# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 13:56:15 2021
#   Inital geometry file: a 126 line input string
#   Ligand name: 1-(5-bromopyridin-3-yl)-4-[cis-4-(3-methylphenyl)cyclohexyl]piperazine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc(c1)[C@H]2CC[C@H](CC2)N3CCN(CC3)c4cncc(Br)c4
#
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
 81F  81F  1-(5-bromopyridin-3-yl)-4-[cis-4-(3-methylphenyl)cyclohexyl]piperazine  ligand  54  26  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_81F
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
 81F  C01   C   CH3   0  -0.699  129.0532  141.8425  114.1014
 81F  N01   N   NT    0  -0.435  130.2189  143.0494  105.4488
 81F  C02   C   CR6   0   0.128  128.3436  142.6694  113.0678
 81F  N02   N   NT    0  -0.521  131.1635  142.1921  102.8966
 81F  C03   C   CR16  0  -0.358  128.7709  142.6815  111.7446
 81F  N03   N   N     0  -0.368  131.5095  142.1666   99.2495
 81F  C04   C   CR6   0   0.223  128.1442  143.4624  110.7716
 81F  C05   C   CH1   0  -0.342  128.6197  143.4516  109.3418
 81F  C06   C   CH2   0  -0.420  130.1184  143.7206  109.1940
 81F  C07   C   CH2   0  -0.420  130.4804  143.9621  107.7229
 81F  C08   C   CH2   0  -0.402  128.2689  142.1234  108.6386
 81F  C09   C   CH2   0  -0.461  129.1601  141.8498  107.4182
 81F  C10   C   CH1   0  -0.052  129.5885  143.1638  106.7601
 81F  C11   C   CH2   0  -0.280  129.2876  142.8038  104.3727
 81F  C12   C   CH2   0  -0.286  129.9579  142.9974  103.0267
 81F  C13   C   CH2   0  -0.292  131.2802  142.0715  105.3538
 81F  C14   C   CH2   0  -0.282  132.0446  142.2340  104.0542
 81F  C15   C   CR6   0   0.341  131.7304  142.0602  101.6497
 81F  C16   C   CR16  0  -0.216  133.0590  141.6410  101.4707
 81F  C17   C   CR6   0  -0.162  133.5488  141.4789  100.1888
 81F  C18   C   CR16  0  -0.086  132.7538  141.7440   99.0860
 81F  C19   C   CR16  0  -0.137  131.0145  142.3274  100.4630
 81F  C20   C   CR16  0  -0.346  127.0563  144.2401  111.1516
 81F  C21   C   CR16  0  -0.207  126.6081  144.2347  112.4680
 81F  C22   C   CR16  0  -0.298  127.2465  143.4571  113.4203
 81F  BR01  BR  BR    0  -0.020  135.3271  140.9068   99.9336
 81F  H1    H   HCH3  0   0.242  129.6133  142.4751  114.7928
 81F  H2    H   HCH3  0   0.235  128.3508  141.2608  114.6991
 81F  H3    H   HCH3  0   0.230  129.7586  141.1499  113.6438
 81F  H5    H   HCR6  0   0.212  129.6201  142.0654  111.4668
 81F  H6    H   HCH1  0   0.231  128.0937  144.2619  108.8247
 81F  H7    H   HCH2  0   0.211  130.6810  142.8664  109.5830
 81F  H8    H   HCH2  0   0.237  130.4164  144.5811  109.7969
 81F  H9    H   HCH2  0   0.220  131.5296  143.6981  107.5689
 81F  H10   H   HCH2  0   0.227  130.3923  145.0247  107.4845
 81F  H11   H   HCH2  0   0.228  127.2180  142.1468  108.3406
 81F  H12   H   HCH2  0   0.227  128.3700  141.2988  109.3483
 81F  H13   H   HCH2  0   0.235  128.6235  141.2129  106.7104
 81F  H14   H   HCH2  0   0.217  130.0483  141.2899  107.7258
 81F  H15   H   HCH1  0   0.219  128.6779  143.7490  106.5888
 81F  H16   H   HCH2  0   0.236  128.4591  143.5126  104.4309
 81F  H17   H   HCH2  0   0.195  128.8541  141.7905  104.4138
 81F  H18   H   HCH2  0   0.222  130.1837  144.0616  102.8751
 81F  H19   H   HCH2  0   0.238  129.2328  142.7048  102.2695
 81F  H20   H   HCH2  0   0.204  130.8995  141.0389  105.4115
 81F  H21   H   HCH2  0   0.238  131.9921  142.1952  106.1711
 81F  H22   H   HCH2  0   0.238  132.7553  141.4105  104.0044
 81F  H23   H   HCH2  0   0.223  132.6213  143.1688  104.0730
 81F  H24   H   HCR6  0   0.271  133.7056  141.4415  102.3121
 81F  H25   H   HCR6  0   0.253  133.1184  141.6267   98.0727
 81F  H26   H   HCR6  0   0.244  129.9948  142.6864  100.4972
 81F  H27   H   HCR6  0   0.220  126.5544  144.8569  110.4150
 81F  H28   H   HCR6  0   0.228  125.7560  144.8410  112.7492
 81F  H29   H   HCR6  0   0.221  126.8939  143.4612  114.4453

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
 81F  C18   N03  aromatic  1.324  0.020  1.324
 81F  C18   C17  aromatic  1.385  0.020  1.385
 81F  N03   C19  aromatic  1.320  0.020  1.320
 81F  BR01  C17  single    1.885  0.020  1.885
 81F  C17   C16  aromatic  1.382  0.020  1.382
 81F  C19   C15  aromatic  1.411  0.020  1.411
 81F  C16   C15  aromatic  1.405  0.020  1.405
 81F  C15   N02  single    1.376  0.020  1.376
 81F  C12   N02  single    1.456  0.020  1.456
 81F  C12   C11  single    1.516  0.020  1.516
 81F  N02   C14  single    1.455  0.020  1.455
 81F  C14   C13  single    1.516  0.020  1.516
 81F  C11   N01  single    1.444  0.020  1.444
 81F  C13   N01  single    1.446  0.020  1.446
 81F  N01   C10  single    1.459  0.020  1.459
 81F  C10   C09  single    1.531  0.020  1.531
 81F  C10   C07  single    1.536  0.020  1.536
 81F  C09   C08  single    1.536  0.020  1.536
 81F  C07   C06  single    1.534  0.020  1.534
 81F  C08   C05  single    1.543  0.020  1.543
 81F  C06   C05  single    1.530  0.020  1.530
 81F  C05   C04  single    1.507  0.020  1.507
 81F  C04   C20  aromatic  1.390  0.020  1.390
 81F  C04   C03  aromatic  1.396  0.020  1.396
 81F  C20   C21  aromatic  1.391  0.020  1.391
 81F  C03   C02  aromatic  1.391  0.020  1.391
 81F  C21   C22  aromatic  1.385  0.020  1.385
 81F  C02   C22  aromatic  1.396  0.020  1.396
 81F  C02   C01  single    1.502  0.020  1.502
 81F  C01   H1   single    0.970  0.020  1.090
 81F  C01   H2   single    0.970  0.020  1.090
 81F  C01   H3   single    0.970  0.020  1.090
 81F  C03   H5   single    0.930  0.020  1.080
 81F  C05   H6   single    0.970  0.020  1.090
 81F  C06   H7   single    0.970  0.020  1.090
 81F  C06   H8   single    0.970  0.020  1.090
 81F  C07   H9   single    0.970  0.020  1.090
 81F  C07   H10  single    0.970  0.020  1.090
 81F  C08   H11  single    0.970  0.020  1.090
 81F  C08   H12  single    0.970  0.020  1.090
 81F  C09   H13  single    0.970  0.020  1.090
 81F  C09   H14  single    0.970  0.020  1.090
 81F  C10   H15  single    0.970  0.020  1.090
 81F  C11   H16  single    0.970  0.020  1.090
 81F  C11   H17  single    0.970  0.020  1.090
 81F  C12   H18  single    0.970  0.020  1.090
 81F  C12   H19  single    0.970  0.020  1.090
 81F  C13   H20  single    0.970  0.020  1.090
 81F  C13   H21  single    0.970  0.020  1.090
 81F  C14   H22  single    0.970  0.020  1.090
 81F  C14   H23  single    0.970  0.020  1.090
 81F  C16   H24  single    0.930  0.020  1.080
 81F  C18   H25  single    0.930  0.020  1.080
 81F  C19   H26  single    0.930  0.020  1.080
 81F  C20   H27  single    0.930  0.020  1.080
 81F  C21   H28  single    0.930  0.020  1.080
 81F  C22   H29  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
 81F  H3    C01  H2   107.95  3.000
 81F  H3    C01  H1   107.59  3.000
 81F  H2    C01  H1   107.00  3.000
 81F  H3    C01  C02  111.52  3.000
 81F  H2    C01  C02  111.51  3.000
 81F  H1    C01  C02  111.05  3.000
 81F  C13   N01  C11  108.01  3.000
 81F  C13   N01  C10  115.41  3.000
 81F  C11   N01  C10  113.85  3.000
 81F  C22   C02  C03  118.48  3.000
 81F  C22   C02  C01  120.55  3.000
 81F  C03   C02  C01  120.97  3.000
 81F  C15   N02  C14  118.30  3.000
 81F  C14   N02  C12  114.48  3.000
 81F  C15   N02  C12  118.37  3.000
 81F  H5    C03  C04  119.36  3.000
 81F  H5    C03  C02  118.62  3.000
 81F  C04   C03  C02  122.01  3.000
 81F  C19   N03  C18  120.30  3.000
 81F  C20   C04  C05  120.68  3.000
 81F  C20   C04  C03  118.27  3.000
 81F  C05   C04  C03  121.04  3.000
 81F  H6    C05  C08  108.20  3.000
 81F  H6    C05  C06  107.14  3.000
 81F  C08   C05  C06  109.26  3.000
 81F  H6    C05  C04  106.92  3.000
 81F  C06   C05  C04  113.55  3.000
 81F  C08   C05  C04  111.52  3.000
 81F  H8    C06  H7   106.18  3.000
 81F  H8    C06  C07  109.93  3.000
 81F  H7    C06  C07  110.03  3.000
 81F  H8    C06  C05  110.64  3.000
 81F  H7    C06  C05  109.39  3.000
 81F  C07   C06  C05  110.58  3.000
 81F  H10   C07  H9   106.36  3.000
 81F  H10   C07  C10  108.77  3.000
 81F  H9    C07  C10  110.09  3.000
 81F  H10   C07  C06  110.08  3.000
 81F  H9    C07  C06  108.88  3.000
 81F  C10   C07  C06  112.47  3.000
 81F  H12   C08  H11  106.39  3.000
 81F  H12   C08  C09  109.15  3.000
 81F  H11   C08  C09  110.20  3.000
 81F  H12   C08  C05  109.42  3.000
 81F  H11   C08  C05  108.93  3.000
 81F  C09   C08  C05  112.56  3.000
 81F  H14   C09  H13  106.41  3.000
 81F  H14   C09  C10  109.44  3.000
 81F  H13   C09  C10  111.05  3.000
 81F  H14   C09  C08  109.81  3.000
 81F  H13   C09  C08  109.49  3.000
 81F  C10   C09  C08  110.55  3.000
 81F  H15   C10  C09  107.04  3.000
 81F  H15   C10  C07  107.63  3.000
 81F  C09   C10  C07  109.82  3.000
 81F  H15   C10  N01  105.09  3.000
 81F  C07   C10  N01  110.68  3.000
 81F  C09   C10  N01  116.10  3.000
 81F  H17   C11  H16  107.22  3.000
 81F  H17   C11  C12  108.92  3.000
 81F  H16   C11  C12  107.45  3.000
 81F  H17   C11  N01  112.45  3.000
 81F  H16   C11  N01  109.83  3.000
 81F  C12   C11  N01  110.78  3.000
 81F  H19   C12  H18  107.54  3.000
 81F  H19   C12  C11  106.78  3.000
 81F  H18   C12  C11  109.70  3.000
 81F  H19   C12  N02  109.93  3.000
 81F  H18   C12  N02  110.70  3.000
 81F  C11   C12  N02  112.02  3.000
 81F  H21   C13  H20  107.00  3.000
 81F  H21   C13  C14  107.52  3.000
 81F  H20   C13  C14  108.63  3.000
 81F  H21   C13  N01  110.67  3.000
 81F  H20   C13  N01  112.12  3.000
 81F  C14   C13  N01  110.72  3.000
 81F  H23   C14  H22  107.56  3.000
 81F  H23   C14  C13  109.95  3.000
 81F  H22   C14  C13  106.68  3.000
 81F  H23   C14  N02  110.86  3.000
 81F  H22   C14  N02  109.69  3.000
 81F  C13   C14  N02  111.92  3.000
 81F  C19   C15  C16  115.41  3.000
 81F  C16   C15  N02  122.26  3.000
 81F  C19   C15  N02  122.33  3.000
 81F  H24   C16  C17  119.27  3.000
 81F  H24   C16  C15  121.49  3.000
 81F  C17   C16  C15  119.24  3.000
 81F  BR01  C17  C18  119.45  3.000
 81F  BR01  C17  C16  119.70  3.000
 81F  C18   C17  C16  120.84  3.000
 81F  H25   C18  C17  122.06  3.000
 81F  H25   C18  N03  117.80  3.000
 81F  C17   C18  N03  120.14  3.000
 81F  H26   C19  C15  120.96  3.000
 81F  H26   C19  N03  115.02  3.000
 81F  C15   C19  N03  124.02  3.000
 81F  H27   C20  C21  119.75  3.000
 81F  H27   C20  C04  119.67  3.000
 81F  C21   C20  C04  120.58  3.000
 81F  H28   C21  C22  119.89  3.000
 81F  H28   C21  C20  119.81  3.000
 81F  C22   C21  C20  120.29  3.000
 81F  H29   C22  C21  119.87  3.000
 81F  H29   C22  C02  119.78  3.000
 81F  C21   C22  C02  120.36  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
 81F  CONST_01  C20   C04  C03  C02     0.00   0.0  0
 81F  CONST_02  C20   C21  C22  C02     0.00   0.0  0
 81F  CONST_03  C21   C20  C04  C03     0.00   0.0  0
 81F  CONST_04  C21   C22  C02  C03     0.00   0.0  0
 81F  CONST_05  C16   C17  C18  N03     0.00   0.0  0
 81F  CONST_06  C16   C15  C19  N03     0.00   0.0  0
 81F  CONST_07  C22   C21  C20  C04     0.00   0.0  0
 81F  CONST_08  C22   C02  C03  C04     0.00   0.0  0
 81F  CONST_09  C18   N03  C19  C15     0.00   0.0  0
 81F  CONST_10  C18   C17  C16  C15     0.00   0.0  0
 81F  CONST_11  C19   N03  C18  C17     0.00   0.0  0
 81F  CONST_12  C19   C15  C16  C17     0.00   0.0  0
 81F  CONST_13  C05   C04  C03  C02   180.00   0.0  0
 81F  CONST_14  N03   C19  C15  N02   180.00   0.0  0
 81F  CONST_15  C17   C16  C15  N02   180.00   0.0  0
 81F  CONST_16  C21   C20  C04  C05   180.00   0.0  0
 81F  CONST_17  C04   C03  C02  C01   180.00   0.0  0
 81F  CONST_18  C21   C22  C02  C01   180.00   0.0  0
 81F  CONST_19  BR01  C17  C18  N03   180.00   0.0  0
 81F  CONST_20  BR01  C17  C16  C15   180.00   0.0  0
 81F  CONST_21  H28   C21  C22  C02   180.00   0.0  0
 81F  CONST_22  H26   C19  C15  N02     0.00   0.0  0
 81F  CONST_23  H24   C16  C15  N02     0.00   0.0  0
 81F  CONST_24  H27   C20  C04  C03   180.00   0.0  0
 81F  CONST_25  H29   C22  C02  C03   180.00   0.0  0
 81F  CONST_26  H5    C03  C04  C05     0.00   0.0  0
 81F  CONST_27  H25   C18  C17  C16   180.00   0.0  0
 81F  Var_01    N02   C12  C11  N01    54.25  30.0  1
 81F  Var_02    N02   C14  C13  N01   -54.44  30.0  1
 81F  Var_03    C10   C09  C08  C05   -31.00  30.0  1
 81F  Var_04    C10   C07  C06  C05   -31.96  30.0  1
 81F  Var_05    C12   C11  N01  C10   167.62  30.0  1
 81F  Var_06    C14   C13  N01  C10  -168.38  30.0  1
 81F  Var_07    C15   N02  C12  C11   167.46  30.0  1
 81F  Var_08    C19   C15  N02  C12   -18.81  30.0  3
 81F  Var_09    C13   C14  N02  C12    45.72  30.0  1
 81F  Var_10    H1    C01  C02  C03   108.59  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
 81F  chir_01  C05  C08  C06  C04  positiv
 81F  chir_02  C10  N01  C09  C07  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
 81F  plan-1  C01   0.020
 81F  plan-1  C02   0.020
 81F  plan-1  C03   0.020
 81F  plan-1  C04   0.020
 81F  plan-1  C05   0.020
 81F  plan-1  C20   0.020
 81F  plan-1  C21   0.020
 81F  plan-1  C22   0.020
 81F  plan-1  H5    0.020
 81F  plan-1  H27   0.020
 81F  plan-1  H28   0.020
 81F  plan-1  H29   0.020
 81F  plan-2  N02   0.020
 81F  plan-2  N03   0.020
 81F  plan-2  C15   0.020
 81F  plan-2  C16   0.020
 81F  plan-2  C17   0.020
 81F  plan-2  C18   0.020
 81F  plan-2  C19   0.020
 81F  plan-2  BR01  0.020
 81F  plan-2  H24   0.020
 81F  plan-2  H25   0.020
 81F  plan-2  H26   0.020

