# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 19:44:40 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: 6-(2,4-difluorophenoxy)-8-methyl-2-{[(1S)-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
 FMK  FMK  6-(2,4-difluorophenoxy)-8-methyl-2-{[(1S)-1-methyl-2-(2H-tetrazol-2-yl)ethyl]amino}pyrido[2,3-d]pyrimidin-7(8H)-one  ligand  46  30  .  2021-08-09  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_FMK
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
 FMK  C21   C  CR6   0   0.491  -5.4648  -0.0309   0.2792
 FMK  C20   C  CR16  0  -0.561  -6.3380   0.9996   0.0072
 FMK  C24   C  CH3   0  -0.536  -0.1156  -0.9757  -2.7725
 FMK  C18   C  CR16  0  -0.415  -4.4926   2.5502   0.1875
 FMK  C6    C  CR16  0  -0.029   1.4025  -1.0715   1.7676
 FMK  C2    C  CH1   0  -0.126   5.2492  -1.3816   0.2694
 FMK  C3    C  CH2   0  -0.273   6.0498  -0.1012   0.0184
 FMK  C4    C  CR6   0   0.620   2.7883  -1.2190  -0.0074
 FMK  C11   C  CR6   0   0.530  -1.7815  -0.9027  -0.9748
 FMK  C12   C  CR6   0   0.140  -2.0419  -0.8760   0.4634
 FMK  C13   C  CR16  0  -0.227  -1.0558  -0.9019   1.3757
 FMK  C16   C  CR6   0   0.216  -4.1150   0.1935   0.5201
 FMK  C17   C  CR16  0  -0.309  -3.6377   1.4927   0.4731
 FMK  C8    C  CR66  0  -0.115   0.2899  -0.9926   0.9326
 FMK  C9    C  CR66  0   0.558   0.5749  -1.0259  -0.4439
 FMK  C19   C  CR6   0   0.529  -5.8268   2.2842  -0.0365
 FMK  F23   F  F     0  -0.312  -6.6627   3.2952  -0.3137
 FMK  F22   F  F     0  -0.300  -5.9230  -1.2851   0.3189
 FMK  O15   O  O2    0  -0.493  -3.3520  -0.8896   0.8367
 FMK  O14   O  O     0  -0.453  -2.6841  -0.8811  -1.7924
 FMK  N10   N  NR6   0  -0.587  -0.4469  -0.9528  -1.3521
 FMK  N5    N  N     0  -0.502   1.8058  -1.1320  -0.9061
 FMK  N7    N  N     0  -0.462   2.6331  -1.1854   1.3271
 FMK  C30   C  CH3   0  -0.651   6.0962  -2.6011  -0.0631
 FMK  N25   N  NR5   0  -0.080   5.2500   1.0731   0.2905
 FMK  N29   N  N     0  -0.252   4.9562   1.4742   1.5015
 FMK  C28   C  CR15  0   0.075   4.1635   2.4965   1.2638
 FMK  N27   N  N     0  -0.320   3.9890   2.6950  -0.0493
 FMK  N26   N  N     0  -0.063   4.6837   1.7795  -0.6453
 FMK  H20   H  HCR6  0   0.309  -7.3865   0.8017  -0.1741
 FMK  H24   H  HCH3  0   0.271  -1.0126  -0.7849  -3.3480
 FMK  H24A  H  HCH3  0   0.262   0.6229  -0.2096  -2.9915
 FMK  H24B  H  HCH3  0   0.260   0.2916  -1.9455  -3.0513
 FMK  H18   H  HCR6  0   0.290  -4.1196   3.5649   0.1598
 FMK  H6    H  HCR6  0   0.282   1.2661  -1.0400   2.8444
 FMK  H2    H  HCH1  0   0.285   4.9749  -1.4133   1.3228
 FMK  H3    H  HCH2  0   0.296   6.9305  -0.0685   0.6573
 FMK  H3A   H  HCH2  0   0.286   6.3742  -0.0372  -1.0193
 FMK  H13   H  HCR6  0   0.293  -1.2757  -0.8774   2.4364
 FMK  H17   H  HCR6  0   0.298  -2.5919   1.6952   0.6662
 FMK  HN1   H  HNH1  0   0.399   4.1067  -1.3405  -1.5070
 FMK  H30   H  HCH3  0   0.252   5.5537  -3.5124   0.1839
 FMK  H30A  H  HCH3  0   0.233   6.3534  -2.6346  -1.1230
 FMK  H30B  H  HCH3  0   0.242   7.0231  -2.5929   0.5104
 FMK  H28   H  HCR5  0   0.299   3.7163   3.1001   2.0359
 FMK  N1    N  NH1   0  -0.647   4.0290  -1.3658  -0.5007

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
 FMK  C21  C20   aromatic  1.378  0.020  1.378
 FMK  C21  C16   aromatic  1.389  0.020  1.389
 FMK  C21  F22   single    1.336  0.020  1.336
 FMK  C20  C19   aromatic  1.383  0.020  1.383
 FMK  C24  N10   single    1.459  0.020  1.459
 FMK  C18  C17   aromatic  1.389  0.020  1.389
 FMK  C18  C19   aromatic  1.379  0.020  1.379
 FMK  C6   C8    aromatic  1.393  0.020  1.393
 FMK  C6   N7    aromatic  1.312  0.020  1.312
 FMK  C2   C3    single    1.531  0.020  1.531
 FMK  C2   N1    single    1.443  0.020  1.443
 FMK  C2   C30   single    1.522  0.020  1.522
 FMK  C3   N25   single    1.447  0.020  1.447
 FMK  C4   N1    single    1.343  0.020  1.343
 FMK  C4   N5    aromatic  1.334  0.020  1.334
 FMK  C4   N7    aromatic  1.344  0.020  1.344
 FMK  C11  C12   single    1.462  0.020  1.462
 FMK  C11  O14   double    1.218  0.020  1.218
 FMK  C11  N10   single    1.388  0.020  1.388
 FMK  C12  C13   double    1.344  0.020  1.344
 FMK  C12  O15   single    1.362  0.020  1.362
 FMK  C13  C8    single    1.420  0.020  1.420
 FMK  C16  C17   aromatic  1.385  0.020  1.385
 FMK  C16  O15   single    1.362  0.020  1.362
 FMK  C8   C9    aromatic  1.406  0.020  1.406
 FMK  C9   N10   single    1.369  0.020  1.369
 FMK  C9   N5    aromatic  1.319  0.020  1.319
 FMK  C19  F23   single    1.341  0.020  1.341
 FMK  N25  N29   aromatic  1.309  0.020  1.309
 FMK  N25  N26   aromatic  1.302  0.020  1.302
 FMK  N29  C28   aromatic  1.315  0.020  1.315
 FMK  C28  N27   aromatic  1.339  0.020  1.339
 FMK  N27  N26   aromatic  1.295  0.020  1.295
 FMK  C20  H20   single    0.930  0.020  1.080
 FMK  C24  H24   single    0.970  0.020  1.090
 FMK  C24  H24A  single    0.970  0.020  1.090
 FMK  C24  H24B  single    0.970  0.020  1.090
 FMK  C18  H18   single    0.930  0.020  1.080
 FMK  C6   H6    single    0.930  0.020  1.080
 FMK  C2   H2    single    0.970  0.020  1.090
 FMK  C3   H3    single    0.970  0.020  1.090
 FMK  C3   H3A   single    0.970  0.020  1.090
 FMK  C13  H13   single    0.930  0.020  1.080
 FMK  C17  H17   single    0.930  0.020  1.080
 FMK  N1   HN1   single    0.860  0.020  1.020
 FMK  C30  H30   single    0.970  0.020  1.090
 FMK  C30  H30A  single    0.970  0.020  1.090
 FMK  C30  H30B  single    0.970  0.020  1.090
 FMK  C28  H28   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
 FMK  F22   C21  C16   118.66  3.000
 FMK  F22   C21  C20   119.38  3.000
 FMK  C16   C21  C20   121.95  3.000
 FMK  H20   C20  C19   121.50  3.000
 FMK  H20   C20  C21   120.69  3.000
 FMK  C19   C20  C21   117.81  3.000
 FMK  H24B  C24  H24A  108.81  3.000
 FMK  H24B  C24  H24   109.32  3.000
 FMK  H24A  C24  H24   109.38  3.000
 FMK  H24B  C24  N10   110.40  3.000
 FMK  H24A  C24  N10   109.85  3.000
 FMK  H24   C24  N10   109.07  3.000
 FMK  H18   C18  C19   120.70  3.000
 FMK  H18   C18  C17   120.47  3.000
 FMK  C19   C18  C17   118.81  3.000
 FMK  H6    C6   N7    116.96  3.000
 FMK  H6    C6   C8    119.49  3.000
 FMK  N7    C6   C8    123.56  3.000
 FMK  H2    C2   C30   109.17  3.000
 FMK  H2    C2   N1    107.67  3.000
 FMK  C30   C2   N1    111.28  3.000
 FMK  H2    C2   C3    108.35  3.000
 FMK  C30   C2   C3    110.08  3.000
 FMK  N1    C2   C3    110.22  3.000
 FMK  H3A   C3   H3    108.45  3.000
 FMK  H3A   C3   N25   107.23  3.000
 FMK  H3    C3   N25   108.21  3.000
 FMK  H3A   C3   C2    111.18  3.000
 FMK  H3    C3   C2    110.61  3.000
 FMK  N25   C3   C2    111.04  3.000
 FMK  N7    C4   N5    125.60  3.000
 FMK  N7    C4   N1    118.30  3.000
 FMK  N5    C4   N1    116.10  3.000
 FMK  N10   C11  O14   122.06  3.000
 FMK  N10   C11  C12   116.06  3.000
 FMK  O14   C11  C12   121.88  3.000
 FMK  O15   C12  C13   121.30  3.000
 FMK  O15   C12  C11   116.15  3.000
 FMK  C13   C12  C11   122.47  3.000
 FMK  H13   C13  C8    119.95  3.000
 FMK  H13   C13  C12   121.02  3.000
 FMK  C8    C13  C12   119.02  3.000
 FMK  O15   C16  C17   124.10  3.000
 FMK  O15   C16  C21   117.14  3.000
 FMK  C17   C16  C21   118.72  3.000
 FMK  H17   C17  C16   120.16  3.000
 FMK  H17   C17  C18   119.25  3.000
 FMK  C16   C17  C18   120.59  3.000
 FMK  C9    C8   C13   119.94  3.000
 FMK  C9    C8   C6    115.05  3.000
 FMK  C13   C8   C6    125.00  3.000
 FMK  N5    C9   N10   117.93  3.000
 FMK  N5    C9   C8    122.28  3.000
 FMK  N10   C9   C8    119.79  3.000
 FMK  F23   C19  C18   119.43  3.000
 FMK  F23   C19  C20   118.45  3.000
 FMK  C18   C19  C20   122.12  3.000
 FMK  C16   O15  C12   117.85  3.000
 FMK  C9    N10  C11   122.65  3.000
 FMK  C9    N10  C24   118.40  3.000
 FMK  C11   N10  C24   118.92  3.000
 FMK  C9    N5   C4    117.15  3.000
 FMK  C4    N7   C6    116.35  3.000
 FMK  H30B  C30  H30A  108.11  3.000
 FMK  H30B  C30  H30   108.09  3.000
 FMK  H30A  C30  H30   108.18  3.000
 FMK  H30B  C30  C2    110.63  3.000
 FMK  H30A  C30  C2    111.60  3.000
 FMK  H30   C30  C2    110.11  3.000
 FMK  N26   N25  N29   113.64  3.000
 FMK  N26   N25  C3    123.07  3.000
 FMK  N29   N25  C3    123.14  3.000
 FMK  C28   N29  N25   101.90  3.000
 FMK  H28   C28  N27   124.44  3.000
 FMK  H28   C28  N29   123.79  3.000
 FMK  N27   C28  N29   111.77  3.000
 FMK  N26   N27  C28   106.05  3.000
 FMK  N27   N26  N25   106.63  3.000
 FMK  HN1   N1   C4    115.75  3.000
 FMK  HN1   N1   C2    117.85  3.000
 FMK  C4    N1   C2    125.89  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
 FMK  CONST_01  C18  C19  C20  C21    0.00   0.0  0
 FMK  CONST_02  C18  C17  C16  C21    0.00   0.0  0
 FMK  CONST_03  C17  C16  C21  C20    0.00   0.0  0
 FMK  CONST_04  C17  C18  C19  C20    0.00   0.0  0
 FMK  CONST_05  N5   C9   C8   C6     0.00   0.0  0
 FMK  CONST_06  N5   C4   N7   C6     0.00   0.0  0
 FMK  CONST_07  C8   C9   N5   C4     0.00   0.0  0
 FMK  CONST_08  C8   C6   N7   C4     0.00   0.0  0
 FMK  CONST_09  C19  C20  C21  C16    0.00   0.0  0
 FMK  CONST_10  C19  C18  C17  C16    0.00   0.0  0
 FMK  CONST_11  N7   C6   C8   C9     0.00   0.0  0
 FMK  CONST_12  N7   C4   N5   C9     0.00   0.0  0
 FMK  CONST_13  N27  C28  N29  N25    0.00   0.0  0
 FMK  CONST_14  C28  N27  N26  N25    0.00   0.0  0
 FMK  CONST_15  N27  N26  N25  N29    0.00   0.0  0
 FMK  CONST_16  N26  N27  C28  N29    0.00   0.0  0
 FMK  CONST_17  N26  N25  N29  C28    0.00   0.0  0
 FMK  CONST_18  C9   N10  C11  C12    0.00   0.0  0
 FMK  CONST_19  F23  C19  C20  C21  180.00   0.0  0
 FMK  CONST_20  O15  C16  C21  C20  180.00   0.0  0
 FMK  CONST_21  O15  C16  C17  C18  180.00   0.0  0
 FMK  CONST_22  N1   C4   N7   C6   180.00   0.0  0
 FMK  CONST_23  C28  N29  N25  C3   180.00   0.0  0
 FMK  CONST_24  N27  N26  N25  C3   180.00   0.0  0
 FMK  CONST_25  F23  C19  C18  C17  180.00   0.0  0
 FMK  CONST_26  F22  C21  C16  C17  180.00   0.0  0
 FMK  CONST_27  N1   C4   N5   C9   180.00   0.0  0
 FMK  CONST_28  F22  C21  C20  C19  180.00   0.0  0
 FMK  CONST_29  C12  C11  N10  C24  180.00   0.0  0
 FMK  CONST_30  O14  C11  N10  C9   180.00   0.0  0
 FMK  CONST_31  H17  C17  C16  C21  180.00   0.0  0
 FMK  CONST_32  H18  C18  C19  C20  180.00   0.0  0
 FMK  CONST_33  H20  C20  C19  C18  180.00   0.0  0
 FMK  CONST_34  H6   C6   N7   C4   180.00   0.0  0
 FMK  CONST_35  H28  C28  N29  N25  180.00   0.0  0
 FMK  CONST_36  N5   C4   N1   C2   180.00   0.0  0
 FMK  CONST_37  N7   C4   N1   C2     0.00   0.0  0
 FMK  CONST_38  O14  C11  N10  C24    0.00   0.0  0
 FMK  CONST_39  HN1  N1   C4   N5     0.00   0.0  0
 FMK  Var_01    C17  C16  O15  C12  -33.29  30.0  2
 FMK  Var_02    N29  N25  C3   C2    74.48  30.0  2
 FMK  Var_03    H24  C24  N10  C11    9.20  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
 FMK  chir_01  C2  C3  N1  C30  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
 FMK  plan-1  C3   0.020
 FMK  plan-1  N25  0.020
 FMK  plan-1  N29  0.020
 FMK  plan-1  C28  0.020
 FMK  plan-1  N27  0.020
 FMK  plan-1  N26  0.020
 FMK  plan-1  H28  0.020
 FMK  plan-2  C21  0.020
 FMK  plan-2  C20  0.020
 FMK  plan-2  C18  0.020
 FMK  plan-2  C16  0.020
 FMK  plan-2  C17  0.020
 FMK  plan-2  C19  0.020
 FMK  plan-2  F23  0.020
 FMK  plan-2  F22  0.020
 FMK  plan-2  O15  0.020
 FMK  plan-2  H20  0.020
 FMK  plan-2  H18  0.020
 FMK  plan-2  H17  0.020
 FMK  plan-3  C24  0.020
 FMK  plan-3  C6   0.020
 FMK  plan-3  C4   0.020
 FMK  plan-3  C11  0.020
 FMK  plan-3  C12  0.020
 FMK  plan-3  C13  0.020
 FMK  plan-3  C8   0.020
 FMK  plan-3  C9   0.020
 FMK  plan-3  O15  0.020
 FMK  plan-3  O14  0.020
 FMK  plan-3  N10  0.020
 FMK  plan-3  N5   0.020
 FMK  plan-3  N7   0.020
 FMK  plan-3  H6   0.020
 FMK  plan-3  H13  0.020
 FMK  plan-3  N1   0.020
 FMK  plan-4  C2   0.020
 FMK  plan-4  C4   0.020
 FMK  plan-4  HN1  0.020
 FMK  plan-4  N1   0.020

