# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 15:27:10 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: 8-cyclopentyl-6-[3-(hydroxymethyl)phenyl]-4-methyl-2-(methylamino)pyrido[2,3-d]pyrimidin-7(8H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1nc(C)c2C=C(C(=O)N(C3CCCC3)c2n1)c4cccc(CO)c4
#
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
 ML8  ML8  8-cyclopentyl-6-[3-(hydroxymethyl)phenyl]-4-methyl-2-(methylamino)pyrido[2,3-d]pyrimidin-7(8H)-one  ligand  51  27  .  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_ML8
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
 ML8  C24   C  CR16  0  -0.233  -4.5974  -0.4370   1.6861
 ML8  C25   C  CR16  0  -0.298  -3.2229  -0.5189   1.5232
 ML8  C23   C  CR16  0  -0.300  -5.3539   0.3955   0.8722
 ML8  C21   C  CR16  0  -0.354  -3.3588   1.0750  -0.2635
 ML8  C14   C  CR6   0   0.120  -2.5838   0.2445   0.5455
 ML8  C1    C  CR66  0  -0.124   0.9909   1.3770   0.1271
 ML8  C22   C  CR6   0   0.110  -4.7380   1.1638  -0.1098
 ML8  C6    C  CR6   0   0.277   1.7919   2.5314   0.0502
 ML8  C2    C  CR66  0   0.573   1.6616   0.1450   0.0135
 ML8  C4    C  CR6   0   0.610   3.6344   1.2342  -0.2186
 ML8  C9    C  CR16  0  -0.216  -0.4125   1.3854   0.3149
 ML8  C10   C  CR6   0  -0.159  -1.1177   0.2336   0.3810
 ML8  C11   C  CR6   0   0.555  -0.4367  -1.0502   0.2433
 ML8  C16   C  CH2   0  -0.454   2.2427  -4.5466   0.5259
 ML8  C17   C  CH2   0  -0.455   2.1105  -4.4402  -1.0160
 ML8  C15   C  CH2   0  -0.439   1.5891  -3.2825   1.1069
 ML8  C18   C  CH2   0  -0.439   1.3344  -3.1462  -1.2931
 ML8  C8    C  CR15  0  -0.113   1.6708  -2.3037  -0.0644
 ML8  C19   C  CH3   0  -0.511   5.8262   2.3075  -0.4932
 ML8  C26   C  CH2   0  -0.231  -5.5547   2.0214  -1.0330
 ML8  N5    N  N     0  -0.487   3.0940   2.4618  -0.1216
 ML8  N3    N  N     0  -0.520   2.9694   0.0806  -0.1575
 ML8  N7    N  NR6   0  -0.626   0.9470  -1.0306   0.0790
 ML8  N20   N  NH1   0  -0.639   4.9574   1.1622  -0.3907
 ML8  O12   O  O     0  -0.465  -1.0434  -2.1093   0.2579
 ML8  O27   O  OH1   0  -0.668  -6.0190   1.2052  -2.0903
 ML8  H24   H  HCR6  0   0.256  -5.0819  -1.0211   2.4579
 ML8  H25   H  HCR6  0   0.249  -2.6455  -1.1569   2.1783
 ML8  H23   H  HCR6  0   0.252  -6.4274   0.4533   1.0090
 ML8  H21   H  HCR6  0   0.249  -2.8744   1.6603  -1.0378
 ML8  H9    H  HCR6  0   0.277  -0.9297   2.3313   0.4227
 ML8  H16   H  HCH2  0   0.233   1.7680  -5.4478   0.9132
 ML8  H16A  H  HCH2  0   0.231   3.2945  -4.6014   0.8101
 ML8  H17   H  HCH2  0   0.230   3.0996  -4.3905  -1.4736
 ML8  H17A  H  HCH2  0   0.234   1.6098  -5.3076  -1.4457
 ML8  H15   H  HCH2  0   0.241   0.5569  -3.4827   1.3859
 ML8  H15A  H  HCH2  0   0.235   2.1091  -2.9083   1.9902
 ML8  H18   H  HCH2  0   0.235   1.6449  -2.6616  -2.2203
 ML8  H18A  H  HCH2  0   0.240   0.2658  -3.3424  -1.3581
 ML8  H8    H  HCR5  0   0.286   2.7147  -2.0154  -0.1592
 ML8  H13   H  HCH3  0   0.263   0.6769   4.0200   1.1164
 ML8  H13A  H  HCH3  0   0.268   1.9553   4.6562   0.0736
 ML8  H13B  H  HCH3  0   0.263   0.4442   4.0600  -0.6231
 ML8  H19   H  HCH3  0   0.239   5.7618   2.9439   0.3892
 ML8  H19A  H  HCH3  0   0.253   6.8468   1.9469  -0.5816
 ML8  H26   H  HCH2  0   0.210  -6.3887   2.4650  -0.4764
 ML8  H26A  H  HCH2  0   0.208  -4.9396   2.8497  -1.4050
 ML8  HO27  H  HOH1  0   0.455  -6.5760   1.7469  -2.6581
 ML8  H231  H  HCH3  0   0.236   5.6016   2.9170  -1.3697
 ML8  H241  H  HNH1  0   0.402   5.3537   0.2420  -0.4823
 ML8  C13   C  CH3   0  -0.760   1.1857   3.8938   0.1597

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
 ML8  C24  H24   single    0.930  0.020  1.080
 ML8  C25  C24   aromatic  1.387  0.020  1.387
 ML8  C25  H25   single    0.930  0.020  1.080
 ML8  C23  C24   aromatic  1.388  0.020  1.388
 ML8  C23  H23   single    0.930  0.020  1.080
 ML8  C21  C22   aromatic  1.391  0.020  1.391
 ML8  C21  C14   aromatic  1.395  0.020  1.395
 ML8  C21  H21   single    0.930  0.020  1.080
 ML8  C14  C25   aromatic  1.395  0.020  1.395
 ML8  C1   C9    single    1.416  0.020  1.416
 ML8  C1   C2    aromatic  1.407  0.020  1.407
 ML8  C22  C23   aromatic  1.391  0.020  1.391
 ML8  C6   C1    aromatic  1.407  0.020  1.407
 ML8  C2   N7    single    1.377  0.020  1.377
 ML8  C4   N3    aromatic  1.333  0.020  1.333
 ML8  C9   C10   double    1.352  0.020  1.352
 ML8  C9   H9    single    0.930  0.020  1.080
 ML8  C10  C14   single    1.475  0.020  1.475
 ML8  C10  C11   single    1.460  0.020  1.460
 ML8  C11  O12   double    1.221  0.020  1.221
 ML8  C16  C17   single    1.551  0.020  1.551
 ML8  C16  H16   single    0.970  0.020  1.090
 ML8  C16  H16A  single    0.970  0.020  1.090
 ML8  C17  H17   single    0.970  0.020  1.090
 ML8  C17  H17A  single    0.970  0.020  1.090
 ML8  C15  C16   single    1.537  0.020  1.537
 ML8  C15  C8    single    1.529  0.020  1.529
 ML8  C15  H15   single    0.970  0.020  1.090
 ML8  C15  H15A  single    0.970  0.020  1.090
 ML8  C18  C17   single    1.534  0.020  1.534
 ML8  C18  H18   single    0.970  0.020  1.090
 ML8  C18  H18A  single    0.970  0.020  1.090
 ML8  C8   C18   single    1.527  0.020  1.527
 ML8  C8   H8    single    0.970  0.020  1.090
 ML8  C13  C6    single    1.495  0.020  1.495
 ML8  C13  H13   single    0.970  0.020  1.090
 ML8  C13  H13A  single    0.970  0.020  1.090
 ML8  C13  H13B  single    0.970  0.020  1.090
 ML8  C19  H19   single    0.970  0.020  1.090
 ML8  C19  H19A  single    0.970  0.020  1.090
 ML8  C26  C22   single    1.502  0.020  1.502
 ML8  C26  H26   single    0.970  0.020  1.090
 ML8  C26  H26A  single    0.970  0.020  1.090
 ML8  N5   C6    aromatic  1.315  0.020  1.315
 ML8  N5   C4    aromatic  1.345  0.020  1.345
 ML8  N3   C2    aromatic  1.320  0.020  1.320
 ML8  N7   C11   single    1.393  0.020  1.393
 ML8  N7   C8    single    1.472  0.020  1.472
 ML8  N20  C4    single    1.336  0.020  1.336
 ML8  N20  C19   single    1.441  0.020  1.441
 ML8  O27  C26   single    1.414  0.020  1.414
 ML8  O27  HO27  single    0.850  0.020  0.980
 ML8  C19  H231  single    0.970  0.020  1.090
 ML8  N20  H241  single    0.860  0.020  1.020

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
 ML8  H24   C24  C23   119.85  3.000
 ML8  C23   C24  C25   120.45  3.000
 ML8  H24   C24  C25   119.71  3.000
 ML8  H25   C25  C14   120.18  3.000
 ML8  C14   C25  C24   120.26  3.000
 ML8  H25   C25  C24   119.54  3.000
 ML8  H23   C23  C22   119.89  3.000
 ML8  C22   C23  C24   120.26  3.000
 ML8  H23   C23  C24   119.85  3.000
 ML8  H21   C21  C22   119.17  3.000
 ML8  H21   C21  C14   119.16  3.000
 ML8  C22   C21  C14   121.67  3.000
 ML8  C10   C14  C21   119.47  3.000
 ML8  C10   C14  C25   121.95  3.000
 ML8  C21   C14  C25   118.54  3.000
 ML8  C9    C1   C2    119.23  3.000
 ML8  C2    C1   C6    116.26  3.000
 ML8  C9    C1   C6    124.51  3.000
 ML8  C26   C22  C21   120.53  3.000
 ML8  C26   C22  C23   120.58  3.000
 ML8  C21   C22  C23   118.82  3.000
 ML8  N5    C6   C13   117.33  3.000
 ML8  N5    C6   C1    121.82  3.000
 ML8  C13   C6   C1    120.85  3.000
 ML8  N7    C2   N3    118.58  3.000
 ML8  N3    C2   C1    121.68  3.000
 ML8  N7    C2   C1    119.74  3.000
 ML8  N20   C4   N3    116.95  3.000
 ML8  N20   C4   N5    117.15  3.000
 ML8  N3    C4   N5    125.89  3.000
 ML8  H9    C9   C10   119.33  3.000
 ML8  H9    C9   C1    119.45  3.000
 ML8  C10   C9   C1    121.22  3.000
 ML8  C11   C10  C9    120.08  3.000
 ML8  C11   C10  C14   118.73  3.000
 ML8  C9    C10  C14   121.16  3.000
 ML8  O12   C11  N7    120.48  3.000
 ML8  N7    C11  C10   117.51  3.000
 ML8  O12   C11  C10   122.01  3.000
 ML8  H16A  C16  H16   106.61  3.000
 ML8  H16A  C16  C15   110.66  3.000
 ML8  H16   C16  C15   111.13  3.000
 ML8  C15   C16  C17   106.44  3.000
 ML8  H16A  C16  C17   110.16  3.000
 ML8  H16   C16  C17   111.89  3.000
 ML8  H17A  C17  H17   106.70  3.000
 ML8  H17A  C17  C18   111.57  3.000
 ML8  H17   C17  C18   110.15  3.000
 ML8  C18   C17  C16   106.29  3.000
 ML8  H17A  C17  C16   112.12  3.000
 ML8  H17   C17  C16   110.04  3.000
 ML8  H15A  C15  H15   107.92  3.000
 ML8  H15A  C15  C8    112.04  3.000
 ML8  H15   C15  C8    111.41  3.000
 ML8  H15A  C15  C16   112.66  3.000
 ML8  H15   C15  C16   110.44  3.000
 ML8  C8    C15  C16   102.37  3.000
 ML8  H18A  C18  H18   107.98  3.000
 ML8  H18A  C18  C8    111.33  3.000
 ML8  H18   C18  C8    112.08  3.000
 ML8  C8    C18  C17   102.04  3.000
 ML8  H18A  C18  C17   110.82  3.000
 ML8  H18   C18  C17   112.58  3.000
 ML8  H8    C8   N7    104.56  3.000
 ML8  N7    C8   C18   116.57  3.000
 ML8  H8    C8   C18   106.72  3.000
 ML8  N7    C8   C15   116.94  3.000
 ML8  H8    C8   C15   106.74  3.000
 ML8  C18   C8   C15   104.57  3.000
 ML8  H231  C19  H19A  108.27  3.000
 ML8  H231  C19  H19   108.19  3.000
 ML8  H19A  C19  H19   108.38  3.000
 ML8  H231  C19  N20   112.15  3.000
 ML8  H19A  C19  N20   107.96  3.000
 ML8  H19   C19  N20   111.77  3.000
 ML8  H26A  C26  H26   107.06  3.000
 ML8  H26A  C26  O27   111.49  3.000
 ML8  H26   C26  O27   111.31  3.000
 ML8  O27   C26  C22   107.97  3.000
 ML8  H26A  C26  C22   109.56  3.000
 ML8  H26   C26  C22   109.43  3.000
 ML8  C4    N5   C6    117.10  3.000
 ML8  C4    N3   C2    117.25  3.000
 ML8  C8    N7   C11   119.19  3.000
 ML8  C8    N7   C2    118.60  3.000
 ML8  C11   N7   C2    122.20  3.000
 ML8  H241  N20  C19   118.87  3.000
 ML8  H241  N20  C4    116.82  3.000
 ML8  C19   N20  C4    124.28  3.000
 ML8  HO27  O27  C26   107.83  3.000
 ML8  H13B  C13  H13A  108.52  3.000
 ML8  H13B  C13  H13   107.13  3.000
 ML8  H13A  C13  H13   108.58  3.000
 ML8  H13B  C13  C6    111.21  3.000
 ML8  H13A  C13  C6    110.26  3.000
 ML8  H13   C13  C6    111.02  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
 ML8  CONST_01  C21   C14  C25  C24     0.00   0.0  0
 ML8  CONST_02  C21   C22  C23  C24     0.00   0.0  0
 ML8  CONST_03  C22   C23  C24  C25     0.00   0.0  0
 ML8  CONST_04  C22   C21  C14  C25     0.00   0.0  0
 ML8  CONST_05  C14   C25  C24  C23     0.00   0.0  0
 ML8  CONST_06  C14   C21  C22  C23     0.00   0.0  0
 ML8  CONST_07  C4    N3   C2   C1      0.00   0.0  0
 ML8  CONST_08  C4    N5   C6   C1      0.00   0.0  0
 ML8  CONST_09  N3    C2   C1   C6      0.00   0.0  0
 ML8  CONST_10  N3    C4   N5   C6      0.00   0.0  0
 ML8  CONST_11  N5    C6   C1   C2      0.00   0.0  0
 ML8  CONST_12  N5    C4   N3   C2      0.00   0.0  0
 ML8  CONST_13  C10   C14  C25  C24   180.00   0.0  0
 ML8  CONST_14  C10   C14  C21  C22   180.00   0.0  0
 ML8  CONST_15  C10   C11  N7   C2      0.00   0.0  0
 ML8  CONST_16  C8    N7   C11  C10   180.00   0.0  0
 ML8  CONST_17  C26   C22  C23  C24   180.00   0.0  0
 ML8  CONST_18  C26   C22  C21  C14   180.00   0.0  0
 ML8  CONST_19  N20   C4   N5   C6    180.00   0.0  0
 ML8  CONST_20  C13   C6   C1   C2    180.00   0.0  0
 ML8  CONST_21  N20   C4   N3   C2    180.00   0.0  0
 ML8  CONST_22  C13   C6   N5   C4    180.00   0.0  0
 ML8  CONST_23  C13   C6   C1   C9      0.00   0.0  0
 ML8  CONST_24  O12   C11  N7   C2    180.00   0.0  0
 ML8  CONST_25  O12   C11  N7   C8      0.00   0.0  0
 ML8  CONST_26  H23   C23  C24  C25   180.00   0.0  0
 ML8  CONST_27  H21   C21  C14  C25   180.00   0.0  0
 ML8  CONST_28  H25   C25  C24  C23   180.00   0.0  0
 ML8  CONST_29  H24   C24  C25  C14   180.00   0.0  0
 ML8  CONST_30  N3    C4   N20  C19   180.00   0.0  0
 ML8  CONST_31  N5    C4   N20  C19     0.00   0.0  0
 ML8  CONST_32  H241  N20  C4   N5    180.00   0.0  0
 ML8  Var_01    C9    C10  C14  C25  -129.86  30.0  2
 ML8  Var_02    C8    C18  C17  C16    26.64  30.0  1
 ML8  Var_03    C8    C15  C16  C17   -23.11  30.0  1
 ML8  Var_04    C18   C17  C16  C15    -2.21  30.0  1
 ML8  Var_05    O27   C26  C22  C23   -83.46  30.0  3
 ML8  Var_06    H13   C13  C6   C1     59.86  30.0  2
 ML8  Var_07    H19   C19  N20  C4     58.31  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
 ML8  chir_01  C8  C15  C18  N7  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
 ML8  plan-1  C24   0.020
 ML8  plan-1  C25   0.020
 ML8  plan-1  C23   0.020
 ML8  plan-1  C21   0.020
 ML8  plan-1  C14   0.020
 ML8  plan-1  C22   0.020
 ML8  plan-1  C10   0.020
 ML8  plan-1  C26   0.020
 ML8  plan-1  H24   0.020
 ML8  plan-1  H25   0.020
 ML8  plan-1  H23   0.020
 ML8  plan-1  H21   0.020
 ML8  plan-2  C14   0.020
 ML8  plan-2  C1    0.020
 ML8  plan-2  C6    0.020
 ML8  plan-2  C2    0.020
 ML8  plan-2  C4    0.020
 ML8  plan-2  C9    0.020
 ML8  plan-2  C10   0.020
 ML8  plan-2  C11   0.020
 ML8  plan-2  C8    0.020
 ML8  plan-2  N5    0.020
 ML8  plan-2  N3    0.020
 ML8  plan-2  N7    0.020
 ML8  plan-2  N20   0.020
 ML8  plan-2  O12   0.020
 ML8  plan-2  H9    0.020
 ML8  plan-2  C13   0.020
 ML8  plan-3  C4    0.020
 ML8  plan-3  C19   0.020
 ML8  plan-3  N20   0.020
 ML8  plan-3  H241  0.020

