# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 00:00:57 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: (3S)-1-[2-(5-chloro-2,4-dimethoxyphenyl)imidazo[1,2-a]pyridin-7-yl]-N-[(pyridin-4-yl)methyl]pyrrolidin-3-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(OC)c(cc1Cl)c2cn3ccc(cc3n2)N4CC[C@@H](C4)NCc5ccncc5
#
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
 NM4  NM4  (3S)-1-[2-(5-chloro-2,4-dimethoxyphenyl)imidazo[1,2-a]pyridin-7-yl]-N-[(pyridin-4-yl)methyl]pyrrolidin-3-amine  ligand  59  33  .  2021-08-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_NM4
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
 NM4  C1   C   CR6   0   0.492   -7.3268   0.4164   0.2533
 NM4  N1   N   NT    0  -0.536    2.6774   0.0658   0.4356
 NM4  O1   O   O2    0  -0.451   -4.2868   2.2555  -0.6383
 NM4  C3   C   CR6   0   0.397   -5.1177   1.2867  -0.2317
 NM4  C4   C   CH3   0  -0.443   -4.8137   3.5236  -0.9755
 NM4  N4   N   N     0  -0.500   -2.1485   0.6369   0.4774
 NM4  C5   C   CR6   0  -0.180   -6.7502  -0.8188   0.5468
 NM4  C6   C   CR16  0  -0.248   -5.3827  -0.9900   0.4596
 NM4  C7   C   CR6   0  -0.128   -4.5378   0.0451   0.0732
 NM4  C8   C   CR5   0   0.126   -3.0958  -0.2033  -0.0316
 NM4  C11  C   CR16  0  -0.564    0.3187   0.4796   0.5346
 NM4  C12  C   CR6   0   0.515    1.4025  -0.3030   0.1719
 NM4  C14  C   CH2   0  -0.490    4.5278   1.4302   0.8399
 NM4  C15  C   CH1   0  -0.085    4.9651  -0.0308   0.9136
 NM4  C22  C   CH2   0  -0.265    3.8440  -0.7495   0.1640
 NM4  C23  C   CR16  0  -0.473    1.1442  -1.5380  -0.5148
 NM4  C24  C   CR16  0   0.047   -0.1205  -1.9243  -0.7982
 NM4  CL   CL  CL    0  -0.123   -7.7633  -2.1330   1.0391
 NM4  O    O   O2    0  -0.455   -8.6554   0.5106   0.3666
 NM4  C    C   CH3   0  -0.441   -9.2820   1.7476   0.0786
 NM4  C2   C   CR16  0  -0.552   -6.4967   1.4650  -0.1364
 NM4  C10  C   CR56  0   0.548   -0.9877   0.0582   0.2278
 NM4  N    N   N     0  -0.527   -1.1704  -1.1432  -0.4330
 NM4  C9   C   CR15  0  -0.134   -2.5258  -1.3107  -0.6022
 NM4  C13  C   CH2   0  -0.274    3.0187   1.3502   1.0159
 NM4  H1   H   HNH1  0   0.353    6.3976  -1.2888   0.2489
 NM4  H4   H   HCH3  0   0.264   -3.9656   4.1391  -1.2640
 NM4  H5   H   HCH3  0   0.231   -5.5089   3.4690  -1.8172
 NM4  H6   H   HCH3  0   0.231   -5.3182   3.9959  -0.1288
 NM4  H7   H   HCR6  0   0.272   -4.9555  -1.9515   0.7133
 NM4  H8   H   HCR6  0   0.273    0.4341   1.4155   1.0625
 NM4  H9   H   HCH2  0   0.257    4.9917   2.0670   1.5925
 NM4  H10  H   HCH2  0   0.242    4.7796   1.8279  -0.1469
 NM4  H11  H   HCH1  0   0.221    4.9364  -0.3471   1.9690
 NM4  H12  H   HCH2  0   0.249    3.7133  -1.7757   0.5158
 NM4  H13  H   HCH2  0   0.229    4.0784  -0.7879  -0.9074
 NM4  H14  H   HCR6  0   0.289    1.9525  -2.1812  -0.8298
 NM4  H15  H   HCR6  0   0.306   -0.3516  -2.8430  -1.3168
 NM4  H16  H   HCH3  0   0.235   -8.9394   2.5417   0.7461
 NM4  H17  H   HCH3  0   0.235   -9.1171   2.0550  -0.9568
 NM4  H18  H   HCH3  0   0.267  -10.3465   1.5935   0.2340
 NM4  H19  H   HCR6  0   0.310   -6.9337   2.4223  -0.3807
 NM4  H20  H   HCR5  0   0.293   -2.9433  -2.1631  -1.1105
 NM4  H21  H   HCH2  0   0.245    2.5021   2.1662   0.5042
 NM4  H22  H   HCH2  0   0.234    2.7317   1.3977   2.0731
 NM4  C17  C   CR6   0   0.162    8.6573   0.1451   0.2518
 NM4  C18  C   CR16  0  -0.366    8.7045   0.0530  -1.1350
 NM4  C19  C   CR16  0  -0.059    9.9369  -0.0564  -1.7610
 NM4  N3   N   N     0  -0.412   11.0964  -0.0809  -1.1131
 NM4  C21  C   CR16  0  -0.062   11.0493   0.0030   0.2119
 NM4  C25  C   CR16  0  -0.373    9.8702   0.1124   0.9316
 NM4  H2   H   HCH2  0   0.262    7.1764   1.3863   1.0950
 NM4  H3   H   HCH2  0   0.225    7.4902  -0.0619   2.0255
 NM4  H23  H   HCR6  0   0.262    7.7972   0.0631  -1.7230
 NM4  H24  H   HCR6  0   0.260    9.9863  -0.1263  -2.8424
 NM4  H25  H   HCR6  0   0.261   12.0001  -0.0229   0.7336
 NM4  H26  H   HCR6  0   0.263    9.9034   0.1671   2.0126
 NM4  N2   N   NH1   0  -0.610    6.2492  -0.2872   0.2978
 NM4  C16  C   CH2   0  -0.305    7.3629   0.3123   0.9988

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
 NM4  C24  C23  aromatic  1.352  0.020  1.352
 NM4  C24  N    aromatic  1.359  0.020  1.359
 NM4  C23  C12  aromatic  1.436  0.020  1.436
 NM4  C9   N    aromatic  1.376  0.020  1.376
 NM4  C9   C8   aromatic  1.370  0.020  1.370
 NM4  C22  C15  single    1.528  0.020  1.528
 NM4  C22  N1   single    1.449  0.020  1.449
 NM4  N    C10  aromatic  1.383  0.020  1.383
 NM4  CL   C5   single    1.731  0.020  1.731
 NM4  C12  N1   single    1.353  0.020  1.353
 NM4  C12  C11  aromatic  1.385  0.020  1.385
 NM4  C15  N2   single    1.447  0.020  1.447
 NM4  C15  C14  single    1.527  0.020  1.527
 NM4  C6   C5   aromatic  1.381  0.020  1.381
 NM4  C6   C7   aromatic  1.391  0.020  1.391
 NM4  N1   C13  single    1.450  0.020  1.450
 NM4  C8   C7   single    1.467  0.020  1.467
 NM4  C8   N4   aromatic  1.365  0.020  1.365
 NM4  C5   C1   aromatic  1.394  0.020  1.394
 NM4  C10  C11  aromatic  1.407  0.020  1.407
 NM4  C10  N4   aromatic  1.321  0.020  1.321
 NM4  C7   C3   aromatic  1.404  0.020  1.404
 NM4  C14  C13  single    1.521  0.020  1.521
 NM4  C1   O    single    1.337  0.020  1.337
 NM4  C1   C2   aromatic  1.393  0.020  1.393
 NM4  O    C    single    1.416  0.020  1.416
 NM4  C3   C2   aromatic  1.394  0.020  1.394
 NM4  C3   O1   single    1.339  0.020  1.339
 NM4  O1   C4   single    1.414  0.020  1.414
 NM4  N2   H1   single    0.890  0.020  1.040
 NM4  C4   H4   single    0.970  0.020  1.090
 NM4  C4   H5   single    0.970  0.020  1.090
 NM4  C4   H6   single    0.970  0.020  1.090
 NM4  C6   H7   single    0.930  0.020  1.080
 NM4  C11  H8   single    0.930  0.020  1.080
 NM4  C14  H9   single    0.970  0.020  1.090
 NM4  C14  H10  single    0.970  0.020  1.090
 NM4  C15  H11  single    0.970  0.020  1.090
 NM4  C22  H12  single    0.970  0.020  1.090
 NM4  C22  H13  single    0.970  0.020  1.090
 NM4  C23  H14  single    0.930  0.020  1.080
 NM4  C24  H15  single    0.930  0.020  1.080
 NM4  C    H16  single    0.970  0.020  1.090
 NM4  C    H17  single    0.970  0.020  1.090
 NM4  C    H18  single    0.970  0.020  1.090
 NM4  C2   H19  single    0.930  0.020  1.080
 NM4  C9   H20  single    0.930  0.020  1.080
 NM4  C13  H21  single    0.970  0.020  1.090
 NM4  C13  H22  single    0.970  0.020  1.090
 NM4  N2   C16  single    1.446  0.020  1.446
 NM4  C16  C17  single    1.504  0.020  1.504
 NM4  C17  C18  aromatic  1.391  0.020  1.391
 NM4  C18  C19  aromatic  1.387  0.020  1.387
 NM4  C19  N3   aromatic  1.328  0.020  1.328
 NM4  N3   C21  aromatic  1.328  0.020  1.328
 NM4  C21  C25  aromatic  1.386  0.020  1.386
 NM4  C25  C17  aromatic  1.391  0.020  1.391
 NM4  C16  H2   single    0.970  0.020  1.090
 NM4  C16  H3   single    0.970  0.020  1.090
 NM4  C18  H23  single    0.930  0.020  1.080
 NM4  C19  H24  single    0.930  0.020  1.080
 NM4  C21  H25  single    0.930  0.020  1.080
 NM4  C25  H26  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
 NM4  C2   C1   O    124.26  3.000
 NM4  C2   C1   C5   118.64  3.000
 NM4  O    C1   C5   117.10  3.000
 NM4  C13  N1   C22  112.58  3.000
 NM4  C13  N1   C12  122.76  3.000
 NM4  C22  N1   C12  124.66  3.000
 NM4  C4   O1   C3   119.33  3.000
 NM4  C2   C3   C7   120.46  3.000
 NM4  C2   C3   O1   122.82  3.000
 NM4  C7   C3   O1   116.70  3.000
 NM4  H6   C4   H5   108.94  3.000
 NM4  H6   C4   H4   108.73  3.000
 NM4  H5   C4   H4   108.67  3.000
 NM4  H6   C4   O1   112.01  3.000
 NM4  H5   C4   O1   112.08  3.000
 NM4  H4   C4   O1   106.28  3.000
 NM4  C10  N4   C8   105.65  3.000
 NM4  CL   C5   C6   120.23  3.000
 NM4  C6   C5   C1   120.40  3.000
 NM4  CL   C5   C1   119.37  3.000
 NM4  H7   C6   C7   119.11  3.000
 NM4  H7   C6   C5   119.09  3.000
 NM4  C7   C6   C5   121.79  3.000
 NM4  C8   C7   C6   119.40  3.000
 NM4  C8   C7   C3   122.70  3.000
 NM4  C6   C7   C3   117.88  3.000
 NM4  C9   C8   C7   125.14  3.000
 NM4  C7   C8   N4   123.46  3.000
 NM4  C9   C8   N4   111.36  3.000
 NM4  H8   C11  C10  117.72  3.000
 NM4  H8   C11  C12  122.25  3.000
 NM4  C10  C11  C12  120.02  3.000
 NM4  C23  C12  C11  118.05  3.000
 NM4  C11  C12  N1   122.15  3.000
 NM4  C23  C12  N1   119.79  3.000
 NM4  H10  C14  H9   108.23  3.000
 NM4  H10  C14  C13  110.61  3.000
 NM4  H9   C14  C13  111.91  3.000
 NM4  H10  C14  C15  109.01  3.000
 NM4  H9   C14  C15  113.83  3.000
 NM4  C13  C14  C15  103.19  3.000
 NM4  H11  C15  C22  108.40  3.000
 NM4  H11  C15  C14  108.26  3.000
 NM4  C22  C15  C14  102.49  3.000
 NM4  H11  C15  N2   112.32  3.000
 NM4  C14  C15  N2   113.77  3.000
 NM4  C22  C15  N2   111.04  3.000
 NM4  H13  C22  H12  107.88  3.000
 NM4  H13  C22  C15  109.80  3.000
 NM4  H12  C22  C15  111.81  3.000
 NM4  H13  C22  N1   112.00  3.000
 NM4  H12  C22  N1   111.83  3.000
 NM4  C15  C22  N1   103.54  3.000
 NM4  H14  C23  C24  117.95  3.000
 NM4  H14  C23  C12  121.13  3.000
 NM4  C24  C23  C12  120.92  3.000
 NM4  H15  C24  N    116.92  3.000
 NM4  H15  C24  C23  122.94  3.000
 NM4  N    C24  C23  120.15  3.000
 NM4  C    O    C1   118.95  3.000
 NM4  H18  C    H17  108.86  3.000
 NM4  H18  C    H16  108.83  3.000
 NM4  H17  C    H16  109.10  3.000
 NM4  H18  C    O    106.29  3.000
 NM4  H17  C    O    111.82  3.000
 NM4  H16  C    O    111.83  3.000
 NM4  H19  C2   C3   119.87  3.000
 NM4  H19  C2   C1   119.29  3.000
 NM4  C3   C2   C1   120.83  3.000
 NM4  N    C10  C11  119.15  3.000
 NM4  C11  C10  N4   130.07  3.000
 NM4  N    C10  N4   110.77  3.000
 NM4  C9   N    C10  107.13  3.000
 NM4  C10  N    C24  121.71  3.000
 NM4  C9   N    C24  131.16  3.000
 NM4  H20  C9   N    122.43  3.000
 NM4  H20  C9   C8   132.47  3.000
 NM4  N    C9   C8   105.09  3.000
 NM4  H22  C13  H21  107.17  3.000
 NM4  H22  C13  C14  111.64  3.000
 NM4  H21  C13  C14  112.05  3.000
 NM4  H22  C13  N1   111.26  3.000
 NM4  H21  C13  N1   111.27  3.000
 NM4  C14  C13  N1   103.52  3.000
 NM4  C25  C17  C18  117.15  3.000
 NM4  C25  C17  C16  120.69  3.000
 NM4  C18  C17  C16  122.14  3.000
 NM4  H23  C18  C19  120.07  3.000
 NM4  H23  C18  C17  120.88  3.000
 NM4  C19  C18  C17  119.05  3.000
 NM4  H24  C19  N3   116.44  3.000
 NM4  H24  C19  C18  119.71  3.000
 NM4  N3   C19  C18  123.85  3.000
 NM4  C21  N3   C19  117.02  3.000
 NM4  H25  C21  C25  119.86  3.000
 NM4  H25  C21  N3   116.56  3.000
 NM4  C25  C21  N3   123.58  3.000
 NM4  H26  C25  C21  119.76  3.000
 NM4  H26  C25  C17  120.90  3.000
 NM4  C21  C25  C17  119.34  3.000
 NM4  C16  N2   H1   108.67  3.000
 NM4  C16  N2   C15  113.81  3.000
 NM4  H1   N2   C15  108.99  3.000
 NM4  H3   C16  H2   105.76  3.000
 NM4  H3   C16  C17  109.04  3.000
 NM4  H2   C16  C17  107.43  3.000
 NM4  H3   C16  N2   113.61  3.000
 NM4  H2   C16  N2   108.55  3.000
 NM4  C17  C16  N2   112.09  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
 NM4  CONST_01  C7   C6   C5   C1      0.00   0.0  0
 NM4  CONST_02  C7   C3   C2   C1      0.00   0.0  0
 NM4  CONST_03  C5   C6   C7   C3      0.00   0.0  0
 NM4  CONST_06  C5   C1   C2   C3      0.00   0.0  0
 NM4  CONST_07  N    C9   C8   N4      0.00   0.0  0
 NM4  CONST_09  C24  N    C10  N4    180.00   0.0  0
 NM4  CONST_10  C9   N    C10  N4      0.00   0.0  0
 NM4  CONST_11  C12  C11  C10  N4    180.00   0.0  0
 NM4  CONST_12  C8   C7   C6   C5    180.00   0.0  0
 NM4  CONST_13  C2   C1   C5   C6      0.00   0.0  0
 NM4  CONST_15  C2   C3   C7   C6      0.00   0.0  0
 NM4  CONST_16  N    C9   C8   C7    180.00   0.0  0
 NM4  CONST_17  C10  N4   C8   C7    180.00   0.0  0
 NM4  CONST_18  C24  N    C9   C8    180.00   0.0  0
 NM4  CONST_19  C10  N    C9   C8      0.00   0.0  0
 NM4  CONST_20  C2   C3   C7   C8    180.00   0.0  0
 NM4  CONST_21  N    C10  N4   C8      0.00   0.0  0
 NM4  CONST_22  C11  C10  N4   C8    180.00   0.0  0
 NM4  CONST_23  C24  C23  C12  C11     0.00   0.0  0
 NM4  CONST_24  C24  N    C10  C11     0.00   0.0  0
 NM4  CONST_25  C9   N    C10  C11   180.00   0.0  0
 NM4  CONST_26  N    C24  C23  C12     0.00   0.0  0
 NM4  CONST_27  N    C10  C11  C12     0.00   0.0  0
 NM4  CONST_28  C9   N    C24  C23   180.00   0.0  0
 NM4  CONST_29  C10  N    C24  C23     0.00   0.0  0
 NM4  CONST_30  C10  C11  C12  C23     0.00   0.0  0
 NM4  CONST_31  C9   C8   N4   C10     0.00   0.0  0
 NM4  CONST_32  N3   C19  C18  C17     0.00   0.0  0
 NM4  CONST_33  N3   C21  C25  C17     0.00   0.0  0
 NM4  CONST_34  C21  C25  C17  C18     0.00   0.0  0
 NM4  CONST_35  C21  N3   C19  C18     0.00   0.0  0
 NM4  CONST_36  C25  C17  C18  C19     0.00   0.0  0
 NM4  CONST_37  C25  C21  N3   C19     0.00   0.0  0
 NM4  CONST_38  C24  C23  C12  N1    180.00   0.0  0
 NM4  CONST_39  C10  C11  C12  N1    180.00   0.0  0
 NM4  CONST_40  O1   C3   C2   C1    180.00   0.0  0
 NM4  CONST_41  C6   C7   C3   O1    180.00   0.0  0
 NM4  CONST_42  C8   C7   C3   O1      0.00   0.0  0
 NM4  CONST_43  O    C1   C2   C3    180.00   0.0  0
 NM4  CONST_44  O    C1   C5   C6    180.00   0.0  0
 NM4  CONST_45  CL   C5   C6   C7    180.00   0.0  0
 NM4  CONST_46  C2   C1   C5   CL    180.00   0.0  0
 NM4  CONST_47  C19  C18  C17  C16   180.00   0.0  0
 NM4  CONST_48  C21  C25  C17  C16   180.00   0.0  0
 NM4  CONST_49  H7   C6   C5   C1    180.00   0.0  0
 NM4  CONST_50  H14  C23  C12  N1      0.00   0.0  0
 NM4  CONST_51  H8   C11  C12  N1      0.00   0.0  0
 NM4  CONST_52  H20  C9   C8   N4    180.00   0.0  0
 NM4  CONST_53  H19  C2   C1   C5    180.00   0.0  0
 NM4  CONST_54  H15  C24  C23  C12   180.00   0.0  0
 NM4  CONST_55  H24  C19  C18  C17   180.00   0.0  0
 NM4  CONST_56  H25  C21  C25  C17   180.00   0.0  0
 NM4  CONST_57  H26  C25  C17  C18   180.00   0.0  0
 NM4  CONST_58  H23  C18  C19  N3    180.00   0.0  0
 NM4  Var_01    C15  C14  C13  N1    -30.68  30.0  1
 NM4  Var_02    C22  N1   C12  C11   175.58  30.0  2
 NM4  Var_03    C15  C22  N1   C12  -167.88  30.0  1
 NM4  Var_04    C14  C13  N1   C12  -168.03  30.0  1
 NM4  Var_05    C18  C17  C16  N2     29.22  30.0  2
 NM4  Var_06    C7   C3   O1   C4    179.24  30.0  2
 NM4  Var_07    C17  C16  N2   C15  -174.02  30.0  3
 NM4  Var_08    C2   C1   O    C      -0.09  30.0  2
 NM4  Var_09    H16  C    O    C1    -61.41  30.0  3
 NM4  Var_10    H4   C4   O1   C3    179.56  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
 NM4  chir_01  C15  C22  N2  C14  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
 NM4  plan-1  C1   0.020
 NM4  plan-1  O1   0.020
 NM4  plan-1  C3   0.020
 NM4  plan-1  C5   0.020
 NM4  plan-1  C6   0.020
 NM4  plan-1  C7   0.020
 NM4  plan-1  C8   0.020
 NM4  plan-1  CL   0.020
 NM4  plan-1  O    0.020
 NM4  plan-1  C2   0.020
 NM4  plan-1  H7   0.020
 NM4  plan-1  H19  0.020
 NM4  plan-2  C17  0.020
 NM4  plan-2  C18  0.020
 NM4  plan-2  C19  0.020
 NM4  plan-2  N3   0.020
 NM4  plan-2  C21  0.020
 NM4  plan-2  C25  0.020
 NM4  plan-2  H23  0.020
 NM4  plan-2  H24  0.020
 NM4  plan-2  H25  0.020
 NM4  plan-2  H26  0.020
 NM4  plan-2  C16  0.020
 NM4  plan-3  N1   0.020
 NM4  plan-3  N4   0.020
 NM4  plan-3  C7   0.020
 NM4  plan-3  C8   0.020
 NM4  plan-3  C11  0.020
 NM4  plan-3  C12  0.020
 NM4  plan-3  C23  0.020
 NM4  plan-3  C24  0.020
 NM4  plan-3  C10  0.020
 NM4  plan-3  N    0.020
 NM4  plan-3  C9   0.020
 NM4  plan-3  H8   0.020
 NM4  plan-3  H14  0.020
 NM4  plan-3  H15  0.020
 NM4  plan-3  H20  0.020

