# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 12:25:19 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 6-{[(3S,4S)-4-(2-{[2-(3-fluorophenyl)ethyl]amino}ethoxy)pyrrolidin-3-yl]methyl}pyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cccc(C[C@H]2CNC[C@H]2OCCNCCc3cccc(F)c3)n1
#
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
 59W  59W  6-{[(3S,4S)-4-(2-{[2-(3-fluorophenyl)ethyl]amino}ethoxy)pyrrolidin-3-yl]methyl}pyridin-2-amine  ligand  53  26  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_59W
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
 59W  C1    C  CH2   0  -0.160  -0.4198   3.4320  -0.3575
 59W  O1    O  O2    0  -0.496  -1.3162   2.3761  -0.1020
 59W  C2    C  CH2   0  -0.296   0.9445   3.0319   0.1578
 59W  N2    N  NH1   0  -0.602   1.4604   1.8817  -0.5579
 59W  C3    C  CH2   0  -0.246   2.7223   1.4096  -0.0286
 59W  C4    C  CH2   0  -0.529   3.2508   0.2344  -0.8489
 59W  N1'   N  NH1   0  -0.599  -3.9307   2.6846   1.2167
 59W  C11   C  CR6   0   0.139   4.5566  -0.2688  -0.3034
 59W  C12   C  CR16  0  -0.467   4.5831  -1.3283   0.6000
 59W  C13   C  CR6   0   0.539   5.7928  -1.7394   1.1259
 59W  F13   F  F     0  -0.319   5.8007  -2.7645   1.9960
 59W  C14   C  CR16  0  -0.427   6.9908  -1.1388   0.7933
 59W  C15   C  CR16  0  -0.225   6.9587  -0.0822  -0.1077
 59W  C16   C  CR16  0  -0.317   5.7570   0.3485  -0.6512
 59W  N1A   N  N     0  -0.472  -3.3450  -1.9546   0.4346
 59W  C2'   C  CH2   0  -0.340  -3.5018   3.4331   0.0394
 59W  C2A   C  CR6   0   0.263  -3.3136  -1.3310  -0.7425
 59W  C3'   C  CH1   0   0.049  -2.5732   2.4937  -0.7271
 59W  C3A   C  CR16  0  -0.380  -4.0321  -1.7795  -1.8424
 59W  C4'   C  CH1   0  -0.300  -3.3203   1.1698  -0.5783
 59W  C4A   C  CR16  0  -0.148  -4.8115  -2.9226  -1.6951
 59W  C5'   C  CH2   0  -0.271  -3.9506   1.2658   0.8301
 59W  C5A   C  CR16  0  -0.393  -4.8546  -3.5725  -0.4809
 59W  C6A   C  CR6   0   0.433  -4.0957  -3.0451   0.5768
 59W  N6A   N  NH2   0  -0.836  -4.1318  -3.6135   1.8175
 59W  C7A   C  CH2   0  -0.499  -2.4808  -0.0826  -0.8258
 59W  H1    H  HCH2  0   0.199  -0.3650   3.6384  -1.4353
 59W  H1A   H  HCH2  0   0.208  -0.7352   4.3605   0.1357
 59W  H2    H  HCH2  0   0.228   1.6238   3.8760   0.0086
 59W  H2A   H  HCH2  0   0.197   0.8879   2.8705   1.2466
 59W  HN2   H  HNH1  0   0.340   0.7802   1.1330  -0.4966
 59W  H3    H  HCH2  0   0.223   3.4463   2.2293  -0.0709
 59W  H3A   H  HCH2  0   0.199   2.6576   1.1125   1.0304
 59W  H4    H  HCH2  0   0.245   2.5108  -0.5706  -0.8460
 59W  H4A   H  HCH2  0   0.248   3.3723   0.5527  -1.8867
 59W  HN1'  H  HNH1  0   0.348  -3.2369   2.8121   1.9404
 59W  H12   H  HCR6  0   0.270   3.6683  -1.8313   0.8906
 59W  H14   H  HCR6  0   0.277   7.9216  -1.4845   1.2231
 59W  H15   H  HCR6  0   0.266   7.8835   0.4059  -0.3858
 59W  H16   H  HCR6  0   0.253   5.7511   1.1719  -1.3548
 59W  H2'   H  HCH2  0   0.222  -4.3622   3.6806  -0.5915
 59W  H2'A  H  HCH2  0   0.245  -3.0378   4.3778   0.3273
 59W  H3'   H  HCH1  0   0.217  -2.4518   2.7818  -1.7806
 59W  H3AA  H  HCR6  0   0.248  -3.9783  -1.2553  -2.7873
 59W  H4'   H  HCH1  0   0.254  -4.1251   1.1895  -1.3212
 59W  H4AA  H  HCR6  0   0.262  -5.3827  -3.3060  -2.5312
 59W  H5'   H  HCH2  0   0.227  -3.3991   0.6646   1.5555
 59W  H5'A  H  HCH2  0   0.215  -4.9731   0.8802   0.8154
 59W  H5A   H  HCR6  0   0.262  -5.4508  -4.4647  -0.3405
 59W  HN6A  H  HNH2  0   0.379  -3.3865  -3.3595   2.4449
 59W  HN6B  H  HNH2  0   0.388  -4.4130  -4.5774   1.8804
 59W  H7A   H  HCH2  0   0.243  -1.6741  -0.1447  -0.0944
 59W  H7AA  H  HCH2  0   0.243  -2.0225  -0.0165  -1.8163

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
 59W  C2   C1    single    1.512  0.020  1.512
 59W  O1   C1    single    1.408  0.020  1.408
 59W  C1   H1    single    0.970  0.020  1.090
 59W  C1   H1A   single    0.970  0.020  1.090
 59W  O1   C3'   single    1.409  0.020  1.409
 59W  N2   C2    single    1.450  0.020  1.450
 59W  C2   H2    single    0.970  0.020  1.090
 59W  C2   H2A   single    0.970  0.020  1.090
 59W  C3   N2    single    1.448  0.020  1.448
 59W  N2   HN2   single    0.890  0.020  1.040
 59W  C3   C4    single    1.528  0.020  1.528
 59W  C3   H3    single    0.970  0.020  1.090
 59W  C3   H3A   single    0.970  0.020  1.090
 59W  C11  C4    single    1.502  0.020  1.502
 59W  C4   H4    single    0.970  0.020  1.090
 59W  C4   H4A   single    0.970  0.020  1.090
 59W  C2'  N1'   single    1.460  0.020  1.460
 59W  N1'  C5'   single    1.471  0.020  1.471
 59W  N1'  HN1'  single    0.890  0.020  1.040
 59W  C12  C11   aromatic  1.393  0.020  1.393
 59W  C16  C11   aromatic  1.394  0.020  1.394
 59W  C13  C12   aromatic  1.382  0.020  1.382
 59W  C12  H12   single    0.930  0.020  1.080
 59W  F13  C13   single    1.345  0.020  1.345
 59W  C14  C13   aromatic  1.381  0.020  1.381
 59W  C14  C15   aromatic  1.389  0.020  1.389
 59W  C14  H14   single    0.930  0.020  1.080
 59W  C15  C16   aromatic  1.387  0.020  1.387
 59W  C15  H15   single    0.930  0.020  1.080
 59W  C16  H16   single    0.930  0.020  1.080
 59W  N1A  C2A   aromatic  1.332  0.020  1.332
 59W  N1A  C6A   aromatic  1.331  0.020  1.331
 59W  C2'  C3'   single    1.527  0.020  1.527
 59W  C2'  H2'   single    0.970  0.020  1.090
 59W  C2'  H2'A  single    0.970  0.020  1.090
 59W  C7A  C2A   single    1.503  0.020  1.503
 59W  C2A  C3A   aromatic  1.388  0.020  1.388
 59W  C3'  C4'   single    1.527  0.020  1.527
 59W  C3'  H3'   single    0.970  0.020  1.090
 59W  C3A  C4A   aromatic  1.391  0.020  1.391
 59W  C3A  H3AA  single    0.930  0.020  1.080
 59W  C7A  C4'   single    1.528  0.020  1.528
 59W  C5'  C4'   single    1.546  0.020  1.546
 59W  C4'  H4'   single    0.970  0.020  1.090
 59W  C5A  C4A   aromatic  1.378  0.020  1.378
 59W  C4A  H4AA  single    0.930  0.020  1.080
 59W  C5'  H5'   single    0.970  0.020  1.090
 59W  C5'  H5'A  single    0.970  0.020  1.090
 59W  C6A  C5A   aromatic  1.405  0.020  1.405
 59W  C5A  H5A   single    0.930  0.020  1.080
 59W  N6A  C6A   single    1.365  0.020  1.365
 59W  N6A  HN6A  single    0.890  0.020  1.040
 59W  N6A  HN6B  single    0.890  0.020  1.040
 59W  C7A  H7A   single    0.970  0.020  1.090
 59W  C7A  H7AA  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
 59W  H1A   C1   H1    107.23  3.000
 59W  H1A   C1   C2    109.26  3.000
 59W  H1    C1   C2    109.81  3.000
 59W  H1A   C1   O1    111.70  3.000
 59W  H1    C1   O1    110.52  3.000
 59W  C2    C1   O1    108.30  3.000
 59W  C3'   O1   C1    115.14  3.000
 59W  H2A   C2   H2    106.24  3.000
 59W  H2A   C2   N2    112.94  3.000
 59W  H2    C2   N2    108.91  3.000
 59W  H2A   C2   C1    109.21  3.000
 59W  H2    C2   C1    108.04  3.000
 59W  N2    C2   C1    111.27  3.000
 59W  HN2   N2   C3    108.79  3.000
 59W  HN2   N2   C2    108.52  3.000
 59W  C3    N2   C2    112.87  3.000
 59W  H3A   C3   H3    106.14  3.000
 59W  H3A   C3   C4    109.21  3.000
 59W  H3    C3   C4    109.06  3.000
 59W  H3A   C3   N2    112.84  3.000
 59W  H3    C3   N2    108.56  3.000
 59W  C4    C3   N2    110.87  3.000
 59W  H4A   C4   H4    107.00  3.000
 59W  H4A   C4   C11   110.25  3.000
 59W  H4    C4   C11   109.92  3.000
 59W  H4A   C4   C3    108.93  3.000
 59W  H4    C4   C3    109.31  3.000
 59W  C11   C4   C3    111.32  3.000
 59W  HN1'  N1'  C5'   108.62  3.000
 59W  HN1'  N1'  C2'   108.14  3.000
 59W  C5'   N1'  C2'   106.66  3.000
 59W  C16   C11  C12   118.84  3.000
 59W  C16   C11  C4    120.64  3.000
 59W  C12   C11  C4    120.47  3.000
 59W  H12   C12  C13   119.93  3.000
 59W  H12   C12  C11   120.73  3.000
 59W  C13   C12  C11   119.34  3.000
 59W  C14   C13  F13   118.85  3.000
 59W  C14   C13  C12   122.58  3.000
 59W  F13   C13  C12   118.57  3.000
 59W  H14   C14  C15   121.37  3.000
 59W  H14   C14  C13   120.78  3.000
 59W  C15   C14  C13   117.85  3.000
 59W  H15   C15  C16   119.97  3.000
 59W  H15   C15  C14   119.35  3.000
 59W  C16   C15  C14   120.68  3.000
 59W  H16   C16  C15   119.69  3.000
 59W  H16   C16  C11   119.60  3.000
 59W  C15   C16  C11   120.71  3.000
 59W  C6A   N1A  C2A   119.40  3.000
 59W  H2'A  C2'  H2'   106.88  3.000
 59W  H2'A  C2'  C3'   113.98  3.000
 59W  H2'   C2'  C3'   109.12  3.000
 59W  H2'A  C2'  N1'   110.86  3.000
 59W  H2'   C2'  N1'   110.47  3.000
 59W  C3'   C2'  N1'   105.55  3.000
 59W  C7A   C2A  C3A   120.75  3.000
 59W  C3A   C2A  N1A   122.45  3.000
 59W  C7A   C2A  N1A   116.79  3.000
 59W  H3'   C3'  C4'   112.00  3.000
 59W  H3'   C3'  C2'   112.77  3.000
 59W  C4'   C3'  C2'   100.77  3.000
 59W  H3'   C3'  O1    110.41  3.000
 59W  C4'   C3'  O1    108.72  3.000
 59W  C2'   C3'  O1    111.79  3.000
 59W  H3AA  C3A  C4A   121.22  3.000
 59W  H3AA  C3A  C2A   120.65  3.000
 59W  C4A   C3A  C2A   118.13  3.000
 59W  H4'   C4'  C7A   107.98  3.000
 59W  H4'   C4'  C5'   108.49  3.000
 59W  C7A   C4'  C5'   114.99  3.000
 59W  H4'   C4'  C3'   106.12  3.000
 59W  C5'   C4'  C3'   103.55  3.000
 59W  C7A   C4'  C3'   115.21  3.000
 59W  H4AA  C4A  C5A   119.80  3.000
 59W  H4AA  C4A  C3A   120.31  3.000
 59W  C5A   C4A  C3A   119.89  3.000
 59W  H5'A  C5'  H5'   106.69  3.000
 59W  H5'A  C5'  C4'   110.32  3.000
 59W  H5'   C5'  C4'   111.42  3.000
 59W  H5'A  C5'  N1'   110.89  3.000
 59W  H5'   C5'  N1'   110.48  3.000
 59W  C4'   C5'  N1'   107.09  3.000
 59W  H5A   C5A  C6A   120.63  3.000
 59W  H5A   C5A  C4A   121.36  3.000
 59W  C6A   C5A  C4A   118.01  3.000
 59W  N6A   C6A  C5A   120.91  3.000
 59W  N6A   C6A  N1A   116.93  3.000
 59W  C5A   C6A  N1A   122.13  3.000
 59W  HN6B  N6A  HN6A  114.18  3.000
 59W  HN6B  N6A  C6A   117.58  3.000
 59W  HN6A  N6A  C6A   116.22  3.000
 59W  H7AA  C7A  H7A   107.51  3.000
 59W  H7AA  C7A  C4'   109.12  3.000
 59W  H7A   C7A  C4'   110.15  3.000
 59W  H7AA  C7A  C2A   109.43  3.000
 59W  H7A   C7A  C2A   108.99  3.000
 59W  C4'   C7A  C2A   111.55  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
 59W  CONST_01  C14   C13  C12  C11     0.00   0.0  0
 59W  CONST_02  C14   C15  C16  C11     0.00   0.0  0
 59W  CONST_03  C15   C16  C11  C12     0.00   0.0  0
 59W  CONST_04  C15   C14  C13  C12     0.00   0.0  0
 59W  CONST_05  C16   C11  C12  C13     0.00   0.0  0
 59W  CONST_06  C16   C15  C14  C13     0.00   0.0  0
 59W  CONST_07  C4A   C3A  C2A  N1A     0.00   0.0  0
 59W  CONST_08  C4A   C5A  C6A  N1A     0.00   0.0  0
 59W  CONST_09  C5A   C6A  N1A  C2A     0.00   0.0  0
 59W  CONST_10  C5A   C4A  C3A  C2A     0.00   0.0  0
 59W  CONST_11  C6A   N1A  C2A  C3A     0.00   0.0  0
 59W  CONST_12  C6A   C5A  C4A  C3A     0.00   0.0  0
 59W  CONST_13  C13   C12  C11  C4    180.00   0.0  0
 59W  CONST_14  C15   C16  C11  C4    180.00   0.0  0
 59W  CONST_15  F13   C13  C12  C11   180.00   0.0  0
 59W  CONST_16  C15   C14  C13  F13   180.00   0.0  0
 59W  CONST_17  N6A   C6A  N1A  C2A   180.00   0.0  0
 59W  CONST_18  C7A   C2A  C3A  C4A   180.00   0.0  0
 59W  CONST_19  N6A   C6A  C5A  C4A   180.00   0.0  0
 59W  CONST_20  C7A   C2A  N1A  C6A   180.00   0.0  0
 59W  CONST_21  H15   C15  C16  C11   180.00   0.0  0
 59W  CONST_22  H16   C16  C11  C12   180.00   0.0  0
 59W  CONST_23  H14   C14  C13  C12   180.00   0.0  0
 59W  CONST_24  H12   C12  C13  C14   180.00   0.0  0
 59W  CONST_25  H3AA  C3A  C2A  N1A   180.00   0.0  0
 59W  CONST_26  H5A   C5A  C6A  N1A   180.00   0.0  0
 59W  CONST_27  H4AA  C4A  C3A  C2A   180.00   0.0  0
 59W  Var_01    C4'   C5'  N1'  C2'     7.90  30.0  1
 59W  Var_02    C5'   N1'  C2'  C3'   -30.66  30.0  1
 59W  Var_03    C4'   C7A  C2A  N1A   -94.28  30.0  1
 59W  Var_04    C12   C11  C4   C3     94.23  30.0  2
 59W  Var_05    C11   C4   C3   N2   -179.67  30.0  3
 59W  Var_06    H1    C1   O1   C3'   -49.09  30.0  3
 59W  Var_07    C3    N2   C2   C1   -175.83  30.0  1
 59W  Var_08    N2    C2   C1   O1     63.65  30.0  2
 59W  Var_09    C4    C3   N2   C2   -177.74  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
 59W  chir_01  C3'  O1   C2'  C4'  positiv
 59W  chir_02  C4'  C3'  C7A  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
 59W  plan-1  C4    0.020
 59W  plan-1  C11   0.020
 59W  plan-1  C12   0.020
 59W  plan-1  C13   0.020
 59W  plan-1  F13   0.020
 59W  plan-1  C14   0.020
 59W  plan-1  C15   0.020
 59W  plan-1  C16   0.020
 59W  plan-1  H12   0.020
 59W  plan-1  H14   0.020
 59W  plan-1  H15   0.020
 59W  plan-1  H16   0.020
 59W  plan-2  N1A   0.020
 59W  plan-2  C2A   0.020
 59W  plan-2  C3A   0.020
 59W  plan-2  C4A   0.020
 59W  plan-2  C5A   0.020
 59W  plan-2  C6A   0.020
 59W  plan-2  N6A   0.020
 59W  plan-2  C7A   0.020
 59W  plan-2  H3AA  0.020
 59W  plan-2  H4AA  0.020
 59W  plan-2  H5A   0.020
 59W  plan-3  C6A   0.020
 59W  plan-3  N6A   0.020
 59W  plan-3  HN6A  0.020
 59W  plan-3  HN6B  0.020

