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: ZY1MN

Calculation Name: 2I5K-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2I5K

Chain ID: A

ChEMBL ID:

UniProt ID: P32861

Base Structure: X-ray

Registration Date: 2023-06-19

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 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 470
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -8896140.700123
FMO2-HF: Nuclear repulsion 8712776.280402
FMO2-HF: Total energy -183364.419721
FMO2-MP2: Total energy -183905.943776


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:22:VAL)


Summations of interaction energy for fragment #1(A:22: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.
-3.1840.6230.133-1.485-2.4530.001
Interaction energy analysis for fragmet #1(A:22:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.052 / q_NPA : 0.013
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].
3A24ALA00.0180.0163.047-3.216-1.0360.029-0.939-1.2700.003
4A25SER00.0220.0003.189-1.212-0.2370.101-0.361-0.714-0.002
5A26GLN0-0.027-0.0283.6500.1230.6410.003-0.158-0.3630.000
6A27MET00.0350.0385.4480.2240.2240.0000.0000.0000.000
7A28ARG10.8440.8948.1350.2490.2490.0000.0000.0000.000
8A29ASN00.0060.0088.4450.1640.1640.0000.0000.0000.000
9A30ALA00.0040.0049.4890.0790.0790.0000.0000.0000.000
10A31LEU00.014-0.00111.2010.0470.0470.0000.0000.0000.000
11A32ASN0-0.0220.00213.3540.0060.0060.0000.0000.0000.000
12A33LYS10.7950.89813.0140.3220.3220.0000.0000.0000.000
13A34LEU0-0.006-0.00716.8560.0240.0240.0000.0000.0000.000
14A35ALA0-0.053-0.05120.6200.0000.0000.0000.0000.0000.000
15A44ALA00.0430.01927.6440.0010.0010.0000.0000.0000.000
16A45ARG10.8840.93329.6590.0320.0320.0000.0000.0000.000
17A46ALA00.0770.04829.214-0.003-0.0030.0000.0000.0000.000
18A47LYS10.8110.89822.2440.0750.0750.0000.0000.0000.000
19A48PHE00.1220.05221.2200.0030.0030.0000.0000.0000.000
20A49GLU-1-0.757-0.89319.090-0.070-0.0700.0000.0000.0000.000
21A50ASN0-0.048-0.01819.0620.0100.0100.0000.0000.0000.000
22A51GLU-1-0.818-0.89820.3990.0330.0330.0000.0000.0000.000
23A52LEU0-0.006-0.00416.8500.0200.0200.0000.0000.0000.000
24A53ASP-1-0.809-0.88514.169-0.073-0.0730.0000.0000.0000.000
25A54SER00.0250.02515.1830.0310.0310.0000.0000.0000.000
26A55PHE00.0320.00313.3700.0390.0390.0000.0000.0000.000
27A56PHE0-0.012-0.0187.5920.0480.0480.0000.0000.0000.000
28A57THR0-0.009-0.01111.2700.0730.0730.0000.0000.0000.000
29A58LEU00.0560.03312.9620.0670.0670.0000.0000.0000.000
30A59PHE0-0.012-0.0157.7410.0940.0940.0000.0000.0000.000
31A60ARG10.8540.9347.5230.0780.0780.0000.0000.0000.000
32A61ARG10.7500.8429.112-0.082-0.0820.0000.0000.0000.000
33A62TYR00.0320.00711.5800.0810.0810.0000.0000.0000.000
34A63LEU0-0.028-0.0164.3440.0280.1620.000-0.027-0.1060.000
35A64VAL00.0030.0058.9730.1430.1430.0000.0000.0000.000
36A65GLU-1-0.808-0.89010.5860.3120.3120.0000.0000.0000.000
37A66LYS10.8790.9519.950-0.871-0.8710.0000.0000.0000.000
38A67SER0-0.038-0.02110.0560.0220.0220.0000.0000.0000.000
39A68SER0-0.036-0.01512.169-0.113-0.1130.0000.0000.0000.000
40A69ARG10.8630.91315.648-0.214-0.2140.0000.0000.0000.000
41A70THR00.0290.01516.663-0.040-0.0400.0000.0000.0000.000
42A71THR0-0.109-0.07519.505-0.021-0.0210.0000.0000.0000.000
43A72LEU0-0.0080.01723.3110.0020.0020.0000.0000.0000.000
44A73GLU-1-0.808-0.88325.8360.1450.1450.0000.0000.0000.000
45A74TRP00.0660.01327.944-0.006-0.0060.0000.0000.0000.000
46A75ASP-1-0.890-0.94731.2780.1130.1130.0000.0000.0000.000
47A76LYS10.8070.90528.716-0.130-0.1300.0000.0000.0000.000
48A77ILE0-0.072-0.03331.826-0.003-0.0030.0000.0000.0000.000
49A78LYS10.8470.92234.141-0.090-0.0900.0000.0000.0000.000
50A79SER00.0040.00137.4570.0020.0020.0000.0000.0000.000
51A80PRO0-0.041-0.01238.751-0.001-0.0010.0000.0000.0000.000
52A81ASN0-0.026-0.02240.334-0.004-0.0040.0000.0000.0000.000
53A82PRO00.004-0.01643.3090.0010.0010.0000.0000.0000.000
54A83ASP-1-0.894-0.94243.0650.0460.0460.0000.0000.0000.000
55A84GLU-1-0.830-0.91737.9420.0700.0700.0000.0000.0000.000
56A85VAL0-0.055-0.04140.0230.0040.0040.0000.0000.0000.000
57A86VAL00.0440.04742.477-0.002-0.0020.0000.0000.0000.000
58A87LYS10.8820.92245.793-0.043-0.0430.0000.0000.0000.000
59A88TYR00.008-0.02448.518-0.002-0.0020.0000.0000.0000.000
60A89GLU-1-0.858-0.93650.1920.0390.0390.0000.0000.0000.000
61A90ILE0-0.0260.00249.722-0.002-0.0020.0000.0000.0000.000
62A91ILE00.0380.02347.052-0.001-0.0010.0000.0000.0000.000
63A92SER0-0.094-0.04351.664-0.002-0.0020.0000.0000.0000.000
64A93GLN0-0.050-0.02654.617-0.002-0.0020.0000.0000.0000.000
65A94GLN00.030-0.00450.0140.0000.0000.0000.0000.0000.000
66A95PRO0-0.024-0.01653.5880.0000.0000.0000.0000.0000.000
67A96GLU-1-0.867-0.92154.6530.0270.0270.0000.0000.0000.000
68A97ASN0-0.0240.00453.250-0.002-0.0020.0000.0000.0000.000
69A98VAL00.0860.04753.4780.0010.0010.0000.0000.0000.000
70A99SER0-0.035-0.03253.9130.0000.0000.0000.0000.0000.000
71A100ASN00.006-0.00149.577-0.001-0.0010.0000.0000.0000.000
72A101LEU00.0430.02449.1740.0010.0010.0000.0000.0000.000
73A102SER0-0.069-0.04649.1940.0000.0000.0000.0000.0000.000
74A103LYS10.8720.93246.055-0.023-0.0230.0000.0000.0000.000
75A104LEU00.0140.01944.0120.0020.0020.0000.0000.0000.000
76A105ALA00.0180.00541.572-0.002-0.0020.0000.0000.0000.000
77A106VAL00.0160.01342.3690.0020.0020.0000.0000.0000.000
78A107LEU00.0050.00335.569-0.001-0.0010.0000.0000.0000.000
79A108LYS10.8520.91339.045-0.042-0.0420.0000.0000.0000.000
80A109LEU0-0.011-0.00832.560-0.001-0.0010.0000.0000.0000.000
81A110ASN00.0140.00135.1230.0020.0020.0000.0000.0000.000
82A111GLY00.0640.05731.988-0.003-0.0030.0000.0000.0000.000
83A112GLY00.0010.01432.0530.0030.0030.0000.0000.0000.000
84A113LEU00.0510.02232.251-0.004-0.0040.0000.0000.0000.000
85A114GLY00.023-0.00535.4640.0030.0030.0000.0000.0000.000
86A115THR00.0320.02034.0350.0000.0000.0000.0000.0000.000
87A116SER0-0.0200.00335.396-0.003-0.0030.0000.0000.0000.000
88A117MET00.0070.00837.2720.0010.0010.0000.0000.0000.000
89A118GLY0-0.018-0.02139.913-0.003-0.0030.0000.0000.0000.000
90A119CYS0-0.0130.01441.310-0.002-0.0020.0000.0000.0000.000
91A120VAL00.0420.00538.0660.0020.0020.0000.0000.0000.000
92A121GLY00.0750.05738.132-0.002-0.0020.0000.0000.0000.000
93A122PRO00.0400.00837.5190.0040.0040.0000.0000.0000.000
94A123LYS10.7730.86337.627-0.053-0.0530.0000.0000.0000.000
95A124SER0-0.033-0.03439.494-0.001-0.0010.0000.0000.0000.000
96A125VAL00.0390.00741.925-0.002-0.0020.0000.0000.0000.000
97A126ILE0-0.030-0.01141.394-0.002-0.0020.0000.0000.0000.000
98A127GLU-1-0.839-0.90645.2430.0270.0270.0000.0000.0000.000
99A128VAL0-0.030-0.02447.0410.0010.0010.0000.0000.0000.000
100A129ARG10.8140.86749.210-0.027-0.0270.0000.0000.0000.000
101A130GLU-1-0.836-0.89752.8980.0230.0230.0000.0000.0000.000
102A131GLY00.0100.01254.193-0.001-0.0010.0000.0000.0000.000
103A132ASN0-0.046-0.01151.528-0.001-0.0010.0000.0000.0000.000
104A133THR0-0.007-0.01846.4820.0020.0020.0000.0000.0000.000
105A134PHE00.021-0.01144.0960.0000.0000.0000.0000.0000.000
106A135LEU00.0260.02442.3950.0000.0000.0000.0000.0000.000
107A136ASP-1-0.726-0.79945.8440.0230.0230.0000.0000.0000.000
108A137LEU0-0.028-0.00648.563-0.001-0.0010.0000.0000.0000.000
109A138SER0-0.017-0.01645.6330.0000.0000.0000.0000.0000.000
110A139VAL00.0250.00747.369-0.001-0.0010.0000.0000.0000.000
111A140ARG10.9050.93349.342-0.022-0.0220.0000.0000.0000.000
112A141GLN0-0.027-0.00948.3060.0000.0000.0000.0000.0000.000
113A142ILE00.0040.00347.221-0.001-0.0010.0000.0000.0000.000
114A143GLU-1-0.757-0.84650.5750.0170.0170.0000.0000.0000.000
115A144TYR0-0.058-0.02053.331-0.002-0.0020.0000.0000.0000.000
116A145LEU00.0160.00750.100-0.001-0.0010.0000.0000.0000.000
117A146ASN0-0.024-0.00450.8740.0000.0000.0000.0000.0000.000
118A147ARG10.8330.89054.663-0.019-0.0190.0000.0000.0000.000
119A148GLN0-0.032-0.01057.744-0.001-0.0010.0000.0000.0000.000
120A149TYR0-0.030-0.02954.8340.0000.0000.0000.0000.0000.000
121A150ASP-1-0.901-0.92557.5520.0150.0150.0000.0000.0000.000
122A151SER0-0.040-0.01253.2020.0000.0000.0000.0000.0000.000
123A152ASP-1-0.819-0.92150.7670.0160.0160.0000.0000.0000.000
124A153VAL00.0320.02246.9380.0000.0000.0000.0000.0000.000
125A154PRO0-0.044-0.01244.045-0.001-0.0010.0000.0000.0000.000
126A155LEU0-0.028-0.00843.3920.0020.0020.0000.0000.0000.000
127A156LEU00.0110.00538.338-0.002-0.0020.0000.0000.0000.000
128A157LEU0-0.029-0.01738.6100.0030.0030.0000.0000.0000.000
129A158MET00.0270.03830.455-0.001-0.0010.0000.0000.0000.000
130A159ASN0-0.019-0.03234.1460.0060.0060.0000.0000.0000.000
131A160SER00.0710.02329.5910.0020.0020.0000.0000.0000.000
132A161PHE00.0440.02025.802-0.006-0.0060.0000.0000.0000.000
133A162ASN0-0.059-0.02228.523-0.005-0.0050.0000.0000.0000.000
134A163THR0-0.049-0.05232.444-0.001-0.0010.0000.0000.0000.000
135A164ASP-1-0.797-0.86934.1150.0210.0210.0000.0000.0000.000
136A165LYS10.8990.93636.120-0.019-0.0190.0000.0000.0000.000
137A166ASP-1-0.845-0.92238.0940.0200.0200.0000.0000.0000.000
138A167THR0-0.042-0.03138.6950.0010.0010.0000.0000.0000.000
139A168GLU-1-0.835-0.89739.6940.0100.0100.0000.0000.0000.000
140A169HIS00.0090.00141.620-0.001-0.0010.0000.0000.0000.000
141A170LEU0-0.0350.00143.885-0.001-0.0010.0000.0000.0000.000
142A171ILE00.030-0.00141.7850.0000.0000.0000.0000.0000.000
143A172LYS10.8440.90144.250-0.011-0.0110.0000.0000.0000.000
144A173LYS10.8260.92348.334-0.021-0.0210.0000.0000.0000.000
145A174TYR0-0.044-0.05246.7070.0000.0000.0000.0000.0000.000
146A175SER0-0.004-0.01651.0670.0000.0000.0000.0000.0000.000
147A176ALA0-0.046-0.02252.6510.0000.0000.0000.0000.0000.000
148A177ASN0-0.021-0.00152.6460.0000.0000.0000.0000.0000.000
149A178ARG10.8200.89351.762-0.017-0.0170.0000.0000.0000.000
150A179ILE0-0.002-0.02647.7470.0010.0010.0000.0000.0000.000
151A180ARG10.8500.93646.093-0.018-0.0180.0000.0000.0000.000
152A181ILE0-0.003-0.00443.9720.0010.0010.0000.0000.0000.000
153A182ARG10.8210.90140.989-0.021-0.0210.0000.0000.0000.000
154A183SER0-0.001-0.01338.2670.0020.0020.0000.0000.0000.000
155A184PHE00.0140.01931.918-0.003-0.0030.0000.0000.0000.000
156A185ASN0-0.021-0.02030.7780.0080.0080.0000.0000.0000.000
157A186GLN0-0.078-0.06826.690-0.002-0.0020.0000.0000.0000.000
158A187SER0-0.027-0.03623.051-0.009-0.0090.0000.0000.0000.000
159A188ARG10.7910.88024.183-0.004-0.0040.0000.0000.0000.000
160A189PHE00.0270.00819.030-0.006-0.0060.0000.0000.0000.000
161A190PRO0-0.0070.01216.428-0.001-0.0010.0000.0000.0000.000
162A191ARG10.8180.88617.176-0.063-0.0630.0000.0000.0000.000
163A192VAL0-0.018-0.00311.169-0.020-0.0200.0000.0000.0000.000
164A193TYR00.0400.02912.9730.0250.0250.0000.0000.0000.000
165A194LYS10.8220.89212.253-0.175-0.1750.0000.0000.0000.000
166A195ASP-1-0.921-0.96711.4760.2780.2780.0000.0000.0000.000
167A196SER00.007-0.0249.7460.0630.0630.0000.0000.0000.000
168A197LEU0-0.077-0.0306.7060.0520.0520.0000.0000.0000.000
169A198LEU00.0140.0308.617-0.014-0.0140.0000.0000.0000.000
170A199PRO0-0.014-0.02710.4630.0470.0470.0000.0000.0000.000
171A200VAL0-0.022-0.00213.672-0.017-0.0170.0000.0000.0000.000
172A201PRO0-0.0450.00016.773-0.013-0.0130.0000.0000.0000.000
173A202THR0-0.055-0.04416.537-0.015-0.0150.0000.0000.0000.000
174A203GLU-1-0.867-0.89818.196-0.070-0.0700.0000.0000.0000.000
175A204TYR0-0.016-0.02121.5120.0120.0120.0000.0000.0000.000
176A205ASP-1-0.826-0.92123.7130.0120.0120.0000.0000.0000.000
177A206SER00.0120.00521.4070.0000.0000.0000.0000.0000.000
178A207PRO00.0580.03322.5340.0040.0040.0000.0000.0000.000
179A208LEU00.0250.02124.3660.0050.0050.0000.0000.0000.000
180A209ASP-1-0.902-0.95524.4330.0420.0420.0000.0000.0000.000
181A210ALA0-0.0010.00520.2810.0160.0160.0000.0000.0000.000
182A211TRP0-0.0110.00520.3740.0100.0100.0000.0000.0000.000
183A212TYR0-0.099-0.08118.5880.0100.0100.0000.0000.0000.000
184A213PRO00.0310.03223.462-0.002-0.0020.0000.0000.0000.000
185A214PRO00.0100.02421.2780.0110.0110.0000.0000.0000.000
186A215GLY00.0350.00523.1670.0100.0100.0000.0000.0000.000
187A216HIS0-0.030-0.04726.135-0.004-0.0040.0000.0000.0000.000
188A217GLY0-0.005-0.01625.719-0.007-0.0070.0000.0000.0000.000
189A218ASP-1-0.713-0.82024.4340.0710.0710.0000.0000.0000.000
190A219LEU00.0070.01625.867-0.010-0.0100.0000.0000.0000.000
191A220PHE0-0.012-0.01027.134-0.008-0.0080.0000.0000.0000.000
192A221GLU-1-0.784-0.91023.2120.0690.0690.0000.0000.0000.000
193A222SER0-0.011-0.01726.614-0.010-0.0100.0000.0000.0000.000
194A223LEU0-0.0210.00328.714-0.007-0.0070.0000.0000.0000.000
195A224HIS0-0.020-0.01027.300-0.003-0.0030.0000.0000.0000.000
196A225VAL0-0.016-0.00625.949-0.005-0.0050.0000.0000.0000.000
197A226SER0-0.082-0.05929.369-0.005-0.0050.0000.0000.0000.000
198A227GLY00.0190.01632.703-0.003-0.0030.0000.0000.0000.000
199A228GLU-1-0.792-0.90134.6880.0200.0200.0000.0000.0000.000
200A229LEU0-0.0290.00331.9770.0000.0000.0000.0000.0000.000
201A230ASP-1-0.825-0.91634.3820.0170.0170.0000.0000.0000.000
202A231ALA00.0030.00237.269-0.001-0.0010.0000.0000.0000.000
203A232LEU0-0.037-0.01838.183-0.001-0.0010.0000.0000.0000.000
204A233ILE00.0100.01237.038-0.001-0.0010.0000.0000.0000.000
205A234ALA0-0.016-0.00741.127-0.001-0.0010.0000.0000.0000.000
206A235GLN0-0.076-0.03042.905-0.001-0.0010.0000.0000.0000.000
207A236GLY00.0130.01045.0220.0000.0000.0000.0000.0000.000
208A237ARG10.7510.87642.536-0.020-0.0200.0000.0000.0000.000
209A238GLU-1-0.808-0.89341.8080.0260.0260.0000.0000.0000.000
210A239ILE0-0.008-0.00340.7170.0020.0020.0000.0000.0000.000
211A240LEU00.0040.00636.219-0.002-0.0020.0000.0000.0000.000
212A241PHE0-0.030-0.00539.8410.0020.0020.0000.0000.0000.000
213A242VAL00.0250.01834.757-0.002-0.0020.0000.0000.0000.000
214A243SER00.0630.04238.1230.0010.0010.0000.0000.0000.000
215A244ASN00.0210.00934.943-0.001-0.0010.0000.0000.0000.000
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