# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 21:20:59 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: 4-[3-(4-chlorophenyl)-2,1-benzisoxazol-5-yl]pyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nccc(n1)c2ccc3noc(c4ccc(Cl)cc4)c3c2
#
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
 VX1  VX1  4-[3-(4-chlorophenyl)-2,1-benzisoxazol-5-yl]pyrimidin-2-amine  ligand  34  23  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_VX1
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
 VX1  N1    N   NH2   0  -0.823   3.3593   3.7149   0.5071
 VX1  C2    C   CR6   0   0.544   3.8217   2.4841   0.2129
 VX1  N3    N   N     0  -0.453   5.1264   2.3730  -0.0717
 VX1  C4    C   CR16  0  -0.018   5.5549   1.1503  -0.3267
 VX1  C5    C   CR16  0  -0.404   4.7380   0.0313  -0.3061
 VX1  C6    C   CR6   0   0.304   3.3984   0.2523   0.0048
 VX1  N7    N   N     0  -0.493   2.9512   1.4766   0.2607
 VX1  C8    C   CR6   0   0.037   2.4014  -0.8375   0.0472
 VX1  C9    C   CR16  0  -0.300   2.8246  -2.2116   0.0918
 VX1  C10   C   CR16  0  -0.275   1.9545  -3.2524   0.1019
 VX1  C11   C   CR56  0   0.227   0.5658  -2.9478   0.0696
 VX1  N12   N   N     0  -0.182  -0.4488  -3.7815   0.0446
 VX1  O13   O   O     0  -0.327  -1.5532  -2.9862   0.0154
 VX1  C14   C   CR5   0   0.465  -1.2419  -1.6977   0.0232
 VX1  C15   C   CR6   0   0.013  -2.3273  -0.7360  -0.0160
 VX1  C16   C   CR16  0  -0.278  -3.5645  -1.0741  -0.5708
 VX1  C17   C   CR16  0  -0.197  -4.5922  -0.1494  -0.6141
 VX1  C18   C   CR6   0  -0.043  -4.3853   1.1218  -0.0985
 VX1  CL19  CL  CL    0  -0.110  -5.6668   2.2793  -0.1536
 VX1  C20   C   CR16  0  -0.188  -3.1687   1.4774   0.4637
 VX1  C21   C   CR16  0  -0.319  -2.1460   0.5463   0.5049
 VX1  C22   C   CR56  0  -0.102   0.1335  -1.5906   0.0552
 VX1  C23   C   CR16  0  -0.358   1.0680  -0.5324   0.0344
 VX1  HN1   H   HNH2  0   0.396   3.9337   4.5104   0.2889
 VX1  HN1A  H   HNH2  0   0.396   2.3655   3.8635   0.5346
 VX1  H4    H   HCR6  0   0.273   6.6082   1.0478  -0.5655
 VX1  H5    H   HCR6  0   0.269   5.1407  -0.9404  -0.5447
 VX1  H9    H   HCR6  0   0.267   3.8825  -2.4318   0.1314
 VX1  H10   H   HCR6  0   0.277   2.2980  -4.2770   0.1361
 VX1  H16   H   HCR6  0   0.278  -3.7331  -2.0573  -0.9888
 VX1  H17   H   HCR6  0   0.291  -5.5437  -0.4180  -1.0515
 VX1  H20   H   HCR6  0   0.291  -3.0187   2.4653   0.8765
 VX1  H21   H   HCR6  0   0.275  -1.2132   0.8255   0.9750
 VX1  H23   H   HCR6  0   0.268   0.7495   0.4996  -0.0100

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
 VX1  N1   C2    single    1.347  0.020  1.347
 VX1  C2   N3    aromatic  1.340  0.020  1.340
 VX1  C2   N7    aromatic  1.332  0.020  1.332
 VX1  N3   C4    aromatic  1.320  0.020  1.320
 VX1  C4   C5    aromatic  1.386  0.020  1.386
 VX1  C5   C6    aromatic  1.393  0.020  1.393
 VX1  C6   N7    aromatic  1.328  0.020  1.328
 VX1  C6   C8    single    1.478  0.020  1.478
 VX1  C8   C9    aromatic  1.438  0.020  1.438
 VX1  C8   C23   aromatic  1.368  0.020  1.368
 VX1  C9   C10   aromatic  1.357  0.020  1.357
 VX1  C10  C11   aromatic  1.422  0.020  1.422
 VX1  C11  N12   aromatic  1.313  0.020  1.313
 VX1  C11  C22   aromatic  1.424  0.020  1.424
 VX1  N12  O13   aromatic  1.361  0.020  1.361
 VX1  O13  C14   aromatic  1.326  0.020  1.326
 VX1  C14  C15   single    1.451  0.020  1.451
 VX1  C14  C22   aromatic  1.380  0.020  1.380
 VX1  C15  C16   aromatic  1.397  0.020  1.397
 VX1  C15  C21   aromatic  1.396  0.020  1.396
 VX1  C16  C17   aromatic  1.383  0.020  1.383
 VX1  C17  C18   aromatic  1.387  0.020  1.387
 VX1  C18  CL19  single    1.728  0.020  1.728
 VX1  C18  C20   aromatic  1.387  0.020  1.387
 VX1  C20  C21   aromatic  1.384  0.020  1.384
 VX1  C22  C23   aromatic  1.412  0.020  1.412
 VX1  N1   HN1   single    0.890  0.020  1.040
 VX1  N1   HN1A  single    0.890  0.020  1.040
 VX1  C4   H4    single    0.930  0.020  1.080
 VX1  C5   H5    single    0.930  0.020  1.080
 VX1  C9   H9    single    0.930  0.020  1.080
 VX1  C10  H10   single    0.930  0.020  1.080
 VX1  C16  H16   single    0.930  0.020  1.080
 VX1  C17  H17   single    0.930  0.020  1.080
 VX1  C20  H20   single    0.930  0.020  1.080
 VX1  C21  H21   single    0.930  0.020  1.080
 VX1  C23  H23   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
 VX1  HN1A  N1   HN1   117.00  3.000
 VX1  HN1A  N1   C2    118.70  3.000
 VX1  HN1   N1   C2    118.64  3.000
 VX1  N7    C2   N3    125.53  3.000
 VX1  N7    C2   N1    117.30  3.000
 VX1  N3    C2   N1    117.15  3.000
 VX1  C4    N3   C2    115.71  3.000
 VX1  H4    C4   C5    119.96  3.000
 VX1  H4    C4   N3    116.43  3.000
 VX1  C5    C4   N3    123.61  3.000
 VX1  H5    C5   C6    123.47  3.000
 VX1  H5    C5   C4    120.28  3.000
 VX1  C6    C5   C4    116.24  3.000
 VX1  C8    C6   N7    116.55  3.000
 VX1  C8    C6   C5    122.57  3.000
 VX1  N7    C6   C5    120.87  3.000
 VX1  C6    N7   C2    118.04  3.000
 VX1  C23   C8   C9    120.01  3.000
 VX1  C23   C8   C6    119.53  3.000
 VX1  C9    C8   C6    120.46  3.000
 VX1  H9    C9   C10   118.10  3.000
 VX1  H9    C9   C8    118.91  3.000
 VX1  C10   C9   C8    122.98  3.000
 VX1  H10   C10  C11   120.92  3.000
 VX1  H10   C10  C9    121.57  3.000
 VX1  C11   C10  C9    117.51  3.000
 VX1  C22   C11  N12   111.72  3.000
 VX1  C22   C11  C10   120.04  3.000
 VX1  N12   C11  C10   128.24  3.000
 VX1  O13   N12  C11   104.85  3.000
 VX1  C14   O13  N12   112.16  3.000
 VX1  C22   C14  C15   134.02  3.000
 VX1  C22   C14  O13   108.04  3.000
 VX1  C15   C14  O13   117.94  3.000
 VX1  C21   C15  C16   119.04  3.000
 VX1  C21   C15  C14   120.11  3.000
 VX1  C16   C15  C14   120.85  3.000
 VX1  H16   C16  C17   118.68  3.000
 VX1  H16   C16  C15   120.75  3.000
 VX1  C17   C16  C15   120.56  3.000
 VX1  H17   C17  C18   120.62  3.000
 VX1  H17   C17  C16   120.03  3.000
 VX1  C18   C17  C16   119.35  3.000
 VX1  C20   C18  CL19  119.46  3.000
 VX1  C20   C18  C17   121.10  3.000
 VX1  CL19  C18  C17   119.43  3.000
 VX1  H20   C20  C21   120.07  3.000
 VX1  H20   C20  C18   120.72  3.000
 VX1  C21   C20  C18   119.21  3.000
 VX1  H21   C21  C20   118.48  3.000
 VX1  H21   C21  C15   120.76  3.000
 VX1  C20   C21  C15   120.74  3.000
 VX1  C23   C22  C14   135.85  3.000
 VX1  C23   C22  C11   120.89  3.000
 VX1  C14   C22  C11   103.22  3.000
 VX1  H23   C23  C22   121.41  3.000
 VX1  H23   C23  C8    120.04  3.000
 VX1  C22   C23  C8    118.54  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
 VX1  CONST_01  C5    C4   N3   C2      0.00  0.0  0
 VX1  CONST_02  C5    C6   N7   C2      0.00  0.0  0
 VX1  CONST_03  C8    C6   N7   C2    180.00  0.0  0
 VX1  CONST_04  C6    N7   C2   N3      0.00  0.0  0
 VX1  CONST_05  C6    C5   C4   N3      0.00  0.0  0
 VX1  CONST_06  N7    C2   N3   C4      0.00  0.0  0
 VX1  CONST_07  N7    C6   C5   C4      0.00  0.0  0
 VX1  CONST_08  C8    C6   C5   C4    180.00  0.0  0
 VX1  CONST_11  C10   C9   C8   C6    180.00  0.0  0
 VX1  CONST_12  C22   C23  C8   C6    180.00  0.0  0
 VX1  CONST_13  C9    C8   C6   N7    180.00  0.0  0
 VX1  CONST_14  C23   C8   C6   N7      0.00  0.0  0
 VX1  CONST_15  C11   C10  C9   C8      0.00  0.0  0
 VX1  CONST_16  C11   C22  C23  C8      0.00  0.0  0
 VX1  CONST_17  C14   C22  C23  C8    180.00  0.0  0
 VX1  CONST_18  C22   C23  C8   C9      0.00  0.0  0
 VX1  CONST_19  N12   C11  C10  C9    180.00  0.0  0
 VX1  CONST_20  C22   C11  C10  C9      0.00  0.0  0
 VX1  CONST_21  C23   C8   C9   C10     0.00  0.0  0
 VX1  CONST_22  O13   N12  C11  C10   180.00  0.0  0
 VX1  CONST_23  C14   C22  C11  C10   180.00  0.0  0
 VX1  CONST_24  C23   C22  C11  C10     0.00  0.0  0
 VX1  CONST_25  C14   O13  N12  C11     0.00  0.0  0
 VX1  CONST_26  O13   C14  C22  C11     0.00  0.0  0
 VX1  CONST_27  C15   C14  C22  C11   180.00  0.0  0
 VX1  CONST_28  C14   C22  C11  N12     0.00  0.0  0
 VX1  CONST_29  C23   C22  C11  N12   180.00  0.0  0
 VX1  CONST_30  C15   C14  O13  N12   180.00  0.0  0
 VX1  CONST_31  C22   C14  O13  N12     0.00  0.0  0
 VX1  CONST_32  C22   C11  N12  O13     0.00  0.0  0
 VX1  CONST_35  C23   C22  C14  O13   180.00  0.0  0
 VX1  CONST_36  C17   C16  C15  C14   180.00  0.0  0
 VX1  CONST_37  C20   C21  C15  C14   180.00  0.0  0
 VX1  CONST_38  C23   C22  C14  C15     0.00  0.0  0
 VX1  CONST_39  C18   C17  C16  C15     0.00  0.0  0
 VX1  CONST_40  C18   C20  C21  C15     0.00  0.0  0
 VX1  CONST_42  C20   C21  C15  C16     0.00  0.0  0
 VX1  CONST_43  C20   C18  C17  C16     0.00  0.0  0
 VX1  CONST_44  C21   C15  C16  C17     0.00  0.0  0
 VX1  CONST_45  C21   C20  C18  C17     0.00  0.0  0
 VX1  CONST_47  C4    N3   C2   N1    180.00  0.0  0
 VX1  CONST_48  C6    N7   C2   N1    180.00  0.0  0
 VX1  CONST_49  CL19  C18  C17  C16   180.00  0.0  0
 VX1  CONST_50  C21   C20  C18  CL19  180.00  0.0  0
 VX1  CONST_51  H4    C4   N3   C2    180.00  0.0  0
 VX1  CONST_52  H5    C5   C4   N3    180.00  0.0  0
 VX1  CONST_53  H9    C9   C8   C6      0.00  0.0  0
 VX1  CONST_54  H23   C23  C8   C6      0.00  0.0  0
 VX1  CONST_55  H10   C10  C9   C8    180.00  0.0  0
 VX1  CONST_56  H16   C16  C15  C14     0.00  0.0  0
 VX1  CONST_57  H21   C21  C15  C14     0.00  0.0  0
 VX1  CONST_58  H17   C17  C16  C15   180.00  0.0  0
 VX1  CONST_59  H20   C20  C21  C15   180.00  0.0  0
 VX1  CONST_60  HN1   N1   C2   N3      0.00  0.0  0
 VX1  CONST_61  HN1A  N1   C2   N3    180.00  0.0  0

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
 VX1  plan-1  N1    0.020
 VX1  plan-1  C2    0.020
 VX1  plan-1  N3    0.020
 VX1  plan-1  C4    0.020
 VX1  plan-1  C5    0.020
 VX1  plan-1  C6    0.020
 VX1  plan-1  N7    0.020
 VX1  plan-1  C8    0.020
 VX1  plan-1  H4    0.020
 VX1  plan-1  H5    0.020
 VX1  plan-2  C14   0.020
 VX1  plan-2  C15   0.020
 VX1  plan-2  C16   0.020
 VX1  plan-2  C17   0.020
 VX1  plan-2  C18   0.020
 VX1  plan-2  CL19  0.020
 VX1  plan-2  C20   0.020
 VX1  plan-2  C21   0.020
 VX1  plan-2  H16   0.020
 VX1  plan-2  H17   0.020
 VX1  plan-2  H20   0.020
 VX1  plan-2  H21   0.020
 VX1  plan-3  C6    0.020
 VX1  plan-3  C8    0.020
 VX1  plan-3  C9    0.020
 VX1  plan-3  C10   0.020
 VX1  plan-3  C11   0.020
 VX1  plan-3  N12   0.020
 VX1  plan-3  O13   0.020
 VX1  plan-3  C14   0.020
 VX1  plan-3  C15   0.020
 VX1  plan-3  C22   0.020
 VX1  plan-3  C23   0.020
 VX1  plan-3  H9    0.020
 VX1  plan-3  H10   0.020
 VX1  plan-3  H23   0.020
 VX1  plan-4  N1    0.020
 VX1  plan-4  C2    0.020
 VX1  plan-4  HN1   0.020
 VX1  plan-4  HN1A  0.020

