FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: YY492

Calculation Name: 3FFV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3FFV

Chain ID: A

ChEMBL ID:

UniProt ID: P0A8U0

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 OptHSide
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 180
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2008276.387557
FMO2-HF: Nuclear repulsion 1935610.124112
FMO2-HF: Total energy -72666.263445
FMO2-MP2: Total energy -72878.585585


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-0.8361.093-0.023-0.82-1.0850.001
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.049 / q_NPA : -0.019
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].
3A3ASP-1-0.801-0.8933.8230.1612.090-0.023-0.820-1.0850.001
4A4LEU00.028-0.0156.060-0.169-0.1690.0000.0000.0000.000
5A5THR0-0.036-0.0159.1060.2130.2130.0000.0000.0000.000
6A6ALA00.0160.0097.1090.0710.0710.0000.0000.0000.000
7A7GLN0-0.070-0.0469.031-0.238-0.2380.0000.0000.0000.000
8A8ALA00.0270.02010.6510.1550.1550.0000.0000.0000.000
9A9LEU0-0.0170.00112.2880.1030.1030.0000.0000.0000.000
10A10LYS10.9710.9948.7961.9191.9190.0000.0000.0000.000
11A11ASP-1-0.842-0.90513.858-1.001-1.0010.0000.0000.0000.000
12A12PHE0-0.059-0.03516.2500.0920.0920.0000.0000.0000.000
13A13THR00.030-0.00716.2450.0690.0690.0000.0000.0000.000
14A14ALA00.0120.00917.6430.0540.0540.0000.0000.0000.000
15A15ARG10.8790.93818.7940.5850.5850.0000.0000.0000.000
16A16TYR0-0.016-0.01421.6490.0550.0550.0000.0000.0000.000
17A17CYS0-0.023-0.02721.1620.0350.0350.0000.0000.0000.000
18A18ASP-1-0.895-0.93723.244-0.463-0.4630.0000.0000.0000.000
19A19ALA0-0.056-0.02825.5620.0320.0320.0000.0000.0000.000
20A20TRP00.0520.01926.5030.0260.0260.0000.0000.0000.000
21A21HIS0-0.0100.01127.7600.0250.0250.0000.0000.0000.000
22A22GLU-1-0.913-0.95429.567-0.239-0.2390.0000.0000.0000.000
23A23GLU-1-0.963-0.96731.585-0.189-0.1890.0000.0000.0000.000
24A24HIS0-0.044-0.02732.0450.0200.0200.0000.0000.0000.000
25A25LYS10.7320.86232.3560.2420.2420.0000.0000.0000.000
26A26SER0-0.047-0.03630.5640.0080.0080.0000.0000.0000.000
27A27TRP00.0220.01221.544-0.027-0.0270.0000.0000.0000.000
28A28PRO00.0160.00024.0760.0210.0210.0000.0000.0000.000
29A29LEU0-0.0050.00327.330-0.003-0.0030.0000.0000.0000.000
30A30SER0-0.032-0.02128.1360.0090.0090.0000.0000.0000.000
31A31GLU-1-0.855-0.94430.172-0.168-0.1680.0000.0000.0000.000
32A32GLU-1-0.984-0.99130.032-0.190-0.1900.0000.0000.0000.000
33A33LEU0-0.021-0.00225.1530.0030.0030.0000.0000.0000.000
34A34TYR0-0.068-0.02029.175-0.003-0.0030.0000.0000.0000.000
35A35GLY0-0.014-0.00531.9230.0100.0100.0000.0000.0000.000
36A36VAL0-0.043-0.01426.5120.0100.0100.0000.0000.0000.000
37A37PRO0-0.017-0.01326.728-0.017-0.0170.0000.0000.0000.000
38A38SER00.038-0.00521.798-0.016-0.0160.0000.0000.0000.000
39A39PRO0-0.024-0.01119.3880.0110.0110.0000.0000.0000.000
40A40CYS0-0.044-0.00720.190-0.028-0.0280.0000.0000.0000.000
41A41ILE0-0.0140.00922.1860.0010.0010.0000.0000.0000.000
42A42ILE0-0.0370.00225.174-0.002-0.0020.0000.0000.0000.000
43A43SER0-0.040-0.03927.4730.0130.0130.0000.0000.0000.000
44A44THR0-0.001-0.00430.983-0.008-0.0080.0000.0000.0000.000
45A45THR0-0.027-0.00533.3010.0040.0040.0000.0000.0000.000
46A46GLU-1-0.931-0.98136.551-0.132-0.1320.0000.0000.0000.000
47A47ASP-1-0.956-0.96937.158-0.148-0.1480.0000.0000.0000.000
48A48ALA00.0600.03433.050-0.004-0.0040.0000.0000.0000.000
49A49VAL0-0.027-0.01527.9180.0000.0000.0000.0000.0000.000
50A50TYR00.0070.01928.874-0.002-0.0020.0000.0000.0000.000
51A51TRP0-0.022-0.01120.326-0.020-0.0200.0000.0000.0000.000
52A52GLN00.001-0.00719.9190.0250.0250.0000.0000.0000.000
53A53PRO00.0030.00416.4340.0090.0090.0000.0000.0000.000
54A54GLN0-0.034-0.01416.920-0.046-0.0460.0000.0000.0000.000
55A55PRO0-0.021-0.02412.667-0.062-0.0620.0000.0000.0000.000
56A56PHE00.0120.02911.1340.0830.0830.0000.0000.0000.000
57A57THR0-0.069-0.07112.193-0.073-0.0730.0000.0000.0000.000
58A58GLY00.0670.02913.3920.0510.0510.0000.0000.0000.000
59A59GLU-1-0.901-0.94411.611-0.093-0.0930.0000.0000.0000.000
60A60GLN0-0.050-0.0307.085-0.069-0.0690.0000.0000.0000.000
61A61ASN0-0.013-0.0138.4950.0140.0140.0000.0000.0000.000
62A62VAL00.0320.00511.114-0.011-0.0110.0000.0000.0000.000
63A63ASN00.0550.00912.3040.0320.0320.0000.0000.0000.000
64A64ALA0-0.056-0.01015.6710.0280.0280.0000.0000.0000.000
65A65VAL00.011-0.00118.1130.0130.0130.0000.0000.0000.000
66A66GLU-1-0.831-0.91215.3540.1940.1940.0000.0000.0000.000
67A67ARG10.7800.88816.104-0.008-0.0080.0000.0000.0000.000
68A68ALA0-0.042-0.01221.0680.0060.0060.0000.0000.0000.000
69A69PHE0-0.055-0.03422.639-0.007-0.0070.0000.0000.0000.000
70A70ASP-1-0.939-0.96522.3340.1450.1450.0000.0000.0000.000
71A71ILE0-0.066-0.03419.819-0.007-0.0070.0000.0000.0000.000
72A72VAL00.0060.01515.9810.0100.0100.0000.0000.0000.000
73A73ILE0-0.043-0.02714.713-0.007-0.0070.0000.0000.0000.000
74A74GLN0-0.009-0.01914.2890.0560.0560.0000.0000.0000.000
75A75PRO00.0400.0109.420-0.069-0.0690.0000.0000.0000.000
76A76THR00.0140.00510.351-0.098-0.0980.0000.0000.0000.000
77A77ILE00.0310.02412.076-0.119-0.1190.0000.0000.0000.000
78A78HIS00.0050.0109.967-0.125-0.1250.0000.0000.0000.000
79A79THR0-0.017-0.0067.308-0.024-0.0240.0000.0000.0000.000
80A80PHE0-0.047-0.0179.584-0.148-0.1480.0000.0000.0000.000
81A81TYR0-0.013-0.02312.836-0.034-0.0340.0000.0000.0000.000
82A82THR0-0.025-0.0019.882-0.017-0.0170.0000.0000.0000.000
83A83THR0-0.015-0.0098.796-0.262-0.2620.0000.0000.0000.000
84A84GLN0-0.104-0.0799.836-0.227-0.2270.0000.0000.0000.000
85A85PHE0-0.036-0.00312.9690.0630.0630.0000.0000.0000.000
86A86ALA00.006-0.02916.536-0.035-0.0350.0000.0000.0000.000
87A87GLY00.0640.02319.0170.0300.0300.0000.0000.0000.000
88A88ASP-1-0.873-0.94421.437-0.309-0.3090.0000.0000.0000.000
89A89MET0-0.094-0.03518.344-0.012-0.0120.0000.0000.0000.000
90A90HIS00.0770.06723.9320.0080.0080.0000.0000.0000.000
91A91ALA00.000-0.01624.205-0.022-0.0220.0000.0000.0000.000
92A92GLN0-0.029-0.03626.3270.0280.0280.0000.0000.0000.000
93A93PHE00.0130.01823.679-0.019-0.0190.0000.0000.0000.000
94A94GLY0-0.014-0.00627.3010.0200.0200.0000.0000.0000.000
95A95ASP-1-0.894-0.95430.418-0.147-0.1470.0000.0000.0000.000
96A96ILE0-0.089-0.04329.4710.0080.0080.0000.0000.0000.000
97A97LYS10.9640.99129.5880.1450.1450.0000.0000.0000.000
98A98LEU0-0.031-0.01124.1300.0130.0130.0000.0000.0000.000
99A99THR00.0410.01825.774-0.007-0.0070.0000.0000.0000.000
100A100LEU0-0.079-0.04318.4470.0110.0110.0000.0000.0000.000
101A101LEU00.0360.02021.464-0.010-0.0100.0000.0000.0000.000
102A102GLN0-0.030-0.01815.938-0.107-0.1070.0000.0000.0000.000
103A103THR0-0.023-0.01815.8210.0650.0650.0000.0000.0000.000
104A104TRP00.0410.03218.051-0.066-0.0660.0000.0000.0000.000
105A105SER00.0230.00019.772-0.008-0.0080.0000.0000.0000.000
106A106GLU-1-0.815-0.88617.772-0.305-0.3050.0000.0000.0000.000
107A107ASP-1-0.807-0.88319.829-0.134-0.1340.0000.0000.0000.000
108A108ASP-1-0.774-0.88021.942-0.210-0.2100.0000.0000.0000.000
109A109PHE00.0160.01214.2540.0090.0090.0000.0000.0000.000
110A110ARG10.7670.86819.5630.1500.1500.0000.0000.0000.000
111A111ARG10.8290.89321.7360.1880.1880.0000.0000.0000.000
112A112VAL00.0040.01518.7520.0210.0210.0000.0000.0000.000
113A113GLN00.0470.00916.8550.0510.0510.0000.0000.0000.000
114A114GLU-1-0.848-0.91020.920-0.077-0.0770.0000.0000.0000.000
115A115ASN0-0.043-0.03924.4300.0230.0230.0000.0000.0000.000
116A116LEU00.0000.01018.8630.0160.0160.0000.0000.0000.000
117A117ILE00.0090.00922.3840.0210.0210.0000.0000.0000.000
118A118GLY0-0.014-0.00424.6920.0130.0130.0000.0000.0000.000
119A119HIS0-0.046-0.02324.6470.0060.0060.0000.0000.0000.000
120A120LEU00.0400.02121.6650.0100.0100.0000.0000.0000.000
121A121VAL0-0.0030.00126.3530.0140.0140.0000.0000.0000.000
122A122THR0-0.018-0.00929.3330.0090.0090.0000.0000.0000.000
123A123GLN00.0390.00826.5450.0130.0130.0000.0000.0000.000
124A124LYS10.9911.01228.589-0.064-0.0640.0000.0000.0000.000
125A125ARG10.8900.94730.8400.0190.0190.0000.0000.0000.000
126A126LEU0-0.030-0.01133.6510.0020.0020.0000.0000.0000.000
127A127LYS10.8980.95632.699-0.035-0.0350.0000.0000.0000.000
128A128LEU0-0.045-0.01630.8010.0020.0020.0000.0000.0000.000
129A129PRO00.014-0.00228.0340.0060.0060.0000.0000.0000.000
130A130PRO00.0210.02223.797-0.012-0.0120.0000.0000.0000.000
131A131THR0-0.082-0.07022.8620.0100.0100.0000.0000.0000.000
132A132LEU00.0320.01917.8010.0040.0040.0000.0000.0000.000
133A133PHE00.0480.02521.027-0.010-0.0100.0000.0000.0000.000
134A134ILE0-0.028-0.00918.218-0.012-0.0120.0000.0000.0000.000
135A135ALA00.0190.00820.996-0.032-0.0320.0000.0000.0000.000
136A136THR00.0360.03124.0760.0190.0190.0000.0000.0000.000
137A137LEU0-0.048-0.04227.779-0.012-0.0120.0000.0000.0000.000
138A138GLU-1-0.877-0.93030.847-0.135-0.1350.0000.0000.0000.000
139A139GLU-1-0.891-0.94634.308-0.105-0.1050.0000.0000.0000.000
140A140GLU-1-0.891-0.94934.098-0.078-0.0780.0000.0000.0000.000
141A141LEU0-0.039-0.02233.936-0.001-0.0010.0000.0000.0000.000
142A142GLU-1-0.785-0.84631.609-0.071-0.0710.0000.0000.0000.000
143A143VAL00.0160.01326.913-0.009-0.0090.0000.0000.0000.000
144A144ILE0-0.0040.00623.2730.0130.0130.0000.0000.0000.000
145A145SER00.015-0.03022.460-0.020-0.0200.0000.0000.0000.000
146A146VAL00.0030.02117.2810.0010.0010.0000.0000.0000.000
147A147CYS0-0.073-0.04820.5510.0290.0290.0000.0000.0000.000
148A148ASN00.032-0.00518.637-0.003-0.0030.0000.0000.0000.000
149A149LEU0-0.055-0.01320.2710.0300.0300.0000.0000.0000.000
150A150SER0-0.042-0.05721.1640.0280.0280.0000.0000.0000.000
151A151GLY00.0250.02117.9630.0200.0200.0000.0000.0000.000
152A152GLU-1-0.865-0.88418.744-0.046-0.0460.0000.0000.0000.000
153A153VAL00.0060.00519.823-0.004-0.0040.0000.0000.0000.000
154A155LYS10.8930.95525.7530.0980.0980.0000.0000.0000.000
155A156GLU-1-0.840-0.88926.665-0.045-0.0450.0000.0000.0000.000
156A157THR0-0.002-0.00830.313-0.006-0.0060.0000.0000.0000.000
157A158LEU00.0290.00529.0120.0120.0120.0000.0000.0000.000
158A159GLY0-0.006-0.01032.6280.0030.0030.0000.0000.0000.000
159A160THR0-0.043-0.01734.0520.0070.0070.0000.0000.0000.000
160A161ARG10.8530.89433.262-0.013-0.0130.0000.0000.0000.000
161A162LYS10.8080.89832.8950.0700.0700.0000.0000.0000.000
162A163ARG10.8890.93927.8170.0240.0240.0000.0000.0000.000
163A164THR0-0.009-0.00529.9980.0070.0070.0000.0000.0000.000
164A165HIS0-0.052-0.03324.247-0.021-0.0210.0000.0000.0000.000
165A166LEU0-0.043-0.01325.279-0.003-0.0030.0000.0000.0000.000
166A167ALA00.0150.00621.904-0.016-0.0160.0000.0000.0000.000
167A168SER0-0.007-0.04120.1540.0320.0320.0000.0000.0000.000
168A169ASN0-0.038-0.01016.405-0.020-0.0200.0000.0000.0000.000
169A170LEU00.0470.02013.754-0.026-0.0260.0000.0000.0000.000
170A171ALA00.0550.02913.457-0.046-0.0460.0000.0000.0000.000
171A172GLU-1-0.859-0.90215.323-0.204-0.2040.0000.0000.0000.000
172A173PHE00.0400.00818.728-0.005-0.0050.0000.0000.0000.000
173A174LEU00.0190.00714.7450.0040.0040.0000.0000.0000.000
174A175ASN0-0.004-0.01215.162-0.054-0.0540.0000.0000.0000.000
175A176GLN0-0.041-0.00919.3350.0190.0190.0000.0000.0000.000
176A177LEU0-0.056-0.00120.4040.0310.0310.0000.0000.0000.000
177A178LYS10.8970.96223.2800.2400.2400.0000.0000.0000.000
178A179PRO00.0390.01624.0920.0150.0150.0000.0000.0000.000
179A180LEU0-0.046-0.01226.1480.0200.0200.0000.0000.0000.000
180A181LEU00.0300.02228.6460.0000.0000.0000.0000.0000.000