FMODB

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

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: 761MK

Calculation Name: 4YWK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4YWK

Chain ID: A

ChEMBL ID:

UniProt ID: Q8U3I4

Base Structure: X-ray

Registration Date: 2023-09-23

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

DOI:

Apendix: None


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 199
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2285863.514593
FMO2-HF: Nuclear repulsion 2206355.496487
FMO2-HF: Total energy -79508.018106
FMO2-MP2: Total energy -79742.99467


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:1:VAL)


Summations of interaction energy for fragment #1(A:1:VAL)
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.
-7.521-2.1362.473-2.607-5.2510.001
Interaction energy analysis for fragmet #1(A:1:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / q_NPA : 0.002
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].
3A3ARG10.8600.9143.8840.6412.332-0.011-0.890-0.7910.003
4A4GLU-1-0.941-0.9656.3710.5030.5030.0000.0000.0000.000
5A5GLU-1-0.822-0.9022.1631.5672.2241.573-0.658-1.5710.001
6A6MET0-0.046-0.0222.337-1.907-0.8820.822-0.481-1.3660.000
7A7ILE0-0.041-0.0094.733-0.704-0.644-0.001-0.008-0.0510.000
8A8GLU-1-0.909-0.9458.4090.5250.5250.0000.0000.0000.000
9A9ARG10.7240.8123.693-1.197-0.7830.006-0.100-0.320-0.001
10A10PHE00.018-0.0036.912-0.275-0.2750.0000.0000.0000.000
11A11ALA0-0.028-0.0149.832-0.096-0.0960.0000.0000.0000.000
12A12ASN0-0.043-0.02711.155-0.110-0.1100.0000.0000.0000.000
13A13PHE00.0040.00311.543-0.073-0.0730.0000.0000.0000.000
14A14LEU0-0.059-0.04513.282-0.040-0.0400.0000.0000.0000.000
15A15ARG10.7160.83115.682-0.223-0.2230.0000.0000.0000.000
16A16GLU-1-0.926-0.97515.4690.1920.1920.0000.0000.0000.000
17A17TYR0-0.0210.00016.034-0.015-0.0150.0000.0000.0000.000
18A18THR0-0.061-0.03017.8890.0030.0030.0000.0000.0000.000
19A19ASP-1-0.819-0.90121.157-0.025-0.0250.0000.0000.0000.000
20A20GLU-1-0.974-0.99623.506-0.034-0.0340.0000.0000.0000.000
21A21ASP-1-0.963-0.96926.038-0.011-0.0110.0000.0000.0000.000
22A22GLY0-0.056-0.02625.2180.0060.0060.0000.0000.0000.000
23A23ASN0-0.079-0.06025.6870.0140.0140.0000.0000.0000.000
24A24PRO00.0170.01722.263-0.006-0.0060.0000.0000.0000.000
25A25VAL00.015-0.01120.8210.0020.0020.0000.0000.0000.000
26A26TYR0-0.010-0.01617.727-0.011-0.0110.0000.0000.0000.000
27A27ARG10.8680.93619.716-0.075-0.0750.0000.0000.0000.000
28A28GLY00.0250.01921.8540.0000.0000.0000.0000.0000.000
29A29LYS10.8460.92120.1170.0640.0640.0000.0000.0000.000
30A30ILE00.0370.02717.891-0.005-0.0050.0000.0000.0000.000
31A31THR0-0.030-0.03121.9990.0010.0010.0000.0000.0000.000
32A32ASP-1-0.823-0.89825.199-0.024-0.0240.0000.0000.0000.000
33A33LEU0-0.044-0.00820.773-0.004-0.0040.0000.0000.0000.000
34A34LEU0-0.040-0.02025.4840.0020.0020.0000.0000.0000.000
35A35THR0-0.044-0.01528.3400.0010.0010.0000.0000.0000.000
36A36ILE0-0.006-0.01631.5070.0000.0000.0000.0000.0000.000
37A37THR0-0.063-0.03733.0630.0000.0000.0000.0000.0000.000
38A38PRO0-0.0310.02727.874-0.003-0.0030.0000.0000.0000.000
39A39LYS10.8600.90225.2280.0260.0260.0000.0000.0000.000
40A40ARG10.8570.89123.9450.0450.0450.0000.0000.0000.000
41A41SER0-0.004-0.03220.722-0.005-0.0050.0000.0000.0000.000
42A42VAL0-0.0140.01117.5810.0080.0080.0000.0000.0000.000
43A43ALA00.0230.01517.860-0.017-0.0170.0000.0000.0000.000
44A44ILE0-0.034-0.02213.5890.0230.0230.0000.0000.0000.000
45A45ASP-1-0.781-0.87416.821-0.164-0.1640.0000.0000.0000.000
46A46TRP00.016-0.03211.4150.0450.0450.0000.0000.0000.000
47A47MET0-0.028-0.00114.446-0.029-0.0290.0000.0000.0000.000
48A48HIS00.0060.01416.3580.0090.0090.0000.0000.0000.000
49A49LEU00.0330.0379.2930.0210.0210.0000.0000.0000.000
50A50ASN0-0.002-0.01611.684-0.043-0.0430.0000.0000.0000.000
51A51SER0-0.126-0.06912.7380.0130.0130.0000.0000.0000.000
52A52PHE0-0.022-0.00711.2230.0170.0170.0000.0000.0000.000
53A53ASP-1-0.779-0.8736.705-0.242-0.2420.0000.0000.0000.000
54A54SER00.0500.0228.716-0.133-0.1330.0000.0000.0000.000
55A55GLU-1-0.924-0.9263.573-1.918-1.4070.005-0.142-0.374-0.001
56A56LEU00.0330.0134.275-0.656-0.507-0.001-0.012-0.1360.000
57A57ALA00.001-0.0035.6350.0290.0290.0000.0000.0000.000
58A58HIS0-0.008-0.0056.7140.1560.1560.0000.0000.0000.000
59A59GLU-1-0.859-0.9292.918-3.693-2.8150.080-0.316-0.642-0.001
60A60VAL0-0.047-0.0206.1310.1700.1700.0000.0000.0000.000
61A61ILE0-0.065-0.0238.7450.1510.1510.0000.0000.0000.000
62A62GLU-1-0.798-0.8977.963-0.399-0.3990.0000.0000.0000.000
63A63ASN0-0.076-0.0474.9980.5860.5860.0000.0000.0000.000
64A64PRO0-0.0070.0148.216-0.049-0.0490.0000.0000.0000.000
65A65GLU-1-0.811-0.88210.758-0.263-0.2630.0000.0000.0000.000
66A66GLU-1-0.884-0.9386.924-1.049-1.0490.0000.0000.0000.000
67A67GLY00.0430.0266.7340.0950.0950.0000.0000.0000.000
68A68ILE0-0.036-0.0247.6440.1860.1860.0000.0000.0000.000
69A69SER0-0.008-0.00310.6350.0850.0850.0000.0000.0000.000
70A70ALA00.0110.0067.1970.1060.1060.0000.0000.0000.000
71A71ALA00.0370.0209.0420.1310.1310.0000.0000.0000.000
72A72GLU-1-0.833-0.92710.981-0.091-0.0910.0000.0000.0000.000
73A73ASP-1-0.857-0.93111.6930.0510.0510.0000.0000.0000.000
74A74ALA00.0150.00810.8980.0310.0310.0000.0000.0000.000
75A75ILE0-0.011-0.00812.9580.0030.0030.0000.0000.0000.000
76A76GLN0-0.069-0.03316.2240.0080.0080.0000.0000.0000.000
77A77ILE0-0.0120.00813.966-0.005-0.0050.0000.0000.0000.000
78A78VAL00.0450.01915.711-0.005-0.0050.0000.0000.0000.000
79A79LEU0-0.042-0.02318.307-0.010-0.0100.0000.0000.0000.000
80A80ARG10.8460.90719.706-0.110-0.1100.0000.0000.0000.000
81A81GLU-1-0.902-0.93918.1840.2210.2210.0000.0000.0000.000
82A82ASP-1-0.793-0.86320.7890.1180.1180.0000.0000.0000.000
83A83PHE0-0.071-0.04721.937-0.013-0.0130.0000.0000.0000.000
84A84GLN0-0.049-0.00424.825-0.014-0.0140.0000.0000.0000.000
85A85ARG10.7940.86524.824-0.033-0.0330.0000.0000.0000.000
86A86GLU-1-0.818-0.89623.6870.0820.0820.0000.0000.0000.000
87A87ASP-1-0.862-0.90224.8020.0210.0210.0000.0000.0000.000
88A88VAL0-0.0030.00324.117-0.005-0.0050.0000.0000.0000.000
89A89GLY0-0.0010.01124.505-0.008-0.0080.0000.0000.0000.000
90A90LYS10.8520.91415.8410.0880.0880.0000.0000.0000.000
91A91ILE0-0.0110.00319.164-0.002-0.0020.0000.0000.0000.000
92A92HIS0-0.030-0.01618.003-0.017-0.0170.0000.0000.0000.000
93A93ALA0-0.0080.00213.8780.0180.0180.0000.0000.0000.000
94A94ARG10.7910.90315.7360.0970.0970.0000.0000.0000.000
95A95PHE00.0630.03010.8790.0120.0120.0000.0000.0000.000
96A96TYR00.0220.01416.1700.0030.0030.0000.0000.0000.000
97A97ASN0-0.029-0.03317.895-0.014-0.0140.0000.0000.0000.000
98A98LEU00.0330.01514.969-0.012-0.0120.0000.0000.0000.000
99A99PRO0-0.021-0.00615.4270.0280.0280.0000.0000.0000.000
100A100GLU-1-0.910-0.95018.560-0.209-0.2090.0000.0000.0000.000
101A101THR0-0.016-0.01920.431-0.011-0.0110.0000.0000.0000.000
102A102LEU0-0.0460.00721.5420.0100.0100.0000.0000.0000.000
103A103MET00.008-0.00425.2700.0100.0100.0000.0000.0000.000
104A104VAL00.0090.00027.710-0.006-0.0060.0000.0000.0000.000
105A105LYS10.7210.84029.0070.0820.0820.0000.0000.0000.000
106A106ASP-1-0.850-0.91326.513-0.115-0.1150.0000.0000.0000.000
107A107ILE0-0.0380.00023.356-0.009-0.0090.0000.0000.0000.000
108A108GLY00.0590.04324.0880.0090.0090.0000.0000.0000.000
109A109ALA0-0.083-0.06022.811-0.005-0.0050.0000.0000.0000.000
110A110GLU-1-0.866-0.94419.450-0.179-0.1790.0000.0000.0000.000
111A111HIS00.0410.01417.981-0.016-0.0160.0000.0000.0000.000
112A112ILE0-0.074-0.04418.012-0.004-0.0040.0000.0000.0000.000
113A113ASN0-0.055-0.03713.9370.0060.0060.0000.0000.0000.000
114A114LYS10.8570.93513.1870.3600.3600.0000.0000.0000.000
115A115LEU0-0.0300.00313.3910.0590.0590.0000.0000.0000.000
116A116ILE0-0.018-0.00814.9660.0030.0030.0000.0000.0000.000
117A117GLN00.035-0.00118.2170.0070.0070.0000.0000.0000.000
118A118VAL0-0.064-0.02820.7950.0060.0060.0000.0000.0000.000
119A119GLU-1-0.779-0.86824.552-0.099-0.0990.0000.0000.0000.000
120A120GLY0-0.017-0.02327.8490.0010.0010.0000.0000.0000.000
121A121ILE0-0.092-0.03331.0430.0030.0030.0000.0000.0000.000
122A122VAL00.0640.04331.947-0.003-0.0030.0000.0000.0000.000
123A123THR0-0.049-0.03234.3390.0050.0050.0000.0000.0000.000
124A124ARG10.8790.92535.7830.0640.0640.0000.0000.0000.000
125A125VAL00.0740.04533.823-0.004-0.0040.0000.0000.0000.000
126A126GLY0-0.028-0.00534.5570.0050.0050.0000.0000.0000.000
127A127GLU-1-0.884-0.91633.812-0.053-0.0530.0000.0000.0000.000
128A128ILE0-0.074-0.04033.3760.0040.0040.0000.0000.0000.000
129A129LYS10.9841.01632.6860.0350.0350.0000.0000.0000.000
130A130PRO0-0.037-0.02629.0710.0030.0030.0000.0000.0000.000
131A182PHE00.0130.00425.320-0.001-0.0010.0000.0000.0000.000
132A183GLN00.0440.01229.2900.0030.0030.0000.0000.0000.000
133A184SER0-0.081-0.04929.338-0.007-0.0070.0000.0000.0000.000
134A185PHE00.0870.03129.0350.0050.0050.0000.0000.0000.000
135A186ARG10.7370.84530.6110.0690.0690.0000.0000.0000.000
136A187ILE00.0590.04027.4010.0050.0050.0000.0000.0000.000
137A188GLN0-0.019-0.02131.365-0.001-0.0010.0000.0000.0000.000
138A189ASP-1-0.701-0.85332.090-0.095-0.0950.0000.0000.0000.000
139A190ARG10.7610.84929.8760.0950.0950.0000.0000.0000.000
140A191PRO00.0100.00735.6310.0000.0000.0000.0000.0000.000
141A192GLU-1-0.756-0.86136.351-0.065-0.0650.0000.0000.0000.000
142A193THR0-0.034-0.02433.162-0.001-0.0010.0000.0000.0000.000
143A194LEU0-0.074-0.01636.300-0.002-0.0020.0000.0000.0000.000
144A195LYS10.8990.93835.8460.0770.0770.0000.0000.0000.000
145A196GLY00.0260.00440.9230.0000.0000.0000.0000.0000.000
146A197GLY0-0.005-0.01243.3350.0020.0020.0000.0000.0000.000
147A198GLU-1-0.851-0.90236.179-0.076-0.0760.0000.0000.0000.000
148A199MET00.005-0.00339.8770.0000.0000.0000.0000.0000.000
149A200PRO0-0.0150.00636.619-0.003-0.0030.0000.0000.0000.000
150A201ARG10.9130.96032.5120.0880.0880.0000.0000.0000.000
151A202PHE00.003-0.01732.7120.0010.0010.0000.0000.0000.000
152A203ILE00.0020.01025.7350.0000.0000.0000.0000.0000.000
153A204ASP-1-0.809-0.86430.077-0.080-0.0800.0000.0000.0000.000
154A205GLY00.0420.02326.628-0.009-0.0090.0000.0000.0000.000
155A206ILE0-0.047-0.03325.7740.0120.0120.0000.0000.0000.000
156A207LEU00.0560.03124.010-0.013-0.0130.0000.0000.0000.000
157A208LEU0-0.021-0.01423.4350.0070.0070.0000.0000.0000.000
158A209ASP-1-0.793-0.90323.644-0.085-0.0850.0000.0000.0000.000
159A210ASP-1-0.748-0.81924.567-0.052-0.0520.0000.0000.0000.000
160A211ILE0-0.106-0.07724.9870.0090.0090.0000.0000.0000.000
161A212VAL0-0.056-0.01327.0810.0040.0040.0000.0000.0000.000
162A213ASP-1-0.882-0.93829.926-0.057-0.0570.0000.0000.0000.000
163A214VAL0-0.080-0.04028.0650.0010.0010.0000.0000.0000.000
164A215ALA0-0.0020.00731.388-0.001-0.0010.0000.0000.0000.000
165A216LEU00.0160.00133.3790.0020.0020.0000.0000.0000.000
166A217PRO0-0.069-0.05236.462-0.002-0.0020.0000.0000.0000.000
167A218GLY0-0.019-0.00537.6880.0040.0040.0000.0000.0000.000
168A219ASP-1-0.817-0.89234.026-0.059-0.0590.0000.0000.0000.000
169A220ARG10.7380.82533.6050.0580.0580.0000.0000.0000.000
170A221VAL00.0210.01128.7990.0020.0020.0000.0000.0000.000
171A222ILE00.0440.02823.865-0.001-0.0010.0000.0000.0000.000
172A223VAL0-0.027-0.01223.7420.0050.0050.0000.0000.0000.000
173A224THR00.0430.00318.204-0.005-0.0050.0000.0000.0000.000
174A225GLY00.001-0.01118.6810.0200.0200.0000.0000.0000.000
175A226ILE00.0460.05514.567-0.015-0.0150.0000.0000.0000.000
176A227LEU0-0.044-0.02018.2840.0370.0370.0000.0000.0000.000
177A228ARG10.7550.83516.6690.2440.2440.0000.0000.0000.000
178A229VAL0-0.018-0.02222.7400.0100.0100.0000.0000.0000.000
179A230VAL00.0310.02126.2380.0040.0040.0000.0000.0000.000
180A231LEU0-0.031-0.01329.6990.0030.0030.0000.0000.0000.000
181A232GLU-1-0.813-0.91232.688-0.070-0.0700.0000.0000.0000.000
182A233LYS10.9300.94535.0560.0590.0590.0000.0000.0000.000
183A234ARG10.8430.88438.4870.0520.0520.0000.0000.0000.000
184A235GLU-1-0.859-0.89440.288-0.048-0.0480.0000.0000.0000.000
185A236LYS10.8630.94336.8430.0690.0690.0000.0000.0000.000
186A237THR00.0340.01239.1350.0010.0010.0000.0000.0000.000
187A238PRO0-0.038-0.02636.689-0.003-0.0030.0000.0000.0000.000
188A239ILE0-0.0140.00732.9920.0000.0000.0000.0000.0000.000
189A240PHE00.0250.00228.1630.0020.0020.0000.0000.0000.000
190A241ARG10.8090.91728.8550.0910.0910.0000.0000.0000.000
191A242LYS10.9050.94524.0850.1540.1540.0000.0000.0000.000
192A243ILE0-0.042-0.01325.6780.0120.0120.0000.0000.0000.000
193A244LEU00.0220.01421.183-0.010-0.0100.0000.0000.0000.000
194A245GLU-1-0.847-0.90319.668-0.174-0.1740.0000.0000.0000.000
195A246VAL0-0.036-0.01820.417-0.020-0.0200.0000.0000.0000.000
196A247ASN00.015-0.00816.066-0.002-0.0020.0000.0000.0000.000
197A248HIS00.015-0.01019.1840.0100.0100.0000.0000.0000.000
198A249ILE0-0.018-0.01721.357-0.006-0.0060.0000.0000.0000.000
199A250GLU-1-0.861-0.90124.532-0.101-0.1010.0000.0000.0000.000