FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 5J31Z

Calculation Name: 1YQF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YQF

Chain ID: A

ChEMBL ID:

UniProt ID: Q4Q7K6

Base Structure: X-ray

Registration Date: 2023-09-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 182
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1816520.5146
FMO2-HF: Nuclear repulsion 1743607.214482
FMO2-HF: Total energy -72913.300118
FMO2-MP2: Total energy -73124.739658


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:14:ALA)


Summations of interaction energy for fragment #1(A:14:ALA)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-9.968-3.3013.422-4.616-5.474-0.035
Interaction energy analysis for fragmet #1(A:14:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.024 / q_NPA : 0.016
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A16ASP-1-0.853-0.9202.645-11.694-5.5971.612-3.717-3.993-0.033
4A17ALA00.0750.0302.3340.9221.1751.807-0.786-1.274-0.002
5A18ALA0-0.027-0.0144.1040.9481.2650.003-0.113-0.2070.000
6A19LEU00.0140.0136.1490.7360.7360.0000.0000.0000.000
7A20ALA00.0230.0247.1170.4260.4260.0000.0000.0000.000
8A21ASP-1-0.776-0.8707.888-0.552-0.5520.0000.0000.0000.000
9A22ALA0-0.037-0.0169.6490.2000.2000.0000.0000.0000.000
10A23THR00.026-0.01611.3120.1670.1670.0000.0000.0000.000
11A24ARG10.7510.86011.7550.6560.6560.0000.0000.0000.000
12A25ARG10.8410.90011.0930.8360.8360.0000.0000.0000.000
13A26GLU-1-0.870-0.92615.931-0.415-0.4150.0000.0000.0000.000
14A27LEU0-0.007-0.00317.1440.0540.0540.0000.0000.0000.000
15A28GLU-1-0.903-0.94316.609-0.363-0.3630.0000.0000.0000.000
16A29GLU-1-0.974-0.98519.847-0.287-0.2870.0000.0000.0000.000
17A30GLU-1-0.730-0.85321.635-0.231-0.2310.0000.0000.0000.000
18A31MET0-0.100-0.03722.6840.0370.0370.0000.0000.0000.000
19A32GLY0-0.035-0.00924.2130.0210.0210.0000.0000.0000.000
20A33ARG10.7420.83825.9490.2310.2310.0000.0000.0000.000
21A34SER0-0.056-0.03328.0190.0050.0050.0000.0000.0000.000
22A35ASP-1-0.889-0.92830.291-0.171-0.1710.0000.0000.0000.000
23A36LYS10.8000.88826.2850.2200.2200.0000.0000.0000.000
24A37PRO00.002-0.00131.2350.0110.0110.0000.0000.0000.000
25A38GLU-1-0.913-0.95133.717-0.113-0.1130.0000.0000.0000.000
26A39GLN0-0.032-0.00736.292-0.001-0.0010.0000.0000.0000.000
27A40PRO0-0.0050.01437.5700.0060.0060.0000.0000.0000.000
28A41THR00.006-0.01441.1250.0000.0000.0000.0000.0000.000
29A42PRO0-0.0090.00243.5400.0000.0000.0000.0000.0000.000
30A43PRO00.0280.01145.6660.0030.0030.0000.0000.0000.000
31A44ALA00.000-0.01349.2760.0000.0000.0000.0000.0000.000
32A45GLY0-0.036-0.02651.7550.0010.0010.0000.0000.0000.000
33A46TRP0-0.0180.00047.3550.0010.0010.0000.0000.0000.000
34A47GLN0-0.038-0.02343.451-0.001-0.0010.0000.0000.0000.000
35A48VAL00.0290.01840.1800.0000.0000.0000.0000.0000.000
36A49VAL0-0.0080.00540.5640.0000.0000.0000.0000.0000.000
37A50ARG10.7990.88830.2900.1590.1590.0000.0000.0000.000
38A51LYS10.9370.96736.3490.1070.1070.0000.0000.0000.000
39A52PRO0-0.002-0.00934.875-0.008-0.0080.0000.0000.0000.000
40A53GLY0-0.011-0.01430.7010.0010.0010.0000.0000.0000.000
41A54THR0-0.055-0.01330.292-0.007-0.0070.0000.0000.0000.000
42A55CYS00.0440.02629.7160.0010.0010.0000.0000.0000.000
43A56THR0-0.0100.00332.5010.0030.0030.0000.0000.0000.000
44A57PHE0-0.009-0.01033.9900.0000.0000.0000.0000.0000.000
45A58ASP-1-0.778-0.85439.058-0.086-0.0860.0000.0000.0000.000
46A59LEU0-0.0130.00442.8110.0000.0000.0000.0000.0000.000
47A60THR0-0.020-0.01245.3110.0040.0040.0000.0000.0000.000
48A61LYS10.9130.95448.2390.0610.0610.0000.0000.0000.000
49A62SER0-0.010-0.00951.8210.0000.0000.0000.0000.0000.000
50A63PHE0-0.042-0.03055.3340.0000.0000.0000.0000.0000.000
51A64GLU-1-0.925-0.96058.139-0.044-0.0440.0000.0000.0000.000
52A65GLY0-0.047-0.01860.3880.0020.0020.0000.0000.0000.000
53A66GLU-1-0.806-0.87057.439-0.049-0.0490.0000.0000.0000.000
54A67ASP-1-0.884-0.93353.048-0.055-0.0550.0000.0000.0000.000
55A68LEU0-0.034-0.01752.200-0.001-0.0010.0000.0000.0000.000
56A69VAL0-0.044-0.04046.268-0.001-0.0010.0000.0000.0000.000
57A70VAL00.0120.01645.4320.0000.0000.0000.0000.0000.000
58A71ARG10.7700.85341.4920.0820.0820.0000.0000.0000.000
59A72TYR00.0320.01038.1390.0030.0030.0000.0000.0000.000
60A73SER0-0.051-0.05534.789-0.004-0.0040.0000.0000.0000.000
61A74THR00.0490.02332.0960.0040.0040.0000.0000.0000.000
62A75ASN0-0.066-0.01830.298-0.019-0.0190.0000.0000.0000.000
63A76GLN0-0.014-0.02229.9210.0150.0150.0000.0000.0000.000
64A77ASP-1-0.855-0.92431.375-0.148-0.1480.0000.0000.0000.000
65A78SER0-0.059-0.03529.564-0.007-0.0070.0000.0000.0000.000
66A79ASP-1-0.862-0.90931.315-0.135-0.1350.0000.0000.0000.000
67A80LYS10.7810.86334.3550.1260.1260.0000.0000.0000.000
68A81ALA00.0240.03032.8590.0010.0010.0000.0000.0000.000
69A82ASN0-0.071-0.05234.7570.0040.0040.0000.0000.0000.000
70A83SER00.0040.01638.3480.0030.0030.0000.0000.0000.000
71A84HIS00.0190.01436.686-0.005-0.0050.0000.0000.0000.000
72A85ASN0-0.020-0.01639.9350.0100.0100.0000.0000.0000.000
73A86ILE0-0.024-0.01741.381-0.004-0.0040.0000.0000.0000.000
74A87PHE0-0.017-0.00441.1770.0020.0020.0000.0000.0000.000
75A88VAL0-0.0020.00046.1530.0000.0000.0000.0000.0000.000
76A89TYR00.011-0.00345.5480.0020.0020.0000.0000.0000.000
77A90ILE0-0.007-0.01050.8250.0000.0000.0000.0000.0000.000
78A91THR0-0.041-0.02353.5430.0000.0000.0000.0000.0000.000
79A92GLN00.0440.02255.5470.0020.0020.0000.0000.0000.000
80A93LYS10.9510.95958.9050.0390.0390.0000.0000.0000.000
81A94ASN0-0.076-0.05360.7710.0010.0010.0000.0000.0000.000
82A95GLY00.0270.02757.1290.0010.0010.0000.0000.0000.000
83A96GLN0-0.017-0.00256.425-0.001-0.0010.0000.0000.0000.000
84A97THR0-0.028-0.01452.318-0.001-0.0010.0000.0000.0000.000
85A98MET0-0.0100.01255.2180.0000.0000.0000.0000.0000.000
86A99GLN0-0.014-0.02447.6440.0000.0000.0000.0000.0000.000
87A100ALA00.0000.00151.2480.0020.0020.0000.0000.0000.000
88A101ASP-1-0.813-0.87847.215-0.077-0.0770.0000.0000.0000.000
89A102LEU0-0.011-0.02947.2340.0030.0030.0000.0000.0000.000
90A103SER0-0.026-0.02344.327-0.002-0.0020.0000.0000.0000.000
91A104ILE0-0.047-0.00443.0530.0040.0040.0000.0000.0000.000
92A105GLU-1-0.824-0.91043.251-0.094-0.0940.0000.0000.0000.000
93A106GLU-1-0.945-0.97844.418-0.090-0.0900.0000.0000.0000.000
94A107GLY0-0.037-0.00746.0570.0020.0020.0000.0000.0000.000
95A108GLU-1-0.969-0.97347.453-0.064-0.0640.0000.0000.0000.000
96A109LEU0-0.043-0.02848.122-0.003-0.0030.0000.0000.0000.000
97A110VAL00.0340.03048.7530.0040.0040.0000.0000.0000.000
98A111LEU0-0.033-0.02549.534-0.002-0.0020.0000.0000.0000.000
99A112ASN0-0.012-0.01347.0770.0040.0040.0000.0000.0000.000
100A113ASN0-0.066-0.05450.3670.0020.0020.0000.0000.0000.000
101A114ILE00.0400.01752.050-0.001-0.0010.0000.0000.0000.000
102A115ARG10.8300.92049.9280.0630.0630.0000.0000.0000.000
103A116PHE0-0.001-0.01355.1640.0000.0000.0000.0000.0000.000
104A117TYR00.017-0.00749.7240.0000.0000.0000.0000.0000.000
105A118ASP-1-0.878-0.94055.745-0.043-0.0430.0000.0000.0000.000
106A119GLU-1-0.919-0.95853.498-0.050-0.0500.0000.0000.0000.000
107A120ALA00.0450.01152.566-0.002-0.0020.0000.0000.0000.000
108A121ALA0-0.0080.01749.573-0.003-0.0030.0000.0000.0000.000
109A122LEU0-0.028-0.01148.878-0.003-0.0030.0000.0000.0000.000
110A123ALA00.0050.01349.582-0.002-0.0020.0000.0000.0000.000
111A124LYS10.8970.95346.7370.0600.0600.0000.0000.0000.000
112A125ASP-1-0.867-0.91545.007-0.069-0.0690.0000.0000.0000.000
113A126THR0-0.042-0.03139.805-0.003-0.0030.0000.0000.0000.000
114A127GLY00.0520.01339.450-0.001-0.0010.0000.0000.0000.000
115A128ALA00.0170.01039.0470.0030.0030.0000.0000.0000.000
116A129GLU-1-0.820-0.90340.976-0.058-0.0580.0000.0000.0000.000
117A130ALA0-0.0030.01543.8890.0040.0040.0000.0000.0000.000
118A131GLU-1-0.785-0.87442.419-0.078-0.0780.0000.0000.0000.000
119A132ALA0-0.038-0.01844.8720.0020.0020.0000.0000.0000.000
120A133LYS10.8580.91246.4690.0600.0600.0000.0000.0000.000
121A134ARG10.7490.83444.2310.0760.0760.0000.0000.0000.000
122A135ASN0-0.049-0.01644.9110.0000.0000.0000.0000.0000.000
123A136GLU-1-0.971-0.97649.305-0.050-0.0500.0000.0000.0000.000
124A137LEU0-0.041-0.01152.3730.0030.0030.0000.0000.0000.000
125A138TYR00.002-0.00453.635-0.002-0.0020.0000.0000.0000.000
126A139THR00.0520.02451.5010.0000.0000.0000.0000.0000.000
127A140GLY00.0070.02953.930-0.002-0.0020.0000.0000.0000.000
128A141PRO0-0.044-0.02656.4470.0000.0000.0000.0000.0000.000
129A142LEU00.0240.01154.086-0.002-0.0020.0000.0000.0000.000
130A143VAL00.0280.01354.1470.0020.0020.0000.0000.0000.000
131A144HIS0-0.017-0.00955.4430.0000.0000.0000.0000.0000.000
132A145GLU-1-0.961-0.99057.247-0.047-0.0470.0000.0000.0000.000
133A146LEU0-0.069-0.01858.6800.0020.0020.0000.0000.0000.000
134A147ASP-1-0.905-0.94861.824-0.041-0.0410.0000.0000.0000.000
135A148TYR0-0.004-0.01961.4800.0000.0000.0000.0000.0000.000
136A149ASP-1-0.892-0.94863.154-0.041-0.0410.0000.0000.0000.000
137A150LEU0-0.0150.00262.0870.0000.0000.0000.0000.0000.000
138A151LEU00.0670.02756.759-0.001-0.0010.0000.0000.0000.000
139A152ASN00.0450.03259.597-0.002-0.0020.0000.0000.0000.000
140A153CYS0-0.070-0.03361.2160.0000.0000.0000.0000.0000.000
141A154VAL0-0.0020.00156.9460.0000.0000.0000.0000.0000.000
142A155MET00.0450.02553.263-0.001-0.0010.0000.0000.0000.000
143A156THR0-0.018-0.02157.5090.0000.0000.0000.0000.0000.000
144A157TYR0-0.111-0.06657.8260.0000.0000.0000.0000.0000.000
145A158LEU00.0210.01853.2600.0000.0000.0000.0000.0000.000
146A159GLU-1-0.883-0.93755.551-0.054-0.0540.0000.0000.0000.000
147A160LYS10.9050.94556.6240.0450.0450.0000.0000.0000.000
148A161ARG10.7600.87255.2200.0520.0520.0000.0000.0000.000
149A162GLY0-0.054-0.02153.764-0.001-0.0010.0000.0000.0000.000
150A163VAL0-0.020-0.01750.175-0.003-0.0030.0000.0000.0000.000
151A164ASP-1-0.797-0.90951.109-0.067-0.0670.0000.0000.0000.000
152A165GLU-1-0.801-0.90549.768-0.071-0.0710.0000.0000.0000.000
153A166LYS10.7800.88748.1860.0690.0690.0000.0000.0000.000
154A167LEU0-0.044-0.01445.596-0.004-0.0040.0000.0000.0000.000
155A168GLY00.0480.01645.251-0.004-0.0040.0000.0000.0000.000
156A169GLU-1-0.883-0.94343.650-0.086-0.0860.0000.0000.0000.000
157A170PHE0-0.001-0.00841.465-0.005-0.0050.0000.0000.0000.000
158A171VAL00.0140.00240.341-0.006-0.0060.0000.0000.0000.000
159A172VAL00.0040.02539.148-0.007-0.0070.0000.0000.0000.000
160A173LEU00.005-0.00237.783-0.009-0.0090.0000.0000.0000.000
161A174TYR0-0.031-0.03236.265-0.008-0.0080.0000.0000.0000.000
162A175SER0-0.018-0.02635.033-0.008-0.0080.0000.0000.0000.000
163A176PHE00.0050.00333.101-0.010-0.0100.0000.0000.0000.000
164A177TRP0-0.025-0.00132.060-0.010-0.0100.0000.0000.0000.000
165A178ALA00.004-0.00831.421-0.010-0.0100.0000.0000.0000.000
166A179GLU-1-0.878-0.91627.571-0.229-0.2290.0000.0000.0000.000
167A180GLN0-0.043-0.02726.190-0.008-0.0080.0000.0000.0000.000
168A181GLN0-0.046-0.02826.573-0.015-0.0150.0000.0000.0000.000
169A182ASP-1-0.783-0.87825.736-0.204-0.2040.0000.0000.0000.000
170A183TYR00.0070.00820.366-0.031-0.0310.0000.0000.0000.000
171A184GLU-1-0.750-0.85921.677-0.277-0.2770.0000.0000.0000.000
172A185ALA0-0.0130.00721.029-0.027-0.0270.0000.0000.0000.000
173A186TRP0-0.012-0.00317.943-0.040-0.0400.0000.0000.0000.000
174A187LEU00.0180.01517.111-0.058-0.0580.0000.0000.0000.000
175A188THR0-0.027-0.02716.078-0.062-0.0620.0000.0000.0000.000
176A189THR0-0.099-0.05316.217-0.018-0.0180.0000.0000.0000.000
177A190MET0-0.011-0.00512.659-0.063-0.0630.0000.0000.0000.000
178A191ASN0-0.023-0.00211.896-0.052-0.0520.0000.0000.0000.000
179A192LYS10.9440.97311.2510.2270.2270.0000.0000.0000.000
180A193PHE0-0.080-0.03911.2210.0230.0230.0000.0000.0000.000
181A194ALA0-0.0050.0177.866-0.041-0.0410.0000.0000.0000.000
182A195SER0-0.122-0.0686.730-0.069-0.0690.0000.0000.0000.000