# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 07:03:06 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: (5-chloro-1'H-spiro[indole-3,4'-piperidin]-1'-yl)[(2R)-2,3-dihydro-1,4-benzodioxin-2-yl]methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc2N=CC3(CCN(CC3)C(=O)[C@H]4COc5ccccc5O4)c2c1
#
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
 R0D  R0D  (5-chloro-1'H-spiro[indole-3,4'-piperidin]-1'-yl)[(2R)-2,3-dihydro-1,4-benzodioxin-2-yl]methanone  ligand  46  27  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_R0D
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
 R0D  C10   C   CH2   0  -0.348  -0.1445   1.2028   0.7795
 R0D  C13   C   CH1   0  -0.138  -2.7306   0.2098  -0.1330
 R0D  C17   C   CR16  0  -0.363  -6.4274  -0.4550   1.4942
 R0D  C20   C   CR16  0  -0.359  -5.6404  -1.8074  -0.7985
 R0D  C21   C   CR6   0   0.303  -4.8182  -0.8248  -0.2618
 R0D  C24   C   CH2   0  -0.329   0.4278   1.8752  -1.4803
 R0D  C26   C   CR56  0   0.180   3.5436   0.2139   0.1105
 R0D  C02   C   CR6   0  -0.040   5.1361  -1.5305  -0.0073
 R0D  C03   C   CR16  0  -0.223   6.1293  -0.6893   0.4788
 R0D  C04   C   CR16  0  -0.321   5.8289   0.6328   0.7894
 R0D  C05   C   CR56  0   0.213   4.5302   1.0683   0.5999
 R0D  C07   C   CR15  0   0.014   2.7819   2.3279   0.5405
 R0D  C08   C   CR5   0  -0.319   2.2705   1.0013   0.0243
 R0D  C09   C   CH2   0  -0.391   1.1601   0.4295   0.9214
 R0D  C12   C   C     0   0.526  -1.7034   0.7582  -1.1248
 R0D  C14   C   CH2   0  -0.203  -3.4708   1.3523   0.5516
 R0D  C16   C   CR6   0   0.320  -5.2191  -0.1393   0.8871
 R0D  C18   C   CR16  0  -0.264  -7.2399  -1.4428   0.9593
 R0D  C19   C   CR16  0  -0.267  -6.8503  -2.1121  -0.1945
 R0D  C25   C   CH2   0  -0.400   1.7491   1.1222  -1.4185
 R0D  C27   C   CR16  0  -0.300   3.8268  -1.0987  -0.2011
 R0D  N06   N   N     0  -0.401   4.0208   2.3559   0.8509
 R0D  N11   N   NT    0  -0.454  -0.5622   1.2580  -0.6116
 R0D  O15   O   O2    0  -0.475  -4.4481   0.8354   1.4309
 R0D  O22   O   O2    0  -0.477  -3.6404  -0.5630  -0.8813
 R0D  O23   O   O     0  -0.473  -1.9685   0.7715  -2.3140
 R0D  CL01  CL  CL    0  -0.127   5.5398  -3.1740  -0.3881
 R0D  H1    H   HCH2  0   0.281  -0.8982   0.7333   1.4044
 R0D  H2    H   HCH2  0   0.269  -0.0307   2.2255   1.1519
 R0D  H3    H   HCH1  0   0.288  -2.2579  -0.4305   0.6208
 R0D  H5    H   HCR6  0   0.268  -5.3211  -2.3276  -1.6931
 R0D  H6    H   HCH2  0   0.259   0.5627   2.9148  -1.1651
 R0D  H7    H   HCH2  0   0.282   0.0558   1.8941  -2.5004
 R0D  H8    H   HCR6  0   0.282   7.1351  -1.0625   0.6153
 R0D  H9    H   HCR6  0   0.271   6.5963   1.2958   1.1670
 R0D  H10   H   HCR5  0   0.281   2.1636   3.2133   0.6464
 R0D  H11   H   HCH2  0   0.267   1.4718   0.4381   1.9674
 R0D  H12   H   HCH2  0   0.261   0.9881  -0.6135   0.6415
 R0D  H13   H   HCH2  0   0.272  -2.7977   1.9633   1.1500
 R0D  H14   H   HCH2  0   0.256  -3.9342   1.9956  -0.2053
 R0D  H15   H   HCR6  0   0.257  -8.1800  -1.6806   1.4385
 R0D  H16   H   HCR6  0   0.258  -7.4825  -2.8783  -0.6227
 R0D  H17   H   HCH2  0   0.260   1.6109   0.1176  -1.8269
 R0D  H18   H   HCH2  0   0.264   2.4852   1.6276  -2.0467
 R0D  H19   H   HCR6  0   0.275   3.0694  -1.7734  -0.5813
 R0D  H4    H   HCR6  0   0.268  -6.7225   0.0822   2.3871

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
 R0D  N06  C07   double    1.278  0.020  1.278
 R0D  N06  C05   single    1.407  0.020  1.407
 R0D  C07  C08   single    1.513  0.020  1.513
 R0D  C04  C05   aromatic  1.383  0.020  1.383
 R0D  C04  C03   aromatic  1.391  0.020  1.391
 R0D  C05  C26   aromatic  1.394  0.020  1.394
 R0D  C25  C24   single    1.522  0.020  1.522
 R0D  C25  C08   single    1.539  0.020  1.539
 R0D  C24  N11   single    1.455  0.020  1.455
 R0D  C03  C02   aromatic  1.389  0.020  1.389
 R0D  C08  C26   single    1.499  0.020  1.499
 R0D  C08  C09   single    1.538  0.020  1.538
 R0D  C26  C27   aromatic  1.378  0.020  1.378
 R0D  C02  C27   aromatic  1.392  0.020  1.392
 R0D  C02  CL01  single    1.735  0.020  1.735
 R0D  N11  C10   single    1.453  0.020  1.453
 R0D  N11  C12   single    1.347  0.020  1.347
 R0D  C09  C10   single    1.523  0.020  1.523
 R0D  O23  C12   double    1.218  0.020  1.218
 R0D  C12  C13   single    1.530  0.020  1.530
 R0D  C13  C14   single    1.524  0.020  1.524
 R0D  C13  O22   single    1.409  0.020  1.409
 R0D  C14  O15   single    1.413  0.020  1.413
 R0D  O22  C21   single    1.356  0.020  1.356
 R0D  O15  C16   single    1.356  0.020  1.356
 R0D  C21  C16   aromatic  1.397  0.020  1.397
 R0D  C21  C20   aromatic  1.389  0.020  1.389
 R0D  C16  C17   aromatic  1.389  0.020  1.389
 R0D  C20  C19   aromatic  1.386  0.020  1.386
 R0D  C17  C18   aromatic  1.386  0.020  1.386
 R0D  C19  C18   aromatic  1.390  0.020  1.390
 R0D  C10  H1    single    0.970  0.020  1.090
 R0D  C10  H2    single    0.970  0.020  1.090
 R0D  C13  H3    single    0.970  0.020  1.090
 R0D  C17  H4    single    0.930  0.020  1.080
 R0D  C20  H5    single    0.930  0.020  1.080
 R0D  C24  H6    single    0.970  0.020  1.090
 R0D  C24  H7    single    0.970  0.020  1.090
 R0D  C03  H8    single    0.930  0.020  1.080
 R0D  C04  H9    single    0.930  0.020  1.080
 R0D  C07  H10   single    0.930  0.020  1.080
 R0D  C09  H11   single    0.970  0.020  1.090
 R0D  C09  H12   single    0.970  0.020  1.090
 R0D  C14  H13   single    0.970  0.020  1.090
 R0D  C14  H14   single    0.970  0.020  1.090
 R0D  C18  H15   single    0.930  0.020  1.080
 R0D  C19  H16   single    0.930  0.020  1.080
 R0D  C25  H17   single    0.970  0.020  1.090
 R0D  C25  H18   single    0.970  0.020  1.090
 R0D  C27  H19   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
 R0D  H2    C10  H1   106.28  3.000
 R0D  H2    C10  N11  108.67  3.000
 R0D  H1    C10  N11  111.58  3.000
 R0D  H2    C10  C09  110.71  3.000
 R0D  H1    C10  C09  108.74  3.000
 R0D  N11   C10  C09  110.77  3.000
 R0D  H3    C13  O22  108.86  3.000
 R0D  H3    C13  C14  109.79  3.000
 R0D  O22   C13  C14  109.65  3.000
 R0D  H3    C13  C12  111.45  3.000
 R0D  O22   C13  C12  106.61  3.000
 R0D  C14   C13  C12  110.41  3.000
 R0D  H4    C17  C18  120.78  3.000
 R0D  H4    C17  C16  119.00  3.000
 R0D  C18   C17  C16  120.22  3.000
 R0D  H5    C20  C19  120.77  3.000
 R0D  H5    C20  C21  118.98  3.000
 R0D  C19   C20  C21  120.25  3.000
 R0D  O22   C21  C16  122.02  3.000
 R0D  C16   C21  C20  119.68  3.000
 R0D  O22   C21  C20  118.30  3.000
 R0D  H7    C24  H6   107.23  3.000
 R0D  H7    C24  N11  109.59  3.000
 R0D  H6    C24  N11  108.35  3.000
 R0D  H7    C24  C25  110.13  3.000
 R0D  H6    C24  C25  110.56  3.000
 R0D  N11   C24  C25  110.89  3.000
 R0D  C27   C26  C08  131.41  3.000
 R0D  C27   C26  C05  121.18  3.000
 R0D  C08   C26  C05  107.41  3.000
 R0D  CL01  C02  C27  118.82  3.000
 R0D  CL01  C02  C03  118.95  3.000
 R0D  C27   C02  C03  122.22  3.000
 R0D  H8    C03  C04  120.04  3.000
 R0D  H8    C03  C02  120.01  3.000
 R0D  C04   C03  C02  119.95  3.000
 R0D  H9    C04  C05  121.39  3.000
 R0D  H9    C04  C03  120.47  3.000
 R0D  C05   C04  C03  118.14  3.000
 R0D  N06   C05  C04  127.13  3.000
 R0D  C04   C05  C26  121.32  3.000
 R0D  N06   C05  C26  111.55  3.000
 R0D  H10   C07  N06  120.73  3.000
 R0D  H10   C07  C08  123.80  3.000
 R0D  N06   C07  C08  115.47  3.000
 R0D  C25   C08  C09  109.36  3.000
 R0D  C09   C08  C07  111.79  3.000
 R0D  C25   C08  C07  111.44  3.000
 R0D  C09   C08  C26  112.60  3.000
 R0D  C25   C08  C26  112.51  3.000
 R0D  C07   C08  C26   98.85  3.000
 R0D  H12   C09  H11  107.32  3.000
 R0D  H12   C09  C08  108.60  3.000
 R0D  H11   C09  C08  110.48  3.000
 R0D  H12   C09  C10  109.01  3.000
 R0D  H11   C09  C10  109.26  3.000
 R0D  C08   C09  C10  112.04  3.000
 R0D  O23   C12  N11  123.50  3.000
 R0D  O23   C12  C13  119.38  3.000
 R0D  N11   C12  C13  117.05  3.000
 R0D  H14   C14  H13  108.16  3.000
 R0D  H14   C14  O15  110.62  3.000
 R0D  H13   C14  O15  106.92  3.000
 R0D  H14   C14  C13  109.58  3.000
 R0D  H13   C14  C13  111.56  3.000
 R0D  O15   C14  C13  109.96  3.000
 R0D  O15   C16  C21  121.28  3.000
 R0D  C21   C16  C17  119.86  3.000
 R0D  O15   C16  C17  118.86  3.000
 R0D  H15   C18  C19  120.37  3.000
 R0D  H15   C18  C17  119.68  3.000
 R0D  C19   C18  C17  119.95  3.000
 R0D  H16   C19  C18  120.40  3.000
 R0D  H16   C19  C20  119.57  3.000
 R0D  C18   C19  C20  120.04  3.000
 R0D  H18   C25  H17  107.20  3.000
 R0D  H18   C25  C08  110.33  3.000
 R0D  H17   C25  C08  108.71  3.000
 R0D  H18   C25  C24  109.44  3.000
 R0D  H17   C25  C24  109.25  3.000
 R0D  C08   C25  C24  111.78  3.000
 R0D  H19   C27  C02  120.88  3.000
 R0D  H19   C27  C26  121.92  3.000
 R0D  C02   C27  C26  117.19  3.000
 R0D  C07   N06  C05  106.72  3.000
 R0D  C12   N11  C24  120.42  3.000
 R0D  C12   N11  C10  126.43  3.000
 R0D  C24   N11  C10  113.09  3.000
 R0D  C16   O15  C14  114.00  3.000
 R0D  C21   O22  C13  115.09  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
 R0D  CONST_01  C20   C21  C16  C17     0.00   0.0  0
 R0D  CONST_02  C20   C19  C18  C17     0.00   0.0  0
 R0D  CONST_03  C18   C17  C16  C21     0.00   0.0  0
 R0D  CONST_04  C18   C19  C20  C21     0.00   0.0  0
 R0D  CONST_05  C03   C04  C05  C26     0.00   0.0  0
 R0D  CONST_06  C03   C02  C27  C26     0.00   0.0  0
 R0D  CONST_07  C05   C04  C03  C02     0.00   0.0  0
 R0D  CONST_08  C05   C26  C27  C02     0.00   0.0  0
 R0D  CONST_09  C27   C26  C05  C04     0.00   0.0  0
 R0D  CONST_10  C27   C02  C03  C04     0.00   0.0  0
 R0D  CONST_11  C19   C20  C21  C16     0.00   0.0  0
 R0D  CONST_12  C19   C18  C17  C16     0.00   0.0  0
 R0D  CONST_13  C08   C26  C27  C02   180.00   0.0  0
 R0D  CONST_14  C08   C26  C05  C04   180.00   0.0  0
 R0D  CONST_15  N06   C05  C26  C08     0.00   0.0  0
 R0D  CONST_16  CL01  C02  C27  C26   180.00   0.0  0
 R0D  CONST_17  CL01  C02  C03  C04   180.00   0.0  0
 R0D  CONST_18  C13   C12  N11  C10     0.00   0.0  0
 R0D  CONST_19  C24   N11  C12  C13   180.00   0.0  0
 R0D  CONST_20  H16   C19  C18  C17   180.00   0.0  0
 R0D  CONST_21  H15   C18  C19  C20   180.00   0.0  0
 R0D  CONST_22  H4    C17  C16  C21   180.00   0.0  0
 R0D  CONST_23  H9    C04  C05  C26   180.00   0.0  0
 R0D  CONST_24  H19   C27  C02  C03   180.00   0.0  0
 R0D  CONST_25  H8    C03  C04  C05   180.00   0.0  0
 R0D  CONST_26  H5    C20  C21  C16   180.00   0.0  0
 R0D  CONST_27  O23   C12  N11  C10   180.00   0.0  0
 R0D  CONST_28  O23   C12  N11  C24     0.00   0.0  0
 R0D  Var_01    C25   C24  N11  C10    58.66  30.0  1
 R0D  Var_02    C07   C08  C09  C10    72.19  30.0  3
 R0D  Var_03    C16   C21  O22  C13    13.80  30.0  1
 R0D  Var_04    C09   C10  N11  C24   -58.39  30.0  1
 R0D  Var_05    N11   C24  C25  C08   -55.21  30.0  1
 R0D  Var_06    N11   C10  C09  C08    54.93  30.0  1
 R0D  Var_07    H13   C14  O15  C16  -168.65  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
 R0D  chir_01  C13  C12  C14  O22  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
 R0D  plan-1  C26   0.020
 R0D  plan-1  C02   0.020
 R0D  plan-1  C03   0.020
 R0D  plan-1  C04   0.020
 R0D  plan-1  C05   0.020
 R0D  plan-1  C07   0.020
 R0D  plan-1  C08   0.020
 R0D  plan-1  C09   0.020
 R0D  plan-1  C25   0.020
 R0D  plan-1  C27   0.020
 R0D  plan-1  N06   0.020
 R0D  plan-1  CL01  0.020
 R0D  plan-1  H8    0.020
 R0D  plan-1  H9    0.020
 R0D  plan-1  H10   0.020
 R0D  plan-1  H19   0.020
 R0D  plan-2  C17   0.020
 R0D  plan-2  C20   0.020
 R0D  plan-2  C21   0.020
 R0D  plan-2  C16   0.020
 R0D  plan-2  C18   0.020
 R0D  plan-2  C19   0.020
 R0D  plan-2  O15   0.020
 R0D  plan-2  O22   0.020
 R0D  plan-2  H5    0.020
 R0D  plan-2  H15   0.020
 R0D  plan-2  H16   0.020
 R0D  plan-2  H4    0.020
 R0D  plan-3  C10   0.020
 R0D  plan-3  C13   0.020
 R0D  plan-3  C24   0.020
 R0D  plan-3  C12   0.020
 R0D  plan-3  N11   0.020
 R0D  plan-3  O23   0.020

