# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 05:39:04 2022
#   Inital geometry file: a 111 line input string
#   Ligand name: [3-(4-amino-4-methylpiperidin-1-yl)-6-(2,3-dichlorophenyl)-5-methylpyrazin-2-yl]methanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nc(N2CCC(C)(N)CC2)c(CO)nc1c3cccc(Cl)c3Cl
#
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
 3CW  3CW  "[3-(4-amino-4-methylpiperidin-1-yl)-6-(2,3-dichlorophenyl)-5-methylpyrazin-2-yl]methanol"  ligand  47  25  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3CW
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
 3CW  C14   C   CR6   0  -0.070  -10.1552  -21.7285  34.6417
 3CW  C11   C   CR16  0  -0.238  -10.8279  -24.3054  33.8745
 3CW  C10   C   CR16  0  -0.294  -11.8080  -23.3355  33.9949
 3CW  C12   C   CR16  0  -0.232   -9.5035  -23.9929  34.1355
 3CW  C13   C   CR6   0   0.023   -9.1700  -22.7057  34.5237
 3CW  C01   C   CR6   0   0.104  -12.5722  -21.0342  34.5053
 3CW  C03   C   CR6   0   0.121  -14.5308  -20.5124  35.5777
 3CW  C04   C   CR6   0   0.440  -14.5232  -19.2439  34.9414
 3CW  C06   C   CR6   0   0.221  -12.6732  -19.8813  33.7304
 3CW  C08   C   CH3   0  -0.734  -11.7630  -19.5625  32.5874
 3CW  C09   C   CR6   0   0.123  -11.4878  -22.0320  34.3654
 3CW  C17   C   CH2   0  -0.355  -15.6502  -17.8772  36.6201
 3CW  C18   C   CH2   0  -0.423  -14.6910  -16.7505  36.9958
 3CW  C19   C   CT    0   0.076  -14.7892  -15.5232  36.0734
 3CW  C20   C   CH2   0  -0.423  -14.6885  -16.0022  34.6209
 3CW  C21   C   CH2   0  -0.336  -15.6280  -17.1642  34.3185
 3CW  C22   C   CH3   0  -0.651  -16.0990  -14.7738  36.3114
 3CW  C24   C   CH2   0  -0.215  -15.6748  -21.0006  36.4281
 3CW  N02   N   N     0  -0.361  -13.5360  -21.3433  35.3695
 3CW  N05   N   N     0  -0.424  -13.6376  -19.0045  33.9879
 3CW  N07   N   NT    0  -0.483  -15.4656  -18.2859  35.2309
 3CW  O25   O   OH1   0  -0.658  -15.8598  -22.3721  36.1900
 3CW  CL15  CL  CL    0  -0.089   -9.7249  -20.1474  35.1744
 3CW  CL16  CL  CL    0  -0.096   -7.5244  -22.3334  34.8752
 3CW  H1    H   HCR6  0   0.274  -11.0914  -25.3109  33.5758
 3CW  H2    H   HCR6  0   0.265  -12.8418  -23.5811  33.7907
 3CW  H3    H   HCR6  0   0.288   -8.7306  -24.7438  34.0442
 3CW  H4    H   HCH3  0   0.258  -12.3483  -19.2030  31.7413
 3CW  H5    H   HCH3  0   0.256  -11.0617  -18.7709  32.8554
 3CW  H6    H   HCH3  0   0.245  -11.1848  -20.4253  32.2632
 3CW  H7    H   HCH2  0   0.247  -16.6897  -17.5665  36.7525
 3CW  H8    H   HCH2  0   0.262  -15.4939  -18.7185  37.2914
 3CW  H9    H   HCH2  0   0.226  -13.6671  -17.1394  36.9560
 3CW  H10   H   HCH2  0   0.233  -14.8745  -16.4517  38.0328
 3CW  H11   H   HCH2  0   0.229  -13.6615  -16.3214  34.4191
 3CW  H12   H   HCH2  0   0.230  -14.9043  -15.1732  33.9411
 3CW  H13   H   HCH2  0   0.245  -16.6690  -16.8379  34.4002
 3CW  H14   H   HCH2  0   0.255  -15.4887  -17.5093  33.2957
 3CW  H15   H   HCH3  0   0.226  -16.1545  -14.4149  37.3418
 3CW  H16   H   HCH3  0   0.228  -16.1645  -13.9090  35.6497
 3CW  H17   H   HCH3  0   0.226  -16.9782  -15.3932  36.1372
 3CW  H18   H   HCH2  0   0.222  -15.4586  -20.8071  37.4888
 3CW  H19   H   HCH2  0   0.222  -16.5718  -20.4189  36.1808
 3CW  H23   H   HOH1  0   0.456  -16.5370  -22.6842  36.7974
 3CW  N23   N   NH2   0  -0.789  -13.7024  -14.5722  36.3033
 3CW  H20   H   HNH2  0   0.335  -13.7309  -14.2578  37.2678
 3CW  H21   H   HNH2  0   0.335  -12.8130  -15.0497  36.2016

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
 3CW  C08  C06   single    1.496  0.020  1.496
 3CW  C11  C10   aromatic  1.384  0.020  1.384
 3CW  C11  C12   aromatic  1.386  0.020  1.386
 3CW  C10  C09   aromatic  1.392  0.020  1.392
 3CW  C12  C13   aromatic  1.385  0.020  1.385
 3CW  C06  N05   aromatic  1.329  0.020  1.329
 3CW  C06  C01   aromatic  1.393  0.020  1.393
 3CW  C09  C01   single    1.480  0.020  1.480
 3CW  C09  C14   aromatic  1.394  0.020  1.394
 3CW  C13  C14   aromatic  1.393  0.020  1.393
 3CW  C13  CL16  single    1.723  0.020  1.723
 3CW  N05  C04   aromatic  1.323  0.020  1.323
 3CW  C21  C20   single    1.525  0.020  1.525
 3CW  C21  N07   single    1.455  0.020  1.455
 3CW  C01  N02   aromatic  1.331  0.020  1.331
 3CW  C14  CL15  single    1.723  0.020  1.723
 3CW  C20  C19   single    1.533  0.020  1.533
 3CW  C04  N07   single    1.375  0.020  1.375
 3CW  C04  C03   aromatic  1.419  0.020  1.419
 3CW  N02  C03   aromatic  1.313  0.020  1.313
 3CW  N07  C17   single    1.460  0.020  1.460
 3CW  C03  C24   single    1.507  0.020  1.507
 3CW  C19  C22   single    1.528  0.020  1.528
 3CW  C19  N23   single    1.462  0.020  1.462
 3CW  C19  C18   single    1.538  0.020  1.538
 3CW  O25  C24   single    1.404  0.020  1.404
 3CW  C17  C18   single    1.527  0.020  1.527
 3CW  C11  H1    single    0.930  0.020  1.080
 3CW  C10  H2    single    0.930  0.020  1.080
 3CW  C12  H3    single    0.930  0.020  1.080
 3CW  C08  H4    single    0.970  0.020  1.090
 3CW  C08  H5    single    0.970  0.020  1.090
 3CW  C08  H6    single    0.970  0.020  1.090
 3CW  C17  H7    single    0.970  0.020  1.090
 3CW  C17  H8    single    0.970  0.020  1.090
 3CW  C18  H9    single    0.970  0.020  1.090
 3CW  C18  H10   single    0.970  0.020  1.090
 3CW  C20  H11   single    0.970  0.020  1.090
 3CW  C20  H12   single    0.970  0.020  1.090
 3CW  C21  H13   single    0.970  0.020  1.090
 3CW  C21  H14   single    0.970  0.020  1.090
 3CW  C22  H15   single    0.970  0.020  1.090
 3CW  C22  H16   single    0.970  0.020  1.090
 3CW  C22  H17   single    0.970  0.020  1.090
 3CW  C24  H18   single    0.970  0.020  1.090
 3CW  C24  H19   single    0.970  0.020  1.090
 3CW  N23  H20   single    0.890  0.020  1.040
 3CW  N23  H21   single    0.890  0.020  1.040
 3CW  O25  H23   single    0.850  0.020  0.980

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
 3CW  CL15  C14  C09  119.98  3.000
 3CW  CL15  C14  C13  119.56  3.000
 3CW  C09   C14  C13  120.44  3.000
 3CW  H1    C11  C12  119.64  3.000
 3CW  H1    C11  C10  120.20  3.000
 3CW  C12   C11  C10  120.16  3.000
 3CW  H2    C10  C09  118.84  3.000
 3CW  H2    C10  C11  120.07  3.000
 3CW  C09   C10  C11  121.09  3.000
 3CW  H3    C12  C13  119.79  3.000
 3CW  H3    C12  C11  120.70  3.000
 3CW  C13   C12  C11  119.50  3.000
 3CW  CL16  C13  C12  119.19  3.000
 3CW  CL16  C13  C14  120.44  3.000
 3CW  C12   C13  C14  120.36  3.000
 3CW  N02   C01  C09  115.80  3.000
 3CW  N02   C01  C06  120.07  3.000
 3CW  C09   C01  C06  123.95  3.000
 3CW  N02   C03  C24  117.37  3.000
 3CW  C24   C03  C04  123.15  3.000
 3CW  N02   C03  C04  119.38  3.000
 3CW  N07   C04  N05  118.98  3.000
 3CW  N07   C04  C03  121.65  3.000
 3CW  N05   C04  C03  119.24  3.000
 3CW  N05   C06  C08  116.69  3.000
 3CW  N05   C06  C01  119.41  3.000
 3CW  C08   C06  C01  123.88  3.000
 3CW  H6    C08  H5   107.88  3.000
 3CW  H6    C08  H4   108.40  3.000
 3CW  H5    C08  H4   107.25  3.000
 3CW  H6    C08  C06  112.46  3.000
 3CW  H5    C08  C06  110.99  3.000
 3CW  H4    C08  C06  109.68  3.000
 3CW  C01   C09  C10  119.19  3.000
 3CW  C01   C09  C14  122.32  3.000
 3CW  C10   C09  C14  118.44  3.000
 3CW  H8    C17  H7   106.37  3.000
 3CW  H8    C17  N07  110.65  3.000
 3CW  H7    C17  N07  108.37  3.000
 3CW  H8    C17  C18  109.19  3.000
 3CW  H7    C17  C18  110.97  3.000
 3CW  N07   C17  C18  111.19  3.000
 3CW  H10   C18  H9   106.73  3.000
 3CW  H10   C18  C19  109.85  3.000
 3CW  H9    C18  C19  108.72  3.000
 3CW  H10   C18  C17  109.22  3.000
 3CW  H9    C18  C17  108.43  3.000
 3CW  C19   C18  C17  113.65  3.000
 3CW  N23   C19  C22  107.08  3.000
 3CW  N23   C19  C20  107.66  3.000
 3CW  C22   C19  C20  110.93  3.000
 3CW  N23   C19  C18  112.15  3.000
 3CW  C22   C19  C18  110.65  3.000
 3CW  C20   C19  C18  108.34  3.000
 3CW  H12   C20  H11  106.97  3.000
 3CW  H12   C20  C21  109.44  3.000
 3CW  H11   C20  C21  108.63  3.000
 3CW  H12   C20  C19  109.83  3.000
 3CW  H11   C20  C19  109.12  3.000
 3CW  C21   C20  C19  112.68  3.000
 3CW  H14   C21  H13  106.65  3.000
 3CW  H14   C21  N07  109.30  3.000
 3CW  H13   C21  N07  106.82  3.000
 3CW  H14   C21  C20  110.44  3.000
 3CW  H13   C21  C20  110.13  3.000
 3CW  N07   C21  C20  113.23  3.000
 3CW  H17   C22  H16  107.78  3.000
 3CW  H17   C22  H15  107.25  3.000
 3CW  H16   C22  H15  107.98  3.000
 3CW  H17   C22  C19  112.83  3.000
 3CW  H16   C22  C19  110.24  3.000
 3CW  H15   C22  C19  110.59  3.000
 3CW  H19   C24  H18  106.55  3.000
 3CW  H19   C24  O25  111.82  3.000
 3CW  H18   C24  O25  111.18  3.000
 3CW  H19   C24  C03  108.76  3.000
 3CW  H18   C24  C03  109.77  3.000
 3CW  O25   C24  C03  108.71  3.000
 3CW  C03   N02  C01  120.31  3.000
 3CW  C06   N05  C04  120.40  3.000
 3CW  C21   N07  C17  111.52  3.000
 3CW  C17   N07  C04  118.83  3.000
 3CW  C21   N07  C04  118.80  3.000
 3CW  H23   O25  C24  107.61  3.000
 3CW  H21   N23  H20  105.41  3.000
 3CW  H21   N23  C19  109.25  3.000
 3CW  H20   N23  C19  109.27  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
 3CW  CONST_01  C11   C10  C09  C14     0.00   0.0  0
 3CW  CONST_04  C11   C12  C13  C14     0.00   0.0  0
 3CW  CONST_05  C01   C09  C10  C11   180.00   0.0  0
 3CW  CONST_06  C13   C12  C11  C10     0.00   0.0  0
 3CW  CONST_09  C13   C14  C09  C10     0.00   0.0  0
 3CW  CONST_10  C09   C10  C11  C12     0.00   0.0  0
 3CW  CONST_11  C09   C14  C13  C12     0.00   0.0  0
 3CW  CONST_12  C01   C09  C14  C13   180.00   0.0  0
 3CW  CONST_13  C04   N05  C06  C01     0.00   0.0  0
 3CW  CONST_14  C04   C03  N02  C01     0.00   0.0  0
 3CW  CONST_15  C06   N05  C04  C03     0.00   0.0  0
 3CW  CONST_16  C06   C01  N02  C03     0.00   0.0  0
 3CW  CONST_17  C09   C01  N02  C03   180.00   0.0  0
 3CW  CONST_18  N05   C06  C01  C09   180.00   0.0  0
 3CW  CONST_19  N05   C06  C01  N02     0.00   0.0  0
 3CW  CONST_20  N05   C04  C03  N02     0.00   0.0  0
 3CW  CONST_21  N07   C04  N05  C06   180.00   0.0  0
 3CW  CONST_22  N07   C04  C03  N02   180.00   0.0  0
 3CW  CONST_23  CL16  C13  C12  C11   180.00   0.0  0
 3CW  CONST_24  CL15  C14  C09  C10   180.00   0.0  0
 3CW  CONST_25  CL15  C14  C13  C12   180.00   0.0  0
 3CW  CONST_26  CL15  C14  C09  C01     0.00   0.0  0
 3CW  CONST_27  C24   C03  N02  C01   180.00   0.0  0
 3CW  CONST_28  C08   C06  N05  C04   180.00   0.0  0
 3CW  CONST_29  C09   C01  C06  C08     0.00   0.0  0
 3CW  CONST_30  N02   C01  C06  C08   180.00   0.0  0
 3CW  CONST_31  CL16  C13  C14  C09   180.00   0.0  0
 3CW  CONST_32  N05   C04  C03  C24   180.00   0.0  0
 3CW  CONST_33  N07   C04  C03  C24     0.00   0.0  0
 3CW  CONST_34  H2    C10  C09  C14   180.00   0.0  0
 3CW  CONST_35  H3    C12  C13  C14   180.00   0.0  0
 3CW  CONST_36  H3    C12  C11  C10   180.00   0.0  0
 3CW  CONST_37  H2    C10  C11  C12   180.00   0.0  0
 3CW  CONST_38  H1    C11  C12  C13   180.00   0.0  0
 3CW  CONST_39  H2    C10  C09  C01     0.00   0.0  0
 3CW  CONST_40  H1    C11  C10  C09   180.00   0.0  0
 3CW  Var_01    C21   N07  C04  C03  -163.94  30.0  2
 3CW  Var_02    C17   N07  C04  C03    54.77  30.0  2
 3CW  Var_03    C20   C21  N07  C04   -87.18  30.0  1
 3CW  Var_04    C18   C17  N07  C04    87.27  30.0  1
 3CW  Var_05    C20   C21  N07  C17    56.74  30.0  1
 3CW  Var_06    N05   C04  N07  C17  -129.37  30.0  3
 3CW  Var_07    C21   N07  C17  C18   -56.64  30.0  1
 3CW  Var_08    N07   C21  C20  C19   -54.02  30.0  1
 3CW  Var_09    N07   C17  C18  C19    55.47  30.0  1
 3CW  Var_10    N05   C04  N07  C21    11.92  30.0  3
 3CW  Var_11    H13   C21  N07  C04   151.41  30.0  1
 3CW  Var_12    H14   C21  N07  C04    36.39  30.0  1
 3CW  Var_13    H7    C17  N07  C04  -150.50  30.0  1
 3CW  Var_14    H8    C17  N07  C04   -34.24  30.0  1
 3CW  Var_15    H13   C21  N07  C17   -64.67  30.0  1
 3CW  Var_16    H14   C21  N07  C17  -179.69  30.0  1
 3CW  Var_17    H13   C21  C20  C19    65.50  30.0  1
 3CW  Var_18    H14   C21  C20  C19  -176.97  30.0  1
 3CW  Var_19    H7    C17  C18  C19   -65.23  30.0  1
 3CW  Var_20    H8    C17  C18  C19   177.84  30.0  1
 3CW  Var_21    H7    C17  N07  C21    65.59  30.0  1
 3CW  Var_22    H8    C17  N07  C21  -178.15  30.0  1
 3CW  Var_23    H11   C20  C21  N07    67.01  30.0  1
 3CW  Var_24    H12   C20  C21  N07  -176.53  30.0  1
 3CW  Var_25    H9    C18  C17  N07   -65.54  30.0  1
 3CW  Var_26    H10   C18  C17  N07   178.52  30.0  1
 3CW  Var_27    O25   C24  C03  C04   141.69  30.0  2
 3CW  Var_28    O25   C24  C03  N02   -34.55  30.0  2
 3CW  Var_29    H4    C08  C06  C01   135.36  30.0  2
 3CW  Var_30    H5    C08  C06  C01  -106.31  30.0  2
 3CW  Var_31    H6    C08  C06  C01    14.66  30.0  2
 3CW  Var_32    H18   C24  C03  C04   -96.50  30.0  2
 3CW  Var_33    H19   C24  C03  C04    19.71  30.0  2
 3CW  Var_34    H18   C24  C03  N02    87.26  30.0  2
 3CW  Var_35    H19   C24  C03  N02  -156.53  30.0  2
 3CW  Var_36    H4    C08  C06  N05   -43.69  30.0  2
 3CW  Var_37    H5    C08  C06  N05    74.64  30.0  2
 3CW  Var_38    H6    C08  C06  N05  -164.39  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
 3CW  chir_01  C19  C20  N23  C18  positiv

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
 3CW  plan-1  C14   0.020
 3CW  plan-1  C11   0.020
 3CW  plan-1  C10   0.020
 3CW  plan-1  C12   0.020
 3CW  plan-1  C13   0.020
 3CW  plan-1  C01   0.020
 3CW  plan-1  C09   0.020
 3CW  plan-1  CL15  0.020
 3CW  plan-1  CL16  0.020
 3CW  plan-1  H1    0.020
 3CW  plan-1  H2    0.020
 3CW  plan-1  H3    0.020
 3CW  plan-2  C01   0.020
 3CW  plan-2  C03   0.020
 3CW  plan-2  C04   0.020
 3CW  plan-2  C06   0.020
 3CW  plan-2  C08   0.020
 3CW  plan-2  C09   0.020
 3CW  plan-2  C24   0.020
 3CW  plan-2  N02   0.020
 3CW  plan-2  N05   0.020
 3CW  plan-2  N07   0.020

