# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 09:17:12 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: 5-chloranyl-4-imidazo[1,2-a]pyridin-3-yl-N-(5-methyl-1-piperidin-4-yl-pyrazol-4-yl)pyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1n(ncc1Nc2ncc(Cl)c(n2)c3cnc4ccccn34)C5CCNCC5
#
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
 GD5  GD5  5-chloranyl-4-imidazo[1,2-a]pyridin-3-yl-N-(5-methyl-1-piperidin-4-yl-pyrazol-4-yl)pyrimidin-2-amine  ligand  50  29  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_GD5
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
 GD5  C1    C   CH3   0  -0.745  -3.3790   2.2962   0.3539
 GD5  C2    C   CR5   0   0.356  -3.2936   0.8710  -0.0624
 GD5  C3    C   CR5   0   0.030  -2.1959   0.0876  -0.3793
 GD5  C4    C   CR15  0  -0.073  -2.7278  -1.1802  -0.6805
 GD5  N1    N   N     0  -0.283  -4.0423  -1.1711  -0.5557
 GD5  N2    N   NR5   0  -0.329  -4.3690   0.0607  -0.1952
 GD5  C5    C   CH1   0  -0.088  -5.7553   0.3930   0.0833
 GD5  C6    C   CH2   0  -0.422  -6.6737   0.0153  -1.0737
 GD5  C7    C   CH2   0  -0.301  -8.1116   0.3693  -0.7191
 GD5  N3    N   NH1   0  -0.595  -8.5019  -0.3147   0.5003
 GD5  C8    C   CH2   0  -0.300  -7.6933   0.1064   1.6297
 GD5  C9    C   CH2   0  -0.421  -6.2331  -0.2472   1.3840
 GD5  N4    N   NH1   0  -0.760  -0.8832   0.5496  -0.3865
 GD5  C10   C   CR6   0   0.589   0.2531  -0.1705  -0.4783
 GD5  N5    N   N     0  -0.454   0.1722  -1.4931  -0.6354
 GD5  C11   C   CR16  0   0.048   1.3155  -2.1411  -0.7552
 GD5  C12   C   CR6   0  -0.203   2.5418  -1.5018  -0.7121
 GD5  C13   C   CR6   0   0.300   2.5351  -0.1202  -0.4900
 GD5  N6    N   N     0  -0.478   1.3874   0.5312  -0.3884
 GD5  C14   C   CR5   0   0.229   3.7446   0.6878  -0.4244
 GD5  C15   C   CR15  0  -0.205   4.0568   1.8365  -1.1163
 GD5  N7    N   N     0  -0.467   5.2993   2.2686  -0.8392
 GD5  C16   C   CR56  0   0.532   5.7801   1.4156   0.0534
 GD5  N8    N   N     0  -0.556   4.8578   0.4247   0.3424
 GD5  C17   C   CR16  0   0.032   5.0862  -0.5204   1.2997
 GD5  C18   C   CR16  0  -0.391   6.2805  -0.5363   1.9431
 GD5  C19   C   CR16  0  -0.150   7.2720   0.4278   1.6378
 GD5  C20   C   CR16  0  -0.403   7.0238   1.3982   0.7120
 GD5  CL    CL  CL    0  -0.099   3.9875  -2.3853  -1.0264
 GD5  H11C  H   HCH3  0   0.266  -4.0331   2.8738  -0.3000
 GD5  H12C  H   HCH3  0   0.265  -3.7516   2.4010   1.3743
 GD5  H13C  H   HCH3  0   0.257  -2.3998   2.7715   0.3251
 GD5  H4    H   HCR5  0   0.268  -2.2084  -2.0750  -0.9749
 GD5  HA    H   HNH1  0   0.407  -0.7439   1.5390  -0.2527
 GD5  H5    H   HCH1  0   0.260  -5.7911   1.4792   0.2005
 GD5  H61C  H   HCH2  0   0.240  -6.3696   0.5420  -1.9810
 GD5  H62C  H   HCH2  0   0.232  -6.5994  -1.0560  -1.2698
 GD5  H91C  H   HCH2  0   0.230  -6.1221  -1.3323   1.3150
 GD5  H92C  H   HCH2  0   0.240  -5.6216   0.0982   2.2210
 GD5  H71C  H   HCH2  0   0.191  -8.1994   1.4655  -0.6328
 GD5  H72C  H   HCH2  0   0.239  -8.7754   0.0612  -1.5288
 GD5  H3    H   HNH1  0   0.354  -9.4768  -0.1283   0.6948
 GD5  H81C  H   HCH2  0   0.192  -7.7683   1.1901   1.8209
 GD5  H82C  H   HCH2  0   0.239  -8.0475  -0.3992   2.5298
 GD5  H11   H   HCR6  0   0.294   1.2625  -3.2132  -0.9102
 GD5  H15   H   HCR5  0   0.273   3.4210   2.3382  -1.8306
 GD5  H20   H   HCR6  0   0.284   7.7496   2.1622   0.4717
 GD5  H17   H   HCR6  0   0.316   4.2861  -1.2087   1.5231
 GD5  H18   H   HCR6  0   0.285   6.4547  -1.2890   2.6977
 GD5  H19   H   HCR6  0   0.278   8.2210   0.3990   2.1549

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
 GD5  C1   C2    single    1.487  0.020  1.487
 GD5  C2   C3    aromatic  1.385  0.020  1.385
 GD5  C2   N2    aromatic  1.353  0.020  1.353
 GD5  C3   C4    aromatic  1.407  0.020  1.407
 GD5  C3   N4    single    1.392  0.020  1.392
 GD5  C4   N1    aromatic  1.320  0.020  1.320
 GD5  N1   N2    aromatic  1.324  0.020  1.324
 GD5  N2   C5    single    1.453  0.020  1.453
 GD5  C5   C6    single    1.525  0.020  1.525
 GD5  C5   C9    single    1.526  0.020  1.526
 GD5  C6   C7    single    1.523  0.020  1.523
 GD5  C7   N3    single    1.452  0.020  1.452
 GD5  N3   C8    single    1.451  0.020  1.451
 GD5  C8   C9    single    1.522  0.020  1.522
 GD5  N4   C10   single    1.348  0.020  1.348
 GD5  C10  N5    aromatic  1.334  0.020  1.334
 GD5  C10  N6    aromatic  1.337  0.020  1.337
 GD5  N5   C11   aromatic  1.320  0.020  1.320
 GD5  C11  C12   aromatic  1.384  0.020  1.384
 GD5  C12  C13   aromatic  1.399  0.020  1.399
 GD5  C12  CL    single    1.723  0.020  1.723
 GD5  C13  N6    aromatic  1.324  0.020  1.324
 GD5  C13  C14   single    1.456  0.020  1.456
 GD5  C14  C15   aromatic  1.377  0.020  1.377
 GD5  C14  N8    aromatic  1.377  0.020  1.377
 GD5  C15  N7    aromatic  1.344  0.020  1.344
 GD5  N7   C16   aromatic  1.325  0.020  1.325
 GD5  C16  N8    aromatic  1.384  0.020  1.384
 GD5  C16  C20   aromatic  1.407  0.020  1.407
 GD5  N8   C17   aromatic  1.365  0.020  1.365
 GD5  C17  C18   aromatic  1.357  0.020  1.357
 GD5  C18  C19   aromatic  1.416  0.020  1.416
 GD5  C19  C20   aromatic  1.364  0.020  1.364
 GD5  C1   H11C  single    0.970  0.020  1.090
 GD5  C1   H12C  single    0.970  0.020  1.090
 GD5  C1   H13C  single    0.970  0.020  1.090
 GD5  C4   H4    single    0.930  0.020  1.080
 GD5  N4   HA    single    0.860  0.020  1.020
 GD5  C5   H5    single    0.970  0.020  1.090
 GD5  C6   H61C  single    0.970  0.020  1.090
 GD5  C6   H62C  single    0.970  0.020  1.090
 GD5  C9   H91C  single    0.970  0.020  1.090
 GD5  C9   H92C  single    0.970  0.020  1.090
 GD5  C7   H71C  single    0.970  0.020  1.090
 GD5  C7   H72C  single    0.970  0.020  1.090
 GD5  N3   H3    single    0.890  0.020  1.040
 GD5  C8   H81C  single    0.970  0.020  1.090
 GD5  C8   H82C  single    0.970  0.020  1.090
 GD5  C11  H11   single    0.930  0.020  1.080
 GD5  C15  H15   single    0.930  0.020  1.080
 GD5  C20  H20   single    0.930  0.020  1.080
 GD5  C17  H17   single    0.930  0.020  1.080
 GD5  C18  H18   single    0.930  0.020  1.080
 GD5  C19  H19   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
 GD5  H13C  C1   H12C  106.86  3.000
 GD5  H13C  C1   H11C  107.00  3.000
 GD5  H12C  C1   H11C  107.76  3.000
 GD5  H13C  C1   C2    111.06  3.000
 GD5  H12C  C1   C2    111.92  3.000
 GD5  H11C  C1   C2    111.97  3.000
 GD5  N2    C2   C3    105.59  3.000
 GD5  N2    C2   C1    123.76  3.000
 GD5  C3    C2   C1    130.65  3.000
 GD5  N4    C3   C4    130.87  3.000
 GD5  N4    C3   C2    124.12  3.000
 GD5  C4    C3   C2    105.00  3.000
 GD5  H4    C4   N1    120.81  3.000
 GD5  H4    C4   C3    128.71  3.000
 GD5  N1    C4   C3    110.47  3.000
 GD5  N2    N1   C4    106.12  3.000
 GD5  C5    N2   N1    120.02  3.000
 GD5  C5    N2   C2    127.07  3.000
 GD5  N1    N2   C2    112.81  3.000
 GD5  H5    C5   C9    108.37  3.000
 GD5  H5    C5   C6    107.92  3.000
 GD5  C9    C5   C6    110.75  3.000
 GD5  H5    C5   N2    106.20  3.000
 GD5  C9    C5   N2    111.48  3.000
 GD5  C6    C5   N2    111.88  3.000
 GD5  H62C  C6   H61C  107.77  3.000
 GD5  H62C  C6   C7    109.52  3.000
 GD5  H61C  C6   C7    110.14  3.000
 GD5  H62C  C6   C5    109.78  3.000
 GD5  H61C  C6   C5    110.08  3.000
 GD5  C7    C6   C5    109.54  3.000
 GD5  H72C  C7   H71C  106.87  3.000
 GD5  H72C  C7   N3    109.07  3.000
 GD5  H71C  C7   N3    112.40  3.000
 GD5  H72C  C7   C6    109.63  3.000
 GD5  H71C  C7   C6    108.93  3.000
 GD5  N3    C7   C6    109.88  3.000
 GD5  H3    N3   C8    109.51  3.000
 GD5  H3    N3   C7    109.51  3.000
 GD5  C8    N3   C7    111.54  3.000
 GD5  H82C  C8   H81C  106.86  3.000
 GD5  H82C  C8   C9    109.68  3.000
 GD5  H81C  C8   C9    108.74  3.000
 GD5  H82C  C8   N3    109.06  3.000
 GD5  H81C  C8   N3    112.46  3.000
 GD5  C9    C8   N3    109.96  3.000
 GD5  H92C  C9   H91C  107.78  3.000
 GD5  H92C  C9   C8    109.87  3.000
 GD5  H91C  C9   C8    109.76  3.000
 GD5  H92C  C9   C5    110.18  3.000
 GD5  H91C  C9   C5    109.32  3.000
 GD5  C8    C9   C5    109.90  3.000
 GD5  HA    N4   C10   114.63  3.000
 GD5  HA    N4   C3    117.10  3.000
 GD5  C10   N4   C3    128.17  3.000
 GD5  N6    C10  N5    125.42  3.000
 GD5  N6    C10  N4    115.48  3.000
 GD5  N5    C10  N4    119.10  3.000
 GD5  C11   N5   C10   116.42  3.000
 GD5  H11   C11  C12   120.30  3.000
 GD5  H11   C11  N5    117.13  3.000
 GD5  C12   C11  N5    122.56  3.000
 GD5  CL    C12  C13   122.63  3.000
 GD5  CL    C12  C11   120.07  3.000
 GD5  C13   C12  C11   117.18  3.000
 GD5  C14   C13  N6    116.34  3.000
 GD5  C14   C13  C12   123.44  3.000
 GD5  N6    C13  C12   120.15  3.000
 GD5  C13   N6   C10   118.18  3.000
 GD5  N8    C14  C15   104.83  3.000
 GD5  N8    C14  C13   126.19  3.000
 GD5  C15   C14  C13   128.95  3.000
 GD5  H15   C15  N7    122.08  3.000
 GD5  H15   C15  C14   125.91  3.000
 GD5  N7    C15  C14   111.97  3.000
 GD5  C16   N7   C15   105.51  3.000
 GD5  C20   C16  N8    118.83  3.000
 GD5  C20   C16  N7    130.08  3.000
 GD5  N8    C16  N7    111.08  3.000
 GD5  C17   N8   C16   122.06  3.000
 GD5  C17   N8   C14   131.17  3.000
 GD5  C16   N8   C14   106.59  3.000
 GD5  H17   C17  C18   123.17  3.000
 GD5  H17   C17  N8    117.59  3.000
 GD5  C18   C17  N8    119.22  3.000
 GD5  H18   C18  C19   120.80  3.000
 GD5  H18   C18  C17   118.79  3.000
 GD5  C19   C18  C17   120.41  3.000
 GD5  H19   C19  C20   120.21  3.000
 GD5  H19   C19  C18   119.56  3.000
 GD5  C20   C19  C18   120.22  3.000
 GD5  H20   C20  C19   122.12  3.000
 GD5  H20   C20  C16   118.73  3.000
 GD5  C19   C20  C16   119.15  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
 GD5  CONST_01  N1    C4   C3   C2     0.00   0.0  0
 GD5  CONST_02  C4    N1   N2   C2     0.00   0.0  0
 GD5  CONST_03  N1    N2   C2   C3     0.00   0.0  0
 GD5  CONST_04  N2    N1   C4   C3     0.00   0.0  0
 GD5  CONST_05  N2    C2   C3   C4     0.00   0.0  0
 GD5  CONST_06  C12   C11  N5   C10    0.00   0.0  0
 GD5  CONST_07  C12   C13  N6   C10    0.00   0.0  0
 GD5  CONST_08  C14   C13  N6   C10  180.00   0.0  0
 GD5  CONST_09  C13   N6   C10  N5     0.00   0.0  0
 GD5  CONST_10  C13   C12  C11  N5     0.00   0.0  0
 GD5  CONST_11  N6    C10  N5   C11    0.00   0.0  0
 GD5  CONST_12  N6    C13  C12  C11    0.00   0.0  0
 GD5  CONST_13  C14   C13  C12  C11  180.00   0.0  0
 GD5  CONST_16  N7    C15  C14  C13  180.00   0.0  0
 GD5  CONST_17  C16   N8   C14  C13  180.00   0.0  0
 GD5  CONST_18  C17   N8   C14  C13    0.00   0.0  0
 GD5  CONST_21  C16   N7   C15  C14    0.00   0.0  0
 GD5  CONST_22  N7    C16  N8   C14    0.00   0.0  0
 GD5  CONST_23  C20   C16  N8   C14  180.00   0.0  0
 GD5  CONST_24  C18   C17  N8   C14  180.00   0.0  0
 GD5  CONST_25  C16   N8   C14  C15    0.00   0.0  0
 GD5  CONST_26  C17   N8   C14  C15  180.00   0.0  0
 GD5  CONST_27  N8    C16  N7   C15    0.00   0.0  0
 GD5  CONST_28  C20   C16  N7   C15  180.00   0.0  0
 GD5  CONST_29  N8    C14  C15  N7     0.00   0.0  0
 GD5  CONST_30  C17   N8   C16  N7   180.00   0.0  0
 GD5  CONST_31  C19   C20  C16  N7   180.00   0.0  0
 GD5  CONST_32  C18   C17  N8   C16    0.00   0.0  0
 GD5  CONST_33  C18   C19  C20  C16    0.00   0.0  0
 GD5  CONST_34  C19   C20  C16  N8     0.00   0.0  0
 GD5  CONST_35  C19   C18  C17  N8     0.00   0.0  0
 GD5  CONST_36  C20   C16  N8   C17    0.00   0.0  0
 GD5  CONST_37  C20   C19  C18  C17    0.00   0.0  0
 GD5  CONST_38  C5    N2   C2   C3   180.00   0.0  0
 GD5  CONST_39  C5    N2   N1   C4   180.00   0.0  0
 GD5  CONST_40  C4    C3   C2   C1   180.00   0.0  0
 GD5  CONST_41  N1    N2   C2   C1   180.00   0.0  0
 GD5  CONST_42  C5    N2   C2   C1     0.00   0.0  0
 GD5  CONST_43  N4    C3   C4   N1   180.00   0.0  0
 GD5  CONST_44  N4    C3   C2   N2   180.00   0.0  0
 GD5  CONST_45  C11   N5   C10  N4   180.00   0.0  0
 GD5  CONST_46  C13   N6   C10  N4   180.00   0.0  0
 GD5  CONST_47  CL    C12  C11  N5   180.00   0.0  0
 GD5  CONST_48  CL    C12  C13  N6   180.00   0.0  0
 GD5  CONST_49  CL    C12  C13  C14    0.00   0.0  0
 GD5  CONST_50  H4    C4   C3   C2   180.00   0.0  0
 GD5  CONST_51  H11   C11  N5   C10  180.00   0.0  0
 GD5  CONST_52  H15   C15  C14  C13    0.00   0.0  0
 GD5  CONST_53  H17   C17  N8   C14    0.00   0.0  0
 GD5  CONST_54  H20   C20  C16  N7     0.00   0.0  0
 GD5  CONST_55  H19   C19  C20  C16  180.00   0.0  0
 GD5  CONST_56  H18   C18  C17  N8   180.00   0.0  0
 GD5  Var_01    N3    C7   C6   C5   -57.78  30.0  1
 GD5  Var_02    N3    C8   C9   C5    56.85  30.0  1
 GD5  Var_03    C8    N3   C7   C6    62.62  30.0  1
 GD5  Var_04    C9    C8   N3   C7   -62.08  30.0  1
 GD5  Var_05    C10   N4   C3   C2   168.90  30.0  2
 GD5  Var_06    N5    C10  N4   C3     2.88  30.0  2
 GD5  Var_07    H11C  C1   C2   C3   124.05  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
 GD5  chir_01  C5  N2  C6  C9  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
 GD5  plan-1  C1   0.020
 GD5  plan-1  C2   0.020
 GD5  plan-1  C3   0.020
 GD5  plan-1  C4   0.020
 GD5  plan-1  N1   0.020
 GD5  plan-1  N2   0.020
 GD5  plan-1  C5   0.020
 GD5  plan-1  N4   0.020
 GD5  plan-1  H4   0.020
 GD5  plan-2  N4   0.020
 GD5  plan-2  C10  0.020
 GD5  plan-2  N5   0.020
 GD5  plan-2  C11  0.020
 GD5  plan-2  C12  0.020
 GD5  plan-2  C13  0.020
 GD5  plan-2  N6   0.020
 GD5  plan-2  C14  0.020
 GD5  plan-2  CL   0.020
 GD5  plan-2  H11  0.020
 GD5  plan-3  C13  0.020
 GD5  plan-3  C14  0.020
 GD5  plan-3  C15  0.020
 GD5  plan-3  N7   0.020
 GD5  plan-3  C16  0.020
 GD5  plan-3  N8   0.020
 GD5  plan-3  C17  0.020
 GD5  plan-3  C18  0.020
 GD5  plan-3  C19  0.020
 GD5  plan-3  C20  0.020
 GD5  plan-3  H15  0.020
 GD5  plan-3  H20  0.020
 GD5  plan-3  H17  0.020
 GD5  plan-3  H18  0.020
 GD5  plan-3  H19  0.020

