# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 12:30:02 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 3-({2-[(2-amino-6-methylpyrimidin-4-yl)ethynyl]benzyl}amino)-1,3-oxazol-2(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(nc(N)n1)C#Cc2ccccc2CNN3C=COC3=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
 A91  A91  3-({2-[(2-amino-6-methylpyrimidin-4-yl)ethynyl]benzyl}amino)-1,3-oxazol-2(3H)-one  ligand  39  24  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A91
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
 A91  C1    C  CR15  0  -0.076  -0.7527  -3.7172  -0.0391
 A91  C2    C  CR15  0  -0.082  -0.5547  -2.4256   0.2148
 A91  N3    N  NR5   0  -0.370  -1.8179  -1.8579   0.3088
 A91  C4    C  CR5   0   0.683  -2.7695  -2.8079   0.1007
 A91  O5    O  O     0  -0.443  -2.1064  -3.9645  -0.1013
 A91  O6    O  O     0  -0.488  -3.9729  -2.7018   0.1069
 A91  N7    N  NH1   0  -0.453  -2.0505  -0.5244   0.5425
 A91  C8    C  CH2   0  -0.382  -2.4069   0.2159  -0.6663
 A91  C9    C  CR6   0   0.085  -2.4560   1.6822  -0.3493
 A91  C10   C  CR6   0  -0.105  -1.2838   2.3904  -0.0340
 A91  C11   C  CR16  0  -0.299  -1.3500   3.7545   0.2611
 A91  C12   C  CR16  0  -0.256  -2.5679   4.4144   0.2543
 A91  C13   C  CR16  0  -0.237  -3.7281   3.7175  -0.0508
 A91  C14   C  CR16  0  -0.304  -3.6655   2.3618  -0.3489
 A91  C15   C  CSP   0   0.175  -0.0189   1.7410  -0.0219
 A91  C16   C  CSP   0   0.102   1.0668   1.2155   0.0035
 A91  C17   C  CR6   0   0.107   2.3551   0.6041   0.0463
 A91  C18   C  CR16  0  -0.420   3.5020   1.3866   0.1066
 A91  C19   C  CR6   0   0.283   4.7162   0.7084   0.1481
 A91  N20   N  N     0  -0.470   4.7709  -0.6161   0.1248
 A91  C21   C  CR6   0   0.543   3.6119  -1.2789   0.0657
 A91  N22   N  N     0  -0.488   2.3972  -0.7251   0.0281
 A91  C23   C  CH3   0  -0.723   6.0138   1.4443   0.2314
 A91  N24   N  NH2   0  -0.823   3.6732  -2.6255   0.0738
 A91  H1    H  HCR5  0   0.302  -0.0864  -4.5468  -0.1987
 A91  H2    H  HCR5  0   0.334   0.3521  -1.8465   0.3119
 A91  HN7   H  HNH1  0   0.385  -2.7590  -0.4305   1.2605
 A91  H81   H  HCH2  0   0.266  -1.6310   0.0211  -1.4096
 A91  H82   H  HCH2  0   0.257  -3.3623  -0.1026  -1.0963
 A91  H11   H  HCR6  0   0.264  -0.4404   4.2919   0.4943
 A91  H12   H  HCR6  0   0.268  -2.6094   5.4707   0.4838
 A91  H13   H  HCR6  0   0.268  -4.6829   4.2265  -0.0567
 A91  H14   H  HCR6  0   0.263  -4.5745   1.8244  -0.5889
 A91  H18   H  HCR6  0   0.273   3.4502   2.4650   0.1183
 A91  H231  H  HCH3  0   0.262   6.4825   1.2658   1.2004
 A91  H232  H  HCH3  0   0.259   6.7061   1.0897  -0.5319
 A91  H233  H  HCH3  0   0.249   5.8770   2.5168   0.1118
 A91  H241  H  HNH2  0   0.397   4.5604  -3.0640  -0.1040
 A91  H242  H  HNH2  0   0.392   2.8549  -3.1466  -0.1889

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
 A91  C1   O5    single    1.377  0.020  1.377
 A91  C1   C2    double    1.331  0.020  1.331
 A91  C1   H1    single    0.930  0.020  1.080
 A91  C2   N3    single    1.388  0.020  1.388
 A91  C2   H2    single    0.930  0.020  1.080
 A91  N3   C4    single    1.361  0.020  1.361
 A91  N3   N7    single    1.374  0.020  1.374
 A91  C4   O5    single    1.348  0.020  1.348
 A91  C4   O6    double    1.208  0.020  1.208
 A91  N7   C8    single    1.462  0.020  1.462
 A91  N7   HN7   single    0.890  0.020  1.040
 A91  C8   C9    single    1.501  0.020  1.501
 A91  C8   H81   single    0.970  0.020  1.090
 A91  C8   H82   single    0.970  0.020  1.090
 A91  C9   C10   aromatic  1.405  0.020  1.405
 A91  C9   C14   aromatic  1.387  0.020  1.387
 A91  C10  C15   single    1.422  0.020  1.422
 A91  C10  C11   aromatic  1.397  0.020  1.397
 A91  C11  C12   aromatic  1.385  0.020  1.385
 A91  C11  H11   single    0.930  0.020  1.080
 A91  C12  C13   aromatic  1.387  0.020  1.387
 A91  C12  H12   single    0.930  0.020  1.080
 A91  C13  C14   aromatic  1.390  0.020  1.390
 A91  C13  H13   single    0.930  0.020  1.080
 A91  C14  H14   single    0.930  0.020  1.080
 A91  C15  C16   triple    1.206  0.020  1.206
 A91  C16  C17   single    1.427  0.020  1.427
 A91  C17  C18   aromatic  1.390  0.020  1.390
 A91  C17  N22   aromatic  1.330  0.020  1.330
 A91  C18  C19   aromatic  1.391  0.020  1.391
 A91  C18  H18   single    0.930  0.020  1.080
 A91  C19  C23   single    1.494  0.020  1.494
 A91  C19  N20   aromatic  1.326  0.020  1.326
 A91  N20  C21   aromatic  1.336  0.020  1.336
 A91  C21  N22   aromatic  1.336  0.020  1.336
 A91  C21  N24   single    1.348  0.020  1.348
 A91  C23  H231  single    0.970  0.020  1.090
 A91  C23  H232  single    0.970  0.020  1.090
 A91  C23  H233  single    0.970  0.020  1.090
 A91  N24  H241  single    0.890  0.020  1.040
 A91  N24  H242  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
 A91  H1    C1   O5    117.61  3.000
 A91  H1    C1   C2    133.18  3.000
 A91  O5    C1   C2    109.21  3.000
 A91  H2    C2   N3    122.58  3.000
 A91  H2    C2   C1    131.46  3.000
 A91  N3    C2   C1    105.93  3.000
 A91  N7    N3   C4    125.83  3.000
 A91  N7    N3   C2    124.24  3.000
 A91  C4    N3   C2    109.91  3.000
 A91  O6    C4   O5    124.47  3.000
 A91  O6    C4   N3    129.39  3.000
 A91  O5    C4   N3    106.13  3.000
 A91  C4    O5   C1    108.81  3.000
 A91  HN7   N7   C8    111.63  3.000
 A91  HN7   N7   N3    109.20  3.000
 A91  C8    N7   N3    113.10  3.000
 A91  H82   C8   H81   107.50  3.000
 A91  H82   C8   C9    109.79  3.000
 A91  H81   C8   C9    109.95  3.000
 A91  H82   C8   N7    112.97  3.000
 A91  H81   C8   N7    107.42  3.000
 A91  C9    C8   N7    109.16  3.000
 A91  C14   C9   C10   118.70  3.000
 A91  C14   C9   C8    120.47  3.000
 A91  C10   C9   C8    120.82  3.000
 A91  C15   C10  C11   119.10  3.000
 A91  C11   C10  C9    119.99  3.000
 A91  C15   C10  C9    120.91  3.000
 A91  H11   C11  C12   120.24  3.000
 A91  H11   C11  C10   119.38  3.000
 A91  C12   C11  C10   120.38  3.000
 A91  H12   C12  C13   120.34  3.000
 A91  H12   C12  C11   119.86  3.000
 A91  C13   C12  C11   119.80  3.000
 A91  H13   C13  C14   119.84  3.000
 A91  H13   C13  C12   120.19  3.000
 A91  C14   C13  C12   119.97  3.000
 A91  H14   C14  C13   119.60  3.000
 A91  H14   C14  C9    119.25  3.000
 A91  C13   C14  C9    121.15  3.000
 A91  C16   C15  C10   180.00  3.000
 A91  C17   C16  C15   180.00  3.000
 A91  N22   C17  C18   122.50  3.000
 A91  N22   C17  C16   117.16  3.000
 A91  C18   C17  C16   120.35  3.000
 A91  H18   C18  C19   121.90  3.000
 A91  H18   C18  C17   121.55  3.000
 A91  C19   C18  C17   116.55  3.000
 A91  C23   C19  N20   117.21  3.000
 A91  N20   C19  C18   121.49  3.000
 A91  C23   C19  C18   121.30  3.000
 A91  C21   N20  C19   117.41  3.000
 A91  N24   C21  N22   117.12  3.000
 A91  N24   C21  N20   117.11  3.000
 A91  N22   C21  N20   125.76  3.000
 A91  C21   N22  C17   116.28  3.000
 A91  H233  C23  H232  108.88  3.000
 A91  H233  C23  H231  108.24  3.000
 A91  H232  C23  H231  107.21  3.000
 A91  H233  C23  C19   111.73  3.000
 A91  H232  C23  C19   110.63  3.000
 A91  H231  C23  C19   110.00  3.000
 A91  H242  N24  H241  116.49  3.000
 A91  H242  N24  C21   118.64  3.000
 A91  H241  N24  C21   118.34  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
 A91  CONST_01  C12   C11  C10  C9      0.00   0.0  0
 A91  CONST_02  C12   C13  C14  C9      0.00   0.0  0
 A91  CONST_03  C13   C14  C9   C10     0.00   0.0  0
 A91  CONST_04  C13   C12  C11  C10     0.00   0.0  0
 A91  CONST_05  C14   C9   C10  C11     0.00   0.0  0
 A91  CONST_06  C14   C13  C12  C11     0.00   0.0  0
 A91  CONST_07  N20   C19  C18  C17     0.00   0.0  0
 A91  CONST_08  N20   C21  N22  C17     0.00   0.0  0
 A91  CONST_09  C21   N22  C17  C18     0.00   0.0  0
 A91  CONST_10  C21   N20  C19  C18     0.00   0.0  0
 A91  CONST_11  N22   C17  C18  C19     0.00   0.0  0
 A91  CONST_12  N22   C21  N20  C19     0.00   0.0  0
 A91  CONST_13  C11   C10  C9   C8    180.00   0.0  0
 A91  CONST_14  C13   C14  C9   C8    180.00   0.0  0
 A91  CONST_15  C15   C10  C11  C12   180.00   0.0  0
 A91  CONST_16  C15   C10  C9   C14   180.00   0.0  0
 A91  CONST_17  C19   C18  C17  C16   180.00   0.0  0
 A91  CONST_18  C21   N22  C17  C16   180.00   0.0  0
 A91  CONST_19  C23   C19  C18  C17   180.00   0.0  0
 A91  CONST_20  N24   C21  N22  C17   180.00   0.0  0
 A91  CONST_21  N24   C21  N20  C19   180.00   0.0  0
 A91  CONST_22  C23   C19  N20  C21   180.00   0.0  0
 A91  CONST_23  H11   C11  C10  C9    180.00   0.0  0
 A91  CONST_24  H13   C13  C14  C9    180.00   0.0  0
 A91  CONST_25  H14   C14  C9   C10   180.00   0.0  0
 A91  CONST_26  H12   C12  C11  C10   180.00   0.0  0
 A91  CONST_27  H18   C18  C19  N20   180.00   0.0  0
 A91  CONST_28  H241  N24  C21  N20     0.00   0.0  0
 A91  CONST_29  H242  N24  C21  N20   180.00   0.0  0
 A91  Var_01    C8    N7   N3   C2    101.56  30.0  2
 A91  Var_02    C9    C8   N7   N3   -172.30  30.0  3
 A91  Var_03    C10   C9   C8   N7     68.15  30.0  2
 A91  Var_04    H231  C23  C19  C18   112.20  30.0  2

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
 A91  plan-1  C1    0.020
 A91  plan-1  C2    0.020
 A91  plan-1  N3    0.020
 A91  plan-1  C4    0.020
 A91  plan-1  O5    0.020
 A91  plan-1  O6    0.020
 A91  plan-1  N7    0.020
 A91  plan-1  H1    0.020
 A91  plan-1  H2    0.020
 A91  plan-2  C8    0.020
 A91  plan-2  C9    0.020
 A91  plan-2  C10   0.020
 A91  plan-2  C11   0.020
 A91  plan-2  C12   0.020
 A91  plan-2  C13   0.020
 A91  plan-2  C14   0.020
 A91  plan-2  C15   0.020
 A91  plan-2  C16   0.020
 A91  plan-2  H11   0.020
 A91  plan-2  H12   0.020
 A91  plan-2  H13   0.020
 A91  plan-2  H14   0.020
 A91  plan-3  C15   0.020
 A91  plan-3  C16   0.020
 A91  plan-3  C17   0.020
 A91  plan-3  C18   0.020
 A91  plan-3  C19   0.020
 A91  plan-3  N20   0.020
 A91  plan-3  C21   0.020
 A91  plan-3  N22   0.020
 A91  plan-3  C23   0.020
 A91  plan-3  N24   0.020
 A91  plan-3  H18   0.020
 A91  plan-4  C21   0.020
 A91  plan-4  N24   0.020
 A91  plan-4  H241  0.020
 A91  plan-4  H242  0.020

