# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 04:39:37 2022
#   Inital geometry file: a 102 line input string
#   Ligand name: (3R)-4-[6-{1-[diamino(hydroxy)-lambda~4~-sulfanyl]cyclopropyl}-2-(methylsulfanyl)pyrimidin-4-yl]-3-methylmorpholine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSc1nc(cc(n1)C2(CC2)[S+](=N)(=N)=O)N3CCOC[C@H]3C
#
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
 EIO  EIO  "(3R)-4-[6-{1-[diamino(hydroxy)-lambda~4~-sulfanyl]cyclopropyl}-2-(methylsulfanyl)pyrimidin-4-yl]-3-methylmorpholine"
  ligand  42  22  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EIO
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
 EIO  C13  C  CH3   0  -0.659  -131.9614  -171.2188  114.0578
 EIO  C15  C  CR6   0   0.255  -127.6918  -171.0990  115.8490
 EIO  C17  C  CH3   0  -0.767  -127.3268  -171.8875  113.2197
 EIO  C20  C  CH2   0  -0.426  -127.1610  -170.8589  120.3107
 EIO  C03  C  CT    0  -0.314  -127.7290  -169.9279  119.2547
 EIO  C04  C  CR6   0   0.355  -128.2094  -170.4659  117.9459
 EIO  C05  C  CR16  0  -0.443  -129.5132  -170.8365  117.7726
 EIO  C06  C  CR6   0   0.624  -129.8411  -171.4378  116.5278
 EIO  C08  C  CH1   0  -0.149  -131.3899  -172.3638  114.8858
 EIO  C09  C  CH2   0  -0.183  -132.3251  -173.5615  114.9754
 EIO  C11  C  CH2   0  -0.183  -133.0932  -172.9892  117.0690
 EIO  C12  C  CH2   0  -0.333  -132.1957  -171.7658  117.1396
 EIO  C19  C  CH2   0  -0.437  -128.4301  -170.1478  120.5694
 EIO  N01  N  N     0  -0.666  -126.6056  -167.7917  120.4203
 EIO  N07  N  NT    0  -0.499  -131.0581  -171.9188  116.2442
 EIO  N14  N  N     0  -0.470  -128.8987  -171.5354  115.5803
 EIO  N18  N  N     0  -0.537  -127.2711  -170.5864  116.9996
 EIO  N21  N  N     0  -0.385  -125.9300  -168.2739  117.7533
 EIO  O10  O  O2    0  -0.470  -133.4688  -173.2884  115.7484
 EIO  O22  O  OS    0  -0.391  -127.3467  -167.6749  117.7649
 EIO  S02  S  S     1   1.216  -126.8662  -168.3988  119.0996
 EIO  H1   H  HCH3  0   0.241  -131.2553  -170.3899  114.0054
 EIO  H2   H  HCH3  0   0.240  -132.1524  -171.5592  113.0396
 EIO  H3   H  HCH3  0   0.234  -132.9004  -170.8416  114.4630
 EIO  H4   H  HCH3  0   0.285  -126.5939  -171.9645  112.4189
 EIO  H5   H  HCH3  0   0.279  -127.7042  -172.8789  113.4559
 EIO  H6   H  HCH3  0   0.278  -128.1426  -171.2463  112.8963
 EIO  H7   H  HCH2  0   0.322  -127.1854  -171.9036  120.0296
 EIO  H8   H  HCH2  0   0.320  -126.2714  -170.5482  120.8429
 EIO  H9   H  HCR6  0   0.298  -130.2421  -170.6676  118.5468
 EIO  H10  H  HCH1  0   0.285  -130.4713  -172.7112  114.4171
 EIO  H11  H  HCH2  0   0.246  -132.6576  -173.8335  113.9725
 EIO  H12  H  HCH2  0   0.222  -131.7762  -174.4177  115.3929
 EIO  H13  H  HCH2  0   0.213  -132.5733  -173.8439  117.5237
 EIO  H14  H  HCH2  0   0.251  -134.0006  -172.8003  117.6434
 EIO  H15  H  HCH2  0   0.258  -132.7568  -170.8621  116.8829
 EIO  H16  H  HCH2  0   0.275  -131.8642  -171.6629  118.1697
 EIO  H17  H  HCH2  0   0.318  -129.3624  -170.6926  120.5098
 EIO  H18  H  HCH2  0   0.322  -128.4297  -169.3370  121.2841
 EIO  H19  H  H     0   0.455  -126.0156  -166.9643  120.4755
 EIO  H21  H  H     0   0.458  -126.0341  -169.1574  117.1978
 EIO  S16  S  S2    0   0.063  -126.4490  -171.1728  114.6217

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
 EIO  C13  C08  single    1.524  0.020  1.524
 EIO  C15  N14  aromatic  1.311  0.020  1.311
 EIO  C15  N18  aromatic  1.328  0.020  1.328
 EIO  C15  S16  single    1.748  0.020  1.748
 EIO  C17  S16  single    1.802  0.020  1.802
 EIO  C20  C03  single    1.518  0.020  1.518
 EIO  C20  C19  single    1.478  0.020  1.478
 EIO  C03  C04  single    1.494  0.020  1.494
 EIO  C03  C19  single    1.506  0.020  1.506
 EIO  C03  S02  single    1.763  0.020  1.763
 EIO  C04  C05  aromatic  1.366  0.020  1.366
 EIO  C04  N18  aromatic  1.338  0.020  1.338
 EIO  C05  C06  aromatic  1.421  0.020  1.421
 EIO  C06  N07  single    1.339  0.020  1.339
 EIO  C06  N14  aromatic  1.340  0.020  1.340
 EIO  C08  C09  single    1.522  0.020  1.522
 EIO  C08  N07  single    1.467  0.020  1.467
 EIO  C09  O10  single    1.407  0.020  1.407
 EIO  C11  C12  single    1.519  0.020  1.519
 EIO  C11  O10  single    1.405  0.020  1.405
 EIO  C12  N07  single    1.456  0.020  1.456
 EIO  N01  S02  double    1.477  0.020  1.477
 EIO  N21  S02  double    1.645  0.020  1.645
 EIO  O22  S02  double    1.593  0.020  1.593
 EIO  C13  H1   single    0.970  0.020  1.090
 EIO  C13  H2   single    0.970  0.020  1.090
 EIO  C13  H3   single    0.970  0.020  1.090
 EIO  C17  H4   single    0.970  0.020  1.090
 EIO  C17  H5   single    0.970  0.020  1.090
 EIO  C17  H6   single    0.970  0.020  1.090
 EIO  C20  H7   single    0.970  0.020  1.090
 EIO  C20  H8   single    0.970  0.020  1.090
 EIO  C05  H9   single    0.930  0.020  1.080
 EIO  C08  H10  single    0.970  0.020  1.090
 EIO  C09  H11  single    0.970  0.020  1.090
 EIO  C09  H12  single    0.970  0.020  1.090
 EIO  C11  H13  single    0.970  0.020  1.090
 EIO  C11  H14  single    0.970  0.020  1.090
 EIO  C12  H15  single    0.970  0.020  1.090
 EIO  C12  H16  single    0.970  0.020  1.090
 EIO  C19  H17  single    0.970  0.020  1.090
 EIO  C19  H18  single    0.970  0.020  1.090
 EIO  N01  H19  single    0.890  0.020  1.040
 EIO  N21  H21  single    0.890  0.020  1.040

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
 EIO  H3   C13  H2   107.72  3.000
 EIO  H3   C13  H1   108.23  3.000
 EIO  H2   C13  H1   107.81  3.000
 EIO  H3   C13  C08  112.39  3.000
 EIO  H2   C13  C08  109.78  3.000
 EIO  H1   C13  C08  110.76  3.000
 EIO  S16  C15  N18  113.54  3.000
 EIO  S16  C15  N14  119.76  3.000
 EIO  N18  C15  N14  126.70  3.000
 EIO  H6   C17  H5   110.01  3.000
 EIO  H6   C17  H4   109.16  3.000
 EIO  H5   C17  H4   109.22  3.000
 EIO  H6   C17  S16  111.30  3.000
 EIO  H5   C17  S16  111.22  3.000
 EIO  H4   C17  S16  105.81  3.000
 EIO  H8   C20  H7   115.05  3.000
 EIO  H8   C20  C19  118.80  3.000
 EIO  H7   C20  C19  119.39  3.000
 EIO  H8   C20  C03  118.27  3.000
 EIO  H7   C20  C03  113.76  3.000
 EIO  C19  C20  C03   60.35  3.000
 EIO  S02  C03  C19  115.55  3.000
 EIO  S02  C03  C04  113.12  3.000
 EIO  C19  C03  C04  124.21  3.000
 EIO  S02  C03  C20  114.21  3.000
 EIO  C19  C03  C20   58.49  3.000
 EIO  C04  C03  C20  120.58  3.000
 EIO  N18  C04  C05  123.70  3.000
 EIO  N18  C04  C03  115.24  3.000
 EIO  C05  C04  C03  121.03  3.000
 EIO  H9   C05  C06  122.69  3.000
 EIO  H9   C05  C04  120.81  3.000
 EIO  C06  C05  C04  116.50  3.000
 EIO  N14  C06  N07  117.61  3.000
 EIO  N14  C06  C05  119.21  3.000
 EIO  N07  C06  C05  123.18  3.000
 EIO  H10  C08  N07  107.75  3.000
 EIO  H10  C08  C09  107.02  3.000
 EIO  N07  C08  C09  108.84  3.000
 EIO  H10  C08  C13  108.81  3.000
 EIO  N07  C08  C13  111.09  3.000
 EIO  C09  C08  C13  113.12  3.000
 EIO  H12  C09  H11  107.89  3.000
 EIO  H12  C09  O10  110.39  3.000
 EIO  H11  C09  O10  107.80  3.000
 EIO  H12  C09  C08  109.17  3.000
 EIO  H11  C09  C08  109.22  3.000
 EIO  O10  C09  C08  112.27  3.000
 EIO  H14  C11  H13  108.09  3.000
 EIO  H14  C11  O10  108.03  3.000
 EIO  H13  C11  O10  110.47  3.000
 EIO  H14  C11  C12  109.13  3.000
 EIO  H13  C11  C12  109.13  3.000
 EIO  O10  C11  C12  111.91  3.000
 EIO  H16  C12  H15  107.49  3.000
 EIO  H16  C12  N07  110.77  3.000
 EIO  H15  C12  N07  110.07  3.000
 EIO  H16  C12  C11  107.48  3.000
 EIO  H15  C12  C11  110.56  3.000
 EIO  N07  C12  C11  110.40  3.000
 EIO  H18  C19  H17  114.50  3.000
 EIO  H18  C19  C03  117.87  3.000
 EIO  H17  C19  C03  115.26  3.000
 EIO  H18  C19  C20  118.46  3.000
 EIO  H17  C19  C20  119.23  3.000
 EIO  C03  C19  C20   61.16  3.000
 EIO  H19  N01  S02  119.02  3.000
 EIO  C12  N07  C08  115.13  3.000
 EIO  C12  N07  C06  122.84  3.000
 EIO  C08  N07  C06  120.69  3.000
 EIO  C06  N14  C15  118.57  3.000
 EIO  C04  N18  C15  115.17  3.000
 EIO  H21  N21  S02  108.25  3.000
 EIO  C11  O10  C09  109.90  3.000
 EIO  O22  S02  N21   56.71  3.000
 EIO  O22  S02  N01  128.02  3.000
 EIO  N21  S02  N01  126.90  3.000
 EIO  O22  S02  C03  108.69  3.000
 EIO  N21  S02  C03  114.62  3.000
 EIO  N01  S02  C03  111.37  3.000
 EIO  C17  S16  C15  102.51  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
 EIO  CONST_01  C05  C06  N14  C15     0.00   0.0  0
 EIO  CONST_02  C05  C04  N18  C15     0.00   0.0  0
 EIO  CONST_03  N14  C06  C05  C04     0.00   0.0  0
 EIO  CONST_04  N14  C15  N18  C04     0.00   0.0  0
 EIO  CONST_05  N18  C04  C05  C06     0.00   0.0  0
 EIO  CONST_06  N18  C15  N14  C06     0.00   0.0  0
 EIO  CONST_07  N07  C06  N14  C15   180.00   0.0  0
 EIO  CONST_08  C03  C04  N18  C15   180.00   0.0  0
 EIO  CONST_09  C06  C05  C04  C03   180.00   0.0  0
 EIO  CONST_10  N07  C06  C05  C04   180.00   0.0  0
 EIO  CONST_11  S16  C15  N18  C04   180.00   0.0  0
 EIO  CONST_12  S16  C15  N14  C06   180.00   0.0  0
 EIO  CONST_13  H9   C05  C04  C03     0.00   0.0  0
 EIO  CONST_14  H9   C05  C06  N07     0.00   0.0  0
 EIO  CONST_15  H9   C05  C06  N14   180.00   0.0  0
 EIO  CONST_16  H9   C05  C04  N18   180.00   0.0  0
 EIO  Var_01    C05  C04  C03  C20    91.30  30.0  2
 EIO  Var_02    N18  C04  C03  C20   -86.87  30.0  2
 EIO  Var_03    C04  C03  C19  C20   107.75  30.0  1
 EIO  Var_04    C19  C03  C04  C05    20.70  30.0  3
 EIO  Var_05    C08  N07  C06  C05   171.72  30.0  2
 EIO  Var_06    C12  N07  C06  C05     5.62  30.0  2
 EIO  Var_07    C11  C12  N07  C06  -145.27  30.0  1
 EIO  Var_08    C11  O10  C09  C08   -62.23  30.0  1
 EIO  Var_09    N14  C06  N07  C08    -8.23  30.0  2
 EIO  Var_10    C11  C12  N07  C08    47.91  30.0  1
 EIO  Var_11    C12  C11  O10  C09    60.82  30.0  1
 EIO  Var_12    N14  C06  N07  C12  -174.33  30.0  2
 EIO  Var_13    N18  C04  C03  C19  -157.47  30.0  2
 EIO  Var_14    O10  C11  C12  N07   -53.15  30.0  1
 EIO  Var_15    S02  C03  C19  C20  -103.89  30.0  1
 EIO  Var_16    S02  C03  C04  C05  -128.33  30.0  3
 EIO  Var_17    S02  C03  C04  N18    53.51  30.0  3
 EIO  Var_18    H17  C19  C03  C20  -110.89  30.0  1
 EIO  Var_19    H18  C19  C03  C20   108.91  30.0  1
 EIO  Var_20    H7   C20  C19  C03  -102.21  30.0  1
 EIO  Var_21    H8   C20  C19  C03   107.99  30.0  1
 EIO  Var_22    H7   C20  C03  C04    -2.33  30.0  1
 EIO  Var_23    H8   C20  C03  C04   137.32  30.0  1
 EIO  Var_24    H17  C19  C03  C04    -3.14  30.0  1
 EIO  Var_25    H18  C19  C03  C04  -143.34  30.0  1
 EIO  Var_26    H15  C12  N07  C06    92.39  30.0  1
 EIO  Var_27    H16  C12  N07  C06   -26.34  30.0  1
 EIO  Var_28    H15  C12  N07  C08   -74.42  30.0  1
 EIO  Var_29    H16  C12  N07  C08   166.84  30.0  1
 EIO  Var_30    H13  C11  O10  C09   -60.99  30.0  1
 EIO  Var_31    H14  C11  O10  C09  -179.03  30.0  1
 EIO  Var_32    H11  C09  O10  C11   177.43  30.0  1
 EIO  Var_33    H12  C09  O10  C11    59.82  30.0  1
 EIO  Var_34    H13  C11  C12  N07    69.43  30.0  1
 EIO  Var_35    H14  C11  C12  N07  -172.66  30.0  1
 EIO  Var_36    H15  C12  C11  O10    68.90  30.0  1
 EIO  Var_37    H16  C12  C11  O10  -174.06  30.0  1
 EIO  Var_38    N14  C15  S16  C17     0.67  30.0  2
 EIO  Var_39    N18  C15  S16  C17  -179.64  30.0  2
 EIO  Var_40    N01  S02  C03  C20   -46.42  30.0  3
 EIO  Var_41    N21  S02  C03  C20   106.26  30.0  3
 EIO  Var_42    O22  S02  C03  C20   167.43  30.0  3
 EIO  Var_43    N01  S02  C03  C04   170.59  30.0  3
 EIO  Var_44    N21  S02  C03  C04   -36.72  30.0  3
 EIO  Var_45    O22  S02  C03  C04    24.44  30.0  3
 EIO  Var_46    N01  S02  C03  C19    18.74  30.0  3
 EIO  Var_47    N21  S02  C03  C19   171.42  30.0  3
 EIO  Var_48    O22  S02  C03  C19  -127.42  30.0  3
 EIO  Var_49    H7   C20  C03  S02  -142.30  30.0  1
 EIO  Var_50    H8   C20  C03  S02    -2.66  30.0  1
 EIO  Var_51    H17  C19  C03  S02   145.22  30.0  1
 EIO  Var_52    H18  C19  C03  S02     5.02  30.0  1
 EIO  Var_53    H4   C17  S16  C15  -179.63  30.0  3
 EIO  Var_54    H5   C17  S16  C15   -61.14  30.0  3
 EIO  Var_55    H6   C17  S16  C15    61.91  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
 EIO  chir_02  C08  C13  C09  N07  positiv
 EIO  chir_03  C03  C04  C19  S02  both

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
 EIO  plan-1  C15  0.020
 EIO  plan-1  C03  0.020
 EIO  plan-1  C04  0.020
 EIO  plan-1  C05  0.020
 EIO  plan-1  C06  0.020
 EIO  plan-1  N07  0.020
 EIO  plan-1  N14  0.020
 EIO  plan-1  N18  0.020
 EIO  plan-1  H9   0.020
 EIO  plan-1  S16  0.020

