# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 17:02:40 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: 2-amino-8-[trans-4-(2-hydroxyethoxy)cyclohexyl]-6-(6-methoxypyridin-3-yl)-4-methylpyrido[2,3-d]pyrimidin-7(8H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cn1)C2=Cc3c(C)nc(N)nc3N([C@H]4CC[C@@H](CC4)OCCO)C2=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
 ML9  ML9  2-amino-8-[trans-4-(2-hydroxyethoxy)cyclohexyl]-6-(6-methoxypyridin-3-yl)-4-methylpyrido[2,3-d]pyrimidin-7(8H)-one  ligand  58  31  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_ML9
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
 ML9  C14   C  CR16  0  -0.186   4.2917  -0.8801  -1.0081
 ML9  C15   C  CR16  0  -0.386   5.2472  -1.8704  -1.0070
 ML9  C18   C  CR16  0  -0.072   3.1336  -2.0638   0.6857
 ML9  C13   C  CR6   0  -0.009   3.1925  -0.9535  -0.1444
 ML9  C5    C  CR66  0  -0.113   1.6002   2.4629  -0.0167
 ML9  C6    C  CR6   0   0.272   1.9055   3.8381   0.0124
 ML9  C4    C  CR66  0   0.575   0.2349   2.1299   0.0030
 ML9  C16   C  CR6   0   0.530   5.0740  -2.9389  -0.1210
 ML9  C2    C  CR6   0   0.569  -0.3113   4.3253   0.0646
 ML9  C10   C  CR16  0  -0.222   2.5635   1.4260  -0.0465
 ML9  C9    C  CR6   0  -0.156   2.1938   0.1253  -0.0893
 ML9  C8    C  CR6   0   0.557   0.7779  -0.2282  -0.1281
 ML9  C23   C  CH2   0  -0.444  -2.1290  -0.0141  -1.3119
 ML9  C27   C  CH2   0  -0.441  -1.9854  -0.4229   1.1840
 ML9  C24   C  CH2   0  -0.471  -3.6490  -0.1338  -1.2321
 ML9  C26   C  CH2   0  -0.480  -3.5094  -0.5060   1.2447
 ML9  C22   C  CH1   0  -0.089  -1.5864   0.4867   0.0239
 ML9  C25   C  CH1   0   0.100  -4.0780  -1.0256  -0.0752
 ML9  C20   C  CH3   0  -0.416   5.8540  -4.9800   0.7800
 ML9  C30   C  CH2   0  -0.183  -7.5332  -2.1680   0.4840
 ML9  N17   N  N     0  -0.461   4.0483  -3.0290   0.6994
 ML9  N1    N  N     0  -0.482   0.9654   4.7551   0.0504
 ML9  N3    N  N     0  -0.512  -0.7080   3.0567   0.0426
 ML9  N7    N  NR6   0  -0.627  -0.1450   0.8081  -0.0202
 ML9  N12   N  NH2   0  -0.813  -1.2566   5.2679   0.1020
 ML9  O11   O  O     0  -0.468   0.4012  -1.3831  -0.2524
 ML9  O31   O  OH1   0  -0.672  -7.8312  -2.4803  -0.8574
 ML9  O19   O  O2    0  -0.473   6.0043  -3.8952  -0.1243
 ML9  O28   O  O2    0  -0.501  -5.4888  -1.0778  -0.0746
 ML9  H14   H  HCR6  0   0.268   4.3890  -0.0461  -1.6923
 ML9  H15   H  HCR6  0   0.274   6.1004  -1.8334  -1.6705
 ML9  H18   H  HCR6  0   0.258   2.3201  -2.1804   1.3914
 ML9  H10   H  HCR6  0   0.277   3.6167   1.6793  -0.0221
 ML9  H23   H  HCH2  0   0.237  -1.6929  -0.9800  -1.5692
 ML9  H23A  H  HCH2  0   0.242  -1.8591   0.6861  -2.1060
 ML9  H27   H  HCH2  0   0.242  -1.5978  -0.0183   2.1217
 ML9  H27A  H  HCH2  0   0.241  -1.5765  -1.4257   1.0689
 ML9  H24   H  HCH2  0   0.223  -4.0880   0.8612  -1.1005
 ML9  H24A  H  HCH2  0   0.242  -4.0379  -0.5330  -2.1716
 ML9  H26   H  HCH2  0   0.243  -3.7971  -1.1562   2.0746
 ML9  H26A  H  HCH2  0   0.222  -3.9324   0.4836   1.4507
 ML9  H22   H  HCH1  0   0.276  -2.0638   1.4457   0.2153
 ML9  H25   H  HCH1  0   0.193  -3.6741  -2.0371  -0.2504
 ML9  H21   H  HCH3  0   0.263   3.8499   3.9496  -0.8864
 ML9  H21A  H  HCH3  0   0.269   3.3638   5.3933   0.0112
 ML9  H21B  H  HCH3  0   0.264   3.8679   3.9329   0.8695
 ML9  H20   H  HCH3  0   0.229   5.8498  -4.6447   1.8180
 ML9  H20A  H  HCH3  0   0.229   4.9394  -5.5434   0.5912
 ML9  H20B  H  HCH3  0   0.246   6.7133  -5.6251   0.6152
 ML9  H30   H  HCH2  0   0.201  -7.9333  -2.9182   1.1782
 ML9  H30A  H  HCH2  0   0.200  -7.9606  -1.2015   0.7816
 ML9  H29   H  HCH2  0   0.204  -5.8416  -2.0183   1.7494
 ML9  H29A  H  HCH2  0   0.200  -5.5996  -3.0955   0.3735
 ML9  HN12  H  HNH2  0   0.406  -2.2296   5.0187   0.1121
 ML9  HN1A  H  HNH2  0   0.406  -1.0038   6.2398   0.1144
 ML9  HO31  H  HOH1  0   0.455  -8.7867  -2.4748  -0.9600
 ML9  C21   C  CH3   0  -0.762   3.3247   4.3071   0.0004
 ML9  C29   C  CH2   0  -0.170  -6.0380  -2.1329   0.6759

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
 ML9  C13  C14   aromatic  1.400  0.020  1.400
 ML9  C14  C15   aromatic  1.376  0.020  1.376
 ML9  C14  H14   single    0.930  0.020  1.080
 ML9  C16  C15   aromatic  1.399  0.020  1.399
 ML9  C15  H15   single    0.930  0.020  1.080
 ML9  C18  N17   aromatic  1.330  0.020  1.330
 ML9  C18  C13   aromatic  1.388  0.020  1.388
 ML9  C18  H18   single    0.930  0.020  1.080
 ML9  C9   C13   single    1.471  0.020  1.471
 ML9  C6   C5    aromatic  1.409  0.020  1.409
 ML9  C5   C4    aromatic  1.405  0.020  1.405
 ML9  C5   C10   single    1.416  0.020  1.416
 ML9  C21  C6    single    1.495  0.020  1.495
 ML9  N1   C6    aromatic  1.314  0.020  1.314
 ML9  N3   C4    aromatic  1.323  0.020  1.323
 ML9  C4   N7    single    1.376  0.020  1.376
 ML9  N17  C16   aromatic  1.317  0.020  1.317
 ML9  C16  O19   single    1.334  0.020  1.334
 ML9  N12  C2    single    1.335  0.020  1.335
 ML9  N1   C2    aromatic  1.347  0.020  1.347
 ML9  C2   N3    aromatic  1.329  0.020  1.329
 ML9  C10  C9    double    1.353  0.020  1.353
 ML9  C10  H10   single    0.930  0.020  1.080
 ML9  C9   C8    single    1.460  0.020  1.460
 ML9  N7   C8    single    1.392  0.020  1.392
 ML9  C8   O11   double    1.221  0.020  1.221
 ML9  C23  C22   single    1.526  0.020  1.526
 ML9  C23  C24   single    1.527  0.020  1.527
 ML9  C23  H23   single    0.970  0.020  1.090
 ML9  C23  H23A  single    0.970  0.020  1.090
 ML9  C22  C27   single    1.527  0.020  1.527
 ML9  C27  C26   single    1.527  0.020  1.527
 ML9  C27  H27   single    0.970  0.020  1.090
 ML9  C27  H27A  single    0.970  0.020  1.090
 ML9  C24  C25   single    1.522  0.020  1.522
 ML9  C24  H24   single    0.970  0.020  1.090
 ML9  C24  H24A  single    0.970  0.020  1.090
 ML9  C25  C26   single    1.528  0.020  1.528
 ML9  C26  H26   single    0.970  0.020  1.090
 ML9  C26  H26A  single    0.970  0.020  1.090
 ML9  N7   C22   single    1.477  0.020  1.477
 ML9  C22  H22   single    0.970  0.020  1.090
 ML9  C25  O28   single    1.412  0.020  1.412
 ML9  C25  H25   single    0.970  0.020  1.090
 ML9  C21  H21   single    0.970  0.020  1.090
 ML9  C21  H21A  single    0.970  0.020  1.090
 ML9  C21  H21B  single    0.970  0.020  1.090
 ML9  C20  O19   single    1.420  0.020  1.420
 ML9  C20  H20   single    0.970  0.020  1.090
 ML9  C20  H20A  single    0.970  0.020  1.090
 ML9  C20  H20B  single    0.970  0.020  1.090
 ML9  O31  C30   single    1.409  0.020  1.409
 ML9  C29  C30   single    1.508  0.020  1.508
 ML9  C30  H30   single    0.970  0.020  1.090
 ML9  C30  H30A  single    0.970  0.020  1.090
 ML9  O28  C29   single    1.406  0.020  1.406
 ML9  C29  H29   single    0.970  0.020  1.090
 ML9  C29  H29A  single    0.970  0.020  1.090
 ML9  N12  HN12  single    0.860  0.020  1.020
 ML9  N12  HN1A  single    0.860  0.020  1.020
 ML9  O31  HO31  single    0.850  0.020  0.980

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
 ML9  H14   C14  C13   120.04  3.000
 ML9  H14   C14  C15   119.48  3.000
 ML9  C13   C14  C15   120.47  3.000
 ML9  H15   C15  C16   120.82  3.000
 ML9  H15   C15  C14   121.52  3.000
 ML9  C16   C15  C14   117.66  3.000
 ML9  H18   C18  N17   115.58  3.000
 ML9  H18   C18  C13   120.52  3.000
 ML9  N17   C18  C13   123.90  3.000
 ML9  C9    C13  C18   122.38  3.000
 ML9  C9    C13  C14   121.18  3.000
 ML9  C18   C13  C14   116.39  3.000
 ML9  C10   C5   C4    119.20  3.000
 ML9  C10   C5   C6    124.60  3.000
 ML9  C4    C5   C6    116.19  3.000
 ML9  N1    C6   C21   117.43  3.000
 ML9  N1    C6   C5    121.79  3.000
 ML9  C21   C6   C5    120.78  3.000
 ML9  N7    C4   N3    118.49  3.000
 ML9  N7    C4   C5    119.72  3.000
 ML9  N3    C4   C5    121.80  3.000
 ML9  O19   C16  N17   119.72  3.000
 ML9  O19   C16  C15   117.36  3.000
 ML9  N17   C16  C15   122.92  3.000
 ML9  N12   C2   N3    117.57  3.000
 ML9  N3    C2   N1    125.95  3.000
 ML9  N12   C2   N1    116.49  3.000
 ML9  H10   C10  C9    119.41  3.000
 ML9  H10   C10  C5    119.32  3.000
 ML9  C9    C10  C5    121.26  3.000
 ML9  C8    C9   C10   119.91  3.000
 ML9  C8    C9   C13   118.68  3.000
 ML9  C10   C9   C13   121.38  3.000
 ML9  O11   C8   N7    120.50  3.000
 ML9  O11   C8   C9    122.07  3.000
 ML9  N7    C8   C9    117.44  3.000
 ML9  H23A  C23  H23   107.30  3.000
 ML9  H23A  C23  C22   109.75  3.000
 ML9  H23   C23  C22   110.79  3.000
 ML9  H23A  C23  C24   109.52  3.000
 ML9  H23   C23  C24   109.94  3.000
 ML9  C22   C23  C24   109.51  3.000
 ML9  H27A  C27  H27   107.37  3.000
 ML9  H27A  C27  C22   111.72  3.000
 ML9  H27   C27  C22   109.80  3.000
 ML9  H27A  C27  C26   109.19  3.000
 ML9  H27   C27  C26   109.88  3.000
 ML9  C22   C27  C26   108.86  3.000
 ML9  H24A  C24  H24   107.01  3.000
 ML9  H24A  C24  C25   109.83  3.000
 ML9  H24   C24  C25   109.14  3.000
 ML9  H24A  C24  C23   109.76  3.000
 ML9  H24   C24  C23   109.51  3.000
 ML9  C25   C24  C23   111.48  3.000
 ML9  H26A  C26  H26   107.04  3.000
 ML9  H26A  C26  C25   109.02  3.000
 ML9  H26   C26  C25   110.84  3.000
 ML9  H26A  C26  C27   110.09  3.000
 ML9  H26   C26  C27   108.97  3.000
 ML9  C25   C26  C27   110.82  3.000
 ML9  H22   C22  N7    103.98  3.000
 ML9  H22   C22  C27   106.06  3.000
 ML9  N7    C22  C27   114.02  3.000
 ML9  H22   C22  C23   106.69  3.000
 ML9  N7    C22  C23   113.08  3.000
 ML9  C27   C22  C23   112.11  3.000
 ML9  H25   C25  O28   109.39  3.000
 ML9  H25   C25  C26   108.22  3.000
 ML9  O28   C25  C26   112.58  3.000
 ML9  H25   C25  C24   108.25  3.000
 ML9  O28   C25  C24   107.68  3.000
 ML9  C26   C25  C24   110.63  3.000
 ML9  H20B  C20  H20A  109.27  3.000
 ML9  H20B  C20  H20   109.26  3.000
 ML9  H20A  C20  H20   108.67  3.000
 ML9  H20B  C20  O19   105.85  3.000
 ML9  H20A  C20  O19   111.90  3.000
 ML9  H20   C20  O19   111.81  3.000
 ML9  H30A  C30  H30   106.76  3.000
 ML9  H30A  C30  O31   111.76  3.000
 ML9  H30   C30  O31   111.93  3.000
 ML9  H30A  C30  C29   109.33  3.000
 ML9  H30   C30  C29   107.27  3.000
 ML9  O31   C30  C29   109.63  3.000
 ML9  C16   N17  C18   118.67  3.000
 ML9  C2    N1   C6    117.11  3.000
 ML9  C2    N3   C4    117.16  3.000
 ML9  C22   N7   C8    119.16  3.000
 ML9  C22   N7   C4    118.55  3.000
 ML9  C8    N7   C4    122.25  3.000
 ML9  HN1A  N12  HN12  118.93  3.000
 ML9  HN1A  N12  C2    120.34  3.000
 ML9  HN12  N12  C2    120.72  3.000
 ML9  HO31  O31  C30   108.10  3.000
 ML9  C20   O19  C16   118.18  3.000
 ML9  C29   O28  C25   114.72  3.000
 ML9  H21B  C21  H21A  108.47  3.000
 ML9  H21B  C21  H21   107.18  3.000
 ML9  H21A  C21  H21   108.56  3.000
 ML9  H21B  C21  C6    111.02  3.000
 ML9  H21A  C21  C6    110.34  3.000
 ML9  H21   C21  C6    111.15  3.000
 ML9  H29A  C29  H29   106.80  3.000
 ML9  H29A  C29  O28   110.74  3.000
 ML9  H29   C29  O28   111.95  3.000
 ML9  H29A  C29  C30   109.87  3.000
 ML9  H29   C29  C30   107.72  3.000
 ML9  O28   C29  C30   109.68  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
 ML9  CONST_01  N17   C18  C13  C14     0.00   0.0  0
 ML9  CONST_02  N17   C16  C15  C14     0.00   0.0  0
 ML9  CONST_03  C18   C13  C14  C15     0.00   0.0  0
 ML9  CONST_04  C18   N17  C16  C15     0.00   0.0  0
 ML9  CONST_05  C16   C15  C14  C13     0.00   0.0  0
 ML9  CONST_06  C16   N17  C18  C13     0.00   0.0  0
 ML9  CONST_07  C2    N1   C6   C5      0.00   0.0  0
 ML9  CONST_08  C2    N3   C4   C5      0.00   0.0  0
 ML9  CONST_09  N3    C4   C5   C6      0.00   0.0  0
 ML9  CONST_10  N3    C2   N1   C6      0.00   0.0  0
 ML9  CONST_11  N1    C6   C5   C4      0.00   0.0  0
 ML9  CONST_12  N1    C2   N3   C4      0.00   0.0  0
 ML9  CONST_13  C9    C13  C14  C15   180.00   0.0  0
 ML9  CONST_14  N17   C18  C13  C9    180.00   0.0  0
 ML9  CONST_15  C9    C8   N7   C4      0.00   0.0  0
 ML9  CONST_16  C22   N7   C8   C9    180.00   0.0  0
 ML9  CONST_17  O19   C16  C15  C14   180.00   0.0  0
 ML9  CONST_18  O19   C16  N17  C18   180.00   0.0  0
 ML9  CONST_19  N12   C2   N1   C6    180.00   0.0  0
 ML9  CONST_20  C21   C6   C5   C4    180.00   0.0  0
 ML9  CONST_21  N12   C2   N3   C4    180.00   0.0  0
 ML9  CONST_22  C21   C6   N1   C2    180.00   0.0  0
 ML9  CONST_23  C21   C6   C5   C10     0.00   0.0  0
 ML9  CONST_24  O11   C8   N7   C4    180.00   0.0  0
 ML9  CONST_25  O11   C8   N7   C22     0.00   0.0  0
 ML9  CONST_26  H18   C18  C13  C14   180.00   0.0  0
 ML9  CONST_27  H14   C14  C13  C18   180.00   0.0  0
 ML9  CONST_28  H15   C15  C14  C13   180.00   0.0  0
 ML9  CONST_29  HN12  N12  C2   N1    180.00   0.0  0
 ML9  CONST_30  HN1A  N12  C2   N1      0.00   0.0  0
 ML9  Var_01    C10   C9   C13  C14   -45.16  30.0  2
 ML9  Var_02    C25   C24  C23  C22   -55.65  30.0  1
 ML9  Var_03    C25   C26  C27  C22    57.81  30.0  1
 ML9  Var_04    N17   C16  O19  C20    -0.62  30.0  1
 ML9  Var_05    H21   C21  C6   C5     58.64  30.0  2
 ML9  Var_06    C30   C29  O28  C25  -174.18  30.0  3
 ML9  Var_07    H20   C20  O19  C16   -60.67  30.0  3
 ML9  Var_08    O28   C29  C30  O31    65.18  30.0  2

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
 ML9  chir_01  C22  C23  C27  N7   negativ
 ML9  chir_02  C25  O28  C24  C26  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
 ML9  plan-1  C14   0.020
 ML9  plan-1  C15   0.020
 ML9  plan-1  C18   0.020
 ML9  plan-1  C13   0.020
 ML9  plan-1  C16   0.020
 ML9  plan-1  C9    0.020
 ML9  plan-1  N17   0.020
 ML9  plan-1  O19   0.020
 ML9  plan-1  H14   0.020
 ML9  plan-1  H15   0.020
 ML9  plan-1  H18   0.020
 ML9  plan-2  C13   0.020
 ML9  plan-2  C5    0.020
 ML9  plan-2  C6    0.020
 ML9  plan-2  C4    0.020
 ML9  plan-2  C2    0.020
 ML9  plan-2  C10   0.020
 ML9  plan-2  C9    0.020
 ML9  plan-2  C8    0.020
 ML9  plan-2  C22   0.020
 ML9  plan-2  N1    0.020
 ML9  plan-2  N3    0.020
 ML9  plan-2  N7    0.020
 ML9  plan-2  N12   0.020
 ML9  plan-2  O11   0.020
 ML9  plan-2  H10   0.020
 ML9  plan-2  C21   0.020
 ML9  plan-3  C2    0.020
 ML9  plan-3  N12   0.020
 ML9  plan-3  HN12  0.020
 ML9  plan-3  HN1A  0.020

