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: 76MRK

Calculation Name: 2YVU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YVU

Chain ID: A

ChEMBL ID:

UniProt ID: Q9YCR6

Base Structure: X-ray

Registration Date: 2023-09-22

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 OptH
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 179
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1941540.215326
FMO2-HF: Nuclear repulsion 1871479.534819
FMO2-HF: Total energy -70060.680507
FMO2-MP2: Total energy -70268.822986


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:8:LYS)


Summations of interaction energy for fragment #1(A:8:LYS)
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.
-103.243-93.03715.777-9.945-16.037-0.106
Interaction energy analysis for fragmet #1(A:8:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.936 / q_NPA : 0.972
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].
3A10ILE00.0200.0312.594-4.306-0.7790.242-1.400-2.369-0.003
4A11GLU-1-0.914-0.9534.747-19.311-19.266-0.001-0.006-0.0380.000
5A12LYS10.8960.9398.52921.84321.8430.0000.0000.0000.000
6A13GLY0-0.0090.0138.655-2.588-2.5880.0000.0000.0000.000
7A14ILE00.013-0.0079.5341.6851.6850.0000.0000.0000.000
8A15VAL00.0100.00812.211-0.253-0.2530.0000.0000.0000.000
9A16VAL0-0.015-0.00113.0070.7280.7280.0000.0000.0000.000
10A17TRP00.016-0.00315.7760.2680.2680.0000.0000.0000.000
11A18LEU0-0.008-0.01218.0840.5400.5400.0000.0000.0000.000
12A19THR0-0.0150.00421.1930.6710.6710.0000.0000.0000.000
13A20GLY00.0660.01724.925-0.068-0.0680.0000.0000.0000.000
14A21LEU00.0020.01427.5960.0520.0520.0000.0000.0000.000
15A22PRO00.002-0.00329.115-0.468-0.4680.0000.0000.0000.000
16A23GLY00.0620.02529.2510.2590.2590.0000.0000.0000.000
17A24SER0-0.022-0.01827.022-0.173-0.1730.0000.0000.0000.000
18A25GLY00.0500.02125.144-0.155-0.1550.0000.0000.0000.000
19A26LYS10.8990.96022.40911.63611.6360.0000.0000.0000.000
20A27THR00.0980.03020.774-0.697-0.6970.0000.0000.0000.000
21A28THR00.0090.01520.119-0.599-0.5990.0000.0000.0000.000
22A29ILE00.0040.00317.678-0.793-0.7930.0000.0000.0000.000
23A30ALA00.0200.00016.438-1.149-1.1490.0000.0000.0000.000
24A31THR00.0230.01615.133-1.375-1.3750.0000.0000.0000.000
25A32ARG10.8840.94914.99415.20115.2010.0000.0000.0000.000
26A33LEU00.0230.01810.927-1.146-1.1460.0000.0000.0000.000
27A34ALA00.021-0.00410.751-2.672-2.6720.0000.0000.0000.000
28A35ASP-1-0.871-0.93610.349-25.462-25.4620.0000.0000.0000.000
29A36LEU0-0.051-0.0269.456-1.792-1.7920.0000.0000.0000.000
30A37LEU00.0230.0116.009-3.899-3.8990.0000.0000.0000.000
31A38GLN00.0180.0135.433-7.174-7.1740.0000.0000.0000.000
32A39LYS10.8910.9656.69919.75219.7520.0000.0000.0000.000
33A40GLU-1-0.779-0.8013.344-55.926-55.5300.011-0.087-0.320-0.001
34A41GLY0-0.051-0.0382.866-25.778-22.2010.444-2.028-1.993-0.020
35A42TYR0-0.020-0.0182.252-28.919-26.66115.068-6.543-10.782-0.082
36A43ARG10.9830.9933.55739.54039.8530.0140.126-0.4520.000
37A44VAL0-0.027-0.0185.851-0.017-0.0170.0000.0000.0000.000
38A45GLU-1-0.892-0.9459.104-19.838-19.8380.0000.0000.0000.000
39A46VAL0-0.018-0.00212.756-0.168-0.1680.0000.0000.0000.000
40A47LEU0-0.0010.00615.7800.9360.9360.0000.0000.0000.000
41A48ASP-1-0.828-0.93618.882-14.271-14.2710.0000.0000.0000.000
42A49GLY0-0.012-0.02622.1570.3070.3070.0000.0000.0000.000
43A50ASP-1-0.936-0.96325.328-11.036-11.0360.0000.0000.0000.000
44A51TRP00.0450.02020.6570.2950.2950.0000.0000.0000.000
45A52ALA00.006-0.00923.8540.3330.3330.0000.0000.0000.000
46A53ARG10.8820.94025.17410.82510.8250.0000.0000.0000.000
47A54THR00.0100.01526.7430.2860.2860.0000.0000.0000.000
48A55THR00.0200.02123.480-0.104-0.1040.0000.0000.0000.000
49A56VAL0-0.027-0.01722.9090.3010.3010.0000.0000.0000.000
50A57SER0-0.082-0.09026.1450.2040.2040.0000.0000.0000.000
51A58GLU-1-0.948-0.95228.919-9.568-9.5680.0000.0000.0000.000
52A59GLY00.0050.02430.9430.1950.1950.0000.0000.0000.000
53A60ALA0-0.066-0.02232.7870.1980.1980.0000.0000.0000.000
54A61GLY00.0340.03534.8450.0510.0510.0000.0000.0000.000
55A62PHE0-0.005-0.03034.160-0.315-0.3150.0000.0000.0000.000
56A63THR00.0710.04137.016-0.060-0.0600.0000.0000.0000.000
57A64ARG11.0051.00235.9898.3098.3090.0000.0000.0000.000
58A65GLU-1-0.892-0.96535.592-8.235-8.2350.0000.0000.0000.000
59A66GLU-1-0.965-0.96834.741-8.809-8.8090.0000.0000.0000.000
60A67ARG10.9480.96632.1838.9638.9630.0000.0000.0000.000
61A68LEU00.0200.01430.730-0.448-0.4480.0000.0000.0000.000
62A69ARG10.9460.97630.3758.3888.3880.0000.0000.0000.000
63A70HIS00.0370.04326.401-0.226-0.2260.0000.0000.0000.000
64A71LEU00.0240.00826.153-0.459-0.4590.0000.0000.0000.000
65A72LYS10.9810.98925.4999.7599.7590.0000.0000.0000.000
66A73ARG10.8840.93825.40810.48310.4830.0000.0000.0000.000
67A74ILE0-0.012-0.00421.301-0.432-0.4320.0000.0000.0000.000
68A75ALA00.0190.00721.165-0.729-0.7290.0000.0000.0000.000
69A76TRP0-0.003-0.00420.845-0.578-0.5780.0000.0000.0000.000
70A77ILE0-0.0170.01018.305-0.440-0.4400.0000.0000.0000.000
71A78ALA00.0210.00316.867-0.851-0.8510.0000.0000.0000.000
72A79ARG10.7950.91115.95312.50812.5080.0000.0000.0000.000
73A80LEU0-0.026-0.02416.190-0.625-0.6250.0000.0000.0000.000
74A81LEU00.0200.01813.038-0.652-0.6520.0000.0000.0000.000
75A82ALA00.0630.03711.736-1.514-1.5140.0000.0000.0000.000
76A83ARG10.8360.93011.51913.85113.8510.0000.0000.0000.000
77A84ASN0-0.108-0.07511.5500.5110.5110.0000.0000.0000.000
78A85GLY00.0670.0427.541-0.902-0.9020.0000.0000.0000.000
79A86VAL0-0.077-0.0266.755-4.186-4.1860.0000.0000.0000.000
80A87ILE00.0090.0085.6412.1152.1150.0000.0000.0000.000
81A88VAL0-0.001-0.0139.3910.6870.6870.0000.0000.0000.000
82A89ILE0-0.0040.00911.3540.8160.8160.0000.0000.0000.000
83A90CYS0-0.029-0.01114.8010.9680.9680.0000.0000.0000.000
84A91SER0-0.0080.00918.5310.3410.3410.0000.0000.0000.000
85A92PHE00.0390.00420.8680.6070.6070.0000.0000.0000.000
86A93VAL0-0.053-0.00824.8110.0480.0480.0000.0000.0000.000
87A94SER00.010-0.01326.3050.0870.0870.0000.0000.0000.000
88A95PRO00.0470.01828.846-0.243-0.2430.0000.0000.0000.000
89A96TYR0-0.049-0.06531.5990.0550.0550.0000.0000.0000.000
90A97LYS10.9470.98030.4058.9848.9840.0000.0000.0000.000
91A98GLN00.0160.01330.210-0.240-0.2400.0000.0000.0000.000
92A99ALA0-0.006-0.00830.263-0.160-0.1600.0000.0000.0000.000
93A100ARG10.8330.89025.78011.00911.0090.0000.0000.0000.000
94A101ASN00.0150.00625.966-0.716-0.7160.0000.0000.0000.000
95A102MET0-0.097-0.03927.286-0.231-0.2310.0000.0000.0000.000
96A103VAL00.0190.00622.471-0.142-0.1420.0000.0000.0000.000
97A104ARG10.8140.90221.57513.48613.4860.0000.0000.0000.000
98A105ARG10.9300.96722.87710.24010.2400.0000.0000.0000.000
99A106ILE0-0.0170.00522.302-0.044-0.0440.0000.0000.0000.000
100A107VAL00.008-0.00717.784-0.195-0.1950.0000.0000.0000.000
101A108GLU-1-0.833-0.93419.461-14.227-14.2270.0000.0000.0000.000
102A109GLU-1-0.908-0.92921.241-11.932-11.9320.0000.0000.0000.000
103A110GLU-1-0.908-0.94117.214-15.018-15.0180.0000.0000.0000.000
104A111GLY00.0160.00018.211-0.502-0.5020.0000.0000.0000.000
105A112ILE0-0.091-0.03414.087-1.003-1.0030.0000.0000.0000.000
106A113PRO00.0380.01713.5030.9980.9980.0000.0000.0000.000
107A114PHE00.0280.00315.793-0.572-0.5720.0000.0000.0000.000
108A115LEU0-0.007-0.01014.1870.7920.7920.0000.0000.0000.000
109A116GLU-1-0.836-0.91718.165-12.715-12.7150.0000.0000.0000.000
110A117ILE0-0.0010.00417.5680.1850.1850.0000.0000.0000.000
111A118TYR00.005-0.01121.1350.4820.4820.0000.0000.0000.000
112A119VAL0-0.0140.00222.169-0.122-0.1220.0000.0000.0000.000
113A120LYS10.9380.96724.72510.72110.7210.0000.0000.0000.000
114A121ALA00.0260.00928.124-0.093-0.0930.0000.0000.0000.000
115A122SER00.0040.02030.8830.1460.1460.0000.0000.0000.000
116A123LEU00.048-0.00434.524-0.121-0.1210.0000.0000.0000.000
117A124GLU-1-0.915-0.96436.478-7.765-7.7650.0000.0000.0000.000
118A125GLU-1-0.840-0.89933.157-9.210-9.2100.0000.0000.0000.000
119A126VAL0-0.046-0.03131.544-0.095-0.0950.0000.0000.0000.000
120A127ILE0-0.039-0.01634.1710.0080.0080.0000.0000.0000.000
121A128ARG10.8940.93037.5028.4388.4380.0000.0000.0000.000
122A129ARG10.8020.91928.75610.60510.6050.0000.0000.0000.000
123A130ASP-1-0.876-0.93734.040-9.298-9.2980.0000.0000.0000.000
124A131PRO00.0500.03036.1350.1160.1160.0000.0000.0000.000
125A132LYS10.9600.97137.9788.4128.4120.0000.0000.0000.000
126A133GLY00.0020.00436.3370.1170.1170.0000.0000.0000.000
127A134LEU0-0.0130.00237.3380.0330.0330.0000.0000.0000.000
128A135TYR00.019-0.00439.5590.1070.1070.0000.0000.0000.000
129A136LYS10.9230.97337.9958.5438.5430.0000.0000.0000.000
130A137LYS10.9580.97233.8679.3529.3520.0000.0000.0000.000
131A138ALA00.0350.02239.9400.0910.0910.0000.0000.0000.000
132A139LEU0-0.038-0.01643.3810.1390.1390.0000.0000.0000.000
133A140LYS10.7850.90438.5968.3008.3000.0000.0000.0000.000
134A141GLY00.0240.01043.032-0.028-0.0280.0000.0000.0000.000
135A142GLU-1-0.909-0.93237.941-8.584-8.5840.0000.0000.0000.000
136A143LEU00.0710.01638.488-0.262-0.2620.0000.0000.0000.000
137A144GLU-1-0.894-0.94339.207-7.823-7.8230.0000.0000.0000.000
138A145ASN0-0.044-0.02534.511-0.036-0.0360.0000.0000.0000.000
139A146PHE0-0.035-0.02634.265-0.373-0.3730.0000.0000.0000.000
140A147THR00.073-0.01133.9250.0780.0780.0000.0000.0000.000
141A148GLY0-0.127-0.03335.8480.0340.0340.0000.0000.0000.000
142A149ILE0-0.020-0.00936.5440.0930.0930.0000.0000.0000.000
143A150THR0-0.014-0.01038.3040.0780.0780.0000.0000.0000.000
144A151ASP-1-0.848-0.87536.332-8.443-8.4430.0000.0000.0000.000
145A152PRO00.0130.02336.353-0.278-0.2780.0000.0000.0000.000
146A153TYR0-0.027-0.02927.941-0.101-0.1010.0000.0000.0000.000
147A154GLU-1-0.861-0.93533.319-8.914-8.9140.0000.0000.0000.000
148A155PRO0-0.004-0.00830.616-0.370-0.3700.0000.0000.0000.000
149A156PRO0-0.031-0.01926.3600.2120.2120.0000.0000.0000.000
150A157GLU-1-0.843-0.91429.119-9.476-9.4760.0000.0000.0000.000
151A158ASN0-0.052-0.03727.417-0.206-0.2060.0000.0000.0000.000
152A159PRO0-0.0310.00923.991-0.338-0.3380.0000.0000.0000.000
153A160GLN00.0880.05519.443-0.205-0.2050.0000.0000.0000.000
154A161LEU00.0090.00717.593-0.405-0.4050.0000.0000.0000.000
155A162VAL0-0.0060.00221.5270.2770.2770.0000.0000.0000.000
156A163LEU0-0.026-0.01318.945-0.207-0.2070.0000.0000.0000.000
157A164ASP-1-0.787-0.89223.308-10.539-10.5390.0000.0000.0000.000
158A165THR0-0.057-0.04424.718-0.046-0.0460.0000.0000.0000.000
159A166GLU-1-0.886-0.95626.958-9.491-9.4910.0000.0000.0000.000
160A167SER0-0.032-0.00828.7390.3190.3190.0000.0000.0000.000
161A168ASN0-0.051-0.01924.4650.0470.0470.0000.0000.0000.000
162A169THR00.0580.03423.690-0.055-0.0550.0000.0000.0000.000
163A170ILE00.019-0.00820.192-0.422-0.4220.0000.0000.0000.000
164A171GLU-1-0.872-0.94319.251-14.936-14.9360.0000.0000.0000.000
165A172HIS00.0100.01718.660-0.863-0.8630.0000.0000.0000.000
166A173ASN00.018-0.01619.284-0.730-0.7300.0000.0000.0000.000
167A174VAL0-0.018-0.00814.607-0.544-0.5440.0000.0000.0000.000
168A175SER0-0.0040.00214.612-1.874-1.8740.0000.0000.0000.000
169A176TYR00.0140.00714.923-0.988-0.9880.0000.0000.0000.000
170A177LEU0-0.005-0.02014.596-0.305-0.3050.0000.0000.0000.000
171A178TYR0-0.077-0.1127.119-0.179-0.1790.0000.0000.0000.000
172A179SER0-0.0030.00410.827-2.325-2.3250.0000.0000.0000.000
173A180LEU0-0.0200.00712.660-0.552-0.5520.0000.0000.0000.000
174A181VAL00.004-0.0108.575-0.403-0.4030.0000.0000.0000.000
175A182LYS10.8150.8893.94857.50257.592-0.001-0.007-0.0830.000
176A183ALA0-0.0230.0008.898-1.011-1.0110.0000.0000.0000.000
177A184VAL0-0.045-0.02211.6610.9130.9130.0000.0000.0000.000
178A185ILE0-0.083-0.0345.5290.0500.0500.0000.0000.0000.000
179A186GLU-1-0.972-0.9736.201-33.630-33.6300.0000.0000.0000.000