# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 13:51:33 2022
#   Inital geometry file: a 120 line input string
#   Ligand name: 4-[[(1~{R},2~{R})-2-[(3~{R})-3-azanylpiperidin-1-yl]-2,3-dihydro-1~{H}-inden-1-yl]oxy]-3-chloranyl-benzenecarbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]1CCCN(C1)[C@@H]2Cc3ccccc3[C@H]2Oc4ccc(cc4Cl)C#N
#
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
 HOR  HOR  "4-[[(1R,2R)-2-[(3R)-3-azanylpiperidin-1-yl]-2,3-dihydro-1H-inden-1-yl]oxy]-3-chloranyl-benzenecarbonitrile"
  ligand  48  26  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_HOR
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
 HOR  N    N   NT    0  -0.440  110.3657  154.3294  154.7108
 HOR  C    C   CR15  0  -0.046  111.4165  155.2821  154.3991
 HOR  O    O   O2    0  -0.458  110.7723  156.6443  152.4965
 HOR  C1   C   CR15  0  -0.095  110.9029  156.6529  153.9168
 HOR  C10  C   CR16  0  -0.318  112.2040  158.9187  153.9588
 HOR  C11  C   CR16  0  -0.331  113.8033  157.7183  155.9242
 HOR  C12  C   CR16  0  -0.256  113.2592  159.6167  154.5337
 HOR  C13  C   CR16  0  -0.250  114.0516  159.0216  155.5106
 HOR  C14  C   CR6   0   0.503  109.8827  157.4169  151.8802
 HOR  C15  C   CR6   0  -0.164  109.7342  157.2068  150.5003
 HOR  C16  C   CR16  0  -0.370  109.1067  158.4027  152.4895
 HOR  C17  C   CR16  0  -0.192  108.8628  157.9633  149.7499
 HOR  C18  C   CR16  0  -0.222  108.2262  159.1641  151.7439
 HOR  C19  C   CR6   0  -0.027  108.1018  158.9527  150.3738
 HOR  C2   C   CH2   0  -0.531  112.2912  155.6245  155.6221
 HOR  C20  C   CSP   0   0.052  107.2113  159.7502  149.5995
 HOR  C3   C   CH2   0  -0.277  110.9406  153.0891  155.2149
 HOR  C4   C   CH2   0  -0.284  109.4947  154.0556  153.5733
 HOR  C5   C   CH1   0  -0.075  109.8737  152.1009  155.6690
 HOR  C6   C   CH2   0  -0.445  108.3860  153.0811  153.9427
 HOR  C7   C   CR56  0   0.112  111.9601  157.6187  154.3776
 HOR  C8   C   CH2   0  -0.440  108.9506  151.7861  154.5044
 HOR  C9   C   CR56  0   0.107  112.7513  157.0225  155.3488
 HOR  N1   N   NH2   0  -0.803  110.5268  150.8916  156.1470
 HOR  N2   N   NS    0  -0.249  106.5005  160.4030  148.9691
 HOR  CL   CL  CL    0  -0.088  110.6718  155.9746  149.7436
 HOR  H2   H   HCR5  0   0.229  112.0826  154.8940  153.6066
 HOR  H3   H   HCR5  0   0.275  109.9330  156.8584  154.3856
 HOR  H4   H   HCR6  0   0.254  111.6017  159.3922  153.1939
 HOR  H5   H   HCR6  0   0.249  114.4295  157.2533  156.6761
 HOR  H6   H   HCR6  0   0.256  113.4689  160.6293  154.2155
 HOR  H7   H   HCR6  0   0.256  114.8739  159.5759  155.9447
 HOR  H8   H   HCR6  0   0.308  109.1913  158.6045  153.5483
 HOR  H9   H   HCR6  0   0.301  108.7697  157.7861  148.6871
 HOR  H10  H   HCR6  0   0.291  107.6394  159.9296  152.2326
 HOR  H11  H   HCH2  0   0.261  111.6839  155.5927  156.5324
 HOR  H12  H   HCH2  0   0.267  113.1198  154.9296  155.7587
 HOR  H13  H   HCH2  0   0.189  111.5718  152.5973  154.4525
 HOR  H14  H   HCH2  0   0.249  111.5894  153.3128  156.0641
 HOR  H15  H   HCH2  0   0.189  110.0677  153.6527  152.7199
 HOR  H16  H   HCH2  0   0.242  109.0297  154.9820  153.2361
 HOR  H17  H   HCH1  0   0.192  109.2755  152.5994  156.4484
 HOR  H18  H   HCH2  0   0.218  107.7294  153.5501  154.6813
 HOR  H19  H   HCH2  0   0.235  107.7782  152.8862  153.0568
 HOR  H20  H   HCH2  0   0.231  108.1454  151.1168  154.8208
 HOR  H21  H   HCH2  0   0.211  109.5233  151.2608  153.7320
 HOR  H22  H   HNH2  0   0.341  111.0531  151.0997  156.9874
 HOR  H23  H   HNH2  0   0.344  109.8210  150.2216  156.4276

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
 HOR  N2   C20  triple    1.153  0.020  1.153
 HOR  C20  C19  single    1.424  0.020  1.424
 HOR  C17  C19  aromatic  1.395  0.020  1.395
 HOR  C17  C15  aromatic  1.377  0.020  1.377
 HOR  CL   C15  single    1.723  0.020  1.723
 HOR  C19  C18  aromatic  1.392  0.020  1.392
 HOR  C15  C14  aromatic  1.404  0.020  1.404
 HOR  C18  C16  aromatic  1.382  0.020  1.382
 HOR  C14  C16  aromatic  1.395  0.020  1.395
 HOR  C14  O    single    1.330  0.020  1.330
 HOR  O    C1   single    1.426  0.020  1.426
 HOR  C4   C6   single    1.522  0.020  1.522
 HOR  C4   N    single    1.459  0.020  1.459
 HOR  C1   C7   single    1.504  0.020  1.504
 HOR  C1   C    single    1.541  0.020  1.541
 HOR  C10  C7   aromatic  1.387  0.020  1.387
 HOR  C10  C12  aromatic  1.390  0.020  1.390
 HOR  C6   C8   single    1.520  0.020  1.520
 HOR  C8   C5   single    1.519  0.020  1.519
 HOR  C7   C9   aromatic  1.387  0.020  1.387
 HOR  C    N    single    1.452  0.020  1.452
 HOR  C    C2   single    1.542  0.020  1.542
 HOR  C12  C13  aromatic  1.392  0.020  1.392
 HOR  N    C3   single    1.457  0.020  1.457
 HOR  C3   C5   single    1.523  0.020  1.523
 HOR  N1   C5   single    1.455  0.020  1.455
 HOR  C9   C2   single    1.497  0.020  1.497
 HOR  C9   C11  aromatic  1.386  0.020  1.386
 HOR  C13  C11  aromatic  1.390  0.020  1.390
 HOR  C    H2   single    0.970  0.020  1.090
 HOR  C1   H3   single    0.970  0.020  1.090
 HOR  C10  H4   single    0.930  0.020  1.080
 HOR  C11  H5   single    0.930  0.020  1.080
 HOR  C12  H6   single    0.930  0.020  1.080
 HOR  C13  H7   single    0.930  0.020  1.080
 HOR  C16  H8   single    0.930  0.020  1.080
 HOR  C17  H9   single    0.930  0.020  1.080
 HOR  C18  H10  single    0.930  0.020  1.080
 HOR  C2   H11  single    0.970  0.020  1.090
 HOR  C2   H12  single    0.970  0.020  1.090
 HOR  C3   H13  single    0.970  0.020  1.090
 HOR  C3   H14  single    0.970  0.020  1.090
 HOR  C4   H15  single    0.970  0.020  1.090
 HOR  C4   H16  single    0.970  0.020  1.090
 HOR  C5   H17  single    0.970  0.020  1.090
 HOR  C6   H18  single    0.970  0.020  1.090
 HOR  C6   H19  single    0.970  0.020  1.090
 HOR  C8   H20  single    0.970  0.020  1.090
 HOR  C8   H21  single    0.970  0.020  1.090
 HOR  N1   H22  single    0.890  0.020  1.040
 HOR  N1   H23  single    0.890  0.020  1.040

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
 HOR  C4   N    C3   110.22  3.000
 HOR  C3   N    C    110.31  3.000
 HOR  C4   N    C    112.82  3.000
 HOR  H2   C    C2   107.74  3.000
 HOR  H2   C    C1   106.78  3.000
 HOR  C2   C    C1   103.87  3.000
 HOR  H2   C    N    111.07  3.000
 HOR  C2   C    N    112.70  3.000
 HOR  C1   C    N    114.17  3.000
 HOR  C14  O    C1   121.29  3.000
 HOR  H3   C1   C7   111.73  3.000
 HOR  H3   C1   O    110.23  3.000
 HOR  C7   C1   O    111.92  3.000
 HOR  H3   C1   C    109.13  3.000
 HOR  C7   C1   C    103.94  3.000
 HOR  O    C1   C    109.68  3.000
 HOR  H4   C10  C7   121.69  3.000
 HOR  H4   C10  C12  119.67  3.000
 HOR  C7   C10  C12  118.63  3.000
 HOR  H5   C11  C9   120.75  3.000
 HOR  H5   C11  C13  120.39  3.000
 HOR  C9   C11  C13  118.86  3.000
 HOR  H6   C12  C13  119.76  3.000
 HOR  H6   C12  C10  119.71  3.000
 HOR  C13  C12  C10  120.53  3.000
 HOR  H7   C13  C12  119.68  3.000
 HOR  H7   C13  C11  119.77  3.000
 HOR  C12  C13  C11  120.55  3.000
 HOR  C16  C14  C15  118.45  3.000
 HOR  C16  C14  O    125.48  3.000
 HOR  C15  C14  O    116.07  3.000
 HOR  CL   C15  C17  119.87  3.000
 HOR  CL   C15  C14  118.75  3.000
 HOR  C17  C15  C14  121.38  3.000
 HOR  H8   C16  C18  118.38  3.000
 HOR  H8   C16  C14  121.08  3.000
 HOR  C18  C16  C14  120.54  3.000
 HOR  H9   C17  C19  120.57  3.000
 HOR  H9   C17  C15  120.01  3.000
 HOR  C19  C17  C15  119.41  3.000
 HOR  H10  C18  C19  120.26  3.000
 HOR  H10  C18  C16  119.47  3.000
 HOR  C19  C18  C16  120.28  3.000
 HOR  C20  C19  C18  120.39  3.000
 HOR  C18  C19  C17  119.94  3.000
 HOR  C20  C19  C17  119.66  3.000
 HOR  H12  C2   H11  107.40  3.000
 HOR  H12  C2   C9   112.62  3.000
 HOR  H11  C2   C9   110.45  3.000
 HOR  H12  C2   C    112.89  3.000
 HOR  H11  C2   C    109.77  3.000
 HOR  C9   C2   C    103.70  3.000
 HOR  N2   C20  C19  180.00  3.000
 HOR  H14  C3   H13  106.76  3.000
 HOR  H14  C3   C5   108.50  3.000
 HOR  H13  C3   C5   108.48  3.000
 HOR  H14  C3   N    109.22  3.000
 HOR  H13  C3   N    111.43  3.000
 HOR  C5   C3   N    112.27  3.000
 HOR  H16  C4   H15  107.01  3.000
 HOR  H16  C4   C6   107.97  3.000
 HOR  H15  C4   C6   109.40  3.000
 HOR  H16  C4   N    109.66  3.000
 HOR  H15  C4   N    111.18  3.000
 HOR  C6   C4   N    111.47  3.000
 HOR  H17  C5   N1   112.78  3.000
 HOR  H17  C5   C8   107.83  3.000
 HOR  N1   C5   C8   110.63  3.000
 HOR  H17  C5   C3   107.32  3.000
 HOR  N1   C5   C3   108.82  3.000
 HOR  C8   C5   C3   109.36  3.000
 HOR  H19  C6   H18  106.87  3.000
 HOR  H19  C6   C8   110.76  3.000
 HOR  H18  C6   C8   109.79  3.000
 HOR  H19  C6   C4   108.84  3.000
 HOR  H18  C6   C4   109.07  3.000
 HOR  C8   C6   C4   111.39  3.000
 HOR  C9   C7   C10  120.91  3.000
 HOR  C9   C7   C1   109.84  3.000
 HOR  C10  C7   C1   129.25  3.000
 HOR  H21  C8   H20  107.17  3.000
 HOR  H21  C8   C6   110.00  3.000
 HOR  H20  C8   C6   110.78  3.000
 HOR  H21  C8   C5   108.79  3.000
 HOR  H20  C8   C5   110.64  3.000
 HOR  C6   C8   C5   109.41  3.000
 HOR  C7   C9   C2   110.73  3.000
 HOR  C2   C9   C11  128.77  3.000
 HOR  C7   C9   C11  120.51  3.000
 HOR  H23  N1   H22  105.55  3.000
 HOR  H23  N1   C5   109.15  3.000
 HOR  H22  N1   C5   109.56  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
 HOR  CONST_01  C11  C9   C7   C10     0.00   0.0  0
 HOR  CONST_02  C11  C13  C12  C10     0.00   0.0  0
 HOR  CONST_03  C9   C7   C10  C12     0.00   0.0  0
 HOR  CONST_04  C9   C11  C13  C12     0.00   0.0  0
 HOR  CONST_05  C7   C10  C12  C13     0.00   0.0  0
 HOR  CONST_06  C7   C9   C11  C13     0.00   0.0  0
 HOR  CONST_07  C19  C17  C15  C14     0.00   0.0  0
 HOR  CONST_08  C19  C18  C16  C14     0.00   0.0  0
 HOR  CONST_09  C18  C19  C17  C15     0.00   0.0  0
 HOR  CONST_10  C18  C16  C14  C15     0.00   0.0  0
 HOR  CONST_11  C17  C19  C18  C16     0.00   0.0  0
 HOR  CONST_12  C17  C15  C14  C16     0.00   0.0  0
 HOR  CONST_13  C17  C15  C14  O     180.00   0.0  0
 HOR  CONST_14  C18  C16  C14  O     180.00   0.0  0
 HOR  CONST_15  C20  C19  C17  C15   180.00   0.0  0
 HOR  CONST_16  C20  C19  C18  C16   180.00   0.0  0
 HOR  CONST_17  CL   C15  C14  C16   180.00   0.0  0
 HOR  CONST_18  CL   C15  C17  C19   180.00   0.0  0
 HOR  CONST_19  H4   C10  C7   C1      0.00   0.0  0
 HOR  CONST_20  H7   C13  C12  C10   180.00   0.0  0
 HOR  CONST_21  H6   C12  C13  C11   180.00   0.0  0
 HOR  CONST_22  H5   C11  C13  C12   180.00   0.0  0
 HOR  CONST_23  H4   C10  C12  C13   180.00   0.0  0
 HOR  CONST_24  H9   C17  C15  C14   180.00   0.0  0
 HOR  CONST_25  H10  C18  C16  C14   180.00   0.0  0
 HOR  CONST_26  H8   C16  C14  C15   180.00   0.0  0
 HOR  CONST_27  H10  C18  C19  C17   180.00   0.0  0
 HOR  CONST_28  H9   C17  C19  C18   180.00   0.0  0
 HOR  CONST_29  H8   C16  C18  C19   180.00   0.0  0
 HOR  CONST_30  H5   C11  C9   C2      0.00   0.0  0
 HOR  CONST_31  H6   C12  C10  C7    180.00   0.0  0
 HOR  CONST_32  H5   C11  C9   C7    180.00   0.0  0
 HOR  CONST_33  H4   C10  C7   C9    180.00   0.0  0
 HOR  CONST_34  H7   C13  C11  C9    180.00   0.0  0
 HOR  Var_01    C8   C6   C4   N     -56.09  30.0  1
 HOR  Var_02    C6   C4   N    C    -178.61  30.0  1
 HOR  Var_03    C5   C3   N    C     175.08  30.0  1
 HOR  Var_04    C7   C9   C2   C      17.40  30.0  1
 HOR  Var_05    C11  C9   C2   C    -162.56  30.0  1
 HOR  Var_06    C6   C4   N    C3     57.58  30.0  1
 HOR  Var_07    C5   C8   C6   C4     54.44  30.0  1
 HOR  Var_08    C5   C3   N    C4    -59.67  30.0  1
 HOR  Var_09    C15  C14  O    C1   -172.62  30.0  2
 HOR  Var_10    C16  C14  O    C1      7.63  30.0  2
 HOR  Var_11    H18  C6   C4   N      65.26  30.0  1
 HOR  Var_12    H19  C6   C4   N    -178.49  30.0  1
 HOR  Var_13    H15  C4   N    C      59.03  30.0  1
 HOR  Var_14    H16  C4   N    C     -59.10  30.0  1
 HOR  Var_15    H13  C3   N    C     -63.01  30.0  1
 HOR  Var_16    H14  C3   N    C      54.70  30.0  1
 HOR  Var_17    H11  C2   C9   C11    79.88  30.0  1
 HOR  Var_18    H12  C2   C9   C11   -40.19  30.0  1
 HOR  Var_19    H15  C4   N    C3    -64.77  30.0  1
 HOR  Var_20    H16  C4   N    C3    177.09  30.0  1
 HOR  Var_21    H20  C8   C6   C4    176.69  30.0  1
 HOR  Var_22    H21  C8   C6   C4    -65.01  30.0  1
 HOR  Var_23    H13  C3   N    C4     62.24  30.0  1
 HOR  Var_24    H14  C3   N    C4    179.95  30.0  1
 HOR  Var_25    H18  C6   C8   C5    -66.47  30.0  1
 HOR  Var_26    H19  C6   C8   C5    175.74  30.0  1
 HOR  Var_27    H11  C2   C9   C7   -100.16  30.0  1
 HOR  Var_28    H12  C2   C9   C7    139.77  30.0  1
 HOR  Var_29    H15  C4   C6   C8     67.29  30.0  1
 HOR  Var_30    H16  C4   C6   C8   -176.59  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
 HOR  chir_01  C   C1  N   C2  positiv
 HOR  chir_02  C1  O   C   C7  negativ
 HOR  chir_03  C5  N1  C3  C8  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
 HOR  plan-1  O    0.020
 HOR  plan-1  C14  0.020
 HOR  plan-1  C15  0.020
 HOR  plan-1  C16  0.020
 HOR  plan-1  C17  0.020
 HOR  plan-1  C18  0.020
 HOR  plan-1  C19  0.020
 HOR  plan-1  C20  0.020
 HOR  plan-1  N2   0.020
 HOR  plan-1  CL   0.020
 HOR  plan-1  H8   0.020
 HOR  plan-1  H9   0.020
 HOR  plan-1  H10  0.020
 HOR  plan-2  C1   0.020
 HOR  plan-2  C10  0.020
 HOR  plan-2  C11  0.020
 HOR  plan-2  C12  0.020
 HOR  plan-2  C13  0.020
 HOR  plan-2  C2   0.020
 HOR  plan-2  C7   0.020
 HOR  plan-2  C9   0.020
 HOR  plan-2  H4   0.020
 HOR  plan-2  H5   0.020
 HOR  plan-2  H6   0.020
 HOR  plan-2  H7   0.020

