  C1   H10  single    0.929  0.020  1.085
 VBD  O2   H11  single    0.832  0.020  0.971
 VBD  C16  H12  single    0.913  0.020  1.066
 VBD  C17  H13  single    0.939  0.020  1.096
 VBD  C17  H14  single    0.939  0.020  1.096
 VBD  C18  H15  single    0.939  0.020  1.096
 VBD  C19  H16  single    0.939  0.020  1.096
 VBD  C19  H17  single    0.939  0.020  1.096
 VBD  C20  H18  single    0.939  0.020  1.096
 VBD  C20  H19  single    0.939  0.020  1.096

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
 VBD  F2   C4   C3   118.54  3.000
 VBD  C3   C4   C5   123.99  3.000
 VBD  F2   C4   C5   117.47  3.000
 VBD  H2   C14  H1   106.55  3.000
 VBD  H2   C14  C15  109.87  3.000
 VBD  H1   C14  C15  110.30  3.000
 VBD  H2   C14  N4   108.59  3.000
 VBD  H1   C14  N4   109.29  3.000
 VBD  C15  C14  N4   112.08  3.000
 VBD  O2   C5   C6   125.27  3.000
 VBD  C6   C5   C4   115.06  3.000
 VBD  O2   C5   C4   119.67  3.000
 VBD  F1   C6   C1   119.06  3.000
 VBD  C1   C6   C5   123.38  3.000
 VBD  F1   C6   C5   117.56  3.000
 VBD  O1   C11  N4   122.87  3.000
 VBD  N4   C11  C12  116.59  3.000
 VBD  O1   C11  C12  120.47  3.000
 VBD  N3   C7   N2   125.93  3.000
 VBD  N2   C7   N1   114.52  3.000
 VBD  N3   C7   N1   119.55  3.000
 VBD  H3   C8   N2   115.58  3.000
 VBD  H3   C8   C9   121.24  3.000
 VBD  N2   C8   C9   123.19  3.000
 VBD  N4   C9   C10  119.51  3.000
 VBD  N4   C9   C8   124.47  3.000
 VBD  C10  C9   C8   115.89  3.000
 VBD  N5   C10  N3   119.75  3.000
 VBD  N3   C10  C9   120.95  3.000
 VBD  N5   C10  C9   119.30  3.000
 VBD  H4   C12  N5   107.64  3.000
 VBD  H4   C12  C13  109.09  3.000
 VBD  N5   C12  C13  112.03  3.000
 VBD  H4   C12  C11  105.87  3.000
 VBD  N5   C12  C11  112.72  3.000
 VBD  C13  C12  C11  109.24  3.000
 VBD  H7   C13  H6   108.31  3.000
 VBD  H7   C13  H5   108.58  3.000
 VBD  H6   C13  H5   107.89  3.000
 VBD  H7   C13  C12  111.23  3.000
 VBD  H6   C13  C12  109.96  3.000
 VBD  H5   C13  C12  110.78  3.000
 VBD  C8   N2   C7   116.19  3.000
 VBD  H9   C3   C2   121.47  3.000
 VBD  H9   C3   C4   119.30  3.000
 VBD  C2   C3   C4   119.23  3.000
 VBD  C10  N3   C7   117.80  3.000
 VBD  H10  C1   C2   121.13  3.000
 VBD  H10  C1   C6   118.99  3.000
 VBD  C2   C1   C6   119.88  3.000
 VBD  C1   C2   C3   118.46  3.000
 VBD  C1   C2   N1   116.85  3.000
 VBD  C3   C2   N1   124.69  3.000
 VBD  C9   N4   C11  121.51  3.000
 VBD  C9   N4   C14  119.36  3.000
 VBD  C11  N4   C14  119.08  3.000
 VBD  C17  N5   C12  117.98  3.000
 VBD  C12  N5   C10  118.58  3.000
 VBD  C17  N5   C10  120.81  3.000
 VBD  H11  O2   C5   110.90  3.000
 VBD  C16  C15  C14  180.00  3.000
 VBD  H12  C16  C15  180.00  3.000
 VBD  H14  C17  H13  106.62  3.000
 VBD  H14  C17  C18  110.70  3.000
 VBD  H13  C17  C18  109.48  3.000
 VBD  H14  C17  N5   110.05  3.000
 VBD  H13  C17  N5   107.33  3.000
 VBD  C18  C17  N5   112.44  3.000
 VBD  H15  C18  C20  116.38  3.000
 VBD  H15  C18  C19  116.44  3.000
 VBD  C20  C18  C19   60.15  3.000
 VBD  H15  C18  C17  114.76  3.000
 VBD  C20  C18  C17  119.03  3.000
 VBD  C19  C18  C17  119.35  3.000
 VBD  H17  C19  H16  114.15  3.000
 VBD  H17  C19  C20  117.78  3.000
 VBD  H16  C19  C20  118.40  3.000
 VBD  H17  C19  C18  117.90  3.000
 VBD  H16  C19  C18  118.30  3.000
 VBD  C20  C19  C18   59.92  3.000
 VBD  H19  C20  H18  114.11  3.000
 VBD  H19  C20  C19  118.48  3.000
 VBD  H18  C20  C19  117.85  3.000
 VBD  H19  C20  C18  118.13  3.000
 VBD  H18  C20  C18  117.97  3.000
 VBD  C19  C20  C18   59.94  3.000
 VBD  H8   N1   C2   115.46  3.000
 VBD  H8   N1   C7   112.59  3.000
 VBD  C2   N1   C7   131.14  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
 VBD  CONST_01  C1   C6   C5   C4      0.00   0.0  0
 VBD  CONST_02  C1   C2   C3   C4      0.00   0.0  0
 VBD  CONST_03  C2   C3   C4   C5      0.00   0.0  0
 VBD  CONST_04  C2   C1   C6   C5      0.00   0.0  0
 VBD  CONST_05  C3   C4   C5   C6      0.00   0.0  0
 VBD  CONST_06  C3   C2   C1   C6      0.00   0.0  0
 VBD  CONST_07  C9   C10  N3   C7      0.00   0.0  0
 VBD  CONST_08  C9   C8   N2   C7      0.00   0.0  0
 VBD  CONST_09  N3   C10  C9   C8      0.00   0.0  0
 VBD  CONST_10  N3   C7   N2   C8      0.00   0.0  0
 VBD  CONST_11  N2   C7   N3   C10     0.00   0.0  0
 VBD  CONST_12  N2   C8   C9   C10     0.00   0.0  0
 VBD  CONST_13  C12  C11  N4   C9      0.00   0.0  0
 VBD  CONST_14  F1   C6   C5   C4    180.00   0.0  0
 VBD  CONST_15  N1   C2   C3   C4    180.00   0.0  0
 VBD  CONST_16  F2   C4   C5   C6    180.00   0.0  0
 VBD  CONST_17  N1   C2   C1   C6    180.00   0.0  0
 VBD  CONST_18  N1   C7   N2   C8    180.00   0.0  0
 VBD  CONST_19  N1   C7   N3   C10   180.00   0.0  0
 VBD  CONST_20  O2   C5   C4   C3    180.00   0.0  0
 VBD  CONST_21  O2   C5   C6   C1    180.00   0.0  0
 VBD  CONST_22  F2   C4   C3   C2    180.00   0.0  0
 VBD  CONST_23  F1   C6   C1   C2    180.00   0.0  0
 VBD  CONST_24  C12  C11  N4   C14   180.00   0.0  0
 VBD  CONST_25  O1   C11  N4   C9    180.00   0.0  0
 VBD  CONST_26  H9   C3   C4   C5    180.00   0.0  0
 VBD  CONST_27  H10  C1   C6   C5    180.00   0.0  0
 VBD  CONST_28  H3   C8   N2   C7    180.00   0.0  0
 VBD  CONST_29  O1   C11  N4   C14     0.00   0.0  0
 VBD  Var_01    C10  C9   N4   C11    15.39  30.0  1
 VBD  Var_02    C12  N5   C10  C9    -23.14  30.0  1
 VBD  Var_03    C3   C2   N1   C7     13.99  30.0  1
 VBD  Var_04    C18  C17  N5   C10   -78.95  30.0  1
 VBD  Var_05    C2   N1   C7   N2    169.66  30.0  2
 VBD  Var_06    C19  C18  C17  N5    -79.13  30.0  1
 VBD  Var_07    C20  C19  C18  C17  -108.61  30.0  1
 VBD  Var_08    H18  C20  C19  C18   107.88  30.0  1
 VBD  Var_09    C15  C14  N4   C11    96.75  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
 VBD  chir_01  C12  C13  N5   C11  positiv
 VBD  chir_02  C18  C19  C20  C17  both

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
 VBD  plan-1  C4   0.020
 VBD  plan-1  C5   0.020
 VBD  plan-1  C6   0.020
 VBD  plan-1  C3   0.020
 VBD  plan-1  C1   0.020
 VBD  plan-1  C2   0.020
 VBD  plan-1  F1   0.020
 VBD  plan-1  F2   0.020
 VBD  plan-1  O2   0.020
 VBD  plan-1  H9   0.020
 VBD  plan-1  H10  0.020
 VBD  plan-1  N1   0.020
 VBD  plan-2  C7   0.020
 VBD  plan-2  C8   0.020
 VBD  plan-2  C9   0.020
 VBD  plan-2  C10  0.020
 VBD  plan-2  N2   0.020
 VBD  plan-2  N3   0.020
 VBD  plan-2  N4   0.020
 VBD  plan-2  N5   0.020
 VBD  plan-2  H3   0.020
 VBD  plan-2  N1   0.020
 VBD  plan-3  C14  0.020
 VBD  plan-3  C11  0.020
 VBD  plan-3  C9   0.020
 VBD  plan-3  C12  0.020
 VBD  plan-3  N4   0.020
 VBD  plan-3  O1   0.020

