Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 3JN8L

Calculation Name: 3VPR-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VPR

Chain ID: A

ChEMBL ID:

UniProt ID: Q53WD9

Base Structure: X-ray

Registration Date: 2023-09-20

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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2043773.762043
FMO2-HF: Nuclear repulsion 1968858.317652
FMO2-HF: Total energy -74915.444391
FMO2-MP2: Total energy -75136.078244


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:VAL)


Summations of interaction energy for fragment #1(A:1:VAL)
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.
-2.5760.4280.317-1.262-2.0590.004
Interaction energy analysis for fragmet #1(A:1:VAL)
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 : 0.007
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].
3A3THR0-0.041-0.0572.813-0.3972.4670.318-1.234-1.9490.004
4A4THR0-0.005-0.0334.262-0.090-0.0290.000-0.019-0.0420.000
5A5ARG10.8240.8967.4360.8400.8400.0000.0000.0000.000
6A6ASP-1-0.787-0.8714.804-3.197-3.118-0.001-0.009-0.0680.000
7A7ARG10.9520.9816.2921.0791.0790.0000.0000.0000.000
8A8ILE00.0070.0079.4370.1780.1780.0000.0000.0000.000
9A9LEU0-0.023-0.00510.7480.1160.1160.0000.0000.0000.000
10A10GLU-1-0.869-0.9269.428-1.044-1.0440.0000.0000.0000.000
11A11GLU-1-0.859-0.92912.411-0.494-0.4940.0000.0000.0000.000
12A12ALA0-0.011-0.00214.9590.0980.0980.0000.0000.0000.000
13A13ALA0-0.014-0.00315.3160.0720.0720.0000.0000.0000.000
14A14LYS10.8170.90112.3570.7420.7420.0000.0000.0000.000
15A15LEU00.0700.03818.0850.0530.0530.0000.0000.0000.000
16A16PHE0-0.041-0.03919.5340.0450.0450.0000.0000.0000.000
17A17THR0-0.062-0.03219.9950.0350.0350.0000.0000.0000.000
18A18GLU-1-0.956-0.97220.550-0.274-0.2740.0000.0000.0000.000
19A19LYS10.8250.90924.1840.2260.2260.0000.0000.0000.000
20A20GLY00.0070.01525.2600.0200.0200.0000.0000.0000.000
21A21TYR0-0.003-0.01222.895-0.006-0.0060.0000.0000.0000.000
22A22GLU-1-0.825-0.91525.735-0.204-0.2040.0000.0000.0000.000
23A23ALA0-0.034-0.00328.9230.0070.0070.0000.0000.0000.000
24A24THR00.0090.00622.6940.0050.0050.0000.0000.0000.000
25A25SER0-0.059-0.06225.609-0.008-0.0080.0000.0000.0000.000
26A26VAL00.0650.00921.521-0.014-0.0140.0000.0000.0000.000
27A27GLN0-0.017-0.02322.309-0.009-0.0090.0000.0000.0000.000
28A28ASP-1-0.755-0.84523.607-0.204-0.2040.0000.0000.0000.000
29A29LEU00.0210.02118.375-0.005-0.0050.0000.0000.0000.000
30A30ALA0-0.031-0.01318.868-0.021-0.0210.0000.0000.0000.000
31A31GLN00.0150.01319.4130.0010.0010.0000.0000.0000.000
32A32ALA0-0.0100.01019.7190.0080.0080.0000.0000.0000.000
33A33LEU0-0.014-0.00413.390-0.016-0.0160.0000.0000.0000.000
34A34GLY0-0.0180.01315.619-0.008-0.0080.0000.0000.0000.000
35A35LEU0-0.059-0.02813.2060.0110.0110.0000.0000.0000.000
36A36SER00.0430.01317.7610.0070.0070.0000.0000.0000.000
37A37LYS10.9700.95319.3840.1470.1470.0000.0000.0000.000
38A38ALA0-0.0120.00220.861-0.014-0.0140.0000.0000.0000.000
39A39ALA00.0380.02715.831-0.008-0.0080.0000.0000.0000.000
40A40LEU00.0270.02715.782-0.036-0.0360.0000.0000.0000.000
41A41TYR0-0.002-0.01917.445-0.019-0.0190.0000.0000.0000.000
42A42HIS00.0080.01317.145-0.009-0.0090.0000.0000.0000.000
43A43HIS0-0.076-0.02411.165-0.040-0.0400.0000.0000.0000.000
44A44PHE00.019-0.00212.061-0.037-0.0370.0000.0000.0000.000
45A45GLY00.0240.03417.2460.0190.0190.0000.0000.0000.000
46A46SER0-0.055-0.04920.4930.0300.0300.0000.0000.0000.000
47A47LYS10.8860.93120.5760.2170.2170.0000.0000.0000.000
48A48GLU-1-0.767-0.86221.498-0.287-0.2870.0000.0000.0000.000
49A49GLU-1-0.840-0.92318.248-0.373-0.3730.0000.0000.0000.000
50A50ILE0-0.0210.00016.281-0.037-0.0370.0000.0000.0000.000
51A51LEU0-0.0120.00117.867-0.046-0.0460.0000.0000.0000.000
52A52TYR0-0.0050.00219.939-0.012-0.0120.0000.0000.0000.000
53A53GLU-1-0.756-0.88313.504-0.726-0.7260.0000.0000.0000.000
54A54ILE0-0.0230.00415.177-0.061-0.0610.0000.0000.0000.000
55A55SER0-0.023-0.02916.2420.0060.0060.0000.0000.0000.000
56A56LEU0-0.027-0.01416.2310.0130.0130.0000.0000.0000.000
57A57LEU0-0.0070.0119.9500.0340.0340.0000.0000.0000.000
58A58ALA00.0270.01813.9950.0020.0020.0000.0000.0000.000
59A59LEU00.022-0.01616.2400.0450.0450.0000.0000.0000.000
60A60LYS10.9190.96514.9690.5190.5190.0000.0000.0000.000
61A61GLY00.0150.01914.3770.0320.0320.0000.0000.0000.000
62A62LEU0-0.010-0.00614.9570.0540.0540.0000.0000.0000.000
63A63VAL0-0.012-0.01218.5240.0380.0380.0000.0000.0000.000
64A64ALA0-0.0010.00715.9520.0370.0370.0000.0000.0000.000
65A65ALA00.0060.00417.7630.0450.0450.0000.0000.0000.000
66A66GLY00.0150.00418.9590.0300.0300.0000.0000.0000.000
67A67GLU-1-0.843-0.92920.150-0.157-0.1570.0000.0000.0000.000
68A68LYS10.8430.91417.0380.1660.1660.0000.0000.0000.000
69A69ALA0-0.006-0.00121.9660.0170.0170.0000.0000.0000.000
70A70LEU0-0.0250.00325.2470.0100.0100.0000.0000.0000.000
71A71GLU-1-0.918-0.95324.101-0.032-0.0320.0000.0000.0000.000
72A72VAL0-0.083-0.02426.3830.0120.0120.0000.0000.0000.000
73A73ALA00.0230.01528.857-0.005-0.0050.0000.0000.0000.000
74A74ASP-1-0.787-0.89832.524-0.026-0.0260.0000.0000.0000.000
75A75PRO00.0770.03532.661-0.003-0.0030.0000.0000.0000.000
76A76LYS10.8910.93733.1150.0170.0170.0000.0000.0000.000
77A77GLU-1-0.797-0.87228.676-0.032-0.0320.0000.0000.0000.000
78A78ALA0-0.010-0.00428.541-0.005-0.0050.0000.0000.0000.000
79A79LEU00.001-0.00128.149-0.011-0.0110.0000.0000.0000.000
80A80ARG10.7830.85527.0930.0260.0260.0000.0000.0000.000
81A81ARG10.9520.97221.5360.0210.0210.0000.0000.0000.000
82A82PHE00.0170.02524.012-0.015-0.0150.0000.0000.0000.000
83A83MET0-0.056-0.02524.196-0.015-0.0150.0000.0000.0000.000
84A84GLU-1-0.741-0.84323.628-0.069-0.0690.0000.0000.0000.000
85A85ALA00.0030.00719.900-0.014-0.0140.0000.0000.0000.000
86A86HIS00.0040.01419.600-0.029-0.0290.0000.0000.0000.000
87A87ALA00.009-0.00920.682-0.028-0.0280.0000.0000.0000.000
88A88ARG10.7940.88916.3570.1050.1050.0000.0000.0000.000
89A89TYR0-0.0020.00512.727-0.050-0.0500.0000.0000.0000.000
90A90PHE0-0.025-0.02316.434-0.054-0.0540.0000.0000.0000.000
91A91GLU-1-0.833-0.91618.381-0.187-0.1870.0000.0000.0000.000
92A92GLU-1-0.884-0.93713.225-0.273-0.2730.0000.0000.0000.000
93A93ASN0-0.060-0.03312.103-0.202-0.2020.0000.0000.0000.000
94A94TYR00.0500.02814.7580.0010.0010.0000.0000.0000.000
95A95PRO00.0550.01615.2110.0220.0220.0000.0000.0000.000
96A96PHE00.0290.01711.2340.0360.0360.0000.0000.0000.000
97A97PHE00.0110.00617.0870.0370.0370.0000.0000.0000.000
98A98VAL00.0080.01420.1570.0330.0330.0000.0000.0000.000
99A99THR0-0.037-0.01619.5410.0280.0280.0000.0000.0000.000
100A100MET0-0.012-0.00420.2840.0260.0260.0000.0000.0000.000
101A101LEU0-0.048-0.02122.1420.0270.0270.0000.0000.0000.000
102A102GLN0-0.019-0.01024.6010.0300.0300.0000.0000.0000.000
103A103GLY00.0350.01225.0940.0170.0170.0000.0000.0000.000
104A104ILE00.0390.04126.1160.0090.0090.0000.0000.0000.000
105A105LYS10.8480.92227.4680.1960.1960.0000.0000.0000.000
106A106SER0-0.052-0.05627.0000.0090.0090.0000.0000.0000.000
107A107LEU0-0.0150.02423.0170.0000.0000.0000.0000.0000.000
108A108SER0-0.004-0.00926.3090.0240.0240.0000.0000.0000.000
109A109PRO0-0.014-0.03128.133-0.008-0.0080.0000.0000.0000.000
110A110GLU-1-0.837-0.91126.913-0.194-0.1940.0000.0000.0000.000
111A111ASN00.0310.01723.173-0.002-0.0020.0000.0000.0000.000
112A112ARG10.8410.91124.6640.1750.1750.0000.0000.0000.000
113A113LEU0-0.0030.00826.9190.0010.0010.0000.0000.0000.000
114A114LYS10.9100.94022.4220.2240.2240.0000.0000.0000.000
115A115THR0-0.015-0.00922.333-0.020-0.0200.0000.0000.0000.000
116A116ILE0-0.017-0.02023.5420.0000.0000.0000.0000.0000.000
117A117ALA00.0130.02425.5710.0100.0100.0000.0000.0000.000
118A118LEU0-0.011-0.00619.3610.0070.0070.0000.0000.0000.000
119A119ARG10.8420.90223.3990.1690.1690.0000.0000.0000.000
120A120ASP-1-0.815-0.90225.267-0.141-0.1410.0000.0000.0000.000
121A121ARG10.8530.92722.6080.1720.1720.0000.0000.0000.000
122A122HIS00.000-0.00922.4880.0100.0100.0000.0000.0000.000
123A123GLU-1-0.795-0.86925.258-0.110-0.1100.0000.0000.0000.000
124A124GLU-1-0.816-0.90628.862-0.080-0.0800.0000.0000.0000.000
125A125ASN00.0170.00624.1090.0180.0180.0000.0000.0000.000
126A126LEU0-0.0120.01128.1200.0100.0100.0000.0000.0000.000
127A127ARG10.8510.90029.6240.1120.1120.0000.0000.0000.000
128A128ALA0-0.0080.00830.6500.0080.0080.0000.0000.0000.000
129A129ILE0-0.013-0.00227.5930.0080.0080.0000.0000.0000.000
130A130LEU0-0.022-0.02032.1820.0070.0070.0000.0000.0000.000
131A131ARG10.8690.92233.9720.0750.0750.0000.0000.0000.000
132A132ARG10.8900.95930.4350.0480.0480.0000.0000.0000.000
133A133GLY00.0120.00136.4140.0050.0050.0000.0000.0000.000
134A134VAL0-0.040-0.01137.9370.0040.0040.0000.0000.0000.000
135A135GLU-1-0.917-0.95838.663-0.042-0.0420.0000.0000.0000.000
136A136GLN0-0.097-0.06236.9280.0000.0000.0000.0000.0000.000
137A137GLY00.0180.01641.5230.0030.0030.0000.0000.0000.000
138A138VAL0-0.091-0.03938.1950.0020.0020.0000.0000.0000.000
139A139PHE0-0.072-0.02834.945-0.001-0.0010.0000.0000.0000.000
140A140ARG10.9900.99141.1180.0430.0430.0000.0000.0000.000
141A141GLU-1-0.892-0.95342.853-0.044-0.0440.0000.0000.0000.000
142A142VAL0-0.047-0.02740.0780.0000.0000.0000.0000.0000.000
143A143ASP-1-0.822-0.90140.784-0.068-0.0680.0000.0000.0000.000
144A144VAL00.0610.01436.253-0.004-0.0040.0000.0000.0000.000
145A145ALA0-0.0120.00636.336-0.006-0.0060.0000.0000.0000.000
146A146LEU0-0.016-0.01036.403-0.007-0.0070.0000.0000.0000.000
147A147ALA00.0150.00437.229-0.004-0.0040.0000.0000.0000.000
148A148GLY00.0460.01033.298-0.003-0.0030.0000.0000.0000.000
149A149ARG10.8190.88931.8220.1080.1080.0000.0000.0000.000
150A150ALA00.0070.01833.901-0.006-0.0060.0000.0000.0000.000
151A151VAL00.0510.01329.862-0.004-0.0040.0000.0000.0000.000
152A152LEU00.0170.00527.242-0.008-0.0080.0000.0000.0000.000
153A153SER0-0.092-0.04729.459-0.011-0.0110.0000.0000.0000.000
154A154MET0-0.042-0.01331.279-0.003-0.0030.0000.0000.0000.000
155A155LEU00.0100.01025.761-0.003-0.0030.0000.0000.0000.000
156A156ASN00.001-0.02525.754-0.022-0.0220.0000.0000.0000.000
157A157TRP00.0230.02027.325-0.012-0.0120.0000.0000.0000.000
158A158MET0-0.0200.00425.5490.0010.0010.0000.0000.0000.000
159A159ILE0-0.031-0.01823.559-0.003-0.0030.0000.0000.0000.000
160A160ARG10.8610.93025.8700.1510.1510.0000.0000.0000.000
161A161TRP0-0.019-0.00329.0150.0050.0050.0000.0000.0000.000
162A162PHE0-0.0280.00222.1400.0080.0080.0000.0000.0000.000
163A163ARG10.9230.96425.7040.0970.0970.0000.0000.0000.000
164A164PRO0-0.005-0.00720.5610.0090.0090.0000.0000.0000.000
165A165ASP-1-0.908-0.96222.505-0.114-0.1140.0000.0000.0000.000
166A166GLY0-0.0020.01524.8040.0120.0120.0000.0000.0000.000
167A167PRO00.0130.00125.104-0.005-0.0050.0000.0000.0000.000
168A168MET0-0.056-0.03125.6190.0010.0010.0000.0000.0000.000
169A169ARG10.8680.92718.8970.1050.1050.0000.0000.0000.000
170A170ALA00.0510.02122.0770.0100.0100.0000.0000.0000.000
171A171GLU-1-0.759-0.86921.270-0.083-0.0830.0000.0000.0000.000
172A172GLU-1-0.838-0.91224.043-0.037-0.0370.0000.0000.0000.000
173A173VAL0-0.026-0.00627.1870.0060.0060.0000.0000.0000.000
174A174ALA00.006-0.00126.0260.0040.0040.0000.0000.0000.000
175A175ARG10.7590.84625.7540.0530.0530.0000.0000.0000.000
176A176ALA0-0.008-0.00229.6330.0060.0060.0000.0000.0000.000
177A177TYR00.009-0.01329.7250.0010.0010.0000.0000.0000.000
178A178HIS0-0.017-0.00830.6720.0030.0030.0000.0000.0000.000
179A179ASP-1-0.820-0.89232.673-0.033-0.0330.0000.0000.0000.000
180A180LEU0-0.016-0.01035.5880.0020.0020.0000.0000.0000.000
181A181ILE0-0.061-0.03833.9060.0020.0020.0000.0000.0000.000
182A182LEU0-0.049-0.01635.6780.0020.0020.0000.0000.0000.000
183A183ARG10.8200.88837.7380.0340.0340.0000.0000.0000.000
184A184GLY00.0180.02940.2260.0020.0020.0000.0000.0000.000
185A185LEU0-0.033-0.03341.6410.0010.0010.0000.0000.0000.000
186A186GLU-1-0.981-0.97443.885-0.032-0.0320.0000.0000.0000.000
187A187ARG10.9570.97446.4650.0210.0210.0000.0000.0000.000
188A188GLY00.0470.01447.8540.0000.0000.0000.0000.0000.000
189A189SER0-0.040-0.00745.6670.0020.0020.0000.0000.0000.000