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: R9RV8

Calculation Name: 2B34-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2B34

Chain ID: A

ChEMBL ID:

UniProt ID: Q20062

Base Structure: X-ray

Registration Date: 2023-09-20

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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2112255.109905
FMO2-HF: Nuclear repulsion 2038921.065075
FMO2-HF: Total energy -73334.04483
FMO2-MP2: Total energy -73549.785611


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:ALA)


Summations of interaction energy for fragment #1(A:8: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.
-6.83-2.063.729-3.332-5.165-0.02
Interaction energy analysis for fragmet #1(A:8:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.026 / q_NPA : 0.015
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].
3A10ILE00.0180.0333.812-1.2400.644-0.028-0.888-0.9670.001
4A11ASN00.0440.0236.0830.1470.1470.0000.0000.0000.000
5A12PRO00.026-0.0169.612-0.054-0.0540.0000.0000.0000.000
6A13THR0-0.058-0.02611.3230.0070.0070.0000.0000.0000.000
7A14ASN00.0340.0255.928-0.227-0.2270.0000.0000.0000.000
8A15SER00.0340.0037.872-0.179-0.1790.0000.0000.0000.000
9A16ALA00.0370.0209.4030.0800.0800.0000.0000.0000.000
10A17LEU0-0.049-0.00610.938-0.083-0.0830.0000.0000.0000.000
11A18PHE00.023-0.01713.1710.0460.0460.0000.0000.0000.000
12A19VAL00.0260.00014.928-0.024-0.0240.0000.0000.0000.000
13A20CYS00.0070.00817.8190.0000.0000.0000.0000.0000.000
14A21ASP-1-0.730-0.86519.594-0.179-0.1790.0000.0000.0000.000
15A22LEU00.0190.02420.4400.0070.0070.0000.0000.0000.000
16A23GLN0-0.027-0.03124.048-0.002-0.0020.0000.0000.0000.000
17A24GLU-1-0.861-0.94827.700-0.088-0.0880.0000.0000.0000.000
18A25LYS10.8480.92931.1030.0850.0850.0000.0000.0000.000
19A26PHE00.0250.01927.2200.0010.0010.0000.0000.0000.000
20A27ALA0-0.0010.00229.804-0.003-0.0030.0000.0000.0000.000
21A28SER0-0.051-0.01730.8730.0000.0000.0000.0000.0000.000
22A29ASN0-0.063-0.04230.8520.0030.0030.0000.0000.0000.000
23A30ILE00.0070.00724.903-0.007-0.0070.0000.0000.0000.000
24A31LYS10.8840.95026.0710.1340.1340.0000.0000.0000.000
25A32TYR00.0500.04324.726-0.017-0.0170.0000.0000.0000.000
26A33PHE00.0610.04825.410-0.008-0.0080.0000.0000.0000.000
27A34PRO00.0280.00226.060-0.005-0.0050.0000.0000.0000.000
28A35GLU-1-0.823-0.92124.412-0.135-0.1350.0000.0000.0000.000
29A36ILE00.0100.02320.661-0.008-0.0080.0000.0000.0000.000
30A37ILE0-0.0050.02121.659-0.012-0.0120.0000.0000.0000.000
31A38THR0-0.018-0.00723.4140.0030.0030.0000.0000.0000.000
32A39THR0-0.007-0.01818.2710.0100.0100.0000.0000.0000.000
33A40SER00.020-0.01418.597-0.022-0.0220.0000.0000.0000.000
34A41ARG10.8090.89319.4810.0980.0980.0000.0000.0000.000
35A42ARG10.8880.95919.4800.1520.1520.0000.0000.0000.000
36A43LEU00.0230.00913.2130.0020.0020.0000.0000.0000.000
37A44ILE00.0050.01416.8850.0030.0030.0000.0000.0000.000
38A45ASP-1-0.815-0.88819.166-0.092-0.0920.0000.0000.0000.000
39A46ALA0-0.002-0.01016.3260.0170.0170.0000.0000.0000.000
40A47ALA0-0.003-0.00115.6330.0150.0150.0000.0000.0000.000
41A48ARG10.8540.92316.8070.1020.1020.0000.0000.0000.000
42A49ILE0-0.075-0.02719.7940.0160.0160.0000.0000.0000.000
43A50LEU0-0.061-0.04214.5330.0240.0240.0000.0000.0000.000
44A51SER0-0.036-0.00916.9500.0190.0190.0000.0000.0000.000
45A52ILE0-0.0420.00112.2040.0080.0080.0000.0000.0000.000
46A53PRO0-0.009-0.00814.027-0.005-0.0050.0000.0000.0000.000
47A54THR00.0060.00515.044-0.040-0.0400.0000.0000.0000.000
48A55ILE0-0.011-0.00516.7030.0250.0250.0000.0000.0000.000
49A56VAL00.0180.01818.134-0.023-0.0230.0000.0000.0000.000
50A57THR0-0.022-0.01220.1590.0050.0050.0000.0000.0000.000
51A58GLU-1-0.760-0.86222.376-0.109-0.1090.0000.0000.0000.000
52A59GLN00.0250.01325.4710.0010.0010.0000.0000.0000.000
53A60TYR0-0.015-0.01926.9350.0080.0080.0000.0000.0000.000
54A61PRO00.1070.04529.1670.0030.0030.0000.0000.0000.000
55A62LYS10.9150.97731.4890.0690.0690.0000.0000.0000.000
56A63GLY0-0.042-0.02034.0150.0040.0040.0000.0000.0000.000
57A64LEU0-0.060-0.04528.7880.0020.0020.0000.0000.0000.000
58A65GLY00.0350.03231.477-0.003-0.0030.0000.0000.0000.000
59A66HIS0-0.036-0.02629.687-0.001-0.0010.0000.0000.0000.000
60A67THR0-0.044-0.05524.553-0.006-0.0060.0000.0000.0000.000
61A68VAL0-0.014-0.01226.8110.0090.0090.0000.0000.0000.000
62A69PRO00.0340.01327.631-0.004-0.0040.0000.0000.0000.000
63A70THR00.0640.02827.227-0.001-0.0010.0000.0000.0000.000
64A71LEU0-0.023-0.00522.252-0.001-0.0010.0000.0000.0000.000
65A72LYS10.9610.97424.5200.0830.0830.0000.0000.0000.000
66A73GLU-1-0.954-0.97126.725-0.070-0.0700.0000.0000.0000.000
67A74GLY0-0.0230.00224.5110.0060.0060.0000.0000.0000.000
68A75LEU0-0.024-0.00621.550-0.003-0.0030.0000.0000.0000.000
69A76ALA00.0150.00421.0990.0110.0110.0000.0000.0000.000
70A77GLU-1-0.933-0.95623.066-0.037-0.0370.0000.0000.0000.000
71A78ASN0-0.033-0.01124.4870.0010.0010.0000.0000.0000.000
72A79THR0-0.049-0.03521.160-0.005-0.0050.0000.0000.0000.000
73A80PRO0-0.0160.00321.0320.0030.0030.0000.0000.0000.000
74A81ILE00.000-0.01122.527-0.013-0.0130.0000.0000.0000.000
75A82PHE0-0.014-0.00621.2390.0090.0090.0000.0000.0000.000
76A83ASP-1-0.912-0.94724.924-0.100-0.1000.0000.0000.0000.000
77A84LYS10.8170.90921.3000.1750.1750.0000.0000.0000.000
78A85THR0-0.008-0.01726.7430.0000.0000.0000.0000.0000.000
79A86LYS10.9910.99621.9520.1620.1620.0000.0000.0000.000
80A87PHE00.0520.01422.759-0.002-0.0020.0000.0000.0000.000
81A88SER0-0.051-0.03318.266-0.013-0.0130.0000.0000.0000.000
82A89MET0-0.010-0.01316.8640.0070.0070.0000.0000.0000.000
83A90CYS0-0.0530.00515.6040.0070.0070.0000.0000.0000.000
84A91ILE0-0.038-0.00718.2230.0150.0150.0000.0000.0000.000
85A92PRO00.0830.03220.824-0.004-0.0040.0000.0000.0000.000
86A93PRO0-0.0040.00022.1580.0040.0040.0000.0000.0000.000
87A94THR0-0.057-0.03117.408-0.003-0.0030.0000.0000.0000.000
88A95GLU-1-0.927-0.97417.324-0.109-0.1090.0000.0000.0000.000
89A96ASP-1-0.898-0.96017.407-0.043-0.0430.0000.0000.0000.000
90A97THR0-0.069-0.03814.7630.0210.0210.0000.0000.0000.000
91A98LEU00.007-0.00512.1180.0010.0010.0000.0000.0000.000
92A99LYS10.9540.98812.8260.0500.0500.0000.0000.0000.000
93A100LYS10.9130.96514.5780.0350.0350.0000.0000.0000.000
94A101VAL0-0.076-0.0149.7730.0420.0420.0000.0000.0000.000
95A102GLN00.009-0.0075.9770.1260.1260.0000.0000.0000.000
96A103ASN0-0.028-0.0093.132-1.916-0.9210.089-0.430-0.654-0.004
97A104VAL00.0390.0236.0040.1810.1810.0000.0000.0000.000
98A105ILE0-0.0050.0087.829-0.144-0.1440.0000.0000.0000.000
99A106LEU0-0.012-0.0019.6850.1030.1030.0000.0000.0000.000
100A107VAL0-0.011-0.00512.414-0.016-0.0160.0000.0000.0000.000
101A108GLY00.0270.00715.7940.0160.0160.0000.0000.0000.000
102A109ILE0-0.029-0.03719.132-0.013-0.0130.0000.0000.0000.000
103A110GLU-1-0.885-0.93021.484-0.176-0.1760.0000.0000.0000.000
104A111ALA00.031-0.00118.682-0.014-0.0140.0000.0000.0000.000
105A112HIS00.0450.01018.513-0.036-0.0360.0000.0000.0000.000
106A113VAL0-0.024-0.01421.0340.0110.0110.0000.0000.0000.000
107A115VAL00.0200.03115.075-0.019-0.0190.0000.0000.0000.000
108A116LEU0-0.0070.02115.305-0.048-0.0480.0000.0000.0000.000
109A117GLN0-0.008-0.01516.089-0.023-0.0230.0000.0000.0000.000
110A118THR00.006-0.01113.9620.0110.0110.0000.0000.0000.000
111A119THR0-0.028-0.02610.960-0.041-0.0410.0000.0000.0000.000
112A120TYR00.012-0.00812.013-0.058-0.0580.0000.0000.0000.000
113A121ASP-1-0.767-0.85613.893-0.243-0.2430.0000.0000.0000.000
114A122LEU0-0.056-0.04810.2400.0220.0220.0000.0000.0000.000
115A123LEU0-0.028-0.0187.608-0.010-0.0100.0000.0000.0000.000
116A124GLU-1-0.949-0.96310.264-0.241-0.2410.0000.0000.0000.000
117A125ARG10.8300.92012.7410.2550.2550.0000.0000.0000.000
118A126GLY0-0.0190.0039.3940.0650.0650.0000.0000.0000.000
119A127LEU0-0.077-0.0187.5380.0180.0180.0000.0000.0000.000
120A128ASN0-0.030-0.0212.617-2.580-1.1891.889-1.308-1.972-0.013
121A129VAL00.0130.0074.6090.1940.208-0.001-0.008-0.0040.000
122A130HIS0-0.020-0.0082.503-0.2590.2450.464-0.274-0.693-0.001
123A131VAL00.0400.0067.1500.1980.1980.0000.0000.0000.000
124A132VAL00.0010.00710.790-0.015-0.0150.0000.0000.0000.000
125A133VAL00.0380.01013.0690.0660.0660.0000.0000.0000.000
126A134ASP-1-0.797-0.89215.373-0.275-0.2750.0000.0000.0000.000
127A135ALA0-0.032-0.03816.4930.0350.0350.0000.0000.0000.000
128A136VAL00.0380.04015.1250.0090.0090.0000.0000.0000.000
129A137SER0-0.005-0.04318.3760.0040.0040.0000.0000.0000.000
130A138SER00.0170.00121.663-0.007-0.0070.0000.0000.0000.000
131A139ARG11.0071.01524.3570.1290.1290.0000.0000.0000.000
132A140SER0-0.037-0.01727.2040.0080.0080.0000.0000.0000.000
133A141HIS00.0860.01425.487-0.003-0.0030.0000.0000.0000.000
134A142THR00.0280.01424.391-0.014-0.0140.0000.0000.0000.000
135A143ASP-1-0.874-0.94124.026-0.182-0.1820.0000.0000.0000.000
136A144ARG10.7790.87719.5320.2300.2300.0000.0000.0000.000
137A145HIS0-0.0080.00019.666-0.029-0.0290.0000.0000.0000.000
138A146PHE00.014-0.02319.375-0.023-0.0230.0000.0000.0000.000
139A147ALA0-0.0080.02818.506-0.015-0.0150.0000.0000.0000.000
140A148PHE00.0490.01215.048-0.032-0.0320.0000.0000.0000.000
141A149LYS10.9300.97414.3900.2570.2570.0000.0000.0000.000
142A150GLN0-0.001-0.01115.579-0.016-0.0160.0000.0000.0000.000
143A151MET0-0.029-0.00512.142-0.034-0.0340.0000.0000.0000.000
144A152GLU-1-0.909-0.95710.620-0.595-0.5950.0000.0000.0000.000
145A153GLN0-0.104-0.05011.432-0.030-0.0300.0000.0000.0000.000
146A154ALA0-0.020-0.00112.3120.0120.0120.0000.0000.0000.000
147A155GLY00.0130.0178.403-0.002-0.0020.0000.0000.0000.000
148A156ALA0-0.049-0.0166.596-0.337-0.3370.0000.0000.0000.000
149A157ILE0-0.011-0.0142.290-0.357-0.3751.316-0.424-0.875-0.003
150A158LEU0-0.033-0.0036.7760.1530.1530.0000.0000.0000.000
151A159THR00.0140.0098.2460.0550.0550.0000.0000.0000.000
152A160THR00.0350.00910.3060.0880.0880.0000.0000.0000.000
153A161SER0-0.012-0.03312.745-0.025-0.0250.0000.0000.0000.000
154A162GLU-1-0.945-0.97314.668-0.157-0.1570.0000.0000.0000.000
155A163ALA00.0210.01611.1520.0250.0250.0000.0000.0000.000
156A164THR0-0.038-0.0289.444-0.062-0.0620.0000.0000.0000.000
157A165ILE0-0.020-0.01411.2220.0260.0260.0000.0000.0000.000
158A166LEU00.013-0.00814.2060.0450.0450.0000.0000.0000.000
159A167GLY0-0.0190.00110.2360.0650.0650.0000.0000.0000.000
160A168LEU0-0.055-0.0219.6390.0800.0800.0000.0000.0000.000
161A169VAL0-0.009-0.00511.4800.0790.0790.0000.0000.0000.000
162A170GLY0-0.0250.00012.9060.0550.0550.0000.0000.0000.000
163A171GLY00.016-0.00713.7040.0310.0310.0000.0000.0000.000
164A172SER0-0.018-0.02217.409-0.017-0.0170.0000.0000.0000.000
165A173ASP-1-0.907-0.94520.5750.0810.0810.0000.0000.0000.000
166A174HIS0-0.0150.01316.447-0.006-0.0060.0000.0000.0000.000
167A175PRO00.0210.00019.638-0.018-0.0180.0000.0000.0000.000
168A176LYS10.9450.96819.878-0.014-0.0140.0000.0000.0000.000
169A177PHE00.0210.02219.254-0.019-0.0190.0000.0000.0000.000
170A178LYS10.9070.93021.040-0.008-0.0080.0000.0000.0000.000
171A179GLU-1-0.922-0.96322.948-0.025-0.0250.0000.0000.0000.000
172A180VAL00.0360.01017.808-0.010-0.0100.0000.0000.0000.000
173A181GLN00.0450.02820.652-0.007-0.0070.0000.0000.0000.000
174A182LYS10.9120.95122.3780.0290.0290.0000.0000.0000.000
175A183LEU0-0.024-0.00519.634-0.001-0.0010.0000.0000.0000.000
176A184ILE0-0.039-0.01018.452-0.012-0.0120.0000.0000.0000.000
177A185LEU0-0.0280.01021.9080.0040.0040.0000.0000.0000.000
178A186THR0-0.0040.00125.3470.0010.0010.0000.0000.0000.000
179A187SER00.0840.02922.405-0.005-0.0050.0000.0000.0000.000
180A188ALA0-0.033-0.01120.1240.0080.0080.0000.0000.0000.000
181A189PRO0-0.021-0.01322.1060.0030.0030.0000.0000.0000.000
182A190ASP-1-0.848-0.91622.988-0.174-0.1740.0000.0000.0000.000
183A191THR0-0.026-0.01221.212-0.002-0.0020.0000.0000.0000.000
184A192GLY00.0390.01423.577-0.009-0.0090.0000.0000.0000.000
185A193LEU0-0.073-0.03017.905-0.001-0.0010.0000.0000.0000.000
186A194VAL0-0.0010.00820.547-0.013-0.0130.0000.0000.0000.000
187A195PRO0-0.009-0.00622.0700.0140.0140.0000.0000.0000.000
188A196LEU0-0.0120.00125.3390.0040.0040.0000.0000.0000.000
189A197SER0-0.001-0.01128.0070.0010.0010.0000.0000.0000.000
190A198LYN00.0190.01129.4720.0050.0050.0000.0000.0000.000
191A199LEU0-0.0050.01133.284-0.001-0.0010.0000.0000.0000.000