# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 18 07:52:54 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: 2-amino-6-(5-fluoro-6-methoxypyridin-3-yl)-4-methyl-8-(pyrrolidin-1-yl)pyrido[2,3-d]pyrimidin-7(8H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ncc(cc1F)C2=Cc3c(C)nc(N)nc3N(N4CCCC4)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
 0TB  0TB  2-amino-6-(5-fluoro-6-methoxypyridin-3-yl)-4-methyl-8-(pyrrolidin-1-yl)pyrido[2,3-d]pyrimidin-7(8H)-one  ligand  46  27  .  2022-03-09  2022-03-09
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_0TB
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
 0TB  N1   N  N     0  -0.479   3.5992  -2.6817  -0.0847
 0TB  N3   N  N     0  -0.463   3.5390  -0.2942   0.0022
 0TB  C4   C  CR66  0   0.555   2.2223  -0.3435  -0.0254
 0TB  C5   C  CR66  0  -0.123   1.5080  -1.5522  -0.0796
 0TB  C6   C  CR6   0   0.276   2.2869  -2.7263  -0.1123
 0TB  C8   C  CH3   0  -0.761   1.6436  -4.0732  -0.1907
 0TB  C13  C  CR6   0  -0.153  -0.5948  -0.3539  -0.1015
 0TB  C15  C  CR6   0   0.007  -2.0656  -0.3335  -0.1146
 0TB  C17  C  CR6   0   0.400  -4.1598  -1.1932   0.6427
 0TB  C20  C  CR16  0  -0.081  -2.7983   0.4919  -0.9541
 0TB  C22  C  CH3   0  -0.419  -6.8021   0.5421  -1.1502
 0TB  C24  C  CH2   0  -0.468   3.1779   4.0026  -0.6253
 0TB  C26  C  CH2   0  -0.260   2.2232   2.7775   1.2794
 0TB  C2   C  CR6   0   0.554   4.1739  -1.4635  -0.0263
 0TB  N7   N  NH2   0  -0.811   5.5093  -1.4390   0.0183
 0TB  N9   N  NR6   0  -0.467   1.5198   0.8413  -0.0022
 0TB  N10  N  NR5   0  -0.303   2.2636   1.9950   0.0566
 0TB  C11  C  CR16  0  -0.227   0.0933  -1.5210  -0.1176
 0TB  C12  C  CR6   0   0.539   0.1225   0.9137  -0.0308
 0TB  O14  O  O     0  -0.452  -0.4306   1.9980   0.0120
 0TB  C16  C  CR16  0  -0.345  -2.7945  -1.2019   0.7095
 0TB  C18  C  CR6   0   0.395  -4.8102  -0.3190  -0.2355
 0TB  N19  N  N     0  -0.450  -4.1283   0.4923  -1.0074
 0TB  O21  O  O2    0  -0.466  -6.1387  -0.3436  -0.2571
 0TB  C23  C  CH2   0  -0.262   2.2566   2.8773  -1.0956
 0TB  C25  C  CH2   0  -0.475   3.1008   3.9823   0.9195
 0TB  F27  F  F     0  -0.301  -4.8915  -2.0025   1.4172
 0TB  H1   H  HCH3  0   0.263   0.9382  -4.2264   0.6266
 0TB  H2   H  HCH3  0   0.266   1.0847  -4.1794  -1.1223
 0TB  H3   H  HCH3  0   0.269   2.3978  -4.8544  -0.1503
 0TB  H4   H  HCR6  0   0.263  -2.3021   1.1762  -1.6300
 0TB  H5   H  HCH3  0   0.234  -6.5707   1.5847  -0.9306
 0TB  H6   H  HCH3  0   0.234  -6.5429   0.3360  -2.1891
 0TB  H7   H  HCH3  0   0.251  -7.8645   0.3697  -1.0026
 0TB  H8   H  HCH2  0   0.241   4.2002   3.8206  -0.9559
 0TB  H9   H  HCH2  0   0.238   2.8680   4.9607  -1.0401
 0TB  H10  H  HCH2  0   0.219   1.2143   3.1026   1.5512
 0TB  H11  H  HCH2  0   0.236   2.6270   2.1966   2.1106
 0TB  H12  H  HNH2  0   0.405   6.0328  -2.2887  -0.0969
 0TB  H13  H  HNH2  0   0.404   6.0006  -0.5636  -0.0236
 0TB  H14  H  HCR6  0   0.282  -0.4537  -2.4546  -0.1753
 0TB  H15  H  HCR6  0   0.294  -2.2939  -1.8662   1.4036
 0TB  H16  H  HCH2  0   0.218   1.2623   3.2648  -1.3411
 0TB  H17  H  HCH2  0   0.238   2.6433   2.3552  -1.9725
 0TB  H18  H  HCH2  0   0.243   4.0969   3.8791   1.3484
 0TB  H19  H  HCH2  0   0.239   2.6738   4.9017   1.3172

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
 0TB  C8   C6   single    1.495  0.020  1.495
 0TB  N1   C6   aromatic  1.313  0.020  1.313
 0TB  N1   C2   aromatic  1.348  0.020  1.348
 0TB  N7   C2   single    1.336  0.020  1.336
 0TB  C6   C5   aromatic  1.409  0.020  1.409
 0TB  C2   N3   aromatic  1.331  0.020  1.331
 0TB  C5   C11  single    1.416  0.020  1.416
 0TB  C5   C4   aromatic  1.405  0.020  1.405
 0TB  N3   C4   aromatic  1.318  0.020  1.318
 0TB  C11  C13  double    1.355  0.020  1.355
 0TB  C4   N9   single    1.378  0.020  1.378
 0TB  C20  N19  aromatic  1.331  0.020  1.331
 0TB  C20  C15  aromatic  1.387  0.020  1.387
 0TB  C23  N10  single    1.451  0.020  1.451
 0TB  C23  C24  single    1.528  0.020  1.528
 0TB  C13  C12  single    1.458  0.020  1.458
 0TB  C13  C15  single    1.471  0.020  1.471
 0TB  N9   N10  single    1.374  0.020  1.374
 0TB  N9   C12  single    1.400  0.020  1.400
 0TB  N19  C18  aromatic  1.311  0.020  1.311
 0TB  N10  C26  single    1.452  0.020  1.452
 0TB  C12  O14  double    1.218  0.020  1.218
 0TB  C15  C16  aromatic  1.402  0.020  1.402
 0TB  C24  C25  single    1.547  0.020  1.547
 0TB  C22  O21  single    1.422  0.020  1.422
 0TB  C18  O21  single    1.329  0.020  1.329
 0TB  C18  C17  aromatic  1.399  0.020  1.399
 0TB  C16  C17  aromatic  1.367  0.020  1.367
 0TB  C26  C25  single    1.533  0.020  1.533
 0TB  C17  F27  single    1.338  0.020  1.338
 0TB  C8   H1   single    0.970  0.020  1.090
 0TB  C8   H2   single    0.970  0.020  1.090
 0TB  C8   H3   single    0.970  0.020  1.090
 0TB  C20  H4   single    0.930  0.020  1.080
 0TB  C22  H5   single    0.970  0.020  1.090
 0TB  C22  H6   single    0.970  0.020  1.090
 0TB  C22  H7   single    0.970  0.020  1.090
 0TB  C24  H8   single    0.970  0.020  1.090
 0TB  C24  H9   single    0.970  0.020  1.090
 0TB  C26  H10  single    0.970  0.020  1.090
 0TB  C26  H11  single    0.970  0.020  1.090
 0TB  N7   H12  single    0.860  0.020  1.020
 0TB  N7   H13  single    0.860  0.020  1.020
 0TB  C11  H14  single    0.930  0.020  1.080
 0TB  C16  H15  single    0.930  0.020  1.080
 0TB  C23  H16  single    0.970  0.020  1.090
 0TB  C23  H17  single    0.970  0.020  1.090
 0TB  C25  H18  single    0.970  0.020  1.090
 0TB  C25  H19  single    0.970  0.020  1.090

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
 0TB  C2   N1   C6   117.23  3.000
 0TB  C2   N3   C4   116.31  3.000
 0TB  N9   C4   C5   118.77  3.000
 0TB  N9   C4   N3   118.48  3.000
 0TB  C5   C4   N3   122.75  3.000
 0TB  C11  C5   C6   124.75  3.000
 0TB  C11  C5   C4   119.35  3.000
 0TB  C6   C5   C4   115.89  3.000
 0TB  C8   C6   C5   120.94  3.000
 0TB  C5   C6   N1   121.56  3.000
 0TB  C8   C6   N1   117.50  3.000
 0TB  H3   C8   H2   108.49  3.000
 0TB  H3   C8   H1   108.66  3.000
 0TB  H2   C8   H1   107.14  3.000
 0TB  H3   C8   C6   110.31  3.000
 0TB  H2   C8   C6   110.66  3.000
 0TB  H1   C8   C6   111.45  3.000
 0TB  C12  C13  C11  119.97  3.000
 0TB  C12  C13  C15  118.70  3.000
 0TB  C11  C13  C15  121.31  3.000
 0TB  C16  C15  C20  116.74  3.000
 0TB  C16  C15  C13  120.40  3.000
 0TB  C20  C15  C13  122.82  3.000
 0TB  F27  C17  C18  119.13  3.000
 0TB  F27  C17  C16  120.93  3.000
 0TB  C18  C17  C16  119.93  3.000
 0TB  H4   C20  N19  115.66  3.000
 0TB  H4   C20  C15  120.81  3.000
 0TB  N19  C20  C15  123.53  3.000
 0TB  H7   C22  H6   109.39  3.000
 0TB  H7   C22  H5   109.39  3.000
 0TB  H6   C22  H5   108.80  3.000
 0TB  H7   C22  O21  105.78  3.000
 0TB  H6   C22  O21  111.70  3.000
 0TB  H5   C22  O21  111.72  3.000
 0TB  H9   C24  H8   107.35  3.000
 0TB  H9   C24  C25  112.20  3.000
 0TB  H8   C24  C25  110.34  3.000
 0TB  H9   C24  C23  111.04  3.000
 0TB  H8   C24  C23  110.43  3.000
 0TB  C25  C24  C23  105.52  3.000
 0TB  H11  C26  H10  108.06  3.000
 0TB  H11  C26  C25  112.65  3.000
 0TB  H10  C26  C25  110.64  3.000
 0TB  H11  C26  N10  110.13  3.000
 0TB  H10  C26  N10  113.26  3.000
 0TB  C25  C26  N10  102.11  3.000
 0TB  N7   C2   N3   117.38  3.000
 0TB  N3   C2   N1   126.26  3.000
 0TB  N7   C2   N1   116.35  3.000
 0TB  H13  N7   H12  118.51  3.000
 0TB  H13  N7   C2   120.21  3.000
 0TB  H12  N7   C2   120.10  3.000
 0TB  C12  N9   N10  119.86  3.000
 0TB  C12  N9   C4   123.59  3.000
 0TB  N10  N9   C4   116.54  3.000
 0TB  C23  N10  N9   118.29  3.000
 0TB  N9   N10  C26  118.26  3.000
 0TB  C23  N10  C26  109.92  3.000
 0TB  H14  C11  C13  119.10  3.000
 0TB  H14  C11  C5   119.14  3.000
 0TB  C13  C11  C5   121.75  3.000
 0TB  O14  C12  N9   119.92  3.000
 0TB  O14  C12  C13  123.52  3.000
 0TB  N9   C12  C13  116.56  3.000
 0TB  H15  C16  C17  119.79  3.000
 0TB  H15  C16  C15  121.08  3.000
 0TB  C17  C16  C15  119.12  3.000
 0TB  O21  C18  N19  121.46  3.000
 0TB  O21  C18  C17  117.60  3.000
 0TB  N19  C18  C17  120.95  3.000
 0TB  C18  N19  C20  119.73  3.000
 0TB  C18  O21  C22  117.71  3.000
 0TB  H17  C23  H16  108.11  3.000
 0TB  H17  C23  N10  110.21  3.000
 0TB  H16  C23  N10  113.43  3.000
 0TB  H17  C23  C24  112.70  3.000
 0TB  H16  C23  C24  110.83  3.000
 0TB  N10  C23  C24  101.56  3.000
 0TB  H19  C25  H18  107.14  3.000
 0TB  H19  C25  C26  110.69  3.000
 0TB  H18  C25  C26  110.89  3.000
 0TB  H19  C25  C24  111.91  3.000
 0TB  H18  C25  C24  110.42  3.000
 0TB  C26  C25  C24  105.85  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
 0TB  CONST_01  C4   C5   C6   N1      0.00   0.0  0
 0TB  CONST_02  C4   N3   C2   N1      0.00   0.0  0
 0TB  CONST_03  C6   N1   C2   N3      0.00   0.0  0
 0TB  CONST_04  C6   C5   C4   N3      0.00   0.0  0
 0TB  CONST_05  C2   N1   C6   C5      0.00   0.0  0
 0TB  CONST_06  C2   N3   C4   C5      0.00   0.0  0
 0TB  CONST_07  C18  N19  C20  C15     0.00   0.0  0
 0TB  CONST_08  C18  C17  C16  C15     0.00   0.0  0
 0TB  CONST_09  C20  N19  C18  C17     0.00   0.0  0
 0TB  CONST_10  C20  C15  C16  C17     0.00   0.0  0
 0TB  CONST_11  N19  C20  C15  C16     0.00   0.0  0
 0TB  CONST_12  N19  C18  C17  C16     0.00   0.0  0
 0TB  CONST_13  N19  C20  C15  C13   180.00   0.0  0
 0TB  CONST_14  C17  C16  C15  C13   180.00   0.0  0
 0TB  CONST_15  C13  C12  N9   C4      0.00   0.0  0
 0TB  CONST_16  N10  N9   C12  C13   180.00   0.0  0
 0TB  CONST_17  C8   C6   C5   C4    180.00   0.0  0
 0TB  CONST_18  N7   C2   N3   C4    180.00   0.0  0
 0TB  CONST_19  N7   C2   N1   C6    180.00   0.0  0
 0TB  CONST_20  C2   N1   C6   C8    180.00   0.0  0
 0TB  CONST_21  C11  C5   C6   C8      0.00   0.0  0
 0TB  CONST_22  F27  C17  C16  C15   180.00   0.0  0
 0TB  CONST_23  O21  C18  N19  C20   180.00   0.0  0
 0TB  CONST_24  O21  C18  C17  C16   180.00   0.0  0
 0TB  CONST_25  F27  C17  C18  N19   180.00   0.0  0
 0TB  CONST_26  O14  C12  N9   C4    180.00   0.0  0
 0TB  CONST_27  O14  C12  N9   N10     0.00   0.0  0
 0TB  CONST_28  H4   C20  C15  C13     0.00   0.0  0
 0TB  CONST_29  H15  C16  C15  C13     0.00   0.0  0
 0TB  CONST_30  H12  N7   C2   N1      0.00   0.0  0
 0TB  CONST_31  H13  N7   C2   N1    180.00   0.0  0
 0TB  Var_01    C23  N10  N9   C4    112.40  30.0  2
 0TB  Var_02    C11  C13  C15  C20  -133.27  30.0  2
 0TB  Var_03    N9   N10  C23  C24   179.92  30.0  1
 0TB  Var_04    N10  C26  C25  C24    18.39  30.0  1
 0TB  Var_05    C23  C24  C25  C26     4.24  30.0  1
 0TB  Var_06    C25  C26  N10  N9   -177.24  30.0  1
 0TB  Var_07    C25  C24  C23  N10   -25.18  30.0  1
 0TB  Var_08    N19  C18  O21  C22     0.07  30.0  2
 0TB  Var_09    H1   C8   C6   N1    124.41  30.0  2
 0TB  Var_10    H5   C22  O21  C18   -60.48  30.0  3

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
 0TB  plan-1  C13  0.020
 0TB  plan-1  C15  0.020
 0TB  plan-1  C17  0.020
 0TB  plan-1  C20  0.020
 0TB  plan-1  C16  0.020
 0TB  plan-1  C18  0.020
 0TB  plan-1  N19  0.020
 0TB  plan-1  O21  0.020
 0TB  plan-1  F27  0.020
 0TB  plan-1  H4   0.020
 0TB  plan-1  H15  0.020
 0TB  plan-2  N1   0.020
 0TB  plan-2  N3   0.020
 0TB  plan-2  C4   0.020
 0TB  plan-2  C5   0.020
 0TB  plan-2  C6   0.020
 0TB  plan-2  C8   0.020
 0TB  plan-2  C13  0.020
 0TB  plan-2  C15  0.020
 0TB  plan-2  C2   0.020
 0TB  plan-2  N7   0.020
 0TB  plan-2  N9   0.020
 0TB  plan-2  N10  0.020
 0TB  plan-2  C11  0.020
 0TB  plan-2  C12  0.020
 0TB  plan-2  O14  0.020
 0TB  plan-2  H14  0.020
 0TB  plan-3  C2   0.020
 0TB  plan-3  N7   0.020
 0TB  plan-3  H12  0.020
 0TB  plan-3  H13  0.020

