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: VR9V1

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 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 180
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2014433.746325
FMO2-HF: Nuclear repulsion 1941767.200248
FMO2-HF: Total energy -72666.546077
FMO2-MP2: Total energy -72878.896297


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.
-1.3140.861-0.02-0.965-1.1890.001
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 : -0.042 / q_NPA : -0.022
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-1-0.778-0.8633.749-0.1482.027-0.020-0.965-1.1890.001
4A4LEU00.034-0.0035.977-0.086-0.0860.0000.0000.0000.000
5A5THR0-0.061-0.0418.8880.2810.2810.0000.0000.0000.000
6A6ALA00.0160.0086.8620.1010.1010.0000.0000.0000.000
7A7GLN0-0.079-0.0448.811-0.269-0.2690.0000.0000.0000.000
8A8ALA00.0200.01110.4400.1940.1940.0000.0000.0000.000
9A9LEU0-0.0120.00412.1970.1220.1220.0000.0000.0000.000
10A10LYS10.9280.9868.7031.9501.9500.0000.0000.0000.000
11A11ASP-1-0.830-0.90813.915-1.096-1.0960.0000.0000.0000.000
12A12PHE0-0.069-0.04316.0240.1090.1090.0000.0000.0000.000
13A13THR00.026-0.01216.2430.0760.0760.0000.0000.0000.000
14A14ALA00.0000.01517.6840.0590.0590.0000.0000.0000.000
15A15ARG10.8850.93618.4450.6520.6520.0000.0000.0000.000
16A16TYR0-0.020-0.00921.6350.0570.0570.0000.0000.0000.000
17A17CYS0-0.022-0.02121.2150.0400.0400.0000.0000.0000.000
18A18ASP-1-0.907-0.95422.557-0.501-0.5010.0000.0000.0000.000
19A19ALA0-0.049-0.02925.2660.0350.0350.0000.0000.0000.000
20A20TRP00.0420.01426.2480.0300.0300.0000.0000.0000.000
21A21HIS00.0030.01527.5290.0240.0240.0000.0000.0000.000
22A22GLU-1-0.924-0.96629.278-0.254-0.2540.0000.0000.0000.000
23A23GLU-1-0.955-0.95631.381-0.204-0.2040.0000.0000.0000.000
24A24HIS0-0.035-0.02531.7840.0220.0220.0000.0000.0000.000
25A25LYS10.7040.84432.0590.2590.2590.0000.0000.0000.000
26A26SER0-0.040-0.02730.5440.0090.0090.0000.0000.0000.000
27A27TRP00.0290.00121.166-0.026-0.0260.0000.0000.0000.000
28A28PRO00.0230.01423.8980.0240.0240.0000.0000.0000.000
29A29LEU0-0.0070.00827.1700.0000.0000.0000.0000.0000.000
30A30SER0-0.021-0.01228.3770.0040.0040.0000.0000.0000.000
31A31GLU-1-0.847-0.93730.385-0.185-0.1850.0000.0000.0000.000
32A32GLU-1-0.949-0.97229.651-0.223-0.2230.0000.0000.0000.000
33A33LEU0-0.0120.00525.0720.0010.0010.0000.0000.0000.000
34A34TYR0-0.067-0.03429.027-0.003-0.0030.0000.0000.0000.000
35A35GLY0-0.033-0.01532.0030.0070.0070.0000.0000.0000.000
36A36VAL0-0.027-0.00426.5680.0100.0100.0000.0000.0000.000
37A37PRO0-0.023-0.01526.956-0.017-0.0170.0000.0000.0000.000
38A38SER00.033-0.00721.733-0.016-0.0160.0000.0000.0000.000
39A39PRO0-0.020-0.01619.7170.0110.0110.0000.0000.0000.000
40A40CYS0-0.0330.01020.179-0.032-0.0320.0000.0000.0000.000
41A41ILE0-0.0240.00422.1470.0000.0000.0000.0000.0000.000
42A42ILE0-0.049-0.00925.2470.0000.0000.0000.0000.0000.000
43A43SER0-0.049-0.04027.5160.0140.0140.0000.0000.0000.000
44A44THR00.0140.00430.880-0.009-0.0090.0000.0000.0000.000
45A45THR0-0.031-0.02733.4410.0030.0030.0000.0000.0000.000
46A46GLU-1-0.941-0.98836.757-0.141-0.1410.0000.0000.0000.000
47A47ASP-1-0.920-0.92337.437-0.160-0.1600.0000.0000.0000.000
48A48ALA00.0330.02733.279-0.004-0.0040.0000.0000.0000.000
49A49VAL0-0.025-0.02228.0600.0020.0020.0000.0000.0000.000
50A50TYR00.0100.01329.087-0.004-0.0040.0000.0000.0000.000
51A51TRP0-0.031-0.01820.598-0.020-0.0200.0000.0000.0000.000
52A52GLN0-0.010-0.00719.8780.0280.0280.0000.0000.0000.000
53A53PRO00.0180.00416.4610.0120.0120.0000.0000.0000.000
54A54GLN0-0.034-0.01916.774-0.037-0.0370.0000.0000.0000.000
55A55PRO0-0.026-0.02612.956-0.085-0.0850.0000.0000.0000.000
56A56PHE00.0170.03211.1510.0780.0780.0000.0000.0000.000
57A57THR0-0.088-0.07712.612-0.049-0.0490.0000.0000.0000.000
58A58GLY00.0810.03913.9610.0340.0340.0000.0000.0000.000
59A59GLU-1-0.859-0.91512.120-0.122-0.1220.0000.0000.0000.000
60A60GLN0-0.035-0.0137.307-0.045-0.0450.0000.0000.0000.000
61A61ASN0-0.061-0.0398.348-0.013-0.0130.0000.0000.0000.000
62A62VAL00.0560.01610.9010.0010.0010.0000.0000.0000.000
63A63ASN00.0390.01012.1480.0110.0110.0000.0000.0000.000
64A64ALA0-0.066-0.01815.2740.0350.0350.0000.0000.0000.000
65A65VAL00.0210.01317.9580.0150.0150.0000.0000.0000.000
66A66GLU-1-0.805-0.90815.0270.0990.0990.0000.0000.0000.000
67A67ARG10.7480.84215.6350.0530.0530.0000.0000.0000.000
68A68ALA0-0.031-0.00320.8130.0060.0060.0000.0000.0000.000
69A69PHE0-0.049-0.03122.561-0.004-0.0040.0000.0000.0000.000
70A70ASP-1-0.863-0.91922.1430.0930.0930.0000.0000.0000.000
71A71ILE0-0.058-0.03019.197-0.009-0.0090.0000.0000.0000.000
72A72VAL00.0150.01815.4000.0150.0150.0000.0000.0000.000
73A73ILE0-0.028-0.01213.955-0.007-0.0070.0000.0000.0000.000
74A74GLN00.000-0.01213.7840.0450.0450.0000.0000.0000.000
75A75PRO00.010-0.0048.737-0.079-0.0790.0000.0000.0000.000
76A76THR00.0270.0189.837-0.121-0.1210.0000.0000.0000.000
77A77ILE00.0330.01011.822-0.121-0.1210.0000.0000.0000.000
78A78HIS0-0.0060.0079.411-0.118-0.1180.0000.0000.0000.000
79A79THR00.0140.0096.695-0.027-0.0270.0000.0000.0000.000
80A80PHE0-0.026-0.0028.958-0.124-0.1240.0000.0000.0000.000
81A81TYR0-0.013-0.02412.321-0.039-0.0390.0000.0000.0000.000
82A82THR0-0.010-0.0129.339-0.038-0.0380.0000.0000.0000.000
83A83THR0-0.025-0.0128.458-0.246-0.2460.0000.0000.0000.000
84A84GLN0-0.098-0.0779.529-0.288-0.2880.0000.0000.0000.000
85A85PHE0-0.0240.00612.6930.0630.0630.0000.0000.0000.000
86A86ALA00.024-0.01816.254-0.046-0.0460.0000.0000.0000.000
87A87GLY00.0590.02618.9130.0320.0320.0000.0000.0000.000
88A88ASP-1-0.869-0.94321.351-0.359-0.3590.0000.0000.0000.000
89A89MET0-0.078-0.03718.048-0.003-0.0030.0000.0000.0000.000
90A90HIS00.0410.04723.5390.0000.0000.0000.0000.0000.000
91A91ALA00.000-0.01724.215-0.021-0.0210.0000.0000.0000.000
92A92GLN0-0.024-0.03426.3000.0300.0300.0000.0000.0000.000
93A93PHE0-0.0010.00223.161-0.024-0.0240.0000.0000.0000.000
94A94GLY0-0.003-0.00127.0480.0220.0220.0000.0000.0000.000
95A95ASP-1-0.896-0.94630.129-0.172-0.1720.0000.0000.0000.000
96A96ILE0-0.070-0.03829.1260.0070.0070.0000.0000.0000.000
97A97LYS10.9480.98228.9650.1670.1670.0000.0000.0000.000
98A98LEU0-0.031-0.00924.0290.0120.0120.0000.0000.0000.000
99A99THR00.0260.01025.425-0.007-0.0070.0000.0000.0000.000
100A100LEU0-0.064-0.02918.0640.0090.0090.0000.0000.0000.000
101A101LEU00.0290.01820.796-0.011-0.0110.0000.0000.0000.000
102A102GLN0-0.031-0.02215.724-0.121-0.1210.0000.0000.0000.000
103A103THR0-0.036-0.02915.4520.0650.0650.0000.0000.0000.000
104A104TRP00.0520.03318.156-0.057-0.0570.0000.0000.0000.000
105A105SER00.026-0.00820.117-0.007-0.0070.0000.0000.0000.000
106A106GLU-1-0.808-0.88617.680-0.328-0.3280.0000.0000.0000.000
107A107ASP-1-0.797-0.87619.680-0.154-0.1540.0000.0000.0000.000
108A108ASP-1-0.793-0.86721.779-0.233-0.2330.0000.0000.0000.000
109A109PHE0-0.0020.00413.8570.0070.0070.0000.0000.0000.000
110A110ARG10.7600.86019.1930.1720.1720.0000.0000.0000.000
111A111ARG10.8260.89321.6280.2070.2070.0000.0000.0000.000
112A112VAL00.0160.02218.4040.0210.0210.0000.0000.0000.000
113A113GLN00.0540.01716.1980.0540.0540.0000.0000.0000.000
114A114GLU-1-0.848-0.91920.569-0.103-0.1030.0000.0000.0000.000
115A115ASN0-0.043-0.03424.2370.0250.0250.0000.0000.0000.000
116A116LEU0-0.0100.00618.5540.0170.0170.0000.0000.0000.000
117A117ILE00.0110.01222.3440.0220.0220.0000.0000.0000.000
118A118GLY0-0.0030.00224.4170.0140.0140.0000.0000.0000.000
119A119HIS0-0.042-0.02024.1780.0100.0100.0000.0000.0000.000
120A120LEU00.0430.02221.1890.0140.0140.0000.0000.0000.000
121A121VAL0-0.004-0.00425.8780.0160.0160.0000.0000.0000.000
122A122THR0-0.025-0.00928.9140.0120.0120.0000.0000.0000.000
123A123GLN00.0220.00225.9010.0130.0130.0000.0000.0000.000
124A124LYS10.8520.92526.439-0.038-0.0380.0000.0000.0000.000
125A125ARG10.8890.93730.1650.0440.0440.0000.0000.0000.000
126A126LEU0-0.028-0.01333.2430.0050.0050.0000.0000.0000.000
127A127LYS10.8910.96332.364-0.011-0.0110.0000.0000.0000.000
128A128LEU0-0.040-0.00130.2900.0010.0010.0000.0000.0000.000
129A129PRO00.0220.00327.6650.0060.0060.0000.0000.0000.000
130A130PRO00.0210.02923.318-0.013-0.0130.0000.0000.0000.000
131A131THR0-0.088-0.07122.2720.0070.0070.0000.0000.0000.000
132A132LEU00.0270.01317.1100.0070.0070.0000.0000.0000.000
133A133PHE00.0500.02720.371-0.015-0.0150.0000.0000.0000.000
134A134ILE0-0.038-0.01417.755-0.019-0.0190.0000.0000.0000.000
135A135ALA00.0200.01120.414-0.032-0.0320.0000.0000.0000.000
136A136THR00.0390.03123.6370.0200.0200.0000.0000.0000.000
137A137LEU0-0.055-0.04527.337-0.013-0.0130.0000.0000.0000.000
138A138GLU-1-0.876-0.92330.451-0.155-0.1550.0000.0000.0000.000
139A139GLU-1-0.875-0.94033.732-0.132-0.1320.0000.0000.0000.000
140A140GLU-1-0.928-0.96633.843-0.096-0.0960.0000.0000.0000.000
141A141LEU0-0.011-0.00333.943-0.001-0.0010.0000.0000.0000.000
142A142GLU-1-0.772-0.85630.964-0.099-0.0990.0000.0000.0000.000
143A143VAL00.0000.00326.327-0.009-0.0090.0000.0000.0000.000
144A144ILE00.005-0.00322.8320.0140.0140.0000.0000.0000.000
145A145SER00.024-0.01721.792-0.024-0.0240.0000.0000.0000.000
146A146VAL00.0250.02516.5290.0010.0010.0000.0000.0000.000
147A147CYS0-0.059-0.03919.8820.0370.0370.0000.0000.0000.000
148A148ASN00.025-0.01018.006-0.008-0.0080.0000.0000.0000.000
149A149LEU0-0.058-0.02419.5450.0290.0290.0000.0000.0000.000
150A150SER0-0.055-0.06120.7450.0250.0250.0000.0000.0000.000
151A151GLY00.0280.01917.2730.0210.0210.0000.0000.0000.000
152A152GLU-1-0.866-0.87917.862-0.103-0.1030.0000.0000.0000.000
153A153VAL00.0000.00118.999-0.005-0.0050.0000.0000.0000.000
154A155LYS10.9000.95724.9990.1310.1310.0000.0000.0000.000
155A156GLU-1-0.826-0.87926.162-0.084-0.0840.0000.0000.0000.000
156A157THR0-0.006-0.00629.864-0.005-0.0050.0000.0000.0000.000
157A158LEU00.0500.03528.5440.0130.0130.0000.0000.0000.000
158A159GLY0-0.004-0.00632.2350.0040.0040.0000.0000.0000.000
159A160THR0-0.052-0.03533.6720.0100.0100.0000.0000.0000.000
160A161ARG10.8560.88832.7480.0110.0110.0000.0000.0000.000
161A162LYS10.7920.90132.6240.0980.0980.0000.0000.0000.000
162A163ARG10.8740.92027.3550.0570.0570.0000.0000.0000.000
163A164THR0-0.029-0.01329.4510.0100.0100.0000.0000.0000.000
164A165HIS0-0.036-0.03123.759-0.023-0.0230.0000.0000.0000.000
165A166LEU0-0.041-0.01024.620-0.001-0.0010.0000.0000.0000.000
166A167ALA00.0270.01721.342-0.014-0.0140.0000.0000.0000.000
167A168SER0-0.008-0.04120.1170.0250.0250.0000.0000.0000.000
168A169ASN0-0.042-0.01315.940-0.030-0.0300.0000.0000.0000.000
169A170LEU00.0440.02213.435-0.022-0.0220.0000.0000.0000.000
170A171ALA00.0710.03712.829-0.048-0.0480.0000.0000.0000.000
171A172GLU-1-0.873-0.90614.751-0.261-0.2610.0000.0000.0000.000
172A173PHE00.0280.00118.397-0.003-0.0030.0000.0000.0000.000
173A174LEU00.0070.00514.2080.0100.0100.0000.0000.0000.000
174A175ASN0-0.005-0.01314.879-0.045-0.0450.0000.0000.0000.000
175A176GLN0-0.026-0.00618.8760.0300.0300.0000.0000.0000.000
176A177LEU0-0.0300.02019.8160.0380.0380.0000.0000.0000.000
177A178LYS10.8690.93722.8400.2810.2810.0000.0000.0000.000
178A179PRO00.0340.01124.0760.0180.0180.0000.0000.0000.000
179A180LEU0-0.044-0.00926.2270.0210.0210.0000.0000.0000.000
180A181LEU00.0240.02628.9430.0050.0050.0000.0000.0000.000