# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 04:20:51 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: 6-(2,4-difluorophenoxy)-8-methyl-2-{[(1R)-1-methyl-2-(2H-tetrazol-2-yl)ethyl]amino}pyrido[2,3-d]pyrimidin-7(8H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](Cn1ncnn1)Nc2ncc3C=C(Oc4ccc(F)cc4F)C(=O)N(C)c3n2
#
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
 533  533  6-(2,4-difluorophenoxy)-8-methyl-2-{[(1R)-1-methyl-2-(2H-tetrazol-2-yl)ethyl]amino}pyrido[2,3-d]pyrimidin-7(8H)-one  ligand  46  30  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_533
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
 533  F23   F  F     0  -0.311  -6.4929  -3.3792  -0.8008
 533  C19   C  CR6   0   0.529  -5.6624  -2.4238  -0.3625
 533  C18   C  CR16  0  -0.417  -4.3063  -2.6680  -0.3207
 533  C17   C  CR16  0  -0.308  -3.4591  -1.6681   0.1389
 533  C20   C  CR16  0  -0.562  -6.2011  -1.2140   0.0367
 533  C21   C  CR6   0   0.491  -5.3365  -0.2358   0.4770
 533  F22   F  F     0  -0.299  -5.8235   0.9467   0.8601
 533  C16   C  CR6   0   0.215  -3.9641  -0.4419   0.5367
 533  O15   O  O2    0  -0.491  -3.2055   0.5741   1.0332
 533  C12   C  CR6   0   0.142  -1.9289   0.6993   0.5785
 533  C11   C  CR6   0   0.530  -1.7751   0.9967  -0.8458
 533  O14   O  O     0  -0.451  -2.7318   1.0883  -1.5915
 533  N10   N  NR6   0  -0.587  -0.4721   1.1673  -1.2938
 533  C24   C  CH3   0  -0.538  -0.2456   1.4450  -2.7059
 533  C9    C  CR66  0   0.557   0.6090   1.1323  -0.4559
 533  N5    N  N     0  -0.498   1.8022   1.3457  -0.9778
 533  C13   C  CR16  0  -0.234  -0.8824   0.6419   1.4188
 533  C8    C  CR66  0  -0.110   0.4241   0.8788   0.9149
 533  C6    C  CR16  0  -0.033   1.5872   0.8907   1.6808
 533  N7    N  N     0  -0.461   2.7800   1.1090   1.1807
 533  C4    C  CR6   0   0.619   2.8399   1.3134  -0.1432
 533  N1    N  NH1   0  -0.645   4.0522   1.5170  -0.6905
 533  C2    C  CH1   0  -0.118   5.3114   1.4370   0.0089
 533  C26   C  CH3   0  -0.669   6.3267   2.3576  -0.6497
 533  C3    C  CH2   0  -0.261   5.8608   0.0049   0.0414
 533  N25   N  NR5   0  -0.080   4.9326  -0.9292   0.6353
 533  N30   N  N     0  -0.253   4.0093  -1.5640  -0.0464
 533  C29   C  CR15  0   0.065   3.3575  -2.1877   0.9105
 533  N28   N  N     0  -0.314   3.8760  -1.9350   2.1193
 533  N27   N  N     0  -0.058   4.8683  -1.1334   1.9207
 533  H18   H  HCR6  0   0.290  -3.9077  -3.6224  -0.6340
 533  H17   H  HCR6  0   0.297  -2.3949  -1.8591   0.1836
 533  H20   H  HCR6  0   0.308  -7.2665  -1.0316  -0.0009
 533  H24   H  HCH3  0   0.270  -1.1721   1.3036  -3.2476
 533  H24A  H  HCH3  0   0.260   0.0960   2.4688  -2.8452
 533  H24B  H  HCH3  0   0.262   0.5077   0.7703  -3.1011
 533  H13   H  HCR6  0   0.293  -1.0310   0.4389   2.4723
 533  H6    H  HCR6  0   0.282   1.5297   0.7169   2.7508
 533  HN1   H  HNH1  0   0.398   4.0677   1.6116  -1.6928
 533  H2    H  HCH1  0   0.275   5.1490   1.7613   1.0369
 533  H26   H  HCH3  0   0.249   7.2739   2.3351  -0.1133
 533  H26A  H  HCH3  0   0.237   6.5260   2.0667  -1.6831
 533  H26B  H  HCH3  0   0.256   5.9659   3.3843  -0.6489
 533  H3    H  HCH2  0   0.282   6.0862  -0.3521  -0.9627
 533  H3A   H  HCH2  0   0.290   6.7775  -0.0289   0.6272
 533  H29   H  HCR5  0   0.297   2.5125  -2.8312   0.7339

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
 533  F23  C19   single    1.340  0.020  1.340
 533  C19  C18   aromatic  1.378  0.020  1.378
 533  C19  C20   aromatic  1.383  0.020  1.383
 533  C18  C17   aromatic  1.389  0.020  1.389
 533  C17  C16   aromatic  1.385  0.020  1.385
 533  C20  C21   aromatic  1.378  0.020  1.378
 533  C21  F22   single    1.335  0.020  1.335
 533  C21  C16   aromatic  1.389  0.020  1.389
 533  C16  O15   single    1.362  0.020  1.362
 533  O15  C12   single    1.361  0.020  1.361
 533  C12  C11   single    1.463  0.020  1.463
 533  C12  C13   double    1.343  0.020  1.343
 533  C11  O14   double    1.216  0.020  1.216
 533  C11  N10   single    1.388  0.020  1.388
 533  N10  C24   single    1.457  0.020  1.457
 533  N10  C9    single    1.368  0.020  1.368
 533  C9   N5    aromatic  1.320  0.020  1.320
 533  C9   C8    aromatic  1.406  0.020  1.406
 533  N5   C4    aromatic  1.332  0.020  1.332
 533  C13  C8    single    1.420  0.020  1.420
 533  C8   C6    aromatic  1.393  0.020  1.393
 533  C6   N7    aromatic  1.312  0.020  1.312
 533  N7   C4    aromatic  1.341  0.020  1.341
 533  C4   N1    single    1.346  0.020  1.346
 533  N1   C2    single    1.443  0.020  1.443
 533  C2   C26   single    1.521  0.020  1.521
 533  C2   C3    single    1.534  0.020  1.534
 533  C3   N25   single    1.445  0.020  1.445
 533  N25  N30   aromatic  1.312  0.020  1.312
 533  N25  N27   aromatic  1.303  0.020  1.303
 533  N30  C29   aromatic  1.315  0.020  1.315
 533  C29  N28   aromatic  1.339  0.020  1.339
 533  N28  N27   aromatic  1.291  0.020  1.291
 533  C18  H18   single    0.930  0.020  1.080
 533  C17  H17   single    0.930  0.020  1.080
 533  C20  H20   single    0.930  0.020  1.080
 533  C24  H24   single    0.970  0.020  1.090
 533  C24  H24A  single    0.970  0.020  1.090
 533  C24  H24B  single    0.970  0.020  1.090
 533  C13  H13   single    0.930  0.020  1.080
 533  C6   H6    single    0.930  0.020  1.080
 533  N1   HN1   single    0.860  0.020  1.020
 533  C2   H2    single    0.970  0.020  1.090
 533  C26  H26   single    0.970  0.020  1.090
 533  C26  H26A  single    0.970  0.020  1.090
 533  C26  H26B  single    0.970  0.020  1.090
 533  C3   H3    single    0.970  0.020  1.090
 533  C3   H3A   single    0.970  0.020  1.090
 533  C29  H29   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
 533  C20   C19  C18   121.97  3.000
 533  C20   C19  F23   118.47  3.000
 533  C18   C19  F23   119.56  3.000
 533  H18   C18  C17   120.45  3.000
 533  H18   C18  C19   120.70  3.000
 533  C17   C18  C19   118.85  3.000
 533  H17   C17  C16   120.21  3.000
 533  H17   C17  C18   119.11  3.000
 533  C16   C17  C18   120.68  3.000
 533  H20   C20  C21   120.63  3.000
 533  H20   C20  C19   121.41  3.000
 533  C21   C20  C19   117.95  3.000
 533  C16   C21  F22   118.65  3.000
 533  C16   C21  C20   121.90  3.000
 533  F22   C21  C20   119.45  3.000
 533  O15   C16  C21   117.09  3.000
 533  O15   C16  C17   124.22  3.000
 533  C21   C16  C17   118.65  3.000
 533  C12   O15  C16   117.99  3.000
 533  C13   C12  C11   122.39  3.000
 533  C13   C12  O15   121.18  3.000
 533  C11   C12  O15   116.27  3.000
 533  N10   C11  O14   122.07  3.000
 533  N10   C11  C12   115.96  3.000
 533  O14   C11  C12   121.96  3.000
 533  C9    N10  C24   118.40  3.000
 533  C9    N10  C11   122.74  3.000
 533  C24   N10  C11   118.82  3.000
 533  H24B  C24  H24A  108.68  3.000
 533  H24B  C24  H24   109.30  3.000
 533  H24A  C24  H24   109.12  3.000
 533  H24B  C24  N10   110.01  3.000
 533  H24A  C24  N10   110.62  3.000
 533  H24   C24  N10   109.10  3.000
 533  C8    C9   N5    122.25  3.000
 533  C8    C9   N10   119.84  3.000
 533  N5    C9   N10   117.91  3.000
 533  C4    N5   C9    116.91  3.000
 533  H13   C13  C8    120.17  3.000
 533  H13   C13  C12   120.64  3.000
 533  C8    C13  C12   119.18  3.000
 533  C6    C8   C13   125.07  3.000
 533  C6    C8   C9    115.13  3.000
 533  C13   C8   C9    119.79  3.000
 533  H6    C6   N7    116.78  3.000
 533  H6    C6   C8    119.77  3.000
 533  N7    C6   C8    123.44  3.000
 533  C4    N7   C6    116.26  3.000
 533  N1    C4   N7    117.70  3.000
 533  N1    C4   N5    116.32  3.000
 533  N7    C4   N5    125.98  3.000
 533  HN1   N1   C2    118.32  3.000
 533  HN1   N1   C4    115.65  3.000
 533  C2    N1   C4    125.51  3.000
 533  H2    C2   C3    108.12  3.000
 533  H2    C2   C26   109.14  3.000
 533  C3    C2   C26   109.58  3.000
 533  H2    C2   N1    108.10  3.000
 533  C3    C2   N1    112.00  3.000
 533  C26   C2   N1    109.83  3.000
 533  H26B  C26  H26A  108.21  3.000
 533  H26B  C26  H26   107.91  3.000
 533  H26A  C26  H26   107.57  3.000
 533  H26B  C26  C2    110.46  3.000
 533  H26A  C26  C2    111.75  3.000
 533  H26   C26  C2    110.79  3.000
 533  H3A   C3   H3    108.16  3.000
 533  H3A   C3   N25   107.45  3.000
 533  H3    C3   N25   107.46  3.000
 533  H3A   C3   C2    110.00  3.000
 533  H3    C3   C2    111.13  3.000
 533  N25   C3   C2    112.47  3.000
 533  N27   N25  N30   113.71  3.000
 533  N27   N25  C3    122.59  3.000
 533  N30   N25  C3    123.48  3.000
 533  C29   N30  N25   101.55  3.000
 533  H29   C29  N28   124.38  3.000
 533  H29   C29  N30   123.58  3.000
 533  N28   C29  N30   112.05  3.000
 533  N27   N28  C29   106.01  3.000
 533  N28   N27  N25   106.68  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
 533  CONST_01  C16  C17  C18  C19    0.00   0.0  0
 533  CONST_02  C16  C21  C20  C19    0.00   0.0  0
 533  CONST_03  C21  C20  C19  C18    0.00   0.0  0
 533  CONST_04  C21  C16  C17  C18    0.00   0.0  0
 533  CONST_05  C20  C19  C18  C17    0.00   0.0  0
 533  CONST_06  C20  C21  C16  C17    0.00   0.0  0
 533  CONST_07  N7   C4   N5   C9     0.00   0.0  0
 533  CONST_08  N7   C6   C8   C9     0.00   0.0  0
 533  CONST_09  C6   C8   C9   N5     0.00   0.0  0
 533  CONST_10  C6   N7   C4   N5     0.00   0.0  0
 533  CONST_11  C4   N5   C9   C8     0.00   0.0  0
 533  CONST_12  C4   N7   C6   C8     0.00   0.0  0
 533  CONST_13  N28  C29  N30  N25    0.00   0.0  0
 533  CONST_14  C29  N28  N27  N25    0.00   0.0  0
 533  CONST_15  N28  N27  N25  N30    0.00   0.0  0
 533  CONST_16  N27  N28  C29  N30    0.00   0.0  0
 533  CONST_17  N27  N25  N30  C29    0.00   0.0  0
 533  CONST_18  C9   N10  C11  C12    0.00   0.0  0
 533  CONST_19  C17  C18  C19  F23  180.00   0.0  0
 533  CONST_20  C21  C20  C19  F23  180.00   0.0  0
 533  CONST_21  F22  C21  C20  C19  180.00   0.0  0
 533  CONST_22  O15  C16  C17  C18  180.00   0.0  0
 533  CONST_23  F22  C21  C16  C17  180.00   0.0  0
 533  CONST_24  O15  C16  C21  C20  180.00   0.0  0
 533  CONST_25  N1   C4   N5   C9   180.00   0.0  0
 533  CONST_26  N1   C4   N7   C6   180.00   0.0  0
 533  CONST_27  C29  N30  N25  C3   180.00   0.0  0
 533  CONST_28  N28  N27  N25  C3   180.00   0.0  0
 533  CONST_29  C24  N10  C11  C12  180.00   0.0  0
 533  CONST_30  C9   N10  C11  O14  180.00   0.0  0
 533  CONST_31  H17  C17  C18  C19  180.00   0.0  0
 533  CONST_32  H20  C20  C19  C18  180.00   0.0  0
 533  CONST_33  H18  C18  C19  C20  180.00   0.0  0
 533  CONST_34  H6   C6   C8   C9   180.00   0.0  0
 533  CONST_35  H29  C29  N30  N25  180.00   0.0  0
 533  CONST_36  C2   N1   C4   N5   180.00   0.0  0
 533  CONST_37  C2   N1   C4   N7     0.00   0.0  0
 533  CONST_38  C24  N10  C11  O14    0.00   0.0  0
 533  CONST_39  HN1  N1   C4   N5     0.00   0.0  0
 533  Var_01    C11  C12  O15  C16   63.57  30.0  3
 533  Var_02    N30  N25  C3   C2    88.36  30.0  2
 533  Var_03    H24  C24  N10  C11   -9.94  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
 533  chir_01  C2  N1  C26  C3  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
 533  plan-1  C3   0.020
 533  plan-1  N25  0.020
 533  plan-1  N30  0.020
 533  plan-1  C29  0.020
 533  plan-1  N28  0.020
 533  plan-1  N27  0.020
 533  plan-1  H29  0.020
 533  plan-2  F23  0.020
 533  plan-2  C19  0.020
 533  plan-2  C18  0.020
 533  plan-2  C17  0.020
 533  plan-2  C20  0.020
 533  plan-2  C21  0.020
 533  plan-2  F22  0.020
 533  plan-2  C16  0.020
 533  plan-2  O15  0.020
 533  plan-2  H18  0.020
 533  plan-2  H17  0.020
 533  plan-2  H20  0.020
 533  plan-3  O15  0.020
 533  plan-3  C12  0.020
 533  plan-3  C11  0.020
 533  plan-3  O14  0.020
 533  plan-3  N10  0.020
 533  plan-3  C24  0.020
 533  plan-3  C9   0.020
 533  plan-3  N5   0.020
 533  plan-3  C13  0.020
 533  plan-3  C8   0.020
 533  plan-3  C6   0.020
 533  plan-3  N7   0.020
 533  plan-3  C4   0.020
 533  plan-3  N1   0.020
 533  plan-3  H13  0.020
 533  plan-3  H6   0.020
 533  plan-4  C4   0.020
 533  plan-4  N1   0.020
 533  plan-4  C2   0.020
 533  plan-4  HN1  0.020

