# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 21:36:59 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: 5-[3-[bis(fluoranyl)methyl]-4-fluoranyl-phenyl]-3-[(2-methylimidazol-1-yl)methyl]pyridazine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nccn1Cc2cc(cnn2)c3ccc(F)c(c3)C(F)F
#
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
 5SM  5SM  5-[3-[bis(fluoranyl)methyl]-4-fluoranyl-phenyl]-3-[(2-methylimidazol-1-yl)methyl]pyridazine  ligand  36  23  .  2022-07-23  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_5SM
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
 5SM  N3   N  N     0  -0.248   1.4381  -1.8058   0.8318
 5SM  C4   C  CR15  0  -0.109   4.7433   1.5673   0.6606
 5SM  N2   N  NR5   0  -0.426   4.5338   0.6085  -0.2964
 5SM  C7   C  CR16  0  -0.327   0.9297   0.4900  -0.5474
 5SM  C6   C  CR6   0   0.248   2.1929  -0.0854  -0.4609
 5SM  C9   C  CR16  0  -0.121   0.2187  -1.3075   0.7895
 5SM  C13  C  CR6   0   0.563  -4.0708   1.3596   0.0527
 5SM  C8   C  CR6   0   0.104  -0.1166  -0.1378   0.0989
 5SM  C2   C  CR5   0   0.442   5.5427  -0.2930  -0.1995
 5SM  N1   N  N     0  -0.469   6.3832   0.0468   0.7468
 5SM  C3   C  CR15  0  -0.224   5.8939   1.2031   1.2900
 5SM  C5   C  CH2   0  -0.384   3.3796   0.5322  -1.1557
 5SM  N4   N  N     0  -0.259   2.4216  -1.2026   0.2083
 5SM  C10  C  CR6   0   0.090  -1.4907   0.3829   0.0825
 5SM  C11  C  CR16  0  -0.283  -1.7287   1.7568   0.0810
 5SM  C12  C  CR16  0  -0.391  -3.0203   2.2532   0.0705
 5SM  C14  C  CR6   0  -0.247  -3.8784  -0.0133   0.0548
 5SM  C15  C  CR16  0  -0.331  -2.5761  -0.4908   0.0694
 5SM  F1   F  F     0  -0.342  -5.5767  -0.9320  -1.2694
 5SM  F2   F  F     0  -0.332  -4.6950  -2.2036   0.2693
 5SM  H1   H  HCR5  0   0.288   4.0728   2.4005   0.7928
 5SM  H2   H  HCR6  0   0.286   0.7846   1.3973  -1.1200
 5SM  H3   H  HCR6  0   0.285  -0.5254  -1.8588   1.3516
 5SM  H4   H  HCH1  0   0.215  -5.8640  -0.6523   0.6851
 5SM  H5   H  HCH3  0   0.255   5.7689  -1.2148  -2.1255
 5SM  H6   H  HCH3  0   0.265   6.5389  -2.0597  -0.7855
 5SM  H7   H  HCH3  0   0.258   4.7858  -2.1337  -0.9873
 5SM  H8   H  HCR5  0   0.247   6.3971   1.7122   2.0975
 5SM  H9   H  HCH2  0   0.298   3.1288   1.5327  -1.5072
 5SM  H10  H  HCH2  0   0.306   3.6345  -0.0546  -2.0391
 5SM  H11  H  HCR6  0   0.282  -0.9027   2.4550   0.1117
 5SM  H12  H  HCR6  0   0.296  -3.2088   3.3182   0.0811
 5SM  H13  H  HCR6  0   0.284  -2.4033  -1.5585   0.0554
 5SM  F3   F  F     0  -0.297  -5.3232   1.8303   0.0416
 5SM  C16  C  CH1   0   0.542  -5.0656  -0.9274  -0.0041
 5SM  C1   C  CH3   0  -0.761   5.6600  -1.4884  -1.0742

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
 5SM  C4   C3   aromatic  1.361  0.020  1.361
 5SM  C4   N2   aromatic  1.371  0.020  1.371
 5SM  C5   N2   single    1.441  0.020  1.441
 5SM  C5   C6   single    1.508  0.020  1.508
 5SM  C3   N1   aromatic  1.368  0.020  1.368
 5SM  N2   C2   aromatic  1.356  0.020  1.356
 5SM  C6   N4   aromatic  1.322  0.020  1.322
 5SM  C6   C7   aromatic  1.391  0.020  1.391
 5SM  N4   N3   aromatic  1.311  0.020  1.311
 5SM  C7   C8   aromatic  1.381  0.020  1.381
 5SM  F2   C16  single    1.357  0.020  1.357
 5SM  N3   C9   aromatic  1.318  0.020  1.318
 5SM  C8   C9   aromatic  1.399  0.020  1.399
 5SM  C8   C10  single    1.470  0.020  1.470
 5SM  N1   C2   aromatic  1.310  0.020  1.310
 5SM  C2   C1   single    1.486  0.020  1.486
 5SM  C15  C10  aromatic  1.393  0.020  1.393
 5SM  C15  C14  aromatic  1.387  0.020  1.387
 5SM  C10  C11  aromatic  1.394  0.020  1.394
 5SM  C16  C14  single    1.499  0.020  1.499
 5SM  C16  F1   single    1.365  0.020  1.365
 5SM  C14  C13  aromatic  1.386  0.020  1.386
 5SM  C11  C12  aromatic  1.384  0.020  1.384
 5SM  C13  C12  aromatic  1.379  0.020  1.379
 5SM  C13  F3   single    1.338  0.020  1.338
 5SM  C4   H1   single    0.930  0.020  1.080
 5SM  C7   H2   single    0.930  0.020  1.080
 5SM  C9   H3   single    0.930  0.020  1.080
 5SM  C16  H4   single    0.970  0.020  1.090
 5SM  C1   H5   single    0.970  0.020  1.090
 5SM  C1   H6   single    0.970  0.020  1.090
 5SM  C1   H7   single    0.970  0.020  1.090
 5SM  C3   H8   single    0.930  0.020  1.080
 5SM  C5   H9   single    0.970  0.020  1.090
 5SM  C5   H10  single    0.970  0.020  1.090
 5SM  C11  H11  single    0.930  0.020  1.080
 5SM  C12  H12  single    0.930  0.020  1.080
 5SM  C15  H13  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
 5SM  N4   N3   C9   120.31  3.000
 5SM  H1   C4   C3   132.54  3.000
 5SM  H1   C4   N2   122.10  3.000
 5SM  C3   C4   N2   105.36  3.000
 5SM  C5   N2   C2   127.10  3.000
 5SM  C2   N2   C4   107.54  3.000
 5SM  C5   N2   C4   125.15  3.000
 5SM  H2   C7   C8   121.80  3.000
 5SM  H2   C7   C6   120.09  3.000
 5SM  C8   C7   C6   118.10  3.000
 5SM  N4   C6   C5   116.31  3.000
 5SM  N4   C6   C7   122.56  3.000
 5SM  C5   C6   C7   121.12  3.000
 5SM  H3   C9   C8   121.13  3.000
 5SM  H3   C9   N3   115.24  3.000
 5SM  C8   C9   N3   123.61  3.000
 5SM  F3   C13  C14  118.58  3.000
 5SM  F3   C13  C12  119.02  3.000
 5SM  C14  C13  C12  122.40  3.000
 5SM  C10  C8   C9   121.72  3.000
 5SM  C10  C8   C7   122.84  3.000
 5SM  C9   C8   C7   115.44  3.000
 5SM  N1   C2   C1   125.67  3.000
 5SM  C1   C2   N2   123.46  3.000
 5SM  N1   C2   N2   110.87  3.000
 5SM  C3   N1   C2   106.05  3.000
 5SM  H8   C3   N1   121.94  3.000
 5SM  H8   C3   C4   127.88  3.000
 5SM  N1   C3   C4   110.18  3.000
 5SM  H10  C5   H9   106.65  3.000
 5SM  H10  C5   C6   109.68  3.000
 5SM  H9   C5   C6   110.10  3.000
 5SM  H10  C5   N2   108.92  3.000
 5SM  H9   C5   N2   109.16  3.000
 5SM  C6   C5   N2   112.17  3.000
 5SM  C6   N4   N3   119.97  3.000
 5SM  C15  C10  C11  119.00  3.000
 5SM  C11  C10  C8   120.58  3.000
 5SM  C15  C10  C8   120.42  3.000
 5SM  H11  C11  C12  118.77  3.000
 5SM  H11  C11  C10  120.37  3.000
 5SM  C12  C11  C10  120.85  3.000
 5SM  H12  C12  C11  121.05  3.000
 5SM  H12  C12  C13  120.36  3.000
 5SM  C11  C12  C13  118.59  3.000
 5SM  C15  C14  C16  122.27  3.000
 5SM  C16  C14  C13  119.59  3.000
 5SM  C15  C14  C13  118.11  3.000
 5SM  H13  C15  C14  119.32  3.000
 5SM  H13  C15  C10  119.64  3.000
 5SM  C14  C15  C10  121.04  3.000
 5SM  H4   C16  F2   108.07  3.000
 5SM  H4   C16  F1   108.22  3.000
 5SM  F2   C16  F1   106.62  3.000
 5SM  H4   C16  C14  113.66  3.000
 5SM  F1   C16  C14  109.57  3.000
 5SM  F2   C16  C14  110.44  3.000
 5SM  H7   C1   H6   108.42  3.000
 5SM  H7   C1   H5   107.77  3.000
 5SM  H6   C1   H5   107.86  3.000
 5SM  H7   C1   C2   111.47  3.000
 5SM  H6   C1   C2   109.28  3.000
 5SM  H5   C1   C2   111.91  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
 5SM  CONST_01  C7   C6   N4   N3      0.00   0.0  0
 5SM  CONST_02  C7   C8   C9   N3      0.00   0.0  0
 5SM  CONST_03  C10  C8   C9   N3    180.00   0.0  0
 5SM  CONST_04  C2   N1   C3   C4      0.00   0.0  0
 5SM  CONST_05  N1   C2   N2   C4      0.00   0.0  0
 5SM  CONST_06  N1   C3   C4   N2      0.00   0.0  0
 5SM  CONST_07  C3   N1   C2   N2      0.00   0.0  0
 5SM  CONST_10  C9   N3   N4   C6      0.00   0.0  0
 5SM  CONST_11  C9   C8   C7   C6      0.00   0.0  0
 5SM  CONST_12  C10  C8   C7   C6    180.00   0.0  0
 5SM  CONST_15  C10  C15  C14  C13     0.00   0.0  0
 5SM  CONST_16  C10  C11  C12  C13     0.00   0.0  0
 5SM  CONST_17  N4   C6   C7   C8      0.00   0.0  0
 5SM  CONST_18  N4   N3   C9   C8      0.00   0.0  0
 5SM  CONST_19  C14  C15  C10  C8    180.00   0.0  0
 5SM  CONST_20  C12  C11  C10  C8    180.00   0.0  0
 5SM  CONST_21  C3   C4   N2   C2      0.00   0.0  0
 5SM  CONST_22  C14  C15  C10  C11     0.00   0.0  0
 5SM  CONST_23  C14  C13  C12  C11     0.00   0.0  0
 5SM  CONST_24  C15  C10  C11  C12     0.00   0.0  0
 5SM  CONST_25  C15  C14  C13  C12     0.00   0.0  0
 5SM  CONST_26  C5   C6   N4   N3    180.00   0.0  0
 5SM  CONST_27  C1   C2   N2   C4    180.00   0.0  0
 5SM  CONST_28  C5   C6   C7   C8    180.00   0.0  0
 5SM  CONST_29  C10  C15  C14  C16   180.00   0.0  0
 5SM  CONST_30  C12  C13  C14  C16   180.00   0.0  0
 5SM  CONST_31  C3   N1   C2   C1    180.00   0.0  0
 5SM  CONST_32  C5   N2   C2   N1    180.00   0.0  0
 5SM  CONST_33  C5   N2   C4   C3    180.00   0.0  0
 5SM  CONST_34  F3   C13  C12  C11   180.00   0.0  0
 5SM  CONST_35  F3   C13  C14  C15   180.00   0.0  0
 5SM  CONST_36  H8   C3   C4   N2    180.00   0.0  0
 5SM  CONST_37  H3   C9   C8   C7    180.00   0.0  0
 5SM  CONST_38  H2   C7   C8   C9    180.00   0.0  0
 5SM  CONST_39  H13  C15  C14  C13   180.00   0.0  0
 5SM  CONST_40  H11  C11  C12  C13   180.00   0.0  0
 5SM  CONST_41  H1   C4   N2   C2    180.00   0.0  0
 5SM  CONST_42  H12  C12  C11  C10   180.00   0.0  0
 5SM  Var_01    C6   C5   N2   C4    -79.95  30.0  2
 5SM  Var_02    N4   C6   C5   N2    -47.30  30.0  2
 5SM  Var_03    F2   C16  C14  C13  -168.09  30.0  2
 5SM  Var_04    H5   C1   C2   N2     61.71  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
 5SM  plan-1  C4   0.020
 5SM  plan-1  N2   0.020
 5SM  plan-1  C2   0.020
 5SM  plan-1  N1   0.020
 5SM  plan-1  C3   0.020
 5SM  plan-1  C5   0.020
 5SM  plan-1  H1   0.020
 5SM  plan-1  H8   0.020
 5SM  plan-1  C1   0.020
 5SM  plan-2  N3   0.020
 5SM  plan-2  C7   0.020
 5SM  plan-2  C6   0.020
 5SM  plan-2  C9   0.020
 5SM  plan-2  C8   0.020
 5SM  plan-2  C5   0.020
 5SM  plan-2  N4   0.020
 5SM  plan-2  C10  0.020
 5SM  plan-2  H2   0.020
 5SM  plan-2  H3   0.020
 5SM  plan-3  C13  0.020
 5SM  plan-3  C8   0.020
 5SM  plan-3  C10  0.020
 5SM  plan-3  C11  0.020
 5SM  plan-3  C12  0.020
 5SM  plan-3  C14  0.020
 5SM  plan-3  C15  0.020
 5SM  plan-3  H11  0.020
 5SM  plan-3  H12  0.020
 5SM  plan-3  H13  0.020
 5SM  plan-3  F3   0.020
 5SM  plan-3  C16  0.020

