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: VR7N1

Calculation Name: 3VJP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VJP

Chain ID: A

ChEMBL ID:

UniProt ID: P40131

Base Structure: X-ray

Registration Date: 2023-06-20

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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1895835.821179
FMO2-HF: Nuclear repulsion 1821013.633371
FMO2-HF: Total energy -74822.187807
FMO2-MP2: Total energy -75040.047434


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:GLN)


Summations of interaction energy for fragment #1(A:1:GLN)
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.
-13.221-8.5721.164-2.283-3.530.014
Interaction energy analysis for fragmet #1(A:1:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.005 / q_NPA : -0.015
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].
3A3ILE00.0420.0143.5701.1743.2900.061-0.763-1.4140.004
4A4ASN00.0540.0222.372-5.647-3.6281.088-1.391-1.7150.010
5A5ALA00.0730.0493.326-1.799-1.4030.016-0.122-0.2910.000
6A6GLN00.0320.0255.0260.3020.420-0.001-0.007-0.1100.000
7A7LEU0-0.025-0.0177.264-0.189-0.1890.0000.0000.0000.000
8A8THR0-0.020-0.0126.575-0.256-0.2560.0000.0000.0000.000
9A9THR00.0100.0098.641-0.145-0.1450.0000.0000.0000.000
10A10TRP00.0300.00710.8080.0190.0190.0000.0000.0000.000
11A11PHE0-0.001-0.03111.863-0.041-0.0410.0000.0000.0000.000
12A12SER00.004-0.01011.897-0.051-0.0510.0000.0000.0000.000
13A13GLN0-0.032-0.00814.381-0.018-0.0180.0000.0000.0000.000
14A14ARG10.8890.94816.476-0.201-0.2010.0000.0000.0000.000
15A15LEU0-0.103-0.04415.9610.0030.0030.0000.0000.0000.000
16A16ALA00.1060.06318.9700.0070.0070.0000.0000.0000.000
17A17GLY0-0.020-0.00720.649-0.002-0.0020.0000.0000.0000.000
18A18PHE0-0.071-0.03521.3770.0060.0060.0000.0000.0000.000
19A19SER0-0.033-0.05718.1080.0300.0300.0000.0000.0000.000
20A20ASP-1-0.798-0.85218.6400.1620.1620.0000.0000.0000.000
21A21GLU-1-0.907-0.93214.8600.3900.3900.0000.0000.0000.000
22A22VAL0-0.004-0.00812.5060.0700.0700.0000.0000.0000.000
23A23VAL00.0300.0208.2610.0230.0230.0000.0000.0000.000
24A24VAL0-0.053-0.0248.713-0.014-0.0140.0000.0000.0000.000
25A25THR00.0160.0056.7901.0151.0150.0000.0000.0000.000
26A26LEU0-0.029-0.0176.566-1.008-1.0080.0000.0000.0000.000
27A27ARG10.8920.9378.299-1.251-1.2510.0000.0000.0000.000
28A28SER00.0050.01111.035-0.149-0.1490.0000.0000.0000.000
29A29SER00.0130.00510.8520.2610.2610.0000.0000.0000.000
30A30PRO00.0620.0157.976-0.191-0.1910.0000.0000.0000.000
31A31ASN00.0160.01310.010-0.163-0.1630.0000.0000.0000.000
32A32LEU0-0.025-0.00312.678-0.145-0.1450.0000.0000.0000.000
33A33LEU0-0.031-0.0158.0270.0520.0520.0000.0000.0000.000
34A34PRO0-0.030-0.02612.560-0.080-0.0800.0000.0000.0000.000
35A35SER00.0450.00811.983-0.053-0.0530.0000.0000.0000.000
36A36CYS0-0.062-0.00412.195-0.174-0.1740.0000.0000.0000.000
37A37GLU-1-0.834-0.9038.277-3.091-3.0910.0000.0000.0000.000
38A38GLN0-0.026-0.0229.161-0.291-0.2910.0000.0000.0000.000
39A39PRO0-0.015-0.00611.1180.1310.1310.0000.0000.0000.000
40A40ALA00.0070.01514.2030.0460.0460.0000.0000.0000.000
41A41PHE00.0410.01310.2250.1250.1250.0000.0000.0000.000
42A42SER0-0.016-0.01016.231-0.059-0.0590.0000.0000.0000.000
43A43MET00.0080.01018.1820.0870.0870.0000.0000.0000.000
44A44THR0-0.034-0.01620.171-0.045-0.0450.0000.0000.0000.000
45A45GLY0-0.008-0.00722.0450.0050.0050.0000.0000.0000.000
46A46SER0-0.040-0.01623.857-0.006-0.0060.0000.0000.0000.000
47A47ALA00.0240.02523.022-0.006-0.0060.0000.0000.0000.000
48A48LYS10.8390.91320.102-0.600-0.6000.0000.0000.0000.000
49A49LEU00.0080.02220.0130.0000.0000.0000.0000.0000.000
50A50TRP00.0890.02617.0500.0500.0500.0000.0000.0000.000
51A51GLY00.0220.01916.951-0.045-0.0450.0000.0000.0000.000
52A52ASN0-0.026-0.01115.8510.1930.1930.0000.0000.0000.000
53A53VAL00.0200.02815.568-0.104-0.1040.0000.0000.0000.000
54A54ASN00.0500.01816.0700.1710.1710.0000.0000.0000.000
55A55VAL00.001-0.00213.044-0.082-0.0820.0000.0000.0000.000
56A56VAL0-0.039-0.03216.2490.0280.0280.0000.0000.0000.000
57A57ALA00.0350.04113.910-0.045-0.0450.0000.0000.0000.000
58A58ARG10.9520.95415.857-0.049-0.0490.0000.0000.0000.000
59A60ALA00.0230.03418.3120.0080.0080.0000.0000.0000.000
60A61ASN0-0.008-0.02021.6630.0440.0440.0000.0000.0000.000
61A62GLU-1-0.837-0.89516.732-0.043-0.0430.0000.0000.0000.000
62A63LYS10.9020.94119.502-0.163-0.1630.0000.0000.0000.000
63A64ARG10.8580.92616.050-0.117-0.1170.0000.0000.0000.000
64A65TYR00.008-0.00217.129-0.016-0.0160.0000.0000.0000.000
65A66LEU00.0330.02911.0940.0320.0320.0000.0000.0000.000
66A67GLN00.001-0.00213.906-0.063-0.0630.0000.0000.0000.000
67A68VAL00.005-0.00410.6300.2790.2790.0000.0000.0000.000
68A69ASN0-0.068-0.05611.287-0.183-0.1830.0000.0000.0000.000
69A70VAL0-0.0060.00411.3960.1970.1970.0000.0000.0000.000
70A71GLN00.0270.00512.521-0.269-0.2690.0000.0000.0000.000
71A72ALA00.0420.02914.246-0.024-0.0240.0000.0000.0000.000
72A73THR0-0.019-0.02916.7020.0020.0020.0000.0000.0000.000
73A74GLY00.0580.04019.264-0.033-0.0330.0000.0000.0000.000
74A75ASN0-0.040-0.02122.4140.0150.0150.0000.0000.0000.000
75A76TYR00.0080.00326.1930.0100.0100.0000.0000.0000.000
76A77VAL00.0150.01028.316-0.012-0.0120.0000.0000.0000.000
77A78ALA0-0.023-0.00831.7560.0120.0120.0000.0000.0000.000
78A79VAL00.001-0.00533.472-0.014-0.0140.0000.0000.0000.000
79A80ALA0-0.007-0.00136.9190.0060.0060.0000.0000.0000.000
80A81ALA00.005-0.00338.570-0.004-0.0040.0000.0000.0000.000
81A82PRO00.001-0.00241.8390.0040.0040.0000.0000.0000.000
82A83ILE0-0.042-0.00740.397-0.007-0.0070.0000.0000.0000.000
83A84ALA00.0160.01844.4260.0050.0050.0000.0000.0000.000
84A85ARG10.8680.89146.410-0.114-0.1140.0000.0000.0000.000
85A86GLY0-0.038-0.01046.627-0.005-0.0050.0000.0000.0000.000
86A87GLY00.0050.02546.400-0.006-0.0060.0000.0000.0000.000
87A88LYS10.8920.92544.889-0.069-0.0690.0000.0000.0000.000
88A89LEU0-0.0050.00738.1350.0000.0000.0000.0000.0000.000
89A90THR0-0.035-0.02542.036-0.006-0.0060.0000.0000.0000.000
90A91PRO00.0440.00040.4920.0050.0050.0000.0000.0000.000
91A92ALA00.0030.02341.2600.0020.0020.0000.0000.0000.000
92A93ASN00.017-0.00542.0920.0060.0060.0000.0000.0000.000
93A94VAL00.0020.01136.9190.0100.0100.0000.0000.0000.000
94A95THR00.0300.01434.269-0.009-0.0090.0000.0000.0000.000
95A96LEU0-0.0030.01330.0630.0120.0120.0000.0000.0000.000
96A97LYS10.9230.96228.040-0.217-0.2170.0000.0000.0000.000
97A98ARG10.8690.89421.459-0.181-0.1810.0000.0000.0000.000
98A99GLY0-0.026-0.02224.071-0.005-0.0050.0000.0000.0000.000
99A100ARG10.8620.89415.497-0.726-0.7260.0000.0000.0000.000
100A101LEU00.0410.02020.291-0.002-0.0020.0000.0000.0000.000
101A102ASP-1-0.836-0.88417.7060.6940.6940.0000.0000.0000.000
102A103GLN0-0.085-0.04918.946-0.008-0.0080.0000.0000.0000.000
103A104LEU0-0.0300.01522.412-0.040-0.0400.0000.0000.0000.000
104A105PRO0-0.0020.01425.3120.0200.0200.0000.0000.0000.000
105A106PRO00.0350.01526.863-0.009-0.0090.0000.0000.0000.000
106A107ARG10.9400.96327.870-0.245-0.2450.0000.0000.0000.000
107A108THR00.0440.01027.664-0.026-0.0260.0000.0000.0000.000
108A109VAL0-0.053-0.03528.8220.0030.0030.0000.0000.0000.000
109A110LEU0-0.0020.00124.8450.0050.0050.0000.0000.0000.000
110A111ASP-1-0.769-0.86828.5770.1000.1000.0000.0000.0000.000
111A112ILE00.0550.01530.8770.0010.0010.0000.0000.0000.000
112A113ARG10.8530.91231.175-0.089-0.0890.0000.0000.0000.000
113A114GLN0-0.001-0.01030.8940.0020.0020.0000.0000.0000.000
114A115ILE0-0.036-0.02035.2960.0010.0010.0000.0000.0000.000
115A116GLN00.0350.03137.805-0.008-0.0080.0000.0000.0000.000
116A117ASP-1-0.899-0.95040.6420.0750.0750.0000.0000.0000.000
117A118ALA00.0280.02640.0600.0010.0010.0000.0000.0000.000
118A119VAL00.005-0.00942.110-0.003-0.0030.0000.0000.0000.000
119A120SER00.0300.00042.0620.0090.0090.0000.0000.0000.000
120A121LEU0-0.044-0.02541.016-0.008-0.0080.0000.0000.0000.000
121A122ARG10.9120.94939.347-0.171-0.1710.0000.0000.0000.000
122A123ASP-1-0.757-0.84543.4910.1150.1150.0000.0000.0000.000
123A124LEU0-0.053-0.02538.3730.0090.0090.0000.0000.0000.000
124A125ALA00.0440.02739.751-0.009-0.0090.0000.0000.0000.000
125A126PRO00.016-0.01538.5160.0070.0070.0000.0000.0000.000
126A127GLY0-0.018-0.00534.4760.0050.0050.0000.0000.0000.000
127A128GLN0-0.009-0.00233.1120.0090.0090.0000.0000.0000.000
128A129PRO00.0260.00729.988-0.010-0.0100.0000.0000.0000.000
129A130VAL00.0390.02632.141-0.001-0.0010.0000.0000.0000.000
130A131GLN00.0140.01131.4050.0040.0040.0000.0000.0000.000
131A132LEU00.000-0.01732.099-0.012-0.0120.0000.0000.0000.000
132A133THR0-0.033-0.01634.526-0.009-0.0090.0000.0000.0000.000
133A134MET0-0.068-0.02035.361-0.008-0.0080.0000.0000.0000.000
134A135ILE00.0050.01536.886-0.008-0.0080.0000.0000.0000.000
135A136ARG10.9570.97940.122-0.097-0.0970.0000.0000.0000.000
136A137GLN0-0.050-0.02836.901-0.001-0.0010.0000.0000.0000.000
137A138ALA00.0390.03841.622-0.002-0.0020.0000.0000.0000.000
138A139TRP0-0.041-0.04243.072-0.001-0.0010.0000.0000.0000.000
139A140ARG10.8780.95841.000-0.059-0.0590.0000.0000.0000.000
140A141VAL00.0350.02542.985-0.006-0.0060.0000.0000.0000.000
141A142LYS10.9530.96445.332-0.048-0.0480.0000.0000.0000.000
142A143ALA00.0090.00548.586-0.003-0.0030.0000.0000.0000.000
143A144GLY0-0.005-0.00250.075-0.001-0.0010.0000.0000.0000.000
144A145GLN00.0100.01048.757-0.001-0.0010.0000.0000.0000.000
145A146ARG10.8700.92249.566-0.021-0.0210.0000.0000.0000.000
146A147VAL0-0.003-0.00544.5640.0020.0020.0000.0000.0000.000
147A148GLN00.0230.01442.334-0.008-0.0080.0000.0000.0000.000
148A149VAL0-0.040-0.03640.5120.0060.0060.0000.0000.0000.000
149A150ILE00.0280.01236.998-0.006-0.0060.0000.0000.0000.000
150A151ALA0-0.0010.00036.1420.0090.0090.0000.0000.0000.000
151A152ASN0-0.0060.02332.209-0.019-0.0190.0000.0000.0000.000
152A153GLY00.0290.00632.2850.0120.0120.0000.0000.0000.000
153A154GLU-1-0.964-0.98428.558-0.089-0.0890.0000.0000.0000.000
154A155GLY00.0120.01031.038-0.005-0.0050.0000.0000.0000.000
155A156PHE0-0.044-0.02332.9570.0010.0010.0000.0000.0000.000
156A157SER00.013-0.00734.6040.0080.0080.0000.0000.0000.000
157A158VAL0-0.022-0.01036.798-0.003-0.0030.0000.0000.0000.000
158A159ASN00.000-0.01039.5060.0090.0090.0000.0000.0000.000
159A160ALA00.003-0.00242.147-0.003-0.0030.0000.0000.0000.000
160A161GLU-1-0.768-0.85144.7280.0210.0210.0000.0000.0000.000
161A162GLY00.0390.01447.077-0.001-0.0010.0000.0000.0000.000
162A163GLN0-0.096-0.04147.9540.0000.0000.0000.0000.0000.000
163A164ALA00.0420.03946.5690.0020.0020.0000.0000.0000.000
164A165MET0-0.034-0.03246.814-0.002-0.0020.0000.0000.0000.000
165A166ASN0-0.036-0.02842.932-0.001-0.0010.0000.0000.0000.000
166A167ASN00.0060.01146.224-0.005-0.0050.0000.0000.0000.000
167A168ALA00.0090.01741.0080.0050.0050.0000.0000.0000.000
168A169ALA0-0.026-0.00639.723-0.006-0.0060.0000.0000.0000.000
169A170VAL00.0470.02035.7020.0010.0010.0000.0000.0000.000
170A171ALA0-0.047-0.04332.8860.0090.0090.0000.0000.0000.000
171A172GLN0-0.0270.00834.4870.0040.0040.0000.0000.0000.000
172A173ASN0-0.055-0.03736.888-0.006-0.0060.0000.0000.0000.000
173A174ALA00.0220.00738.213-0.001-0.0010.0000.0000.0000.000
174A175ARG10.9350.96241.089-0.077-0.0770.0000.0000.0000.000
175A176VAL00.0350.01342.822-0.001-0.0010.0000.0000.0000.000
176A177ARG10.9540.97845.345-0.037-0.0370.0000.0000.0000.000
177A178MET00.0130.00444.7150.0000.0000.0000.0000.0000.000
178A179THR00.0470.00947.9950.0000.0000.0000.0000.0000.000
179A180SER0-0.027-0.00848.4020.0010.0010.0000.0000.0000.000
180A181GLY00.0070.00450.9780.0000.0000.0000.0000.0000.000
181A182GLN0-0.031-0.00243.2780.0000.0000.0000.0000.0000.000
182A183ILE0-0.026-0.02744.8050.0020.0020.0000.0000.0000.000
183A184VAL00.0060.00940.0020.0020.0020.0000.0000.0000.000
184A185SER0-0.039-0.01638.5300.0050.0050.0000.0000.0000.000
185A186GLY00.0920.04636.541-0.002-0.0020.0000.0000.0000.000
186A187THR0-0.033-0.00633.0340.0080.0080.0000.0000.0000.000
187A188VAL0-0.0090.01136.111-0.009-0.0090.0000.0000.0000.000
188A189ASP-1-0.742-0.87235.4400.0620.0620.0000.0000.0000.000
189A190SER0-0.018-0.03636.1780.0000.0000.0000.0000.0000.000
190A191ASP-1-0.897-0.93938.0150.0390.0390.0000.0000.0000.000
191A192GLY0-0.066-0.03440.142-0.004-0.0040.0000.0000.0000.000
192A193ASN00.0020.02339.286-0.005-0.0050.0000.0000.0000.000
193A194ILE0-0.030-0.02739.0880.0080.0080.0000.0000.0000.000
194A195LEU00.0000.01333.362-0.007-0.0070.0000.0000.0000.000
195A196ILE0-0.005-0.02235.1660.0110.0110.0000.0000.0000.000
196A197ASN00.0000.00627.786-0.021-0.0210.0000.0000.0000.000
197A198LEU0-0.035-0.01329.0860.0030.0030.0000.0000.0000.000