# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 15:30:34 2022
#   Inital geometry file: a 136 line input string
#   Ligand name: (3R)-3-methyl-4-{6-[1-(S-methylsulfonimidoyl)cyclopropyl]-2-(naphthalen-1-yl)pyrimidin-4-yl}morpholine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1COCCN1c2cc(nc(n2)c3cccc4ccccc34)C5(CC5)[S@](C)(=N)=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
 XWY  XWY  (3R)-3-methyl-4-{6-[1-(S-methylsulfonimidoyl)cyclopropyl]-2-(naphthalen-1-yl)pyrimidin-4-yl}morpholine  ligand  56  30  .  2022-08-11  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_XWY
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
 XWY  C10   C  CH1   0  -0.144  -130.4644  -173.9657  113.1919
 XWY  C13   C  CH2   0  -0.184  -132.2361  -174.9600  115.1687
 XWY  C15   C  CH3   0  -0.661  -130.9228  -172.5942  112.7053
 XWY  C17   C  CR6   0   0.290  -126.6918  -173.1156  114.3550
 XWY  C20   C  CR16  0  -0.247  -123.8874  -171.7396  112.2578
 XWY  C21   C  CR16  0  -0.314  -123.8176  -172.6118  111.2092
 XWY  C22   C  CR66  0   0.105  -124.6654  -173.7417  111.1575
 XWY  C24   C  CR16  0  -0.336  -126.4034  -175.1423  112.1227
 XWY  C26   C  CR16  0  -0.260  -125.3509  -175.7779  110.0433
 XWY  C03   C  CT    0  -0.306  -126.7433  -172.5125  117.9136
 XWY  C04   C  CH2   0  -0.457  -127.1759  -173.3309  119.0920
 XWY  C05   C  CH2   0  -0.453  -125.7600  -173.3841  118.6278
 XWY  C06   C  CR6   0   0.316  -127.1976  -172.8615  116.5395
 XWY  C07   C  CR16  0  -0.435  -128.5082  -173.1981  116.3031
 XWY  C08   C  CR6   0   0.597  -128.8571  -173.5258  114.9760
 XWY  C11   C  CH2   0  -0.184  -131.5180  -175.0442  112.9850
 XWY  C14   C  CH2   0  -0.329  -131.2088  -173.9052  115.5416
 XWY  C18   C  CR6   0   0.022  -125.6909  -173.0185  113.2620
 XWY  C19   C  CR16  0  -0.311  -124.8220  -171.9532  113.2856
 XWY  C23   C  CR66  0   0.126  -125.6173  -173.9638  112.1928
 XWY  C25   C  CR16  0  -0.247  -126.2719  -176.0205  111.0812
 XWY  C27   C  CR16  0  -0.305  -124.5629  -174.6629  110.0876
 XWY  C29   C  CH3   0  -0.769  -125.0773  -170.3025  117.3819
 XWY  N01   N  N     0  -0.853  -126.2928  -170.4166  119.6753
 XWY  N09   N  NT    0  -0.510  -130.0944  -173.9269  114.6092
 XWY  N16   N  N     0  -0.488  -127.9265  -173.4474  114.0196
 XWY  N28   N  N     0  -0.447  -126.2707  -172.8228  115.5781
 XWY  O12   O  O2    0  -0.472  -132.6339  -174.8632  113.8235
 XWY  O30   O  OS    0  -0.677  -127.7265  -170.1186  117.4980
 XWY  S02   S  S     0   1.056  -126.5908  -170.7347  118.2039
 XWY  H101  H  HCH1  0   0.277  -129.5858  -174.2682  112.6245
 XWY  H131  H  HCH2  0   0.247  -133.1224  -174.8323  115.7914
 XWY  H132  H  HCH2  0   0.209  -131.8204  -175.9568  115.3737
 XWY  H152  H  HCH3  0   0.238  -130.1374  -171.8520  112.8480
 XWY  H153  H  HCH3  0   0.235  -131.1579  -172.6323  111.6411
 XWY  H151  H  HCH3  0   0.231  -131.8136  -172.2517  113.2317
 XWY  H201  H  HCR6  0   0.259  -123.2340  -170.8784  112.3020
 XWY  H211  H  HCR6  0   0.258  -123.1055  -172.4535  110.4083
 XWY  H241  H  HCR6  0   0.255  -127.1194  -175.3561  112.9012
 XWY  H261  H  HCR6  0   0.257  -125.2632  -176.4781  109.2229
 XWY  H041  H  HCH2  0   0.274  -127.3865  -172.8293  120.0276
 XWY  H042  H  HCH2  0   0.281  -127.8249  -174.1706  118.8809
 XWY  H052  H  HCH2  0   0.278  -125.4160  -174.2604  118.0941
 XWY  H051  H  HCH2  0   0.277  -125.0103  -172.9041  119.2451
 XWY  H071  H  HCR6  0   0.283  -129.2153  -173.1989  117.1173
 XWY  H111  H  HCH2  0   0.242  -131.8695  -175.0125  111.9524
 XWY  H112  H  HCH2  0   0.219  -131.0664  -176.0317  113.1569
 XWY  H141  H  HCH2  0   0.268  -130.8651  -174.1356  116.5480
 XWY  H142  H  HCH2  0   0.246  -131.6723  -172.9129  115.5727
 XWY  H191  H  HCR6  0   0.275  -124.8749  -171.2470  114.1034
 XWY  H251  H  HCR6  0   0.257  -126.8819  -176.9143  111.0564
 XWY  H271  H  HCR6  0   0.256  -123.8377  -174.4695  109.3061
 XWY  H292  H  HCH3  0   0.290  -124.2471  -170.8406  117.8302
 XWY  H293  H  HCH3  0   0.301  -125.1670  -170.5530  116.3292
 XWY  H291  H  HCH3  0   0.302  -124.9445  -169.2296  117.5083
 XWY  H011  H  H     0   0.362  -127.1096  -170.5613  120.2620

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
 XWY  C26  C27   aromatic  1.366  0.020  1.366
 XWY  C26  C25   aromatic  1.409  0.020  1.409
 XWY  C27  C22   aromatic  1.416  0.020  1.416
 XWY  C25  C24   aromatic  1.369  0.020  1.369
 XWY  C22  C21   aromatic  1.414  0.020  1.414
 XWY  C22  C23   aromatic  1.424  0.020  1.424
 XWY  C21  C20   aromatic  1.366  0.020  1.366
 XWY  C24  C23   aromatic  1.418  0.020  1.418
 XWY  C23  C18   aromatic  1.429  0.020  1.429
 XWY  C20  C19   aromatic  1.405  0.020  1.405
 XWY  C15  C10   single    1.526  0.020  1.526
 XWY  C11  C10   single    1.522  0.020  1.522
 XWY  C11  O12   single    1.407  0.020  1.407
 XWY  C18  C19   aromatic  1.375  0.020  1.375
 XWY  C18  C17   single    1.485  0.020  1.485
 XWY  C10  N09   single    1.465  0.020  1.465
 XWY  N16  C17   aromatic  1.322  0.020  1.322
 XWY  N16  C08   aromatic  1.337  0.020  1.337
 XWY  O12  C13   single    1.406  0.020  1.406
 XWY  C17  N28   aromatic  1.326  0.020  1.326
 XWY  N09  C08   single    1.351  0.020  1.351
 XWY  N09  C14   single    1.453  0.020  1.453
 XWY  C08  C07   aromatic  1.411  0.020  1.411
 XWY  C13  C14   single    1.519  0.020  1.519
 XWY  N28  C06   aromatic  1.336  0.020  1.336
 XWY  C07  C06   aromatic  1.374  0.020  1.374
 XWY  C06  C03   single    1.489  0.020  1.489
 XWY  O30  S02   double    1.472  0.020  1.472
 XWY  C29  S02   single    1.776  0.020  1.776
 XWY  S02  C03   single    1.808  0.020  1.808
 XWY  S02  N01   double    1.535  0.020  1.535
 XWY  C03  C05   single    1.496  0.020  1.496
 XWY  C03  C04   single    1.499  0.020  1.499
 XWY  C05  C04   single    1.491  0.020  1.491
 XWY  C10  H101  single    0.970  0.020  1.090
 XWY  C13  H131  single    0.970  0.020  1.090
 XWY  C13  H132  single    0.970  0.020  1.090
 XWY  C15  H152  single    0.970  0.020  1.090
 XWY  C15  H153  single    0.970  0.020  1.090
 XWY  C15  H151  single    0.970  0.020  1.090
 XWY  C20  H201  single    0.930  0.020  1.080
 XWY  C21  H211  single    0.930  0.020  1.080
 XWY  C24  H241  single    0.930  0.020  1.080
 XWY  C26  H261  single    0.930  0.020  1.080
 XWY  C04  H041  single    0.970  0.020  1.090
 XWY  C04  H042  single    0.970  0.020  1.090
 XWY  C05  H052  single    0.970  0.020  1.090
 XWY  C05  H051  single    0.970  0.020  1.090
 XWY  C07  H071  single    0.930  0.020  1.080
 XWY  C11  H111  single    0.970  0.020  1.090
 XWY  C11  H112  single    0.970  0.020  1.090
 XWY  C14  H141  single    0.970  0.020  1.090
 XWY  C14  H142  single    0.970  0.020  1.090
 XWY  C19  H191  single    0.930  0.020  1.080
 XWY  C25  H251  single    0.930  0.020  1.080
 XWY  C27  H271  single    0.930  0.020  1.080
 XWY  C29  H292  single    0.970  0.020  1.090
 XWY  C29  H293  single    0.970  0.020  1.090
 XWY  C29  H291  single    0.970  0.020  1.090
 XWY  N01  H011  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
 XWY  H101  C10  N09   107.92  3.000
 XWY  H101  C10  C11   106.91  3.000
 XWY  N09   C10  C11   108.97  3.000
 XWY  H101  C10  C15   109.02  3.000
 XWY  N09   C10  C15   111.13  3.000
 XWY  C11   C10  C15   112.69  3.000
 XWY  H132  C13  H131  107.88  3.000
 XWY  H132  C13  O12   110.36  3.000
 XWY  H131  C13  O12   107.95  3.000
 XWY  H132  C13  C14   109.16  3.000
 XWY  H131  C13  C14   109.16  3.000
 XWY  O12   C13  C14   112.23  3.000
 XWY  H151  C15  H153  107.82  3.000
 XWY  H151  C15  H152  108.16  3.000
 XWY  H153  C15  H152  107.87  3.000
 XWY  H151  C15  C10   111.96  3.000
 XWY  H153  C15  C10   110.16  3.000
 XWY  H152  C15  C10   110.73  3.000
 XWY  N28   C17  N16   125.88  3.000
 XWY  N28   C17  C18   116.76  3.000
 XWY  N16   C17  C18   117.33  3.000
 XWY  H201  C20  C19   119.51  3.000
 XWY  H201  C20  C21   120.59  3.000
 XWY  C19   C20  C21   119.90  3.000
 XWY  H211  C21  C22   118.94  3.000
 XWY  H211  C21  C20   120.53  3.000
 XWY  C22   C21  C20   120.53  3.000
 XWY  C27   C22  C23   119.76  3.000
 XWY  C23   C22  C21   119.94  3.000
 XWY  C27   C22  C21   120.30  3.000
 XWY  H241  C24  C25   119.05  3.000
 XWY  H241  C24  C23   119.78  3.000
 XWY  C25   C24  C23   121.16  3.000
 XWY  H261  C26  C27   120.40  3.000
 XWY  H261  C26  C25   120.01  3.000
 XWY  C27   C26  C25   119.59  3.000
 XWY  S02   C03  C06   113.86  3.000
 XWY  S02   C03  C05   116.16  3.000
 XWY  C06   C03  C05   120.31  3.000
 XWY  C05   C03  C04    59.73  3.000
 XWY  S02   C03  C04   115.79  3.000
 XWY  C06   C03  C04   120.64  3.000
 XWY  H042  C04  H041  114.31  3.000
 XWY  H042  C04  C05   118.76  3.000
 XWY  H041  C04  C05   118.07  3.000
 XWY  H042  C04  C03   116.33  3.000
 XWY  H041  C04  C03   118.87  3.000
 XWY  C05   C04  C03    60.03  3.000
 XWY  H051  C05  H052  114.82  3.000
 XWY  H051  C05  C04   117.64  3.000
 XWY  H052  C05  C04   118.97  3.000
 XWY  H051  C05  C03   117.96  3.000
 XWY  H052  C05  C03   116.45  3.000
 XWY  C04   C05  C03    60.23  3.000
 XWY  N28   C06  C07   123.04  3.000
 XWY  C07   C06  C03   120.49  3.000
 XWY  N28   C06  C03   116.46  3.000
 XWY  H071  C07  C08   123.22  3.000
 XWY  H071  C07  C06   119.72  3.000
 XWY  C08   C07  C06   117.05  3.000
 XWY  N16   C08  N09   117.42  3.000
 XWY  N09   C08  C07   123.41  3.000
 XWY  N16   C08  C07   119.16  3.000
 XWY  H112  C11  H111  107.84  3.000
 XWY  H112  C11  O12   110.37  3.000
 XWY  H111  C11  O12   107.74  3.000
 XWY  H112  C11  C10   109.32  3.000
 XWY  H111  C11  C10   109.33  3.000
 XWY  O12   C11  C10   112.13  3.000
 XWY  H142  C14  H141  107.41  3.000
 XWY  H142  C14  N09   110.87  3.000
 XWY  H141  C14  N09   110.37  3.000
 XWY  H142  C14  C13   110.48  3.000
 XWY  H141  C14  C13   107.07  3.000
 XWY  N09   C14  C13   110.53  3.000
 XWY  C23   C18  C19   119.53  3.000
 XWY  C19   C18  C17   117.64  3.000
 XWY  C23   C18  C17   122.83  3.000
 XWY  H191  C19  C18   119.20  3.000
 XWY  H191  C19  C20   119.09  3.000
 XWY  C18   C19  C20   121.69  3.000
 XWY  C18   C23  C24   123.92  3.000
 XWY  C18   C23  C22   118.38  3.000
 XWY  C24   C23  C22   117.66  3.000
 XWY  H251  C25  C26   119.59  3.000
 XWY  H251  C25  C24   119.55  3.000
 XWY  C26   C25  C24   120.86  3.000
 XWY  H271  C27  C26   120.56  3.000
 XWY  H271  C27  C22   118.51  3.000
 XWY  C26   C27  C22   120.93  3.000
 XWY  H291  C29  H293  110.49  3.000
 XWY  H291  C29  H292  110.31  3.000
 XWY  H293  C29  H292  110.42  3.000
 XWY  H291  C29  S02   106.87  3.000
 XWY  H293  C29  S02   108.80  3.000
 XWY  H292  C29  S02   109.87  3.000
 XWY  H011  N01  S02   111.60  3.000
 XWY  C14   N09  C08   121.57  3.000
 XWY  C14   N09  C10   115.30  3.000
 XWY  C08   N09  C10   120.11  3.000
 XWY  C08   N16  C17   118.91  3.000
 XWY  C06   N28  C17   115.91  3.000
 XWY  C11   O12  C13   109.69  3.000
 XWY  O30   S02  N01   121.52  3.000
 XWY  N01   S02  C29   103.18  3.000
 XWY  O30   S02  C29   109.49  3.000
 XWY  N01   S02  C03   111.98  3.000
 XWY  C29   S02  C03   103.70  3.000
 XWY  O30   S02  C03   105.63  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
 XWY  CONST_01  C22   C23  C18  C17   180.00   0.0  0
 XWY  CONST_02  C24   C23  C18  C17     0.00   0.0  0
 XWY  CONST_03  C20   C19  C18  C17   180.00   0.0  0
 XWY  CONST_04  C07   C08  N16  C17     0.00   0.0  0
 XWY  CONST_05  C07   C06  N28  C17     0.00   0.0  0
 XWY  CONST_06  C27   C22  C21  C20   180.00   0.0  0
 XWY  CONST_07  C23   C22  C21  C20     0.00   0.0  0
 XWY  CONST_08  C23   C18  C19  C20     0.00   0.0  0
 XWY  CONST_09  C26   C27  C22  C21   180.00   0.0  0
 XWY  CONST_10  C24   C23  C22  C21   180.00   0.0  0
 XWY  CONST_11  C18   C23  C22  C21     0.00   0.0  0
 XWY  CONST_12  C18   C19  C20  C21     0.00   0.0  0
 XWY  CONST_13  C25   C26  C27  C22     0.00   0.0  0
 XWY  CONST_14  C19   C20  C21  C22     0.00   0.0  0
 XWY  CONST_15  C25   C24  C23  C22     0.00   0.0  0
 XWY  CONST_16  C19   C18  C23  C22     0.00   0.0  0
 XWY  CONST_17  C27   C26  C25  C24     0.00   0.0  0
 XWY  CONST_18  C27   C22  C23  C24     0.00   0.0  0
 XWY  CONST_19  C19   C18  C23  C24   180.00   0.0  0
 XWY  CONST_20  C23   C22  C27  C26     0.00   0.0  0
 XWY  CONST_21  C23   C24  C25  C26     0.00   0.0  0
 XWY  CONST_22  C18   C17  N28  C06   180.00   0.0  0
 XWY  CONST_23  N16   C17  N28  C06     0.00   0.0  0
 XWY  CONST_24  N16   C08  C07  C06     0.00   0.0  0
 XWY  CONST_25  C18   C17  N16  C08   180.00   0.0  0
 XWY  CONST_26  N28   C17  N16  C08     0.00   0.0  0
 XWY  CONST_27  N28   C06  C07  C08     0.00   0.0  0
 XWY  CONST_28  C27   C22  C23  C18   180.00   0.0  0
 XWY  CONST_29  C25   C24  C23  C18   180.00   0.0  0
 XWY  CONST_34  N09   C08  N16  C17   180.00   0.0  0
 XWY  CONST_35  C03   C06  N28  C17   180.00   0.0  0
 XWY  CONST_36  C08   C07  C06  C03   180.00   0.0  0
 XWY  CONST_37  N09   C08  C07  C06   180.00   0.0  0
 XWY  CONST_38  H191  C19  C18  C17     0.00   0.0  0
 XWY  CONST_39  H271  C27  C22  C21     0.00   0.0  0
 XWY  CONST_40  H261  C26  C27  C22   180.00   0.0  0
 XWY  CONST_41  H201  C20  C21  C22   180.00   0.0  0
 XWY  CONST_42  H241  C24  C23  C22   180.00   0.0  0
 XWY  CONST_43  H071  C07  C06  C03     0.00   0.0  0
 XWY  CONST_44  H211  C21  C20  C19   180.00   0.0  0
 XWY  CONST_45  H251  C25  C24  C23   180.00   0.0  0
 XWY  Var_01    N16   C08  N09  C10   -13.81  30.0  2
 XWY  Var_02    C13   C14  N09  C10    47.08  30.0  1
 XWY  Var_03    N28   C06  C03  C04  -136.09  30.0  2
 XWY  Var_04    C06   C03  C05  C04  -110.02  30.0  1
 XWY  Var_05    C14   C13  O12  C11    60.59  30.0  1
 XWY  Var_06    O12   C13  C14  N09   -52.43  30.0  1
 XWY  Var_07    H111  C11  O12  C13   177.24  30.0  1
 XWY  Var_08    H041  C04  C05  C03  -108.92  30.0  1
 XWY  Var_09    O30   S02  C03  C04  -107.84  30.0  3
 XWY  Var_10    H292  C29  S02  C03   -61.43  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
 XWY  chir_01  C10  C15  C11  N09  positiv
 XWY  chir_02  S02  C29  C03  N01  both
 XWY  chir_03  C03  C04  C05  C06  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
 XWY  plan-1  C17   0.020
 XWY  plan-1  C03   0.020
 XWY  plan-1  C06   0.020
 XWY  plan-1  C07   0.020
 XWY  plan-1  C08   0.020
 XWY  plan-1  C18   0.020
 XWY  plan-1  N09   0.020
 XWY  plan-1  N16   0.020
 XWY  plan-1  N28   0.020
 XWY  plan-1  H071  0.020
 XWY  plan-2  C17   0.020
 XWY  plan-2  C20   0.020
 XWY  plan-2  C21   0.020
 XWY  plan-2  C22   0.020
 XWY  plan-2  C24   0.020
 XWY  plan-2  C26   0.020
 XWY  plan-2  C18   0.020
 XWY  plan-2  C19   0.020
 XWY  plan-2  C23   0.020
 XWY  plan-2  C25   0.020
 XWY  plan-2  C27   0.020
 XWY  plan-2  H201  0.020
 XWY  plan-2  H211  0.020
 XWY  plan-2  H241  0.020
 XWY  plan-2  H261  0.020
 XWY  plan-2  H191  0.020
 XWY  plan-2  H251  0.020
 XWY  plan-2  H271  0.020

