# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 12:07:29 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: (2~{S})-2-(diphenylmethyl)pyrrolidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CN[C@@H](C1)C(c2ccccc2)c3ccccc3
#
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
 60H  60H  (2~{S})-2-(diphenylmethyl)pyrrolidine  ligand  37  18  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_60H
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
 60H  N10  N  NH1   0  -0.607  -0.4968   2.0143  -0.7525
 60H  C38  C  CH1   0  -0.035  -0.4977   1.5455   0.6217
 60H  C39  C  CH1   0  -0.418   0.0013   0.1019   0.8076
 60H  C46  C  CR6   0   0.137  -0.8857  -0.9942   0.2603
 60H  C51  C  CR16  0  -0.312  -1.0881  -2.1329   1.0398
 60H  C50  C  CR16  0  -0.243  -1.8648  -3.1909   0.5875
 60H  C49  C  CR16  0  -0.272  -2.4633  -3.1277  -0.6637
 60H  C48  C  CR16  0  -0.244  -2.2761  -1.9978  -1.4484
 60H  C47  C  CR16  0  -0.308  -1.4953  -0.9424  -0.9940
 60H  C40  C  CR6   0   0.162   1.4377  -0.0169   0.3349
 60H  C45  C  CR16  0  -0.316   2.4725   0.2176   1.2389
 60H  C44  C  CR16  0  -0.241   3.8011   0.1654   0.8392
 60H  C43  C  CR16  0  -0.274   4.1198  -0.1229  -0.4809
 60H  C42  C  CR16  0  -0.237   3.0985  -0.3585  -1.3917
 60H  C41  C  CR16  0  -0.306   1.7709  -0.3072  -0.9869
 60H  C37  C  CH2   0  -0.430  -1.9404   1.7978   1.0487
 60H  C36  C  CH2   0  -0.481  -2.2984   3.1147   0.3446
 60H  C35  C  CH2   0  -0.273  -1.2334   3.2738  -0.7594
 60H  H1   H  HNH1  0   0.350   0.4438   2.1368  -1.1047
 60H  H66  H  HCH1  0   0.211   0.1580   2.1666   1.2577
 60H  H67  H  HCH1  0   0.259   0.0253  -0.0391   1.8936
 60H  H77  H  HCR6  0   0.247  -0.6312  -2.1931   2.0212
 60H  H76  H  HCR6  0   0.252  -2.0050  -4.0609   1.2165
 60H  H75  H  HCR6  0   0.251  -3.0726  -3.9479  -1.0211
 60H  H74  H  HCR6  0   0.249  -2.7433  -1.9325  -2.4231
 60H  H73  H  HCR6  0   0.262  -1.3716  -0.0607  -1.6085
 60H  H72  H  HCR6  0   0.248   2.2362   0.4402   2.2734
 60H  H71  H  HCR6  0   0.253   4.5871   0.3442   1.5619
 60H  H70  H  HCR6  0   0.253   5.1544  -0.1695  -0.7958
 60H  H69  H  HCR6  0   0.253   3.3346  -0.5863  -2.4234
 60H  H68  H  HCR6  0   0.254   0.9912  -0.5019  -1.7124
 60H  H65  H  HCH2  0   0.232  -2.5817   0.9877   0.6977
 60H  H64  H  HCH2  0   0.233  -2.0410   1.8531   2.1328
 60H  H63  H  HCH2  0   0.237  -3.3095   3.0916  -0.0611
 60H  H62  H  HCH2  0   0.234  -2.2527   3.9555   1.0366
 60H  H60  H  HCH2  0   0.203  -0.5895   4.1327  -0.5326
 60H  H61  H  HCH2  0   0.220  -1.6734   3.4572  -1.7417

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
 60H  C49  C50  aromatic  1.388  0.020  1.388
 60H  C49  C48  aromatic  1.388  0.020  1.388
 60H  C50  C51  aromatic  1.388  0.020  1.388
 60H  C48  C47  aromatic  1.389  0.020  1.389
 60H  C51  C46  aromatic  1.395  0.020  1.395
 60H  C47  C46  aromatic  1.396  0.020  1.396
 60H  C46  C39  single    1.512  0.020  1.512
 60H  C39  C40  single    1.517  0.020  1.517
 60H  C39  C38  single    1.539  0.020  1.539
 60H  C41  C40  aromatic  1.394  0.020  1.394
 60H  C41  C42  aromatic  1.389  0.020  1.389
 60H  C40  C45  aromatic  1.394  0.020  1.394
 60H  C38  N10  single    1.452  0.020  1.452
 60H  C38  C37  single    1.526  0.020  1.526
 60H  N10  C35  single    1.459  0.020  1.459
 60H  C42  C43  aromatic  1.389  0.020  1.389
 60H  C45  C44  aromatic  1.388  0.020  1.388
 60H  C43  C44  aromatic  1.388  0.020  1.388
 60H  C37  C36  single    1.536  0.020  1.536
 60H  C35  C36  single    1.542  0.020  1.542
 60H  N10  H1   single    0.890  0.020  1.040
 60H  C38  H66  single    0.970  0.020  1.090
 60H  C39  H67  single    0.970  0.020  1.090
 60H  C51  H77  single    0.930  0.020  1.080
 60H  C50  H76  single    0.930  0.020  1.080
 60H  C49  H75  single    0.930  0.020  1.080
 60H  C48  H74  single    0.930  0.020  1.080
 60H  C47  H73  single    0.930  0.020  1.080
 60H  C45  H72  single    0.930  0.020  1.080
 60H  C44  H71  single    0.930  0.020  1.080
 60H  C43  H70  single    0.930  0.020  1.080
 60H  C42  H69  single    0.930  0.020  1.080
 60H  C41  H68  single    0.930  0.020  1.080
 60H  C37  H65  single    0.970  0.020  1.090
 60H  C37  H64  single    0.970  0.020  1.090
 60H  C36  H63  single    0.970  0.020  1.090
 60H  C36  H62  single    0.970  0.020  1.090
 60H  C35  H60  single    0.970  0.020  1.090
 60H  C35  H61  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
 60H  H1   N10  C35  111.29  3.000
 60H  H1   N10  C38  111.66  3.000
 60H  C35  N10  C38  106.43  3.000
 60H  H66  C38  C37  107.89  3.000
 60H  H66  C38  C39  105.39  3.000
 60H  C37  C38  C39  115.34  3.000
 60H  H66  C38  N10  111.29  3.000
 60H  C37  C38  N10  102.25  3.000
 60H  C39  C38  N10  114.65  3.000
 60H  H67  C39  C40  106.15  3.000
 60H  H67  C39  C46  106.16  3.000
 60H  C40  C39  C46  112.70  3.000
 60H  H67  C39  C38  104.34  3.000
 60H  C40  C39  C38  110.06  3.000
 60H  C46  C39  C38  116.49  3.000
 60H  C47  C46  C51  117.98  3.000
 60H  C47  C46  C39  123.67  3.000
 60H  C51  C46  C39  118.33  3.000
 60H  H77  C51  C50  119.23  3.000
 60H  H77  C51  C46  119.35  3.000
 60H  C50  C51  C46  121.42  3.000
 60H  H76  C50  C49  120.29  3.000
 60H  H76  C50  C51  119.70  3.000
 60H  C49  C50  C51  120.01  3.000
 60H  H75  C49  C48  120.39  3.000
 60H  H75  C49  C50  120.38  3.000
 60H  C48  C49  C50  119.23  3.000
 60H  H74  C48  C47  119.41  3.000
 60H  H74  C48  C49  119.98  3.000
 60H  C47  C48  C49  120.61  3.000
 60H  H73  C47  C48  119.84  3.000
 60H  H73  C47  C46  119.40  3.000
 60H  C48  C47  C46  120.75  3.000
 60H  C41  C40  C45  118.20  3.000
 60H  C45  C40  C39  119.19  3.000
 60H  C41  C40  C39  122.57  3.000
 60H  H72  C45  C44  119.40  3.000
 60H  H72  C45  C40  119.44  3.000
 60H  C44  C45  C40  121.16  3.000
 60H  H71  C44  C43  120.16  3.000
 60H  H71  C44  C45  119.76  3.000
 60H  C43  C44  C45  120.08  3.000
 60H  H70  C43  C42  120.32  3.000
 60H  H70  C43  C44  120.33  3.000
 60H  C42  C43  C44  119.35  3.000
 60H  H69  C42  C41  119.60  3.000
 60H  H69  C42  C43  120.02  3.000
 60H  C41  C42  C43  120.37  3.000
 60H  H68  C41  C42  119.11  3.000
 60H  H68  C41  C40  120.05  3.000
 60H  C42  C41  C40  120.84  3.000
 60H  H64  C37  H65  107.65  3.000
 60H  H64  C37  C36  113.01  3.000
 60H  H65  C37  C36  110.62  3.000
 60H  H64  C37  C38  111.96  3.000
 60H  H65  C37  C38  110.06  3.000
 60H  C36  C37  C38  103.53  3.000
 60H  H62  C36  H63  106.95  3.000
 60H  H62  C36  C35  110.25  3.000
 60H  H63  C36  C35  112.12  3.000
 60H  H62  C36  C37  111.14  3.000
 60H  H63  C36  C37  111.64  3.000
 60H  C35  C36  C37  104.82  3.000
 60H  H61  C35  H60  106.91  3.000
 60H  H61  C35  C36  112.53  3.000
 60H  H60  C35  C36  109.76  3.000
 60H  H61  C35  N10  110.65  3.000
 60H  H60  C35  N10  112.24  3.000
 60H  C36  C35  N10  104.85  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
 60H  CONST_01  C49  C50  C51  C46     0.00   0.0  0
 60H  CONST_02  C49  C48  C47  C46     0.00   0.0  0
 60H  CONST_03  C48  C49  C50  C51     0.00   0.0  0
 60H  CONST_04  C48  C47  C46  C51     0.00   0.0  0
 60H  CONST_05  C47  C48  C49  C50     0.00   0.0  0
 60H  CONST_06  C47  C46  C51  C50     0.00   0.0  0
 60H  CONST_07  C43  C42  C41  C40     0.00   0.0  0
 60H  CONST_08  C43  C44  C45  C40     0.00   0.0  0
 60H  CONST_09  C42  C41  C40  C45     0.00   0.0  0
 60H  CONST_10  C42  C43  C44  C45     0.00   0.0  0
 60H  CONST_11  C41  C40  C45  C44     0.00   0.0  0
 60H  CONST_12  C41  C42  C43  C44     0.00   0.0  0
 60H  CONST_13  C50  C51  C46  C39   180.00   0.0  0
 60H  CONST_14  C48  C47  C46  C39   180.00   0.0  0
 60H  CONST_15  C42  C41  C40  C39   180.00   0.0  0
 60H  CONST_16  C44  C45  C40  C39   180.00   0.0  0
 60H  CONST_17  H76  C50  C51  C46   180.00   0.0  0
 60H  CONST_18  H74  C48  C47  C46   180.00   0.0  0
 60H  CONST_19  H75  C49  C50  C51   180.00   0.0  0
 60H  CONST_20  H73  C47  C46  C51   180.00   0.0  0
 60H  CONST_21  H77  C51  C50  C49   180.00   0.0  0
 60H  CONST_22  H69  C42  C41  C40   180.00   0.0  0
 60H  CONST_23  H71  C44  C45  C40   180.00   0.0  0
 60H  CONST_24  H68  C41  C40  C45   180.00   0.0  0
 60H  CONST_25  H70  C43  C44  C45   180.00   0.0  0
 60H  CONST_26  H72  C45  C44  C43   180.00   0.0  0
 60H  Var_01    C37  C36  C35  N10     7.90  30.0  1
 60H  Var_02    C36  C35  N10  C38   -32.29  30.0  1
 60H  Var_03    C35  C36  C37  C38    17.55  30.0  1
 60H  Var_04    C51  C46  C39  C38  -136.85  30.0  2
 60H  Var_05    C41  C40  C39  C38   -88.10  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
 60H  chir_01  C38  C39  N10  C37  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
 60H  plan-1  C39  0.020
 60H  plan-1  C46  0.020
 60H  plan-1  C51  0.020
 60H  plan-1  C50  0.020
 60H  plan-1  C49  0.020
 60H  plan-1  C48  0.020
 60H  plan-1  C47  0.020
 60H  plan-1  H77  0.020
 60H  plan-1  H76  0.020
 60H  plan-1  H75  0.020
 60H  plan-1  H74  0.020
 60H  plan-1  H73  0.020
 60H  plan-2  C39  0.020
 60H  plan-2  C40  0.020
 60H  plan-2  C45  0.020
 60H  plan-2  C44  0.020
 60H  plan-2  C43  0.020
 60H  plan-2  C42  0.020
 60H  plan-2  C41  0.020
 60H  plan-2  H72  0.020
 60H  plan-2  H71  0.020
 60H  plan-2  H70  0.020
 60H  plan-2  H69  0.020
 60H  plan-2  H68  0.020

