# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 08:19:24 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: (3aS,7aR)-7a-[3-(pyrimidin-5-yl)phenyl]-3a,6,7,7a-tetrahydro-4H-pyrano[4,3-d][1,3]oxazol-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=N[C@]2(CCOC[C@H]2O1)c3cccc(c3)c4cncnc4
#
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
 1W0  1W0  (3aS,7aR)-7a-[3-(pyrimidin-5-yl)phenyl]-3a,6,7,7a-tetrahydro-4H-pyrano[4,3-d][1,3]oxazol-2-amine  ligand  38  22  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_1W0
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
 1W0  C4   C  CR16  0  -0.379  -0.6588   0.1322  -0.1956
 1W0  C5   C  CR6   0   0.198   0.5602   0.7661  -0.4190
 1W0  C6   C  CR16  0  -0.326   0.5630   2.1400  -0.6320
 1W0  C7   C  CR5   0  -0.056   1.8497  -0.0499  -0.4783
 1W0  C8   C  CH2   0  -0.447   1.8319  -0.9081  -1.7491
 1W0  C17  C  CR6   0  -0.048  -3.1254   0.1462   0.0981
 1W0  C20  C  CR16  0   0.049  -5.4297  -1.1213   0.5751
 1W0  C22  C  CR16  0  -0.046  -4.3130   0.4874  -0.5434
 1W0  C1   C  CR16  0  -0.218  -0.6257   2.8587  -0.6134
 1W0  C2   C  CR16  0  -0.325  -1.8311   2.2207  -0.3770
 1W0  C3   C  CR6   0   0.115  -1.8567   0.8420  -0.1629
 1W0  C9   C  CH2   0  -0.192   2.8569  -2.0206  -1.7053
 1W0  O10  O  O2    0  -0.480   2.6509  -2.8230  -0.5597
 1W0  C11  C  CH2   0  -0.180   2.9558  -2.1084   0.6074
 1W0  C12  C  CR15  0  -0.033   2.0420  -0.8904   0.8051
 1W0  O13  O  O     0  -0.474   2.7324   0.0328   1.6569
 1W0  C14  C  CR5   0   0.665   3.3696   0.8593   0.7997
 1W0  N15  N  N     0  -0.485   3.0135   0.8266  -0.4278
 1W0  N16  N  NH2   0  -0.842   4.3441   1.6050   1.3414
 1W0  C18  C  CR16  0  -0.048  -3.2279  -0.9016   1.0089
 1W0  N19  N  N     0  -0.386  -4.3664  -1.5361   1.2466
 1W0  N21  N  N     0  -0.386  -5.4587  -0.1355  -0.3088
 1W0  H1   H  HCR6  0   0.253  -0.6849  -0.9442  -0.0616
 1W0  H2   H  HCR6  0   0.252   1.4988   2.6503  -0.8124
 1W0  H3   H  HCH2  0   0.243   0.8421  -1.3516  -1.8804
 1W0  H4   H  HCH2  0   0.248   2.0025  -0.2589  -2.6107
 1W0  H5   H  HCR6  0   0.268  -6.3638  -1.6370   0.7670
 1W0  H6   H  HCR6  0   0.276  -4.3332   1.2826  -1.2813
 1W0  H7   H  HCR6  0   0.259  -0.6084   3.9287  -0.7740
 1W0  H8   H  HCR6  0   0.258  -2.7460   2.7988  -0.3395
 1W0  H9   H  HCH2  0   0.245   2.7562  -2.6685  -2.5771
 1W0  H10  H  HCH2  0   0.208   3.8768  -1.6128  -1.7083
 1W0  H11  H  HCH2  0   0.252   2.8479  -2.7912   1.4515
 1W0  H12  H  HCH2  0   0.213   4.0031  -1.7747   0.5854
 1W0  H13  H  HCR5  0   0.268   1.1078  -1.1738   1.2899
 1W0  H14  H  HNH2  0   0.406   4.4281   1.6536   2.3424
 1W0  H15  H  HNH2  0   0.405   4.6550   2.4132   0.8303
 1W0  H16  H  HCR6  0   0.275  -2.3613  -1.2272   1.5757

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
 1W0  N19  C18  aromatic  1.325  0.020  1.325
 1W0  N19  C20  aromatic  1.324  0.020  1.324
 1W0  C18  C17  aromatic  1.392  0.020  1.392
 1W0  C20  N21  aromatic  1.324  0.020  1.324
 1W0  N16  C14  single    1.341  0.020  1.341
 1W0  C17  C3   single    1.470  0.020  1.470
 1W0  C17  C22  aromatic  1.392  0.020  1.392
 1W0  N15  C14  double    1.279  0.020  1.279
 1W0  N15  C7   single    1.458  0.020  1.458
 1W0  N21  C22  aromatic  1.325  0.020  1.325
 1W0  C14  O13  single    1.351  0.020  1.351
 1W0  C3   C4   aromatic  1.393  0.020  1.393
 1W0  C3   C2   aromatic  1.395  0.020  1.395
 1W0  C4   C5   aromatic  1.392  0.020  1.392
 1W0  C2   C1   aromatic  1.384  0.020  1.384
 1W0  C5   C7   single    1.527  0.020  1.527
 1W0  C5   C6   aromatic  1.390  0.020  1.390
 1W0  C7   C8   single    1.534  0.020  1.534
 1W0  C7   C12  single    1.546  0.020  1.546
 1W0  C1   C6   aromatic  1.389  0.020  1.389
 1W0  O13  C12  single    1.433  0.020  1.433
 1W0  C8   C9   single    1.513  0.020  1.513
 1W0  C9   O10  single    1.414  0.020  1.414
 1W0  C12  C11  single    1.536  0.020  1.536
 1W0  O10  C11  single    1.402  0.020  1.402
 1W0  C4   H1   single    0.930  0.020  1.080
 1W0  C6   H2   single    0.930  0.020  1.080
 1W0  C8   H3   single    0.970  0.020  1.090
 1W0  C8   H4   single    0.970  0.020  1.090
 1W0  C20  H5   single    0.930  0.020  1.080
 1W0  C22  H6   single    0.930  0.020  1.080
 1W0  C1   H7   single    0.930  0.020  1.080
 1W0  C2   H8   single    0.930  0.020  1.080
 1W0  C9   H9   single    0.970  0.020  1.090
 1W0  C9   H10  single    0.970  0.020  1.090
 1W0  C11  H11  single    0.970  0.020  1.090
 1W0  C11  H12  single    0.970  0.020  1.090
 1W0  C12  H13  single    0.970  0.020  1.090
 1W0  N16  H14  single    0.890  0.020  1.040
 1W0  N16  H15  single    0.890  0.020  1.040
 1W0  C18  H16  single    0.930  0.020  1.080

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
 1W0  H1   C4   C3   118.82  3.000
 1W0  H1   C4   C5   119.52  3.000
 1W0  C3   C4   C5   121.66  3.000
 1W0  C7   C5   C6   121.36  3.000
 1W0  C6   C5   C4   118.45  3.000
 1W0  C7   C5   C4   120.15  3.000
 1W0  H2   C6   C1   119.92  3.000
 1W0  H2   C6   C5   119.59  3.000
 1W0  C1   C6   C5   120.49  3.000
 1W0  N15  C7   C12  101.47  3.000
 1W0  C12  C7   C8   112.65  3.000
 1W0  N15  C7   C8   111.99  3.000
 1W0  C12  C7   C5   111.30  3.000
 1W0  C8   C7   C5   108.75  3.000
 1W0  N15  C7   C5   110.58  3.000
 1W0  H4   C8   H3   106.74  3.000
 1W0  H4   C8   C9   110.73  3.000
 1W0  H3   C8   C9   108.58  3.000
 1W0  H4   C8   C7   108.62  3.000
 1W0  H3   C8   C7   109.71  3.000
 1W0  C9   C8   C7   112.31  3.000
 1W0  C18  C17  C3   122.41  3.000
 1W0  C3   C17  C22  122.56  3.000
 1W0  C18  C17  C22  115.03  3.000
 1W0  H5   C20  N21  116.96  3.000
 1W0  H5   C20  N19  116.94  3.000
 1W0  N21  C20  N19  126.10  3.000
 1W0  H6   C22  N21  116.67  3.000
 1W0  H6   C22  C17  120.59  3.000
 1W0  N21  C22  C17  122.73  3.000
 1W0  H7   C1   C2   119.67  3.000
 1W0  H7   C1   C6   119.72  3.000
 1W0  C2   C1   C6   120.60  3.000
 1W0  H8   C2   C3   120.44  3.000
 1W0  H8   C2   C1   119.71  3.000
 1W0  C3   C2   C1   119.84  3.000
 1W0  C2   C3   C17  120.71  3.000
 1W0  C2   C3   C4   118.96  3.000
 1W0  C17  C3   C4   120.34  3.000
 1W0  H10  C9   H9   107.70  3.000
 1W0  H10  C9   O10  110.38  3.000
 1W0  H9   C9   O10  107.28  3.000
 1W0  H10  C9   C8   110.85  3.000
 1W0  H9   C9   C8   110.55  3.000
 1W0  O10  C9   C8   110.00  3.000
 1W0  C11  O10  C9   110.71  3.000
 1W0  H12  C11  H11  107.44  3.000
 1W0  H12  C11  C12  109.19  3.000
 1W0  H11  C11  C12  109.76  3.000
 1W0  H12  C11  O10  110.20  3.000
 1W0  H11  C11  O10  107.67  3.000
 1W0  C12  C11  O10  112.46  3.000
 1W0  H13  C12  O13  108.41  3.000
 1W0  H13  C12  C11  111.17  3.000
 1W0  O13  C12  C11  107.50  3.000
 1W0  H13  C12  C7   113.83  3.000
 1W0  C11  C12  C7   113.48  3.000
 1W0  O13  C12  C7   101.71  3.000
 1W0  C14  O13  C12  104.14  3.000
 1W0  N16  C14  N15  127.18  3.000
 1W0  N15  C14  O13  117.54  3.000
 1W0  N16  C14  O13  115.26  3.000
 1W0  C14  N15  C7   105.72  3.000
 1W0  H15  N16  H14  116.19  3.000
 1W0  H15  N16  C14  117.79  3.000
 1W0  H14  N16  C14  119.31  3.000
 1W0  H16  C18  N19  116.66  3.000
 1W0  H16  C18  C17  120.57  3.000
 1W0  N19  C18  C17  122.76  3.000
 1W0  C18  N19  C20  116.68  3.000
 1W0  C22  N21  C20  116.69  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
 1W0  CONST_03  C1   C2   C3   C4     0.00   0.0  0
 1W0  CONST_04  C1   C6   C5   C4     0.00   0.0  0
 1W0  CONST_05  C17  C3   C4   C5   180.00   0.0  0
 1W0  CONST_06  C2   C3   C4   C5     0.00   0.0  0
 1W0  CONST_07  C2   C1   C6   C5     0.00   0.0  0
 1W0  CONST_08  C3   C4   C5   C6     0.00   0.0  0
 1W0  CONST_09  C3   C2   C1   C6     0.00   0.0  0
 1W0  CONST_10  C20  N19  C18  C17    0.00   0.0  0
 1W0  CONST_11  C1   C2   C3   C17  180.00   0.0  0
 1W0  CONST_12  C20  N21  C22  C17    0.00   0.0  0
 1W0  CONST_13  N19  C18  C17  C22    0.00   0.0  0
 1W0  CONST_15  N19  C20  N21  C22    0.00   0.0  0
 1W0  CONST_17  N19  C18  C17  C3   180.00   0.0  0
 1W0  CONST_18  N21  C22  C17  C3   180.00   0.0  0
 1W0  CONST_19  N21  C20  N19  C18    0.00   0.0  0
 1W0  CONST_20  N21  C22  C17  C18    0.00   0.0  0
 1W0  CONST_21  C3   C4   C5   C7   180.00   0.0  0
 1W0  CONST_22  C1   C6   C5   C7   180.00   0.0  0
 1W0  CONST_23  O13  C14  N15  C7     0.00   0.0  0
 1W0  CONST_24  N16  C14  N15  C7   180.00   0.0  0
 1W0  CONST_25  H8   C2   C3   C4   180.00   0.0  0
 1W0  CONST_26  H2   C6   C5   C4   180.00   0.0  0
 1W0  CONST_27  H7   C1   C6   C5   180.00   0.0  0
 1W0  CONST_28  H1   C4   C5   C6   180.00   0.0  0
 1W0  CONST_29  H16  C18  N19  C20  180.00   0.0  0
 1W0  CONST_30  H6   C22  N21  C20  180.00   0.0  0
 1W0  CONST_31  H5   C20  N21  C22  180.00   0.0  0
 1W0  CONST_32  H14  N16  C14  O13    0.00   0.0  0
 1W0  Var_01    O10  C9   C8   C7    56.33  30.0  1
 1W0  Var_02    C12  C11  O10  C9    62.87  30.0  1
 1W0  Var_03    N15  C14  O13  C12   14.06  30.0  1

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
 1W0  chir_01  C7   C5   C8  C12  positiv
 1W0  chir_02  C12  O13  C7  C11  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
 1W0  plan-1  C4   0.020
 1W0  plan-1  C5   0.020
 1W0  plan-1  C6   0.020
 1W0  plan-1  C7   0.020
 1W0  plan-1  C17  0.020
 1W0  plan-1  C1   0.020
 1W0  plan-1  C2   0.020
 1W0  plan-1  C3   0.020
 1W0  plan-1  H1   0.020
 1W0  plan-1  H2   0.020
 1W0  plan-1  H7   0.020
 1W0  plan-1  H8   0.020
 1W0  plan-2  C17  0.020
 1W0  plan-2  C20  0.020
 1W0  plan-2  C22  0.020
 1W0  plan-2  C3   0.020
 1W0  plan-2  C18  0.020
 1W0  plan-2  N19  0.020
 1W0  plan-2  N21  0.020
 1W0  plan-2  H5   0.020
 1W0  plan-2  H6   0.020
 1W0  plan-2  H16  0.020
 1W0  plan-3  C7   0.020
 1W0  plan-3  O13  0.020
 1W0  plan-3  C14  0.020
 1W0  plan-3  N15  0.020
 1W0  plan-3  N16  0.020
 1W0  plan-3  H14  0.020
 1W0  plan-3  H15  0.020

