# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 01:58:26 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: 2-methyl-3-{(3S)-1-[(1-pyridin-2-ylcyclopropyl)carbonyl]pyrrolidin-3-yl}-1H-pyrrolo[2,3-b]pyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1[nH]c2ncccc2c1[C@@H]3CCN(C3)C(=O)C4(CC4)c5ccccn5
#
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
 2M3  2M3  2-methyl-3-{(3S)-1-[(1-pyridin-2-ylcyclopropyl)carbonyl]pyrrolidin-3-yl}-1H-pyrrolo[2,3-b]pyridine  ligand  48  26  .  2022-09-22  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_2M3
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
 2M3  C1    C  CR16  0  -0.342  -3.3183   2.7981  -0.8508
 2M3  C2    C  CR16  0  -0.096  -4.7081   2.6603  -0.8381
 2M3  C4    C  CR16  0  -0.266  -2.5141   1.7225  -0.5075
 2M3  C5    C  CR56  0   0.004  -3.1389   0.5273  -0.1588
 2M3  C6    C  CR56  0   0.450  -4.5537   0.5262  -0.1881
 2M3  C8    C  CR5   0   0.299  -3.8774  -1.5069   0.4451
 2M3  C11   C  CR15  0  -0.445  -1.3303  -1.2721   0.4395
 2M3  C12   C  CH2   0  -0.443  -0.5118  -0.5292   1.5010
 2M3  C15   C  CH2   0  -0.230  -0.4424  -1.1758  -0.8067
 2M3  C17   C  CT    0  -0.213   3.3208  -1.0174  -0.3874
 2M3  C19   C  CR6   0   0.301   3.7205   0.3644   0.0122
 2M3  C21   C  CR16  0  -0.076   5.2228   1.6791   1.1323
 2M3  C23   C  CR16  0  -0.150   3.4391   2.7425  -0.0147
 2M3  C24   C  CR16  0  -0.339   3.0062   1.4861  -0.4072
 2M3  N3    N  N     0  -0.428  -5.3387   1.5390  -0.5112
 2M3  N7    N  NR15  0  -0.710  -4.9674  -0.7149   0.1800
 2M3  C9    C  CR5   0   0.002  -2.7262  -0.7859   0.2481
 2M3  C10   C  CH3   0  -0.739  -4.0734  -2.9175   0.8699
 2M3  C13   C  CH2   0  -0.282   0.9162  -0.9454   1.1875
 2M3  N14   N  NR5   0  -0.461   0.9079  -1.0837  -0.2669
 2M3  O18   O  O     0  -0.492   1.8805  -1.2858  -2.2809
 2M3  N20   N  N     0  -0.433   4.8098   0.4736   0.7671
 2M3  C22   C  CR16  0  -0.332   4.5735   2.8503   0.7740
 2M3  C25   C  CH2   0  -0.451   3.7795  -2.1778   0.4586
 2M3  C26   C  CH2   0  -0.468   4.4154  -1.9338  -0.8637
 2M3  H1    H  HCR6  0   0.261  -2.8816   3.7466  -1.1312
 2M3  H2    H  HCR6  0   0.253  -5.3347   3.5031  -1.1075
 2M3  H4    H  HCR6  0   0.246  -1.4360   1.8245  -0.5157
 2M3  H11   H  HCR5  0   0.267  -1.3654  -2.3246   0.7342
 2M3  H12   H  HCH2  0   0.241  -0.6210   0.5523   1.3922
 2M3  H12A  H  HCH2  0   0.259  -0.8071  -0.7929   2.5156
 2M3  H15   H  HCH2  0   0.256  -0.5532  -2.0467  -1.4540
 2M3  H15A  H  HCH2  0   0.237  -0.6725  -0.2931  -1.4101
 2M3  H21   H  HCR6  0   0.263   6.1176   1.7149   1.7438
 2M3  H23   H  HCR6  0   0.275   2.8959   3.6253  -0.3256
 2M3  H24   H  HCR6  0   0.269   2.1315   1.3944  -1.0369
 2M3  HN7   H  HNR5  0   0.406  -5.9292  -1.0041   0.2588
 2M3  H10   H  HCH3  0   0.259  -4.5324  -3.5091   0.0756
 2M3  H10A  H  HCH3  0   0.259  -3.1282  -3.3877   1.1307
 2M3  H10B  H  HCH3  0   0.258  -4.7281  -2.9777   1.7410
 2M3  H13   H  HCH2  0   0.260   1.6422  -0.2058   1.5203
 2M3  H13A  H  HCH2  0   0.247   1.1653  -1.8975   1.6644
 2M3  H22   H  HCR6  0   0.270   4.9486   3.8100   1.1007
 2M3  H25   H  HCH2  0   0.262   4.3364  -1.9389   1.3549
 2M3  H25A  H  HCH2  0   0.264   3.1032  -3.0193   0.5494
 2M3  H26   H  HCH2  0   0.263   4.1879  -2.6037  -1.6826
 2M3  H26A  H  HCH2  0   0.262   5.4166  -1.5230  -0.8786
 2M3  C16   C  C     0   0.502   1.9808  -1.1459  -1.0677

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
 2M3  C1   C2    aromatic  1.397  0.020  1.397
 2M3  C1   C4    aromatic  1.386  0.020  1.386
 2M3  C2   N3    aromatic  1.327  0.020  1.327
 2M3  C4   C5    aromatic  1.393  0.020  1.393
 2M3  C5   C6    aromatic  1.415  0.020  1.415
 2M3  C5   C9    aromatic  1.435  0.020  1.435
 2M3  C6   N3    aromatic  1.322  0.020  1.322
 2M3  C6   N7    aromatic  1.359  0.020  1.359
 2M3  C8   N7    aromatic  1.373  0.020  1.373
 2M3  C8   C9    aromatic  1.373  0.020  1.373
 2M3  C8   C10   single    1.486  0.020  1.486
 2M3  C11  C12   single    1.533  0.020  1.533
 2M3  C11  C15   single    1.533  0.020  1.533
 2M3  C11  C9    single    1.491  0.020  1.491
 2M3  C12  C13   single    1.520  0.020  1.520
 2M3  C15  N14   single    1.457  0.020  1.457
 2M3  C16  C17   single    1.508  0.020  1.508
 2M3  C16  N14   single    1.340  0.020  1.340
 2M3  C16  O18   double    1.225  0.020  1.225
 2M3  C17  C19   single    1.493  0.020  1.493
 2M3  C17  C25   single    1.508  0.020  1.508
 2M3  C17  C26   single    1.505  0.020  1.505
 2M3  C19  C24   aromatic  1.394  0.020  1.394
 2M3  C19  N20   aromatic  1.330  0.020  1.330
 2M3  C21  N20   aromatic  1.326  0.020  1.326
 2M3  C21  C22   aromatic  1.386  0.020  1.386
 2M3  C23  C24   aromatic  1.386  0.020  1.386
 2M3  C23  C22   aromatic  1.386  0.020  1.386
 2M3  C13  N14   single    1.461  0.020  1.461
 2M3  C25  C26   single    1.487  0.020  1.487
 2M3  C1   H1    single    0.930  0.020  1.080
 2M3  C2   H2    single    0.930  0.020  1.080
 2M3  C4   H4    single    0.930  0.020  1.080
 2M3  C11  H11   single    0.970  0.020  1.090
 2M3  C12  H12   single    0.970  0.020  1.090
 2M3  C12  H12A  single    0.970  0.020  1.090
 2M3  C15  H15   single    0.970  0.020  1.090
 2M3  C15  H15A  single    0.970  0.020  1.090
 2M3  C21  H21   single    0.930  0.020  1.080
 2M3  C23  H23   single    0.930  0.020  1.080
 2M3  C24  H24   single    0.930  0.020  1.080
 2M3  N7   HN7   single    0.860  0.020  1.020
 2M3  C10  H10   single    0.970  0.020  1.090
 2M3  C10  H10A  single    0.970  0.020  1.090
 2M3  C10  H10B  single    0.970  0.020  1.090
 2M3  C13  H13   single    0.970  0.020  1.090
 2M3  C13  H13A  single    0.970  0.020  1.090
 2M3  C22  H22   single    0.930  0.020  1.080
 2M3  C25  H25   single    0.970  0.020  1.090
 2M3  C25  H25A  single    0.970  0.020  1.090
 2M3  C26  H26   single    0.970  0.020  1.090
 2M3  C26  H26A  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
 2M3  H1    C1   C4    120.70  3.000
 2M3  H1    C1   C2    119.39  3.000
 2M3  C4    C1   C2    119.90  3.000
 2M3  H2    C2   N3    116.32  3.000
 2M3  H2    C2   C1    119.74  3.000
 2M3  N3    C2   C1    123.94  3.000
 2M3  H4    C4   C5    121.95  3.000
 2M3  H4    C4   C1    120.18  3.000
 2M3  C5    C4   C1    117.87  3.000
 2M3  C9    C5   C6    107.01  3.000
 2M3  C9    C5   C4    136.63  3.000
 2M3  C6    C5   C4    116.35  3.000
 2M3  N7    C6   N3    125.82  3.000
 2M3  N7    C6   C5    107.43  3.000
 2M3  N3    C6   C5    126.75  3.000
 2M3  C10   C8   C9    130.56  3.000
 2M3  C10   C8   N7    119.86  3.000
 2M3  C9    C8   N7    109.57  3.000
 2M3  H11   C11  C9    108.57  3.000
 2M3  H11   C11  C15   107.34  3.000
 2M3  C9    C11  C15   114.68  3.000
 2M3  H11   C11  C12   107.28  3.000
 2M3  C9    C11  C12   115.53  3.000
 2M3  C15   C11  C12   102.90  3.000
 2M3  H12A  C12  H12   107.78  3.000
 2M3  H12A  C12  C13   112.37  3.000
 2M3  H12   C12  C13   110.15  3.000
 2M3  H12A  C12  C11   112.52  3.000
 2M3  H12   C12  C11   110.95  3.000
 2M3  C13   C12  C11   103.07  3.000
 2M3  H15A  C15  H15   107.20  3.000
 2M3  H15A  C15  N14   110.38  3.000
 2M3  H15   C15  N14   111.38  3.000
 2M3  H15A  C15  C11   112.16  3.000
 2M3  H15   C15  C11   111.93  3.000
 2M3  N14   C15  C11   103.86  3.000
 2M3  C26   C17  C25    59.18  3.000
 2M3  C26   C17  C19   116.97  3.000
 2M3  C25   C17  C19   118.73  3.000
 2M3  C26   C17  C16   116.85  3.000
 2M3  C25   C17  C16   117.25  3.000
 2M3  C19   C17  C16   115.94  3.000
 2M3  N20   C19  C24   121.62  3.000
 2M3  N20   C19  C17   116.57  3.000
 2M3  C24   C19  C17   121.80  3.000
 2M3  H21   C21  C22   120.28  3.000
 2M3  H21   C21  N20   116.26  3.000
 2M3  C22   C21  N20   123.46  3.000
 2M3  H23   C23  C22   120.73  3.000
 2M3  H23   C23  C24   120.10  3.000
 2M3  C22   C23  C24   119.17  3.000
 2M3  H24   C24  C23   119.63  3.000
 2M3  H24   C24  C19   121.41  3.000
 2M3  C23   C24  C19   118.96  3.000
 2M3  C6    N3   C2    115.18  3.000
 2M3  HN7   N7   C8    125.25  3.000
 2M3  HN7   N7   C6    125.03  3.000
 2M3  C8    N7   C6    109.72  3.000
 2M3  C11   C9   C8    126.56  3.000
 2M3  C11   C9   C5    127.16  3.000
 2M3  C8    C9   C5    106.27  3.000
 2M3  H10B  C10  H10A  107.83  3.000
 2M3  H10B  C10  H10   107.38  3.000
 2M3  H10A  C10  H10   107.80  3.000
 2M3  H10B  C10  C8    111.08  3.000
 2M3  H10A  C10  C8    111.36  3.000
 2M3  H10   C10  C8    111.22  3.000
 2M3  H13A  C13  H13   107.84  3.000
 2M3  H13A  C13  N14   110.67  3.000
 2M3  H13   C13  N14   111.87  3.000
 2M3  H13A  C13  C12   111.24  3.000
 2M3  H13   C13  C12   112.18  3.000
 2M3  N14   C13  C12   103.05  3.000
 2M3  C13   N14  C16   126.48  3.000
 2M3  C13   N14  C15   112.34  3.000
 2M3  C16   N14  C15   121.17  3.000
 2M3  C21   N20  C19   119.09  3.000
 2M3  H22   C22  C23   121.67  3.000
 2M3  H22   C22  C21   120.63  3.000
 2M3  C23   C22  C21   117.69  3.000
 2M3  H25A  C25  H25   115.05  3.000
 2M3  H25A  C25  C26   117.95  3.000
 2M3  H25   C25  C26   118.69  3.000
 2M3  H25A  C25  C17   117.06  3.000
 2M3  H25   C25  C17   116.84  3.000
 2M3  C26   C25  C17    60.32  3.000
 2M3  H26A  C26  H26   114.77  3.000
 2M3  H26A  C26  C25   118.04  3.000
 2M3  H26   C26  C25   118.77  3.000
 2M3  H26A  C26  C17   116.50  3.000
 2M3  H26   C26  C17   117.61  3.000
 2M3  C25   C26  C17    60.50  3.000
 2M3  O18   C16  N14   122.10  3.000
 2M3  O18   C16  C17   121.93  3.000
 2M3  N14   C16  C17   115.96  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
 2M3  CONST_01  C6   N3   C2   C1      0.00   0.0  0
 2M3  CONST_02  C6   C5   C4   C1      0.00   0.0  0
 2M3  CONST_03  C9   C5   C4   C1    180.00   0.0  0
 2M3  CONST_04  C5   C4   C1   C2      0.00   0.0  0
 2M3  CONST_05  C5   C6   N3   C2      0.00   0.0  0
 2M3  CONST_06  N7   C6   N3   C2    180.00   0.0  0
 2M3  CONST_07  N3   C2   C1   C4      0.00   0.0  0
 2M3  CONST_08  N3   C6   C5   C4      0.00   0.0  0
 2M3  CONST_09  N7   C6   C5   C4    180.00   0.0  0
 2M3  CONST_10  C8   C9   C5   C4    180.00   0.0  0
 2M3  CONST_11  C8   N7   C6   C5      0.00   0.0  0
 2M3  CONST_12  N7   C8   C9   C5      0.00   0.0  0
 2M3  CONST_13  C8   C9   C5   C6      0.00   0.0  0
 2M3  CONST_14  C9   C8   N7   C6      0.00   0.0  0
 2M3  CONST_15  N3   C6   N7   C8    180.00   0.0  0
 2M3  CONST_16  C22  C23  C24  C19     0.00   0.0  0
 2M3  CONST_17  C22  C21  N20  C19     0.00   0.0  0
 2M3  CONST_18  C24  C19  N20  C21     0.00   0.0  0
 2M3  CONST_19  C24  C23  C22  C21     0.00   0.0  0
 2M3  CONST_20  N20  C19  C24  C23     0.00   0.0  0
 2M3  CONST_21  N20  C21  C22  C23     0.00   0.0  0
 2M3  CONST_22  C9   C5   C6   N3    180.00   0.0  0
 2M3  CONST_23  C9   C5   C6   N7      0.00   0.0  0
 2M3  CONST_24  C11  C9   C5   C4      0.00   0.0  0
 2M3  CONST_25  C11  C9   C5   C6    180.00   0.0  0
 2M3  CONST_26  N7   C8   C9   C11   180.00   0.0  0
 2M3  CONST_27  C23  C24  C19  C17   180.00   0.0  0
 2M3  CONST_28  C21  N20  C19  C17   180.00   0.0  0
 2M3  CONST_29  C10  C8   C9   C5    180.00   0.0  0
 2M3  CONST_30  C10  C8   N7   C6    180.00   0.0  0
 2M3  CONST_31  C10  C8   C9   C11     0.00   0.0  0
 2M3  CONST_32  C17  C16  N14  C15   180.00   0.0  0
 2M3  CONST_33  C13  N14  C16  C17     0.00   0.0  0
 2M3  CONST_34  H4   C4   C1   C2    180.00   0.0  0
 2M3  CONST_35  H2   C2   C1   C4    180.00   0.0  0
 2M3  CONST_36  H1   C1   C4   C5    180.00   0.0  0
 2M3  CONST_37  HN7  N7   C6   C5    180.00   0.0  0
 2M3  CONST_38  H24  C24  C19  C17     0.00   0.0  0
 2M3  CONST_39  H23  C23  C24  C19   180.00   0.0  0
 2M3  CONST_40  H21  C21  N20  C19   180.00   0.0  0
 2M3  CONST_41  H22  C22  C23  C24   180.00   0.0  0
 2M3  CONST_42  O18  C16  N14  C15     0.00   0.0  0
 2M3  CONST_43  O18  C16  N14  C13   180.00   0.0  0
 2M3  Var_01    N14  C13  C12  C11    33.69  30.0  1
 2M3  Var_02    C13  N14  C15  C11    -7.21  30.0  1
 2M3  Var_03    C15  N14  C13  C12   -16.78  30.0  1
 2M3  Var_04    C26  C25  C17  C19  -105.98  30.0  1
 2M3  Var_05    C25  C17  C19  C24  -157.90  30.0  3
 2M3  Var_06    N14  C16  C17  C19   -77.13  30.0  2
 2M3  Var_07    H26  C26  C25  C17  -107.27  30.0  1
 2M3  Var_08    H10  C10  C8   N7     64.98  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
 2M3  chir_01  C11  C12  C15  C9   positiv
 2M3  chir_02  C17  C19  C25  C26  both

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
 2M3  plan-1  C17  0.020
 2M3  plan-1  C19  0.020
 2M3  plan-1  C21  0.020
 2M3  plan-1  C23  0.020
 2M3  plan-1  C24  0.020
 2M3  plan-1  N20  0.020
 2M3  plan-1  C22  0.020
 2M3  plan-1  H21  0.020
 2M3  plan-1  H23  0.020
 2M3  plan-1  H24  0.020
 2M3  plan-1  H22  0.020
 2M3  plan-2  C1   0.020
 2M3  plan-2  C2   0.020
 2M3  plan-2  C4   0.020
 2M3  plan-2  C5   0.020
 2M3  plan-2  C6   0.020
 2M3  plan-2  C8   0.020
 2M3  plan-2  C11  0.020
 2M3  plan-2  N3   0.020
 2M3  plan-2  N7   0.020
 2M3  plan-2  C9   0.020
 2M3  plan-2  C10  0.020
 2M3  plan-2  H1   0.020
 2M3  plan-2  H2   0.020
 2M3  plan-2  H4   0.020
 2M3  plan-2  HN7  0.020
 2M3  plan-3  C15  0.020
 2M3  plan-3  C17  0.020
 2M3  plan-3  C13  0.020
 2M3  plan-3  N14  0.020
 2M3  plan-3  O18  0.020
 2M3  plan-3  C16  0.020

