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: 3JZ1L

Calculation Name: 1VF7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VF7

Chain ID: A

ChEMBL ID:

UniProt ID: P52477

Base Structure: X-ray

Registration Date: 2023-09-23

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 237
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2355598.19265
FMO2-HF: Nuclear repulsion 2266231.359744
FMO2-HF: Total energy -89366.832906
FMO2-MP2: Total energy -89632.246694


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:26:THR)


Summations of interaction energy for fragment #1(A:26:THR)
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.
-3.2171.7730.325-2.268-3.048-0.009
Interaction energy analysis for fragmet #1(A:26:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.020 / 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].
3A28ASN0-0.020-0.0042.710-0.3412.2560.163-1.139-1.621-0.003
4A29THR0-0.021-0.0205.3100.3300.402-0.001-0.004-0.0670.000
5A30GLU-1-0.761-0.8648.892-0.832-0.8320.0000.0000.0000.000
6A31LEU0-0.054-0.02811.9290.0790.0790.0000.0000.0000.000
7A32PRO00.0250.02915.1570.0100.0100.0000.0000.0000.000
8A33GLY00.0210.01018.5090.0250.0250.0000.0000.0000.000
9A34ARG10.9160.96220.9720.1760.1760.0000.0000.0000.000
10A35THR00.027-0.00223.4570.0040.0040.0000.0000.0000.000
11A36ASN0-0.080-0.05625.1850.0240.0240.0000.0000.0000.000
12A37ALA00.0280.01727.962-0.004-0.0040.0000.0000.0000.000
13A38PHE0-0.0070.01928.1000.0060.0060.0000.0000.0000.000
14A39ARG10.8980.92430.5340.0980.0980.0000.0000.0000.000
15A40ILE00.0070.00334.212-0.001-0.0010.0000.0000.0000.000
16A41ALA0-0.0090.00437.1190.0030.0030.0000.0000.0000.000
17A42GLU-1-0.830-0.89540.819-0.067-0.0670.0000.0000.0000.000
18A43VAL0-0.014-0.00343.8930.0020.0020.0000.0000.0000.000
19A44ARG10.7980.86746.7010.0590.0590.0000.0000.0000.000
20A45PRO00.0250.02550.0830.0000.0000.0000.0000.0000.000
21A46GLN00.016-0.00951.1870.0010.0010.0000.0000.0000.000
22A47VAL0-0.030-0.00955.1220.0010.0010.0000.0000.0000.000
23A48ASN00.0580.02958.172-0.002-0.0020.0000.0000.0000.000
24A49GLY00.0440.03060.7310.0010.0010.0000.0000.0000.000
25A50ILE00.0620.05560.545-0.001-0.0010.0000.0000.0000.000
26A51ILE0-0.040-0.00754.1820.0000.0000.0000.0000.0000.000
27A52LEU00.0500.04658.1480.0000.0000.0000.0000.0000.000
28A53LYS10.7980.86555.4440.0410.0410.0000.0000.0000.000
29A54ARG10.8690.93248.5670.0560.0560.0000.0000.0000.000
30A55LEU0-0.016-0.00850.711-0.001-0.0010.0000.0000.0000.000
31A56PHE00.0410.03745.073-0.001-0.0010.0000.0000.0000.000
32A57LYS10.9270.96242.2830.0720.0720.0000.0000.0000.000
33A58GLU-1-0.787-0.86944.002-0.063-0.0630.0000.0000.0000.000
34A59GLY0-0.027-0.00939.8350.0000.0000.0000.0000.0000.000
35A60SER0-0.124-0.08439.3650.0000.0000.0000.0000.0000.000
36A61ASP-1-0.780-0.88435.745-0.099-0.0990.0000.0000.0000.000
37A62VAL0-0.029-0.00138.8760.0050.0050.0000.0000.0000.000
38A63LYS10.9670.97339.4670.0630.0630.0000.0000.0000.000
39A64ALA00.0150.00040.3600.0030.0030.0000.0000.0000.000
40A65GLY0-0.009-0.01842.1860.0020.0020.0000.0000.0000.000
41A66GLN00.0060.01343.5990.0010.0010.0000.0000.0000.000
42A67GLN0-0.066-0.06546.7550.0000.0000.0000.0000.0000.000
43A68LEU0-0.059-0.03544.890-0.001-0.0010.0000.0000.0000.000
44A69TYR00.0980.01948.732-0.001-0.0010.0000.0000.0000.000
45A70GLN0-0.0390.00552.5330.0000.0000.0000.0000.0000.000
46A71ILE0-0.0060.00055.7720.0000.0000.0000.0000.0000.000
47A72ASP-1-0.860-0.94258.429-0.032-0.0320.0000.0000.0000.000
48A73PRO0-0.004-0.00161.2590.0000.0000.0000.0000.0000.000
49A74ALA00.0000.00662.9680.0010.0010.0000.0000.0000.000
50A75THR00.037-0.00166.7650.0010.0010.0000.0000.0000.000
51A76TYR0-0.022-0.01562.5340.0010.0010.0000.0000.0000.000
52A77GLU-1-0.868-0.93165.080-0.029-0.0290.0000.0000.0000.000
53A78ALA00.005-0.00466.5060.0010.0010.0000.0000.0000.000
54A79ASP-1-0.902-0.97167.923-0.027-0.0270.0000.0000.0000.000
55A80TYR0-0.058-0.03965.1120.0000.0000.0000.0000.0000.000
56A81GLN0-0.062-0.02567.9560.0010.0010.0000.0000.0000.000
57A82SER0-0.007-0.00170.6880.0010.0010.0000.0000.0000.000
58A83ALA00.0090.01369.5490.0010.0010.0000.0000.0000.000
59A84GLN00.024-0.00867.8950.0000.0000.0000.0000.0000.000
60A85ALA0-0.0110.01271.3680.0010.0010.0000.0000.0000.000
61A86ASN0-0.0030.00074.4300.0010.0010.0000.0000.0000.000
62A87LEU00.0110.01970.0250.0010.0010.0000.0000.0000.000
63A88ALA00.001-0.00774.0750.0010.0010.0000.0000.0000.000
64A89SER0-0.0250.00975.8410.0010.0010.0000.0000.0000.000
65A90THR00.009-0.02076.2370.0010.0010.0000.0000.0000.000
66A91GLN00.0140.01373.0460.0000.0000.0000.0000.0000.000
67A92GLU-1-0.841-0.90176.938-0.016-0.0160.0000.0000.0000.000
68A93GLN00.0430.03080.0550.0010.0010.0000.0000.0000.000
69A94ALA0-0.011-0.00478.3360.0000.0000.0000.0000.0000.000
70A95GLN0-0.010-0.01376.8710.0000.0000.0000.0000.0000.000
71A96ARG10.8670.91580.6630.0160.0160.0000.0000.0000.000
72A97TYR0-0.011-0.02783.5860.0000.0000.0000.0000.0000.000
73A98LYS10.9070.96378.1410.0170.0170.0000.0000.0000.000
74A99LEU00.0100.00483.2820.0000.0000.0000.0000.0000.000
75A100LEU00.0350.01885.8090.0000.0000.0000.0000.0000.000
76A101VAL0-0.070-0.01984.7740.0000.0000.0000.0000.0000.000
77A102ALA0-0.058-0.02086.1600.0000.0000.0000.0000.0000.000
78A103ASP-1-0.902-0.93787.957-0.012-0.0120.0000.0000.0000.000
79A104GLN0-0.136-0.07890.6930.0000.0000.0000.0000.0000.000
80A105ALA00.0440.02891.5620.0000.0000.0000.0000.0000.000
81A106VAL0-0.068-0.02787.4340.0000.0000.0000.0000.0000.000
82A107SER00.026-0.01589.9170.0000.0000.0000.0000.0000.000
83A108LYS10.9970.96786.1030.0140.0140.0000.0000.0000.000
84A109GLN0-0.046-0.01583.7410.0000.0000.0000.0000.0000.000
85A110GLN00.1290.08884.9900.0000.0000.0000.0000.0000.000
86A111TYR00.0070.00278.6080.0000.0000.0000.0000.0000.000
87A112ALA0-0.017-0.00980.968-0.001-0.0010.0000.0000.0000.000
88A113ASP-1-0.832-0.91080.198-0.017-0.0170.0000.0000.0000.000
89A114ALA0-0.012-0.00880.440-0.001-0.0010.0000.0000.0000.000
90A115ASN0-0.026-0.01775.5700.0000.0000.0000.0000.0000.000
91A116ALA00.001-0.00476.083-0.001-0.0010.0000.0000.0000.000
92A117ALA00.0090.00875.511-0.001-0.0010.0000.0000.0000.000
93A118TYR00.017-0.00272.155-0.001-0.0010.0000.0000.0000.000
94A119LEU0-0.022-0.01370.948-0.001-0.0010.0000.0000.0000.000
95A120GLN00.0190.00870.7620.0000.0000.0000.0000.0000.000
96A121SER0-0.007-0.00270.850-0.001-0.0010.0000.0000.0000.000
97A122LYS10.9070.94367.6820.0230.0230.0000.0000.0000.000
98A123ALA0-0.021-0.00866.667-0.001-0.0010.0000.0000.0000.000
99A124ALA00.010-0.00566.355-0.001-0.0010.0000.0000.0000.000
100A125VAL00.0090.00966.506-0.001-0.0010.0000.0000.0000.000
101A126GLU-1-0.790-0.84760.289-0.033-0.0330.0000.0000.0000.000
102A127GLN0-0.028-0.02660.860-0.001-0.0010.0000.0000.0000.000
103A128ALA00.0110.00262.706-0.001-0.0010.0000.0000.0000.000
104A129ARG10.8390.88658.0130.0320.0320.0000.0000.0000.000
105A130ILE0-0.072-0.02557.187-0.002-0.0020.0000.0000.0000.000
106A131ASN00.0140.00358.528-0.002-0.0020.0000.0000.0000.000
107A132LEU00.0550.04259.866-0.001-0.0010.0000.0000.0000.000
108A133ARG10.8660.95754.4950.0390.0390.0000.0000.0000.000
109A134TYR0-0.005-0.03353.024-0.001-0.0010.0000.0000.0000.000
110A135THR0-0.029-0.01055.706-0.001-0.0010.0000.0000.0000.000
111A136LYS10.8680.94853.6220.0380.0380.0000.0000.0000.000
112A137VAL00.0400.02449.737-0.001-0.0010.0000.0000.0000.000
113A138LEU0-0.024-0.00748.062-0.001-0.0010.0000.0000.0000.000
114A139SER0-0.012-0.01341.999-0.001-0.0010.0000.0000.0000.000
115A140PRO00.0330.04142.5010.0010.0010.0000.0000.0000.000
116A141ILE00.002-0.00736.7690.0000.0000.0000.0000.0000.000
117A142SER00.002-0.00736.7270.0040.0040.0000.0000.0000.000
118A143GLY0-0.006-0.01035.609-0.004-0.0040.0000.0000.0000.000
119A144ARG10.8980.96334.2120.1030.1030.0000.0000.0000.000
120A145ILE0-0.0180.00637.306-0.001-0.0010.0000.0000.0000.000
121A146GLY00.0340.01640.655-0.001-0.0010.0000.0000.0000.000
122A147ARG10.9660.95941.4330.0760.0760.0000.0000.0000.000
123A148SER0-0.057-0.01844.793-0.001-0.0010.0000.0000.0000.000
124A149ALA0-0.053-0.02747.8210.0010.0010.0000.0000.0000.000
125A150VAL0-0.0200.00049.3610.0020.0020.0000.0000.0000.000
126A151THR00.0250.01252.432-0.001-0.0010.0000.0000.0000.000
127A152GLU-1-0.772-0.89854.806-0.043-0.0430.0000.0000.0000.000
128A153GLY0-0.010-0.01256.7750.0000.0000.0000.0000.0000.000
129A154ALA0-0.0300.00456.8250.0010.0010.0000.0000.0000.000
130A155LEU0-0.005-0.00758.8910.0000.0000.0000.0000.0000.000
131A156VAL0-0.011-0.01355.195-0.001-0.0010.0000.0000.0000.000
132A157THR0-0.038-0.02457.3570.0020.0020.0000.0000.0000.000
133A158ASN00.013-0.00556.199-0.003-0.0030.0000.0000.0000.000
134A159GLY00.0230.01554.1500.0010.0010.0000.0000.0000.000
135A160GLN0-0.0120.01052.7880.0020.0020.0000.0000.0000.000
136A161ALA00.0440.00452.411-0.002-0.0020.0000.0000.0000.000
137A162ASN0-0.0030.01149.849-0.003-0.0030.0000.0000.0000.000
138A163ALA00.0400.02746.4960.0020.0020.0000.0000.0000.000
139A164MET0-0.032-0.01248.5580.0010.0010.0000.0000.0000.000
140A165ALA00.0450.02744.8640.0000.0000.0000.0000.0000.000
141A166THR0-0.002-0.00439.6430.0020.0020.0000.0000.0000.000
142A167VAL00.0060.01438.331-0.002-0.0020.0000.0000.0000.000
143A168GLN00.014-0.00434.389-0.005-0.0050.0000.0000.0000.000
144A169GLN00.0570.03032.0980.0040.0040.0000.0000.0000.000
145A170LEU0-0.003-0.02530.004-0.005-0.0050.0000.0000.0000.000
146A171ASP-1-0.827-0.89328.766-0.139-0.1390.0000.0000.0000.000
147A172PRO0-0.0290.00826.451-0.009-0.0090.0000.0000.0000.000
148A173ILE0-0.053-0.03124.2010.0110.0110.0000.0000.0000.000
149A174TYR0-0.012-0.01724.509-0.008-0.0080.0000.0000.0000.000
150A175VAL00.006-0.01419.0690.0000.0000.0000.0000.0000.000
151A176ASP-1-0.876-0.92321.952-0.192-0.1920.0000.0000.0000.000
152A177VAL00.0290.01017.492-0.008-0.0080.0000.0000.0000.000
153A178THR00.0020.00020.8320.0220.0220.0000.0000.0000.000
154A179GLN0-0.013-0.01316.717-0.046-0.0460.0000.0000.0000.000
155A180PRO00.0750.03019.5390.0210.0210.0000.0000.0000.000
156A181SER00.0980.04220.970-0.016-0.0160.0000.0000.0000.000
157A182THR00.0030.00419.067-0.001-0.0010.0000.0000.0000.000
158A183ALA0-0.032-0.01516.7620.0020.0020.0000.0000.0000.000
159A184LEU00.0480.04417.139-0.009-0.0090.0000.0000.0000.000
160A185LEU0-0.014-0.02218.7860.0040.0040.0000.0000.0000.000
161A186ARG10.8230.91111.8690.4180.4180.0000.0000.0000.000
162A187LEU00.0160.01412.6410.0240.0240.0000.0000.0000.000
163A188ARG10.9330.95615.5820.1360.1360.0000.0000.0000.000
164A189ARG10.9340.97114.1980.0660.0660.0000.0000.0000.000
165A190GLH0-0.063-0.08110.8120.0390.0390.0000.0000.0000.000
166A191LEU00.0200.03613.9710.0210.0210.0000.0000.0000.000
167A192ALA0-0.095-0.05315.8390.0170.0170.0000.0000.0000.000
168A193SER0-0.051-0.02915.0540.0040.0040.0000.0000.0000.000
169A194GLY00.0250.01815.0380.0210.0210.0000.0000.0000.000
170A195GLN0-0.054-0.02210.408-0.029-0.0290.0000.0000.0000.000
171A196LEU0-0.012-0.0069.870-0.004-0.0040.0000.0000.0000.000
172A197GLU-1-0.847-0.92810.954-0.307-0.3070.0000.0000.0000.000
173A198ARG10.8720.92012.9450.0540.0540.0000.0000.0000.000
174A199ALA0-0.008-0.00316.546-0.002-0.0020.0000.0000.0000.000
175A200GLY0-0.001-0.01118.5110.0160.0160.0000.0000.0000.000
176A201ASP-1-0.889-0.95621.156-0.086-0.0860.0000.0000.0000.000
177A202ASN0-0.075-0.04122.1060.0030.0030.0000.0000.0000.000
178A203ALA00.0230.02619.620-0.007-0.0070.0000.0000.0000.000
179A204ALA00.0240.02913.9990.0170.0170.0000.0000.0000.000
180A205LYS10.8400.92513.2760.2700.2700.0000.0000.0000.000
181A206VAL0-0.067-0.01712.832-0.045-0.0450.0000.0000.0000.000
182A207SER00.0570.01911.6820.0400.0400.0000.0000.0000.000
183A208LEU0-0.014-0.01113.802-0.019-0.0190.0000.0000.0000.000
184A209LYS10.8510.93512.3410.7230.7230.0000.0000.0000.000
185A210LEU00.0200.00515.9440.0210.0210.0000.0000.0000.000
186A211GLU-1-0.851-0.92019.264-0.235-0.2350.0000.0000.0000.000
187A212ASP-1-0.855-0.89721.247-0.262-0.2620.0000.0000.0000.000
188A213GLY0-0.070-0.03617.4180.0030.0030.0000.0000.0000.000
189A214SER0-0.090-0.06416.617-0.043-0.0430.0000.0000.0000.000
190A215GLN0-0.042-0.05012.450-0.006-0.0060.0000.0000.0000.000
191A216TYR0-0.006-0.04216.2540.0440.0440.0000.0000.0000.000
192A217PRO0-0.0200.00016.811-0.038-0.0380.0000.0000.0000.000
193A218LEU0-0.047-0.04218.0350.0300.0300.0000.0000.0000.000
194A219GLU-1-0.869-0.91413.945-0.349-0.3490.0000.0000.0000.000
195A220GLY00.0150.01416.8860.0400.0400.0000.0000.0000.000
196A221ARG10.8110.86217.4880.1550.1550.0000.0000.0000.000
197A222LEU0-0.0050.00115.7400.0100.0100.0000.0000.0000.000
198A223GLU-1-0.764-0.86918.559-0.154-0.1540.0000.0000.0000.000
199A224PHE00.0200.00115.925-0.005-0.0050.0000.0000.0000.000
200A225SER0-0.092-0.03722.1830.0100.0100.0000.0000.0000.000
201A226GLU-1-0.901-0.96023.945-0.152-0.1520.0000.0000.0000.000
202A227VAL00.0190.00826.7330.0020.0020.0000.0000.0000.000
203A228SER0-0.0340.01027.5720.0100.0100.0000.0000.0000.000
204A229VAL00.015-0.01827.882-0.006-0.0060.0000.0000.0000.000
205A230ASP-1-0.881-0.93828.853-0.114-0.1140.0000.0000.0000.000
206A231GLU-1-0.943-0.95130.598-0.074-0.0740.0000.0000.0000.000
207A232GLY0-0.023-0.00133.5120.0040.0040.0000.0000.0000.000
208A233THR0-0.060-0.03428.508-0.002-0.0020.0000.0000.0000.000
209A234GLY00.0340.01027.7300.0010.0010.0000.0000.0000.000
210A235SER0-0.105-0.05325.015-0.011-0.0110.0000.0000.0000.000
211A236VAL00.0100.00523.6890.0120.0120.0000.0000.0000.000
212A237THR00.0010.00023.710-0.018-0.0180.0000.0000.0000.000
213A238ILE0-0.010-0.00818.4520.0150.0150.0000.0000.0000.000
214A239ARG10.9060.94922.5260.1390.1390.0000.0000.0000.000
215A240ALA00.0140.00918.7770.0000.0000.0000.0000.0000.000
216A241VAL0-0.023-0.01720.8040.0130.0130.0000.0000.0000.000
217A242PHE00.0230.01316.237-0.011-0.0110.0000.0000.0000.000
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