# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 11:57:24 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: pyridin-4-yl[4-(2-pyrrolidin-1-ylethoxy)phenyl]methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(c1ccncc1)c2ccc(OCCN3CCCC3)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
 52D  52D  pyridin-4-yl[4-(2-pyrrolidin-1-ylethoxy)phenyl]methanone  ligand  42  22  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_52D
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
 52D  O8    O  O     0  -0.388   3.7879   2.0863  -1.0742
 52D  C7    C  C     0   0.365   3.3284   1.0751  -0.5804
 52D  C9    C  CR6   0   0.041   4.2577  -0.0507  -0.2508
 52D  C14   C  CR16  0  -0.349   3.9732  -1.3682  -0.5886
 52D  C13   C  CR16  0  -0.054   4.9245  -2.3424  -0.3209
 52D  N12   N  N     0  -0.398   6.0886  -2.0880   0.2621
 52D  C11   C  CR16  0  -0.059   6.3545  -0.8272   0.5857
 52D  C10   C  CR16  0  -0.344   5.4865   0.2242   0.3385
 52D  C6    C  CR6   0  -0.061   1.8914   0.9274  -0.2980
 52D  C1    C  CR16  0  -0.262   1.4010  -0.0061   0.6131
 52D  C5    C  CR16  0  -0.241   0.9801   1.7960  -0.9142
 52D  C4    C  CR16  0  -0.340  -0.3656   1.7157  -0.6464
 52D  C3    C  CR6   0   0.406  -0.8482   0.7712   0.2712
 52D  C2    C  CR16  0  -0.374   0.0493  -0.0879   0.9060
 52D  O15   O  O2    0  -0.453  -2.1664   0.7709   0.4748
 52D  C16   C  CH2   0  -0.217  -2.7279  -0.1425   1.4083
 52D  C17   C  CH2   0  -0.297  -4.2173   0.1069   1.4773
 52D  N23   N  NT    0  -0.420  -4.8960  -0.1089   0.2247
 52D  C19   C  CH2   0  -0.284  -4.9304  -1.4902  -0.2245
 52D  C22   C  CH2   0  -0.274  -6.2872   0.3053   0.2463
 52D  C21   C  CH2   0  -0.464  -6.8398  -0.2409  -1.0672
 52D  C20   C  CH2   0  -0.467  -5.9801  -1.4928  -1.3416
 52D  H14   H  HCR6  0   0.286   3.0440  -1.6441  -1.0691
 52D  H13   H  HCR6  0   0.272   4.7286  -3.3744  -0.5887
 52D  H11   H  HCR6  0   0.271   7.3088  -0.6390   1.0644
 52D  H10   H  HCR6  0   0.279   5.7645   1.2321   0.6151
 52D  H1    H  HCR6  0   0.275   2.0748  -0.6728   1.1344
 52D  H5    H  HCR6  0   0.267   1.3341   2.5354  -1.6205
 52D  H4    H  HCR6  0   0.271  -1.0630   2.3827  -1.1368
 52D  H2    H  HCR6  0   0.289  -0.2839  -0.8180   1.6301
 52D  H16   H  HCH2  0   0.237  -2.5107  -1.1724   1.1071
 52D  H16A  H  HCH2  0   0.246  -2.2950   0.0109   2.4021
 52D  H17   H  HCH2  0   0.205  -4.6141  -0.5354   2.2833
 52D  H17A  H  HCH2  0   0.245  -4.3871   1.1392   1.7957
 52D  H19   H  HCH2  0   0.235  -3.9511  -1.8270  -0.5692
 52D  H19A  H  HCH2  0   0.192  -5.2395  -2.1677   0.5900
 52D  H22   H  HCH2  0   0.189  -6.8301  -0.1346   1.1012
 52D  H22A  H  HCH2  0   0.233  -6.3710   1.3909   0.3332
 52D  H21   H  HCH2  0   0.233  -7.9035  -0.4654  -0.9963
 52D  H21A  H  HCH2  0   0.234  -6.7158   0.4920  -1.8649
 52D  H20   H  HCH2  0   0.236  -5.5091  -1.4340  -2.3230
 52D  H20A  H  HCH2  0   0.234  -6.5664  -2.4111  -1.3229

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
 52D  C7   O8    double    1.216  0.020  1.216
 52D  C6   C7    single    1.472  0.020  1.472
 52D  C7   C9    single    1.497  0.020  1.497
 52D  C14  C9    aromatic  1.390  0.020  1.390
 52D  C9   C10   aromatic  1.390  0.020  1.390
 52D  C14  C13   aromatic  1.388  0.020  1.388
 52D  C14  H14   single    0.930  0.020  1.080
 52D  C13  N12   aromatic  1.327  0.020  1.327
 52D  C13  H13   single    0.930  0.020  1.080
 52D  N12  C11   aromatic  1.329  0.020  1.329
 52D  C10  C11   aromatic  1.386  0.020  1.386
 52D  C11  H11   single    0.930  0.020  1.080
 52D  C10  H10   single    0.930  0.020  1.080
 52D  C5   C6    aromatic  1.402  0.020  1.402
 52D  C6   C1    aromatic  1.394  0.020  1.394
 52D  C2   C1    aromatic  1.385  0.020  1.385
 52D  C1   H1    single    0.930  0.020  1.080
 52D  C4   C5    aromatic  1.374  0.020  1.374
 52D  C5   H5    single    0.930  0.020  1.080
 52D  C4   C3    aromatic  1.402  0.020  1.402
 52D  C4   H4    single    0.930  0.020  1.080
 52D  O15  C3    single    1.334  0.020  1.334
 52D  C3   C2    aromatic  1.395  0.020  1.395
 52D  C2   H2    single    0.930  0.020  1.080
 52D  O15  C16   single    1.422  0.020  1.422
 52D  C17  C16   single    1.512  0.020  1.512
 52D  C16  H16   single    0.970  0.020  1.090
 52D  C16  H16A  single    0.970  0.020  1.090
 52D  C17  N23   single    1.441  0.020  1.441
 52D  C17  H17   single    0.970  0.020  1.090
 52D  C17  H17A  single    0.970  0.020  1.090
 52D  C19  N23   single    1.453  0.020  1.453
 52D  N23  C22   single    1.452  0.020  1.452
 52D  C19  C20   single    1.533  0.020  1.533
 52D  C19  H19   single    0.970  0.020  1.090
 52D  C19  H19A  single    0.970  0.020  1.090
 52D  C22  C21   single    1.526  0.020  1.526
 52D  C22  H22   single    0.970  0.020  1.090
 52D  C22  H22A  single    0.970  0.020  1.090
 52D  C20  C21   single    1.543  0.020  1.543
 52D  C21  H21   single    0.970  0.020  1.090
 52D  C21  H21A  single    0.970  0.020  1.090
 52D  C20  H20   single    0.970  0.020  1.090
 52D  C20  H20A  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
 52D  C6    C7   C9   119.24  3.000
 52D  C9    C7   O8   118.72  3.000
 52D  C6    C7   O8   122.04  3.000
 52D  C10   C9   C14  118.13  3.000
 52D  C10   C9   C7   119.57  3.000
 52D  C14   C9   C7   122.18  3.000
 52D  H14   C14  C13  119.70  3.000
 52D  H14   C14  C9   121.71  3.000
 52D  C13   C14  C9   118.58  3.000
 52D  H13   C13  N12  116.73  3.000
 52D  H13   C13  C14  119.79  3.000
 52D  N12   C13  C14  123.48  3.000
 52D  C11   N12  C13  117.69  3.000
 52D  H11   C11  C10  119.90  3.000
 52D  H11   C11  N12  116.64  3.000
 52D  C10   C11  N12  123.46  3.000
 52D  H10   C10  C11  120.04  3.000
 52D  H10   C10  C9   121.32  3.000
 52D  C11   C10  C9   118.64  3.000
 52D  C5    C6   C1   118.28  3.000
 52D  C1    C6   C7   122.43  3.000
 52D  C5    C6   C7   119.22  3.000
 52D  H1    C1   C2   118.00  3.000
 52D  H1    C1   C6   120.57  3.000
 52D  C2    C1   C6   121.41  3.000
 52D  H5    C5   C4   119.17  3.000
 52D  H5    C5   C6   119.85  3.000
 52D  C4    C5   C6   120.97  3.000
 52D  H4    C4   C3   119.32  3.000
 52D  H4    C4   C5   120.43  3.000
 52D  C3    C4   C5   120.25  3.000
 52D  O15   C3   C2   124.48  3.000
 52D  C2    C3   C4   119.40  3.000
 52D  O15   C3   C4   116.12  3.000
 52D  H2    C2   C3   121.49  3.000
 52D  H2    C2   C1   118.83  3.000
 52D  C3    C2   C1   119.67  3.000
 52D  C16   O15  C3   119.39  3.000
 52D  H16A  C16  H16  107.64  3.000
 52D  H16A  C16  C17  108.97  3.000
 52D  H16   C16  C17  111.30  3.000
 52D  H16A  C16  O15  110.48  3.000
 52D  H16   C16  O15  110.20  3.000
 52D  C17   C16  O15  108.24  3.000
 52D  H17A  C17  H17  106.30  3.000
 52D  H17A  C17  N23  108.74  3.000
 52D  H17   C17  N23  112.22  3.000
 52D  H17A  C17  C16  108.79  3.000
 52D  H17   C17  C16  106.94  3.000
 52D  N23   C17  C16  113.56  3.000
 52D  C22   N23  C19  104.67  3.000
 52D  C22   N23  C17  113.31  3.000
 52D  C19   N23  C17  114.98  3.000
 52D  H19A  C19  H19  107.16  3.000
 52D  H19A  C19  C20  110.18  3.000
 52D  H19   C19  C20  112.56  3.000
 52D  H19A  C19  N23  111.23  3.000
 52D  H19   C19  N23  111.70  3.000
 52D  C20   C19  N23  104.07  3.000
 52D  H22A  C22  H22  107.26  3.000
 52D  H22A  C22  C21  113.35  3.000
 52D  H22   C22  C21  110.23  3.000
 52D  H22A  C22  N23  111.00  3.000
 52D  H22   C22  N23  111.66  3.000
 52D  C21   C22  N23  103.42  3.000
 52D  H21A  C21  H21  107.29  3.000
 52D  H21A  C21  C20  110.60  3.000
 52D  H21   C21  C20  112.85  3.000
 52D  H21A  C21  C22  110.36  3.000
 52D  H21   C21  C22  111.79  3.000
 52D  C20   C21  C22  103.98  3.000
 52D  H20A  C20  H20  107.06  3.000
 52D  H20A  C20  C21  112.38  3.000
 52D  H20   C20  C21  110.91  3.000
 52D  H20A  C20  C19  110.94  3.000
 52D  H20   C20  C19  111.11  3.000
 52D  C21   C20  C19  104.51  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
 52D  CONST_01  N12  C13  C14  C9      0.00   0.0  0
 52D  CONST_02  N12  C11  C10  C9      0.00   0.0  0
 52D  CONST_03  C11  C10  C9   C14     0.00   0.0  0
 52D  CONST_04  C11  N12  C13  C14     0.00   0.0  0
 52D  CONST_05  C10  C9   C14  C13     0.00   0.0  0
 52D  CONST_06  C10  C11  N12  C13     0.00   0.0  0
 52D  CONST_07  C3   C4   C5   C6      0.00   0.0  0
 52D  CONST_08  C3   C2   C1   C6      0.00   0.0  0
 52D  CONST_09  C4   C5   C6   C1      0.00   0.0  0
 52D  CONST_10  C4   C3   C2   C1      0.00   0.0  0
 52D  CONST_11  C2   C1   C6   C5      0.00   0.0  0
 52D  CONST_12  C2   C3   C4   C5      0.00   0.0  0
 52D  CONST_13  C4   C5   C6   C7    180.00   0.0  0
 52D  CONST_14  C2   C1   C6   C7    180.00   0.0  0
 52D  CONST_15  C13  C14  C9   C7    180.00   0.0  0
 52D  CONST_16  C11  C10  C9   C7    180.00   0.0  0
 52D  CONST_17  O15  C3   C2   C1    180.00   0.0  0
 52D  CONST_18  O15  C3   C4   C5    180.00   0.0  0
 52D  CONST_19  H13  C13  C14  C9    180.00   0.0  0
 52D  CONST_20  H11  C11  C10  C9    180.00   0.0  0
 52D  CONST_21  H10  C10  C9   C14   180.00   0.0  0
 52D  CONST_22  H14  C14  C13  N12   180.00   0.0  0
 52D  CONST_23  H4   C4   C5   C6    180.00   0.0  0
 52D  CONST_24  H2   C2   C1   C6    180.00   0.0  0
 52D  CONST_25  H5   C5   C6   C1    180.00   0.0  0
 52D  CONST_26  H1   C1   C6   C5    180.00   0.0  0
 52D  Var_01    C21  C20  C19  N23   -21.46  30.0  1
 52D  Var_02    C20  C21  C22  N23    29.19  30.0  1
 52D  Var_03    C21  C22  N23  C19   -44.28  30.0  1
 52D  Var_04    C22  C21  C20  C19    -4.65  30.0  1
 52D  Var_05    C20  C19  N23  C22    41.16  30.0  1
 52D  Var_06    C5   C6   C7   C9   -163.00  30.0  2
 52D  Var_07    C6   C7   C9   C14    46.48  30.0  2
 52D  Var_08    C19  N23  C17  C16    67.61  30.0  3
 52D  Var_09    C17  C16  O15  C3    177.95  30.0  3
 52D  Var_10    N23  C17  C16  O15    61.63  30.0  2

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
 52D  plan-1  C7   0.020
 52D  plan-1  C9   0.020
 52D  plan-1  C14  0.020
 52D  plan-1  C13  0.020
 52D  plan-1  N12  0.020
 52D  plan-1  C11  0.020
 52D  plan-1  C10  0.020
 52D  plan-1  H14  0.020
 52D  plan-1  H13  0.020
 52D  plan-1  H11  0.020
 52D  plan-1  H10  0.020
 52D  plan-2  C7   0.020
 52D  plan-2  C6   0.020
 52D  plan-2  C1   0.020
 52D  plan-2  C5   0.020
 52D  plan-2  C4   0.020
 52D  plan-2  C3   0.020
 52D  plan-2  C2   0.020
 52D  plan-2  O15  0.020
 52D  plan-2  H1   0.020
 52D  plan-2  H5   0.020
 52D  plan-2  H4   0.020
 52D  plan-2  H2   0.020
 52D  plan-3  O8   0.020
 52D  plan-3  C7   0.020
 52D  plan-3  C9   0.020
 52D  plan-3  C6   0.020

