# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 08:45:56 2022
#   Inital geometry file: a 116 line input string
#   Ligand name: 2-azanyl-9-cyclohexyl-8-(2-methoxyphenyl)-3~{H}-purine-6-thione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccccc1c2nc3C(=S)N=C(N)Nc3n2C4CCCCC4
#
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
 RTW  RTW  2-azanyl-9-cyclohexyl-8-(2-methoxyphenyl)-3~{H}-purine-6-thione  ligand  46  25  .  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_RTW
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
 RTW  C01  C  CH3   0  -0.441   8.3149  -10.3534  -3.4945
 RTW  C03  C  CR6   0   0.390   8.5934   -8.0206  -3.1399
 RTW  C04  C  CR16  0  -0.375   7.7666   -7.6805  -4.2065
 RTW  C05  C  CR16  0  -0.236   7.5216   -6.3421  -4.4877
 RTW  C06  C  CR16  0  -0.272   8.0896   -5.3355  -3.7229
 RTW  C07  C  CR16  0  -0.258   8.9078   -5.6784  -2.6554
 RTW  C08  C  CR6   0  -0.154   9.1584   -7.0093  -2.3486
 RTW  C09  C  CR5   0   0.459  10.0432   -7.3486  -1.2248
 RTW  C11  C  CR56  0   0.039  11.7427   -7.5470   0.0358
 RTW  C12  C  CR56  0   0.639  10.6687   -8.0565   0.7280
 RTW  C14  C  CR6   0   0.676  12.0582   -8.5613   2.5124
 RTW  C17  C  CR6   0   0.056  13.0336   -7.5538   0.6420
 RTW  C20  C  CH1   0  -0.114   8.1866   -8.2542   0.2530
 RTW  C21  C  CH2   0  -0.441   7.9720   -9.7378   0.5392
 RTW  C22  C  CH2   0  -0.439   6.4884  -10.0116   0.7687
 RTW  C23  C  CH2   0  -0.434   5.9305   -9.1378   1.8873
 RTW  C24  C  CH2   0  -0.439   6.1663   -7.6591   1.5986
 RTW  C25  C  CH2   0  -0.428   7.6459   -7.3642   1.3702
 RTW  N10  N  N     0  -0.430  11.3195   -7.1065  -1.1873
 RTW  N13  N  NR16  0  -0.733  10.8020   -8.5600   1.9807
 RTW  N15  N  NH2   0  -0.827  12.1974   -9.0554   3.7447
 RTW  N16  N  N     0  -0.487  13.1115   -8.0901   1.8841
 RTW  N19  N  NR5   0  -0.527   9.5802   -7.9398  -0.0604
 RTW  O02  O  O2    0  -0.465   8.9099   -9.2778  -2.7922
 RTW  S18  S  S1    0  -0.451  14.3958   -6.9431  -0.1198
 RTW  H1   H  HCH3  0   0.262   8.6869  -11.2637  -3.0317
 RTW  H2   H  HCH3  0   0.233   7.2254  -10.3355  -3.4147
 RTW  H3   H  HCH3  0   0.236   8.5953  -10.3535  -4.5505
 RTW  H4   H  HCR6  0   0.284   7.3144   -8.4408  -4.8285
 RTW  H5   H  HCR6  0   0.264   6.8778   -6.0923  -5.3210
 RTW  H6   H  HCR6  0   0.257   7.8961   -4.2960  -3.9492
 RTW  H7   H  HCR6  0   0.260   9.3534   -4.9059  -2.0415
 RTW  H8   H  HCH1  0   0.277   7.6294   -8.0079  -0.6527
 RTW  H9   H  HCH2  0   0.260   8.3519  -10.3307  -0.2939
 RTW  H10  H  HCH2  0   0.221   8.5263  -10.0503   1.4298
 RTW  H11  H  HCH2  0   0.222   5.9369   -9.8155  -0.1568
 RTW  H12  H  HCH2  0   0.240   6.3445  -11.0687   0.9995
 RTW  H13  H  HCH2  0   0.236   4.8638   -9.3301   2.0198
 RTW  H14  H  HCH2  0   0.216   6.4171   -9.4043   2.8316
 RTW  H15  H  HCH2  0   0.240   5.7944   -7.0437   2.4200
 RTW  H16  H  HCH2  0   0.222   5.6003   -7.3664   0.7081
 RTW  H17  H  HCH2  0   0.224   8.1939   -7.5365   2.3016
 RTW  H18  H  HCH2  0   0.253   7.7934   -6.3154   1.1036
 RTW  H19  H  HNR6  0   0.447  10.0176   -8.9085   2.5138
 RTW  H20  H  HNH2  0   0.417  13.1266   -9.1337   4.1212
 RTW  H21  H  HNH2  0   0.420  11.4607   -9.5525   4.2169

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
 RTW  C05  C04  aromatic  1.389  0.020  1.389
 RTW  C05  C06  aromatic  1.386  0.020  1.386
 RTW  C04  C03  aromatic  1.392  0.020  1.392
 RTW  C06  C07  aromatic  1.388  0.020  1.388
 RTW  C01  O02  single    1.416  0.020  1.416
 RTW  C03  O02  single    1.342  0.020  1.342
 RTW  C03  C08  aromatic  1.403  0.020  1.403
 RTW  C07  C08  aromatic  1.389  0.020  1.389
 RTW  C08  C09  single    1.470  0.020  1.470
 RTW  C09  N10  aromatic  1.300  0.020  1.300
 RTW  C09  N19  aromatic  1.385  0.020  1.385
 RTW  N10  C11  aromatic  1.367  0.020  1.367
 RTW  N19  C20  single    1.463  0.020  1.463
 RTW  N19  C12  aromatic  1.349  0.020  1.349
 RTW  S18  C17  double    1.676  0.020  1.676
 RTW  C11  C17  single    1.426  0.020  1.426
 RTW  C11  C12  aromatic  1.376  0.020  1.376
 RTW  C20  C21  single    1.526  0.020  1.526
 RTW  C20  C25  single    1.527  0.020  1.527
 RTW  C21  C22  single    1.526  0.020  1.526
 RTW  C17  N16  single    1.355  0.020  1.355
 RTW  C12  N13  single    1.357  0.020  1.357
 RTW  C22  C23  single    1.525  0.020  1.525
 RTW  C25  C24  single    1.526  0.020  1.526
 RTW  C24  C23  single    1.525  0.020  1.525
 RTW  N16  C14  double    1.314  0.020  1.314
 RTW  N13  C14  single    1.364  0.020  1.364
 RTW  C14  N15  single    1.335  0.020  1.335
 RTW  C01  H1   single    0.970  0.020  1.090
 RTW  C01  H2   single    0.970  0.020  1.090
 RTW  C01  H3   single    0.970  0.020  1.090
 RTW  C04  H4   single    0.930  0.020  1.080
 RTW  C05  H5   single    0.930  0.020  1.080
 RTW  C06  H6   single    0.930  0.020  1.080
 RTW  C07  H7   single    0.930  0.020  1.080
 RTW  C20  H8   single    0.970  0.020  1.090
 RTW  C21  H9   single    0.970  0.020  1.090
 RTW  C21  H10  single    0.970  0.020  1.090
 RTW  C22  H11  single    0.970  0.020  1.090
 RTW  C22  H12  single    0.970  0.020  1.090
 RTW  C23  H13  single    0.970  0.020  1.090
 RTW  C23  H14  single    0.970  0.020  1.090
 RTW  C24  H15  single    0.970  0.020  1.090
 RTW  C24  H16  single    0.970  0.020  1.090
 RTW  C25  H17  single    0.970  0.020  1.090
 RTW  C25  H18  single    0.970  0.020  1.090
 RTW  N13  H19  single    0.860  0.020  1.020
 RTW  N15  H20  single    0.860  0.020  1.020
 RTW  N15  H21  single    0.860  0.020  1.020

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
 RTW  H3   C01  H2   109.05  3.000
 RTW  H3   C01  H1   108.89  3.000
 RTW  H2   C01  H1   108.90  3.000
 RTW  H3   C01  O02  111.82  3.000
 RTW  H2   C01  O02  111.74  3.000
 RTW  H1   C01  O02  106.34  3.000
 RTW  O02  C03  C08  115.73  3.000
 RTW  C08  C03  C04  119.69  3.000
 RTW  O02  C03  C04  124.57  3.000
 RTW  H4   C04  C05  119.16  3.000
 RTW  H4   C04  C03  121.16  3.000
 RTW  C05  C04  C03  119.69  3.000
 RTW  H5   C05  C06  120.07  3.000
 RTW  H5   C05  C04  118.89  3.000
 RTW  C06  C05  C04  121.04  3.000
 RTW  H6   C06  C07  120.26  3.000
 RTW  H6   C06  C05  120.62  3.000
 RTW  C07  C06  C05  119.12  3.000
 RTW  H7   C07  C08  118.97  3.000
 RTW  H7   C07  C06  120.16  3.000
 RTW  C08  C07  C06  120.86  3.000
 RTW  C09  C08  C07  119.92  3.000
 RTW  C09  C08  C03  120.48  3.000
 RTW  C07  C08  C03  119.58  3.000
 RTW  N19  C09  N10  112.55  3.000
 RTW  N19  C09  C08  122.67  3.000
 RTW  N10  C09  C08  124.76  3.000
 RTW  N10  C11  C17  131.45  3.000
 RTW  C17  C11  C12  119.41  3.000
 RTW  N10  C11  C12  109.14  3.000
 RTW  N19  C12  N13  130.62  3.000
 RTW  N13  C12  C11  121.69  3.000
 RTW  N19  C12  C11  107.69  3.000
 RTW  N16  C14  N15  119.38  3.000
 RTW  N15  C14  N13  117.14  3.000
 RTW  N16  C14  N13  123.47  3.000
 RTW  S18  C17  N16  120.94  3.000
 RTW  N16  C17  C11  116.33  3.000
 RTW  S18  C17  C11  122.73  3.000
 RTW  H8   C20  N19  105.08  3.000
 RTW  H8   C20  C25  107.14  3.000
 RTW  N19  C20  C25  111.64  3.000
 RTW  H8   C20  C21  107.65  3.000
 RTW  C25  C20  C21  112.30  3.000
 RTW  N19  C20  C21  112.53  3.000
 RTW  H10  C21  H9   106.85  3.000
 RTW  H10  C21  C22  108.59  3.000
 RTW  H9   C21  C22  110.85  3.000
 RTW  H10  C21  C20  111.03  3.000
 RTW  H9   C21  C20  109.64  3.000
 RTW  C22  C21  C20  109.84  3.000
 RTW  H12  C22  H11  106.60  3.000
 RTW  H12  C22  C23  110.58  3.000
 RTW  H11  C22  C23  109.45  3.000
 RTW  H12  C22  C21  109.50  3.000
 RTW  H11  C22  C21  109.30  3.000
 RTW  C23  C22  C21  111.29  3.000
 RTW  H14  C23  H13  106.65  3.000
 RTW  H14  C23  C24  109.29  3.000
 RTW  H13  C23  C24  110.16  3.000
 RTW  H14  C23  C22  109.30  3.000
 RTW  H13  C23  C22  110.21  3.000
 RTW  C24  C23  C22  111.11  3.000
 RTW  H16  C24  H15  106.57  3.000
 RTW  H16  C24  C25  109.13  3.000
 RTW  H15  C24  C25  109.51  3.000
 RTW  H16  C24  C23  109.46  3.000
 RTW  H15  C24  C23  110.58  3.000
 RTW  C25  C24  C23  111.45  3.000
 RTW  H18  C25  H17  106.94  3.000
 RTW  H18  C25  C24  110.68  3.000
 RTW  H17  C25  C24  109.13  3.000
 RTW  H18  C25  C20  109.46  3.000
 RTW  H17  C25  C20  110.70  3.000
 RTW  C24  C25  C20  109.89  3.000
 RTW  C11  N10  C09  105.65  3.000
 RTW  H19  N13  C14  120.59  3.000
 RTW  H19  N13  C12  122.61  3.000
 RTW  C14  N13  C12  116.79  3.000
 RTW  H21  N15  H20  117.53  3.000
 RTW  H21  N15  C14  122.66  3.000
 RTW  H20  N15  C14  118.09  3.000
 RTW  C17  N16  C14  122.29  3.000
 RTW  C20  N19  C12  128.68  3.000
 RTW  C12  N19  C09  104.98  3.000
 RTW  C20  N19  C09  126.17  3.000
 RTW  C03  O02  C01  118.95  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
 RTW  CONST_01  C06  C05  C04  C03     0.00   0.0  0
 RTW  CONST_02  C06  C07  C08  C03     0.00   0.0  0
 RTW  CONST_05  C07  C06  C05  C04     0.00   0.0  0
 RTW  CONST_06  C07  C08  C03  C04     0.00   0.0  0
 RTW  CONST_07  C09  C08  C03  C04   180.00   0.0  0
 RTW  CONST_08  C08  C03  C04  C05     0.00   0.0  0
 RTW  CONST_09  C08  C07  C06  C05     0.00   0.0  0
 RTW  CONST_10  C09  C08  C07  C06   180.00   0.0  0
 RTW  CONST_13  C11  N10  C09  C08   180.00   0.0  0
 RTW  CONST_14  C12  N19  C09  C08   180.00   0.0  0
 RTW  CONST_15  C12  C11  N10  C09     0.00   0.0  0
 RTW  CONST_16  C11  C12  N19  C09     0.00   0.0  0
 RTW  CONST_17  N19  C09  N10  C11     0.00   0.0  0
 RTW  CONST_18  N10  C09  N19  C12     0.00   0.0  0
 RTW  CONST_19  N19  C12  C11  N10     0.00   0.0  0
 RTW  CONST_20  C20  N19  C09  C08     0.00   0.0  0
 RTW  CONST_21  C20  N19  C12  C11   180.00   0.0  0
 RTW  CONST_22  N10  C09  N19  C20   180.00   0.0  0
 RTW  CONST_23  N13  C12  N19  C20     0.00   0.0  0
 RTW  CONST_24  N16  C14  N13  C12     0.00   0.0  0
 RTW  CONST_25  N13  C14  N16  C17     0.00   0.0  0
 RTW  CONST_26  O02  C03  C04  C05   180.00   0.0  0
 RTW  CONST_27  O02  C03  C08  C07   180.00   0.0  0
 RTW  CONST_28  O02  C03  C08  C09     0.00   0.0  0
 RTW  CONST_29  N15  C14  N13  C12   180.00   0.0  0
 RTW  CONST_30  N15  C14  N16  C17   180.00   0.0  0
 RTW  CONST_31  H5   C05  C04  C03   180.00   0.0  0
 RTW  CONST_32  H7   C07  C08  C03   180.00   0.0  0
 RTW  CONST_33  H6   C06  C05  C04   180.00   0.0  0
 RTW  CONST_34  H4   C04  C05  C06   180.00   0.0  0
 RTW  CONST_35  H19  N13  C14  N16   180.00   0.0  0
 RTW  CONST_36  H20  N15  C14  N13   180.00   0.0  0
 RTW  CONST_37  H21  N15  C14  N13     0.00   0.0  0
 RTW  Var_01    C23  C22  C21  C20   -55.91  30.0  1
 RTW  Var_02    C23  C24  C25  C20    55.46  30.0  1
 RTW  Var_03    C24  C23  C22  C21    56.20  30.0  1
 RTW  Var_04    C25  C24  C23  C22   -56.00  30.0  1
 RTW  Var_05    C04  C03  O02  C01    -3.82  30.0  1
 RTW  Var_06    H1   C01  O02  C03  -178.34  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
 RTW  chir_01  C20  N19  C21  C25  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
 RTW  plan-1  C03  0.020
 RTW  plan-1  C04  0.020
 RTW  plan-1  C05  0.020
 RTW  plan-1  C06  0.020
 RTW  plan-1  C07  0.020
 RTW  plan-1  C08  0.020
 RTW  plan-1  C09  0.020
 RTW  plan-1  O02  0.020
 RTW  plan-1  H4   0.020
 RTW  plan-1  H5   0.020
 RTW  plan-1  H6   0.020
 RTW  plan-1  H7   0.020
 RTW  plan-2  C08  0.020
 RTW  plan-2  C09  0.020
 RTW  plan-2  C11  0.020
 RTW  plan-2  C12  0.020
 RTW  plan-2  C14  0.020
 RTW  plan-2  C17  0.020
 RTW  plan-2  C20  0.020
 RTW  plan-2  N10  0.020
 RTW  plan-2  N13  0.020
 RTW  plan-2  N15  0.020
 RTW  plan-2  N16  0.020
 RTW  plan-2  N19  0.020
 RTW  plan-2  S18  0.020
 RTW  plan-2  H19  0.020
 RTW  plan-2  H20  0.020
 RTW  plan-2  H21  0.020

