# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 16:09:28 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: (1S,2S)-N-{4-[(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)methyl]phenyl}-2-(pyridin-3-yl)cyclopropane-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(Nc1ccc(CN2C(=O)c3ccccc3C2=O)cc1)[C@H]4C[C@@H]4c5cccnc5
#
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
 C5V  C5V  (1S,2S)-N-{4-[(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)methyl]phenyl}-2-(pyridin-3-yl)cyclopropane-1-carboxamide  ligand  49  30  .  2022-09-16  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_C5V
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
 C5V  C1   C  CH2   0  -0.428   3.2902   1.3510   1.6287
 C5V  C2   C  CR6   0   0.123   1.8931   0.9923   1.1987
 C5V  C3   C  CR16  0  -0.287   1.1538   0.0393   1.8854
 C5V  C11  C  CR56  0  -0.028   5.6975  -0.8413  -0.1260
 C5V  C12  C  CR56  0  -0.024   5.8307   0.3244  -0.8622
 C5V  C13  C  CR5   0   0.584   4.9240   1.3410  -0.2784
 C5V  C14  C  CR16  0  -0.296   6.4159  -1.9771  -0.4310
 C5V  C15  C  CR16  0  -0.241   7.2874  -1.9055  -1.5167
 C5V  C16  C  CR16  0  -0.241   7.4209  -0.7342  -2.2568
 C5V  C17  C  CR16  0  -0.296   6.6886   0.4083  -1.9376
 C5V  C21  C  CH1   0  -0.429  -4.1759  -0.8577  -0.4298
 C5V  C23  C  CH1   0  -0.353  -5.4941  -1.0130   0.3048
 C5V  C24  C  CH2   0  -0.450  -4.9465  -2.1413  -0.4994
 C5V  C25  C  CR6   0   0.125  -6.6777  -0.2360  -0.1276
 C5V  C26  C  CR16  0  -0.135  -7.0097  -0.0487  -1.4691
 C5V  C28  C  CR16  0  -0.079  -8.8490   1.1964  -0.9690
 C5V  C29  C  CR16  0  -0.313  -8.6193   1.0748   0.3922
 C5V  C30  C  CR16  0  -0.207  -7.5170   0.3494   0.8150
 C5V  C4   C  CR16  0  -0.305  -0.1305  -0.3153   1.4941
 C5V  C5   C  CR6   0   0.366  -0.7034   0.2924   0.3768
 C5V  C6   C  CR16  0  -0.339   0.0352   1.2545  -0.3188
 C5V  C7   C  CR16  0  -0.281   1.3100   1.5980   0.0882
 C5V  N8   N  NH1   0  -0.760  -1.9806   0.0091  -0.1133
 C5V  N9   N  NR5   0  -0.587   4.3013   0.7247   0.7960
 C5V  C10  C  CR5   0   0.587   4.7047  -0.5929   0.9457
 C5V  O18  O  O     0  -0.397   4.3065  -1.3502   1.7940
 C5V  O22  O  O     0  -0.473  -2.7993  -1.4836   1.4008
 C5V  N27  N  N     0  -0.398  -8.0596   0.6453  -1.8847
 C5V  H1   H  HCH2  0   0.290   3.4486   2.4277   1.5791
 C5V  H2   H  HCH2  0   0.290   3.4644   1.0481   2.6607
 C5V  H3   H  HCR6  0   0.255   1.5818  -0.4476   2.7528
 C5V  H4   H  HCR6  0   0.276   6.3121  -2.8879   0.1435
 C5V  H5   H  HCR6  0   0.279   7.8709  -2.7742  -1.7906
 C5V  H6   H  HCR6  0   0.280   8.1049  -0.7122  -3.0943
 C5V  H7   H  HCR6  0   0.276   6.7926   1.3183  -2.5132
 C5V  H8   H  HCH1  0   0.294  -4.1957  -0.2291  -1.3135
 C5V  H9   H  HCH1  0   0.279  -5.4020  -1.1191   1.3798
 C5V  H10  H  HCH2  0   0.274  -5.4164  -2.3823  -1.4446
 C5V  H11  H  HCH2  0   0.277  -4.5518  -2.9923   0.0397
 C5V  H12  H  HCR6  0   0.256  -6.3937  -0.4827  -2.2512
 C5V  H13  H  HCR6  0   0.263  -9.7013   1.7577  -1.3349
 C5V  H14  H  HCR6  0   0.271  -9.2892   1.5383   1.1034
 C5V  H15  H  HCR6  0   0.270  -7.3087   0.2363   1.8722
 C5V  H16  H  HCR6  0   0.281  -0.6678  -1.0578   2.0598
 C5V  H17  H  HCR6  0   0.271  -0.3968   1.7436  -1.1842
 C5V  H18  H  HCR6  0   0.257   1.8527   2.3533  -0.4673
 C5V  H19  H  HNH1  0   0.419  -2.2240   0.5004  -0.9599
 C5V  O19  O  O     0  -0.404   4.7397   2.4765  -0.6378
 C5V  C20  C  C     0   0.608  -2.9315  -0.8219   0.3850

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
 C5V  C15  C14  aromatic  1.394  0.020  1.394
 C5V  C15  C16  aromatic  1.392  0.020  1.392
 C5V  C14  C11  aromatic  1.378  0.020  1.378
 C5V  C16  C17  aromatic  1.394  0.020  1.394
 C5V  C11  C12  aromatic  1.385  0.020  1.385
 C5V  C11  C10  single    1.482  0.020  1.482
 C5V  C17  C12  aromatic  1.378  0.020  1.378
 C5V  O18  C10  double    1.205  0.020  1.205
 C5V  C12  C13  single    1.482  0.020  1.482
 C5V  C10  N9   single    1.386  0.020  1.386
 C5V  C13  N9   single    1.386  0.020  1.386
 C5V  C13  O19  double    1.205  0.020  1.205
 C5V  N9   C1   single    1.452  0.020  1.452
 C5V  C7   C6   aromatic  1.382  0.020  1.382
 C5V  C7   C2   aromatic  1.393  0.020  1.393
 C5V  C6   C5   aromatic  1.398  0.020  1.398
 C5V  C1   C2   single    1.505  0.020  1.505
 C5V  C2   C3   aromatic  1.388  0.020  1.388
 C5V  C5   N8   single    1.397  0.020  1.397
 C5V  C5   C4   aromatic  1.395  0.020  1.395
 C5V  N8   C20  single    1.358  0.020  1.358
 C5V  C3   C4   aromatic  1.389  0.020  1.389
 C5V  C20  C21  single    1.488  0.020  1.488
 C5V  C20  O22  double    1.220  0.020  1.220
 C5V  C21  C24  single    1.499  0.020  1.499
 C5V  C21  C23  single    1.517  0.020  1.517
 C5V  C30  C29  aromatic  1.386  0.020  1.386
 C5V  C30  C25  aromatic  1.391  0.020  1.391
 C5V  C29  C28  aromatic  1.386  0.020  1.386
 C5V  C24  C23  single    1.490  0.020  1.490
 C5V  C23  C25  single    1.480  0.020  1.480
 C5V  C25  C26  aromatic  1.395  0.020  1.395
 C5V  C28  N27  aromatic  1.329  0.020  1.329
 C5V  C26  N27  aromatic  1.325  0.020  1.325
 C5V  C1   H1   single    0.970  0.020  1.090
 C5V  C1   H2   single    0.970  0.020  1.090
 C5V  C3   H3   single    0.930  0.020  1.080
 C5V  C14  H4   single    0.930  0.020  1.080
 C5V  C15  H5   single    0.930  0.020  1.080
 C5V  C16  H6   single    0.930  0.020  1.080
 C5V  C17  H7   single    0.930  0.020  1.080
 C5V  C21  H8   single    0.970  0.020  1.090
 C5V  C23  H9   single    0.970  0.020  1.090
 C5V  C24  H10  single    0.970  0.020  1.090
 C5V  C24  H11  single    0.970  0.020  1.090
 C5V  C26  H12  single    0.930  0.020  1.080
 C5V  C28  H13  single    0.930  0.020  1.080
 C5V  C29  H14  single    0.930  0.020  1.080
 C5V  C30  H15  single    0.930  0.020  1.080
 C5V  C4   H16  single    0.930  0.020  1.080
 C5V  C6   H17  single    0.930  0.020  1.080
 C5V  C7   H18  single    0.930  0.020  1.080
 C5V  N8   H19  single    0.860  0.020  1.020

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
 C5V  H2   C1   H1   107.13  3.000
 C5V  H2   C1   N9   108.17  3.000
 C5V  H1   C1   N9   107.39  3.000
 C5V  H2   C1   C2   110.66  3.000
 C5V  H1   C1   C2   110.95  3.000
 C5V  N9   C1   C2   112.32  3.000
 C5V  C7   C2   C3   118.03  3.000
 C5V  C3   C2   C1   121.11  3.000
 C5V  C7   C2   C1   120.85  3.000
 C5V  H3   C3   C4   118.45  3.000
 C5V  H3   C3   C2   119.64  3.000
 C5V  C4   C3   C2   121.91  3.000
 C5V  C10  C11  C14  130.35  3.000
 C5V  C10  C11  C12  107.92  3.000
 C5V  C14  C11  C12  121.72  3.000
 C5V  C17  C12  C13  130.27  3.000
 C5V  C13  C12  C11  108.00  3.000
 C5V  C17  C12  C11  121.72  3.000
 C5V  O19  C13  N9   125.53  3.000
 C5V  O19  C13  C12  128.49  3.000
 C5V  N9   C13  C12  105.97  3.000
 C5V  H4   C14  C15  121.12  3.000
 C5V  H4   C14  C11  121.75  3.000
 C5V  C15  C14  C11  117.12  3.000
 C5V  H5   C15  C16  119.31  3.000
 C5V  H5   C15  C14  119.54  3.000
 C5V  C16  C15  C14  121.15  3.000
 C5V  H6   C16  C17  119.54  3.000
 C5V  H6   C16  C15  119.30  3.000
 C5V  C17  C16  C15  121.16  3.000
 C5V  H7   C17  C16  121.13  3.000
 C5V  H7   C17  C12  121.75  3.000
 C5V  C16  C17  C12  117.12  3.000
 C5V  H8   C21  C24  116.69  3.000
 C5V  H8   C21  C23  115.98  3.000
 C5V  C24  C21  C23   59.20  3.000
 C5V  H8   C21  C20  116.58  3.000
 C5V  C23  C21  C20  117.65  3.000
 C5V  C24  C21  C20  118.42  3.000
 C5V  H9   C23  C25  114.13  3.000
 C5V  H9   C23  C24  115.46  3.000
 C5V  C25  C23  C24  122.26  3.000
 C5V  H9   C23  C21  114.61  3.000
 C5V  C25  C23  C21  119.97  3.000
 C5V  C24  C23  C21   59.79  3.000
 C5V  H11  C24  H10  114.72  3.000
 C5V  H11  C24  C23  117.44  3.000
 C5V  H10  C24  C23  118.70  3.000
 C5V  H11  C24  C21  117.58  3.000
 C5V  H10  C24  C21  117.02  3.000
 C5V  C23  C24  C21   61.01  3.000
 C5V  C30  C25  C26  116.85  3.000
 C5V  C26  C25  C23  122.80  3.000
 C5V  C30  C25  C23  120.35  3.000
 C5V  H12  C26  N27  115.64  3.000
 C5V  H12  C26  C25  120.26  3.000
 C5V  N27  C26  C25  124.09  3.000
 C5V  H13  C28  N27  116.69  3.000
 C5V  H13  C28  C29  120.48  3.000
 C5V  N27  C28  C29  122.83  3.000
 C5V  H14  C29  C30  121.10  3.000
 C5V  H14  C29  C28  120.38  3.000
 C5V  C30  C29  C28  118.52  3.000
 C5V  H15  C30  C29  120.35  3.000
 C5V  H15  C30  C25  120.08  3.000
 C5V  C29  C30  C25  119.57  3.000
 C5V  H16  C4   C5   121.08  3.000
 C5V  H16  C4   C3   119.30  3.000
 C5V  C5   C4   C3   119.63  3.000
 C5V  N8   C5   C6   116.61  3.000
 C5V  N8   C5   C4   124.62  3.000
 C5V  C6   C5   C4   118.77  3.000
 C5V  H17  C6   C7   119.39  3.000
 C5V  H17  C6   C5   119.81  3.000
 C5V  C7   C6   C5   120.79  3.000
 C5V  H18  C7   C6   118.99  3.000
 C5V  H18  C7   C2   120.15  3.000
 C5V  C6   C7   C2   120.87  3.000
 C5V  H19  N8   C5   114.60  3.000
 C5V  H19  N8   C20  115.93  3.000
 C5V  C5   N8   C20  129.47  3.000
 C5V  C10  N9   C13  112.05  3.000
 C5V  C13  N9   C1   124.44  3.000
 C5V  C10  N9   C1   123.42  3.000
 C5V  O18  C10  N9   125.26  3.000
 C5V  N9   C10  C11  106.04  3.000
 C5V  O18  C10  C11  128.70  3.000
 C5V  C28  N27  C26  118.15  3.000
 C5V  O22  C20  N8   124.19  3.000
 C5V  O22  C20  C21  122.26  3.000
 C5V  N8   C20  C21  113.55  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
 C5V  CONST_01  C5   C6   C7   C2      0.00   0.0  0
 C5V  CONST_02  C5   C4   C3   C2      0.00   0.0  0
 C5V  CONST_03  C6   C7   C2   C3      0.00   0.0  0
 C5V  CONST_04  C6   C5   C4   C3      0.00   0.0  0
 C5V  CONST_05  C16  C15  C14  C11     0.00   0.0  0
 C5V  CONST_06  C16  C17  C12  C11     0.00   0.0  0
 C5V  CONST_07  C15  C14  C11  C12     0.00   0.0  0
 C5V  CONST_08  C15  C16  C17  C12     0.00   0.0  0
 C5V  CONST_09  C17  C16  C15  C14     0.00   0.0  0
 C5V  CONST_10  C17  C12  C11  C14     0.00   0.0  0
 C5V  CONST_11  C28  C29  C30  C25     0.00   0.0  0
 C5V  CONST_12  C28  N27  C26  C25     0.00   0.0  0
 C5V  CONST_13  C29  C30  C25  C26     0.00   0.0  0
 C5V  CONST_14  C29  C28  N27  C26     0.00   0.0  0
 C5V  CONST_15  N27  C28  C29  C30     0.00   0.0  0
 C5V  CONST_16  N27  C26  C25  C30     0.00   0.0  0
 C5V  CONST_17  C7   C6   C5   C4      0.00   0.0  0
 C5V  CONST_18  C7   C2   C3   C4      0.00   0.0  0
 C5V  CONST_19  C29  C30  C25  C23   180.00   0.0  0
 C5V  CONST_20  N27  C26  C25  C23   180.00   0.0  0
 C5V  CONST_21  C10  N9   C13  C12     0.00   0.0  0
 C5V  CONST_22  C6   C7   C2   C1    180.00   0.0  0
 C5V  CONST_23  C4   C3   C2   C1    180.00   0.0  0
 C5V  CONST_24  N8   C5   C4   C3    180.00   0.0  0
 C5V  CONST_25  N8   C5   C6   C7    180.00   0.0  0
 C5V  CONST_26  C12  C13  N9   C1    180.00   0.0  0
 C5V  CONST_27  O19  C13  N9   C10   180.00   0.0  0
 C5V  CONST_28  H17  C6   C7   C2    180.00   0.0  0
 C5V  CONST_29  H16  C4   C3   C2    180.00   0.0  0
 C5V  CONST_30  H18  C7   C2   C3    180.00   0.0  0
 C5V  CONST_31  H5   C15  C14  C11   180.00   0.0  0
 C5V  CONST_32  H7   C17  C12  C11   180.00   0.0  0
 C5V  CONST_33  H4   C14  C11  C12   180.00   0.0  0
 C5V  CONST_34  H6   C16  C17  C12   180.00   0.0  0
 C5V  CONST_35  H15  C30  C25  C23     0.00   0.0  0
 C5V  CONST_36  H12  C26  C25  C23     0.00   0.0  0
 C5V  CONST_37  H14  C29  C30  C25   180.00   0.0  0
 C5V  CONST_38  H13  C28  N27  C26   180.00   0.0  0
 C5V  CONST_39  H3   C3   C4   C5    180.00   0.0  0
 C5V  CONST_40  C5   N8   C20  C21   180.00   0.0  0
 C5V  CONST_41  C6   C5   N8   C20   180.00   0.0  0
 C5V  CONST_42  C4   C5   N8   C20     0.00   0.0  0
 C5V  CONST_43  O19  C13  N9   C1      0.00   0.0  0
 C5V  CONST_44  H19  N8   C5   C4    180.00   0.0  0
 C5V  CONST_45  O22  C20  N8   C5      0.00   0.0  0
 C5V  Var_01    C25  C23  C24  C21   108.43  30.0  1
 C5V  Var_02    C30  C25  C23  C21  -138.14  30.0  2
 C5V  Var_03    C10  N9   C1   C2    -79.95  30.0  2
 C5V  Var_04    N9   C1   C2   C3    101.83  30.0  2
 C5V  Var_05    C23  C24  C21  C20   106.96  30.0  1
 C5V  Var_06    N8   C20  C21  C23  -144.81  30.0  1

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
 C5V  chir_01  C21  C20  C24  C23  both
 C5V  chir_02  C23  C21  C24  C25  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
 C5V  plan-1  C23  0.020
 C5V  plan-1  C25  0.020
 C5V  plan-1  C26  0.020
 C5V  plan-1  C28  0.020
 C5V  plan-1  C29  0.020
 C5V  plan-1  C30  0.020
 C5V  plan-1  N27  0.020
 C5V  plan-1  H12  0.020
 C5V  plan-1  H13  0.020
 C5V  plan-1  H14  0.020
 C5V  plan-1  H15  0.020
 C5V  plan-2  C1   0.020
 C5V  plan-2  C2   0.020
 C5V  plan-2  C3   0.020
 C5V  plan-2  C4   0.020
 C5V  plan-2  C5   0.020
 C5V  plan-2  C6   0.020
 C5V  plan-2  C7   0.020
 C5V  plan-2  N8   0.020
 C5V  plan-2  H3   0.020
 C5V  plan-2  H16  0.020
 C5V  plan-2  H17  0.020
 C5V  plan-2  H18  0.020
 C5V  plan-3  C1   0.020
 C5V  plan-3  C11  0.020
 C5V  plan-3  C12  0.020
 C5V  plan-3  C13  0.020
 C5V  plan-3  C14  0.020
 C5V  plan-3  C15  0.020
 C5V  plan-3  C16  0.020
 C5V  plan-3  C17  0.020
 C5V  plan-3  N9   0.020
 C5V  plan-3  C10  0.020
 C5V  plan-3  O18  0.020
 C5V  plan-3  H4   0.020
 C5V  plan-3  H5   0.020
 C5V  plan-3  H6   0.020
 C5V  plan-3  H7   0.020
 C5V  plan-3  O19  0.020
 C5V  plan-4  C21  0.020
 C5V  plan-4  C5   0.020
 C5V  plan-4  N8   0.020
 C5V  plan-4  O22  0.020
 C5V  plan-4  H19  0.020
 C5V  plan-4  C20  0.020

