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: ZN2QN

Calculation Name: 2FBE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2FBE

Chain ID: A

ChEMBL ID:

UniProt ID: A6NLU0

Base Structure: X-ray

Registration Date: 2023-09-26

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 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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2109132.202169
FMO2-HF: Nuclear repulsion 2034167.966494
FMO2-HF: Total energy -74964.235675
FMO2-MP2: Total energy -75180.148102


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:GLY)


Summations of interaction energy for fragment #1(A:1:GLY)
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.
-4.8450.1832.753-3.902-3.878-0.027
Interaction energy analysis for fragmet #1(A:1:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.037 / q_NPA : 0.007
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].
3A3LEU0-0.051-0.0073.1761.0732.6630.017-0.768-0.8390.001
4A4GLY00.0310.0135.246-0.095-0.0950.0000.0000.0000.000
5A5SER0-0.030-0.0077.5670.3020.3020.0000.0000.0000.000
6A6PRO00.0480.0087.406-0.020-0.0200.0000.0000.0000.000
7A7GLU-1-0.882-0.9478.468-0.780-0.7800.0000.0000.0000.000
8A8PHE0-0.030-0.02110.2760.1570.1570.0000.0000.0000.000
9A9GLN0-0.003-0.0064.8760.3490.3490.0000.0000.0000.000
10A10VAL0-0.061-0.0289.3430.1670.1670.0000.0000.0000.000
11A11ASP-1-0.868-0.93511.394-0.058-0.0580.0000.0000.0000.000
12A12MET0-0.053-0.02112.2280.0430.0430.0000.0000.0000.000
13A13THR00.0120.01314.2990.0310.0310.0000.0000.0000.000
14A14PHE0-0.016-0.01716.128-0.026-0.0260.0000.0000.0000.000
15A15ASP-1-0.825-0.90019.554-0.029-0.0290.0000.0000.0000.000
16A16VAL0-0.0110.00323.0570.0050.0050.0000.0000.0000.000
17A17ASP-1-0.855-0.91625.707-0.003-0.0030.0000.0000.0000.000
18A18THR0-0.027-0.07924.599-0.001-0.0010.0000.0000.0000.000
19A19ALA0-0.062-0.01624.9570.0030.0030.0000.0000.0000.000
20A20ASN00.0450.04126.3060.0040.0040.0000.0000.0000.000
21A21ASN00.0830.02128.6490.0060.0060.0000.0000.0000.000
22A22TYR0-0.076-0.02729.8580.0050.0050.0000.0000.0000.000
23A23LEU0-0.034-0.00624.0060.0110.0110.0000.0000.0000.000
24A24ILE0-0.036-0.01124.432-0.008-0.0080.0000.0000.0000.000
25A25ILE0-0.067-0.04120.7960.0100.0100.0000.0000.0000.000
26A26SER0-0.076-0.08919.125-0.008-0.0080.0000.0000.0000.000
27A27GLU-1-0.865-0.95321.4730.1480.1480.0000.0000.0000.000
28A28ASP-1-0.834-0.85516.8290.1810.1810.0000.0000.0000.000
29A29LEU0-0.052-0.02418.564-0.019-0.0190.0000.0000.0000.000
30A30ARG10.9720.97613.081-0.084-0.0840.0000.0000.0000.000
31A31SER00.004-0.00614.9900.0700.0700.0000.0000.0000.000
32A32PHE0-0.033-0.01217.237-0.032-0.0320.0000.0000.0000.000
33A33ARG10.9991.01019.989-0.134-0.1340.0000.0000.0000.000
34A34SER00.0060.00822.702-0.015-0.0150.0000.0000.0000.000
35A35GLY0-0.051-0.05225.9350.0130.0130.0000.0000.0000.000
36A36ASP-1-0.915-0.94129.1730.0830.0830.0000.0000.0000.000
37A37LEU0-0.033-0.00631.631-0.006-0.0060.0000.0000.0000.000
38A38SER00.0380.01232.8900.0010.0010.0000.0000.0000.000
39A39GLN0-0.004-0.00829.111-0.005-0.0050.0000.0000.0000.000
40A40ASN0-0.035-0.02232.904-0.005-0.0050.0000.0000.0000.000
41A41ARG10.9010.95726.633-0.050-0.0500.0000.0000.0000.000
42A42LYS10.9300.95131.096-0.021-0.0210.0000.0000.0000.000
43A43GLU-1-0.924-0.94634.174-0.001-0.0010.0000.0000.0000.000
44A44GLN00.024-0.01132.0650.0040.0040.0000.0000.0000.000
45A45ALA00.0490.02433.6230.0010.0010.0000.0000.0000.000
46A46GLU-1-0.927-0.96629.012-0.028-0.0280.0000.0000.0000.000
47A47ARG10.8200.94128.621-0.011-0.0110.0000.0000.0000.000
48A48PHE0-0.018-0.00724.891-0.002-0.0020.0000.0000.0000.000
49A49ASP-1-0.801-0.90130.0940.0100.0100.0000.0000.0000.000
50A50THR0-0.075-0.04532.5550.0050.0050.0000.0000.0000.000
51A51ALA0-0.024-0.00927.5370.0060.0060.0000.0000.0000.000
52A52LEU0-0.013-0.01625.574-0.001-0.0010.0000.0000.0000.000
53A53CYS0-0.016-0.01623.1990.0090.0090.0000.0000.0000.000
54A54VAL00.0190.00820.7410.0000.0000.0000.0000.0000.000
55A55LEU0-0.0040.00620.591-0.008-0.0080.0000.0000.0000.000
56A56GLY00.0320.01017.7160.0100.0100.0000.0000.0000.000
57A57THR00.0130.00618.638-0.004-0.0040.0000.0000.0000.000
58A58PRO0-0.045-0.01716.460-0.002-0.0020.0000.0000.0000.000
59A59ARG10.9630.98619.7310.0980.0980.0000.0000.0000.000
60A60PHE0-0.0040.01015.154-0.009-0.0090.0000.0000.0000.000
61A61THR00.0620.02720.5860.0050.0050.0000.0000.0000.000
62A62SER00.0280.01121.5830.0010.0010.0000.0000.0000.000
63A63GLY00.0370.04519.084-0.010-0.0100.0000.0000.0000.000
64A64ARG10.8700.95114.0510.6140.6140.0000.0000.0000.000
65A65HIS10.8110.87613.0760.3940.3940.0000.0000.0000.000
66A66TYR0-0.002-0.0163.469-0.0170.1530.001-0.050-0.1210.000
67A67TRP00.0210.0268.326-0.019-0.0190.0000.0000.0000.000
68A68GLU-1-0.812-0.9122.518-4.371-1.5691.345-2.133-2.015-0.025
69A69VAL00.0120.0057.2840.0520.0520.0000.0000.0000.000
70A70ASP-1-0.829-0.9129.7651.0461.0460.0000.0000.0000.000
71A71VAL0-0.009-0.00310.958-0.090-0.0900.0000.0000.0000.000
72A72GLY00.0430.01513.265-0.051-0.0510.0000.0000.0000.000
73A73THR0-0.048-0.04414.742-0.007-0.0070.0000.0000.0000.000
74A74SER0-0.0150.00417.589-0.047-0.0470.0000.0000.0000.000
75A75GLN00.016-0.00719.006-0.004-0.0040.0000.0000.0000.000
76A76VAL0-0.038-0.01021.697-0.018-0.0180.0000.0000.0000.000
77A77TRP0-0.016-0.02314.3560.0040.0040.0000.0000.0000.000
78A78ASP-1-0.754-0.86418.7400.0200.0200.0000.0000.0000.000
79A79VAL0-0.028-0.01412.8570.0060.0060.0000.0000.0000.000
80A80GLY00.0550.02915.356-0.018-0.0180.0000.0000.0000.000
81A81VAL0-0.0540.00516.253-0.007-0.0070.0000.0000.0000.000
82A82CYS0-0.0210.00818.7980.0140.0140.0000.0000.0000.000
83A83LYS10.9540.97822.5770.0860.0860.0000.0000.0000.000
84A84GLU-1-0.880-0.95725.278-0.063-0.0630.0000.0000.0000.000
85A85SER0-0.106-0.10526.6800.0100.0100.0000.0000.0000.000
86A86VAL0-0.045-0.00226.2520.0050.0050.0000.0000.0000.000
87A87ASN00.008-0.00829.3990.0020.0020.0000.0000.0000.000
88A88ARG10.8870.95526.6600.0430.0430.0000.0000.0000.000
89A89GLN0-0.0110.00630.6760.0030.0030.0000.0000.0000.000
90A90GLY0-0.028-0.00433.859-0.003-0.0030.0000.0000.0000.000
91A91LYS10.9230.95032.6710.0020.0020.0000.0000.0000.000
92A92ILE00.0200.01426.751-0.004-0.0040.0000.0000.0000.000
93A93GLU-1-0.965-0.98528.691-0.021-0.0210.0000.0000.0000.000
94A94LEU0-0.015-0.00222.767-0.007-0.0070.0000.0000.0000.000
95A95SER00.0840.04525.927-0.005-0.0050.0000.0000.0000.000
96A96SER00.0550.01724.512-0.003-0.0030.0000.0000.0000.000
97A97GLU-1-0.991-1.00125.777-0.071-0.0710.0000.0000.0000.000
98A98HIS0-0.054-0.01528.4200.0020.0020.0000.0000.0000.000
99A99GLY0-0.055-0.02626.4570.0010.0010.0000.0000.0000.000
100A100PHE00.024-0.00623.157-0.008-0.0080.0000.0000.0000.000
101A101LEU0-0.0320.00119.6910.0010.0010.0000.0000.0000.000
102A102THR0-0.020-0.03518.092-0.009-0.0090.0000.0000.0000.000
103A103VAL00.0270.02214.939-0.002-0.0020.0000.0000.0000.000
104A104GLY00.0620.02317.4580.0150.0150.0000.0000.0000.000
105A105CYS0-0.090-0.01418.2790.0030.0030.0000.0000.0000.000
106A106ARG10.8060.88420.184-0.050-0.0500.0000.0000.0000.000
107A107GLU-1-0.877-0.95823.5250.0950.0950.0000.0000.0000.000
108A108GLY00.0220.01325.305-0.009-0.0090.0000.0000.0000.000
109A109LYS10.8510.92718.868-0.230-0.2300.0000.0000.0000.000
110A110VAL00.0170.02121.568-0.005-0.0050.0000.0000.0000.000
111A111PHE00.000-0.01815.9870.0080.0080.0000.0000.0000.000
112A112ALA0-0.003-0.01320.409-0.013-0.0130.0000.0000.0000.000
113A113ALA00.0570.03619.1660.0040.0040.0000.0000.0000.000
114A114SER0-0.010-0.00220.7410.0030.0030.0000.0000.0000.000
115A115THR0-0.069-0.07122.725-0.008-0.0080.0000.0000.0000.000
116A116VAL00.0050.00725.0600.0100.0100.0000.0000.0000.000
117A117PRO00.0230.00528.859-0.002-0.0020.0000.0000.0000.000
118A118MET00.0050.06125.247-0.006-0.0060.0000.0000.0000.000
119A119THR0-0.016-0.00822.3990.0030.0030.0000.0000.0000.000
120A120PRO0-0.006-0.01122.6150.0040.0040.0000.0000.0000.000
121A121LEU0-0.0130.00017.719-0.013-0.0130.0000.0000.0000.000
122A122TRP0-0.031-0.00819.5980.0200.0200.0000.0000.0000.000
123A123VAL00.0200.01714.527-0.019-0.0190.0000.0000.0000.000
124A124SER00.0130.00413.0680.0210.0210.0000.0000.0000.000
125A125PRO00.0590.01615.1960.0250.0250.0000.0000.0000.000
126A126GLN0-0.023-0.02013.540-0.054-0.0540.0000.0000.0000.000
127A127LEU0-0.0070.00910.2520.1180.1180.0000.0000.0000.000
128A128HIS10.8970.9488.869-1.166-1.1660.0000.0000.0000.000
129A129ARG10.9140.9585.480-2.312-2.3120.0000.0000.0000.000
130A130VAL00.0350.0357.8730.0240.0240.0000.0000.0000.000
131A131GLY00.0190.0026.0310.0180.0180.0000.0000.0000.000
132A132ILE0-0.0040.0016.7740.0100.0100.0000.0000.0000.000
133A133PHE00.016-0.0019.189-0.115-0.1150.0000.0000.0000.000
134A134LEU00.0090.01211.1280.0780.0780.0000.0000.0000.000
135A135ASP-1-0.831-0.92714.745-0.483-0.4830.0000.0000.0000.000
136A136VAL00.0350.00916.8420.0360.0360.0000.0000.0000.000
137A137GLY0-0.038-0.00919.9610.0280.0280.0000.0000.0000.000
138A138MET0-0.042-0.03218.6000.0260.0260.0000.0000.0000.000
139A139ARG10.9060.96920.9940.1930.1930.0000.0000.0000.000
140A140SER00.0100.01317.7750.0060.0060.0000.0000.0000.000
141A141ILE00.0130.00114.572-0.027-0.0270.0000.0000.0000.000
142A142ALA00.0030.02212.4150.0420.0420.0000.0000.0000.000
143A143PHE00.0110.00110.946-0.044-0.0440.0000.0000.0000.000
144A144TYR00.007-0.0047.132-0.052-0.0520.0000.0000.0000.000
145A145ASN00.0330.0358.1690.3280.3280.0000.0000.0000.000
146A146VAL00.002-0.0192.532-0.399-0.4471.371-0.713-0.609-0.001
147A147SER0-0.094-0.0563.5290.3870.9010.019-0.238-0.294-0.002
148A148ASP-1-0.834-0.9236.0980.1350.1350.0000.0000.0000.000
149A149GLY0-0.0060.0086.197-0.327-0.3270.0000.0000.0000.000
150A150CYS0-0.077-0.0287.031-0.059-0.0590.0000.0000.0000.000
151A151HIS00.0180.06210.2960.0080.0080.0000.0000.0000.000
152A152ILE0-0.051-0.01811.2650.0750.0750.0000.0000.0000.000
153A153TYR00.0210.00014.0250.0280.0280.0000.0000.0000.000
154A154THR00.006-0.06514.953-0.060-0.0600.0000.0000.0000.000
155A155PHE0-0.054-0.01416.9540.0280.0280.0000.0000.0000.000
156A156ILE00.016-0.01319.446-0.034-0.0340.0000.0000.0000.000
157A157GLU-1-0.944-0.96321.970-0.125-0.1250.0000.0000.0000.000
158A158ILE0-0.0260.00019.8770.0160.0160.0000.0000.0000.000
159A159PRO0-0.031-0.01823.977-0.005-0.0050.0000.0000.0000.000
160A160VAL00.002-0.01623.083-0.007-0.0070.0000.0000.0000.000
161A161CYS0-0.031-0.02225.824-0.001-0.0010.0000.0000.0000.000
162A162GLU-1-0.762-0.83026.691-0.082-0.0820.0000.0000.0000.000
163A163PRO0-0.022-0.01624.109-0.012-0.0120.0000.0000.0000.000
164A164TRP0-0.0030.00519.9170.0110.0110.0000.0000.0000.000
165A165ARG10.7920.86020.4310.0690.0690.0000.0000.0000.000
166A166PRO0-0.0100.00215.7160.0070.0070.0000.0000.0000.000
167A167PHE00.0520.00917.4780.0230.0230.0000.0000.0000.000
168A168PHE00.000-0.01313.7210.0040.0040.0000.0000.0000.000
169A169ALA00.0500.02618.665-0.005-0.0050.0000.0000.0000.000
170A170HIS00.000-0.00419.7400.0000.0000.0000.0000.0000.000
171A171LYS10.9830.99321.808-0.087-0.0870.0000.0000.0000.000
172A172ARG10.8050.93924.212-0.112-0.1120.0000.0000.0000.000
173A173GLY0-0.008-0.00525.637-0.011-0.0110.0000.0000.0000.000
174A174SER0-0.002-0.01926.829-0.008-0.0080.0000.0000.0000.000
175A175GLN00.029-0.02728.8500.0070.0070.0000.0000.0000.000
176A176ASP-1-0.859-0.92629.6810.1260.1260.0000.0000.0000.000
177A177ASP-1-0.876-0.91423.8080.2040.2040.0000.0000.0000.000
178A178GLN0-0.017-0.01423.331-0.016-0.0160.0000.0000.0000.000
179A179SER0-0.057-0.00519.5580.0210.0210.0000.0000.0000.000
180A180ILE0-0.016-0.02516.685-0.033-0.0330.0000.0000.0000.000
181A181LEU0-0.0220.01015.3840.0400.0400.0000.0000.0000.000
182A182SER0-0.009-0.00712.751-0.027-0.0270.0000.0000.0000.000
183A183ILE0-0.018-0.00711.0700.0490.0490.0000.0000.0000.000
184A184CYS0-0.093-0.0586.6790.2050.2050.0000.0000.0000.000
185A185SER0-0.075-0.0797.170-0.146-0.1460.0000.0000.0000.000
186A186VAL00.0180.0367.818-0.037-0.0370.0000.0000.0000.000
187A187ILE0-0.0070.0137.291-0.099-0.0990.0000.0000.0000.000
188A188ASN00.0750.0689.6790.0980.0980.0000.0000.0000.000