# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 13 07:00:42 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: 6-{[(3S,4S)-4-{2-[(2-methoxybenzyl)amino]ethoxy}pyrrolidin-3-yl]methyl}-4-methylpyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccccc1CNCCO[C@@H]2CNC[C@@H]2Cc3cc(C)cc(N)n3
#
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
 08R  08R  6-{[(3S,4S)-4-{2-[(2-methoxybenzyl)amino]ethoxy}pyrrolidin-3-yl]methyl}-4-methylpyridin-2-amine  ligand  57  27  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_08R
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
 08R  N02  N  NH2   0  -0.839   4.9676   2.2791   2.0918
 08R  C02  C  CR6   0   0.440   4.1782   2.2130   0.9769
 08R  C03  C  CR16  0  -0.447   4.2696   3.1934  -0.0254
 08R  C04  C  CR6   0   0.205   3.4210   3.1210  -1.1118
 08R  C07  C  CH3   0  -0.727   3.4585   4.1501  -2.2000
 08R  C05  C  CR16  0  -0.433   2.5075   2.0634  -1.1639
 08R  N01  N  N     0  -0.472   3.3047   1.2135   0.9171
 08R  C06  C  CR6   0   0.268   2.4871   1.1370  -0.1350
 08R  C08  C  CH2   0  -0.490   1.5554  -0.0411  -0.1802
 08R  C3'  C  CH1   0  -0.277   2.2801  -1.3162  -0.6098
 08R  C2'  C  CH2   0  -0.288   3.2185  -1.9495   0.4186
 08R  N1'  N  NH1   0  -0.603   3.4851  -3.2952  -0.0799
 08R  C5'  C  CH2   0  -0.305   2.3067  -3.7098  -0.8548
 08R  C4'  C  CH1   0   0.021   1.3655  -2.4917  -0.9558
 08R  O09  O  O2    0  -0.500   0.3232  -2.5411  -0.0075
 08R  C10  C  CH2   0  -0.157  -0.7634  -3.3642  -0.3584
 08R  C11  C  CH2   0  -0.303  -1.9127  -3.0675   0.5787
 08R  N12  N  NH1   0  -0.587  -2.3787  -1.7048   0.4159
 08R  C13  C  CH2   0  -0.315  -3.4534  -1.3675   1.3331
 08R  C21  C  CR6   0  -0.010  -3.8576   0.0707   1.1708
 08R  C22  C  CR6   0   0.360  -4.6186   0.4927   0.0683
 08R  O22  O  O2    0  -0.462  -5.0035  -0.4687  -0.7917
 08R  C27  C  CH3   0  -0.436  -5.8157  -0.1142  -1.8917
 08R  C26  C  CR16  0  -0.289  -3.4431   1.0216   2.0917
 08R  C25  C  CR16  0  -0.273  -3.7630   2.3682   1.9515
 08R  C24  C  CR16  0  -0.253  -4.5146   2.7675   0.8607
 08R  C23  C  CR16  0  -0.385  -4.9465   1.8380  -0.0800
 08R  H1   H  HNH2  0   0.378   5.0672   1.4180   2.6047
 08R  H2   H  HNH2  0   0.386   5.8227   2.8052   2.0181
 08R  H3   H  HCR6  0   0.255   4.9982   3.9906   0.0596
 08R  H4   H  HCH3  0   0.249   3.4647   3.6820  -3.1848
 08R  H5   H  HCH3  0   0.254   2.5734   4.7869  -2.1546
 08R  H6   H  HCH3  0   0.246   4.3349   4.7912  -2.1210
 08R  H7   H  HCR6  0   0.241   1.8253   1.9658  -1.9994
 08R  H8   H  HCH2  0   0.238   1.1055  -0.1816   0.8050
 08R  H9   H  HCH2  0   0.243   0.7427   0.1704  -0.8791
 08R  H10  H  HCH1  0   0.245   2.8657  -1.0969  -1.5111
 08R  H11  H  HCH2  0   0.239   4.1480  -1.3995   0.5554
 08R  H12  H  HCH2  0   0.207   2.7247  -1.9920   1.3962
 08R  H13  H  HNH1  0   0.348   4.2804  -3.2505  -0.7017
 08R  H15  H  HCH2  0   0.231   2.6039  -4.0573  -1.8455
 08R  H16  H  HCH2  0   0.222   1.7909  -4.5451  -0.3714
 08R  H17  H  HCH1  0   0.227   0.9409  -2.3923  -1.9638
 08R  H18  H  HCH2  0   0.198  -1.0767  -3.1698  -1.3936
 08R  H19  H  HCH2  0   0.205  -0.5034  -4.4289  -0.2909
 08R  H20  H  HCH2  0   0.227  -2.7299  -3.7526   0.3349
 08R  H21  H  HCH2  0   0.198  -1.6135  -3.2994   1.6140
 08R  H22  H  HNH1  0   0.339  -1.6030  -1.0751   0.5831
 08R  H24  H  HCH2  0   0.231  -4.2993  -2.0305   1.1313
 08R  H25  H  HCH2  0   0.209  -3.1761  -1.5381   2.3849
 08R  H26  H  HCH3  0   0.227  -5.3118   0.5834  -2.5661
 08R  H27  H  HCH3  0   0.258  -6.0215  -1.0350  -2.4323
 08R  H28  H  HCH3  0   0.227  -6.7644   0.3276  -1.5759
 08R  H29  H  HCR6  0   0.249  -2.8571   0.6964   2.9440
 08R  H30  H  HCR6  0   0.249  -3.4284   3.0892   2.6854
 08R  H31  H  HCR6  0   0.257  -4.7773   3.8094   0.7287
 08R  H32  H  HCR6  0   0.276  -5.5332   2.1812  -0.9213

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
 08R  C07  C04  single    1.498  0.020  1.498
 08R  C04  C03  aromatic  1.380  0.020  1.380
 08R  C04  C05  aromatic  1.399  0.020  1.399
 08R  C03  C02  aromatic  1.405  0.020  1.405
 08R  C05  C06  aromatic  1.385  0.020  1.385
 08R  C02  N02  single    1.368  0.020  1.368
 08R  C02  N01  aromatic  1.329  0.020  1.329
 08R  C06  N01  aromatic  1.335  0.020  1.335
 08R  C06  C08  single    1.503  0.020  1.503
 08R  C3'  C2'  single    1.529  0.020  1.529
 08R  C3'  C08  single    1.528  0.020  1.528
 08R  C3'  C4'  single    1.529  0.020  1.529
 08R  C2'  N1'  single    1.460  0.020  1.460
 08R  C10  O09  single    1.408  0.020  1.408
 08R  C10  C11  single    1.512  0.020  1.512
 08R  C4'  O09  single    1.410  0.020  1.410
 08R  C4'  C5'  single    1.543  0.020  1.543
 08R  N1'  C5'  single    1.470  0.020  1.470
 08R  C11  N12  single    1.449  0.020  1.449
 08R  N12  C13  single    1.453  0.020  1.453
 08R  C13  C21  single    1.503  0.020  1.503
 08R  O22  C22  single    1.346  0.020  1.346
 08R  O22  C27  single    1.413  0.020  1.413
 08R  C21  C22  aromatic  1.405  0.020  1.405
 08R  C21  C26  aromatic  1.387  0.020  1.387
 08R  C22  C23  aromatic  1.393  0.020  1.393
 08R  C26  C25  aromatic  1.391  0.020  1.391
 08R  C23  C24  aromatic  1.391  0.020  1.391
 08R  C25  C24  aromatic  1.384  0.020  1.384
 08R  N02  H1   single    0.890  0.020  1.040
 08R  N02  H2   single    0.890  0.020  1.040
 08R  C03  H3   single    0.930  0.020  1.080
 08R  C07  H4   single    0.970  0.020  1.090
 08R  C07  H5   single    0.970  0.020  1.090
 08R  C07  H6   single    0.970  0.020  1.090
 08R  C05  H7   single    0.930  0.020  1.080
 08R  C08  H8   single    0.970  0.020  1.090
 08R  C08  H9   single    0.970  0.020  1.090
 08R  C3'  H10  single    0.970  0.020  1.090
 08R  C2'  H11  single    0.970  0.020  1.090
 08R  C2'  H12  single    0.970  0.020  1.090
 08R  N1'  H13  single    0.890  0.020  1.040
 08R  C5'  H15  single    0.970  0.020  1.090
 08R  C5'  H16  single    0.970  0.020  1.090
 08R  C4'  H17  single    0.970  0.020  1.090
 08R  C10  H18  single    0.970  0.020  1.090
 08R  C10  H19  single    0.970  0.020  1.090
 08R  C11  H20  single    0.970  0.020  1.090
 08R  C11  H21  single    0.970  0.020  1.090
 08R  N12  H22  single    0.890  0.020  1.040
 08R  C13  H24  single    0.970  0.020  1.090
 08R  C13  H25  single    0.970  0.020  1.090
 08R  C27  H26  single    0.970  0.020  1.090
 08R  C27  H27  single    0.970  0.020  1.090
 08R  C27  H28  single    0.970  0.020  1.090
 08R  C26  H29  single    0.930  0.020  1.080
 08R  C25  H30  single    0.930  0.020  1.080
 08R  C24  H31  single    0.930  0.020  1.080
 08R  C23  H32  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
 08R  H2   N02  H1   113.59  3.000
 08R  H2   N02  C02  117.11  3.000
 08R  H1   N02  C02  115.52  3.000
 08R  N01  C02  C03  122.38  3.000
 08R  N01  C02  N02  116.90  3.000
 08R  C03  C02  N02  120.68  3.000
 08R  H3   C03  C04  120.91  3.000
 08R  H3   C03  C02  120.09  3.000
 08R  C04  C03  C02  119.00  3.000
 08R  C05  C04  C07  120.58  3.000
 08R  C05  C04  C03  118.07  3.000
 08R  C07  C04  C03  121.35  3.000
 08R  H6   C07  H5   107.84  3.000
 08R  H6   C07  H4   108.29  3.000
 08R  H5   C07  H4   107.02  3.000
 08R  H6   C07  C04  111.83  3.000
 08R  H5   C07  C04  110.50  3.000
 08R  H4   C07  C04  111.18  3.000
 08R  H7   C05  C06  120.24  3.000
 08R  H7   C05  C04  120.55  3.000
 08R  C06  C05  C04  119.20  3.000
 08R  C06  N01  C02  118.77  3.000
 08R  C08  C06  N01  116.65  3.000
 08R  C08  C06  C05  120.75  3.000
 08R  N01  C06  C05  122.57  3.000
 08R  H9   C08  H8   107.19  3.000
 08R  H9   C08  C3'  109.54  3.000
 08R  H8   C08  C3'  109.98  3.000
 08R  H9   C08  C06  109.19  3.000
 08R  H8   C08  C06  109.21  3.000
 08R  C3'  C08  C06  111.63  3.000
 08R  H10  C3'  C4'  106.68  3.000
 08R  H10  C3'  C2'  107.92  3.000
 08R  C4'  C3'  C2'  101.58  3.000
 08R  H10  C3'  C08  108.50  3.000
 08R  C4'  C3'  C08  114.92  3.000
 08R  C2'  C3'  C08  116.58  3.000
 08R  H12  C2'  H11  106.98  3.000
 08R  H12  C2'  N1'  110.56  3.000
 08R  H11  C2'  N1'  110.65  3.000
 08R  H12  C2'  C3'  109.84  3.000
 08R  H11  C2'  C3'  113.53  3.000
 08R  N1'  C2'  C3'  105.32  3.000
 08R  H13  N1'  C5'  108.61  3.000
 08R  H13  N1'  C2'  108.24  3.000
 08R  C5'  N1'  C2'  107.07  3.000
 08R  H16  C5'  H15  106.64  3.000
 08R  H16  C5'  C4'  110.12  3.000
 08R  H15  C5'  C4'  110.99  3.000
 08R  H16  C5'  N1'  111.12  3.000
 08R  H15  C5'  N1'  110.49  3.000
 08R  C4'  C5'  N1'  107.51  3.000
 08R  H17  C4'  O09  109.55  3.000
 08R  H17  C4'  C5'  111.56  3.000
 08R  O09  C4'  C5'  112.29  3.000
 08R  H17  C4'  C3'  111.67  3.000
 08R  C5'  C4'  C3'  103.14  3.000
 08R  O09  C4'  C3'  108.47  3.000
 08R  C10  O09  C4'  115.05  3.000
 08R  H19  C10  H18  107.27  3.000
 08R  H19  C10  C11  109.40  3.000
 08R  H18  C10  C11  109.41  3.000
 08R  H19  C10  O09  111.65  3.000
 08R  H18  C10  O09  110.58  3.000
 08R  C11  C10  O09  108.51  3.000
 08R  H21  C11  H20  106.28  3.000
 08R  H21  C11  N12  112.99  3.000
 08R  H20  C11  N12  108.88  3.000
 08R  H21  C11  C10  109.54  3.000
 08R  H20  C11  C10  107.86  3.000
 08R  N12  C11  C10  111.06  3.000
 08R  H22  N12  C13  108.54  3.000
 08R  H22  N12  C11  108.64  3.000
 08R  C13  N12  C11  112.67  3.000
 08R  H25  C13  H24  106.09  3.000
 08R  H25  C13  C21  108.61  3.000
 08R  H24  C13  C21  110.63  3.000
 08R  H25  C13  N12  112.39  3.000
 08R  H24  C13  N12  108.36  3.000
 08R  C21  C13  N12  110.68  3.000
 08R  C26  C21  C22  118.49  3.000
 08R  C26  C21  C13  120.27  3.000
 08R  C22  C21  C13  121.20  3.000
 08R  C23  C22  O22  123.68  3.000
 08R  C23  C22  C21  120.09  3.000
 08R  O22  C22  C21  116.22  3.000
 08R  C27  O22  C22  118.86  3.000
 08R  H28  C27  H27  108.76  3.000
 08R  H28  C27  H26  108.68  3.000
 08R  H27  C27  H26  108.72  3.000
 08R  H28  C27  O22  112.05  3.000
 08R  H27  C27  O22  106.47  3.000
 08R  H26  C27  O22  112.05  3.000
 08R  H29  C26  C25  119.59  3.000
 08R  H29  C26  C21  118.54  3.000
 08R  C25  C26  C21  121.87  3.000
 08R  H30  C25  C24  120.70  3.000
 08R  H30  C25  C26  120.37  3.000
 08R  C24  C25  C26  118.93  3.000
 08R  H31  C24  C23  119.03  3.000
 08R  H31  C24  C25  120.37  3.000
 08R  C23  C24  C25  120.59  3.000
 08R  H32  C23  C24  118.84  3.000
 08R  H32  C23  C22  121.14  3.000
 08R  C24  C23  C22  120.02  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
 08R  CONST_01  C05  C04  C03  C02     0.00   0.0  0
 08R  CONST_02  C05  C06  N01  C02     0.00   0.0  0
 08R  CONST_03  C06  C05  C04  C03     0.00   0.0  0
 08R  CONST_04  C06  N01  C02  C03     0.00   0.0  0
 08R  CONST_05  N01  C02  C03  C04     0.00   0.0  0
 08R  CONST_06  N01  C06  C05  C04     0.00   0.0  0
 08R  CONST_07  C24  C23  C22  C21     0.00   0.0  0
 08R  CONST_08  C24  C25  C26  C21     0.00   0.0  0
 08R  CONST_09  C25  C26  C21  C22     0.00   0.0  0
 08R  CONST_10  C25  C24  C23  C22     0.00   0.0  0
 08R  CONST_11  C23  C22  C21  C26     0.00   0.0  0
 08R  CONST_12  C23  C24  C25  C26     0.00   0.0  0
 08R  CONST_13  C04  C03  C02  N02   180.00   0.0  0
 08R  CONST_14  C06  N01  C02  N02   180.00   0.0  0
 08R  CONST_15  C07  C04  C03  C02   180.00   0.0  0
 08R  CONST_16  C08  C06  N01  C02   180.00   0.0  0
 08R  CONST_17  C08  C06  C05  C04   180.00   0.0  0
 08R  CONST_18  C06  C05  C04  C07   180.00   0.0  0
 08R  CONST_19  C23  C22  C21  C13   180.00   0.0  0
 08R  CONST_20  C25  C26  C21  C13   180.00   0.0  0
 08R  CONST_21  C26  C21  C22  O22   180.00   0.0  0
 08R  CONST_22  C24  C23  C22  O22   180.00   0.0  0
 08R  CONST_23  H7   C05  C04  C03   180.00   0.0  0
 08R  CONST_24  H3   C03  C04  C05   180.00   0.0  0
 08R  CONST_25  H32  C23  C22  C21   180.00   0.0  0
 08R  CONST_26  H30  C25  C26  C21   180.00   0.0  0
 08R  CONST_27  H29  C26  C21  C22   180.00   0.0  0
 08R  CONST_28  H31  C24  C23  C22   180.00   0.0  0
 08R  Var_01    C5'  N1'  C2'  C3'   -28.91  30.0  1
 08R  Var_02    C4'  C5'  N1'  C2'     6.69  30.0  1
 08R  Var_03    C3'  C08  C06  C05   101.11  30.0  2
 08R  Var_04    C22  C21  C13  N12    74.94  30.0  2
 08R  Var_05    C23  C22  O22  C27    -1.76  30.0  2
 08R  Var_06    H4   C07  C04  C03   132.88  30.0  2
 08R  Var_07    C11  C10  O09  C4'  -167.05  30.0  2
 08R  Var_08    C21  C13  N12  C11   177.34  30.0  3
 08R  Var_09    H26  C27  O22  C22    62.51  30.0  3
 08R  Var_10    N12  C11  C10  O09    64.03  30.0  3
 08R  Var_11    C13  N12  C11  C10  -178.00  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
 08R  chir_01  C3'  C2'  C08  C4'  positiv
 08R  chir_02  C4'  O09  C3'  C5'  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
 08R  plan-1  N02  0.020
 08R  plan-1  C02  0.020
 08R  plan-1  C03  0.020
 08R  plan-1  C04  0.020
 08R  plan-1  C07  0.020
 08R  plan-1  C05  0.020
 08R  plan-1  N01  0.020
 08R  plan-1  C06  0.020
 08R  plan-1  C08  0.020
 08R  plan-1  H3   0.020
 08R  plan-1  H7   0.020
 08R  plan-2  C13  0.020
 08R  plan-2  C21  0.020
 08R  plan-2  C22  0.020
 08R  plan-2  O22  0.020
 08R  plan-2  C26  0.020
 08R  plan-2  C25  0.020
 08R  plan-2  C24  0.020
 08R  plan-2  C23  0.020
 08R  plan-2  H29  0.020
 08R  plan-2  H30  0.020
 08R  plan-2  H31  0.020
 08R  plan-2  H32  0.020
 08R  plan-3  N02  0.020
 08R  plan-3  C02  0.020
 08R  plan-3  H1   0.020
 08R  plan-3  H2   0.020

