# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 20:54:43 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: 4-[(1S,4S)-5-(3-chlorophenyl)-2,5-diazabicyclo[2.2.1]heptan-2-yl]-2-(pyridin-3-yl)pyrimidine-5-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cccc(c1)N2C[C@@H]3C[C@H]2CN3c4nc(ncc4C#N)c5cccnc5
#
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
 M5V  M5V  4-[(1S,4S)-5-(3-chlorophenyl)-2,5-diazabicyclo[2.2.1]heptan-2-yl]-2-(pyridin-3-yl)pyrimidine-5-carbonitrile  ligand  45  28  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_M5V
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
 M5V  C2   C   CH2   0  -0.253  -0.5934   0.9371   0.9717
 M5V  C3   C   CH1   0  -0.207  -1.4129   2.2048   0.7171
 M5V  C4   C   CH2   0  -0.429  -2.7979   1.7486   1.1549
 M5V  C5   C   CH1   0  -0.212  -2.8098   0.5962   0.1566
 M5V  C6   C   CH2   0  -0.256  -2.5751   1.3355  -1.1594
 M5V  C8   C   CR6   0   0.388  -0.6868   2.8890  -1.5702
 M5V  C11  C   CR16  0  -0.269   1.1944   4.0286  -3.3488
 M5V  C12  C   CR6   0  -0.023   1.3718   4.0749  -1.9762
 M5V  C15  C   CR6   0   0.609  -1.2179  -1.3531   0.3557
 M5V  C17  C   CR6   0   0.424   0.3626  -2.9600   0.7999
 M5V  C19  C   CR16  0   0.009  -1.4906  -3.6499  -0.2633
 M5V  C21  C   CSP   0   0.024  -3.2154  -2.1427  -0.9803
 M5V  N22  N   NS    0  -0.249  -4.1976  -2.0279  -1.5756
 M5V  C23  C   CR6   0  -0.106   1.6845  -3.2796   1.3697
 M5V  C24  C   CR16  0  -0.062   2.5025  -2.2758   1.8896
 M5V  C27  C   CR16  0  -0.313   3.4083  -4.8295   1.9564
 M5V  N1   N   NT    0  -0.477  -1.5539  -0.0762   0.5062
 M5V  N7   N   NT    0  -0.504  -1.6180   2.3572  -0.7218
 M5V  C9   C   CR16  0  -0.349  -0.8787   2.8398  -2.9620
 M5V  C10  C   CR16  0  -0.244   0.0489   3.4000  -3.8210
 M5V  CL1  CL  CL    0  -0.136   2.7911   4.8461  -1.3344
 M5V  C14  C   CR16  0  -0.314   0.4689   3.5223  -1.0854
 M5V  N16  N   N     0  -0.490  -0.0266  -1.7046   0.8551
 M5V  N18  N   N     0  -0.457  -0.3326  -3.9727   0.2760
 M5V  C20  C   CR6   0  -0.166  -2.0035  -2.3574  -0.2808
 M5V  N25  N   N     0  -0.401   3.6983  -2.5019   2.4126
 M5V  C26  C   CR16  0  -0.058   4.1380  -3.7558   2.4444
 M5V  C28  C   CR16  0  -0.158   2.1611  -4.5875   1.4085
 M5V  H1   H   HCH2  0   0.269   0.3317   0.8985   0.3957
 M5V  H2   H   HCH2  0   0.267  -0.3494   0.8086   2.0282
 M5V  H3   H   HCH1  0   0.288  -1.0258   3.1009   1.1954
 M5V  H4   H   HCH2  0   0.278  -2.8424   1.4217   2.1931
 M5V  H5   H   HCH2  0   0.279  -3.5778   2.4844   0.9642
 M5V  H6   H   HCH1  0   0.299  -3.6761  -0.0545   0.1887
 M5V  H7   H   HCH2  0   0.256  -2.1519   0.6808  -1.9257
 M5V  H8   H   HCH2  0   0.260  -3.4988   1.7694  -1.5524
 M5V  H9   H   HCR6  0   0.270   1.9167   4.4636  -4.0247
 M5V  H10  H   HCR6  0   0.296  -2.0601  -4.4493  -0.7246
 M5V  H11  H   HCR6  0   0.273   2.1650  -1.2463   1.8758
 M5V  H12  H   HCR6  0   0.277   3.8108  -5.8314   2.0077
 M5V  H13  H   HCR6  0   0.273  -1.7640   2.3759  -3.3748
 M5V  H14  H   HCR6  0   0.264  -0.1259   3.3493  -4.8880
 M5V  H15  H   HCR6  0   0.282   0.6689   3.5859  -0.0253
 M5V  H16  H   HCR6  0   0.273   5.1178  -3.9149   2.8806
 M5V  H17  H   HCR6  0   0.274   1.5622  -5.3987   1.0179

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
 M5V  C10  C11  aromatic  1.389  0.020  1.389
 M5V  C10  C9   aromatic  1.383  0.020  1.383
 M5V  C11  C12  aromatic  1.385  0.020  1.385
 M5V  C9   C8   aromatic  1.406  0.020  1.406
 M5V  C12  CL1  single    1.738  0.020  1.738
 M5V  C12  C14  aromatic  1.384  0.020  1.384
 M5V  C26  C27  aromatic  1.387  0.020  1.387
 M5V  C26  N25  aromatic  1.329  0.020  1.329
 M5V  C27  C28  aromatic  1.384  0.020  1.384
 M5V  N25  C24  aromatic  1.325  0.020  1.325
 M5V  C28  C23  aromatic  1.393  0.020  1.393
 M5V  C24  C23  aromatic  1.395  0.020  1.395
 M5V  C23  C17  single    1.475  0.020  1.475
 M5V  C8   C14  aromatic  1.404  0.020  1.404
 M5V  C8   N7   single    1.367  0.020  1.367
 M5V  N18  C17  aromatic  1.335  0.020  1.335
 M5V  N18  C19  aromatic  1.318  0.020  1.318
 M5V  C17  N16  aromatic  1.315  0.020  1.315
 M5V  C19  C20  aromatic  1.391  0.020  1.391
 M5V  C6   N7   single    1.467  0.020  1.467
 M5V  C6   C5   single    1.528  0.020  1.528
 M5V  N16  C15  aromatic  1.339  0.020  1.339
 M5V  N7   C3   single    1.461  0.020  1.461
 M5V  C20  C15  aromatic  1.425  0.020  1.425
 M5V  C20  C21  single    1.416  0.020  1.416
 M5V  C15  N1   single    1.329  0.020  1.329
 M5V  C21  N22  triple    1.154  0.020  1.154
 M5V  C5   N1   single    1.467  0.020  1.467
 M5V  C5   C4   single    1.525  0.020  1.525
 M5V  C2   N1   single    1.472  0.020  1.472
 M5V  C2   C3   single    1.531  0.020  1.531
 M5V  C3   C4   single    1.523  0.020  1.523
 M5V  C2   H1   single    0.970  0.020  1.090
 M5V  C2   H2   single    0.970  0.020  1.090
 M5V  C3   H3   single    0.970  0.020  1.090
 M5V  C4   H4   single    0.970  0.020  1.090
 M5V  C4   H5   single    0.970  0.020  1.090
 M5V  C5   H6   single    0.970  0.020  1.090
 M5V  C6   H7   single    0.970  0.020  1.090
 M5V  C6   H8   single    0.970  0.020  1.090
 M5V  C11  H9   single    0.930  0.020  1.080
 M5V  C19  H10  single    0.930  0.020  1.080
 M5V  C24  H11  single    0.930  0.020  1.080
 M5V  C27  H12  single    0.930  0.020  1.080
 M5V  C9   H13  single    0.930  0.020  1.080
 M5V  C10  H14  single    0.930  0.020  1.080
 M5V  C14  H15  single    0.930  0.020  1.080
 M5V  C26  H16  single    0.930  0.020  1.080
 M5V  C28  H17  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
 M5V  H2   C2   H1   108.51  3.000
 M5V  H2   C2   N1   111.77  3.000
 M5V  H1   C2   N1   111.23  3.000
 M5V  H2   C2   C3   112.21  3.000
 M5V  H1   C2   C3   113.31  3.000
 M5V  N1   C2   C3    99.68  3.000
 M5V  H3   C3   N7   113.40  3.000
 M5V  H3   C3   C4   116.39  3.000
 M5V  N7   C3   C4   100.76  3.000
 M5V  H3   C3   C2   114.76  3.000
 M5V  C4   C3   C2   101.01  3.000
 M5V  N7   C3   C2   108.98  3.000
 M5V  H5   C4   H4   109.90  3.000
 M5V  H5   C4   C5   112.98  3.000
 M5V  H4   C4   C5   113.39  3.000
 M5V  H5   C4   C3   113.49  3.000
 M5V  H4   C4   C3   113.65  3.000
 M5V  C5   C4   C3    92.59  3.000
 M5V  H6   C5   N1   113.71  3.000
 M5V  H6   C5   C6   116.03  3.000
 M5V  N1   C5   C6   107.20  3.000
 M5V  H6   C5   C4   116.13  3.000
 M5V  N1   C5   C4   100.59  3.000
 M5V  C6   C5   C4   101.37  3.000
 M5V  H8   C6   H7   108.22  3.000
 M5V  H8   C6   N7   112.45  3.000
 M5V  H7   C6   N7   111.95  3.000
 M5V  H8   C6   C5   111.83  3.000
 M5V  H7   C6   C5   111.94  3.000
 M5V  N7   C6   C5   100.39  3.000
 M5V  C14  C8   C9   118.03  3.000
 M5V  C14  C8   N7   121.44  3.000
 M5V  C9   C8   N7   120.51  3.000
 M5V  H9   C11  C10  121.38  3.000
 M5V  H9   C11  C12  121.39  3.000
 M5V  C10  C11  C12  117.24  3.000
 M5V  C14  C12  CL1  118.19  3.000
 M5V  C14  C12  C11  122.77  3.000
 M5V  CL1  C12  C11  119.04  3.000
 M5V  C20  C15  N16  118.17  3.000
 M5V  C20  C15  N1   126.04  3.000
 M5V  N16  C15  N1   115.79  3.000
 M5V  N18  C17  N16  125.89  3.000
 M5V  N16  C17  C23  117.12  3.000
 M5V  N18  C17  C23  116.99  3.000
 M5V  H10  C19  C20  119.08  3.000
 M5V  H10  C19  N18  117.07  3.000
 M5V  C20  C19  N18  123.85  3.000
 M5V  C20  C21  N22  180.00  3.000
 M5V  C28  C23  C24  117.69  3.000
 M5V  C24  C23  C17  120.90  3.000
 M5V  C28  C23  C17  121.41  3.000
 M5V  H11  C24  N25  116.64  3.000
 M5V  H11  C24  C23  119.75  3.000
 M5V  N25  C24  C23  123.61  3.000
 M5V  H12  C27  C28  121.10  3.000
 M5V  H12  C27  C26  120.33  3.000
 M5V  C28  C27  C26  118.57  3.000
 M5V  C15  N1   C5   129.05  3.000
 M5V  C5   N1   C2   108.58  3.000
 M5V  C15  N1   C2   122.16  3.000
 M5V  C8   N7   C6   122.01  3.000
 M5V  C6   N7   C3   108.22  3.000
 M5V  C8   N7   C3   123.78  3.000
 M5V  H13  C9   C10  119.07  3.000
 M5V  H13  C9   C8   120.31  3.000
 M5V  C10  C9   C8   120.61  3.000
 M5V  H14  C10  C9   119.02  3.000
 M5V  H14  C10  C11  119.30  3.000
 M5V  C9   C10  C11  121.68  3.000
 M5V  H15  C14  C12  119.16  3.000
 M5V  H15  C14  C8   121.17  3.000
 M5V  C12  C14  C8   119.67  3.000
 M5V  C17  N16  C15  119.88  3.000
 M5V  C19  N18  C17  115.62  3.000
 M5V  C21  C20  C19  117.58  3.000
 M5V  C21  C20  C15  125.85  3.000
 M5V  C19  C20  C15  116.49  3.000
 M5V  C26  N25  C24  117.97  3.000
 M5V  H16  C26  N25  116.55  3.000
 M5V  H16  C26  C27  120.23  3.000
 M5V  N25  C26  C27  123.22  3.000
 M5V  H17  C28  C27  120.74  3.000
 M5V  H17  C28  C23  120.33  3.000
 M5V  C27  C28  C23  118.93  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
 M5V  CONST_01  C11  C10  C9   C8     0.00   0.0  0
 M5V  CONST_02  C11  C12  C14  C8     0.00   0.0  0
 M5V  CONST_03  C9   C10  C11  C12    0.00   0.0  0
 M5V  CONST_04  C9   C8   C14  C12    0.00   0.0  0
 M5V  CONST_05  C23  C17  N16  C15  180.00   0.0  0
 M5V  CONST_06  N18  C17  N16  C15    0.00   0.0  0
 M5V  CONST_07  N18  C19  C20  C15    0.00   0.0  0
 M5V  CONST_08  C27  C28  C23  C17  180.00   0.0  0
 M5V  CONST_09  N25  C24  C23  C17  180.00   0.0  0
 M5V  CONST_10  C20  C19  N18  C17    0.00   0.0  0
 M5V  CONST_11  C20  C15  N16  C17    0.00   0.0  0
 M5V  CONST_12  C23  C17  N18  C19  180.00   0.0  0
 M5V  CONST_13  N16  C17  N18  C19    0.00   0.0  0
 M5V  CONST_14  N16  C15  C20  C19    0.00   0.0  0
 M5V  CONST_15  C26  C27  C28  C23    0.00   0.0  0
 M5V  CONST_16  C26  N25  C24  C23    0.00   0.0  0
 M5V  CONST_17  C27  C26  N25  C24    0.00   0.0  0
 M5V  CONST_18  C27  C28  C23  C24    0.00   0.0  0
 M5V  CONST_19  N18  C17  C23  C24  180.00   0.0  0
 M5V  CONST_20  N16  C17  C23  C24    0.00   0.0  0
 M5V  CONST_21  C14  C12  C11  C10    0.00   0.0  0
 M5V  CONST_22  C14  C8   C9   C10    0.00   0.0  0
 M5V  CONST_23  C28  C23  C17  N16  180.00   0.0  0
 M5V  CONST_24  C28  C23  C17  N18    0.00   0.0  0
 M5V  CONST_25  C28  C27  C26  N25    0.00   0.0  0
 M5V  CONST_26  C28  C23  C24  N25    0.00   0.0  0
 M5V  CONST_27  N7   C8   C14  C12  180.00   0.0  0
 M5V  CONST_28  N1   C15  N16  C17  180.00   0.0  0
 M5V  CONST_29  N1   C15  C20  C19  180.00   0.0  0
 M5V  CONST_30  C10  C9   C8   N7   180.00   0.0  0
 M5V  CONST_31  CL1  C12  C14  C8   180.00   0.0  0
 M5V  CONST_32  N18  C19  C20  C21  180.00   0.0  0
 M5V  CONST_33  N16  C15  C20  C21  180.00   0.0  0
 M5V  CONST_34  N1   C15  C20  C21    0.00   0.0  0
 M5V  CONST_35  CL1  C12  C11  C10  180.00   0.0  0
 M5V  CONST_36  H14  C10  C9   C8   180.00   0.0  0
 M5V  CONST_37  H13  C9   C10  C11  180.00   0.0  0
 M5V  CONST_38  H15  C14  C12  C11  180.00   0.0  0
 M5V  CONST_39  H10  C19  C20  C15  180.00   0.0  0
 M5V  CONST_40  H17  C28  C23  C17    0.00   0.0  0
 M5V  CONST_41  H11  C24  C23  C17    0.00   0.0  0
 M5V  CONST_42  H12  C27  C28  C23  180.00   0.0  0
 M5V  CONST_43  H16  C26  N25  C24  180.00   0.0  0
 M5V  CONST_44  H9   C11  C10  C9   180.00   0.0  0
 M5V  Var_01    N16  C15  N1   C2    10.45  30.0  3
 M5V  Var_02    C9   C8   N7   C3   171.37  30.0  2
 M5V  Var_03    C5   C6   N7   C3    -2.31  30.0  1
 M5V  Var_04    C15  N1   C2   C3   170.36  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
 M5V  chir_01  C3  N7  C2  C4  positiv
 M5V  chir_02  C5  N1  C6  C4  positiv

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
 M5V  plan-1  C8   0.020
 M5V  plan-1  C11  0.020
 M5V  plan-1  C12  0.020
 M5V  plan-1  N7   0.020
 M5V  plan-1  C9   0.020
 M5V  plan-1  C10  0.020
 M5V  plan-1  CL1  0.020
 M5V  plan-1  C14  0.020
 M5V  plan-1  H9   0.020
 M5V  plan-1  H13  0.020
 M5V  plan-1  H14  0.020
 M5V  plan-1  H15  0.020
 M5V  plan-2  C15  0.020
 M5V  plan-2  C17  0.020
 M5V  plan-2  C19  0.020
 M5V  plan-2  C21  0.020
 M5V  plan-2  N22  0.020
 M5V  plan-2  C23  0.020
 M5V  plan-2  N1   0.020
 M5V  plan-2  N16  0.020
 M5V  plan-2  N18  0.020
 M5V  plan-2  C20  0.020
 M5V  plan-2  H10  0.020
 M5V  plan-3  C17  0.020
 M5V  plan-3  C23  0.020
 M5V  plan-3  C24  0.020
 M5V  plan-3  C27  0.020
 M5V  plan-3  N25  0.020
 M5V  plan-3  C26  0.020
 M5V  plan-3  C28  0.020
 M5V  plan-3  H11  0.020
 M5V  plan-3  H12  0.020
 M5V  plan-3  H16  0.020
 M5V  plan-3  H17  0.020

