# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 21:55:52 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: 2-({(1R)-1-[7-methyl-2-(morpholin-4-yl)-4-oxo-4H-pyrido[1,2-a]pyrimidin-9-yl]ethyl}amino)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](Nc1ccccc1C(O)=O)C2=CC(=CN3C(=O)C=C(N=C23)N4CCOCC4)C
#
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
 A82  A82  '2-({(1R)-1-[7-methyl-2-(morpholin-4-yl)-4-oxo-4H-pyrido[1,2-a]pyrimidin-9-yl]ethyl}amino)benzoic acid'  ligand  54  30  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A82
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
 A82  C1    C  CR6   0  -0.025  -2.9559   3.2538  -0.2859
 A82  C2    C  CR16  0  -0.018  -3.5818   2.0911  -0.5782
 A82  N3    N  N     0  -0.627  -2.9886   0.8767  -0.3529
 A82  C4    C  CR66  0   0.578  -1.7322   0.7652   0.1854
 A82  N5    N  N     0  -0.556  -1.1505  -0.3876   0.4039
 A82  C6    C  CR6   0   0.613  -1.7893  -1.5309   0.1021
 A82  C7    C  CR16  0  -0.613  -3.0797  -1.5124  -0.4265
 A82  C8    C  CR6   0   0.584  -3.7411  -0.3069  -0.6915
 A82  O9    O  O     0  -0.512  -4.8650  -0.1643  -1.1588
 A82  N10   N  NT    0  -0.518  -1.1055  -2.6740   0.3398
 A82  C11   C  CH2   0  -0.321  -1.6965  -3.9855   0.1547
 A82  C12   C  CH2   0  -0.183  -0.6317  -4.9850  -0.2666
 A82  O13   O  O2    0  -0.482   0.4547  -5.0135   0.6271
 A82  C14   C  CH2   0  -0.195   1.0553  -3.7395   0.7028
 A82  C15   C  CH2   0  -0.318   0.0771  -2.6885   1.1865
 A82  C16   C  CR6   0   0.011  -1.0408   1.9786   0.5035
 A82  C17   C  CR16  0  -0.194  -1.6509   3.1699   0.2649
 A82  C18   C  CH1   0  -0.185   0.3370   1.9433   1.1278
 A82  C19   C  CH3   0  -0.655   0.3135   1.4237   2.5668
 A82  C20   C  CH3   0  -0.723  -3.5994   4.5827  -0.5280
 A82  N21   N  NH1   0  -0.720   1.2629   1.2226   0.2786
 A82  C22   C  CR6   0   0.396   2.5941   1.4579   0.2203
 A82  C23   C  CR16  0  -0.262   4.8385   0.9485  -0.6056
 A82  C24   C  CR6   0  -0.187   3.4720   0.6388  -0.5496
 A82  C25   C  CR16  0  -0.285   5.3744   2.0241   0.0659
 A82  C26   C  CR16  0  -0.358   3.1743   2.5462   0.9108
 A82  C27   C  CR16  0  -0.234   4.5204   2.8198   0.8281
 A82  C28   C  C     0   0.559   2.9670  -0.5235  -1.2894
 A82  O29   O  OH1   0  -0.599   3.9088  -1.1862  -1.9552
 A82  O30   O  O     0  -0.466   1.8053  -0.8852  -1.3169
 A82  H2    H  HCR6  0   0.310  -4.5719   2.0448  -1.0032
 A82  H17   H  HCR6  0   0.273  -1.1282   4.0896   0.5020
 A82  H201  H  HCH3  0   0.252  -4.5971   4.4734  -0.9498
 A82  H202  H  HCH3  0   0.253  -3.6865   5.1471   0.4014
 A82  H203  H  HCH3  0   0.253  -3.0054   5.1840  -1.2176
 A82  H7    H  HCR6  0   0.271  -3.6312  -2.4131  -0.6460
 A82  H111  H  HCH2  0   0.241  -2.1858  -4.3183   1.0783
 A82  H112  H  HCH2  0   0.267  -2.4486  -3.9631  -0.6302
 A82  H151  H  HCH2  0   0.275   0.5565  -1.7150   1.1712
 A82  H152  H  HCH2  0   0.234  -0.2152  -2.9029   2.2224
 A82  H121  H  HCH2  0   0.247  -1.0678  -5.9844  -0.2937
 A82  H122  H  HCH2  0   0.209  -0.2889  -4.7358  -1.2805
 A82  H141  H  HCH2  0   0.243   1.8907  -3.8072   1.4008
 A82  H142  H  HCH2  0   0.210   1.4532  -3.4435  -0.2770
 A82  H18   H  HCH1  0   0.268   0.6548   2.9866   1.1614
 A82  H191  H  HCH3  0   0.238   1.3120   1.4811   3.0016
 A82  H192  H  HCH3  0   0.233  -0.3534   2.0298   3.1806
 A82  H193  H  HCH3  0   0.244  -0.0189   0.3886   2.6087
 A82  H21   H  HNH1  0   0.440   0.9360   0.3468  -0.1061
 A82  H26   H  HCR6  0   0.272   2.5601   3.1880   1.5251
 A82  H23   H  HCR6  0   0.265   5.4957   0.3256  -1.1955
 A82  H25   H  HCR6  0   0.253   6.4314   2.2415   0.0049
 A82  H27   H  HCR6  0   0.262   4.9139   3.6690   1.3726
 A82  H29   H  HOH1  0   0.483   3.5048  -1.9352  -2.4167

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
 A82  C1   C2    double    1.352  0.020  1.352
 A82  C1   C17   single    1.419  0.020  1.419
 A82  C1   C20   single    1.496  0.020  1.496
 A82  C2   N3    single    1.370  0.020  1.370
 A82  N3   C4    single    1.371  0.020  1.371
 A82  N3   C8    single    1.443  0.020  1.443
 A82  C4   N5    double    1.310  0.020  1.310
 A82  C4   C16   single    1.432  0.020  1.432
 A82  N5   C6    single    1.344  0.020  1.344
 A82  C6   C7    double    1.395  0.020  1.395
 A82  C6   N10   single    1.353  0.020  1.353
 A82  C7   C8    single    1.400  0.020  1.400
 A82  C8   O9    double    1.226  0.020  1.226
 A82  N10  C11   single    1.450  0.020  1.450
 A82  N10  C15   single    1.454  0.020  1.454
 A82  C11  C12   single    1.520  0.020  1.520
 A82  C12  O13   single    1.407  0.020  1.407
 A82  O13  C14   single    1.410  0.020  1.410
 A82  C14  C15   single    1.515  0.020  1.515
 A82  C16  C17   double    1.360  0.020  1.360
 A82  C16  C18   single    1.513  0.020  1.513
 A82  C18  C19   single    1.530  0.020  1.530
 A82  C18  N21   single    1.448  0.020  1.448
 A82  N21  C22   single    1.353  0.020  1.353
 A82  C22  C24   aromatic  1.426  0.020  1.426
 A82  C22  C26   aromatic  1.413  0.020  1.413
 A82  C23  C24   aromatic  1.402  0.020  1.402
 A82  C23  C25   aromatic  1.377  0.020  1.377
 A82  C24  C28   single    1.467  0.020  1.467
 A82  C25  C27   aromatic  1.394  0.020  1.394
 A82  C26  C27   aromatic  1.376  0.020  1.376
 A82  C28  O29   single    1.330  0.020  1.330
 A82  C28  O30   double    1.217  0.020  1.217
 A82  C2   H2    single    0.930  0.020  1.080
 A82  C17  H17   single    0.930  0.020  1.080
 A82  C20  H201  single    0.970  0.020  1.090
 A82  C20  H202  single    0.970  0.020  1.090
 A82  C20  H203  single    0.970  0.020  1.090
 A82  C7   H7    single    0.930  0.020  1.080
 A82  C11  H111  single    0.970  0.020  1.090
 A82  C11  H112  single    0.970  0.020  1.090
 A82  C15  H151  single    0.970  0.020  1.090
 A82  C15  H152  single    0.970  0.020  1.090
 A82  C12  H121  single    0.970  0.020  1.090
 A82  C12  H122  single    0.970  0.020  1.090
 A82  C14  H141  single    0.970  0.020  1.090
 A82  C14  H142  single    0.970  0.020  1.090
 A82  C18  H18   single    0.970  0.020  1.090
 A82  C19  H191  single    0.970  0.020  1.090
 A82  C19  H192  single    0.970  0.020  1.090
 A82  C19  H193  single    0.970  0.020  1.090
 A82  N21  H21   single    0.860  0.020  1.020
 A82  C26  H26   single    0.930  0.020  1.080
 A82  C23  H23   single    0.930  0.020  1.080
 A82  C25  H25   single    0.930  0.020  1.080
 A82  C27  H27   single    0.930  0.020  1.080
 A82  O29  H29   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
 A82  C20   C1   C17   120.72  3.000
 A82  C20   C1   C2    121.98  3.000
 A82  C17   C1   C2    117.30  3.000
 A82  H2    C2   N3    115.10  3.000
 A82  H2    C2   C1    123.16  3.000
 A82  N3    C2   C1    121.74  3.000
 A82  C8    N3   C4    120.21  3.000
 A82  C8    N3   C2    117.56  3.000
 A82  C4    N3   C2    122.23  3.000
 A82  C16   C4   N5    119.62  3.000
 A82  C16   C4   N3    117.42  3.000
 A82  N5    C4   N3    122.96  3.000
 A82  C6    N5   C4    120.02  3.000
 A82  N10   C6   C7    123.05  3.000
 A82  N10   C6   N5    116.04  3.000
 A82  C7    C6   N5    120.90  3.000
 A82  H7    C7   C8    116.03  3.000
 A82  H7    C7   C6    122.62  3.000
 A82  C8    C7   C6    121.34  3.000
 A82  O9    C8   C7    127.26  3.000
 A82  O9    C8   N3    118.18  3.000
 A82  C7    C8   N3    114.55  3.000
 A82  C15   N10  C11   113.37  3.000
 A82  C15   N10  C6    121.44  3.000
 A82  C11   N10  C6    122.38  3.000
 A82  H112  C11  H111  107.79  3.000
 A82  H112  C11  C12   107.34  3.000
 A82  H111  C11  C12   110.27  3.000
 A82  H112  C11  N10   110.82  3.000
 A82  H111  C11  N10   110.40  3.000
 A82  C12   C11  N10   110.15  3.000
 A82  H122  C12  H121  108.03  3.000
 A82  H122  C12  O13   110.47  3.000
 A82  H121  C12  O13   107.82  3.000
 A82  H122  C12  C11   108.97  3.000
 A82  H121  C12  C11   109.23  3.000
 A82  O13   C12  C11   112.22  3.000
 A82  C14   O13  C12   110.16  3.000
 A82  H142  C14  H141  108.07  3.000
 A82  H142  C14  C15   109.38  3.000
 A82  H141  C14  C15   109.47  3.000
 A82  H142  C14  O13   110.48  3.000
 A82  H141  C14  O13   107.72  3.000
 A82  C15   C14  O13   111.64  3.000
 A82  H152  C15  H151  107.82  3.000
 A82  H152  C15  C14   109.75  3.000
 A82  H151  C15  C14   109.43  3.000
 A82  H152  C15  N10   109.56  3.000
 A82  H151  C15  N10   110.00  3.000
 A82  C14   C15  N10   110.25  3.000
 A82  C18   C16  C17   120.10  3.000
 A82  C18   C16  C4    120.76  3.000
 A82  C17   C16  C4    119.13  3.000
 A82  H17   C17  C16   119.26  3.000
 A82  H17   C17  C1    118.56  3.000
 A82  C16   C17  C1    122.18  3.000
 A82  H18   C18  N21   107.91  3.000
 A82  H18   C18  C19   107.47  3.000
 A82  N21   C18  C19   113.09  3.000
 A82  H18   C18  C16   104.81  3.000
 A82  N21   C18  C16   110.60  3.000
 A82  C19   C18  C16   112.45  3.000
 A82  H193  C19  H192  108.68  3.000
 A82  H193  C19  H191  108.33  3.000
 A82  H192  C19  H191  107.84  3.000
 A82  H193  C19  C18   111.34  3.000
 A82  H192  C19  C18   110.49  3.000
 A82  H191  C19  C18   110.06  3.000
 A82  H203  C20  H202  107.27  3.000
 A82  H203  C20  H201  108.02  3.000
 A82  H202  C20  H201  107.99  3.000
 A82  H203  C20  C1    110.96  3.000
 A82  H202  C20  C1    110.86  3.000
 A82  H201  C20  C1    111.57  3.000
 A82  H21   N21  C22   116.90  3.000
 A82  H21   N21  C18   116.58  3.000
 A82  C22   N21  C18   124.59  3.000
 A82  C26   C22  C24   116.95  3.000
 A82  C26   C22  N21   121.11  3.000
 A82  C24   C22  N21   121.94  3.000
 A82  H23   C23  C25   118.67  3.000
 A82  H23   C23  C24   119.16  3.000
 A82  C25   C23  C24   122.17  3.000
 A82  C28   C24  C23   119.35  3.000
 A82  C28   C24  C22   121.01  3.000
 A82  C23   C24  C22   119.64  3.000
 A82  H25   C25  C27   121.00  3.000
 A82  H25   C25  C23   120.69  3.000
 A82  C27   C25  C23   118.31  3.000
 A82  H26   C26  C27   118.18  3.000
 A82  H26   C26  C22   120.13  3.000
 A82  C27   C26  C22   121.69  3.000
 A82  H27   C27  C26   118.77  3.000
 A82  H27   C27  C25   119.99  3.000
 A82  C26   C27  C25   121.24  3.000
 A82  O30   C28  O29   121.09  3.000
 A82  O30   C28  C24   125.12  3.000
 A82  O29   C28  C24   113.79  3.000
 A82  H29   O29  C28   109.19  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
 A82  CONST_01  C25   C23  C24  C22     0.00   0.0  0
 A82  CONST_02  C25   C27  C26  C22     0.00   0.0  0
 A82  CONST_03  C26   C22  C24  C23     0.00   0.0  0
 A82  CONST_04  C26   C27  C25  C23     0.00   0.0  0
 A82  CONST_05  C27   C26  C22  C24     0.00   0.0  0
 A82  CONST_06  C27   C25  C23  C24     0.00   0.0  0
 A82  CONST_07  N5    C4   N3   C2    180.00   0.0  0
 A82  CONST_08  C16   C4   N3   C2      0.00   0.0  0
 A82  CONST_09  C7    C8   N3   C2    180.00   0.0  0
 A82  CONST_10  C6    N5   C4   N3      0.00   0.0  0
 A82  CONST_11  C7    C8   N3   C4      0.00   0.0  0
 A82  CONST_12  C7    C6   N5   C4      0.00   0.0  0
 A82  CONST_13  N10   C6   N5   C4    180.00   0.0  0
 A82  CONST_14  C8    N3   C4   N5      0.00   0.0  0
 A82  CONST_15  C11   N10  C6   N5    180.00   0.0  0
 A82  CONST_17  C16   C4   N5   C6    180.00   0.0  0
 A82  CONST_18  C11   N10  C6   C7      0.00   0.0  0
 A82  CONST_20  C16   C4   N3   C8    180.00   0.0  0
 A82  CONST_21  C23   C24  C22  N21   180.00   0.0  0
 A82  CONST_22  C27   C26  C22  N21   180.00   0.0  0
 A82  CONST_23  C28   C24  C23  C25   180.00   0.0  0
 A82  CONST_24  C28   C24  C22  C26   180.00   0.0  0
 A82  CONST_25  O9    C8   N3   C2      0.00   0.0  0
 A82  CONST_26  O9    C8   N3   C4    180.00   0.0  0
 A82  CONST_27  H23   C23  C24  C22   180.00   0.0  0
 A82  CONST_28  H27   C27  C26  C22   180.00   0.0  0
 A82  CONST_29  H26   C26  C22  C24   180.00   0.0  0
 A82  CONST_30  H25   C25  C23  C24   180.00   0.0  0
 A82  CONST_31  C24   C22  N21  C18   180.00   0.0  0
 A82  CONST_32  C26   C22  N21  C18     0.00   0.0  0
 A82  CONST_33  H21   N21  C22  C24     0.00   0.0  0
 A82  CONST_34  H29   O29  C28  C24   180.00   0.0  0
 A82  Var_01    C12   C11  N10  C6    148.56  30.0  1
 A82  Var_02    C14   C15  N10  C6   -147.59  30.0  1
 A82  Var_03    O13   C12  C11  N10    54.25  30.0  1
 A82  Var_04    O13   C14  C15  N10   -55.34  30.0  1
 A82  Var_05    C15   C14  O13  C12    59.96  30.0  1
 A82  Var_06    O29   C28  C24  C22  -179.86  30.0  2
 A82  Var_07    H201  C20  C1   C2      0.20  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
 A82  chir_01  C18  C16  C19  N21  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
 A82  plan-1  N21  0.020
 A82  plan-1  C22  0.020
 A82  plan-1  C23  0.020
 A82  plan-1  C24  0.020
 A82  plan-1  C25  0.020
 A82  plan-1  C26  0.020
 A82  plan-1  C27  0.020
 A82  plan-1  C28  0.020
 A82  plan-1  H26  0.020
 A82  plan-1  H23  0.020
 A82  plan-1  H25  0.020
 A82  plan-1  H27  0.020
 A82  plan-2  C1   0.020
 A82  plan-2  C2   0.020
 A82  plan-2  N3   0.020
 A82  plan-2  C4   0.020
 A82  plan-2  N5   0.020
 A82  plan-2  C6   0.020
 A82  plan-2  C7   0.020
 A82  plan-2  C8   0.020
 A82  plan-2  O9   0.020
 A82  plan-2  N10  0.020
 A82  plan-2  C11  0.020
 A82  plan-2  C15  0.020
 A82  plan-2  C16  0.020
 A82  plan-2  C17  0.020
 A82  plan-2  C18  0.020
 A82  plan-2  C20  0.020
 A82  plan-2  H2   0.020
 A82  plan-2  H17  0.020
 A82  plan-2  H7   0.020
 A82  plan-3  C18  0.020
 A82  plan-3  N21  0.020
 A82  plan-3  C22  0.020
 A82  plan-3  H21  0.020
 A82  plan-4  C24  0.020
 A82  plan-4  C28  0.020
 A82  plan-4  O29  0.020
 A82  plan-4  O30  0.020
 A82  plan-4  H29  0.020

