# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 28 23:55:49 2022
#   Inital geometry file: a 88 line input string
#   Ligand name: 1-[(2~{S})-2-(4-methoxyphenyl)pyrrolidin-1-yl]propan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)N1CCC[C@H]1c2ccc(OC)cc2
#
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
 06D  06D  "1-[(2~{S})-2-(4-methoxyphenyl)pyrrolidin-1-yl]propan-1-one"  ligand  36  17  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_06D
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
 06D  C13  C  CH1   0  -0.141   -7.2245  3.6598  6.9584
 06D  C14  C  CR6   0   0.123   -5.8267  4.1286  7.2945
 06D  C15  C  CR16  0  -0.299   -5.4267  5.4512  7.1931
 06D  C03  C  CH2   0  -0.560   -9.8742  6.1376  8.1171
 06D  C04  C  CH3   0  -0.665  -11.2213  5.4139  8.0682
 06D  C16  C  CR16  0  -0.366   -4.1151  5.8390  7.4559
 06D  C17  C  CR6   0   0.366   -3.1724  4.8877  7.8317
 06D  C19  C  CH3   0  -0.434   -1.4318  6.4905  7.9958
 06D  C20  C  CR16  0  -0.328   -3.5651  3.5519  7.9460
 06D  C21  C  CR16  0  -0.282   -4.8711  3.1883  7.6811
 06D  C22  C  CH2   0  -0.457   -7.3369  3.1681  5.5090
 06D  C23  C  CH2   0  -0.479   -7.6786  4.4359  4.7380
 06D  C24  C  CH2   0  -0.279   -8.6370  5.1637  5.6742
 06D  N12  N  NT    0  -0.467   -8.2192  4.7233  7.0048
 06D  O01  O  O     0  -0.497   -8.3406  4.6998  9.2496
 06D  O18  O  O2    0  -0.469   -1.8801  5.1562  8.1065
 06D  H1   H  HCH1  0   0.263   -7.5014  2.8659  7.6561
 06D  H2   H  HCR6  0   0.250   -6.1409  6.2152  6.9111
 06D  H3   H  HCH2  0   0.250   -9.7853  6.8108  7.2646
 06D  H4   H  HCH2  0   0.260   -9.8210  6.7511  9.0169
 06D  H5   H  HCH3  0   0.242  -12.0389  6.1336  8.0742
 06D  H6   H  HCH3  0   0.233  -11.3217  4.8063  7.1685
 06D  H7   H  HCH3  0   0.233  -11.3456  4.7600  8.9312
 06D  H8   H  HCR6  0   0.273   -3.8550  6.8848  7.3628
 06D  H9   H  HCH3  0   0.257   -0.3733  6.4836  8.2452
 06D  H10  H  HCH3  0   0.225   -1.5496  6.8791  6.9805
 06D  H11  H  HCH3  0   0.225   -1.9506  7.1582  8.6891
 06D  H12  H  HCR6  0   0.257   -2.8398  2.8062  8.2476
 06D  H13  H  HCR6  0   0.247   -5.1552  2.1463  7.7787
 06D  H14  H  HCH2  0   0.244   -8.1522  2.4451  5.4290
 06D  H15  H  HCH2  0   0.255   -6.4253  2.6809  5.1648
 06D  H16  H  HCH2  0   0.242   -6.7822  5.0357  4.5694
 06D  H17  H  HCH2  0   0.257   -8.1308  4.2389  3.7670
 06D  H18  H  HCH2  0   0.254   -8.5653  6.2467  5.5679
 06D  H19  H  HCH2  0   0.247   -9.6730  4.8744  5.4778
 06D  C02  C  C     0   0.522   -8.7367  5.1410  8.1772

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
 06D  C23  C22  single    1.523  0.020  1.523
 06D  C23  C24  single    1.525  0.020  1.525
 06D  C22  C13  single    1.535  0.020  1.535
 06D  C24  N12  single    1.462  0.020  1.462
 06D  C13  N12  single    1.457  0.020  1.457
 06D  C13  C14  single    1.512  0.020  1.512
 06D  N12  C02  single    1.348  0.020  1.348
 06D  C15  C14  aromatic  1.386  0.020  1.386
 06D  C15  C16  aromatic  1.393  0.020  1.393
 06D  C14  C21  aromatic  1.395  0.020  1.395
 06D  C16  C17  aromatic  1.391  0.020  1.391
 06D  C04  C03  single    1.530  0.020  1.530
 06D  C19  O18  single    1.412  0.020  1.412
 06D  C21  C20  aromatic  1.381  0.020  1.381
 06D  C17  C20  aromatic  1.397  0.020  1.397
 06D  C17  O18  single    1.348  0.020  1.348
 06D  C02  C03  single    1.514  0.020  1.514
 06D  C02  O01  double    1.225  0.020  1.225
 06D  C13  H1   single    0.970  0.020  1.090
 06D  C15  H2   single    0.930  0.020  1.080
 06D  C03  H3   single    0.970  0.020  1.090
 06D  C03  H4   single    0.970  0.020  1.090
 06D  C04  H5   single    0.970  0.020  1.090
 06D  C04  H6   single    0.970  0.020  1.090
 06D  C04  H7   single    0.970  0.020  1.090
 06D  C16  H8   single    0.930  0.020  1.080
 06D  C19  H9   single    0.970  0.020  1.090
 06D  C19  H10  single    0.970  0.020  1.090
 06D  C19  H11  single    0.970  0.020  1.090
 06D  C20  H12  single    0.930  0.020  1.080
 06D  C21  H13  single    0.930  0.020  1.080
 06D  C22  H14  single    0.970  0.020  1.090
 06D  C22  H15  single    0.970  0.020  1.090
 06D  C23  H16  single    0.970  0.020  1.090
 06D  C23  H17  single    0.970  0.020  1.090
 06D  C24  H18  single    0.970  0.020  1.090
 06D  C24  H19  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
 06D  H1   C13  N12  109.70  3.000
 06D  H1   C13  C22  110.59  3.000
 06D  N12  C13  C22  102.35  3.000
 06D  H1   C13  C14  108.52  3.000
 06D  N12  C13  C14  113.44  3.000
 06D  C22  C13  C14  112.14  3.000
 06D  C21  C14  C15  117.76  3.000
 06D  C21  C14  C13  119.07  3.000
 06D  C15  C14  C13  123.13  3.000
 06D  H2   C15  C16  118.28  3.000
 06D  H2   C15  C14  120.13  3.000
 06D  C16  C15  C14  121.59  3.000
 06D  H4   C03  H3   107.10  3.000
 06D  H4   C03  C04  109.60  3.000
 06D  H3   C03  C04  109.82  3.000
 06D  H4   C03  C02  107.52  3.000
 06D  H3   C03  C02  112.12  3.000
 06D  C04  C03  C02  110.58  3.000
 06D  H7   C04  H6   107.97  3.000
 06D  H7   C04  H5   107.85  3.000
 06D  H6   C04  H5   107.68  3.000
 06D  H7   C04  C03  111.03  3.000
 06D  H6   C04  C03  111.78  3.000
 06D  H5   C04  C03  110.38  3.000
 06D  H8   C16  C17  121.43  3.000
 06D  H8   C16  C15  118.64  3.000
 06D  C17  C16  C15  119.92  3.000
 06D  O18  C17  C20  116.31  3.000
 06D  O18  C17  C16  124.64  3.000
 06D  C20  C17  C16  119.04  3.000
 06D  H11  C19  H10  108.69  3.000
 06D  H11  C19  H9   108.68  3.000
 06D  H10  C19  H9   108.67  3.000
 06D  H11  C19  O18  112.13  3.000
 06D  H10  C19  O18  111.99  3.000
 06D  H9   C19  O18  106.57  3.000
 06D  H12  C20  C21  120.35  3.000
 06D  H12  C20  C17  119.52  3.000
 06D  C21  C20  C17  120.12  3.000
 06D  H13  C21  C20  118.91  3.000
 06D  H13  C21  C14  119.54  3.000
 06D  C20  C21  C14  121.55  3.000
 06D  H15  C22  H14  107.78  3.000
 06D  H15  C22  C23  113.59  3.000
 06D  H14  C22  C23  110.27  3.000
 06D  H15  C22  C13  112.36  3.000
 06D  H14  C22  C13  109.62  3.000
 06D  C23  C22  C13  103.17  3.000
 06D  H17  C23  H16  107.62  3.000
 06D  H17  C23  C24  111.88  3.000
 06D  H16  C23  C24  110.41  3.000
 06D  H17  C23  C22  113.21  3.000
 06D  H16  C23  C22  110.57  3.000
 06D  C24  C23  C22  103.15  3.000
 06D  H19  C24  H18  107.90  3.000
 06D  H19  C24  N12  110.76  3.000
 06D  H18  C24  N12  111.65  3.000
 06D  H19  C24  C23  111.04  3.000
 06D  H18  C24  C23  111.89  3.000
 06D  N12  C24  C23  103.61  3.000
 06D  C24  N12  C02  126.04  3.000
 06D  C02  N12  C13  121.07  3.000
 06D  C24  N12  C13  112.70  3.000
 06D  C19  O18  C17  118.46  3.000
 06D  O01  C02  N12  121.70  3.000
 06D  O01  C02  C03  120.99  3.000
 06D  N12  C02  C03  117.26  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
 06D  CONST_01  C17  C16  C15  C14     0.00   0.0  0
 06D  CONST_02  C17  C20  C21  C14     0.00   0.0  0
 06D  CONST_03  C20  C21  C14  C15     0.00   0.0  0
 06D  CONST_04  C20  C17  C16  C15     0.00   0.0  0
 06D  CONST_05  C21  C14  C15  C16     0.00   0.0  0
 06D  CONST_06  C21  C20  C17  C16     0.00   0.0  0
 06D  CONST_07  C16  C15  C14  C13   180.00   0.0  0
 06D  CONST_08  C20  C21  C14  C13   180.00   0.0  0
 06D  CONST_09  O18  C17  C16  C15   180.00   0.0  0
 06D  CONST_10  O18  C17  C20  C21   180.00   0.0  0
 06D  CONST_11  H2   C15  C14  C13     0.00   0.0  0
 06D  CONST_12  H13  C21  C14  C13     0.00   0.0  0
 06D  CONST_13  H8   C16  C15  C14   180.00   0.0  0
 06D  CONST_14  H12  C20  C21  C14   180.00   0.0  0
 06D  CONST_15  H13  C21  C14  C15   180.00   0.0  0
 06D  CONST_16  H12  C20  C17  C16   180.00   0.0  0
 06D  CONST_17  H2   C15  C16  C17   180.00   0.0  0
 06D  CONST_18  H13  C21  C20  C17   180.00   0.0  0
 06D  CONST_19  H8   C16  C17  C20   180.00   0.0  0
 06D  CONST_20  H2   C15  C14  C21   180.00   0.0  0
 06D  CONST_21  C03  C02  N12  C13   180.00   0.0  0
 06D  CONST_22  O01  C02  N12  C13     0.00   0.0  0
 06D  CONST_23  C24  N12  C02  C03     0.00   0.0  0
 06D  CONST_24  O01  C02  N12  C24   180.00   0.0  0
 06D  Var_01    C24  C23  C22  C13   -38.82  30.0  1
 06D  Var_02    C23  C24  N12  C13    -7.98  30.0  1
 06D  Var_03    N12  C24  C23  C22    28.84  30.0  1
 06D  Var_04    C23  C24  N12  C02   177.10  30.0  1
 06D  Var_05    H16  C23  C22  C13    79.22  30.0  1
 06D  Var_06    H17  C23  C22  C13  -159.93  30.0  1
 06D  Var_07    H18  C24  N12  C13  -128.57  30.0  1
 06D  Var_08    H19  C24  N12  C13   111.15  30.0  1
 06D  Var_09    H18  C24  C23  C22   149.26  30.0  1
 06D  Var_10    H19  C24  C23  C22   -90.10  30.0  1
 06D  Var_11    H14  C22  C23  C24    78.18  30.0  1
 06D  Var_12    H15  C22  C23  C24  -160.72  30.0  1
 06D  Var_13    H16  C23  C24  N12   -89.32  30.0  1
 06D  Var_14    H17  C23  C24  N12   150.85  30.0  1
 06D  Var_15    C19  O18  C17  C16    -0.72  30.0  2
 06D  Var_16    C20  C17  O18  C19   179.54  30.0  1
 06D  Var_17    H18  C24  N12  C02    56.51  30.0  1
 06D  Var_18    H19  C24  N12  C02   -63.77  30.0  1
 06D  Var_19    N12  C02  C03  C04    90.19  30.0  1
 06D  Var_20    H9   C19  O18  C17  -179.30  30.0  3
 06D  Var_21    H10  C19  O18  C17   -60.60  30.0  3
 06D  Var_22    H11  C19  O18  C17    61.91  30.0  3
 06D  Var_23    H3   C03  C02  N12   -32.74  30.0  3
 06D  Var_24    H4   C03  C02  N12  -150.19  30.0  3
 06D  Var_25    O01  C02  C03  C04   -87.24  30.0  1
 06D  Var_26    H5   C04  C03  C02   177.24  30.0  3
 06D  Var_27    H6   C04  C03  C02   -62.94  30.0  3
 06D  Var_28    H7   C04  C03  C02    57.69  30.0  3
 06D  Var_29    H3   C03  C02  O01   149.84  30.0  3
 06D  Var_30    H4   C03  C02  O01    32.39  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
 06D  chir_01  C13  C22  N12  C14  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
 06D  plan-1  C13  0.020
 06D  plan-1  C14  0.020
 06D  plan-1  C15  0.020
 06D  plan-1  C16  0.020
 06D  plan-1  C17  0.020
 06D  plan-1  C20  0.020
 06D  plan-1  C21  0.020
 06D  plan-1  O18  0.020
 06D  plan-1  H2   0.020
 06D  plan-1  H8   0.020
 06D  plan-1  H12  0.020
 06D  plan-1  H13  0.020
 06D  plan-2  C13  0.020
 06D  plan-2  C03  0.020
 06D  plan-2  C24  0.020
 06D  plan-2  N12  0.020
 06D  plan-2  O01  0.020
 06D  plan-2  C02  0.020

