# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 16:41:58 2021
#   Inital geometry file: a 109 line input string
#   Ligand name: [(2R)-7-(2-aminopyridin-4-yl)-5-chloro-2,3-dihydro-1-benzofuran-2-yl](piperazin-1-yl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cc(ccn1)c2cc(Cl)cc3C[C@@H](Oc23)C(=O)N4CCNCC4
#
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
 R41  R41  '[(2R)-7-(2-aminopyridin-4-yl)-5-chloro-2,3-dihydro-1-benzofuran-2-yl](piperazin-1-yl)methanone'  ligand  44  25  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_R41
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
 R41  C2    C   CR6   0   0.465  4.7256   4.8842  90.6069
 R41  C4    C   CR16  0  -0.058  6.8912   5.5334  90.3106
 R41  C5    C   CR16  0  -0.390  7.3559   4.7451  91.3428
 R41  C6    C   CR6   0   0.187  6.4235   3.9725  92.0446
 R41  C7    C   CR16  0  -0.436  5.0954   4.0420  91.6698
 R41  C8    C   CR6   0  -0.042  6.8304   3.1006  93.1624
 R41  C12   C   CR16  0  -0.297  7.5490   1.4634  95.3658
 R41  C15   C   CR15  0  -0.186  8.5749   5.0042  95.6385
 R41  C17   C   CR56  0   0.395  7.6345   3.5568  94.1957
 R41  C18   C   C     0   0.568  7.4416   5.7217  96.3923
 R41  C21   C   CH2   0  -0.324  7.6290   7.6434  94.7956
 R41  C24   C   CH2   0  -0.313  4.8412   7.7155  95.3681
 R41  N1    N   NH2   0  -0.838  3.4167   5.0190  90.2516
 R41  N3    N   N     0  -0.460  5.6167   5.6145  89.9408
 R41  C9    C   CR16  0  -0.269  6.3851   1.7781  93.2578
 R41  C10   C   CR6   0  -0.041  6.7440   0.9854  94.3343
 R41  CL11  CL  CL    0  -0.134  6.1718  -0.6527  94.4025
 R41  C13   C   CR56  0  -0.007  7.9836   2.7682  95.2823
 R41  C14   C   CH2   0  -0.482  8.8463   3.5982  96.1858
 R41  O16   O   O     0  -0.475  8.1363   4.8069  94.2806
 R41  O19   O   O     0  -0.488  6.9074   5.1824  97.3525
 R41  N20   N   NT    0  -0.450  7.0741   6.9332  95.9394
 R41  C22   C   CH2   0  -0.314  6.5711   7.7655  93.7009
 R41  N23   N   NH1   0  -0.578  5.3346   8.3695  94.1682
 R41  C25   C   CH2   0  -0.325  5.8904   7.5945  96.4711
 R41  H1    H   HCR6  0   0.256  7.5883   6.1387  89.7410
 R41  H2    H   HCR6  0   0.253  8.4098   4.7210  91.5784
 R41  H3    H   HCR6  0   0.267  4.3395   3.4741  92.1982
 R41  H4    H   HCR6  0   0.281  7.8181   0.8314  96.2015
 R41  H5    H   HCR5  0   0.299  9.4764   5.6183  95.6148
 R41  H7    H   HCH2  0   0.247  7.9206   8.6433  95.1337
 R41  H8    H   HCH2  0   0.245  3.9769   8.2650  95.7451
 R41  H9    H   HCH2  0   0.226  4.4936   6.7122  95.1010
 R41  H10   H   HNH2  0   0.383  3.2363   5.4141  89.3434
 R41  H11   H   HNH2  0   0.391  2.7795   4.2883  90.5202
 R41  H12   H   HCR6  0   0.279  5.7605   1.3716  92.4731
 R41  H13   H   HCH2  0   0.283  8.5974   3.5018  97.2399
 R41  H14   H   HCH2  0   0.284  9.8997   3.3349  96.0643
 R41  H15   H   HCH2  0   0.242  6.3510   6.7702  93.3052
 R41  H16   H   HCH2  0   0.240  6.9691   8.3585  92.8755
 R41  H17   H   HNH1  0   0.343  5.4997   9.3489  94.3718
 R41  H19   H   HCH2  0   0.243  6.1760   8.5903  96.8264
 R41  H20   H   HCH2  0   0.264  5.5053   7.0380  97.3212
 R41  H6    H   HCH2  0   0.270  8.5285   7.1672  94.4190

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
 R41  N3    C4   aromatic  1.330  0.020  1.330
 R41  N3    C2   aromatic  1.331  0.020  1.331
 R41  N1    C2   single    1.363  0.020  1.363
 R41  C4    C5   aromatic  1.379  0.020  1.379
 R41  C2    C7   aromatic  1.406  0.020  1.406
 R41  C5    C6   aromatic  1.400  0.020  1.400
 R41  C7    C6   aromatic  1.382  0.020  1.382
 R41  C6    C8   single    1.475  0.020  1.475
 R41  C8    C9   aromatic  1.399  0.020  1.399
 R41  C8    C17  aromatic  1.387  0.020  1.387
 R41  C9    C10  aromatic  1.384  0.020  1.384
 R41  C22   N23  single    1.453  0.020  1.453
 R41  C22   C21  single    1.527  0.020  1.527
 R41  C17   O16  single    1.350  0.020  1.350
 R41  C17   C13  aromatic  1.387  0.020  1.387
 R41  CL11  C10  single    1.737  0.020  1.737
 R41  C10   C12  aromatic  1.393  0.020  1.393
 R41  O16   C15  single    1.441  0.020  1.441
 R41  N23   C24  single    1.453  0.020  1.453
 R41  C21   N20  single    1.456  0.020  1.456
 R41  C13   C12  aromatic  1.378  0.020  1.378
 R41  C13   C14  single    1.500  0.020  1.500
 R41  C15   C14  single    1.533  0.020  1.533
 R41  C15   C18  single    1.539  0.020  1.539
 R41  C24   C25  single    1.527  0.020  1.527
 R41  N20   C18  single    1.345  0.020  1.345
 R41  N20   C25  single    1.456  0.020  1.456
 R41  C18   O19  double    1.224  0.020  1.224
 R41  C4    H1   single    0.930  0.020  1.080
 R41  C5    H2   single    0.930  0.020  1.080
 R41  C7    H3   single    0.930  0.020  1.080
 R41  C12   H4   single    0.930  0.020  1.080
 R41  C15   H5   single    0.970  0.020  1.090
 R41  C21   H6   single    0.970  0.020  1.090
 R41  C21   H7   single    0.970  0.020  1.090
 R41  C24   H8   single    0.970  0.020  1.090
 R41  C24   H9   single    0.970  0.020  1.090
 R41  N1    H10  single    0.890  0.020  1.040
 R41  N1    H11  single    0.890  0.020  1.040
 R41  C9    H12  single    0.930  0.020  1.080
 R41  C14   H13  single    0.970  0.020  1.090
 R41  C14   H14  single    0.970  0.020  1.090
 R41  C22   H15  single    0.970  0.020  1.090
 R41  C22   H16  single    0.970  0.020  1.090
 R41  N23   H17  single    0.890  0.020  1.040
 R41  C25   H19  single    0.970  0.020  1.090
 R41  C25   H20  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
 R41  N3    C2   N1   117.28  3.000
 R41  N1    C2   C7   120.60  3.000
 R41  N3    C2   C7   122.08  3.000
 R41  H1    C4   N3   115.84  3.000
 R41  H1    C4   C5   119.69  3.000
 R41  N3    C4   C5   124.47  3.000
 R41  H2    C5   C6   121.89  3.000
 R41  H2    C5   C4   120.31  3.000
 R41  C6    C5   C4   117.79  3.000
 R41  C8    C6   C7   120.03  3.000
 R41  C8    C6   C5   121.51  3.000
 R41  C7    C6   C5   118.46  3.000
 R41  H3    C7   C6   120.81  3.000
 R41  H3    C7   C2   119.96  3.000
 R41  C6    C7   C2   119.22  3.000
 R41  C9    C8   C17  116.42  3.000
 R41  C17   C8   C6   122.03  3.000
 R41  C9    C8   C6   121.52  3.000
 R41  H4    C12  C13  121.44  3.000
 R41  H4    C12  C10  121.02  3.000
 R41  C13   C12  C10  117.54  3.000
 R41  H5    C15  O16  107.95  3.000
 R41  H5    C15  C14  112.19  3.000
 R41  O16   C15  C14  105.36  3.000
 R41  H5    C15  C18  110.91  3.000
 R41  C14   C15  C18  112.53  3.000
 R41  O16   C15  C18  107.55  3.000
 R41  O16   C17  C13  112.56  3.000
 R41  C13   C17  C8   122.86  3.000
 R41  O16   C17  C8   124.56  3.000
 R41  N20   C18  O19  122.82  3.000
 R41  O19   C18  C15  120.02  3.000
 R41  N20   C18  C15  117.16  3.000
 R41  H7    C21  H6   106.68  3.000
 R41  H7    C21  C22  109.43  3.000
 R41  H6    C21  C22  111.13  3.000
 R41  H7    C21  N20  107.71  3.000
 R41  H6    C21  N20  111.99  3.000
 R41  C22   C21  N20  109.76  3.000
 R41  H9    C24  H8   107.11  3.000
 R41  H9    C24  C25  108.77  3.000
 R41  H8    C24  C25  109.54  3.000
 R41  H9    C24  N23  108.60  3.000
 R41  H8    C24  N23  109.13  3.000
 R41  C25   C24  N23  113.50  3.000
 R41  H11   N1   H10  114.36  3.000
 R41  H11   N1   C2   117.83  3.000
 R41  H10   N1   C2   116.49  3.000
 R41  C4    N3   C2   117.98  3.000
 R41  H12   C9   C10  119.90  3.000
 R41  H12   C9   C8   119.30  3.000
 R41  C10   C9   C8   120.79  3.000
 R41  CL11  C10  C9   119.03  3.000
 R41  CL11  C10  C12  119.02  3.000
 R41  C9    C10  C12  121.95  3.000
 R41  C14   C13  C17  107.58  3.000
 R41  C14   C13  C12  131.99  3.000
 R41  C17   C13  C12  120.43  3.000
 R41  H14   C14  H13  107.89  3.000
 R41  H14   C14  C13  110.75  3.000
 R41  H13   C14  C13  113.78  3.000
 R41  H14   C14  C15  110.61  3.000
 R41  H13   C14  C15  112.76  3.000
 R41  C13   C14  C15  100.99  3.000
 R41  C17   O16  C15  107.41  3.000
 R41  C25   N20  C21  112.03  3.000
 R41  C25   N20  C18  120.55  3.000
 R41  C21   N20  C18  126.86  3.000
 R41  H16   C22  H15  107.11  3.000
 R41  H16   C22  N23  109.12  3.000
 R41  H15   C22  N23  108.87  3.000
 R41  H16   C22  C21  109.45  3.000
 R41  H15   C22  C21  109.03  3.000
 R41  N23   C22  C21  113.08  3.000
 R41  H17   N23  C22  109.12  3.000
 R41  H17   N23  C24  108.92  3.000
 R41  C22   N23  C24  111.56  3.000
 R41  H20   C25  H19  107.72  3.000
 R41  H20   C25  N20  109.95  3.000
 R41  H19   C25  N20  108.62  3.000
 R41  H20   C25  C24  111.23  3.000
 R41  H19   C25  C24  109.96  3.000
 R41  N20   C25  C24  109.31  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
 R41  CONST_01  C5    C4   N3   C2       0.00   0.0  0
 R41  CONST_02  C5    C6   C7   C2       0.00   0.0  0
 R41  CONST_03  C8    C6   C7   C2     180.00   0.0  0
 R41  CONST_04  C7    C2   N3   C4       0.00   0.0  0
 R41  CONST_05  C7    C6   C5   C4       0.00   0.0  0
 R41  CONST_06  C8    C6   C5   C4     180.00   0.0  0
 R41  CONST_09  N3    C4   C5   C6       0.00   0.0  0
 R41  CONST_10  N3    C2   C7   C6       0.00   0.0  0
 R41  CONST_11  C10   C9   C8   C6     180.00   0.0  0
 R41  CONST_12  C13   C17  C8   C6     180.00   0.0  0
 R41  CONST_15  C12   C10  C9   C8       0.00   0.0  0
 R41  CONST_16  C12   C13  C17  C8       0.00   0.0  0
 R41  CONST_17  C10   C9   C8   C17      0.00   0.0  0
 R41  CONST_18  C10   C12  C13  C17      0.00   0.0  0
 R41  CONST_19  C13   C17  C8   C9       0.00   0.0  0
 R41  CONST_20  C13   C12  C10  C9       0.00   0.0  0
 R41  CONST_21  O16   C17  C8   C6       0.00   0.0  0
 R41  CONST_22  N1    C2   N3   C4     180.00   0.0  0
 R41  CONST_23  N1    C2   C7   C6     180.00   0.0  0
 R41  CONST_24  CL11  C10  C9   C8     180.00   0.0  0
 R41  CONST_25  C13   C12  C10  CL11   180.00   0.0  0
 R41  CONST_26  C21   N20  C18  C15      0.00   0.0  0
 R41  CONST_27  C25   N20  C18  C15    180.00   0.0  0
 R41  CONST_28  H1    C4   N3   C2     180.00   0.0  0
 R41  CONST_29  H3    C7   C6   C5     180.00   0.0  0
 R41  CONST_30  H12   C9   C8   C6       0.00   0.0  0
 R41  CONST_31  H2    C5   C6   C7     180.00   0.0  0
 R41  CONST_32  H4    C12  C13  C17    180.00   0.0  0
 R41  CONST_33  O19   C18  N20  C21    180.00   0.0  0
 R41  CONST_34  C25   N20  C18  O19      0.00   0.0  0
 R41  Var_01    C15   C14  C13  C12   -165.63  30.0  1
 R41  Var_02    C13   C17  O16  C15    -14.79  30.0  1
 R41  Var_03    C24   N23  C22  C21    -51.14  30.0  1
 R41  Var_04    C24   C25  N20  C21     57.64  30.0  1
 R41  Var_05    N23   C22  C21  N20     54.18  30.0  1
 R41  Var_06    N23   C24  C25  N20    -54.30  30.0  1
 R41  Var_07    C25   C24  N23  C22     51.43  30.0  1
 R41  Var_08    C25   N20  C21  C22    -57.84  30.0  1

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
 R41  chir_01  C15  O16  C14  C18  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
 R41  plan-1  C2    0.020
 R41  plan-1  C4    0.020
 R41  plan-1  C5    0.020
 R41  plan-1  C6    0.020
 R41  plan-1  C7    0.020
 R41  plan-1  C8    0.020
 R41  plan-1  N1    0.020
 R41  plan-1  N3    0.020
 R41  plan-1  H1    0.020
 R41  plan-1  H2    0.020
 R41  plan-1  H3    0.020
 R41  plan-2  C6    0.020
 R41  plan-2  C8    0.020
 R41  plan-2  C12   0.020
 R41  plan-2  C17   0.020
 R41  plan-2  C9    0.020
 R41  plan-2  C10   0.020
 R41  plan-2  CL11  0.020
 R41  plan-2  C13   0.020
 R41  plan-2  C14   0.020
 R41  plan-2  O16   0.020
 R41  plan-2  H4    0.020
 R41  plan-2  H12   0.020
 R41  plan-3  C15   0.020
 R41  plan-3  C18   0.020
 R41  plan-3  C21   0.020
 R41  plan-3  O19   0.020
 R41  plan-3  N20   0.020
 R41  plan-3  C25   0.020
 R41  plan-4  C2    0.020
 R41  plan-4  N1    0.020
 R41  plan-4  H10   0.020
 R41  plan-4  H11   0.020

