# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 10:52:02 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 6-{[(3S,4S)-4-{2-[(furan-2-ylmethyl)amino]ethoxy}pyrrolidin-3-yl]methyl}-4-methylpyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(N)nc(C[C@H]2CNC[C@H]2OCCNCc3occc3)c1
#
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
 DXW  DXW  6-{[(3S,4S)-4-{2-[(furan-2-ylmethyl)amino]ethoxy}pyrrolidin-3-yl]methyl}-4-methylpyridin-2-amine  ligand  50  24  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DXW
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
 DXW  N02  N  NH2   0  -0.839   3.6171   2.4752   2.4439
 DXW  C02  C  CR6   0   0.440   3.2544   2.2512   1.1452
 DXW  C03  C  CR16  0  -0.447   3.8190   3.0052   0.1033
 DXW  C04  C  CR6   0   0.204   3.3887   2.7876  -1.1905
 DXW  C05  C  CR16  0  -0.424   2.4020   1.8202  -1.4025
 DXW  C07  C  CH3   0  -0.727   3.9630   3.5567  -2.3407
 DXW  N01  N  N     0  -0.476   2.3203   1.3298   0.9312
 DXW  C06  C  CR6   0   0.268   1.9046   1.1165  -0.3185
 DXW  C08  C  CH2   0  -0.493   0.8910   0.0245  -0.5129
 DXW  C3'  C  CH1   0  -0.277   1.5686  -1.3247  -0.7411
 DXW  C4'  C  CH1   0   0.021   0.6270  -2.4676  -1.1188
 DXW  C5'  C  CH2   0  -0.303   1.4617  -3.7264  -0.8045
 DXW  N1'  N  NH1   0  -0.602   2.5595  -3.3177   0.0844
 DXW  C2'  C  CH2   0  -0.292   2.3172  -1.9245   0.4493
 DXW  O09  O  O2    0  -0.501  -0.5262  -2.3868  -0.3100
 DXW  C10  C  CH2   0  -0.159  -1.6302  -3.1192  -0.7837
 DXW  C11  C  CH2   0  -0.303  -2.8184  -2.8194   0.1021
 DXW  N12  N  NH1   0  -0.600  -3.1788  -1.4153   0.0399
 DXW  C13  C  CH2   0  -0.358  -4.2598  -1.0909   0.9574
 DXW  C22  C  CR5   0   0.353  -4.6074   0.3525   0.9173
 DXW  O21  O  O     0  -0.414  -3.6808   1.2298   1.3687
 DXW  C23  C  CR15  0  -0.014  -4.1907   2.4731   1.2393
 DXW  C24  C  CR15  0  -0.331  -5.4360   2.4149   0.7155
 DXW  C25  C  CR15  0  -0.391  -5.7072   1.0273   0.5027
 DXW  H1   H  HNH2  0   0.378   3.3992   1.7382   3.0946
 DXW  H2   H  HNH2  0   0.386   4.5089   2.9120   2.6064
 DXW  H3   H  HCR6  0   0.254   4.5800   3.7469   0.3159
 DXW  H4   H  HCR6  0   0.240   2.0336   1.6154  -2.4007
 DXW  H5   H  HCH3  0   0.252   4.5007   2.8921  -3.0186
 DXW  H6   H  HCH3  0   0.250   3.1755   4.0359  -2.9233
 DXW  H7   H  HCH3  0   0.246   4.6547   4.3284  -2.0067
 DXW  H8   H  HCH2  0   0.239   0.2445  -0.0224   0.3647
 DXW  H9   H  HCH2  0   0.242   0.2583   0.2575  -1.3731
 DXW  H10  H  HCH1  0   0.248   2.2855  -1.2198  -1.5650
 DXW  H11  H  HCH1  0   0.228   0.3401  -2.4219  -2.1776
 DXW  H12  H  HCH2  0   0.222   0.8304  -4.4830  -0.3283
 DXW  H13  H  HCH2  0   0.232   1.8572  -4.1748  -1.7172
 DXW  H14  H  HNH1  0   0.348   3.4257  -3.3611  -0.4341
 DXW  H16  H  HCH2  0   0.238   3.2561  -1.4200   0.6744
 DXW  H17  H  HCH2  0   0.210   1.6974  -1.8681   1.3511
 DXW  H18  H  HCH2  0   0.201  -1.8586  -2.8413  -1.8220
 DXW  H19  H  HCH2  0   0.207  -1.4371  -4.2003  -0.7705
 DXW  H20  H  HCH2  0   0.231  -3.6626  -3.4186  -0.2507
 DXW  H21  H  HCH2  0   0.201  -2.6037  -3.1592   1.1281
 DXW  H22  H  HNH1  0   0.344  -2.3624  -0.8692   0.2878
 DXW  H24  H  HCH2  0   0.251  -5.1510  -1.6506   0.6646
 DXW  H25  H  HCH2  0   0.220  -4.0347  -1.3904   1.9939
 DXW  H26  H  HCR5  0   0.276  -3.5631   3.2902   1.5565
 DXW  H27  H  HCR5  0   0.261  -6.0823   3.2512   0.5039
 DXW  H28  H  HCR5  0   0.260  -6.6038   0.5902   0.0935

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
 DXW  C07  C04  single    1.498  0.020  1.498
 DXW  C04  C03  aromatic  1.381  0.020  1.381
 DXW  C04  C05  aromatic  1.398  0.020  1.398
 DXW  C03  C02  aromatic  1.405  0.020  1.405
 DXW  C05  C06  aromatic  1.385  0.020  1.385
 DXW  C02  N02  single    1.367  0.020  1.367
 DXW  C02  N01  aromatic  1.329  0.020  1.329
 DXW  C3'  C2'  single    1.529  0.020  1.529
 DXW  C3'  C08  single    1.527  0.020  1.527
 DXW  C3'  C4'  single    1.528  0.020  1.528
 DXW  C06  N01  aromatic  1.334  0.020  1.334
 DXW  C06  C08  single    1.503  0.020  1.503
 DXW  C2'  N1'  single    1.460  0.020  1.460
 DXW  C4'  O09  single    1.411  0.020  1.411
 DXW  C4'  C5'  single    1.543  0.020  1.543
 DXW  O09  C10  single    1.407  0.020  1.407
 DXW  C10  C11  single    1.512  0.020  1.512
 DXW  C11  N12  single    1.451  0.020  1.451
 DXW  N1'  C5'  single    1.471  0.020  1.471
 DXW  N12  C13  single    1.454  0.020  1.454
 DXW  C25  C24  aromatic  1.430  0.020  1.430
 DXW  C25  C22  aromatic  1.355  0.020  1.355
 DXW  C24  C23  aromatic  1.352  0.020  1.352
 DXW  C13  C22  single    1.485  0.020  1.485
 DXW  C22  O21  aromatic  1.354  0.020  1.354
 DXW  C23  O21  aromatic  1.350  0.020  1.350
 DXW  N02  H1   single    0.890  0.020  1.040
 DXW  N02  H2   single    0.890  0.020  1.040
 DXW  C03  H3   single    0.930  0.020  1.080
 DXW  C05  H4   single    0.930  0.020  1.080
 DXW  C07  H5   single    0.970  0.020  1.090
 DXW  C07  H6   single    0.970  0.020  1.090
 DXW  C07  H7   single    0.970  0.020  1.090
 DXW  C08  H8   single    0.970  0.020  1.090
 DXW  C08  H9   single    0.970  0.020  1.090
 DXW  C3'  H10  single    0.970  0.020  1.090
 DXW  C4'  H11  single    0.970  0.020  1.090
 DXW  C5'  H12  single    0.970  0.020  1.090
 DXW  C5'  H13  single    0.970  0.020  1.090
 DXW  N1'  H14  single    0.890  0.020  1.040
 DXW  C2'  H16  single    0.970  0.020  1.090
 DXW  C2'  H17  single    0.970  0.020  1.090
 DXW  C10  H18  single    0.970  0.020  1.090
 DXW  C10  H19  single    0.970  0.020  1.090
 DXW  C11  H20  single    0.970  0.020  1.090
 DXW  C11  H21  single    0.970  0.020  1.090
 DXW  N12  H22  single    0.890  0.020  1.040
 DXW  C13  H24  single    0.970  0.020  1.090
 DXW  C13  H25  single    0.970  0.020  1.090
 DXW  C23  H26  single    0.930  0.020  1.080
 DXW  C24  H27  single    0.930  0.020  1.080
 DXW  C25  H28  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
 DXW  H2   N02  H1   113.90  3.000
 DXW  H2   N02  C02  117.37  3.000
 DXW  H1   N02  C02  115.89  3.000
 DXW  N01  C02  C03  122.35  3.000
 DXW  N01  C02  N02  116.94  3.000
 DXW  C03  C02  N02  120.67  3.000
 DXW  H3   C03  C04  120.70  3.000
 DXW  H3   C03  C02  120.27  3.000
 DXW  C04  C03  C02  119.03  3.000
 DXW  C07  C04  C05  120.62  3.000
 DXW  C05  C04  C03  118.11  3.000
 DXW  C07  C04  C03  121.27  3.000
 DXW  H4   C05  C06  120.19  3.000
 DXW  H4   C05  C04  120.70  3.000
 DXW  C06  C05  C04  119.11  3.000
 DXW  H7   C07  H6   108.13  3.000
 DXW  H7   C07  H5   108.01  3.000
 DXW  H6   C07  H5   106.96  3.000
 DXW  H7   C07  C04  111.83  3.000
 DXW  H6   C07  C04  111.04  3.000
 DXW  H5   C07  C04  110.68  3.000
 DXW  C06  N01  C02  118.72  3.000
 DXW  C08  C06  N01  116.59  3.000
 DXW  C08  C06  C05  120.69  3.000
 DXW  N01  C06  C05  122.69  3.000
 DXW  H9   C08  H8   107.41  3.000
 DXW  H9   C08  C3'  109.12  3.000
 DXW  H8   C08  C3'  110.19  3.000
 DXW  H9   C08  C06  109.72  3.000
 DXW  H8   C08  C06  109.08  3.000
 DXW  C3'  C08  C06  111.24  3.000
 DXW  H10  C3'  C2'  107.59  3.000
 DXW  H10  C3'  C4'  106.77  3.000
 DXW  C2'  C3'  C4'  101.58  3.000
 DXW  H10  C3'  C08  108.52  3.000
 DXW  C4'  C3'  C08  115.11  3.000
 DXW  C2'  C3'  C08  116.59  3.000
 DXW  H11  C4'  O09  109.68  3.000
 DXW  H11  C4'  C5'  111.83  3.000
 DXW  O09  C4'  C5'  111.85  3.000
 DXW  H11  C4'  C3'  111.61  3.000
 DXW  C5'  C4'  C3'  103.09  3.000
 DXW  O09  C4'  C3'  108.61  3.000
 DXW  H13  C5'  H12  106.79  3.000
 DXW  H13  C5'  N1'  110.45  3.000
 DXW  H12  C5'  N1'  111.08  3.000
 DXW  H13  C5'  C4'  111.16  3.000
 DXW  H12  C5'  C4'  109.92  3.000
 DXW  N1'  C5'  C4'  107.48  3.000
 DXW  H14  N1'  C2'  108.14  3.000
 DXW  H14  N1'  C5'  108.53  3.000
 DXW  C2'  N1'  C5'  106.99  3.000
 DXW  H17  C2'  H16  107.07  3.000
 DXW  H17  C2'  N1'  110.40  3.000
 DXW  H16  C2'  N1'  110.51  3.000
 DXW  H17  C2'  C3'  110.10  3.000
 DXW  H16  C2'  C3'  113.65  3.000
 DXW  N1'  C2'  C3'  105.13  3.000
 DXW  C10  O09  C4'  114.74  3.000
 DXW  H19  C10  H18  107.26  3.000
 DXW  H19  C10  C11  109.04  3.000
 DXW  H18  C10  C11  109.88  3.000
 DXW  H19  C10  O09  111.74  3.000
 DXW  H18  C10  O09  110.46  3.000
 DXW  C11  C10  O09  108.43  3.000
 DXW  H21  C11  H20  106.37  3.000
 DXW  H21  C11  N12  112.75  3.000
 DXW  H20  C11  N12  108.94  3.000
 DXW  H21  C11  C10  109.35  3.000
 DXW  H20  C11  C10  108.00  3.000
 DXW  N12  C11  C10  111.22  3.000
 DXW  H22  N12  C13  108.93  3.000
 DXW  H22  N12  C11  108.12  3.000
 DXW  C13  N12  C11  111.93  3.000
 DXW  H25  C13  H24  106.23  3.000
 DXW  H25  C13  C22  109.71  3.000
 DXW  H24  C13  C22  107.44  3.000
 DXW  H25  C13  N12  112.39  3.000
 DXW  H24  C13  N12  108.84  3.000
 DXW  C22  C13  N12  111.94  3.000
 DXW  C25  C22  O21  109.57  3.000
 DXW  O21  C22  C13  117.43  3.000
 DXW  C25  C22  C13  133.00  3.000
 DXW  C23  O21  C22  107.84  3.000
 DXW  H26  C23  C24  133.06  3.000
 DXW  H26  C23  O21  116.73  3.000
 DXW  C24  C23  O21  110.20  3.000
 DXW  H27  C24  C25  127.60  3.000
 DXW  H27  C24  C23  126.50  3.000
 DXW  C25  C24  C23  105.91  3.000
 DXW  H28  C25  C24  127.42  3.000
 DXW  H28  C25  C22  126.10  3.000
 DXW  C24  C25  C22  106.49  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
 DXW  CONST_01  C05  C04  C03  C02     0.00   0.0  0
 DXW  CONST_02  C05  C06  N01  C02     0.00   0.0  0
 DXW  CONST_03  C06  C05  C04  C03     0.00   0.0  0
 DXW  CONST_04  C06  N01  C02  C03     0.00   0.0  0
 DXW  CONST_05  N01  C02  C03  C04     0.00   0.0  0
 DXW  CONST_06  N01  C06  C05  C04     0.00   0.0  0
 DXW  CONST_07  C23  C24  C25  C22     0.00   0.0  0
 DXW  CONST_08  C24  C23  O21  C22     0.00   0.0  0
 DXW  CONST_09  C24  C25  C22  O21     0.00   0.0  0
 DXW  CONST_10  C25  C24  C23  O21     0.00   0.0  0
 DXW  CONST_11  C25  C22  O21  C23     0.00   0.0  0
 DXW  CONST_12  C04  C03  C02  N02   180.00   0.0  0
 DXW  CONST_13  C06  N01  C02  N02   180.00   0.0  0
 DXW  CONST_14  C07  C04  C03  C02   180.00   0.0  0
 DXW  CONST_15  C08  C06  N01  C02   180.00   0.0  0
 DXW  CONST_16  C08  C06  C05  C04   180.00   0.0  0
 DXW  CONST_17  C06  C05  C04  C07   180.00   0.0  0
 DXW  CONST_18  C24  C25  C22  C13   180.00   0.0  0
 DXW  CONST_19  C23  O21  C22  C13   180.00   0.0  0
 DXW  CONST_20  H4   C05  C04  C03   180.00   0.0  0
 DXW  CONST_21  H3   C03  C04  C05   180.00   0.0  0
 DXW  CONST_22  H27  C24  C25  C22   180.00   0.0  0
 DXW  CONST_23  H26  C23  O21  C22   180.00   0.0  0
 DXW  CONST_24  H28  C25  C22  O21   180.00   0.0  0
 DXW  Var_01    C5'  N1'  C2'  C3'   -29.50  30.0  1
 DXW  Var_02    C2'  N1'  C5'  C4'     7.18  30.0  1
 DXW  Var_03    C3'  C08  C06  C05    89.13  30.0  2
 DXW  Var_04    C25  C22  C13  N12   113.12  30.0  2
 DXW  Var_05    H5   C07  C04  C03   115.26  30.0  2
 DXW  Var_06    C11  C10  O09  C4'  -174.17  30.0  3
 DXW  Var_07    C22  C13  N12  C11   178.65  30.0  3
 DXW  Var_08    N12  C11  C10  O09    62.47  30.0  3
 DXW  Var_09    C13  N12  C11  C10  -175.96  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
 DXW  chir_01  C3'  C2'  C08  C4'  positiv
 DXW  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
 DXW  plan-1  C13  0.020
 DXW  plan-1  C22  0.020
 DXW  plan-1  O21  0.020
 DXW  plan-1  C23  0.020
 DXW  plan-1  C24  0.020
 DXW  plan-1  C25  0.020
 DXW  plan-1  H26  0.020
 DXW  plan-1  H27  0.020
 DXW  plan-1  H28  0.020
 DXW  plan-2  N02  0.020
 DXW  plan-2  C02  0.020
 DXW  plan-2  C03  0.020
 DXW  plan-2  C04  0.020
 DXW  plan-2  C05  0.020
 DXW  plan-2  C07  0.020
 DXW  plan-2  N01  0.020
 DXW  plan-2  C06  0.020
 DXW  plan-2  C08  0.020
 DXW  plan-2  H3   0.020
 DXW  plan-2  H4   0.020
 DXW  plan-3  N02  0.020
 DXW  plan-3  C02  0.020
 DXW  plan-3  H1   0.020
 DXW  plan-3  H2   0.020

