# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  3 13:10:41 2022
#   Inital geometry file: a 106 line input string
#   Ligand name: 4-(hydroxymethyl)-1-[[2-(3-methoxyphenyl)-1,3-thiazol-5-yl]methyl]piperidin-4-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(c1)c2sc(CN3CCC(O)(CO)CC3)cn2
#
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
 YAG  YAG  "4-(hydroxymethyl)-1-[[2-(3-methoxyphenyl)-1,3-thiazol-5-yl]methyl]piperidin-4-ol"
  ligand  45  23  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_YAG
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
 YAG  C17  C  CH2   0  -0.508   3.1114   7.7580  61.4592
 YAG  C20  C  CH2   0  -0.285   4.9445   5.8342  60.9275
 YAG  C21  C  CH2   0  -0.164   4.2077   9.4618  60.0064
 YAG  C01  C  CR5   0   0.019   4.0338   4.7033  66.8815
 YAG  C02  C  CR6   0   0.124   3.6566   4.3558  68.2528
 YAG  C03  C  CR16  0  -0.311   4.4975   4.7239  69.3079
 YAG  C04  C  CR16  0  -0.221   4.1430   4.3989  70.6029
 YAG  C05  C  CR16  0  -0.387   2.9664   3.7123  70.8834
 YAG  C06  C  CR6   0   0.417   2.1270   3.3467  69.8343
 YAG  C08  C  CH3   0  -0.436   0.5364   2.3554  71.2890
 YAG  C09  C  CR16  0  -0.431   2.4777   3.6720  68.5240
 YAG  C11  C  CR5   0  -0.239   4.2159   4.9992  64.4639
 YAG  C12  C  CR15  0  -0.014   5.1892   5.5749  65.2217
 YAG  C16  C  CH2   0  -0.318   4.0561   7.3749  62.5902
 YAG  C18  C  CT    0   0.232   3.8796   7.9788  60.1411
 YAG  C19  C  CH2   0  -0.481   5.1588   7.1271  60.1615
 YAG  N13  N  N     0  -0.393   5.0791   5.4041  66.5676
 YAG  N15  N  NT    0  -0.417   4.7271   6.0967  62.3496
 YAG  O07  O  O2    0  -0.468   0.9659   2.6856  69.9836
 YAG  O22  O  OH1   0  -0.667   4.9982   9.6758  58.8634
 YAG  O23  O  OH1   0  -0.676   3.1158   7.5392  59.0298
 YAG  S10  S  S2    0   0.227   3.1030   4.2054  65.5051
 YAG  H1   H  HCH2  0   0.242   2.5389   8.6504  61.7309
 YAG  H2   H  HCH2  0   0.246   2.3828   6.9542  61.3152
 YAG  H3   H  HCH2  0   0.201   4.0927   5.2979  60.4800
 YAG  H4   H  HCH2  0   0.237   5.8113   5.1769  60.8174
 YAG  H5   H  HCH2  0   0.196   4.7197   9.7900  60.9218
 YAG  H6   H  HCH2  0   0.200   3.2629  10.0255  59.9576
 YAG  H7   H  HCR6  0   0.253   5.4167   5.2558  69.1078
 YAG  H8   H  HCR6  0   0.262   4.7917   4.6823  71.4216
 YAG  H9   H  HCR6  0   0.283   2.7249   3.4773  71.9110
 YAG  H10  H  HCH3  0   0.259  -0.4177   1.8458  71.1795
 YAG  H11  H  HCH3  0   0.229   1.2368   1.6853  71.7940
 YAG  H12  H  HCH3  0   0.229   0.3902   3.2444  71.9081
 YAG  H13  H  HCR6  0   0.258   1.8009   3.3797  67.7286
 YAG  H14  H  HCR5  0   0.264   6.0104   6.1504  64.8192
 YAG  H15  H  HCH2  0   0.226   3.0012   4.8961  62.7031
 YAG  H16  H  HCH2  0   0.270   4.5322   4.0559  62.6008
 YAG  H17  H  HCH2  0   0.231   4.8047   8.1627  62.7268
 YAG  H18  H  HCH2  0   0.250   3.5112   7.3212  63.5336
 YAG  H19  H  HCH2  0   0.251   5.4730   6.9025  59.1414
 YAG  H20  H  HCH2  0   0.239   5.9781   7.6863  60.6207
 YAG  H22  H  HOH1  0   0.452   5.2666  10.5983  58.8505
 YAG  H23  H  HOH1  0   0.440   2.2534   7.9671  59.0671
 YAG  C14  C  CH2   0  -0.321   4.0675   4.9739  62.9751

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
 YAG  O22  C21  single    1.406  0.020  1.406
 YAG  O23  C18  single    1.418  0.020  1.418
 YAG  C19  C18  single    1.537  0.020  1.537
 YAG  C19  C20  single    1.518  0.020  1.518
 YAG  C21  C18  single    1.525  0.020  1.525
 YAG  C18  C17  single    1.542  0.020  1.542
 YAG  C20  N15  single    1.462  0.020  1.462
 YAG  C17  C16  single    1.523  0.020  1.523
 YAG  N15  C14  single    1.445  0.020  1.445
 YAG  N15  C16  single    1.464  0.020  1.464
 YAG  C14  C11  single    1.496  0.020  1.496
 YAG  C11  C12  aromatic  1.361  0.020  1.361
 YAG  C11  S10  aromatic  1.718  0.020  1.718
 YAG  C12  N13  aromatic  1.361  0.020  1.361
 YAG  S10  C01  aromatic  1.735  0.020  1.735
 YAG  N13  C01  aromatic  1.297  0.020  1.297
 YAG  C01  C02  single    1.464  0.020  1.464
 YAG  C02  C09  aromatic  1.390  0.020  1.390
 YAG  C02  C03  aromatic  1.399  0.020  1.399
 YAG  C09  C06  aromatic  1.395  0.020  1.395
 YAG  C03  C04  aromatic  1.381  0.020  1.381
 YAG  C06  O07  single    1.344  0.020  1.344
 YAG  C06  C05  aromatic  1.392  0.020  1.392
 YAG  O07  C08  single    1.413  0.020  1.413
 YAG  C04  C05  aromatic  1.391  0.020  1.391
 YAG  C17  H1   single    0.970  0.020  1.090
 YAG  C17  H2   single    0.970  0.020  1.090
 YAG  C20  H3   single    0.970  0.020  1.090
 YAG  C20  H4   single    0.970  0.020  1.090
 YAG  C21  H5   single    0.970  0.020  1.090
 YAG  C21  H6   single    0.970  0.020  1.090
 YAG  C03  H7   single    0.930  0.020  1.080
 YAG  C04  H8   single    0.930  0.020  1.080
 YAG  C05  H9   single    0.930  0.020  1.080
 YAG  C08  H10  single    0.970  0.020  1.090
 YAG  C08  H11  single    0.970  0.020  1.090
 YAG  C08  H12  single    0.970  0.020  1.090
 YAG  C09  H13  single    0.930  0.020  1.080
 YAG  C12  H14  single    0.930  0.020  1.080
 YAG  C14  H15  single    0.970  0.020  1.090
 YAG  C14  H16  single    0.970  0.020  1.090
 YAG  C16  H17  single    0.970  0.020  1.090
 YAG  C16  H18  single    0.970  0.020  1.090
 YAG  C19  H19  single    0.970  0.020  1.090
 YAG  C19  H20  single    0.970  0.020  1.090
 YAG  O22  H22  single    0.850  0.020  0.980
 YAG  O23  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
 YAG  H2   C17  H1   106.46  3.000
 YAG  H2   C17  C18  108.93  3.000
 YAG  H1   C17  C18  110.86  3.000
 YAG  H2   C17  C16  109.03  3.000
 YAG  H1   C17  C16  110.20  3.000
 YAG  C18  C17  C16  111.22  3.000
 YAG  H4   C20  H3   106.23  3.000
 YAG  H4   C20  N15  108.89  3.000
 YAG  H3   C20  N15  111.56  3.000
 YAG  H4   C20  C19  110.44  3.000
 YAG  H3   C20  C19  108.59  3.000
 YAG  N15  C20  C19  111.03  3.000
 YAG  H6   C21  H5   106.48  3.000
 YAG  H6   C21  O22  111.61  3.000
 YAG  H5   C21  O22  111.70  3.000
 YAG  H6   C21  C18  108.49  3.000
 YAG  H5   C21  C18  108.49  3.000
 YAG  O22  C21  C18  109.92  3.000
 YAG  S10  C01  N13  113.30  3.000
 YAG  N13  C01  C02  124.23  3.000
 YAG  S10  C01  C02  122.47  3.000
 YAG  C09  C02  C03  119.50  3.000
 YAG  C03  C02  C01  119.29  3.000
 YAG  C09  C02  C01  121.21  3.000
 YAG  H7   C03  C04  120.51  3.000
 YAG  H7   C03  C02  120.09  3.000
 YAG  C04  C03  C02  119.40  3.000
 YAG  H8   C04  C05  118.93  3.000
 YAG  H8   C04  C03  119.59  3.000
 YAG  C05  C04  C03  121.48  3.000
 YAG  H9   C05  C06  121.62  3.000
 YAG  H9   C05  C04  119.20  3.000
 YAG  C06  C05  C04  119.19  3.000
 YAG  O07  C06  C09  115.86  3.000
 YAG  O07  C06  C05  124.48  3.000
 YAG  C09  C06  C05  119.66  3.000
 YAG  H12  C08  H11  108.82  3.000
 YAG  H12  C08  H10  108.71  3.000
 YAG  H11  C08  H10  108.76  3.000
 YAG  H12  C08  O07  111.95  3.000
 YAG  H11  C08  O07  112.04  3.000
 YAG  H10  C08  O07  106.45  3.000
 YAG  H13  C09  C06  117.98  3.000
 YAG  H13  C09  C02  121.26  3.000
 YAG  C06  C09  C02  120.76  3.000
 YAG  S10  C11  C14  122.06  3.000
 YAG  S10  C11  C12  108.73  3.000
 YAG  C14  C11  C12  129.19  3.000
 YAG  H14  C12  N13  119.78  3.000
 YAG  H14  C12  C11  124.15  3.000
 YAG  N13  C12  C11  116.07  3.000
 YAG  H18  C16  H17  105.60  3.000
 YAG  H18  C16  N15  109.16  3.000
 YAG  H17  C16  N15  109.60  3.000
 YAG  H18  C16  C17  110.17  3.000
 YAG  H17  C16  C17  109.62  3.000
 YAG  N15  C16  C17  112.47  3.000
 YAG  O23  C18  C19  106.67  3.000
 YAG  C19  C18  C21  111.17  3.000
 YAG  O23  C18  C21  110.37  3.000
 YAG  C21  C18  C17  108.79  3.000
 YAG  C19  C18  C17  108.91  3.000
 YAG  O23  C18  C17  110.93  3.000
 YAG  H20  C19  H19  106.40  3.000
 YAG  H20  C19  C18  110.23  3.000
 YAG  H19  C19  C18  109.96  3.000
 YAG  H20  C19  C20  109.24  3.000
 YAG  H19  C19  C20  109.71  3.000
 YAG  C18  C19  C20  111.17  3.000
 YAG  C12  N13  C01  111.86  3.000
 YAG  C16  N15  C14  113.47  3.000
 YAG  C16  N15  C20  112.63  3.000
 YAG  C14  N15  C20  110.45  3.000
 YAG  C08  O07  C06  118.68  3.000
 YAG  H22  O22  C21  108.30  3.000
 YAG  H23  O23  C18  108.31  3.000
 YAG  C11  S10  C01   90.04  3.000
 YAG  H16  C14  H15  105.48  3.000
 YAG  H16  C14  N15  108.05  3.000
 YAG  H15  C14  N15  112.92  3.000
 YAG  H16  C14  C11  108.19  3.000
 YAG  H15  C14  C11  110.02  3.000
 YAG  N15  C14  C11  111.86  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
 YAG  CONST_01  C12  C11  S10  C01     0.00   0.0  0
 YAG  CONST_02  C11  C12  N13  C01     0.00   0.0  0
 YAG  CONST_03  C06  C09  C02  C01   180.00   0.0  0
 YAG  CONST_04  C04  C03  C02  C01   180.00   0.0  0
 YAG  CONST_05  C11  S10  C01  C02   180.00   0.0  0
 YAG  CONST_06  C12  N13  C01  C02   180.00   0.0  0
 YAG  CONST_07  C05  C06  C09  C02     0.00   0.0  0
 YAG  CONST_08  C05  C04  C03  C02     0.00   0.0  0
 YAG  CONST_09  S10  C01  C02  C03   180.00   0.0  0
 YAG  CONST_10  N13  C01  C02  C03     0.00   0.0  0
 YAG  CONST_11  C06  C09  C02  C03     0.00   0.0  0
 YAG  CONST_12  C06  C05  C04  C03     0.00   0.0  0
 YAG  CONST_13  C09  C02  C03  C04     0.00   0.0  0
 YAG  CONST_14  C09  C06  C05  C04     0.00   0.0  0
 YAG  CONST_15  S10  C01  C02  C09     0.00   0.0  0
 YAG  CONST_16  N13  C01  C02  C09   180.00   0.0  0
 YAG  CONST_17  N13  C01  S10  C11     0.00   0.0  0
 YAG  CONST_18  S10  C01  N13  C12     0.00   0.0  0
 YAG  CONST_19  S10  C11  C12  N13     0.00   0.0  0
 YAG  CONST_20  C14  C11  S10  C01   180.00   0.0  0
 YAG  CONST_21  O07  C06  C09  C02   180.00   0.0  0
 YAG  CONST_22  O07  C06  C05  C04   180.00   0.0  0
 YAG  CONST_23  N13  C12  C11  C14   180.00   0.0  0
 YAG  CONST_24  H14  C12  N13  C01   180.00   0.0  0
 YAG  CONST_25  H13  C09  C02  C01     0.00   0.0  0
 YAG  CONST_26  H7   C03  C02  C01     0.00   0.0  0
 YAG  CONST_27  H8   C04  C03  C02   180.00   0.0  0
 YAG  CONST_28  H13  C09  C02  C03   180.00   0.0  0
 YAG  CONST_29  H9   C05  C04  C03   180.00   0.0  0
 YAG  CONST_30  H13  C09  C06  C05   180.00   0.0  0
 YAG  CONST_31  H7   C03  C04  C05   180.00   0.0  0
 YAG  CONST_32  H8   C04  C05  C06   180.00   0.0  0
 YAG  CONST_33  H7   C03  C02  C09   180.00   0.0  0
 YAG  CONST_34  H9   C05  C06  C09   180.00   0.0  0
 YAG  CONST_35  H14  C12  C11  S10   180.00   0.0  0
 YAG  Var_01    C20  N15  C16  C17    30.90  30.0  1
 YAG  Var_02    C19  C20  N15  C16    31.54  30.0  1
 YAG  Var_03    N15  C20  C19  C18   -67.01  30.0  1
 YAG  Var_04    N15  C16  C17  C18   -63.66  30.0  1
 YAG  Var_05    C14  N15  C16  C17   -95.53  30.0  1
 YAG  Var_06    C11  C14  N15  C20   161.72  30.0  3
 YAG  Var_07    C16  N15  C14  C11   -70.71  30.0  2
 YAG  Var_08    N15  C14  C11  C12   -25.47  30.0  2
 YAG  Var_09    C19  C20  N15  C14   159.57  30.0  1
 YAG  Var_10    S10  C11  C14  N15   156.16  30.0  2
 YAG  Var_11    H17  C16  N15  C20   -91.30  30.0  1
 YAG  Var_12    H18  C16  N15  C20   153.49  30.0  1
 YAG  Var_13    H3   C20  N15  C16   -89.74  30.0  1
 YAG  Var_14    H4   C20  N15  C16   153.34  30.0  1
 YAG  Var_15    H3   C20  C19  C18    55.99  30.0  1
 YAG  Var_16    H4   C20  C19  C18   172.10  30.0  1
 YAG  Var_17    H17  C16  C17  C18    58.52  30.0  1
 YAG  Var_18    H18  C16  C17  C18   174.31  30.0  1
 YAG  Var_19    H19  C19  C20  N15   171.14  30.0  1
 YAG  Var_20    H20  C19  C20  N15    54.86  30.0  1
 YAG  Var_21    H1   C17  C16  N15   172.98  30.0  1
 YAG  Var_22    H2   C17  C16  N15    56.47  30.0  1
 YAG  Var_23    C08  O07  C06  C05     1.44  30.0  2
 YAG  Var_24    C09  C06  O07  C08  -178.45  30.0  2
 YAG  Var_25    H15  C14  N15  C20   -73.53  30.0  3
 YAG  Var_26    H16  C14  N15  C20    42.74  30.0  3
 YAG  Var_27    H15  C14  C11  C12  -151.81  30.0  2
 YAG  Var_28    H16  C14  C11  C12    93.43  30.0  2
 YAG  Var_29    H3   C20  N15  C14    38.29  30.0  1
 YAG  Var_30    H4   C20  N15  C14   -78.63  30.0  1
 YAG  Var_31    H17  C16  N15  C14   142.28  30.0  1
 YAG  Var_32    H18  C16  N15  C14    27.07  30.0  1
 YAG  Var_33    H15  C14  N15  C16    54.04  30.0  3
 YAG  Var_34    H16  C14  N15  C16   170.30  30.0  3
 YAG  Var_35    H15  C14  C11  S10    29.82  30.0  2
 YAG  Var_36    H16  C14  C11  S10   -84.94  30.0  2
 YAG  Var_37    H10  C08  O07  C06   179.15  30.0  3
 YAG  Var_38    H11  C08  O07  C06   -62.08  30.0  3
 YAG  Var_39    H12  C08  O07  C06    60.49  30.0  3

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
 YAG  chir_01  C18  C19  C21  C17  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
 YAG  plan-1  C01  0.020
 YAG  plan-1  C02  0.020
 YAG  plan-1  C11  0.020
 YAG  plan-1  C12  0.020
 YAG  plan-1  N13  0.020
 YAG  plan-1  S10  0.020
 YAG  plan-1  H14  0.020
 YAG  plan-1  C14  0.020
 YAG  plan-2  C01  0.020
 YAG  plan-2  C02  0.020
 YAG  plan-2  C03  0.020
 YAG  plan-2  C04  0.020
 YAG  plan-2  C05  0.020
 YAG  plan-2  C06  0.020
 YAG  plan-2  C09  0.020
 YAG  plan-2  O07  0.020
 YAG  plan-2  H7   0.020
 YAG  plan-2  H8   0.020
 YAG  plan-2  H9   0.020
 YAG  plan-2  H13  0.020

