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: YV732

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 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 179
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1579693.433064
FMO2-HF: Nuclear repulsion 1508284.662152
FMO2-HF: Total energy -71408.770912
FMO2-MP2: Total energy -71615.143395


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.
-55.931-53.56522.088-12.712-11.741-0.026
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 : 0.000 / 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].
3A5LEU0-0.0180.0102.503-7.236-2.6672.027-3.093-3.5020.023
4A6GLU-1-0.812-0.9011.775-41.181-43.98220.050-9.443-7.806-0.051
5A7ALA00.0380.0283.883-3.838-3.3740.012-0.170-0.3060.002
6A8LEU0-0.040-0.0225.556-1.134-1.1340.0000.0000.0000.000
7A9GLN0-0.053-0.0536.427-0.601-0.6010.0000.0000.0000.000
8A10GLN00.012-0.0046.357-0.484-0.4840.0000.0000.0000.000
9A11ARG10.8650.9199.324-0.528-0.5280.0000.0000.0000.000
10A12LEU00.0010.01411.061-0.168-0.1680.0000.0000.0000.000
11A13GLU-1-0.831-0.89611.6500.2850.2850.0000.0000.0000.000
12A14LYS10.9190.98513.904-0.172-0.1720.0000.0000.0000.000
13A15TYR0-0.007-0.02215.187-0.106-0.1060.0000.0000.0000.000
14A16GLN00.017-0.00715.852-0.028-0.0280.0000.0000.0000.000
15A17SER0-0.082-0.04818.113-0.064-0.0640.0000.0000.0000.000
16A18VAL0-0.004-0.01620.005-0.037-0.0370.0000.0000.0000.000
17A19GLU-1-0.809-0.89821.6120.2430.2430.0000.0000.0000.000
18A20ALA0-0.0030.00422.627-0.018-0.0180.0000.0000.0000.000
19A21ALA00.0220.01224.237-0.016-0.0160.0000.0000.0000.000
20A22ALA00.002-0.00825.958-0.011-0.0110.0000.0000.0000.000
21A23LYS10.7440.85126.203-0.180-0.1800.0000.0000.0000.000
22A24ALA00.0160.01829.225-0.007-0.0070.0000.0000.0000.000
23A25GLU-1-0.835-0.90429.6010.0630.0630.0000.0000.0000.000
24A26ASN0-0.054-0.02232.3180.0030.0030.0000.0000.0000.000
25A27ASN00.0190.02330.8040.0060.0060.0000.0000.0000.000
26A28SER00.0540.00830.8610.0150.0150.0000.0000.0000.000
27A29GLY0-0.003-0.00330.9840.0140.0140.0000.0000.0000.000
28A30LYS10.9120.95026.698-0.063-0.0630.0000.0000.0000.000
29A31ALA00.005-0.00926.8040.0200.0200.0000.0000.0000.000
30A32ARG10.8210.89326.505-0.123-0.1230.0000.0000.0000.000
31A33ARG10.7940.86425.961-0.110-0.1100.0000.0000.0000.000
32A34PHE0-0.002-0.01221.1580.0300.0300.0000.0000.0000.000
33A35GLY00.0300.02421.7370.0390.0390.0000.0000.0000.000
34A36ARG10.6730.77722.525-0.199-0.1990.0000.0000.0000.000
35A37ILE00.0170.02518.0450.0430.0430.0000.0000.0000.000
36A38VAL00.0100.00317.3910.0940.0940.0000.0000.0000.000
37A39LYS10.9460.98117.641-0.261-0.2610.0000.0000.0000.000
38A40GLN00.0210.01917.6270.0240.0240.0000.0000.0000.000
39A41TYR00.007-0.00911.1320.1270.1270.0000.0000.0000.000
40A42GLU-1-0.880-0.93313.6760.8170.8170.0000.0000.0000.000
41A43ASP-1-0.939-0.97115.6380.7150.7150.0000.0000.0000.000
42A44ALA0-0.016-0.01212.3790.0670.0670.0000.0000.0000.000
43A45ILE0-0.019-0.01210.2050.2790.2790.0000.0000.0000.000
44A46LYS10.8070.89711.998-0.622-0.6220.0000.0000.0000.000
45A47LEU0-0.038-0.01814.151-0.038-0.0380.0000.0000.0000.000
46A48TYR00.0400.0204.6750.7110.845-0.001-0.006-0.1270.000
47A49LYS10.9220.95910.343-1.533-1.5330.0000.0000.0000.000
48A50ALA0-0.042-0.00811.644-0.172-0.1720.0000.0000.0000.000
49A51GLY00.0040.01011.698-0.155-0.1550.0000.0000.0000.000
50A52LYS10.8930.95612.754-0.868-0.8680.0000.0000.0000.000
51A53PRO00.002-0.00313.2550.1500.1500.0000.0000.0000.000
52A54VAL00.0290.01210.725-0.028-0.0280.0000.0000.0000.000
53A55PRO00.0150.01013.490-0.037-0.0370.0000.0000.0000.000
54A56TYR00.028-0.0158.053-0.048-0.0480.0000.0000.0000.000
55A57ASP-1-0.918-0.95313.6890.4020.4020.0000.0000.0000.000
56A58GLU-1-0.971-0.97816.7730.4380.4380.0000.0000.0000.000
57A59LEU0-0.054-0.00912.544-0.005-0.0050.0000.0000.0000.000
58A60PRO00.0500.05016.091-0.046-0.0460.0000.0000.0000.000
59A61VAL0-0.015-0.00512.8480.0960.0960.0000.0000.0000.000
60A62PRO00.0090.01414.225-0.052-0.0520.0000.0000.0000.000
61A63PRO00.038-0.00215.768-0.052-0.0520.0000.0000.0000.000
62A64GLY00.0250.01615.921-0.008-0.0080.0000.0000.0000.000
63A65PHE0-0.025-0.00211.525-0.099-0.0990.0000.0000.0000.000
64A66GLY00.0260.02010.1810.0040.0040.0000.0000.0000.000
65A76GLY00.0410.01039.144-0.001-0.0010.0000.0000.0000.000
66A77THR00.0520.01135.8700.0030.0030.0000.0000.0000.000
67A78THR00.0210.01533.0940.0050.0050.0000.0000.0000.000
68A79GLY00.0540.02434.3030.0040.0040.0000.0000.0000.000
69A80GLU-1-0.875-0.93836.944-0.011-0.0110.0000.0000.0000.000
70A81ALA0-0.034-0.01331.9430.0060.0060.0000.0000.0000.000
71A82ILE00.0370.02431.9010.0080.0080.0000.0000.0000.000
72A83GLN00.0090.01133.5910.0130.0130.0000.0000.0000.000
73A84LYS10.9250.95434.5680.0140.0140.0000.0000.0000.000
74A85LEU00.0110.02328.3630.0080.0080.0000.0000.0000.000
75A86ARG10.9720.98232.189-0.009-0.0090.0000.0000.0000.000
76A87GLU-1-0.959-0.96434.3390.0360.0360.0000.0000.0000.000
77A88THR0-0.019-0.03131.1450.0070.0070.0000.0000.0000.000
78A89GLU-1-0.798-0.90530.0860.0590.0590.0000.0000.0000.000
79A90ASN0-0.068-0.04432.4500.0120.0120.0000.0000.0000.000
80A91MET0-0.047-0.01335.2810.0070.0070.0000.0000.0000.000
81A92LEU00.0070.00728.9080.0080.0080.0000.0000.0000.000
82A93ILE00.0090.00532.2030.0130.0130.0000.0000.0000.000
83A94LYS10.9880.99433.664-0.056-0.0560.0000.0000.0000.000
84A95LYS10.8870.96233.672-0.118-0.1180.0000.0000.0000.000
85A96GLN0-0.004-0.00330.2830.0040.0040.0000.0000.0000.000
86A97GLU-1-0.904-0.95532.8920.1060.1060.0000.0000.0000.000
87A98PHE0-0.009-0.00835.9660.0020.0020.0000.0000.0000.000
88A99LEU0-0.027-0.02131.7450.0000.0000.0000.0000.0000.000
89A100GLU-1-0.750-0.83431.4320.1730.1730.0000.0000.0000.000
90A101ALA00.0330.02634.7030.0030.0030.0000.0000.0000.000
91A102LYS10.9480.98337.701-0.120-0.1200.0000.0000.0000.000
92A103ILE0-0.024-0.02031.7490.0020.0020.0000.0000.0000.000
93A104GLU-1-0.922-0.96036.0340.1380.1380.0000.0000.0000.000
94A105ASP-1-0.896-0.94338.0740.1090.1090.0000.0000.0000.000
95A106GLU-1-0.903-0.98238.0420.1280.1280.0000.0000.0000.000
96A107LEU0-0.0100.00135.7350.0020.0020.0000.0000.0000.000
97A108ASN0-0.005-0.00238.8740.0000.0000.0000.0000.0000.000
98A109ILE0-0.031-0.01042.422-0.005-0.0050.0000.0000.0000.000
99A110ALA0-0.005-0.01139.967-0.004-0.0040.0000.0000.0000.000
100A111ARG10.9160.94838.575-0.151-0.1510.0000.0000.0000.000
101A112LYS10.9330.97643.065-0.108-0.1080.0000.0000.0000.000
102A113ASN0-0.106-0.06445.730-0.009-0.0090.0000.0000.0000.000
103A114ALA00.0360.03343.5420.0000.0000.0000.0000.0000.000
104A115SER00.002-0.00145.0330.0010.0010.0000.0000.0000.000
105A116LYS10.9320.98448.209-0.097-0.0970.0000.0000.0000.000
106A117ASN00.0340.01249.0180.0010.0010.0000.0000.0000.000
107A118LYS10.9600.96443.594-0.126-0.1260.0000.0000.0000.000
108A119GLU-1-0.762-0.88644.7890.1310.1310.0000.0000.0000.000
109A120VAL0-0.032-0.01144.7240.0040.0040.0000.0000.0000.000
110A121ALA00.0210.01442.8490.0040.0040.0000.0000.0000.000
111A122LEU0-0.010-0.00238.8640.0090.0090.0000.0000.0000.000
112A123GLN00.013-0.00239.6310.0070.0070.0000.0000.0000.000
113A124ALA00.0160.01139.9940.0040.0040.0000.0000.0000.000
114A125LEU00.0260.01336.0850.0080.0080.0000.0000.0000.000
115A126LYS10.9030.95434.285-0.178-0.1780.0000.0000.0000.000
116A127LYS10.9080.96635.161-0.116-0.1160.0000.0000.0000.000
117A128LYS10.8360.90931.612-0.224-0.2240.0000.0000.0000.000
118A129LYS10.9730.98828.241-0.281-0.2810.0000.0000.0000.000
119A130GLU-1-0.846-0.90430.4690.2140.2140.0000.0000.0000.000
120A131LEU00.007-0.00531.4880.0010.0010.0000.0000.0000.000
121A132GLU-1-0.782-0.88128.4060.2480.2480.0000.0000.0000.000
122A133LYS10.8740.93526.760-0.220-0.2200.0000.0000.0000.000
123A134GLN0-0.058-0.04127.109-0.005-0.0050.0000.0000.0000.000
124A135LEU0-0.020-0.01128.294-0.007-0.0070.0000.0000.0000.000
125A136GLN0-0.001-0.00221.6110.0030.0030.0000.0000.0000.000
126A137GLN00.0070.00023.986-0.007-0.0070.0000.0000.0000.000
127A138ILE0-0.032-0.01625.443-0.016-0.0160.0000.0000.0000.000
128A139ASP-1-0.742-0.84123.8650.2290.2290.0000.0000.0000.000
129A140GLY00.0410.03721.672-0.007-0.0070.0000.0000.0000.000
130A141THR0-0.020-0.00322.399-0.024-0.0240.0000.0000.0000.000
131A142LEU0-0.022-0.01224.548-0.023-0.0230.0000.0000.0000.000
132A143SER0-0.002-0.01322.151-0.013-0.0130.0000.0000.0000.000
133A144THR0-0.036-0.03620.424-0.020-0.0200.0000.0000.0000.000
134A145ILE00.007-0.00322.505-0.030-0.0300.0000.0000.0000.000
135A146GLU-1-0.740-0.83925.9540.1030.1030.0000.0000.0000.000
136A147MET0-0.035-0.00719.361-0.022-0.0220.0000.0000.0000.000
137A148GLN0-0.020-0.00523.511-0.015-0.0150.0000.0000.0000.000
138A149ARG10.7420.84224.642-0.043-0.0430.0000.0000.0000.000
139A150GLU-1-0.865-0.92926.2550.0190.0190.0000.0000.0000.000
140A151ALA0-0.0210.00123.869-0.015-0.0150.0000.0000.0000.000
141A152LEU0-0.005-0.00225.973-0.015-0.0150.0000.0000.0000.000
142A153GLU-1-0.815-0.90528.720-0.008-0.0080.0000.0000.0000.000
143A154SER0-0.019-0.00927.716-0.004-0.0040.0000.0000.0000.000
144A155ALA0-0.019-0.00727.512-0.009-0.0090.0000.0000.0000.000
145A156ASN0-0.023-0.01029.483-0.008-0.0080.0000.0000.0000.000
146A157THR0-0.006-0.01232.8700.0020.0020.0000.0000.0000.000
147A158ASN00.014-0.00228.7380.0050.0050.0000.0000.0000.000
148A159THR0-0.0020.00332.232-0.007-0.0070.0000.0000.0000.000
149A160ALA00.0060.01334.3050.0010.0010.0000.0000.0000.000
150A161VAL0-0.002-0.01035.5360.0020.0020.0000.0000.0000.000
151A162LEU00.003-0.00931.892-0.001-0.0010.0000.0000.0000.000
152A163THR0-0.038-0.01336.541-0.001-0.0010.0000.0000.0000.000
153A164THR0-0.013-0.01239.5350.0010.0010.0000.0000.0000.000
154A165MET00.0160.00837.3890.0020.0020.0000.0000.0000.000
155A166LYS10.8310.91639.6910.0930.0930.0000.0000.0000.000
156A167ASN00.022-0.00341.451-0.001-0.0010.0000.0000.0000.000
157A168ALA00.0010.00843.8540.0030.0030.0000.0000.0000.000
158A169ALA00.0140.00642.4860.0020.0020.0000.0000.0000.000
159A170ASP-1-0.830-0.90644.586-0.086-0.0860.0000.0000.0000.000
160A171ALA0-0.020-0.00546.8260.0030.0030.0000.0000.0000.000
161A172LEU0-0.009-0.01245.8260.0020.0020.0000.0000.0000.000
162A173LYS10.9360.96945.4850.0870.0870.0000.0000.0000.000
163A174ARG10.9140.96649.5440.0570.0570.0000.0000.0000.000
164A175ALA0-0.042-0.01852.4070.0030.0030.0000.0000.0000.000
165A176HIS0-0.028-0.00950.3150.0020.0020.0000.0000.0000.000
166A177GLN0-0.023-0.00953.712-0.003-0.0030.0000.0000.0000.000
167A178ASN00.0360.02254.1930.0020.0020.0000.0000.0000.000
168A179MET00.0310.00057.9880.0010.0010.0000.0000.0000.000
169A180ASP-1-0.876-0.93059.720-0.056-0.0560.0000.0000.0000.000
170A181VAL0-0.033-0.02957.8980.0000.0000.0000.0000.0000.000
171A182ASP-1-0.895-0.95061.013-0.055-0.0550.0000.0000.0000.000
172A183LYS10.8050.90563.1890.0440.0440.0000.0000.0000.000
173A184VAL0-0.022-0.02364.0710.0010.0010.0000.0000.0000.000
174A185HIS00.027-0.00360.1420.0010.0010.0000.0000.0000.000
175A186ASP-1-0.868-0.92165.724-0.041-0.0410.0000.0000.0000.000
176A187MET0-0.071-0.03768.5670.0020.0020.0000.0000.0000.000
177A188MET0-0.097-0.03765.2100.0000.0000.0000.0000.0000.000
178A189ASP-1-0.940-0.95667.819-0.048-0.0480.0000.0000.0000.000
179A190ASP-1-1.067-1.01570.875-0.036-0.0360.0000.0000.0000.000