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: MV2YZ

Calculation Name: 5EIQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5EIQ

Chain ID: A

ChEMBL ID:

UniProt ID: Q8IYS5

Base Structure: X-ray

Registration Date: 2023-06-26

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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1794230.77308
FMO2-HF: Nuclear repulsion 1721962.906875
FMO2-HF: Total energy -72267.866205
FMO2-MP2: Total energy -72479.639819


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:3:SER)


Summations of interaction energy for fragment #1(A:3:SER)
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.
-15.068-14.4125.952-2.832-3.7750.028
Interaction energy analysis for fragmet #1(A:3:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.027 / 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].
3A5HIS10.8570.9321.947-16.036-15.5165.953-2.828-3.6450.028
4A6PRO00.0490.0205.7310.0640.0640.0000.0000.0000.000
5A7LYS10.8750.9549.1320.0020.0020.0000.0000.0000.000
6A8PRO0-0.0050.00512.156-0.011-0.0110.0000.0000.0000.000
7A9TRP0-0.012-0.00414.614-0.023-0.0230.0000.0000.0000.000
8A10LEU0-0.004-0.01618.2360.0180.0180.0000.0000.0000.000
9A11GLY00.0150.00921.052-0.011-0.0110.0000.0000.0000.000
10A12ALA00.0250.00324.7130.0050.0050.0000.0000.0000.000
11A13GLN0-0.065-0.01428.114-0.006-0.0060.0000.0000.0000.000
12A14PRO00.0560.03031.2180.0020.0020.0000.0000.0000.000
13A15ALA00.0100.00132.621-0.001-0.0010.0000.0000.0000.000
14A16THR0-0.008-0.00628.8320.0020.0020.0000.0000.0000.000
15A17VAL0-0.022-0.01531.629-0.001-0.0010.0000.0000.0000.000
16A18VAL0-0.016-0.01334.939-0.001-0.0010.0000.0000.0000.000
17A19THR00.0530.03537.5820.0000.0000.0000.0000.0000.000
18A20PRO0-0.031-0.02339.2370.0030.0030.0000.0000.0000.000
19A21GLY00.0240.02339.993-0.002-0.0020.0000.0000.0000.000
20A22VAL0-0.064-0.02136.3950.0000.0000.0000.0000.0000.000
21A23ASN00.026-0.00135.7690.0010.0010.0000.0000.0000.000
22A24VAL0-0.028-0.00530.4190.0000.0000.0000.0000.0000.000
23A25THR0-0.027-0.01427.9390.0030.0030.0000.0000.0000.000
24A26LEU00.0070.00924.9970.0000.0000.0000.0000.0000.000
25A27ARG10.8250.89023.636-0.093-0.0930.0000.0000.0000.000
26A28CYS0-0.0190.00317.8210.0130.0130.0000.0000.0000.000
27A29ARG10.8520.92117.073-0.161-0.1610.0000.0000.0000.000
28A30ALA00.0290.01912.321-0.010-0.0100.0000.0000.0000.000
29A31PRO0-0.048-0.02410.528-0.024-0.0240.0000.0000.0000.000
30A32GLN00.0250.0056.6620.2550.2550.0000.0000.0000.000
31A33PRO00.0100.01212.0080.0330.0330.0000.0000.0000.000
32A34ALA0-0.022-0.01111.5260.1540.1540.0000.0000.0000.000
33A35TRP00.007-0.00112.580-0.061-0.0610.0000.0000.0000.000
34A36ARG10.8730.90213.822-0.294-0.2940.0000.0000.0000.000
35A37PHE00.010-0.01314.1570.0820.0820.0000.0000.0000.000
36A38GLY00.0250.00216.544-0.028-0.0280.0000.0000.0000.000
37A39LEU0-0.040-0.01518.0800.0140.0140.0000.0000.0000.000
38A40PHE0-0.002-0.00515.985-0.001-0.0010.0000.0000.0000.000
39A41LYS10.8440.91121.163-0.085-0.0850.0000.0000.0000.000
40A42PRO0-0.023-0.03322.7920.0040.0040.0000.0000.0000.000
41A43GLY0-0.0050.00422.751-0.004-0.0040.0000.0000.0000.000
42A44GLU-1-0.825-0.90022.4480.0950.0950.0000.0000.0000.000
43A45ILE0-0.010-0.01717.9680.0120.0120.0000.0000.0000.000
44A46ALA0-0.025-0.01818.1930.0140.0140.0000.0000.0000.000
45A47PRO0-0.070-0.01618.182-0.006-0.0060.0000.0000.0000.000
46A48LEU00.0390.02720.751-0.004-0.0040.0000.0000.0000.000
47A49LEU00.0040.00322.946-0.006-0.0060.0000.0000.0000.000
48A50PHE0-0.024-0.02619.1010.0190.0190.0000.0000.0000.000
49A51ARG10.9070.94819.667-0.155-0.1550.0000.0000.0000.000
50A52ASP-1-0.767-0.83618.5730.2470.2470.0000.0000.0000.000
51A53VAL0-0.044-0.03718.022-0.024-0.0240.0000.0000.0000.000
52A54SER0-0.038-0.01216.596-0.005-0.0050.0000.0000.0000.000
53A55SER00.0440.03516.857-0.025-0.0250.0000.0000.0000.000
54A56GLU-1-0.803-0.89515.0870.2700.2700.0000.0000.0000.000
55A57LEU0-0.063-0.02716.4540.0020.0020.0000.0000.0000.000
56A58ALA00.0140.01619.2620.0010.0010.0000.0000.0000.000
57A59GLU-1-0.825-0.90220.9370.0990.0990.0000.0000.0000.000
58A60PHE0-0.004-0.00820.3120.0040.0040.0000.0000.0000.000
59A61PHE00.0130.00926.011-0.003-0.0030.0000.0000.0000.000
60A62LEU0-0.039-0.01928.3770.0010.0010.0000.0000.0000.000
61A63GLU-1-0.873-0.93831.7110.0560.0560.0000.0000.0000.000
62A64GLU-1-0.949-0.97335.3620.0420.0420.0000.0000.0000.000
63A65VAL0-0.065-0.00433.764-0.001-0.0010.0000.0000.0000.000
64A66THR00.0610.00636.172-0.004-0.0040.0000.0000.0000.000
65A67PRO00.033-0.00835.7360.0030.0030.0000.0000.0000.000
66A68ALA0-0.0210.00634.4110.0020.0020.0000.0000.0000.000
67A69GLN00.0520.04431.5240.0010.0010.0000.0000.0000.000
68A70GLY00.0560.04531.0020.0050.0050.0000.0000.0000.000
69A71GLY00.0150.01730.5820.0030.0030.0000.0000.0000.000
70A72SER0-0.082-0.08225.5560.0040.0040.0000.0000.0000.000
71A73TYR0-0.043-0.02723.4760.0030.0030.0000.0000.0000.000
72A74ARG10.8780.93718.322-0.119-0.1190.0000.0000.0000.000
73A76CYS0-0.0110.00712.885-0.006-0.0060.0000.0000.0000.000
74A77TYR00.021-0.0198.7040.0300.0300.0000.0000.0000.000
75A78ARG10.8210.8879.448-0.375-0.3750.0000.0000.0000.000
76A79ARG10.8970.9607.656-1.216-1.2160.0000.0000.0000.000
77A80PRO00.0500.0219.6900.0470.0470.0000.0000.0000.000
78A81ASP-1-0.859-0.9376.9801.4651.4650.0000.0000.0000.000
79A82TRP0-0.069-0.0235.2800.2600.396-0.001-0.004-0.1300.000
80A83GLY00.0860.0396.424-0.224-0.2240.0000.0000.0000.000
81A84PRO00.0390.0098.4900.1790.1790.0000.0000.0000.000
82A85GLY00.0390.02211.7230.0540.0540.0000.0000.0000.000
83A86VAL0-0.082-0.0275.4190.0150.0150.0000.0000.0000.000
84A87TRP00.0400.0138.9140.1550.1550.0000.0000.0000.000
85A88SER0-0.019-0.0137.6090.2430.2430.0000.0000.0000.000
86A89GLN0-0.025-0.0038.604-0.139-0.1390.0000.0000.0000.000
87A90PRO00.0690.02710.8580.0390.0390.0000.0000.0000.000
88A91SER00.0000.00014.582-0.016-0.0160.0000.0000.0000.000
89A92ASP-1-0.855-0.91516.8600.0930.0930.0000.0000.0000.000
90A93VAL0-0.020-0.00919.8430.0090.0090.0000.0000.0000.000
91A94LEU0-0.0090.01923.005-0.006-0.0060.0000.0000.0000.000
92A95GLU-1-0.826-0.90025.2260.0680.0680.0000.0000.0000.000
93A96LEU0-0.025-0.00328.617-0.001-0.0010.0000.0000.0000.000
94A97LEU0-0.028-0.01030.899-0.002-0.0020.0000.0000.0000.000
95A98VAL00.0270.00834.4620.0000.0000.0000.0000.0000.000
96A99THR0-0.054-0.04737.105-0.002-0.0020.0000.0000.0000.000
97A100GLU-1-0.802-0.91940.7140.0360.0360.0000.0000.0000.000
98A101GLU-1-0.889-0.92643.6970.0270.0270.0000.0000.0000.000
99A102LEU0-0.053-0.02139.4610.0010.0010.0000.0000.0000.000
100A103PRO00.017-0.00840.178-0.002-0.0020.0000.0000.0000.000
101A104ARG10.8670.93643.386-0.023-0.0230.0000.0000.0000.000
102A105PRO0-0.056-0.00545.1850.0000.0000.0000.0000.0000.000
103A106SER0-0.062-0.04145.834-0.001-0.0010.0000.0000.0000.000
104A107LEU00.023-0.00747.9170.0010.0010.0000.0000.0000.000
105A108VAL0-0.027-0.00448.992-0.001-0.0010.0000.0000.0000.000
106A109ALA00.0510.01651.7740.0000.0000.0000.0000.0000.000
107A110LEU0-0.071-0.03448.2670.0000.0000.0000.0000.0000.000
108A111PRO00.009-0.00550.950-0.001-0.0010.0000.0000.0000.000
109A112GLY00.0220.01252.9640.0000.0000.0000.0000.0000.000
110A113PRO0-0.036-0.01454.6420.0000.0000.0000.0000.0000.000
111A114VAL00.0150.00656.940-0.001-0.0010.0000.0000.0000.000
112A115VAL0-0.009-0.00359.1040.0000.0000.0000.0000.0000.000
113A116GLY00.0510.02361.7060.0000.0000.0000.0000.0000.000
114A117PRO00.002-0.01464.4570.0000.0000.0000.0000.0000.000
115A118GLY00.0130.01565.9340.0000.0000.0000.0000.0000.000
116A119ALA00.0090.01861.6110.0000.0000.0000.0000.0000.000
117A120ASN0-0.001-0.01258.0590.0000.0000.0000.0000.0000.000
118A121VAL00.0250.02556.4160.0000.0000.0000.0000.0000.000
119A122SER0-0.0060.00051.0360.0010.0010.0000.0000.0000.000
120A123LEU00.0240.01951.9580.0000.0000.0000.0000.0000.000
121A124ARG10.8570.89743.052-0.023-0.0230.0000.0000.0000.000
122A125CYS0-0.0410.01846.9920.0000.0000.0000.0000.0000.000
123A126ALA00.007-0.01343.2580.0010.0010.0000.0000.0000.000
124A127GLY00.0700.04541.947-0.001-0.0010.0000.0000.0000.000
125A128ARG10.8940.93337.633-0.031-0.0310.0000.0000.0000.000
126A129LEU00.0370.03035.3460.0020.0020.0000.0000.0000.000
127A130ARG10.9090.94331.316-0.044-0.0440.0000.0000.0000.000
128A131ASN0-0.019-0.01231.087-0.001-0.0010.0000.0000.0000.000
129A132MET00.0310.04035.5060.0010.0010.0000.0000.0000.000
130A133SER00.002-0.00339.040-0.001-0.0010.0000.0000.0000.000
131A134PHE00.0180.01240.5610.0000.0000.0000.0000.0000.000
132A135VAL0-0.001-0.00545.260-0.001-0.0010.0000.0000.0000.000
133A136LEU0-0.0080.00249.0430.0000.0000.0000.0000.0000.000
134A137TYR00.0600.01452.0030.0000.0000.0000.0000.0000.000
135A138ARG10.8610.92855.661-0.015-0.0150.0000.0000.0000.000
136A139GLU-1-0.854-0.91558.3300.0180.0180.0000.0000.0000.000
137A140GLY00.002-0.00161.473-0.001-0.0010.0000.0000.0000.000
138A141VAL0-0.080-0.04560.1840.0000.0000.0000.0000.0000.000
139A142ALA00.0160.00659.7510.0010.0010.0000.0000.0000.000
140A143ALA0-0.0060.00857.1740.0010.0010.0000.0000.0000.000
141A144PRO0-0.0100.00352.6460.0000.0000.0000.0000.0000.000
142A145LEU0-0.023-0.01654.8000.0000.0000.0000.0000.0000.000
143A146GLN0-0.050-0.04251.2260.0000.0000.0000.0000.0000.000
144A147TYR00.0580.02443.6340.0000.0000.0000.0000.0000.000
145A148ARG10.8320.90543.420-0.024-0.0240.0000.0000.0000.000
146A149HIS0-0.0370.00137.5500.0020.0020.0000.0000.0000.000
147A150SER0-0.034-0.03939.509-0.002-0.0020.0000.0000.0000.000
148A151ALA00.0540.02733.9130.0020.0020.0000.0000.0000.000
149A152GLN00.0280.02135.0970.0040.0040.0000.0000.0000.000
150A153PRO0-0.0020.01136.0060.0000.0000.0000.0000.0000.000
151A154TRP0-0.042-0.05238.4280.0000.0000.0000.0000.0000.000
152A155ALA00.0340.03741.8210.0010.0010.0000.0000.0000.000
153A156ASP-1-0.778-0.84344.6200.0220.0220.0000.0000.0000.000
154A157PHE00.0070.00047.2660.0000.0000.0000.0000.0000.000
155A158THR0-0.0020.00650.6170.0000.0000.0000.0000.0000.000
156A159LEU0-0.0010.01353.7070.0000.0000.0000.0000.0000.000
157A160LEU00.0400.00857.4210.0000.0000.0000.0000.0000.000
158A161GLY00.0910.03660.3080.0000.0000.0000.0000.0000.000
159A162ALA0-0.039-0.02662.8240.0000.0000.0000.0000.0000.000
160A163ARG10.9080.94762.318-0.013-0.0130.0000.0000.0000.000
161A164ALA00.0220.03560.5480.0000.0000.0000.0000.0000.000
162A165PRO00.0370.03461.3550.0000.0000.0000.0000.0000.000
163A166GLY00.0210.01362.9720.0000.0000.0000.0000.0000.000
164A167THR00.0140.01360.1920.0000.0000.0000.0000.0000.000
165A168TYR0-0.032-0.03456.0170.0000.0000.0000.0000.0000.000
166A169SER00.015-0.01254.3590.0000.0000.0000.0000.0000.000
167A171TYR00.0690.03848.0340.0000.0000.0000.0000.0000.000
168A172TYR0-0.053-0.05940.4290.0000.0000.0000.0000.0000.000
169A173HIS00.0320.00942.758-0.001-0.0010.0000.0000.0000.000
170A174THR00.0530.00937.879-0.001-0.0010.0000.0000.0000.000
171A175PRO0-0.056-0.01636.515-0.002-0.0020.0000.0000.0000.000
172A176SER0-0.015-0.00236.683-0.001-0.0010.0000.0000.0000.000
173A177ALA00.0060.02339.022-0.001-0.0010.0000.0000.0000.000
174A178PRO00.0350.01137.3180.0030.0030.0000.0000.0000.000
175A179TYR00.0370.00940.1920.0000.0000.0000.0000.0000.000
176A180VAL00.0360.02339.840-0.001-0.0010.0000.0000.0000.000
177A181LEU0-0.008-0.00842.5090.0000.0000.0000.0000.0000.000
178A182SER0-0.044-0.01744.4160.0000.0000.0000.0000.0000.000
179A183GLN00.0080.00245.583-0.002-0.0020.0000.0000.0000.000
180A184ARG10.9190.95248.521-0.020-0.0200.0000.0000.0000.000
181A185SER0-0.001-0.01950.1520.0000.0000.0000.0000.0000.000
182A186GLU-1-0.827-0.88151.0880.0200.0200.0000.0000.0000.000
183A187VAL0-0.0170.00053.9300.0000.0000.0000.0000.0000.000
184A188LEU0-0.0070.00254.1440.0000.0000.0000.0000.0000.000
185A189VAL00.000-0.00457.2610.0000.0000.0000.0000.0000.000
186A190ILE0-0.0070.00257.4140.0000.0000.0000.0000.0000.000