# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 03:11:49 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: 4-methyl-6-{[(3R,4R)-4-{[5-(pyridin-2-yl)pentyl]oxy}pyrrolidin-3-yl]methyl}pyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(N)nc(C[C@@H]2CNC[C@@H]2OCCCCCc3ccccn3)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
 HW8  HW8  4-methyl-6-{[(3R,4R)-4-{[5-(pyridin-2-yl)pentyl]oxy}pyrrolidin-3-yl]methyl}pyridin-2-amine  ligand  56  26  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HW8
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
 HW8  N02  N  NH2   0  -0.840  -7.2498  -0.7712   1.8025
 HW8  C02  C  CR6   0   0.440  -6.2717  -1.1262   0.9189
 HW8  C03  C  CR16  0  -0.450  -6.5537  -2.0015  -0.1453
 HW8  C04  C  CR6   0   0.206  -5.5563  -2.2969  -1.0508
 HW8  C07  C  CH3   0  -0.727  -5.8054  -3.2062  -2.2148
 HW8  C05  C  CR16  0  -0.437  -4.2999  -1.7084  -0.8629
 HW8  C06  C  CR6   0   0.285  -4.1066  -0.8629   0.2144
 HW8  N01  N  N     0  -0.487  -5.0737  -0.5795   1.0902
 HW8  C08  C  CH2   0  -0.489  -2.7776  -0.2006   0.4516
 HW8  C4'  C  CH1   0  -0.277  -2.8792   1.3166   0.3534
 HW8  C5'  C  CH2   0  -0.292  -3.2302   1.8716  -1.0266
 HW8  N1'  N  NH1   0  -0.600  -2.9370   3.2986  -0.9523
 HW8  C3'  C  CH1   0   0.020  -1.6012   2.0864   0.6867
 HW8  C2'  C  CH2   0  -0.308  -1.8258   3.4521  -0.0026
 HW8  O09  O  O2    0  -0.497  -0.4981   1.3907   0.1485
 HW8  C10  C  CH2   0  -0.125   0.7526   1.8268   0.6222
 HW8  C11  C  CH2   0  -0.460   1.8357   0.9092   0.0906
 HW8  C12  C  CH2   0  -0.429   3.2213   1.3299   0.5647
 HW8  C13  C  CH2   0  -0.416   4.3184   0.3929   0.0770
 HW8  C14  C  CH2   0  -0.486   5.7070   0.8186   0.5568
 HW8  C26  C  CR6   0   0.257   6.7715  -0.1445   0.1187
 HW8  N21  N  N     0  -0.422   6.8234  -1.3143   0.7555
 HW8  C22  C  CR16  0  -0.082   7.7280  -2.2078   0.3754
 HW8  C23  C  CR16  0  -0.332   8.6315  -1.9940  -0.6547
 HW8  C24  C  CR16  0  -0.151   8.5822  -0.7780  -1.3189
 HW8  C25  C  CR16  0  -0.350   7.6393   0.1594  -0.9273
 HW8  H1   H  HNH2  0   0.387  -8.0481  -1.3777   1.8862
 HW8  H2   H  HNH2  0   0.379  -6.9420  -0.3696   2.6728
 HW8  H3   H  HCR6  0   0.253  -7.5427  -2.4328  -0.2458
 HW8  H4   H  HCH3  0   0.253  -5.8100  -2.6405  -3.1483
 HW8  H5   H  HCH3  0   0.249  -5.0213  -3.9587  -2.3027
 HW8  H6   H  HCH3  0   0.246  -6.7628  -3.7187  -2.1317
 HW8  H7   H  HCR6  0   0.240  -3.4873  -1.9140  -1.5488
 HW8  H8   H  HCH2  0   0.244  -2.4152  -0.4754   1.4473
 HW8  H9   H  HCH2  0   0.240  -2.0497  -0.5796  -0.2670
 HW8  H10  H  HCH1  0   0.243  -3.6497   1.6546   1.0551
 HW8  H11  H  HCH2  0   0.211  -2.6117   1.3922  -1.7945
 HW8  H12  H  HCH2  0   0.237  -4.2716   1.7087  -1.3069
 HW8  H13  H  HNH1  0   0.348  -3.7494   3.7662  -0.5735
 HW8  H15  H  HCH1  0   0.223  -1.4700   2.1977   1.7718
 HW8  H16  H  HCH2  0   0.223  -0.9120   3.7647  -0.5169
 HW8  H17  H  HCH2  0   0.232  -2.0544   4.2317   0.7256
 HW8  H18  H  HCH2  0   0.191   0.9590   2.8611   0.3107
 HW8  H19  H  HCH2  0   0.192   0.7674   1.8229   1.7224
 HW8  H20  H  HCH2  0   0.221   1.6323  -0.1156   0.4155
 HW8  H21  H  HCH2  0   0.221   1.8062   0.9070  -1.0034
 HW8  H22  H  HCH2  0   0.218   3.4324   2.3486   0.2231
 HW8  H23  H  HCH2  0   0.217   3.2403   1.3648   1.6593
 HW8  H24  H  HCH2  0   0.223   4.1162  -0.6239   0.4264
 HW8  H25  H  HCH2  0   0.223   4.3082   0.3524  -1.0169
 HW8  H26  H  HCH2  0   0.239   5.9334   1.8192   0.1815
 HW8  H27  H  HCH2  0   0.240   5.7074   0.8783   1.6487
 HW8  H28  H  HCR6  0   0.259   7.7367  -3.1453   0.9215
 HW8  H29  H  HCR6  0   0.267   9.3480  -2.7579  -0.9229
 HW8  H30  H  HCR6  0   0.271   9.2673  -0.5629  -2.1287
 HW8  H31  H  HCR6  0   0.262   7.5752   1.1195  -1.4229

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
 HW8  C24  C23  aromatic  1.387  0.020  1.387
 HW8  C24  C25  aromatic  1.386  0.020  1.386
 HW8  C23  C22  aromatic  1.387  0.020  1.387
 HW8  C25  C26  aromatic  1.393  0.020  1.393
 HW8  C22  N21  aromatic  1.327  0.020  1.327
 HW8  C26  N21  aromatic  1.333  0.020  1.333
 HW8  C26  C14  single    1.501  0.020  1.501
 HW8  C13  C14  single    1.530  0.020  1.530
 HW8  C13  C12  single    1.523  0.020  1.523
 HW8  C11  C12  single    1.524  0.020  1.524
 HW8  C11  C10  single    1.516  0.020  1.516
 HW8  C10  O09  single    1.407  0.020  1.407
 HW8  O09  C3'  single    1.411  0.020  1.411
 HW8  C08  C06  single    1.504  0.020  1.504
 HW8  C08  C4'  single    1.524  0.020  1.524
 HW8  C3'  C4'  single    1.529  0.020  1.529
 HW8  C3'  C2'  single    1.546  0.020  1.546
 HW8  C06  N01  aromatic  1.335  0.020  1.335
 HW8  C06  C05  aromatic  1.383  0.020  1.383
 HW8  N01  C02  aromatic  1.328  0.020  1.328
 HW8  C4'  C5'  single    1.528  0.020  1.528
 HW8  C05  C04  aromatic  1.400  0.020  1.400
 HW8  C02  N02  single    1.365  0.020  1.365
 HW8  C02  C03  aromatic  1.406  0.020  1.406
 HW8  C2'  N1'  single    1.470  0.020  1.470
 HW8  C04  C03  aromatic  1.379  0.020  1.379
 HW8  C04  C07  single    1.498  0.020  1.498
 HW8  C5'  N1'  single    1.459  0.020  1.459
 HW8  N02  H1   single    0.890  0.020  1.040
 HW8  N02  H2   single    0.890  0.020  1.040
 HW8  C03  H3   single    0.930  0.020  1.080
 HW8  C07  H4   single    0.970  0.020  1.090
 HW8  C07  H5   single    0.970  0.020  1.090
 HW8  C07  H6   single    0.970  0.020  1.090
 HW8  C05  H7   single    0.930  0.020  1.080
 HW8  C08  H8   single    0.970  0.020  1.090
 HW8  C08  H9   single    0.970  0.020  1.090
 HW8  C4'  H10  single    0.970  0.020  1.090
 HW8  C5'  H11  single    0.970  0.020  1.090
 HW8  C5'  H12  single    0.970  0.020  1.090
 HW8  N1'  H13  single    0.890  0.020  1.040
 HW8  C3'  H15  single    0.970  0.020  1.090
 HW8  C2'  H16  single    0.970  0.020  1.090
 HW8  C2'  H17  single    0.970  0.020  1.090
 HW8  C10  H18  single    0.970  0.020  1.090
 HW8  C10  H19  single    0.970  0.020  1.090
 HW8  C11  H20  single    0.970  0.020  1.090
 HW8  C11  H21  single    0.970  0.020  1.090
 HW8  C12  H22  single    0.970  0.020  1.090
 HW8  C12  H23  single    0.970  0.020  1.090
 HW8  C13  H24  single    0.970  0.020  1.090
 HW8  C13  H25  single    0.970  0.020  1.090
 HW8  C14  H26  single    0.970  0.020  1.090
 HW8  C14  H27  single    0.970  0.020  1.090
 HW8  C22  H28  single    0.930  0.020  1.080
 HW8  C23  H29  single    0.930  0.020  1.080
 HW8  C24  H30  single    0.930  0.020  1.080
 HW8  C25  H31  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
 HW8  H2   N02  H1   114.27  3.000
 HW8  H2   N02  C02  116.38  3.000
 HW8  H1   N02  C02  117.75  3.000
 HW8  N01  C02  C03  122.32  3.000
 HW8  C03  C02  N02  120.53  3.000
 HW8  N01  C02  N02  117.12  3.000
 HW8  H3   C03  C04  120.92  3.000
 HW8  H3   C03  C02  120.06  3.000
 HW8  C04  C03  C02  119.02  3.000
 HW8  C05  C04  C07  120.58  3.000
 HW8  C07  C04  C03  121.33  3.000
 HW8  C05  C04  C03  118.09  3.000
 HW8  H6   C07  H5   108.28  3.000
 HW8  H6   C07  H4   107.79  3.000
 HW8  H5   C07  H4   106.96  3.000
 HW8  H6   C07  C04  111.88  3.000
 HW8  H5   C07  C04  111.22  3.000
 HW8  H4   C07  C04  110.52  3.000
 HW8  H7   C05  C06  120.29  3.000
 HW8  H7   C05  C04  120.56  3.000
 HW8  C06  C05  C04  119.14  3.000
 HW8  C08  C06  N01  116.31  3.000
 HW8  N01  C06  C05  122.64  3.000
 HW8  C08  C06  C05  121.05  3.000
 HW8  C06  N01  C02  118.78  3.000
 HW8  H9   C08  H8   106.92  3.000
 HW8  H9   C08  C4'  110.37  3.000
 HW8  H8   C08  C4'  109.31  3.000
 HW8  H9   C08  C06  109.44  3.000
 HW8  H8   C08  C06  109.00  3.000
 HW8  C4'  C08  C06  111.68  3.000
 HW8  H10  C4'  C3'  107.04  3.000
 HW8  H10  C4'  C5'  107.75  3.000
 HW8  C3'  C4'  C5'  101.89  3.000
 HW8  H10  C4'  C08  108.23  3.000
 HW8  C5'  C4'  C08  115.79  3.000
 HW8  C3'  C4'  C08  115.56  3.000
 HW8  H12  C5'  H11  107.06  3.000
 HW8  H12  C5'  N1'  110.55  3.000
 HW8  H11  C5'  N1'  110.49  3.000
 HW8  H12  C5'  C4'  113.40  3.000
 HW8  H11  C5'  C4'  110.13  3.000
 HW8  N1'  C5'  C4'  105.25  3.000
 HW8  H13  N1'  C2'  108.50  3.000
 HW8  H13  N1'  C5'  108.06  3.000
 HW8  C2'  N1'  C5'  106.68  3.000
 HW8  H15  C3'  O09  109.47  3.000
 HW8  H15  C3'  C2'  111.60  3.000
 HW8  O09  C3'  C2'  112.27  3.000
 HW8  H15  C3'  C4'  111.48  3.000
 HW8  C2'  C3'  C4'  103.07  3.000
 HW8  O09  C3'  C4'  108.80  3.000
 HW8  H17  C2'  H16  106.53  3.000
 HW8  H17  C2'  C3'  111.35  3.000
 HW8  H16  C2'  C3'  109.92  3.000
 HW8  H17  C2'  N1'  110.33  3.000
 HW8  H16  C2'  N1'  110.95  3.000
 HW8  C3'  C2'  N1'  107.80  3.000
 HW8  C10  O09  C3'  114.45  3.000
 HW8  H19  C10  H18  106.50  3.000
 HW8  H19  C10  C11  109.81  3.000
 HW8  H18  C10  C11  109.63  3.000
 HW8  H19  C10  O09  110.34  3.000
 HW8  H18  C10  O09  111.29  3.000
 HW8  C11  C10  O09  109.24  3.000
 HW8  H21  C11  H20  106.85  3.000
 HW8  H21  C11  C12  109.64  3.000
 HW8  H20  C11  C12  109.59  3.000
 HW8  H21  C11  C10  109.42  3.000
 HW8  H20  C11  C10  109.27  3.000
 HW8  C12  C11  C10  111.93  3.000
 HW8  H23  C12  H22  106.18  3.000
 HW8  H23  C12  C13  109.09  3.000
 HW8  H22  C12  C13  109.49  3.000
 HW8  H23  C12  C11  109.60  3.000
 HW8  H22  C12  C11  109.58  3.000
 HW8  C13  C12  C11  112.68  3.000
 HW8  H25  C13  H24  106.44  3.000
 HW8  H25  C13  C14  109.41  3.000
 HW8  H24  C13  C14  109.05  3.000
 HW8  H25  C13  C12  109.63  3.000
 HW8  H24  C13  C12  109.65  3.000
 HW8  C14  C13  C12  112.47  3.000
 HW8  H27  C14  H26  107.04  3.000
 HW8  H27  C14  C26  109.04  3.000
 HW8  H26  C14  C26  109.91  3.000
 HW8  H27  C14  C13  109.19  3.000
 HW8  H26  C14  C13  109.59  3.000
 HW8  C26  C14  C13  111.94  3.000
 HW8  C25  C26  N21  121.74  3.000
 HW8  N21  C26  C14  116.83  3.000
 HW8  C25  C26  C14  121.41  3.000
 HW8  C22  N21  C26  118.73  3.000
 HW8  H28  C22  C23  120.12  3.000
 HW8  H28  C22  N21  116.31  3.000
 HW8  C23  C22  N21  123.58  3.000
 HW8  H29  C23  C24  121.63  3.000
 HW8  H29  C23  C22  120.48  3.000
 HW8  C24  C23  C22  117.90  3.000
 HW8  H30  C24  C25  120.51  3.000
 HW8  H30  C24  C23  120.68  3.000
 HW8  C25  C24  C23  118.82  3.000
 HW8  H31  C25  C24  120.72  3.000
 HW8  H31  C25  C26  120.04  3.000
 HW8  C24  C25  C26  119.24  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
 HW8  CONST_01  C05  C06  N01  C02     0.00   0.0  0
 HW8  CONST_02  C05  C04  C03  C02     0.00   0.0  0
 HW8  CONST_03  C06  N01  C02  C03     0.00   0.0  0
 HW8  CONST_04  C06  C05  C04  C03     0.00   0.0  0
 HW8  CONST_05  N01  C06  C05  C04     0.00   0.0  0
 HW8  CONST_06  N01  C02  C03  C04     0.00   0.0  0
 HW8  CONST_07  C23  C24  C25  C26     0.00   0.0  0
 HW8  CONST_08  C23  C22  N21  C26     0.00   0.0  0
 HW8  CONST_09  C24  C23  C22  N21     0.00   0.0  0
 HW8  CONST_10  C24  C25  C26  N21     0.00   0.0  0
 HW8  CONST_11  C25  C24  C23  C22     0.00   0.0  0
 HW8  CONST_12  C25  C26  N21  C22     0.00   0.0  0
 HW8  CONST_13  C06  N01  C02  N02   180.00   0.0  0
 HW8  CONST_14  C04  C03  C02  N02   180.00   0.0  0
 HW8  CONST_15  C08  C06  N01  C02   180.00   0.0  0
 HW8  CONST_16  C07  C04  C03  C02   180.00   0.0  0
 HW8  CONST_17  C08  C06  C05  C04   180.00   0.0  0
 HW8  CONST_18  C06  C05  C04  C07   180.00   0.0  0
 HW8  CONST_19  C24  C25  C26  C14   180.00   0.0  0
 HW8  CONST_20  C22  N21  C26  C14   180.00   0.0  0
 HW8  CONST_21  H7   C05  C04  C03   180.00   0.0  0
 HW8  CONST_22  H3   C03  C04  C05   180.00   0.0  0
 HW8  CONST_23  H30  C24  C25  C26   180.00   0.0  0
 HW8  CONST_24  H28  C22  N21  C26   180.00   0.0  0
 HW8  CONST_25  H29  C23  C22  N21   180.00   0.0  0
 HW8  CONST_26  H31  C25  C26  N21   180.00   0.0  0
 HW8  Var_01    C2'  N1'  C5'  C4'    30.70  30.0  1
 HW8  Var_02    C3'  C2'  N1'  C5'    -9.38  30.0  1
 HW8  Var_03    C4'  C08  C06  C05   116.77  30.0  2
 HW8  Var_04    C25  C26  C14  C13   104.34  30.0  2
 HW8  Var_05    H4   C07  C04  C03   109.36  30.0  2
 HW8  Var_06    C11  C10  O09  C3'   173.86  30.0  2
 HW8  Var_07    C26  C14  C13  C12   177.57  30.0  3
 HW8  Var_08    C12  C11  C10  O09   179.83  30.0  2
 HW8  Var_09    C13  C12  C11  C10   178.16  30.0  3
 HW8  Var_10    C14  C13  C12  C11  -179.94  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
 HW8  chir_01  C4'  C08  C3'  C5'  negativ
 HW8  chir_02  C3'  O09  C4'  C2'  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
 HW8  plan-1  N02  0.020
 HW8  plan-1  C02  0.020
 HW8  plan-1  C03  0.020
 HW8  plan-1  C04  0.020
 HW8  plan-1  C07  0.020
 HW8  plan-1  C05  0.020
 HW8  plan-1  C06  0.020
 HW8  plan-1  N01  0.020
 HW8  plan-1  C08  0.020
 HW8  plan-1  H3   0.020
 HW8  plan-1  H7   0.020
 HW8  plan-2  C14  0.020
 HW8  plan-2  C26  0.020
 HW8  plan-2  N21  0.020
 HW8  plan-2  C22  0.020
 HW8  plan-2  C23  0.020
 HW8  plan-2  C24  0.020
 HW8  plan-2  C25  0.020
 HW8  plan-2  H28  0.020
 HW8  plan-2  H29  0.020
 HW8  plan-2  H30  0.020
 HW8  plan-2  H31  0.020
 HW8  plan-3  N02  0.020
 HW8  plan-3  C02  0.020
 HW8  plan-3  H1   0.020
 HW8  plan-3  H2   0.020

