# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 06:01:04 2021
#   Inital geometry file: a 106 line input string
#   Ligand name: N~4~,N~6~-dicyclopentyl-2-(methylsulfanyl)-5-nitropyrimidine-4,6-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSc1nc(NC2CCCC2)c(c(NC3CCCC3)n1)[N+]([O-])=O
#
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
 QDA  QDA  N~4~,N~6~-dicyclopentyl-2-(methylsulfanyl)-5-nitropyrimidine-4,6-diamine  ligand  46  23  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QDA
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
 QDA  C04  C  CR6    0   0.025  142.6766  139.1222  100.4038
 QDA  C05  C  CR6    0   0.543  142.4066  137.7096  100.3837
 QDA  C07  C  CH1    0  -0.107  141.0922  135.7095  100.9433
 QDA  C08  C  CH2    0  -0.438  140.4865  135.2853   99.6049
 QDA  C09  C  CH2    0  -0.450  139.0451  135.8002   99.6710
 QDA  C10  C  CH2    0  -0.459  138.6677  135.7816  101.1706
 QDA  C11  C  CH2    0  -0.478  139.9593  135.4059  101.9214
 QDA  C13  C  CR6    0   0.235  144.2762  137.4096   99.1380
 QDA  C15  C  CH3    0  -0.763  144.6174  134.7296   98.5205
 QDA  C17  C  CR6    0   0.531  143.8586  139.5651   99.7083
 QDA  C19  C  CH1    0  -0.108  145.4571  141.2797   98.9698
 QDA  C20  C  CH2    0  -0.477  145.4389  142.8044   98.8872
 QDA  C21  C  CH2    0  -0.460  145.8971  143.2880  100.2763
 QDA  C22  C  CH2    0  -0.452  146.6298  142.0871  100.9177
 QDA  C23  C  CH2    0  -0.438  146.6986  141.0169   99.8235
 QDA  N02  N  N      1   0.365  141.8348  140.0181  101.0660
 QDA  N06  N  NH1    0  -0.646  141.3698  137.1402  100.9805
 QDA  N12  N  N      0  -0.473  143.2368  136.8821   99.7386
 QDA  N16  N  N      0  -0.497  144.6346  138.6771   99.0818
 QDA  N18  N  NH1    0  -0.649  144.2414  140.8327   99.6361
 QDA  O01  O  O      0  -0.451  140.8406  139.6041  101.6532
 QDA  O03  O  O     -1  -0.451  142.0885  141.2182  101.0597
 QDA  S14  S  S2     0   0.059  145.3721  136.3496   98.2828
 QDA  H1   H  HCH1   0   0.264  142.0068  135.1651  101.1793
 QDA  H2   H  HCH2   0   0.248  141.0448  135.6580   98.7466
 QDA  H3   H  HCH2   0   0.232  140.5055  134.1934   99.5551
 QDA  H4   H  HCH2   0   0.236  138.3694  135.1971   99.0647
 QDA  H5   H  HCH2   0   0.229  138.9929  136.8178   99.2794
 QDA  H6   H  HCH2   0   0.239  137.8734  135.0657  101.3821
 QDA  H7   H  HCH2   0   0.233  138.2954  136.7564  101.4899
 QDA  H8   H  HCH2   0   0.253  139.9780  134.3359  102.1339
 QDA  H9   H  HCH2   0   0.249  140.0722  135.9198  102.8781
 QDA  H10  H  HCH3   0   0.279  145.2625  134.0204   98.0055
 QDA  H11  H  HCH3   0   0.276  144.5669  134.4713   99.5748
 QDA  H12  H  HCH3   0   0.278  143.6220  134.6929   98.0859
 QDA  H13  H  HCH1   0   0.262  145.5187  140.8093   97.9885
 QDA  H14  H  HCH2   0   0.252  146.1566  143.1074   98.1231
 QDA  H15  H  HCH2   0   0.249  144.4680  143.2025   98.5866
 QDA  H16  H  HCH2   0   0.233  145.0468  143.5985  100.8863
 QDA  H17  H  HCH2   0   0.240  146.5452  144.1599  100.1884
 QDA  H18  H  HCH2   0   0.230  146.0679  141.7134  101.7755
 QDA  H19  H  HCH2   0   0.237  147.6203  142.3538  101.2864
 QDA  H20  H  HCH2   0   0.233  147.5793  141.1659   99.1933
 QDA  H21  H  HCH2   0   0.247  146.7438  139.9987  100.2083
 QDA  H22  H  HNH1   0   0.419  140.7509  137.7496  101.4920
 QDA  H23  H  HNH1   0   0.419  143.6541  141.5111  100.0959

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
 QDA  C15  S14  single    1.803  0.020  1.803
 QDA  S14  C13  single    1.748  0.020  1.748
 QDA  C13  N12  aromatic  1.311  0.020  1.311
 QDA  C13  N16  aromatic  1.318  0.020  1.318
 QDA  N12  C05  aromatic  1.338  0.020  1.338
 QDA  C23  C22  single    1.532  0.020  1.532
 QDA  C23  C19  single    1.529  0.020  1.529
 QDA  N16  C17  aromatic  1.335  0.020  1.335
 QDA  C22  C21  single    1.546  0.020  1.546
 QDA  C05  N06  single    1.325  0.020  1.325
 QDA  C05  C04  aromatic  1.438  0.020  1.438
 QDA  N06  C07  single    1.458  0.020  1.458
 QDA  C17  C04  aromatic  1.441  0.020  1.441
 QDA  C17  N18  single    1.326  0.020  1.326
 QDA  C19  N18  single    1.457  0.020  1.457
 QDA  C19  C20  single    1.527  0.020  1.527
 QDA  C04  N02  single    1.396  0.020  1.396
 QDA  O01  N02  double    1.227  0.020  1.227
 QDA  C21  C20  single    1.541  0.020  1.541
 QDA  C11  C07  single    1.527  0.020  1.527
 QDA  C11  C10  single    1.541  0.020  1.541
 QDA  N02  O03  single    1.227  0.020  1.227
 QDA  C07  C08  single    1.529  0.020  1.529
 QDA  C10  C09  single    1.546  0.020  1.546
 QDA  C08  C09  single    1.532  0.020  1.532
 QDA  C07  H1   single    0.970  0.020  1.090
 QDA  C08  H2   single    0.970  0.020  1.090
 QDA  C08  H3   single    0.970  0.020  1.090
 QDA  C09  H4   single    0.970  0.020  1.090
 QDA  C09  H5   single    0.970  0.020  1.090
 QDA  C10  H6   single    0.970  0.020  1.090
 QDA  C10  H7   single    0.970  0.020  1.090
 QDA  C11  H8   single    0.970  0.020  1.090
 QDA  C11  H9   single    0.970  0.020  1.090
 QDA  C15  H10  single    0.970  0.020  1.090
 QDA  C15  H11  single    0.970  0.020  1.090
 QDA  C15  H12  single    0.970  0.020  1.090
 QDA  C19  H13  single    0.970  0.020  1.090
 QDA  C20  H14  single    0.970  0.020  1.090
 QDA  C20  H15  single    0.970  0.020  1.090
 QDA  C21  H16  single    0.970  0.020  1.090
 QDA  C21  H17  single    0.970  0.020  1.090
 QDA  C22  H18  single    0.970  0.020  1.090
 QDA  C22  H19  single    0.970  0.020  1.090
 QDA  C23  H20  single    0.970  0.020  1.090
 QDA  C23  H21  single    0.970  0.020  1.090
 QDA  N06  H22  single    0.860  0.020  1.020
 QDA  N18  H23  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
 QDA  N02  C04  C17  121.74  3.000
 QDA  N02  C04  C05  121.58  3.000
 QDA  C17  C04  C05  116.68  3.000
 QDA  N12  C05  N06  115.91  3.000
 QDA  N06  C05  C04  124.24  3.000
 QDA  N12  C05  C04  119.85  3.000
 QDA  H1   C07  N06  108.95  3.000
 QDA  H1   C07  C11  112.60  3.000
 QDA  N06  C07  C11  108.66  3.000
 QDA  H1   C07  C08  112.53  3.000
 QDA  C11  C07  C08  102.22  3.000
 QDA  N06  C07  C08  111.72  3.000
 QDA  H3   C08  H2   107.27  3.000
 QDA  H3   C08  C09  110.74  3.000
 QDA  H2   C08  C09  113.65  3.000
 QDA  H3   C08  C07  108.06  3.000
 QDA  H2   C08  C07  113.05  3.000
 QDA  C09  C08  C07  103.98  3.000
 QDA  H5   C09  H4   106.65  3.000
 QDA  H5   C09  C10  110.33  3.000
 QDA  H4   C09  C10  112.42  3.000
 QDA  H5   C09  C08  110.05  3.000
 QDA  H4   C09  C08  111.92  3.000
 QDA  C10  C09  C08  105.51  3.000
 QDA  H7   C10  H6   106.34  3.000
 QDA  H7   C10  C11  111.18  3.000
 QDA  H6   C10  C11  110.87  3.000
 QDA  H7   C10  C09  110.87  3.000
 QDA  H6   C10  C09  111.96  3.000
 QDA  C11  C10  C09  105.72  3.000
 QDA  H9   C11  H8   106.81  3.000
 QDA  H9   C11  C10  113.52  3.000
 QDA  H8   C11  C10  110.39  3.000
 QDA  H9   C11  C07  113.01  3.000
 QDA  H8   C11  C07  107.88  3.000
 QDA  C10  C11  C07  105.15  3.000
 QDA  S14  C13  N16  113.06  3.000
 QDA  N16  C13  N12  128.45  3.000
 QDA  S14  C13  N12  118.50  3.000
 QDA  H12  C15  H11  109.72  3.000
 QDA  H12  C15  H10  109.37  3.000
 QDA  H11  C15  H10  109.38  3.000
 QDA  H12  C15  S14  111.16  3.000
 QDA  H11  C15  S14  111.16  3.000
 QDA  H10  C15  S14  105.96  3.000
 QDA  N18  C17  N16  116.26  3.000
 QDA  N18  C17  C04  123.83  3.000
 QDA  N16  C17  C04  119.91  3.000
 QDA  H13  C19  N18  109.06  3.000
 QDA  H13  C19  C23  112.49  3.000
 QDA  N18  C19  C23  111.68  3.000
 QDA  H13  C19  C20  112.51  3.000
 QDA  N18  C19  C20  108.73  3.000
 QDA  C23  C19  C20  102.20  3.000
 QDA  H15  C20  H14  106.92  3.000
 QDA  H15  C20  C21  113.48  3.000
 QDA  H14  C20  C21  110.40  3.000
 QDA  H15  C20  C19  112.93  3.000
 QDA  H14  C20  C19  107.90  3.000
 QDA  C21  C20  C19  105.13  3.000
 QDA  H17  C21  H16  106.30  3.000
 QDA  H17  C21  C22  111.91  3.000
 QDA  H16  C21  C22  110.99  3.000
 QDA  H17  C21  C20  110.81  3.000
 QDA  H16  C21  C20  111.19  3.000
 QDA  C22  C21  C20  105.74  3.000
 QDA  H19  C22  H18  106.61  3.000
 QDA  H19  C22  C23  111.82  3.000
 QDA  H18  C22  C23  110.20  3.000
 QDA  H19  C22  C21  112.39  3.000
 QDA  H18  C22  C21  110.36  3.000
 QDA  C23  C22  C21  105.51  3.000
 QDA  H21  C23  H20  107.31  3.000
 QDA  H21  C23  C22  113.72  3.000
 QDA  H20  C23  C22  110.65  3.000
 QDA  H21  C23  C19  113.04  3.000
 QDA  H20  C23  C19  107.99  3.000
 QDA  C22  C23  C19  104.02  3.000
 QDA  O03  N02  O01  120.02  3.000
 QDA  O03  N02  C04  120.04  3.000
 QDA  O01  N02  C04  119.94  3.000
 QDA  H22  N06  C07  119.30  3.000
 QDA  H22  N06  C05  116.70  3.000
 QDA  C07  N06  C05  124.00  3.000
 QDA  C13  N12  C05  117.64  3.000
 QDA  C17  N16  C13  117.47  3.000
 QDA  H23  N18  C19  119.23  3.000
 QDA  H23  N18  C17  116.75  3.000
 QDA  C19  N18  C17  124.00  3.000
 QDA  C15  S14  C13  102.59  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
 QDA  CONST_01  C13  N12  C05  C04     0.00   0.0  0
 QDA  CONST_02  C13  N16  C17  C04     0.00   0.0  0
 QDA  CONST_03  N16  C13  N12  C05     0.00   0.0  0
 QDA  CONST_04  N16  C17  C04  C05     0.00   0.0  0
 QDA  CONST_05  N12  C13  N16  C17     0.00   0.0  0
 QDA  CONST_06  N12  C05  C04  C17     0.00   0.0  0
 QDA  CONST_07  S14  C13  N12  C05   180.00   0.0  0
 QDA  CONST_08  N18  C17  C04  C05   180.00   0.0  0
 QDA  CONST_09  N06  C05  N12  C13   180.00   0.0  0
 QDA  CONST_10  N18  C17  N16  C13   180.00   0.0  0
 QDA  CONST_11  S14  C13  N16  C17   180.00   0.0  0
 QDA  CONST_12  N06  C05  C04  C17   180.00   0.0  0
 QDA  CONST_13  N12  C05  C04  N02   180.00   0.0  0
 QDA  CONST_14  N16  C17  C04  N02   180.00   0.0  0
 QDA  CONST_15  C07  N06  C05  C04   180.00   0.0  0
 QDA  CONST_16  C19  N18  C17  C04   180.00   0.0  0
 QDA  CONST_17  N12  C05  N06  C07     0.00   0.0  0
 QDA  CONST_18  N16  C17  N18  C19     0.00   0.0  0
 QDA  CONST_19  O01  N02  C04  C05     0.00   0.0  0
 QDA  CONST_20  O03  N02  C04  C05   180.00   0.0  0
 QDA  CONST_21  O01  N02  C04  C17   180.00   0.0  0
 QDA  CONST_22  O03  N02  C04  C17     0.00   0.0  0
 QDA  CONST_23  H22  N06  C05  C04     0.00   0.0  0
 QDA  CONST_24  H23  N18  C17  C04     0.00   0.0  0
 QDA  Var_01    C09  C10  C11  C07    19.60  30.0  1
 QDA  Var_02    C10  C09  C08  C07   -29.56  30.0  1
 QDA  Var_03    C11  C10  C09  C08     6.15  30.0  1
 QDA  Var_04    C21  C22  C23  C19   -29.40  30.0  1
 QDA  Var_05    C22  C21  C20  C19    19.76  30.0  1
 QDA  Var_06    C23  C22  C21  C20     5.96  30.0  1
 QDA  Var_07    N12  C13  S14  C15     0.78  30.0  2
 QDA  Var_08    H10  C15  S14  C13  -179.95  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
 QDA  chir_01  C07  N06  C11  C08  negativ
 QDA  chir_02  C19  N18  C23  C20  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
 QDA  plan-1  C04  0.020
 QDA  plan-1  C05  0.020
 QDA  plan-1  C13  0.020
 QDA  plan-1  C17  0.020
 QDA  plan-1  N02  0.020
 QDA  plan-1  N06  0.020
 QDA  plan-1  N12  0.020
 QDA  plan-1  N16  0.020
 QDA  plan-1  N18  0.020
 QDA  plan-1  S14  0.020
 QDA  plan-2  C05  0.020
 QDA  plan-2  C07  0.020
 QDA  plan-2  N06  0.020
 QDA  plan-2  H22  0.020
 QDA  plan-3  C17  0.020
 QDA  plan-3  C19  0.020
 QDA  plan-3  N18  0.020
 QDA  plan-3  H23  0.020
 QDA  plan-4  C04  0.020
 QDA  plan-4  N02  0.020
 QDA  plan-4  O01  0.020
 QDA  plan-4  O03  0.020

