# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 10:38:25 2022
#   Inital geometry file: a 131 line input string
#   Ligand name: (6R,7S)-6,7-bis(4-bromophenyl)-7,11-dihydro-6H-chromeno[4,3-d][1,2,4]triazolo[1,5-a]pyrimidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Brc1ccc(cc1)[C@H]2Oc3ccccc3C4=C2[C@@H](N5N=CNC5=N4)c6ccc(Br)cc6
#
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
 YIN  YIN  (6R,7S)-6,7-bis(4-bromophenyl)-7,11-dihydro-6H-chromeno[4,3-d][1,2,4]triazolo[1,5-a]pyrimidine  ligand  47  31  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_YIN
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
 YIN  C1   C   CR6   0   0.143  -0.2437  -1.9979   0.6348
 YIN  N1   N   NR5   0  -0.405  -2.4060  -2.7599  -0.2430
 YIN  O1   O   O     0  -0.476  -2.6281   1.4838   1.9016
 YIN  BR1  BR  BR    0  -0.050   4.3837  -1.5502   0.3938
 YIN  C2   C   CR16  0  -0.315   0.5497  -2.3370   1.7188
 YIN  N2   N   NR15  0  -0.678  -3.7364  -3.3947  -1.7789
 YIN  C3   C   CR16  0  -0.214   1.9331  -2.2263   1.6547
 YIN  N3   N   N     0  -0.569  -3.9401  -1.1293  -1.0475
 YIN  C4   C   CR6   0  -0.110   2.5111  -1.7723   0.4821
 YIN  N4   N   N     0  -0.240  -2.1121  -4.0664  -0.4688
 YIN  C5   C   CR16  0  -0.199   1.7374  -1.4566  -0.6276
 YIN  C6   C   CR16  0  -0.263   0.3622  -1.5770  -0.5434
 YIN  C7   C   CR16  0  -0.131  -1.6973   0.4617   1.5520
 YIN  C8   C   CR15  0   0.117  -2.9259  -4.4199  -1.4019
 YIN  C9   C   CR6   0  -0.049  -2.3201  -0.5860   0.6773
 YIN  C10  C   CH1   0  -0.111  -1.7502  -1.9806   0.7822
 YIN  C11  C   CR5   0   0.746  -3.4111  -2.3121  -1.0256
 YIN  C12  C   CR6   0   0.234  -3.3321  -0.2670  -0.1590
 YIN  C13  C   CR16  0  -0.310  -4.7340   1.6052  -1.0722
 YIN  C14  C   CR16  0  -0.262  -5.2279   2.8976  -0.9737
 YIN  C15  C   CR16  0  -0.258  -4.8422   3.7013   0.0918
 YIN  C16  C   CR16  0  -0.350  -3.9569   3.2230   1.0478
 YIN  C17  C   CR66  0   0.331  -3.4597   1.9320   0.9358
 YIN  C18  C   CR66  0  -0.072  -3.8471   1.1050  -0.1230
 YIN  C19  C   CR16  0  -0.284  -0.4133   1.5686  -0.3457
 YIN  C20  C   CR6   0   0.159  -0.4412   1.0688   0.9539
 YIN  C21  C   CR16  0  -0.296   0.7262   1.1053   1.7038
 YIN  C22  C   CR16  0  -0.206   1.9106   1.5985   1.1748
 YIN  C23  C   CR6   0  -0.116   1.9102   2.0861  -0.1206
 YIN  C24  C   CR16  0  -0.214   0.7520   2.0876  -0.8853
 YIN  H2   H   HCR6  0   0.264   0.0900  -2.6756   2.6397
 YIN  H3   H   HCR6  0   0.278   2.5350  -2.4821   2.5162
 YIN  H5   H   HCR6  0   0.276   2.1918  -1.1004  -1.5420
 YIN  H6   H   HCR6  0   0.264  -0.2402  -1.3049  -1.4017
 YIN  H8   H   HCR5  0   0.318  -2.9748  -5.4022  -1.8413
 YIN  H13  H   HCR6  0   0.253  -5.0416   0.9664  -1.8894
 YIN  H14  H   HCR6  0   0.253  -5.9122   3.2748  -1.7218
 YIN  H15  H   HCR6  0   0.259  -5.2227   4.7106   0.1792
 YIN  H16  H   HCR6  0   0.264  -3.6477   3.8463   1.8773
 YIN  H19  H   HCR6  0   0.267  -1.2945   1.5306  -0.9728
 YIN  H21  H   HCR6  0   0.261   0.7274   0.7191   2.7156
 YIN  H22  H   HCR6  0   0.275   2.8124   1.5873   1.7717
 YIN  H24  H   HCR6  0   0.276   0.7528   2.4647  -1.8992
 YIN  HN2  H   HNR5  0   0.441  -4.4520  -3.4168  -2.4890
 YIN  H10  H   HCH1  0   0.284  -1.9886  -2.4113   1.7661
 YIN  H7   H   HCR6  0   0.271  -1.4195   0.0087   2.5100
 YIN  BR2  BR  BR    0  -0.054   3.5179   2.7361  -0.8698

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
 YIN  C1   C2   aromatic  1.385  0.020  1.385
 YIN  C1   C6   aromatic  1.390  0.020  1.390
 YIN  C1   C10  single    1.514  0.020  1.514
 YIN  N1   N4   single    1.358  0.020  1.358
 YIN  N1   C10  single    1.445  0.020  1.445
 YIN  N1   C11  single    1.350  0.020  1.350
 YIN  O1   C7   single    1.426  0.020  1.426
 YIN  O1   C17  single    1.351  0.020  1.351
 YIN  BR1  C4   single    1.888  0.020  1.888
 YIN  C2   C3   aromatic  1.389  0.020  1.389
 YIN  C2   H2   single    0.930  0.020  1.080
 YIN  N2   C8   single    1.360  0.020  1.360
 YIN  N2   C11  single    1.358  0.020  1.358
 YIN  BR2  C23  single    1.889  0.020  1.889
 YIN  C3   C4   aromatic  1.384  0.020  1.384
 YIN  C3   H3   single    0.930  0.020  1.080
 YIN  N3   C11  double    1.296  0.020  1.296
 YIN  N3   C12  single    1.379  0.020  1.379
 YIN  C4   C5   aromatic  1.389  0.020  1.389
 YIN  N4   C8   double    1.288  0.020  1.288
 YIN  C5   C6   aromatic  1.383  0.020  1.383
 YIN  C5   H5   single    0.930  0.020  1.080
 YIN  C6   H6   single    0.930  0.020  1.080
 YIN  C7   C9   single    1.500  0.020  1.500
 YIN  C7   C20  single    1.518  0.020  1.518
 YIN  C7   H7   single    0.970  0.020  1.090
 YIN  C8   H8   single    0.930  0.020  1.080
 YIN  C9   C10  single    1.510  0.020  1.510
 YIN  C9   C12  double    1.351  0.020  1.351
 YIN  C12  C18  single    1.466  0.020  1.466
 YIN  C13  C14  aromatic  1.387  0.020  1.387
 YIN  C13  C18  aromatic  1.392  0.020  1.392
 YIN  C13  H13  single    0.930  0.020  1.080
 YIN  C14  C15  aromatic  1.389  0.020  1.389
 YIN  C14  H14  single    0.930  0.020  1.080
 YIN  C15  C16  aromatic  1.388  0.020  1.388
 YIN  C15  H15  single    0.930  0.020  1.080
 YIN  C16  C17  aromatic  1.388  0.020  1.388
 YIN  C16  H16  single    0.930  0.020  1.080
 YIN  C17  C18  aromatic  1.398  0.020  1.398
 YIN  C19  C20  aromatic  1.393  0.020  1.393
 YIN  C19  C24  aromatic  1.385  0.020  1.385
 YIN  C19  H19  single    0.930  0.020  1.080
 YIN  C20  C21  aromatic  1.388  0.020  1.388
 YIN  C21  C22  aromatic  1.388  0.020  1.388
 YIN  C21  H21  single    0.930  0.020  1.080
 YIN  C22  C23  aromatic  1.384  0.020  1.384
 YIN  C22  H22  single    0.930  0.020  1.080
 YIN  C23  C24  aromatic  1.388  0.020  1.388
 YIN  C24  H24  single    0.930  0.020  1.080
 YIN  N2   HN2  single    0.860  0.020  1.020
 YIN  C10  H10  single    0.970  0.020  1.090

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
 YIN  C10  C1   C6   120.85  3.000
 YIN  C10  C1   C2   119.77  3.000
 YIN  C6   C1   C2   119.18  3.000
 YIN  C11  N1   C10  124.76  3.000
 YIN  C11  N1   N4   112.57  3.000
 YIN  C10  N1   N4   122.58  3.000
 YIN  C17  O1   C7   117.67  3.000
 YIN  H2   C2   C3   119.11  3.000
 YIN  H2   C2   C1   119.90  3.000
 YIN  C3   C2   C1   120.97  3.000
 YIN  HN2  N2   C11  125.31  3.000
 YIN  HN2  N2   C8   126.98  3.000
 YIN  C11  N2   C8   107.72  3.000
 YIN  H3   C3   C4   121.34  3.000
 YIN  H3   C3   C2   119.90  3.000
 YIN  C4   C3   C2   118.76  3.000
 YIN  C12  N3   C11  112.32  3.000
 YIN  C5   C4   C3   121.25  3.000
 YIN  C5   C4   BR1  119.23  3.000
 YIN  C3   C4   BR1  119.51  3.000
 YIN  C8   N4   N1   104.35  3.000
 YIN  H5   C5   C6   119.86  3.000
 YIN  H5   C5   C4   121.09  3.000
 YIN  C6   C5   C4   119.04  3.000
 YIN  H6   C6   C5   118.87  3.000
 YIN  H6   C6   C1   120.34  3.000
 YIN  C5   C6   C1   120.76  3.000
 YIN  H7   C7   C20  107.46  3.000
 YIN  H7   C7   C9   109.05  3.000
 YIN  C20  C7   C9   113.15  3.000
 YIN  H7   C7   O1   104.33  3.000
 YIN  C20  C7   O1   110.49  3.000
 YIN  C9   C7   O1   111.87  3.000
 YIN  H8   C8   N4   125.07  3.000
 YIN  H8   C8   N2   123.18  3.000
 YIN  N4   C8   N2   111.75  3.000
 YIN  C12  C9   C10  122.94  3.000
 YIN  C12  C9   C7   120.46  3.000
 YIN  C10  C9   C7   116.60  3.000
 YIN  H10  C10  C9   109.99  3.000
 YIN  H10  C10  N1   108.97  3.000
 YIN  C9   C10  N1   106.11  3.000
 YIN  H10  C10  C1   107.35  3.000
 YIN  C9   C10  C1   112.30  3.000
 YIN  N1   C10  C1   112.10  3.000
 YIN  N3   C11  N2   128.33  3.000
 YIN  N3   C11  N1   128.05  3.000
 YIN  N2   C11  N1   103.62  3.000
 YIN  C18  C12  C9   117.97  3.000
 YIN  C18  C12  N3   116.49  3.000
 YIN  C9   C12  N3   125.54  3.000
 YIN  H13  C13  C18  118.95  3.000
 YIN  H13  C13  C14  120.17  3.000
 YIN  C18  C13  C14  120.88  3.000
 YIN  H14  C14  C15  120.28  3.000
 YIN  H14  C14  C13  120.07  3.000
 YIN  C15  C14  C13  119.65  3.000
 YIN  H15  C15  C16  119.34  3.000
 YIN  H15  C15  C14  120.26  3.000
 YIN  C16  C15  C14  120.40  3.000
 YIN  H16  C16  C17  119.67  3.000
 YIN  H16  C16  C15  120.76  3.000
 YIN  C17  C16  C15  119.57  3.000
 YIN  C18  C17  C16  120.80  3.000
 YIN  C18  C17  O1   121.04  3.000
 YIN  C16  C17  O1   118.12  3.000
 YIN  C17  C18  C13  118.71  3.000
 YIN  C17  C18  C12  118.35  3.000
 YIN  C13  C18  C12  122.91  3.000
 YIN  H19  C19  C24  118.20  3.000
 YIN  H19  C19  C20  120.78  3.000
 YIN  C24  C19  C20  120.99  3.000
 YIN  C21  C20  C19  118.55  3.000
 YIN  C21  C20  C7   119.58  3.000
 YIN  C19  C20  C7   121.86  3.000
 YIN  H21  C21  C22  118.81  3.000
 YIN  H21  C21  C20  119.76  3.000
 YIN  C22  C21  C20  121.41  3.000
 YIN  H22  C22  C23  121.36  3.000
 YIN  H22  C22  C21  119.84  3.000
 YIN  C23  C22  C21  118.80  3.000
 YIN  C24  C23  C22  121.08  3.000
 YIN  C24  C23  BR2  119.43  3.000
 YIN  C22  C23  BR2  119.48  3.000
 YIN  H24  C24  C23  121.08  3.000
 YIN  H24  C24  C19  119.76  3.000
 YIN  C23  C24  C19  119.15  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
 YIN  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 YIN  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 YIN  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 YIN  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 YIN  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 YIN  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 YIN  CONST_07  C16  C15  C14  C13     0.00   0.0  0
 YIN  CONST_08  C16  C17  C18  C13     0.00   0.0  0
 YIN  CONST_09  C17  C18  C13  C14     0.00   0.0  0
 YIN  CONST_10  C17  C16  C15  C14     0.00   0.0  0
 YIN  CONST_11  C18  C13  C14  C15     0.00   0.0  0
 YIN  CONST_12  C18  C17  C16  C15     0.00   0.0  0
 YIN  CONST_13  C22  C21  C20  C19     0.00   0.0  0
 YIN  CONST_14  C22  C23  C24  C19     0.00   0.0  0
 YIN  CONST_15  C23  C24  C19  C20     0.00   0.0  0
 YIN  CONST_16  C23  C22  C21  C20     0.00   0.0  0
 YIN  CONST_17  C24  C19  C20  C21     0.00   0.0  0
 YIN  CONST_18  C24  C23  C22  C21     0.00   0.0  0
 YIN  CONST_19  C10  C1   C2   C3    180.00   0.0  0
 YIN  CONST_20  C10  C1   C6   C5    180.00   0.0  0
 YIN  CONST_21  C24  C19  C20  C7    180.00   0.0  0
 YIN  CONST_22  C22  C21  C20  C7    180.00   0.0  0
 YIN  CONST_23  N2   C8   N4   N1      0.00   0.0  0
 YIN  CONST_24  C8   N2   C11  N1      0.00   0.0  0
 YIN  CONST_25  C12  N3   C11  N1      0.00   0.0  0
 YIN  CONST_26  N4   N1   C11  N2      0.00   0.0  0
 YIN  CONST_27  C10  N1   C11  N2    180.00   0.0  0
 YIN  CONST_28  C12  N3   C11  N2    180.00   0.0  0
 YIN  CONST_29  N4   N1   C11  N3    180.00   0.0  0
 YIN  CONST_30  C10  N1   C11  N3      0.00   0.0  0
 YIN  CONST_31  C8   N2   C11  N3    180.00   0.0  0
 YIN  CONST_32  C11  N2   C8   N4      0.00   0.0  0
 YIN  CONST_33  C10  N1   N4   C8    180.00   0.0  0
 YIN  CONST_34  C11  N1   N4   C8      0.00   0.0  0
 YIN  CONST_35  C2   C3   C4   BR1   180.00   0.0  0
 YIN  CONST_36  C6   C5   C4   BR1   180.00   0.0  0
 YIN  CONST_37  C21  C22  C23  BR2   180.00   0.0  0
 YIN  CONST_38  C19  C24  C23  BR2   180.00   0.0  0
 YIN  CONST_39  H3   C3   C2   C1    180.00   0.0  0
 YIN  CONST_40  H5   C5   C6   C1    180.00   0.0  0
 YIN  CONST_41  H16  C16  C17  O1      0.00   0.0  0
 YIN  CONST_42  H6   C6   C1   C2    180.00   0.0  0
 YIN  CONST_43  H2   C2   C3   C4    180.00   0.0  0
 YIN  CONST_44  H19  C19  C20  C7      0.00   0.0  0
 YIN  CONST_45  H21  C21  C20  C7      0.00   0.0  0
 YIN  CONST_46  H13  C13  C18  C12     0.00   0.0  0
 YIN  CONST_47  H15  C15  C14  C13   180.00   0.0  0
 YIN  CONST_48  H14  C14  C15  C16   180.00   0.0  0
 YIN  CONST_49  H24  C24  C19  C20   180.00   0.0  0
 YIN  CONST_50  H22  C22  C21  C20   180.00   0.0  0
 YIN  CONST_51  H8   C8   N4   N1    180.00   0.0  0
 YIN  CONST_52  HN2  N2   C11  N1    180.00   0.0  0
 YIN  Var_01    C7   C9   C12  N3    177.02  30.0  1
 YIN  Var_02    C13  C18  C12  N3    -10.89  30.0  1
 YIN  Var_03    C16  C17  O1   C7   -153.90  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
 YIN  chir_01  C7   O1  C9  C20  negativ
 YIN  chir_02  C10  N1  C9  C1   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
 YIN  plan-1  C1   0.020
 YIN  plan-1  BR1  0.020
 YIN  plan-1  C2   0.020
 YIN  plan-1  C3   0.020
 YIN  plan-1  C4   0.020
 YIN  plan-1  C5   0.020
 YIN  plan-1  C6   0.020
 YIN  plan-1  C10  0.020
 YIN  plan-1  H2   0.020
 YIN  plan-1  H3   0.020
 YIN  plan-1  H5   0.020
 YIN  plan-1  H6   0.020
 YIN  plan-2  C7   0.020
 YIN  plan-2  C19  0.020
 YIN  plan-2  C20  0.020
 YIN  plan-2  C21  0.020
 YIN  plan-2  C22  0.020
 YIN  plan-2  C23  0.020
 YIN  plan-2  C24  0.020
 YIN  plan-2  H19  0.020
 YIN  plan-2  H21  0.020
 YIN  plan-2  H22  0.020
 YIN  plan-2  H24  0.020
 YIN  plan-2  BR2  0.020
 YIN  plan-3  O1   0.020
 YIN  plan-3  C12  0.020
 YIN  plan-3  C13  0.020
 YIN  plan-3  C14  0.020
 YIN  plan-3  C15  0.020
 YIN  plan-3  C16  0.020
 YIN  plan-3  C17  0.020
 YIN  plan-3  C18  0.020
 YIN  plan-3  H13  0.020
 YIN  plan-3  H14  0.020
 YIN  plan-3  H15  0.020
 YIN  plan-3  H16  0.020
 YIN  plan-4  N1   0.020
 YIN  plan-4  N2   0.020
 YIN  plan-4  N3   0.020
 YIN  plan-4  N4   0.020
 YIN  plan-4  C8   0.020
 YIN  plan-4  C10  0.020
 YIN  plan-4  C11  0.020
 YIN  plan-4  C12  0.020
 YIN  plan-4  H8   0.020
 YIN  plan-4  HN2  0.020

