FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: K9NM3

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:

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 191
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2115038.327832
FMO2-HF: Nuclear repulsion 2041703.390023
FMO2-HF: Total energy -73334.937809
FMO2-MP2: Total energy -73550.688876


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.
-8.017-3.0765.56-4.044-6.455-0.03
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 : 0.041 / q_NPA : 0.024
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].
3A10ILE00.0470.0343.864-0.6590.810-0.013-0.675-0.7800.001
4A11ASN00.0090.0266.1400.0910.0910.0000.0000.0000.000
5A12PRO00.034-0.0039.482-0.021-0.0210.0000.0000.0000.000
6A13THR0-0.053-0.02911.804-0.006-0.0060.0000.0000.0000.000
7A14ASN00.016-0.0015.801-0.392-0.3920.0000.0000.0000.000
8A15SER00.012-0.0027.703-0.166-0.1660.0000.0000.0000.000
9A16ALA00.0300.0179.1700.0650.0650.0000.0000.0000.000
10A17LEU0-0.048-0.01011.173-0.090-0.0900.0000.0000.0000.000
11A18PHE00.021-0.01413.3180.0410.0410.0000.0000.0000.000
12A19VAL00.011-0.00715.075-0.025-0.0250.0000.0000.0000.000
13A20CYS00.0220.01617.7750.0040.0040.0000.0000.0000.000
14A21ASP-1-0.717-0.84419.372-0.143-0.1430.0000.0000.0000.000
15A22LEU00.0280.03120.0750.0070.0070.0000.0000.0000.000
16A23GLN0-0.049-0.05523.8910.0020.0020.0000.0000.0000.000
17A24GLU-1-0.854-0.93727.601-0.068-0.0680.0000.0000.0000.000
18A25LYS10.8410.91730.9220.0660.0660.0000.0000.0000.000
19A26PHE00.0050.00626.5830.0000.0000.0000.0000.0000.000
20A27ALA0-0.0010.00729.458-0.004-0.0040.0000.0000.0000.000
21A28SER0-0.013-0.01130.5780.0000.0000.0000.0000.0000.000
22A29ASN0-0.093-0.04630.8640.0040.0040.0000.0000.0000.000
23A30ILE00.0010.00124.438-0.006-0.0060.0000.0000.0000.000
24A31LYS10.8450.93525.5140.1170.1170.0000.0000.0000.000
25A32TYR00.0540.03624.287-0.013-0.0130.0000.0000.0000.000
26A33PHE00.0610.05125.007-0.006-0.0060.0000.0000.0000.000
27A34PRO00.0360.00925.494-0.004-0.0040.0000.0000.0000.000
28A35GLU-1-0.810-0.90024.247-0.110-0.1100.0000.0000.0000.000
29A36ILE00.0080.01120.235-0.006-0.0060.0000.0000.0000.000
30A37ILE0-0.0140.00621.271-0.009-0.0090.0000.0000.0000.000
31A38THR0-0.022-0.02323.2360.0050.0050.0000.0000.0000.000
32A39THR0-0.040-0.03517.7710.0110.0110.0000.0000.0000.000
33A40SER00.006-0.01918.478-0.015-0.0150.0000.0000.0000.000
34A41ARG10.7670.86319.5640.0660.0660.0000.0000.0000.000
35A42ARG10.8320.91719.6160.1140.1140.0000.0000.0000.000
36A43LEU00.016-0.00113.4890.0040.0040.0000.0000.0000.000
37A44ILE00.0020.01617.2830.0070.0070.0000.0000.0000.000
38A45ASP-1-0.790-0.86819.583-0.045-0.0450.0000.0000.0000.000
39A46ALA00.002-0.00917.0860.0160.0160.0000.0000.0000.000
40A47ALA0-0.003-0.00116.1460.0180.0180.0000.0000.0000.000
41A48ARG10.8150.88817.4330.0620.0620.0000.0000.0000.000
42A49ILE0-0.077-0.03320.5580.0160.0160.0000.0000.0000.000
43A50LEU0-0.045-0.03214.9670.0220.0220.0000.0000.0000.000
44A51SER0-0.040-0.01517.1480.0240.0240.0000.0000.0000.000
45A52ILE0-0.0230.00812.6980.0120.0120.0000.0000.0000.000
46A53PRO0-0.001-0.00114.043-0.018-0.0180.0000.0000.0000.000
47A54THR00.0010.00115.134-0.039-0.0390.0000.0000.0000.000
48A55ILE0-0.010-0.00317.0800.0190.0190.0000.0000.0000.000
49A56VAL00.0250.01218.335-0.023-0.0230.0000.0000.0000.000
50A57THR0-0.048-0.04520.6660.0030.0030.0000.0000.0000.000
51A58GLU-1-0.725-0.82222.777-0.078-0.0780.0000.0000.0000.000
52A59GLN00.0470.03725.3920.0040.0040.0000.0000.0000.000
53A60TYR00.0450.01526.9760.0070.0070.0000.0000.0000.000
54A61PRO00.0900.04829.4670.0020.0020.0000.0000.0000.000
55A62LYS10.8800.94631.6480.0540.0540.0000.0000.0000.000
56A63GLY0-0.041-0.01533.9080.0030.0030.0000.0000.0000.000
57A64LEU0-0.020-0.02028.3950.0020.0020.0000.0000.0000.000
58A65GLY00.0220.02531.384-0.002-0.0020.0000.0000.0000.000
59A66HIS0-0.045-0.04029.936-0.001-0.0010.0000.0000.0000.000
60A67THR0-0.032-0.05924.445-0.006-0.0060.0000.0000.0000.000
61A68VAL00.007-0.00226.9710.0080.0080.0000.0000.0000.000
62A69PRO00.0440.01727.718-0.003-0.0030.0000.0000.0000.000
63A70THR00.004-0.00427.5540.0000.0000.0000.0000.0000.000
64A71LEU0-0.040-0.01022.299-0.002-0.0020.0000.0000.0000.000
65A72LYS10.8570.91324.9340.0690.0690.0000.0000.0000.000
66A73GLU-1-0.850-0.90027.063-0.049-0.0490.0000.0000.0000.000
67A74GLY0-0.0020.00924.8750.0060.0060.0000.0000.0000.000
68A75LEU0-0.017-0.00221.872-0.001-0.0010.0000.0000.0000.000
69A76ALA00.0210.01221.4280.0090.0090.0000.0000.0000.000
70A77GLU-1-0.900-0.93923.4220.0010.0010.0000.0000.0000.000
71A78ASN0-0.051-0.02524.900-0.002-0.0020.0000.0000.0000.000
72A79THR0-0.046-0.03721.329-0.002-0.0020.0000.0000.0000.000
73A80PRO0-0.020-0.00221.201-0.001-0.0010.0000.0000.0000.000
74A81ILE0-0.007-0.01322.674-0.012-0.0120.0000.0000.0000.000
75A82PHE0-0.010-0.00621.6010.0080.0080.0000.0000.0000.000
76A83ASP-1-0.924-0.95725.068-0.076-0.0760.0000.0000.0000.000
77A84LYS10.7630.86321.4630.1420.1420.0000.0000.0000.000
78A85THR0-0.005-0.01626.9680.0010.0010.0000.0000.0000.000
79A86LYS10.8700.93720.2740.1550.1550.0000.0000.0000.000
80A87PHE00.0530.01622.573-0.002-0.0020.0000.0000.0000.000
81A88SER0-0.027-0.02518.108-0.007-0.0070.0000.0000.0000.000
82A89MET0-0.029-0.00217.0070.0060.0060.0000.0000.0000.000
83A90CYS0-0.0310.01915.8040.0090.0090.0000.0000.0000.000
84A91ILE00.0120.00718.4520.0100.0100.0000.0000.0000.000
85A92PRO00.0700.03021.1610.0000.0000.0000.0000.0000.000
86A93PRO0-0.0030.00022.0870.0060.0060.0000.0000.0000.000
87A94THR0-0.017-0.01317.949-0.001-0.0010.0000.0000.0000.000
88A95GLU-1-0.819-0.90717.426-0.091-0.0910.0000.0000.0000.000
89A96ASP-1-0.870-0.93917.1650.0110.0110.0000.0000.0000.000
90A97THR0-0.053-0.02014.8060.0240.0240.0000.0000.0000.000
91A98LEU00.010-0.00112.6360.0160.0160.0000.0000.0000.000
92A99LYS10.8490.91412.4760.0200.0200.0000.0000.0000.000
93A100LYS10.8950.95913.965-0.042-0.0420.0000.0000.0000.000
94A101VAL0-0.060-0.0119.3980.0480.0480.0000.0000.0000.000
95A102GLN00.0250.0075.3560.3690.3690.0000.0000.0000.000
96A103ASN0-0.036-0.0122.954-2.559-1.5180.211-0.528-0.724-0.005
97A104VAL00.0150.0125.9530.2230.2230.0000.0000.0000.000
98A105ILE00.0150.0198.294-0.123-0.1230.0000.0000.0000.000
99A106LEU0-0.036-0.0089.6260.0990.0990.0000.0000.0000.000
100A107VAL00.0140.00412.159-0.014-0.0140.0000.0000.0000.000
101A108GLY00.0540.01515.5640.0120.0120.0000.0000.0000.000
102A109ILE0-0.047-0.02618.761-0.005-0.0050.0000.0000.0000.000
103A110GLU-1-0.841-0.93321.135-0.151-0.1510.0000.0000.0000.000
104A111ALA00.0330.01118.126-0.010-0.0100.0000.0000.0000.000
105A112HIS00.0440.01418.046-0.032-0.0320.0000.0000.0000.000
106A113VAL0-0.014-0.01020.4550.0030.0030.0000.0000.0000.000
107A115VAL00.0200.03014.448-0.016-0.0160.0000.0000.0000.000
108A116LEU0-0.0080.02214.962-0.045-0.0450.0000.0000.0000.000
109A117GLN0-0.003-0.01015.567-0.023-0.0230.0000.0000.0000.000
110A118THR00.000-0.02013.8220.0110.0110.0000.0000.0000.000
111A119THR0-0.026-0.02610.284-0.039-0.0390.0000.0000.0000.000
112A120TYR00.0130.00011.858-0.052-0.0520.0000.0000.0000.000
113A121ASP-1-0.714-0.80914.054-0.199-0.1990.0000.0000.0000.000
114A122LEU0-0.003-0.00510.2970.0320.0320.0000.0000.0000.000
115A123LEU0-0.022-0.0067.736-0.008-0.0080.0000.0000.0000.000
116A124GLU-1-0.971-0.97710.602-0.213-0.2130.0000.0000.0000.000
117A125ARG10.6980.82613.0880.2120.2120.0000.0000.0000.000
118A126GLY0-0.0040.0069.9700.0670.0670.0000.0000.0000.000
119A127LEU0-0.068-0.0207.335-0.010-0.0100.0000.0000.0000.000
120A128ASN0-0.026-0.0262.565-4.487-2.2412.266-1.748-2.764-0.020
121A129VAL00.0090.0034.7580.2590.270-0.001-0.007-0.0030.000
122A130HIS0-0.020-0.0112.695-0.4560.4670.552-0.486-0.988-0.003
123A131VAL00.0360.0066.7590.1730.1730.0000.0000.0000.000
124A132VAL00.0000.00410.296-0.002-0.0020.0000.0000.0000.000
125A133VAL00.0310.01412.6150.0500.0500.0000.0000.0000.000
126A134ASP-1-0.772-0.86715.058-0.230-0.2300.0000.0000.0000.000
127A135ALA0-0.030-0.02515.9850.0300.0300.0000.0000.0000.000
128A136VAL00.0510.04014.6110.0040.0040.0000.0000.0000.000
129A137SER0-0.007-0.02617.7550.0030.0030.0000.0000.0000.000
130A138SER0-0.004-0.01321.048-0.006-0.0060.0000.0000.0000.000
131A139ARG10.9991.01623.7910.1140.1140.0000.0000.0000.000
132A140SER0-0.057-0.02326.6750.0080.0080.0000.0000.0000.000
133A141HIS00.1100.03724.930-0.003-0.0030.0000.0000.0000.000
134A142THR00.0180.00723.857-0.012-0.0120.0000.0000.0000.000
135A143ASP-1-0.848-0.93723.461-0.156-0.1560.0000.0000.0000.000
136A144ARG10.8120.88919.2070.1910.1910.0000.0000.0000.000
137A145HIS00.0070.01119.066-0.027-0.0270.0000.0000.0000.000
138A146PHE00.030-0.01018.950-0.019-0.0190.0000.0000.0000.000
139A147ALA0-0.0050.03017.662-0.012-0.0120.0000.0000.0000.000
140A148PHE00.0500.01214.468-0.031-0.0310.0000.0000.0000.000
141A149LYS10.8350.90914.1550.2660.2660.0000.0000.0000.000
142A150GLN0-0.043-0.03715.541-0.010-0.0100.0000.0000.0000.000
143A151MET0-0.0310.00411.413-0.028-0.0280.0000.0000.0000.000
144A152GLU-1-0.820-0.89610.261-0.480-0.4800.0000.0000.0000.000
145A153GLN0-0.064-0.03710.954-0.032-0.0320.0000.0000.0000.000
146A154ALA0-0.0130.00812.1620.0210.0210.0000.0000.0000.000
147A155GLY00.0100.0118.230-0.010-0.0100.0000.0000.0000.000
148A156ALA0-0.052-0.0186.299-0.304-0.3040.0000.0000.0000.000
149A157ILE0-0.026-0.0212.3950.343-0.4062.545-0.600-1.196-0.003
150A158LEU0-0.030-0.0046.3740.0800.0800.0000.0000.0000.000
151A159THR0-0.002-0.0058.0080.0070.0070.0000.0000.0000.000
152A160THR00.0390.00910.0680.0680.0680.0000.0000.0000.000
153A161SER0-0.020-0.03012.661-0.016-0.0160.0000.0000.0000.000
154A162GLU-1-0.871-0.93314.397-0.126-0.1260.0000.0000.0000.000
155A163ALA00.0340.01611.7450.0240.0240.0000.0000.0000.000
156A164THR0-0.018-0.0229.344-0.050-0.0500.0000.0000.0000.000
157A165ILE0-0.025-0.01811.1310.0280.0280.0000.0000.0000.000
158A166LEU00.0190.00514.2440.0450.0450.0000.0000.0000.000
159A167GLY0-0.023-0.01010.1550.0610.0610.0000.0000.0000.000
160A168LEU0-0.044-0.0169.9880.0950.0950.0000.0000.0000.000
161A169VAL0-0.021-0.01611.6860.0740.0740.0000.0000.0000.000
162A170GLY0-0.030-0.00813.2380.0460.0460.0000.0000.0000.000
163A171GLY00.001-0.01513.9900.0060.0060.0000.0000.0000.000
164A172SER0-0.040-0.05017.779-0.009-0.0090.0000.0000.0000.000
165A173ASP-1-0.897-0.92420.9200.0870.0870.0000.0000.0000.000
166A174HIS00.0170.03115.896-0.009-0.0090.0000.0000.0000.000
167A175PRO00.011-0.00619.648-0.021-0.0210.0000.0000.0000.000
168A176LYS10.8770.92719.866-0.049-0.0490.0000.0000.0000.000
169A177PHE0-0.0230.01219.146-0.021-0.0210.0000.0000.0000.000
170A178LYS10.9030.92521.106-0.032-0.0320.0000.0000.0000.000
171A179GLU-1-0.830-0.89623.1410.0180.0180.0000.0000.0000.000
172A180VAL00.0570.01118.211-0.011-0.0110.0000.0000.0000.000
173A181GLN00.0560.03321.066-0.005-0.0050.0000.0000.0000.000
174A182LYS10.9030.94822.7240.0050.0050.0000.0000.0000.000
175A183LEU0-0.0180.00320.424-0.003-0.0030.0000.0000.0000.000
176A184ILE0-0.017-0.01018.473-0.016-0.0160.0000.0000.0000.000
177A185LEU0-0.0290.00921.9380.0030.0030.0000.0000.0000.000
178A186THR0-0.0040.00225.0490.0020.0020.0000.0000.0000.000
179A187SER00.0590.02621.788-0.001-0.0010.0000.0000.0000.000
180A188ALA0-0.042-0.01319.7200.0080.0080.0000.0000.0000.000
181A189PRO0-0.013-0.00921.7440.0040.0040.0000.0000.0000.000
182A190ASP-1-0.802-0.90222.567-0.157-0.1570.0000.0000.0000.000
183A191THR0-0.059-0.02521.2570.0000.0000.0000.0000.0000.000
184A192GLY00.0060.00523.463-0.007-0.0070.0000.0000.0000.000
185A193LEU0-0.058-0.02617.913-0.005-0.0050.0000.0000.0000.000
186A194VAL00.0010.00820.848-0.014-0.0140.0000.0000.0000.000
187A195PRO0-0.026-0.01621.9740.0120.0120.0000.0000.0000.000
188A196LEU0-0.021-0.00125.1260.0040.0040.0000.0000.0000.000
189A197SER0-0.001-0.02227.853-0.001-0.0010.0000.0000.0000.000
190A198LYN00.0180.02329.5890.0040.0040.0000.0000.0000.000
191A199LEU00.0050.01233.106-0.002-0.0020.0000.0000.0000.000