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: VQ821

Calculation Name: 1VL5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VL5

Chain ID: A

ChEMBL ID:

UniProt ID: Q9KAF6

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 230
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2932800.052272
FMO2-HF: Nuclear repulsion 2840065.636141
FMO2-HF: Total energy -92734.41613
FMO2-MP2: Total energy -93005.510381


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:28:GLY)


Summations of interaction energy for fragment #1(A:28:GLY)
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.
-1.9171.4620.252-1.64-1.990.001
Interaction energy analysis for fragmet #1(A:28:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.074 / q_NPA : 0.036
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].
3A30ASP-1-0.861-0.9403.631-5.002-2.6560.014-1.239-1.1210.003
4A31LEU00.025-0.0035.0710.3240.356-0.001-0.007-0.0240.000
5A32ALA00.0320.0256.6640.3410.3410.0000.0000.0000.000
6A33LYS10.8770.9454.9422.7712.7710.0000.0000.0000.000
7A34LEU00.003-0.0037.0430.5490.5490.0000.0000.0000.000
8A35MET00.0070.00910.0850.2800.2800.0000.0000.0000.000
9A36GLN0-0.019-0.0039.185-0.003-0.0030.0000.0000.0000.000
10A37ILE0-0.033-0.0149.6050.1470.1470.0000.0000.0000.000
11A38ALA00.0040.01812.4450.1830.1830.0000.0000.0000.000
12A39ALA0-0.0250.00215.3150.1110.1110.0000.0000.0000.000
13A40LEU0-0.022-0.00317.0560.0680.0680.0000.0000.0000.000
14A41LYS10.8480.88219.4010.3830.3830.0000.0000.0000.000
15A42GLY00.0280.03722.8120.0280.0280.0000.0000.0000.000
16A43ASN0-0.042-0.02624.1670.0030.0030.0000.0000.0000.000
17A44GLU-1-0.790-0.87922.501-0.396-0.3960.0000.0000.0000.000
18A45GLU-1-0.781-0.88325.040-0.226-0.2260.0000.0000.0000.000
19A46VAL0-0.008-0.01419.671-0.004-0.0040.0000.0000.0000.000
20A47LEU00.0140.02222.7130.0230.0230.0000.0000.0000.000
21A48ASP-1-0.794-0.88317.596-0.564-0.5640.0000.0000.0000.000
22A49VAL00.030-0.01119.9810.0430.0430.0000.0000.0000.000
23A50ALA0-0.0210.00219.158-0.035-0.0350.0000.0000.0000.000
24A51THR0-0.037-0.02818.734-0.018-0.0180.0000.0000.0000.000
25A52GLY00.0260.00618.200-0.031-0.0310.0000.0000.0000.000
26A53GLY0-0.025-0.02017.8030.0200.0200.0000.0000.0000.000
27A54GLY00.0380.01918.2970.0110.0110.0000.0000.0000.000
28A55HIS0-0.079-0.05812.954-0.012-0.0120.0000.0000.0000.000
29A56VAL00.0250.01212.858-0.103-0.1030.0000.0000.0000.000
30A57ALA00.0520.02115.088-0.014-0.0140.0000.0000.0000.000
31A58ASN0-0.017-0.00316.5260.0530.0530.0000.0000.0000.000
32A59ALA0-0.030-0.01213.8540.0070.0070.0000.0000.0000.000
33A60PHE00.046-0.00714.023-0.016-0.0160.0000.0000.0000.000
34A61ALA0-0.0120.00917.9290.0290.0290.0000.0000.0000.000
35A62PRO00.0130.00918.9840.0310.0310.0000.0000.0000.000
36A63PHE0-0.032-0.00916.6080.0140.0140.0000.0000.0000.000
37A64VAL0-0.045-0.01320.396-0.002-0.0020.0000.0000.0000.000
38A65LYS10.8560.93523.1500.2660.2660.0000.0000.0000.000
39A66LYS10.8130.88825.9700.2270.2270.0000.0000.0000.000
40A67VAL00.0160.01921.072-0.023-0.0230.0000.0000.0000.000
41A68VAL0-0.043-0.00824.2800.0270.0270.0000.0000.0000.000
42A69ALA00.0050.00422.573-0.028-0.0280.0000.0000.0000.000
43A70PHE00.0240.00122.9570.0300.0300.0000.0000.0000.000
44A71ASP-1-0.775-0.89121.990-0.251-0.2510.0000.0000.0000.000
45A72LEU00.0010.00924.9100.0150.0150.0000.0000.0000.000
46A73THR0-0.025-0.02227.1550.0090.0090.0000.0000.0000.000
47A74GLU-1-0.813-0.92028.006-0.135-0.1350.0000.0000.0000.000
48A75ASP-1-0.879-0.92928.909-0.094-0.0940.0000.0000.0000.000
49A76ILE0-0.025-0.00122.817-0.001-0.0010.0000.0000.0000.000
50A77LEU0-0.014-0.00524.516-0.015-0.0150.0000.0000.0000.000
51A78LYS10.8330.91026.2950.0880.0880.0000.0000.0000.000
52A79VAL0-0.023-0.00522.0150.0000.0000.0000.0000.0000.000
53A80ALA0-0.0030.00821.584-0.010-0.0100.0000.0000.0000.000
54A81ARG10.8350.88922.5820.1290.1290.0000.0000.0000.000
55A82ALA0-0.0080.01125.054-0.002-0.0020.0000.0000.0000.000
56A83PHE00.0040.00116.299-0.011-0.0110.0000.0000.0000.000
57A84ILE0-0.023-0.01720.439-0.013-0.0130.0000.0000.0000.000
58A85GLU-1-0.853-0.91522.271-0.154-0.1540.0000.0000.0000.000
59A86GLY00.0000.01124.2750.0120.0120.0000.0000.0000.000
60A87ASN0-0.122-0.05919.3530.0170.0170.0000.0000.0000.000
61A88GLY0-0.0160.00722.826-0.010-0.0100.0000.0000.0000.000
62A89HIS0-0.0140.00219.7460.0060.0060.0000.0000.0000.000
63A90GLN00.000-0.02024.9750.0060.0060.0000.0000.0000.000
64A91GLN0-0.059-0.02324.2340.0170.0170.0000.0000.0000.000
65A92VAL0-0.006-0.00923.252-0.020-0.0200.0000.0000.0000.000
66A93GLU-1-0.845-0.90826.324-0.174-0.1740.0000.0000.0000.000
67A94TYR00.0550.01824.235-0.022-0.0220.0000.0000.0000.000
68A95VAL0-0.011-0.01027.3490.0160.0160.0000.0000.0000.000
69A96GLN00.0330.01327.698-0.009-0.0090.0000.0000.0000.000
70A97GLY0-0.036-0.04028.5460.0060.0060.0000.0000.0000.000
71A98ASP-1-0.866-0.94127.463-0.164-0.1640.0000.0000.0000.000
72A99ALA00.001-0.00423.737-0.010-0.0100.0000.0000.0000.000
73A101GLN0-0.039-0.00629.1110.0070.0070.0000.0000.0000.000
74A102MET0-0.026-0.01125.111-0.005-0.0050.0000.0000.0000.000
75A103PRO0-0.0170.01229.9730.0040.0040.0000.0000.0000.000
76A104PHE0-0.035-0.03527.3890.0000.0000.0000.0000.0000.000
77A105THR00.0270.00932.2390.0050.0050.0000.0000.0000.000
78A106ASP-1-0.817-0.91432.144-0.170-0.1700.0000.0000.0000.000
79A107GLU-1-0.873-0.91730.731-0.181-0.1810.0000.0000.0000.000
80A108ARG10.8560.94529.6770.2170.2170.0000.0000.0000.000
81A109PHE0-0.003-0.01425.110-0.003-0.0030.0000.0000.0000.000
82A110HIS00.0040.01024.719-0.004-0.0040.0000.0000.0000.000
83A111ILE0-0.026-0.01018.748-0.019-0.0190.0000.0000.0000.000
84A112VAL00.0320.03720.5360.0250.0250.0000.0000.0000.000
85A113THR0-0.013-0.02715.859-0.043-0.0430.0000.0000.0000.000
86A114CYS0-0.042-0.01715.9740.0760.0760.0000.0000.0000.000
87A115ARG10.9420.9626.6161.5171.5170.0000.0000.0000.000
88A116ILE0-0.082-0.04210.1820.0570.0570.0000.0000.0000.000
89A117ALA00.0470.02313.2440.0820.0820.0000.0000.0000.000
90A118ALA00.0710.03416.4840.0480.0480.0000.0000.0000.000
91A119HIS10.7950.87814.8700.2350.2350.0000.0000.0000.000
92A120HIS10.8350.89918.3370.1620.1620.0000.0000.0000.000
93A121PHE0-0.0130.00820.6500.0140.0140.0000.0000.0000.000
94A122PRO00.0720.04523.2740.0050.0050.0000.0000.0000.000
95A123ASN0-0.030-0.03426.2930.0110.0110.0000.0000.0000.000
96A124PRO00.0230.01721.934-0.009-0.0090.0000.0000.0000.000
97A125ALA00.0790.02623.842-0.019-0.0190.0000.0000.0000.000
98A126SER00.0200.01325.846-0.004-0.0040.0000.0000.0000.000
99A127PHE00.0270.02019.466-0.007-0.0070.0000.0000.0000.000
100A128VAL0-0.020-0.00621.561-0.017-0.0170.0000.0000.0000.000
101A129SER00.0740.02724.143-0.005-0.0050.0000.0000.0000.000
102A130GLU-1-0.801-0.86627.252-0.170-0.1700.0000.0000.0000.000
103A131ALA0-0.011-0.01823.010-0.005-0.0050.0000.0000.0000.000
104A132TYR00.0210.00525.083-0.001-0.0010.0000.0000.0000.000
105A133ARG10.7530.84326.9150.1710.1710.0000.0000.0000.000
106A134VAL0-0.011-0.00326.5220.0050.0050.0000.0000.0000.000
107A135LEU0-0.0280.01222.941-0.006-0.0060.0000.0000.0000.000
108A136LYS10.8310.90327.3010.2400.2400.0000.0000.0000.000
109A137LYS10.8760.92227.9910.1570.1570.0000.0000.0000.000
110A138GLY00.003-0.00226.8400.0020.0020.0000.0000.0000.000
111A139GLY0-0.0360.00124.655-0.025-0.0250.0000.0000.0000.000
112A140GLN0-0.022-0.02918.549-0.007-0.0070.0000.0000.0000.000
113A141LEU00.0090.01118.457-0.001-0.0010.0000.0000.0000.000
114A142LEU0-0.024-0.01514.113-0.044-0.0440.0000.0000.0000.000
115A143LEU00.0030.00514.7410.0090.0090.0000.0000.0000.000
116A144VAL0-0.014-0.0178.765-0.119-0.1190.0000.0000.0000.000
117A145ASP-1-0.721-0.84310.850-0.217-0.2170.0000.0000.0000.000
118A146ASN0-0.036-0.0219.956-0.110-0.1100.0000.0000.0000.000
119A147SER0-0.036-0.04411.525-0.051-0.0510.0000.0000.0000.000
120A148ALA00.0030.01713.3650.0820.0820.0000.0000.0000.000
121A149PRO0-0.076-0.05815.727-0.015-0.0150.0000.0000.0000.000
122A150GLU-1-0.718-0.85717.198-0.078-0.0780.0000.0000.0000.000
123A151ASN00.0000.00920.018-0.003-0.0030.0000.0000.0000.000
124A152ASP-1-0.751-0.88121.5230.0230.0230.0000.0000.0000.000
125A153ALA00.0070.02023.864-0.001-0.0010.0000.0000.0000.000
126A154PHE0-0.009-0.03319.1300.0140.0140.0000.0000.0000.000
127A155ASP-1-0.781-0.83719.2930.0140.0140.0000.0000.0000.000
128A156VAL00.0590.02320.352-0.002-0.0020.0000.0000.0000.000
129A157PHE0-0.022-0.00819.543-0.002-0.0020.0000.0000.0000.000
130A158TYR0-0.072-0.06213.2970.0080.0080.0000.0000.0000.000
131A159ASN00.0290.00218.609-0.014-0.0140.0000.0000.0000.000
132A160TYR0-0.074-0.04220.076-0.005-0.0050.0000.0000.0000.000
133A161VAL00.0240.00218.510-0.002-0.0020.0000.0000.0000.000
134A162GLU-1-0.818-0.90714.4220.1250.1250.0000.0000.0000.000
135A163LYS10.8080.90818.9460.0020.0020.0000.0000.0000.000
136A164GLU-1-0.829-0.88322.3550.0590.0590.0000.0000.0000.000
137A165ARG10.8850.96515.390-0.106-0.1060.0000.0000.0000.000
138A166ASP-1-0.813-0.88819.656-0.050-0.0500.0000.0000.0000.000
139A167DTY00.0350.02221.725-0.013-0.0130.0000.0000.0000.000
140A168SER0-0.048-0.05022.292-0.014-0.0140.0000.0000.0000.000
141A169HIS0-0.025-0.00417.480-0.040-0.0400.0000.0000.0000.000
142A170HIS0-0.035-0.00621.2610.0230.0230.0000.0000.0000.000
143A171ARG10.7610.83720.4600.0700.0700.0000.0000.0000.000
144A172ALA0-0.026-0.00615.354-0.037-0.0370.0000.0000.0000.000
145A173TRP00.0320.01117.2400.0410.0410.0000.0000.0000.000
146A174LYS10.7810.87416.495-0.004-0.0040.0000.0000.0000.000
147A175LYS10.8310.88612.5920.0160.0160.0000.0000.0000.000
148A176SER0-0.013-0.02816.640-0.026-0.0260.0000.0000.0000.000
149A177ASP-1-0.758-0.87120.132-0.095-0.0950.0000.0000.0000.000
150A178TRP00.018-0.01315.853-0.021-0.0210.0000.0000.0000.000
151A179LEU0-0.0100.00018.447-0.014-0.0140.0000.0000.0000.000
152A180LYS10.9680.99220.8950.1090.1090.0000.0000.0000.000
153A181MET00.0190.01120.9710.0010.0010.0000.0000.0000.000
154A182LEU0-0.069-0.02818.397-0.010-0.0100.0000.0000.0000.000
155A183GLU-1-0.933-0.96423.026-0.153-0.1530.0000.0000.0000.000
156A184GLU-1-0.964-0.98825.815-0.123-0.1230.0000.0000.0000.000
157A185ALA0-0.051-0.02025.7830.0080.0080.0000.0000.0000.000
158A186GLY0-0.0070.00227.5910.0010.0010.0000.0000.0000.000
159A187PHE0-0.072-0.04822.806-0.012-0.0120.0000.0000.0000.000
160A188GLU-1-0.910-0.95523.799-0.208-0.2080.0000.0000.0000.000
161A189LEU0-0.058-0.03716.389-0.035-0.0350.0000.0000.0000.000
162A190GLU-1-0.788-0.85518.058-0.423-0.4230.0000.0000.0000.000
163A191GLU-1-0.849-0.92513.122-0.862-0.8620.0000.0000.0000.000
164A192LEU00.004-0.00512.169-0.036-0.0360.0000.0000.0000.000
165A193HIS0-0.035-0.0257.512-0.184-0.1840.0000.0000.0000.000
166A194CYS0-0.032-0.0218.359-0.051-0.0510.0000.0000.0000.000
167A195PHE0-0.019-0.0172.843-1.208-0.4350.241-0.371-0.643-0.002
168A196HIS00.0340.0044.782-0.152-0.125-0.001-0.003-0.0220.000
169A197LYS10.9120.9614.2400.8581.059-0.001-0.020-0.1800.000
170A198THR00.0200.0066.464-0.407-0.4070.0000.0000.0000.000
171A199PHE0-0.055-0.0189.7600.0820.0820.0000.0000.0000.000
172A200ILE00.0800.04112.015-0.010-0.0100.0000.0000.0000.000
173A201PHE0-0.016-0.01514.893-0.060-0.0600.0000.0000.0000.000
174A202GLU-1-0.678-0.81217.7960.1780.1780.0000.0000.0000.000
175A203ASP-1-0.822-0.91815.3370.3840.3840.0000.0000.0000.000
176A204TRP0-0.148-0.08913.655-0.032-0.0320.0000.0000.0000.000
177A205CYS0-0.029-0.01816.046-0.055-0.0550.0000.0000.0000.000
178A206ASP-1-0.774-0.87119.7390.1330.1330.0000.0000.0000.000
179A207ARG10.8670.94812.350-0.306-0.3060.0000.0000.0000.000
180A208MET0-0.059-0.01718.615-0.037-0.0370.0000.0000.0000.000
181A209ASN0-0.074-0.02920.922-0.006-0.0060.0000.0000.0000.000
182A210VAL00.0210.02122.336-0.008-0.0080.0000.0000.0000.000
183A211THR00.0520.02724.8700.0100.0100.0000.0000.0000.000
184A212THR00.044-0.00427.3540.0080.0080.0000.0000.0000.000
185A213GLU-1-0.921-0.95428.6740.0810.0810.0000.0000.0000.000
186A214LYS10.8670.93326.147-0.069-0.0690.0000.0000.0000.000
187A215LYS10.7640.84823.053-0.158-0.1580.0000.0000.0000.000
188A216GLN0-0.032-0.03125.5290.0230.0230.0000.0000.0000.000
189A217GLU-1-0.898-0.94528.1700.0910.0910.0000.0000.0000.000
190A218LEU00.0040.00021.2600.0060.0060.0000.0000.0000.000
191A219SER00.0270.01123.6800.0220.0220.0000.0000.0000.000
192A220ASP-1-0.818-0.88824.6840.1580.1580.0000.0000.0000.000
193A221PHE00.0440.01524.4460.0010.0010.0000.0000.0000.000
194A222ILE0-0.017-0.01120.1700.0000.0000.0000.0000.0000.000
195A223LYS10.8680.94324.012-0.165-0.1650.0000.0000.0000.000
196A224SER0-0.068-0.02425.7290.0000.0000.0000.0000.0000.000
197A225LYS10.7810.91124.346-0.155-0.1550.0000.0000.0000.000
198A226PRO00.0650.02926.7470.0110.0110.0000.0000.0000.000
199A227THR00.0510.01525.0980.0150.0150.0000.0000.0000.000
200A228GLU-1-0.842-0.92123.4790.1910.1910.0000.0000.0000.000
201A229TYR0-0.008-0.01621.4890.0200.0200.0000.0000.0000.000
202A230TYR00.006-0.01619.8860.0440.0440.0000.0000.0000.000
203A231GLN0-0.014-0.00319.0990.0410.0410.0000.0000.0000.000
204A232LYS10.8860.96515.352-0.209-0.2090.0000.0000.0000.000
205A233PHE0-0.051-0.03414.7360.0410.0410.0000.0000.0000.000
206A234LYS10.8380.91613.760-0.492-0.4920.0000.0000.0000.000
207A235ILE00.0010.01416.1060.0600.0600.0000.0000.0000.000
208A236VAL00.0040.01717.122-0.015-0.0150.0000.0000.0000.000
209A237VAL0-0.023-0.01319.634-0.009-0.0090.0000.0000.0000.000
210A238GLU-1-0.927-0.96521.8360.4000.4000.0000.0000.0000.000
211A239ASP-1-0.898-0.94724.6710.2170.2170.0000.0000.0000.000
212A240GLY0-0.040-0.01727.431-0.016-0.0160.0000.0000.0000.000
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