# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 20:56:44 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: (3R,4R)-4-(pyrrolidin-1-ylcarbonyl)-1-(quinoxalin-2-ylcarbonyl)pyrrolidin-3-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1CN(C[C@H]1C(=O)N2CCCC2)C(=O)c3cnc4ccccc4n3
#
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
 34Q  34Q  (3R,4R)-4-(pyrrolidin-1-ylcarbonyl)-1-(quinoxalin-2-ylcarbonyl)pyrrolidin-3-amine  ligand  46  25  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_34Q
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
 34Q  N1    N  NT    0  -0.467   0.0211   0.8640  -0.1211
 34Q  N3    N  NH2   0  -0.791   1.7228  -0.2044   2.0542
 34Q  C4    C  C     0   0.573   3.6990   0.7001   0.1155
 34Q  C5    C  CH2   0  -0.258   6.0732   0.1381   0.0892
 34Q  C6    C  CH2   0  -0.488   6.8463  -0.8843  -0.7358
 34Q  C7    C  CH2   0  -0.281   4.5274  -1.3927  -0.9854
 34Q  C8    C  CH2   0  -0.472   5.8851  -2.0642  -0.8236
 34Q  C10   C  C     0   0.536  -1.0800   1.6162  -0.1048
 34Q  C13   C  CR66  0   0.232  -4.8689  -0.0707   0.3445
 34Q  C15   C  CR16  0  -0.304  -4.1585  -1.9602  -1.0341
 34Q  C17   C  CR6   0   0.051  -2.4061   0.9387   0.0714
 34Q  O2    O  O     0  -0.492  -1.0622   2.8352  -0.2440
 34Q  C18   C  CR16  0  -0.086  -3.4177   1.6094   0.8111
 34Q  N5    N  N     0  -0.382  -4.6104   1.1106   0.9539
 34Q  C14   C  CR66  0   0.233  -3.8660  -0.7321  -0.4044
 34Q  N4    N  N     0  -0.385  -2.6292  -0.2002  -0.5179
 34Q  C16   C  CR16  0  -0.250  -5.4090  -2.5021  -0.9134
 34Q  C12   C  CR16  0  -0.298  -6.1493  -0.6511   0.4539
 34Q  C11   C  CR16  0  -0.248  -6.4096  -1.8435  -0.1659
 34Q  C1    C  CH2   0  -0.205   1.3235   1.4910  -0.3188
 34Q  C2    C  CH1   0  -0.471   2.2876   0.3117  -0.2826
 34Q  C3    C  CH1   0  -0.126   1.5969  -0.6673   0.6852
 34Q  C9    C  CH2   0  -0.262   0.1479  -0.5467   0.2324
 34Q  O1    O  O     0  -0.500   3.9340   1.7355   0.7299
 34Q  N2    N  NT    0  -0.473   4.6759  -0.1528  -0.2250
 34Q  HN3   H  HNH2  0   0.354   1.1883  -0.8140   2.6607
 34Q  HN3A  H  HNH2  0   0.354   2.6818  -0.2864   2.3687
 34Q  H5A   H  HCH2  0   0.247   6.3259   1.1659  -0.1711
 34Q  H6    H  HCH2  0   0.239   7.0483  -0.4871  -1.7328
 34Q  H6A   H  HCH2  0   0.253   7.8020  -1.1414  -0.2812
 34Q  H7    H  HCH2  0   0.245   4.3153  -1.1798  -2.0377
 34Q  H7A   H  HCH2  0   0.257   3.7201  -2.0124  -0.5981
 34Q  H8    H  HCH2  0   0.253   6.1040  -2.7447  -1.6455
 34Q  H8A   H  HCH2  0   0.241   5.9060  -2.6426   0.1025
 34Q  H15   H  HCR6  0   0.273  -3.3812  -2.4523  -1.6040
 34Q  H18   H  HCR6  0   0.280  -3.2055   2.5577   1.2904
 34Q  H16   H  HCR6  0   0.273  -5.6392  -3.4444  -1.3920
 34Q  H12   H  HCR6  0   0.273  -6.9071  -0.1372   1.0306
 34Q  H11   H  HCR6  0   0.273  -7.3918  -2.2898  -0.0861
 34Q  H1    H  HCH2  0   0.255   1.3612   2.0255  -1.2686
 34Q  H1A   H  HCH2  0   0.248   1.5304   2.2046   0.4788
 34Q  H2    H  HCH1  0   0.294   2.3052  -0.1612  -1.2691
 34Q  H3    H  HCH1  0   0.253   1.9457  -1.6955   0.5305
 34Q  H9    H  HCH2  0   0.262  -0.5498  -0.8329   1.0187
 34Q  H9A   H  HCH2  0   0.254  -0.0357  -1.1892  -0.6298
 34Q  H5    H  HCH2  0   0.237   6.2560   0.0119   1.1600

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
 34Q  N1   C10   single    1.334  0.020  1.334
 34Q  N1   C1    single    1.459  0.020  1.459
 34Q  N1   C9    single    1.460  0.020  1.460
 34Q  N3   C3    single    1.451  0.020  1.451
 34Q  C4   C2    single    1.517  0.020  1.517
 34Q  C4   O1    double    1.227  0.020  1.227
 34Q  C4   N2    single    1.341  0.020  1.341
 34Q  C5   C6    single    1.524  0.020  1.524
 34Q  C5   N2    single    1.461  0.020  1.461
 34Q  C6   C8    single    1.524  0.020  1.524
 34Q  C7   C8    single    1.523  0.020  1.523
 34Q  C7   N2    single    1.462  0.020  1.462
 34Q  C10  C17   single    1.499  0.020  1.499
 34Q  C10  O2    double    1.227  0.020  1.227
 34Q  C13  N5    aromatic  1.354  0.020  1.354
 34Q  C13  C14   aromatic  1.416  0.020  1.416
 34Q  C13  C12   aromatic  1.410  0.020  1.410
 34Q  C15  C14   aromatic  1.411  0.020  1.411
 34Q  C15  C16   aromatic  1.368  0.020  1.368
 34Q  C17  C18   aromatic  1.421  0.020  1.421
 34Q  C17  N4    aromatic  1.302  0.020  1.302
 34Q  C18  N5    aromatic  1.301  0.020  1.301
 34Q  C14  N4    aromatic  1.351  0.020  1.351
 34Q  C16  C11   aromatic  1.412  0.020  1.412
 34Q  C12  C11   aromatic  1.369  0.020  1.369
 34Q  C1   C2    single    1.524  0.020  1.524
 34Q  C2   C3    single    1.540  0.020  1.540
 34Q  C3   C9    single    1.523  0.020  1.523
 34Q  N3   HN3   single    0.890  0.020  1.040
 34Q  N3   HN3A  single    0.890  0.020  1.040
 34Q  C5   H5    single    0.970  0.020  1.090
 34Q  C5   H5A   single    0.970  0.020  1.090
 34Q  C6   H6    single    0.970  0.020  1.090
 34Q  C6   H6A   single    0.970  0.020  1.090
 34Q  C7   H7    single    0.970  0.020  1.090
 34Q  C7   H7A   single    0.970  0.020  1.090
 34Q  C8   H8    single    0.970  0.020  1.090
 34Q  C8   H8A   single    0.970  0.020  1.090
 34Q  C15  H15   single    0.930  0.020  1.080
 34Q  C18  H18   single    0.930  0.020  1.080
 34Q  C16  H16   single    0.930  0.020  1.080
 34Q  C12  H12   single    0.930  0.020  1.080
 34Q  C11  H11   single    0.930  0.020  1.080
 34Q  C1   H1    single    0.970  0.020  1.090
 34Q  C1   H1A   single    0.970  0.020  1.090
 34Q  C2   H2    single    0.970  0.020  1.090
 34Q  C3   H3    single    0.970  0.020  1.090
 34Q  C9   H9    single    0.970  0.020  1.090
 34Q  C9   H9A   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
 34Q  C9    N1   C1   111.75  3.000
 34Q  C9    N1   C10  127.86  3.000
 34Q  C1    N1   C10  119.76  3.000
 34Q  HN3A  N3   HN3  105.38  3.000
 34Q  HN3A  N3   C3   110.45  3.000
 34Q  HN3   N3   C3   109.10  3.000
 34Q  N2    C4   O1   121.63  3.000
 34Q  N2    C4   C2   116.64  3.000
 34Q  O1    C4   C2   121.73  3.000
 34Q  H5A   C5   H5   107.69  3.000
 34Q  H5A   C5   N2   110.98  3.000
 34Q  H5    C5   N2   110.33  3.000
 34Q  H5A   C5   C6   112.68  3.000
 34Q  H5    C5   C6   111.58  3.000
 34Q  N2    C5   C6   103.59  3.000
 34Q  H6A   C6   H6   107.73  3.000
 34Q  H6A   C6   C8   113.25  3.000
 34Q  H6    C6   C8   110.22  3.000
 34Q  H6A   C6   C5   112.17  3.000
 34Q  H6    C6   C5   110.12  3.000
 34Q  C8    C6   C5   103.33  3.000
 34Q  H7A   C7   H7   108.00  3.000
 34Q  H7A   C7   N2   111.90  3.000
 34Q  H7    C7   N2   110.78  3.000
 34Q  H7A   C7   C8   111.85  3.000
 34Q  H7    C7   C8   111.13  3.000
 34Q  N2    C7   C8   103.18  3.000
 34Q  H8A   C8   H8   107.76  3.000
 34Q  H8A   C8   C7   109.92  3.000
 34Q  H8    C8   C7   111.99  3.000
 34Q  H8A   C8   C6   110.43  3.000
 34Q  H8    C8   C6   113.60  3.000
 34Q  C7    C8   C6   103.12  3.000
 34Q  O2    C10  C17  118.36  3.000
 34Q  O2    C10  N1   123.15  3.000
 34Q  C17   C10  N1   118.48  3.000
 34Q  C12   C13  C14  119.47  3.000
 34Q  C12   C13  N5   119.84  3.000
 34Q  C14   C13  N5   120.69  3.000
 34Q  H15   C15  C16  121.52  3.000
 34Q  H15   C15  C14  118.82  3.000
 34Q  C16   C15  C14  119.66  3.000
 34Q  N4    C17  C18  121.77  3.000
 34Q  N4    C17  C10  119.59  3.000
 34Q  C18   C17  C10  118.51  3.000
 34Q  H18   C18  N5   117.82  3.000
 34Q  H18   C18  C17  120.25  3.000
 34Q  N5    C18  C17  121.92  3.000
 34Q  C18   N5   C13  117.40  3.000
 34Q  N4    C14  C15  119.67  3.000
 34Q  N4    C14  C13  120.60  3.000
 34Q  C15   C14  C13  119.73  3.000
 34Q  C14   N4   C17  117.61  3.000
 34Q  H16   C16  C11  119.33  3.000
 34Q  H16   C16  C15  120.03  3.000
 34Q  C11   C16  C15  120.64  3.000
 34Q  H12   C12  C11  121.45  3.000
 34Q  H12   C12  C13  118.80  3.000
 34Q  C11   C12  C13  119.74  3.000
 34Q  H11   C11  C12  119.91  3.000
 34Q  H11   C11  C16  119.34  3.000
 34Q  C12   C11  C16  120.75  3.000
 34Q  H1A   C1   H1   108.05  3.000
 34Q  H1A   C1   C2   111.67  3.000
 34Q  H1    C1   C2   112.22  3.000
 34Q  H1A   C1   N1   110.59  3.000
 34Q  H1    C1   N1   111.07  3.000
 34Q  C2    C1   N1   103.24  3.000
 34Q  H2    C2   C3   107.40  3.000
 34Q  H2    C2   C1   108.86  3.000
 34Q  C3    C2   C1   102.89  3.000
 34Q  H2    C2   C4   109.41  3.000
 34Q  C3    C2   C4   114.52  3.000
 34Q  C1    C2   C4   113.37  3.000
 34Q  H3    C3   C9   109.56  3.000
 34Q  H3    C3   C2   111.39  3.000
 34Q  C9    C3   C2   100.93  3.000
 34Q  H3    C3   N3   113.87  3.000
 34Q  C9    C3   N3   109.75  3.000
 34Q  C2    C3   N3   110.57  3.000
 34Q  H9A   C9   H9   107.93  3.000
 34Q  H9A   C9   C3   110.40  3.000
 34Q  H9    C9   C3   111.96  3.000
 34Q  H9A   C9   N1   111.29  3.000
 34Q  H9    C9   N1   111.90  3.000
 34Q  C3    C9   N1   103.37  3.000
 34Q  C7    N2   C5   112.19  3.000
 34Q  C7    N2   C4   126.69  3.000
 34Q  C5    N2   C4   121.03  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
 34Q  CONST_01  C17  C18  N5   C13    0.00   0.0  0
 34Q  CONST_02  C16  C15  C14  C13    0.00   0.0  0
 34Q  CONST_03  C17  N4   C14  C13    0.00   0.0  0
 34Q  CONST_04  C16  C11  C12  C13    0.00   0.0  0
 34Q  CONST_05  N5   C13  C14  C15  180.00   0.0  0
 34Q  CONST_06  C12  C13  C14  C15    0.00   0.0  0
 34Q  CONST_07  C17  N4   C14  C15  180.00   0.0  0
 34Q  CONST_08  C12  C11  C16  C15    0.00   0.0  0
 34Q  CONST_09  C14  N4   C17  C18    0.00   0.0  0
 34Q  CONST_10  C14  C13  N5   C18    0.00   0.0  0
 34Q  CONST_11  C12  C13  N5   C18  180.00   0.0  0
 34Q  CONST_12  N4   C14  C13  N5     0.00   0.0  0
 34Q  CONST_13  C11  C12  C13  N5   180.00   0.0  0
 34Q  CONST_14  N4   C17  C18  N5     0.00   0.0  0
 34Q  CONST_15  C11  C12  C13  C14    0.00   0.0  0
 34Q  CONST_16  C11  C16  C15  C14    0.00   0.0  0
 34Q  CONST_17  C12  C13  C14  N4   180.00   0.0  0
 34Q  CONST_18  C16  C15  C14  N4   180.00   0.0  0
 34Q  CONST_19  N5   C18  C17  C10  180.00   0.0  0
 34Q  CONST_20  C14  N4   C17  C10  180.00   0.0  0
 34Q  CONST_21  C2   C4   N2   C5   180.00   0.0  0
 34Q  CONST_22  C2   C4   N2   C7     0.00   0.0  0
 34Q  CONST_23  C1   N1   C10  C17  180.00   0.0  0
 34Q  CONST_24  C9   N1   C10  C17    0.00   0.0  0
 34Q  CONST_25  H18  C18  N5   C13  180.00   0.0  0
 34Q  CONST_26  H15  C15  C14  C13  180.00   0.0  0
 34Q  CONST_27  H11  C11  C12  C13  180.00   0.0  0
 34Q  CONST_28  H12  C12  C13  N5     0.00   0.0  0
 34Q  CONST_29  H16  C16  C15  C14  180.00   0.0  0
 34Q  CONST_30  O1   C4   N2   C5     0.00   0.0  0
 34Q  CONST_31  O1   C4   N2   C7   180.00   0.0  0
 34Q  CONST_32  C1   N1   C10  O2     0.00   0.0  0
 34Q  CONST_33  C9   N1   C10  O2   180.00   0.0  0
 34Q  Var_01    C7   C8   C6   C5    38.42  30.0  1
 34Q  Var_02    C8   C7   N2   C5    14.34  30.0  1
 34Q  Var_03    C7   N2   C5   C6     9.53  30.0  1
 34Q  Var_04    N2   C7   C8   C6   -32.23  30.0  1
 34Q  Var_05    N2   C5   C6   C8   -29.46  30.0  1
 34Q  Var_06    C3   C9   N1   C1    17.72  30.0  1
 34Q  Var_07    C9   N1   C1   C2     8.79  30.0  1
 34Q  Var_08    C18  C17  C10  N1   144.98  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
 34Q  chir_01  C2  C4  C1  C3  positiv
 34Q  chir_02  C3  N3  C2  C9  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
 34Q  plan-1  C4   0.020
 34Q  plan-1  C5   0.020
 34Q  plan-1  C7   0.020
 34Q  plan-1  C2   0.020
 34Q  plan-1  O1   0.020
 34Q  plan-1  N2   0.020
 34Q  plan-2  C10  0.020
 34Q  plan-2  C13  0.020
 34Q  plan-2  C15  0.020
 34Q  plan-2  C17  0.020
 34Q  plan-2  C18  0.020
 34Q  plan-2  N5   0.020
 34Q  plan-2  C14  0.020
 34Q  plan-2  N4   0.020
 34Q  plan-2  C16  0.020
 34Q  plan-2  C12  0.020
 34Q  plan-2  C11  0.020
 34Q  plan-2  H15  0.020
 34Q  plan-2  H18  0.020
 34Q  plan-2  H16  0.020
 34Q  plan-2  H12  0.020
 34Q  plan-2  H11  0.020
 34Q  plan-3  N1   0.020
 34Q  plan-3  C10  0.020
 34Q  plan-3  C17  0.020
 34Q  plan-3  O2   0.020
 34Q  plan-3  C1   0.020
 34Q  plan-3  C9   0.020

