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

tag_button

FMODB ID: VQZM1

Calculation Name: 5VO5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5VO5

Chain ID: A

ChEMBL ID:

UniProt ID: Q9VKJ9

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 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 179
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1586293.483817
FMO2-HF: Nuclear repulsion 1514884.237311
FMO2-HF: Total energy -71409.246506
FMO2-MP2: Total energy -71615.554286


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:3:ASN)


Summations of interaction energy for fragment #1(A:3:ASN)
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.
-56.478-53.21420.856-12.069-12.048-0.018
Interaction energy analysis for fragmet #1(A:3:ASN)
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 : -0.004
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].
3A5LEU0-0.0270.0122.372-8.549-4.3992.873-3.185-3.8370.029
4A6GLU-1-0.834-0.9191.806-41.624-43.12517.973-8.679-7.792-0.048
5A7ALA00.0240.0183.962-3.146-2.6490.011-0.202-0.3050.001
6A8LEU0-0.045-0.0175.715-0.812-0.8120.0000.0000.0000.000
7A9GLN0-0.054-0.0526.609-0.447-0.4470.0000.0000.0000.000
8A10GLN00.0540.0216.196-0.381-0.3810.0000.0000.0000.000
9A11ARG10.8550.9289.260-0.323-0.3230.0000.0000.0000.000
10A12LEU0-0.0070.00611.182-0.141-0.1410.0000.0000.0000.000
11A13GLU-1-0.840-0.90211.5310.1540.1540.0000.0000.0000.000
12A14LYS10.9090.97413.831-0.079-0.0790.0000.0000.0000.000
13A15TYR0-0.033-0.04315.083-0.093-0.0930.0000.0000.0000.000
14A16GLN00.0340.00115.916-0.048-0.0480.0000.0000.0000.000
15A17SER0-0.063-0.03418.223-0.055-0.0550.0000.0000.0000.000
16A18VAL00.012-0.00420.152-0.032-0.0320.0000.0000.0000.000
17A19GLU-1-0.843-0.92121.6120.2290.2290.0000.0000.0000.000
18A20ALA0-0.0040.00622.671-0.012-0.0120.0000.0000.0000.000
19A21ALA00.0240.01324.265-0.013-0.0130.0000.0000.0000.000
20A22ALA0-0.003-0.01326.031-0.008-0.0080.0000.0000.0000.000
21A23LYS10.7660.87126.350-0.148-0.1480.0000.0000.0000.000
22A24ALA00.0260.02529.208-0.006-0.0060.0000.0000.0000.000
23A25GLU-1-0.844-0.90529.0590.0370.0370.0000.0000.0000.000
24A26ASN0-0.039-0.02332.3920.0050.0050.0000.0000.0000.000
25A27ASN00.0140.01530.6970.0150.0150.0000.0000.0000.000
26A28SER00.046-0.00130.7100.0140.0140.0000.0000.0000.000
27A29GLY0-0.0150.00531.1040.0140.0140.0000.0000.0000.000
28A30LYS10.8220.88926.241-0.023-0.0230.0000.0000.0000.000
29A31ALA0-0.003-0.01126.5730.0200.0200.0000.0000.0000.000
30A32ARG10.7630.86426.395-0.107-0.1070.0000.0000.0000.000
31A33ARG10.7890.86825.802-0.087-0.0870.0000.0000.0000.000
32A34PHE00.017-0.00320.9090.0330.0330.0000.0000.0000.000
33A35GLY00.0480.03521.4950.0450.0450.0000.0000.0000.000
34A36ARG10.7010.80922.970-0.197-0.1970.0000.0000.0000.000
35A37ILE00.0200.02217.6790.0530.0530.0000.0000.0000.000
36A38VAL0-0.004-0.01117.1660.0950.0950.0000.0000.0000.000
37A39LYS10.8880.94717.143-0.273-0.2730.0000.0000.0000.000
38A40GLN00.0230.01117.4110.0430.0430.0000.0000.0000.000
39A41TYR00.004-0.02110.9880.1420.1420.0000.0000.0000.000
40A42GLU-1-0.881-0.92613.1590.8480.8480.0000.0000.0000.000
41A43ASP-1-0.908-0.96814.9290.7840.7840.0000.0000.0000.000
42A44ALA0-0.0100.00112.0080.0710.0710.0000.0000.0000.000
43A45ILE0-0.011-0.0109.7120.2980.2980.0000.0000.0000.000
44A46LYS10.8020.89311.625-0.661-0.6610.0000.0000.0000.000
45A47LEU0-0.058-0.02513.908-0.071-0.0710.0000.0000.0000.000
46A48TYR00.0460.0214.8160.7400.858-0.001-0.003-0.1140.000
47A49LYS10.9200.9579.662-1.758-1.7580.0000.0000.0000.000
48A50ALA0-0.039-0.00511.517-0.201-0.2010.0000.0000.0000.000
49A51GLY0-0.0010.00111.870-0.167-0.1670.0000.0000.0000.000
50A52LYS10.8950.95912.937-0.944-0.9440.0000.0000.0000.000
51A53PRO00.002-0.00112.9390.1830.1830.0000.0000.0000.000
52A54VAL00.0240.00810.572-0.047-0.0470.0000.0000.0000.000
53A55PRO00.0280.02213.445-0.038-0.0380.0000.0000.0000.000
54A56TYR00.016-0.0247.824-0.075-0.0750.0000.0000.0000.000
55A57ASP-1-0.908-0.94713.4250.4340.4340.0000.0000.0000.000
56A58GLU-1-0.955-0.97216.5010.4300.4300.0000.0000.0000.000
57A59LEU0-0.065-0.01412.224-0.005-0.0050.0000.0000.0000.000
58A60PRO00.0550.05415.435-0.047-0.0470.0000.0000.0000.000
59A61VAL0-0.0100.00512.5420.0840.0840.0000.0000.0000.000
60A62PRO00.0070.01113.906-0.049-0.0490.0000.0000.0000.000
61A63PRO00.0300.00315.472-0.065-0.0650.0000.0000.0000.000
62A64GLY00.0350.02215.555-0.010-0.0100.0000.0000.0000.000
63A65PHE0-0.0120.00611.349-0.126-0.1260.0000.0000.0000.000
64A66GLY00.0150.0079.7850.0250.0250.0000.0000.0000.000
65A76GLY00.0540.01639.096-0.002-0.0020.0000.0000.0000.000
66A77THR00.0360.00935.3880.0010.0010.0000.0000.0000.000
67A78THR0-0.0020.00533.1900.0030.0030.0000.0000.0000.000
68A79GLY00.0500.02133.7710.0020.0020.0000.0000.0000.000
69A80GLU-1-0.886-0.94336.401-0.025-0.0250.0000.0000.0000.000
70A81ALA0-0.022-0.00431.2470.0070.0070.0000.0000.0000.000
71A82ILE00.0290.02131.3950.0080.0080.0000.0000.0000.000
72A83GLN00.0280.01632.9460.0120.0120.0000.0000.0000.000
73A84LYS10.9370.95334.2830.0270.0270.0000.0000.0000.000
74A85LEU00.0000.02228.1180.0090.0090.0000.0000.0000.000
75A86ARG10.9570.97531.6930.0100.0100.0000.0000.0000.000
76A87GLU-1-0.964-0.97333.9940.0230.0230.0000.0000.0000.000
77A88THR0-0.018-0.02930.4870.0090.0090.0000.0000.0000.000
78A89GLU-1-0.796-0.90729.6870.0350.0350.0000.0000.0000.000
79A90ASN0-0.041-0.02532.0680.0150.0150.0000.0000.0000.000
80A91MET0-0.0340.00234.8070.0060.0060.0000.0000.0000.000
81A92LEU00.0100.00628.4640.0090.0090.0000.0000.0000.000
82A93ILE00.0320.01132.1850.0130.0130.0000.0000.0000.000
83A94LYS10.9040.95133.460-0.046-0.0460.0000.0000.0000.000
84A95LYS10.8990.96833.278-0.116-0.1160.0000.0000.0000.000
85A96GLN00.003-0.00129.8320.0020.0020.0000.0000.0000.000
86A97GLU-1-0.854-0.92632.4480.1040.1040.0000.0000.0000.000
87A98PHE0-0.011-0.00535.5060.0030.0030.0000.0000.0000.000
88A99LEU0-0.048-0.02231.5470.0010.0010.0000.0000.0000.000
89A100GLU-1-0.730-0.84430.9150.1650.1650.0000.0000.0000.000
90A101ALA00.0230.03034.2160.0030.0030.0000.0000.0000.000
91A102LYS10.9130.95237.643-0.119-0.1190.0000.0000.0000.000
92A103ILE0-0.017-0.01631.4320.0040.0040.0000.0000.0000.000
93A104GLU-1-0.862-0.92635.6920.1480.1480.0000.0000.0000.000
94A105ASP-1-0.891-0.94038.0420.1080.1080.0000.0000.0000.000
95A106GLU-1-0.798-0.89737.9490.1260.1260.0000.0000.0000.000
96A107LEU00.0140.01235.5160.0020.0020.0000.0000.0000.000
97A108ASN00.0010.00938.732-0.001-0.0010.0000.0000.0000.000
98A109ILE0-0.034-0.00842.286-0.004-0.0040.0000.0000.0000.000
99A110ALA00.0180.00639.921-0.003-0.0030.0000.0000.0000.000
100A111ARG10.8570.90738.284-0.151-0.1510.0000.0000.0000.000
101A112LYS10.9430.98142.682-0.108-0.1080.0000.0000.0000.000
102A113ASN0-0.067-0.05545.192-0.011-0.0110.0000.0000.0000.000
103A114ALA00.0350.03042.841-0.002-0.0020.0000.0000.0000.000
104A115SER00.0050.00944.5800.0010.0010.0000.0000.0000.000
105A116LYS10.8780.95047.931-0.103-0.1030.0000.0000.0000.000
106A117ASN00.009-0.00748.3240.0000.0000.0000.0000.0000.000
107A118LYS10.9330.95643.583-0.132-0.1320.0000.0000.0000.000
108A119GLU-1-0.755-0.86744.1490.1360.1360.0000.0000.0000.000
109A120VAL0-0.0050.00044.1370.0040.0040.0000.0000.0000.000
110A121ALA00.0190.00942.5930.0040.0040.0000.0000.0000.000
111A122LEU00.0020.00538.4910.0090.0090.0000.0000.0000.000
112A123GLN00.009-0.00739.1880.0080.0080.0000.0000.0000.000
113A124ALA0-0.0010.00839.6560.0040.0040.0000.0000.0000.000
114A125LEU00.0190.00435.9040.0070.0070.0000.0000.0000.000
115A126LYS10.8950.94434.396-0.179-0.1790.0000.0000.0000.000
116A127LYS10.8410.91634.957-0.121-0.1210.0000.0000.0000.000
117A128LYS10.8110.89531.351-0.226-0.2260.0000.0000.0000.000
118A129LYS10.9990.99727.749-0.299-0.2990.0000.0000.0000.000
119A130GLU-1-0.838-0.89130.2560.2120.2120.0000.0000.0000.000
120A131LEU00.002-0.01031.1740.0020.0020.0000.0000.0000.000
121A132GLU-1-0.766-0.87828.2020.2500.2500.0000.0000.0000.000
122A133LYS10.8830.94126.548-0.220-0.2200.0000.0000.0000.000
123A134GLN0-0.061-0.03726.950-0.008-0.0080.0000.0000.0000.000
124A135LEU0-0.035-0.00828.095-0.009-0.0090.0000.0000.0000.000
125A136GLN00.0170.00421.5890.0020.0020.0000.0000.0000.000
126A137GLN0-0.004-0.01023.811-0.005-0.0050.0000.0000.0000.000
127A138ILE0-0.034-0.00125.349-0.018-0.0180.0000.0000.0000.000
128A139ASP-1-0.736-0.85324.1630.2060.2060.0000.0000.0000.000
129A140GLY00.0370.03421.684-0.010-0.0100.0000.0000.0000.000
130A141THR0-0.044-0.01922.060-0.027-0.0270.0000.0000.0000.000
131A142LEU0-0.041-0.01624.401-0.025-0.0250.0000.0000.0000.000
132A143SER00.018-0.00722.133-0.017-0.0170.0000.0000.0000.000
133A144THR0-0.026-0.02519.998-0.026-0.0260.0000.0000.0000.000
134A145ILE00.007-0.00621.988-0.033-0.0330.0000.0000.0000.000
135A146GLU-1-0.736-0.84325.4490.0760.0760.0000.0000.0000.000
136A147MET0-0.055-0.01619.038-0.028-0.0280.0000.0000.0000.000
137A148GLN0-0.0070.00323.254-0.019-0.0190.0000.0000.0000.000
138A149ARG10.7270.81924.259-0.015-0.0150.0000.0000.0000.000
139A150GLU-1-0.777-0.87225.853-0.003-0.0030.0000.0000.0000.000
140A151ALA0-0.0150.01023.402-0.014-0.0140.0000.0000.0000.000
141A152LEU00.000-0.00225.505-0.013-0.0130.0000.0000.0000.000
142A153GLU-1-0.819-0.90628.275-0.030-0.0300.0000.0000.0000.000
143A154SER0-0.014-0.00127.250-0.003-0.0030.0000.0000.0000.000
144A155ALA0-0.012-0.00327.096-0.007-0.0070.0000.0000.0000.000
145A156ASN00.0080.00929.046-0.005-0.0050.0000.0000.0000.000
146A157THR0-0.012-0.02132.5810.0040.0040.0000.0000.0000.000
147A158ASN00.009-0.00928.6750.0060.0060.0000.0000.0000.000
148A159THR0-0.011-0.00231.895-0.006-0.0060.0000.0000.0000.000
149A160ALA00.0170.02133.9370.0010.0010.0000.0000.0000.000
150A161VAL00.0140.01635.0260.0030.0030.0000.0000.0000.000
151A162LEU00.0140.00431.4180.0000.0000.0000.0000.0000.000
152A163THR0-0.032-0.01836.1090.0000.0000.0000.0000.0000.000
153A164THR0-0.042-0.03838.9890.0030.0030.0000.0000.0000.000
154A165MET00.001-0.00236.8910.0020.0020.0000.0000.0000.000
155A166LYS10.8250.90939.2040.1110.1110.0000.0000.0000.000
156A167ASN00.0270.00340.9880.0000.0000.0000.0000.0000.000
157A168ALA00.0110.00943.5620.0040.0040.0000.0000.0000.000
158A169ALA00.0120.00742.1530.0020.0020.0000.0000.0000.000
159A170ASP-1-0.837-0.90944.255-0.100-0.1000.0000.0000.0000.000
160A171ALA0-0.005-0.00146.4910.0030.0030.0000.0000.0000.000
161A172LEU00.001-0.00445.6370.0030.0030.0000.0000.0000.000
162A173LYS10.9150.94944.9540.1000.1000.0000.0000.0000.000
163A174ARG10.9010.96249.1210.0650.0650.0000.0000.0000.000
164A175ALA00.0020.00551.9840.0040.0040.0000.0000.0000.000
165A176HIS0-0.042-0.01249.9450.0030.0030.0000.0000.0000.000
166A177GLN0-0.018-0.00853.362-0.003-0.0030.0000.0000.0000.000
167A178ASN00.0260.02254.1800.0020.0020.0000.0000.0000.000
168A179MET00.027-0.00857.7640.0010.0010.0000.0000.0000.000
169A180ASP-1-0.891-0.93959.565-0.063-0.0630.0000.0000.0000.000
170A181VAL0-0.017-0.01457.9170.0010.0010.0000.0000.0000.000
171A182ASP-1-0.903-0.95060.646-0.062-0.0620.0000.0000.0000.000
172A183LYS10.7670.86562.8820.0500.0500.0000.0000.0000.000
173A184VAL0-0.007-0.00463.8670.0020.0020.0000.0000.0000.000
174A185HIS00.0380.00459.9860.0020.0020.0000.0000.0000.000
175A186ASP-1-0.836-0.89565.577-0.046-0.0460.0000.0000.0000.000
176A187MET0-0.058-0.03568.5560.0020.0020.0000.0000.0000.000
177A188MET0-0.111-0.04264.8730.0000.0000.0000.0000.0000.000
178A189ASP-1-0.917-0.94467.681-0.053-0.0530.0000.0000.0000.000
179A190ASP-1-1.100-1.04070.699-0.040-0.0400.0000.0000.0000.000