Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 2J2VR

Calculation Name: 3QKS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3QKS

Chain ID: A

ChEMBL ID:

UniProt ID: Q8U1N9

Base Structure: X-ray

Registration Date: 2023-06-21

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 OptHSide
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
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2085953.260795
FMO2-HF: Nuclear repulsion 2006577.73688
FMO2-HF: Total energy -79375.523915
FMO2-MP2: Total energy -79611.403058


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-16.649-9.26918.069-7.45-17.998-0.035
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.016 / q_NPA : 0.006
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].
3A3LEU00.0110.0022.558-1.7701.3750.543-1.416-2.2720.006
4A4GLU-1-0.830-0.8925.008-1.602-1.518-0.001-0.006-0.0770.000
5A5ARG10.8970.9438.4090.9990.9990.0000.0000.0000.000
6A6VAL0-0.0240.0048.770-0.049-0.0490.0000.0000.0000.000
7A7THR0-0.027-0.01310.4110.1010.1010.0000.0000.0000.000
8A8VAL0-0.022-0.01713.1680.0150.0150.0000.0000.0000.000
9A9LYS10.8290.89515.4870.3160.3160.0000.0000.0000.000
10A10ASN00.002-0.01519.1030.0200.0200.0000.0000.0000.000
11A11PHE00.0040.01815.4960.0150.0150.0000.0000.0000.000
12A12ARG10.7860.83617.1540.0440.0440.0000.0000.0000.000
13A13SER00.0320.01821.4650.0000.0000.0000.0000.0000.000
14A14HIS0-0.0080.03416.606-0.020-0.0200.0000.0000.0000.000
15A15SER00.0350.01320.2330.0060.0060.0000.0000.0000.000
16A16ASP-1-0.835-0.92619.988-0.299-0.2990.0000.0000.0000.000
17A17THR0-0.001-0.00315.6230.0000.0000.0000.0000.0000.000
18A18VAL00.017-0.00214.936-0.030-0.0300.0000.0000.0000.000
19A19VAL0-0.015-0.00312.3250.0350.0350.0000.0000.0000.000
20A20GLU-1-0.822-0.90211.987-0.957-0.9570.0000.0000.0000.000
21A21PHE0-0.057-0.0298.1840.1070.1070.0000.0000.0000.000
22A22LYS10.9490.95810.5470.7280.7280.0000.0000.0000.000
23A23GLU-1-0.865-0.9288.607-1.871-1.8710.0000.0000.0000.000
24A24GLY00.0130.0189.9580.2690.2690.0000.0000.0000.000
25A25ILE00.010-0.00411.027-0.170-0.1700.0000.0000.0000.000
26A26ASN0-0.034-0.02011.0080.1390.1390.0000.0000.0000.000
27A27LEU00.0280.01613.7140.0410.0410.0000.0000.0000.000
28A28ILE0-0.013-0.00713.0070.0120.0120.0000.0000.0000.000
29A29ILE00.0300.00916.2460.0500.0500.0000.0000.0000.000
30A30GLY00.0650.02619.878-0.003-0.0030.0000.0000.0000.000
31A31GLN00.0520.03422.0750.0130.0130.0000.0000.0000.000
32A32ASN00.0070.00822.923-0.020-0.0200.0000.0000.0000.000
33A33GLY00.0500.02822.6980.0030.0030.0000.0000.0000.000
34A34SER0-0.043-0.04121.355-0.014-0.0140.0000.0000.0000.000
35A35GLY00.0510.02719.455-0.010-0.0100.0000.0000.0000.000
36A36LYS10.9000.94216.4960.1800.1800.0000.0000.0000.000
37A37SER00.0240.01215.099-0.013-0.0130.0000.0000.0000.000
38A38SER00.015-0.00114.9580.0130.0130.0000.0000.0000.000
39A39LEU00.0090.02111.8910.0100.0100.0000.0000.0000.000
40A40LEU00.0510.01810.186-0.057-0.0570.0000.0000.0000.000
41A41ASP-1-0.786-0.85710.0690.0090.0090.0000.0000.0000.000
42A42ALA00.000-0.00111.2810.0320.0320.0000.0000.0000.000
43A43ILE00.0250.0155.874-0.036-0.0360.0000.0000.0000.000
44A44LEU00.0250.0146.778-0.076-0.0760.0000.0000.0000.000
45A45VAL0-0.018-0.0107.9640.0820.0820.0000.0000.0000.000
46A46GLY0-0.006-0.0068.7740.0510.0510.0000.0000.0000.000
47A47LEU0-0.0090.0042.617-0.702-0.1880.790-0.188-1.116-0.002
48A48TYR0-0.013-0.0334.611-0.0280.172-0.001-0.012-0.1880.000
49A49TRP0-0.0140.0498.7000.0530.0530.0000.0000.0000.000
50A50PRO0-0.055-0.05012.0360.0180.0180.0000.0000.0000.000
51A51LEU00.0160.00010.902-0.030-0.0300.0000.0000.0000.000
52A52ARG10.8700.93813.692-0.250-0.2500.0000.0000.0000.000
53A53ILE00.0730.04610.0790.0670.0670.0000.0000.0000.000
54A54LYS10.8810.91613.853-0.097-0.0970.0000.0000.0000.000
55A55ASP-1-0.787-0.89416.5610.1310.1310.0000.0000.0000.000
56A56ILE0-0.067-0.01714.238-0.026-0.0260.0000.0000.0000.000
57A57LYS10.8980.94618.179-0.076-0.0760.0000.0000.0000.000
58A58LYS10.9110.95717.870-0.106-0.1060.0000.0000.0000.000
59A59ASP-1-0.865-0.93819.4170.0310.0310.0000.0000.0000.000
60A60GLU-1-0.814-0.87619.215-0.047-0.0470.0000.0000.0000.000
61A61PHE0-0.024-0.01914.377-0.016-0.0160.0000.0000.0000.000
62A62THR0-0.050-0.03719.453-0.010-0.0100.0000.0000.0000.000
63A63LYS10.9210.94922.132-0.023-0.0230.0000.0000.0000.000
64A64VAL00.0140.03823.569-0.002-0.0020.0000.0000.0000.000
65A65GLY00.0160.01424.262-0.013-0.0130.0000.0000.0000.000
66A66ALA00.0300.01426.5670.0070.0070.0000.0000.0000.000
67A67ARG10.9040.95324.3940.1560.1560.0000.0000.0000.000
68A68ASP-1-0.773-0.88121.832-0.114-0.1140.0000.0000.0000.000
69A69THR0-0.046-0.00617.303-0.007-0.0070.0000.0000.0000.000
70A70TYR0-0.050-0.02215.6920.0270.0270.0000.0000.0000.000
71A71ILE00.0130.00610.818-0.018-0.0180.0000.0000.0000.000
72A72ASP-1-0.822-0.86411.919-0.534-0.5340.0000.0000.0000.000
73A73LEU0-0.0060.0125.936-0.048-0.0480.0000.0000.0000.000
74A74ILE00.0080.0047.9500.0800.0800.0000.0000.0000.000
75A75PHE00.001-0.0072.670-2.472-1.1572.202-0.730-2.786-0.008
76A76GLU-1-0.863-0.9304.336-1.426-1.059-0.001-0.087-0.2790.000
77A77LYS10.8590.9102.353-10.839-7.8644.095-3.101-3.968-0.026
78A78ASP-1-0.816-0.8933.4713.3453.5700.0200.028-0.2740.000
79A79GLY00.0350.0266.048-0.254-0.2540.0000.0000.0000.000
80A80THR0-0.049-0.0117.184-0.142-0.1420.0000.0000.0000.000
81A81LYS10.8310.9096.8351.3121.3120.0000.0000.0000.000
82A82TYR00.021-0.0145.8080.3830.3830.0000.0000.0000.000
83A83ARG10.8480.8887.7410.2420.2420.0000.0000.0000.000
84A84ILE0-0.017-0.0036.2720.1980.1980.0000.0000.0000.000
85A85THR0-0.041-0.0339.515-0.065-0.0650.0000.0000.0000.000
86A86ARG10.7920.8809.1160.1390.1390.0000.0000.0000.000
87A87ARG10.8930.94114.7620.1330.1330.0000.0000.0000.000
88A88PHE0-0.034-0.02015.0580.0260.0260.0000.0000.0000.000
89A89LEU00.0290.00620.417-0.011-0.0110.0000.0000.0000.000
90A90LYS10.8100.88321.9900.1000.1000.0000.0000.0000.000
91A91GLY00.0410.01826.589-0.002-0.0020.0000.0000.0000.000
92A92TYR0-0.013-0.01230.3740.0050.0050.0000.0000.0000.000
93A93SER00.0240.02230.2030.0070.0070.0000.0000.0000.000
94A94SER0-0.0200.00124.762-0.003-0.0030.0000.0000.0000.000
95A95GLY00.0190.01024.5280.0110.0110.0000.0000.0000.000
96A96GLU-1-0.829-0.91918.6410.0230.0230.0000.0000.0000.000
97A97ILE00.0030.00818.8720.0110.0110.0000.0000.0000.000
98A98HIS00.001-0.01114.522-0.043-0.0430.0000.0000.0000.000
99A99ALA0-0.004-0.01214.1920.0350.0350.0000.0000.0000.000
100A100MET00.0140.0246.736-0.030-0.0300.0000.0000.0000.000
101A101LYS10.8910.94811.0600.2620.2620.0000.0000.0000.000
102A102ARG10.9900.99110.401-0.341-0.3410.0000.0000.0000.000
103A103LEU0-0.026-0.01311.7830.0260.0260.0000.0000.0000.000
104A104VAL0-0.008-0.00913.7920.0410.0410.0000.0000.0000.000
105A105GLY00.0470.03116.8060.0080.0080.0000.0000.0000.000
106A106ASN00.004-0.00417.431-0.036-0.0360.0000.0000.0000.000
107A107GLU-1-0.809-0.89318.871-0.137-0.1370.0000.0000.0000.000
108A108TRP0-0.010-0.00210.3730.0190.0190.0000.0000.0000.000
109A109LYS10.8360.90215.5230.1380.1380.0000.0000.0000.000
110A110HIS00.0020.00214.776-0.029-0.0290.0000.0000.0000.000
111A111VAL0-0.040-0.00810.8910.0190.0190.0000.0000.0000.000
112A112THR0-0.012-0.01113.5110.0570.0570.0000.0000.0000.000
113A113GLU-1-0.821-0.87915.9330.0860.0860.0000.0000.0000.000
114A114PRO0-0.033-0.01016.6540.0080.0080.0000.0000.0000.000
115A115SER00.005-0.03716.937-0.007-0.0070.0000.0000.0000.000
116A116SER00.0470.00615.2900.0100.0100.0000.0000.0000.000
117A117LYS10.9580.97714.926-0.182-0.1820.0000.0000.0000.000
118A118ALA00.0120.02016.0980.0600.0600.0000.0000.0000.000
119A119ILE00.0100.01010.4610.0690.0690.0000.0000.0000.000
120A120SER00.0280.01611.0930.0750.0750.0000.0000.0000.000
121A121ALA0-0.040-0.01811.9310.1270.1270.0000.0000.0000.000
122A122PHE0-0.024-0.0258.8420.1090.1090.0000.0000.0000.000
123A123MET00.0360.0113.9640.0350.1720.000-0.018-0.1190.000
124A124GLU-1-0.841-0.9008.2941.7391.7390.0000.0000.0000.000
125A125LYS10.8880.94210.816-0.623-0.6230.0000.0000.0000.000
126A126LEU0-0.062-0.0085.2230.0880.0880.0000.0000.0000.000
127A127ILE0-0.002-0.0372.6151.146-1.3506.990-0.950-3.544-0.002
128A128PRO00.0520.0516.303-0.341-0.319-0.001-0.003-0.0180.000
129A129TYR00.027-0.0258.0720.3690.3690.0000.0000.0000.000
130A130ASN00.001-0.0049.030-0.043-0.0430.0000.0000.0000.000
131A131ILE00.0220.0176.545-0.104-0.1040.0000.0000.0000.000
132A132PHE00.0370.0052.510-2.131-1.9443.139-0.778-2.548-0.003
133A133LEU0-0.054-0.0496.777-0.455-0.4550.0000.0000.0000.000
134A134ASN0-0.042-0.0119.773-0.281-0.2810.0000.0000.0000.000
135A135ALA0-0.0160.0068.651-0.141-0.1410.0000.0000.0000.000
136A136ILE0-0.064-0.0233.277-0.6590.0460.294-0.189-0.8090.000
137A137TYR0-0.052-0.0277.348-0.541-0.5410.0000.0000.0000.000
138A138ILE00.0510.0319.759-0.002-0.0020.0000.0000.0000.000
139A139ARG10.8070.88213.426-0.399-0.3990.0000.0000.0000.000
140A140GLN00.000-0.01115.283-0.039-0.0390.0000.0000.0000.000
141A141GLY00.0160.00718.4120.0240.0240.0000.0000.0000.000
142A142GLN0-0.009-0.00515.9580.0040.0040.0000.0000.0000.000
143A143ILE00.0310.00317.5910.0100.0100.0000.0000.0000.000
144A144ASP-1-0.877-0.94521.1420.0130.0130.0000.0000.0000.000
145A145ALA00.0240.01223.1400.0020.0020.0000.0000.0000.000
146A146ILE0-0.048-0.02519.7430.0070.0070.0000.0000.0000.000
147A147LEU0-0.035-0.02324.226-0.001-0.0010.0000.0000.0000.000
148A148GLU-1-0.987-0.96327.0490.0780.0780.0000.0000.0000.000
149A149SER00.003-0.03628.964-0.005-0.0050.0000.0000.0000.000
150A150ASP-1-0.796-0.89029.0620.1130.1130.0000.0000.0000.000
151A151GLU-1-0.891-0.92129.5030.1150.1150.0000.0000.0000.000
152A152ALA0-0.0040.00527.2030.0180.0180.0000.0000.0000.000
153A153ARG10.8140.88724.755-0.095-0.0950.0000.0000.0000.000
154A154GLU-1-0.757-0.83324.4080.2450.2450.0000.0000.0000.000
155A155LYS10.9450.98922.071-0.188-0.1880.0000.0000.0000.000
156A156VAL0-0.043-0.02319.6860.0320.0320.0000.0000.0000.000
157A157VAL00.003-0.00320.1500.0510.0510.0000.0000.0000.000
158A158ARG10.7580.83320.796-0.181-0.1810.0000.0000.0000.000
159A159GLU-1-0.872-0.91517.7170.3300.3300.0000.0000.0000.000
160A160VAL00.0370.01815.0490.0610.0610.0000.0000.0000.000
161A161LEU0-0.078-0.02716.0300.1130.1130.0000.0000.0000.000
162A162ASN0-0.040-0.00916.1060.0120.0120.0000.0000.0000.000
163A163LEU0-0.003-0.00417.149-0.049-0.0490.0000.0000.0000.000
164A164ASP-1-0.751-0.87618.4490.5270.5270.0000.0000.0000.000
165A165LYS10.9030.96420.148-0.458-0.4580.0000.0000.0000.000
166A166PHE0-0.037-0.04122.579-0.038-0.0380.0000.0000.0000.000
167A167GLU-1-0.885-0.94023.0760.3280.3280.0000.0000.0000.000
168A168THR00.003-0.01421.568-0.026-0.0260.0000.0000.0000.000
169A169ALA0-0.061-0.02624.290-0.024-0.0240.0000.0000.0000.000
170A170TYR00.0200.00927.632-0.027-0.0270.0000.0000.0000.000
171A171LYS10.9380.96926.301-0.255-0.2550.0000.0000.0000.000
172A172LYS10.9750.97124.721-0.349-0.3490.0000.0000.0000.000
173A173LEU00.0430.02629.748-0.019-0.0190.0000.0000.0000.000
174A174SER00.0180.01432.522-0.020-0.0200.0000.0000.0000.000
175A175GLU-1-0.834-0.90630.5700.1780.1780.0000.0000.0000.000
176A176LEU0-0.0090.00633.847-0.011-0.0110.0000.0000.0000.000
177A177LYS10.9970.99635.514-0.151-0.1510.0000.0000.0000.000
178A178LYS10.8630.92234.110-0.175-0.1750.0000.0000.0000.000
179A179THR0-0.0190.00036.300-0.009-0.0090.0000.0000.0000.000
180A180ILE0-0.002-0.00739.019-0.008-0.0080.0000.0000.0000.000
181A181ASN0-0.010-0.00741.530-0.010-0.0100.0000.0000.0000.000
182A182ASN00.022-0.00640.257-0.010-0.0100.0000.0000.0000.000
183A183ARG10.9711.00440.000-0.133-0.1330.0000.0000.0000.000
184A184ILE0-0.0060.00044.806-0.005-0.0050.0000.0000.0000.000
185A185LYS10.8760.93545.763-0.103-0.1030.0000.0000.0000.000
186A186GLU-1-0.861-0.92546.8420.0830.0830.0000.0000.0000.000
187A187TYR0-0.012-0.02046.1790.0000.0000.0000.0000.0000.000
188A188ARG10.9540.97850.709-0.087-0.0870.0000.0000.0000.000
189A189ASP-1-0.801-0.87652.1210.0680.0680.0000.0000.0000.000
190A190ILE0-0.0080.00250.520-0.003-0.0030.0000.0000.0000.000
191A191LEU0-0.011-0.00454.429-0.002-0.0020.0000.0000.0000.000
192A192ALA00.0310.02656.657-0.002-0.0020.0000.0000.0000.000
193A193ARG10.7620.85254.047-0.069-0.0690.0000.0000.0000.000
194A194THR0-0.072-0.04857.614-0.002-0.0020.0000.0000.0000.000
195A195GLU-1-0.958-0.96360.3040.0580.0580.0000.0000.0000.000
196A196GLY0-0.0430.00863.040-0.001-0.0010.0000.0000.0000.000
197A197GLY0-0.012-0.01166.7910.0010.0010.0000.0000.0000.000
198A198HIS0-0.027-0.03663.906-0.003-0.0030.0000.0000.0000.000
199A199HIS00.0170.01867.9000.0000.0000.0000.0000.0000.000