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: LN6V9

Calculation Name: 1VLW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VLW

Chain ID: A

ChEMBL ID:

UniProt ID: Q9WXS1

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 204
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2339238.612344
FMO2-HF: Nuclear repulsion 2260650.402087
FMO2-HF: Total energy -78588.210257
FMO2-MP2: Total energy -78815.378528


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:HIS)


Summations of interaction energy for fragment #1(A:-1:HIS)
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.
-54.374-45.99111.938-7.442-12.8770.016
Interaction energy analysis for fragmet #1(A:-1:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.086 / q_NPA : 0.014
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].
3A1MET00.0240.0033.862-2.117-0.765-0.008-0.568-0.7770.001
4A2LYS10.9600.9922.014-26.094-26.58610.554-3.636-6.4260.033
5A3MET00.0360.0302.869-4.534-2.5871.026-0.717-2.2550.003
6A4GLU-1-0.828-0.9065.5430.5360.5360.0000.0000.0000.000
7A5GLU-1-0.833-0.9178.1150.8480.8480.0000.0000.0000.000
8A6LEU0-0.0150.0034.499-0.690-0.504-0.001-0.017-0.1680.000
9A7PHE00.024-0.0057.979-0.165-0.1650.0000.0000.0000.000
10A8LYS10.8320.91511.432-1.140-1.1400.0000.0000.0000.000
11A9LYS10.8750.95611.0130.5480.5480.0000.0000.0000.000
12A10HIS00.024-0.0049.5660.2550.2550.0000.0000.0000.000
13A11LYS10.9120.96713.7490.0160.0160.0000.0000.0000.000
14A12ILE00.0350.01115.4620.0650.0650.0000.0000.0000.000
15A13VAL0-0.022-0.01112.530-0.144-0.1440.0000.0000.0000.000
16A14ALA00.0220.01814.9080.1670.1670.0000.0000.0000.000
17A15VAL0-0.047-0.02115.685-0.152-0.1520.0000.0000.0000.000
18A16LEU00.0470.01816.7740.1280.1280.0000.0000.0000.000
19A17ARG10.8560.94819.0860.6630.6630.0000.0000.0000.000
20A18ALA00.000-0.01421.9570.0160.0160.0000.0000.0000.000
21A19ASN0-0.058-0.04323.922-0.003-0.0030.0000.0000.0000.000
22A20SER00.004-0.02525.1460.0230.0230.0000.0000.0000.000
23A21VAL00.0810.04421.124-0.048-0.0480.0000.0000.0000.000
24A22GLU-1-0.834-0.91322.282-0.733-0.7330.0000.0000.0000.000
25A23GLU-1-0.747-0.84424.013-0.620-0.6200.0000.0000.0000.000
26A24ALA0-0.001-0.01919.637-0.021-0.0210.0000.0000.0000.000
27A25LYS10.8040.90518.8780.8360.8360.0000.0000.0000.000
28A26GLU-1-0.880-0.94819.914-0.665-0.6650.0000.0000.0000.000
29A27LYS10.7920.88721.4020.6730.6730.0000.0000.0000.000
30A28ALA0-0.008-0.01716.088-0.012-0.0120.0000.0000.0000.000
31A29LEU0-0.0090.00417.282-0.082-0.0820.0000.0000.0000.000
32A30ALA00.0230.02219.0970.0050.0050.0000.0000.0000.000
33A31VAL0-0.001-0.02316.9130.0480.0480.0000.0000.0000.000
34A32PHE0-0.022-0.00312.5520.0080.0080.0000.0000.0000.000
35A33GLU-1-0.849-0.91516.927-0.664-0.6640.0000.0000.0000.000
36A34GLY0-0.027-0.00320.0490.0740.0740.0000.0000.0000.000
37A35GLY0-0.022-0.01417.8980.0720.0720.0000.0000.0000.000
38A36VAL0-0.056-0.02515.226-0.011-0.0110.0000.0000.0000.000
39A37HIS00.004-0.00810.799-0.062-0.0620.0000.0000.0000.000
40A38LEU0-0.0360.0138.936-0.455-0.4550.0000.0000.0000.000
41A39ILE00.0160.00811.0020.3670.3670.0000.0000.0000.000
42A40GLU-1-0.808-0.91611.671-1.450-1.4500.0000.0000.0000.000
43A41ILE00.0290.01213.1010.2660.2660.0000.0000.0000.000
44A42THR0-0.080-0.06215.010-0.008-0.0080.0000.0000.0000.000
45A43PHE00.0710.00314.2190.0170.0170.0000.0000.0000.000
46A44THR0-0.032-0.01118.6350.0680.0680.0000.0000.0000.000
47A45VAL0-0.078-0.01319.6920.0610.0610.0000.0000.0000.000
48A46PRO00.0210.01121.246-0.035-0.0350.0000.0000.0000.000
49A47ASP-1-0.879-0.94221.212-0.756-0.7560.0000.0000.0000.000
50A48ALA00.0210.02316.991-0.079-0.0790.0000.0000.0000.000
51A49ASP-1-0.812-0.92215.277-1.173-1.1730.0000.0000.0000.000
52A50THR00.0370.03215.779-0.172-0.1720.0000.0000.0000.000
53A51VAL00.0110.01716.611-0.032-0.0320.0000.0000.0000.000
54A52ILE0-0.039-0.02211.113-0.062-0.0620.0000.0000.0000.000
55A53LYS10.9400.97213.5621.2171.2170.0000.0000.0000.000
56A54GLU-1-0.822-0.89514.867-1.015-1.0150.0000.0000.0000.000
57A55LEU0-0.0130.00414.1330.1070.1070.0000.0000.0000.000
58A56SER00.007-0.00812.007-0.140-0.1400.0000.0000.0000.000
59A57PHE00.0580.03112.999-0.097-0.0970.0000.0000.0000.000
60A58LEU00.0010.00913.6640.0700.0700.0000.0000.0000.000
61A59LYS10.8380.9024.6177.7377.777-0.0010.001-0.0390.000
62A60GLU-1-0.933-0.9689.720-1.609-1.6090.0000.0000.0000.000
63A61LYS10.7810.89412.1831.4211.4210.0000.0000.0000.000
64A62GLY00.0100.0159.3740.1970.1970.0000.0000.0000.000
65A63ALA0-0.054-0.0199.561-0.065-0.0650.0000.0000.0000.000
66A64ILE0-0.035-0.0274.867-0.567-0.5670.0000.0000.0000.000
67A65ILE00.0280.0177.5040.8780.8780.0000.0000.0000.000
68A66GLY00.0360.0307.812-0.938-0.9380.0000.0000.0000.000
69A67ALA0-0.0090.0139.0940.4410.4410.0000.0000.0000.000
70A68GLY00.0420.00212.0240.0160.0160.0000.0000.0000.000
71A69THR0-0.081-0.05314.7920.0950.0950.0000.0000.0000.000
72A70VAL00.0100.02613.4880.0490.0490.0000.0000.0000.000
73A71THR0-0.023-0.04716.6400.0650.0650.0000.0000.0000.000
74A72SER00.0330.01518.4040.0640.0640.0000.0000.0000.000
75A73VAL00.0910.02415.118-0.129-0.1290.0000.0000.0000.000
76A74GLU-1-0.886-0.93716.508-0.651-0.6510.0000.0000.0000.000
77A75GLN00.0410.04317.027-0.074-0.0740.0000.0000.0000.000
78A76CYS0-0.0090.01012.090-0.253-0.2530.0000.0000.0000.000
79A77ARG10.9670.99512.5390.4280.4280.0000.0000.0000.000
80A78LYS10.8770.93613.7230.7620.7620.0000.0000.0000.000
81A79ALA0-0.022-0.01411.610-0.130-0.1300.0000.0000.0000.000
82A80VAL0-0.013-0.0208.420-0.306-0.3060.0000.0000.0000.000
83A81GLU-1-0.937-0.9729.845-1.305-1.3050.0000.0000.0000.000
84A82SER0-0.097-0.07512.6420.1320.1320.0000.0000.0000.000
85A83GLY0-0.0120.0188.6980.0640.0640.0000.0000.0000.000
86A84ALA0-0.068-0.0247.744-0.704-0.7040.0000.0000.0000.000
87A85GLU-1-0.839-0.9383.213-16.593-15.0060.032-0.809-0.810-0.007
88A86PHE0-0.069-0.0363.580-2.096-1.2950.009-0.322-0.487-0.002
89A87ILE00.0310.0206.4470.4700.4700.0000.0000.0000.000
90A88VAL0-0.010-0.0059.8200.2770.2770.0000.0000.0000.000
91A89SER0-0.014-0.00912.717-0.021-0.0210.0000.0000.0000.000
92A90PRO0-0.039-0.01515.9790.0410.0410.0000.0000.0000.000
93A91HIS00.0440.02118.8990.0440.0440.0000.0000.0000.000
94A92LEU00.0040.01515.733-0.062-0.0620.0000.0000.0000.000
95A93ASP-1-0.772-0.88416.357-0.367-0.3670.0000.0000.0000.000
96A94GLU-1-0.801-0.92515.554-0.001-0.0010.0000.0000.0000.000
97A95GLU-1-0.878-0.92815.657-0.210-0.2100.0000.0000.0000.000
98A96ILE00.001-0.00512.253-0.066-0.0660.0000.0000.0000.000
99A97SER0-0.007-0.00911.354-0.074-0.0740.0000.0000.0000.000
100A98GLN0-0.062-0.02710.5740.0710.0710.0000.0000.0000.000
101A99PHE00.0700.03311.3750.0760.0760.0000.0000.0000.000
102A100CYS0-0.035-0.0157.574-0.193-0.1930.0000.0000.0000.000
103A101LYS10.8550.9346.628-0.664-0.6640.0000.0000.0000.000
104A102GLU-1-0.900-0.9367.403-0.052-0.0520.0000.0000.0000.000
105A103LYS10.8210.9108.2850.7750.7750.0000.0000.0000.000
106A104GLY00.0130.0204.392-0.352-0.251-0.001-0.013-0.0870.000
107A105VAL0-0.077-0.0482.856-6.541-4.3620.311-1.193-1.297-0.012
108A106PHE0-0.010-0.0153.3430.8731.4640.018-0.160-0.4490.000
109A107TYR00.028-0.0174.855-0.120-0.029-0.001-0.008-0.0820.000
110A108MET0-0.051-0.0218.6120.4910.4910.0000.0000.0000.000
111A109PRO00.0070.00611.102-0.070-0.0700.0000.0000.0000.000
112A110GLY0-0.0040.00414.4690.0720.0720.0000.0000.0000.000
113A111VAL0-0.059-0.03217.7510.0580.0580.0000.0000.0000.000
114A112MET00.008-0.00320.491-0.028-0.0280.0000.0000.0000.000
115A113THR0-0.010-0.03623.8870.0330.0330.0000.0000.0000.000
116A114PRO00.0750.00923.5680.0110.0110.0000.0000.0000.000
117A115THR0-0.0060.00123.8320.0340.0340.0000.0000.0000.000
118A116GLU-1-0.783-0.86421.674-0.069-0.0690.0000.0000.0000.000
119A117LEU0-0.0110.00919.5300.0130.0130.0000.0000.0000.000
120A118VAL00.005-0.00518.9440.0560.0560.0000.0000.0000.000
121A119LYS10.8380.91219.7440.0350.0350.0000.0000.0000.000
122A120ALA00.0540.02615.7300.0200.0200.0000.0000.0000.000
123A121MET0-0.018-0.01415.0210.0540.0540.0000.0000.0000.000
124A122LYS10.9100.96715.493-0.187-0.1870.0000.0000.0000.000
125A123LEU0-0.0240.01114.2170.0350.0350.0000.0000.0000.000
126A124GLY00.003-0.01011.5010.0050.0050.0000.0000.0000.000
127A125HIS10.8110.9239.1490.1720.1720.0000.0000.0000.000
128A126THR00.0470.01911.633-0.088-0.0880.0000.0000.0000.000
129A127ILE0-0.0040.0069.054-0.049-0.0490.0000.0000.0000.000
130A128LEU0-0.007-0.00412.321-0.132-0.1320.0000.0000.0000.000
131A129LYS10.8510.92514.9030.8490.8490.0000.0000.0000.000
132A130LEU0-0.055-0.00516.2230.0560.0560.0000.0000.0000.000
133A131PHE0-0.042-0.00319.902-0.072-0.0720.0000.0000.0000.000
134A132PRO00.0450.02221.9190.0220.0220.0000.0000.0000.000
135A133GLY00.052-0.00223.6950.0380.0380.0000.0000.0000.000
136A134GLU-1-0.871-0.95924.679-0.299-0.2990.0000.0000.0000.000
137A135VAL0-0.057-0.01327.6880.0210.0210.0000.0000.0000.000
138A136VAL0-0.0150.00724.6190.0280.0280.0000.0000.0000.000
139A137GLY00.0720.02525.358-0.016-0.0160.0000.0000.0000.000
140A138PRO00.010-0.00625.8930.0260.0260.0000.0000.0000.000
141A139GLN00.0400.00226.9360.0330.0330.0000.0000.0000.000
142A140PHE0-0.0040.00922.8370.0240.0240.0000.0000.0000.000
143A141VAL00.0070.00021.6960.0280.0280.0000.0000.0000.000
144A142LYS10.8790.95424.151-0.063-0.0630.0000.0000.0000.000
145A143ALA0-0.021-0.00626.8730.0310.0310.0000.0000.0000.000
146A144MET0-0.020-0.00823.0160.0290.0290.0000.0000.0000.000
147A145LYS10.8880.95420.958-0.380-0.3800.0000.0000.0000.000
148A146GLY00.009-0.00524.5480.0390.0390.0000.0000.0000.000
149A147PRO0-0.0130.00125.9100.0320.0320.0000.0000.0000.000
150A148PHE0-0.004-0.01320.9830.0300.0300.0000.0000.0000.000
151A149PRO00.0510.04621.0570.0120.0120.0000.0000.0000.000
152A150ASN00.005-0.01116.8980.0200.0200.0000.0000.0000.000
153A151VAL0-0.023-0.01216.0810.1110.1110.0000.0000.0000.000
154A152LYS10.8170.89812.600-1.155-1.1550.0000.0000.0000.000
155A153PHE00.0600.01815.333-0.024-0.0240.0000.0000.0000.000
156A154VAL00.0180.00413.1270.0130.0130.0000.0000.0000.000
157A155PRO00.0160.01916.435-0.060-0.0600.0000.0000.0000.000
158A156THR0-0.045-0.02518.447-0.135-0.1350.0000.0000.0000.000
159A157GLY00.0790.04820.4530.0320.0320.0000.0000.0000.000
160A158GLY00.019-0.00124.1680.0210.0210.0000.0000.0000.000
161A159VAL0-0.0260.01721.9570.0360.0360.0000.0000.0000.000
162A160ASN00.021-0.00625.203-0.027-0.0270.0000.0000.0000.000
163A161LEU00.0830.02526.3030.0150.0150.0000.0000.0000.000
164A162ASP-1-0.873-0.92128.223-0.184-0.1840.0000.0000.0000.000
165A163ASN00.006-0.00627.5540.0010.0010.0000.0000.0000.000
166A164VAL00.0090.01122.9970.0230.0230.0000.0000.0000.000
167A203CYS0-0.089-0.07923.8700.0670.0670.0000.0000.0000.000
168A166GLU-1-0.873-0.91226.954-0.024-0.0240.0000.0000.0000.000
169A167TRP0-0.022-0.02823.0360.0410.0410.0000.0000.0000.000
170A168PHE00.0040.00118.8640.0260.0260.0000.0000.0000.000
171A169LYS10.8480.92623.5410.0630.0630.0000.0000.0000.000
172A170ALA0-0.057-0.04925.0310.0390.0390.0000.0000.0000.000
173A171GLY0-0.027-0.00222.5220.0300.0300.0000.0000.0000.000
174A172VAL0-0.056-0.01518.9240.0470.0470.0000.0000.0000.000
175A173LEU0-0.043-0.01011.7460.0500.0500.0000.0000.0000.000
176A174ALA0-0.012-0.01714.588-0.027-0.0270.0000.0000.0000.000
177A175VAL0-0.006-0.00116.5590.0470.0470.0000.0000.0000.000
178A176GLY00.0420.03517.188-0.113-0.1130.0000.0000.0000.000
179A177VAL0-0.045-0.03217.9150.0940.0940.0000.0000.0000.000
180A178GLY00.0810.04820.112-0.074-0.0740.0000.0000.0000.000
181A179SER00.006-0.00222.172-0.001-0.0010.0000.0000.0000.000
182A180ALA00.010-0.01325.5070.0080.0080.0000.0000.0000.000
183A181LEU0-0.0370.00219.3620.0210.0210.0000.0000.0000.000
184A182VAL00.0560.01520.3820.0090.0090.0000.0000.0000.000
185A183LYS10.9050.96023.4150.4020.4020.0000.0000.0000.000
186A184GLY00.0370.03227.0000.0200.0200.0000.0000.0000.000
187A185THR0-0.009-0.03427.976-0.038-0.0380.0000.0000.0000.000
188A186PRO00.0730.02925.240-0.001-0.0010.0000.0000.0000.000
189A187ASP-1-0.813-0.89625.962-0.473-0.4730.0000.0000.0000.000
190A188GLU-1-0.852-0.90327.950-0.397-0.3970.0000.0000.0000.000
191A189VAL0-0.082-0.03922.4440.0030.0030.0000.0000.0000.000
192A190ARG10.8260.90223.1440.5510.5510.0000.0000.0000.000
193A191GLU-1-0.812-0.89124.229-0.430-0.4300.0000.0000.0000.000
194A192LYS10.8370.91025.7030.4820.4820.0000.0000.0000.000
195A193ALA0-0.007-0.00420.5150.0140.0140.0000.0000.0000.000
196A194LYS10.8680.92122.0450.4580.4580.0000.0000.0000.000
197A195ALA0-0.039-0.01623.7770.0320.0320.0000.0000.0000.000
198A196PHE00.001-0.02621.8580.0410.0410.0000.0000.0000.000
199A197VAL0-0.0070.00818.7250.0390.0390.0000.0000.0000.000
200A198GLU-1-0.860-0.88821.401-0.203-0.2030.0000.0000.0000.000
201A199LYS10.8480.90424.8060.2460.2460.0000.0000.0000.000
202A200ILE00.0150.00219.8740.0400.0400.0000.0000.0000.000
203A201ARG10.7900.91521.9170.3190.3190.0000.0000.0000.000
204A202GLY0-0.0100.00423.3110.0410.0410.0000.0000.0000.000