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: YVLN2

Calculation Name: 3USW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3USW

Chain ID: A

ChEMBL ID:

UniProt ID: O25119

Base Structure: X-ray

Registration Date: 2023-09-24

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 OptH
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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2129469.330578
FMO2-HF: Nuclear repulsion 2046370.956508
FMO2-HF: Total energy -83098.37407
FMO2-MP2: Total energy -83341.001267


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:117:LYS)


Summations of interaction energy for fragment #1(A:117:LYS)
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.
-102.497-92.97821.526-11.273-19.771-0.105
Interaction energy analysis for fragmet #1(A:117:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.911 / q_NPA : 0.970
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].
3A119PHE00.0780.0513.027-4.272-1.3520.129-1.370-1.679-0.005
4A120ALA00.0310.0015.7263.8973.8970.0000.0000.0000.000
5A121TYR0-0.016-0.0435.3861.9841.9840.0000.0000.0000.000
6A122LEU00.0230.0068.9542.0652.0650.0000.0000.0000.000
7A123GLY0-0.0200.00711.4861.3251.3250.0000.0000.0000.000
8A124LYS10.8840.93513.30419.47819.4780.0000.0000.0000.000
9A125ILE00.0280.02812.8470.9560.9560.0000.0000.0000.000
10A126LYS10.9500.97516.65212.58012.5800.0000.0000.0000.000
11A127PRO00.0850.03717.579-0.188-0.1880.0000.0000.0000.000
12A128GLN00.0080.01118.6340.0770.0770.0000.0000.0000.000
13A129GLN0-0.026-0.00718.6280.0880.0880.0000.0000.0000.000
14A130LEU00.0120.01013.417-0.218-0.2180.0000.0000.0000.000
15A131ALA00.003-0.00217.269-0.496-0.4960.0000.0000.0000.000
16A132ASP-1-0.932-0.98519.237-13.432-13.4320.0000.0000.0000.000
17A133PHE0-0.063-0.02314.8960.2150.2150.0000.0000.0000.000
18A134ILE0-0.035-0.03213.537-0.328-0.3280.0000.0000.0000.000
19A135ILE00.0050.01716.656-0.290-0.2900.0000.0000.0000.000
20A136ASN0-0.031-0.02319.7220.4890.4890.0000.0000.0000.000
21A137GLU-1-0.930-0.95014.607-19.306-19.3060.0000.0000.0000.000
22A138HIS00.0190.00815.560-0.546-0.5460.0000.0000.0000.000
23A139PRO00.1210.04615.052-1.686-1.6860.0000.0000.0000.000
24A140GLN0-0.0020.00111.129-1.487-1.4870.0000.0000.0000.000
25A141THR0-0.010-0.01110.742-3.109-3.1090.0000.0000.0000.000
26A142ILE00.0190.01410.615-2.792-2.7920.0000.0000.0000.000
27A143ALA00.0290.01710.980-1.283-1.2830.0000.0000.0000.000
28A144LEU0-0.050-0.0284.250-4.298-4.187-0.001-0.008-0.1010.000
29A145ILE0-0.005-0.0016.387-6.103-6.1030.0000.0000.0000.000
30A146LEU00.022-0.0068.290-1.555-1.5550.0000.0000.0000.000
31A147ALA0-0.0130.0006.1390.4370.4370.0000.0000.0000.000
32A148HIS0-0.084-0.0472.177-47.161-44.0146.620-4.770-4.996-0.080
33A149MET0-0.065-0.0166.1752.2302.2300.0000.0000.0000.000
34A150GLU-1-0.892-0.9439.911-23.090-23.0900.0000.0000.0000.000
35A151ALA00.0340.00112.5930.6200.6200.0000.0000.0000.000
36A152PRO00.009-0.00114.2610.6300.6300.0000.0000.0000.000
37A153ASN00.0550.03014.6051.5581.5580.0000.0000.0000.000
38A154ALA00.0080.01012.3530.5470.5470.0000.0000.0000.000
39A155ALA0-0.010-0.00614.4070.6570.6570.0000.0000.0000.000
40A156GLU-1-0.851-0.93317.642-14.332-14.3320.0000.0000.0000.000
41A157THR0-0.0150.01915.5260.6240.6240.0000.0000.0000.000
42A158LEU0-0.005-0.00916.1230.6050.6050.0000.0000.0000.000
43A159SER0-0.104-0.08918.2810.9340.9340.0000.0000.0000.000
44A160TYR0-0.0020.00320.8321.0061.0060.0000.0000.0000.000
45A161PHE0-0.025-0.00416.8980.4020.4020.0000.0000.0000.000
46A162PRO00.0740.01722.3960.1750.1750.0000.0000.0000.000
47A163ASP-1-0.851-0.93223.219-12.970-12.9700.0000.0000.0000.000
48A164GLU-1-0.938-0.97223.264-12.544-12.5440.0000.0000.0000.000
49A165MET00.0300.03219.182-0.169-0.1690.0000.0000.0000.000
50A166LYS10.8220.91219.03412.78912.7890.0000.0000.0000.000
51A167ALA00.0160.02218.461-1.057-1.0570.0000.0000.0000.000
52A168GLU-1-0.886-0.94618.989-15.289-15.2890.0000.0000.0000.000
53A169ILE0-0.046-0.02213.995-1.188-1.1880.0000.0000.0000.000
54A170SER0-0.030-0.02914.352-1.772-1.7720.0000.0000.0000.000
55A171ILE0-0.041-0.02415.181-0.858-0.8580.0000.0000.0000.000
56A172ARG10.8820.95413.07618.67918.6790.0000.0000.0000.000
57A173MET00.003-0.0039.347-1.217-1.2170.0000.0000.0000.000
58A174ALA0-0.041-0.00610.741-1.973-1.9730.0000.0000.0000.000
59A175ASN0-0.102-0.05311.8431.3341.3340.0000.0000.0000.000
60A176LEU00.0660.0486.815-0.715-0.7150.0000.0000.0000.000
61A177GLY0-0.056-0.0156.785-5.539-5.5390.0000.0000.0000.000
62A178GLU-1-0.881-0.9488.590-27.432-27.4320.0000.0000.0000.000
63A179ILE0-0.011-0.0015.8101.9051.9050.0000.0000.0000.000
64A180SER00.0180.0066.023-5.432-5.4320.0000.0000.0000.000
65A181PRO00.0960.0232.890-3.648-2.7390.171-0.235-0.8460.000
66A182GLN0-0.017-0.0102.849-1.4970.1480.304-0.717-1.231-0.009
67A183VAL0-0.0030.0005.5362.5562.5560.0000.0000.0000.000
68A184VAL00.0400.0212.061-1.187-1.6266.011-1.628-3.944-0.010
69A185LYS10.9460.9642.23623.88426.8218.001-5.192-5.7460.002
70A186ARG10.9740.9983.17624.59121.8210.0863.154-0.4710.000
71A187VAL00.0060.0005.8541.9181.9180.0000.0000.0000.000
72A188SER0-0.005-0.0092.6793.4434.4470.206-0.502-0.708-0.003
73A189THR00.0200.0344.5103.1423.197-0.001-0.005-0.0490.000
74A190VAL0-0.047-0.0276.1651.7531.7530.0000.0000.0000.000
75A191LEU00.0000.0008.2401.6291.6290.0000.0000.0000.000
76A192GLU-1-0.931-0.9696.829-23.672-23.6720.0000.0000.0000.000
77A193ASN0-0.015-0.0249.2151.2381.2380.0000.0000.0000.000
78A194LYS10.8460.94711.90918.82218.8220.0000.0000.0000.000
79A195LEU0-0.052-0.03410.9390.6200.6200.0000.0000.0000.000
80A196GLU-1-0.990-0.96314.285-14.100-14.1000.0000.0000.0000.000
81A204GLU-1-0.964-0.98325.472-10.205-10.2050.0000.0000.0000.000
82A205VAL00.002-0.01128.510-0.031-0.0310.0000.0000.0000.000
83A206GLY00.0040.02231.3580.0480.0480.0000.0000.0000.000
84A207GLY00.0350.00430.272-0.199-0.1990.0000.0000.0000.000
85A208LEU00.006-0.01329.8960.2600.2600.0000.0000.0000.000
86A209ARG11.0060.99129.8789.9199.9190.0000.0000.0000.000
87A210ALA00.0400.02833.1720.2460.2460.0000.0000.0000.000
88A211VAL00.0160.01735.0610.2880.2880.0000.0000.0000.000
89A212ALA00.0350.01535.9710.2630.2630.0000.0000.0000.000
90A213GLU-1-0.945-0.97736.612-8.178-8.1780.0000.0000.0000.000
91A214ILE0-0.0160.00139.2160.2510.2510.0000.0000.0000.000
92A215PHE0-0.014-0.03940.4270.2220.2220.0000.0000.0000.000
93A216ASN00.0190.01339.5750.1940.1940.0000.0000.0000.000
94A217ARG10.8600.95043.1087.1587.1580.0000.0000.0000.000
95A218LEU0-0.0230.01644.3310.2000.2000.0000.0000.0000.000
96A219GLY00.0290.01747.2350.0230.0230.0000.0000.0000.000
97A220GLN00.0670.02248.123-0.134-0.1340.0000.0000.0000.000
98A221LYS10.9330.96648.9075.9225.9220.0000.0000.0000.000
99A222SER00.0040.01449.078-0.076-0.0760.0000.0000.0000.000
100A223ALA00.0870.06044.667-0.073-0.0730.0000.0000.0000.000
101A224LYS10.9991.00244.6636.2996.2990.0000.0000.0000.000
102A225THR0-0.087-0.06946.077-0.004-0.0040.0000.0000.0000.000
103A226THR0-0.011-0.03343.2140.0060.0060.0000.0000.0000.000
104A227LEU00.0180.01739.592-0.079-0.0790.0000.0000.0000.000
105A228ALA00.0030.01241.897-0.135-0.1350.0000.0000.0000.000
106A229ARG10.9340.96744.0026.4766.4760.0000.0000.0000.000
107A230ILE00.0070.03837.977-0.020-0.0200.0000.0000.0000.000
108A231GLU-1-0.928-0.97139.290-7.915-7.9150.0000.0000.0000.000
109A232SER0-0.089-0.06840.055-0.061-0.0610.0000.0000.0000.000
110A233VAL0-0.060-0.02738.8610.0320.0320.0000.0000.0000.000
111A234ASP-1-0.892-0.94933.974-9.514-9.5140.0000.0000.0000.000
112A235ASN00.0540.01634.7710.1820.1820.0000.0000.0000.000
113A236LYS10.9510.96527.46711.48511.4850.0000.0000.0000.000
114A237LEU00.0370.04032.616-0.088-0.0880.0000.0000.0000.000
115A238ALA00.0210.01633.9200.0590.0590.0000.0000.0000.000
116A239GLY00.0110.00135.5270.1280.1280.0000.0000.0000.000
117A240ALA00.0120.00831.379-0.023-0.0230.0000.0000.0000.000
118A241ILE0-0.010-0.02133.2020.0130.0130.0000.0000.0000.000
119A242LYS10.9200.94335.8647.8937.8930.0000.0000.0000.000
120A243GLU-1-0.983-0.99032.645-9.614-9.6140.0000.0000.0000.000
121A244MET0-0.0310.00830.490-0.112-0.1120.0000.0000.0000.000
122A245MET0-0.129-0.05835.1950.1520.1520.0000.0000.0000.000
123A246PHE0-0.0070.00038.893-0.053-0.0530.0000.0000.0000.000
124A247THR0-0.025-0.02040.2150.3370.3370.0000.0000.0000.000
125A248PHE00.015-0.01542.6950.0260.0260.0000.0000.0000.000
126A249GLU-1-0.837-0.92541.350-7.682-7.6820.0000.0000.0000.000
127A250ASP-1-0.841-0.91838.854-8.516-8.5160.0000.0000.0000.000
128A251ILE0-0.032-0.02440.944-0.056-0.0560.0000.0000.0000.000
129A252VAL0-0.034-0.00539.6950.0510.0510.0000.0000.0000.000
130A253LYS10.9100.94835.0759.0159.0150.0000.0000.0000.000
131A254LEU0-0.0060.03039.801-0.058-0.0580.0000.0000.0000.000
132A255ASP-1-0.837-0.92242.170-7.321-7.3210.0000.0000.0000.000
133A256ASN00.026-0.01943.4710.1180.1180.0000.0000.0000.000
134A257PHE0-0.004-0.00646.3020.1920.1920.0000.0000.0000.000
135A258ALA00.0690.03945.3370.1600.1600.0000.0000.0000.000
136A259ILE00.0000.00546.0100.1540.1540.0000.0000.0000.000
137A260ARG10.8720.93849.0066.5506.5500.0000.0000.0000.000
138A261GLU-1-0.843-0.91650.199-5.899-5.8990.0000.0000.0000.000
139A262ILE00.0080.00547.5890.1180.1180.0000.0000.0000.000
140A263LEU0-0.076-0.04252.0130.1490.1490.0000.0000.0000.000
141A264LYS10.7860.90154.7845.9575.9570.0000.0000.0000.000
142A265VAL0-0.037-0.01055.0740.1190.1190.0000.0000.0000.000
143A266ALA0-0.023-0.01354.6900.0690.0690.0000.0000.0000.000
144A267ASP-1-0.859-0.92656.757-5.177-5.1770.0000.0000.0000.000
145A268LYS10.9390.95058.1195.5065.5060.0000.0000.0000.000
146A269LYS10.9911.00659.2204.9464.9460.0000.0000.0000.000
147A270ASP-1-0.881-0.93956.907-5.567-5.5670.0000.0000.0000.000
148A271LEU0-0.002-0.00852.316-0.095-0.0950.0000.0000.0000.000
149A272SER00.0040.00954.615-0.146-0.1460.0000.0000.0000.000
150A273LEU00.023-0.00655.857-0.067-0.0670.0000.0000.0000.000
151A274ALA0-0.031-0.01751.993-0.094-0.0940.0000.0000.0000.000
152A275LEU0-0.002-0.00749.586-0.151-0.1510.0000.0000.0000.000
153A276LYS10.8000.92151.2105.7095.7090.0000.0000.0000.000
154A277THR0-0.044-0.02548.990-0.023-0.0230.0000.0000.0000.000
155A278SER00.0160.02546.734-0.176-0.1760.0000.0000.0000.000
156A279THR00.0560.02441.6690.0950.0950.0000.0000.0000.000
157A280LYS10.9620.97545.0786.8546.8540.0000.0000.0000.000
158A281ASP-1-0.874-0.93140.997-7.768-7.7680.0000.0000.0000.000
159A282LEU0-0.022-0.01644.3560.0680.0680.0000.0000.0000.000
160A283THR00.011-0.00445.8480.1560.1560.0000.0000.0000.000
161A284ASP-1-0.846-0.93847.291-6.579-6.5790.0000.0000.0000.000
162A285LYS10.8320.95042.4827.7467.7460.0000.0000.0000.000
163A286PHE00.0310.00747.6850.0940.0940.0000.0000.0000.000
164A287LEU0-0.006-0.00650.9260.1180.1180.0000.0000.0000.000
165A288ASN0-0.009-0.01648.2750.2190.2190.0000.0000.0000.000
166A289ASN0-0.095-0.05748.4090.0410.0410.0000.0000.0000.000
167A290MET0-0.059-0.00552.5660.1480.1480.0000.0000.0000.000
168A291SER0-0.0020.00356.2200.0090.0090.0000.0000.0000.000
169A292SER00.0850.02058.3120.0100.0100.0000.0000.0000.000
170A293ARG11.0001.01059.2675.0985.0980.0000.0000.0000.000
171A294ALA0-0.074-0.04759.8750.0350.0350.0000.0000.0000.000
172A295ALA00.0330.00656.584-0.001-0.0010.0000.0000.0000.000
173A296GLU-1-0.908-0.95658.273-5.252-5.2520.0000.0000.0000.000
174A297GLN00.0360.02460.731-0.017-0.0170.0000.0000.0000.000
175A298PHE00.0030.00654.9000.0110.0110.0000.0000.0000.000
176A299VAL00.0170.00455.957-0.041-0.0410.0000.0000.0000.000
177A300GLU-1-0.918-0.95558.462-5.082-5.0820.0000.0000.0000.000
178A301GLU-1-0.951-0.99160.892-5.324-5.3240.0000.0000.0000.000
179A302MET0-0.029-0.01253.104-0.016-0.0160.0000.0000.0000.000
180A303GLN0-0.052-0.02058.806-0.019-0.0190.0000.0000.0000.000
181A304TYR0-0.036-0.02460.1180.0590.0590.0000.0000.0000.000
182A305LEU0-0.0220.00058.6530.0540.0540.0000.0000.0000.000
183A306GLY0-0.0100.01860.9010.0170.0170.0000.0000.0000.000
184A307ALA0-0.031-0.02057.930-0.126-0.1260.0000.0000.0000.000
185A308VAL00.0480.02455.3600.0750.0750.0000.0000.0000.000
186A309LYS10.9380.96156.2085.4795.4790.0000.0000.0000.000
187A310ILE00.0790.03049.6360.0360.0360.0000.0000.0000.000
188A311LYS10.9310.96153.1605.6365.6360.0000.0000.0000.000
189A312ASP-1-0.900-0.94055.006-5.535-5.5350.0000.0000.0000.000
190A313VAL00.0130.00851.2010.0290.0290.0000.0000.0000.000
191A314ASP-1-0.857-0.93249.798-6.622-6.6220.0000.0000.0000.000
192A315VAL0-0.082-0.04752.038-0.025-0.0250.0000.0000.0000.000
193A316ALA00.0030.00654.8860.0320.0320.0000.0000.0000.000
194A317GLN00.008-0.02048.378-0.066-0.0660.0000.0000.0000.000
195A318ARG10.8860.95047.0946.4796.4790.0000.0000.0000.000
196A319LYS10.9540.98151.4165.4855.4850.0000.0000.0000.000
197A320ILE00.0030.01649.6790.0120.0120.0000.0000.0000.000
198A321ILE00.0250.01745.460-0.035-0.0350.0000.0000.0000.000
199A322GLU-1-0.949-0.97848.434-6.067-6.0670.0000.0000.0000.000
200A323ILE0-0.0120.00650.9750.0260.0260.0000.0000.0000.000
201A324VAL00.0060.00545.079-0.002-0.0020.0000.0000.0000.000
202A325GLN0-0.034-0.02345.696-0.171-0.1710.0000.0000.0000.000
203A326SER00.0130.01247.4150.0140.0140.0000.0000.0000.000
204A327LEU0-0.009-0.02348.9550.0320.0320.0000.0000.0000.000
205A328GLN00.0080.00041.443-0.030-0.0300.0000.0000.0000.000
206A329GLU-1-0.932-0.96845.461-6.537-6.5370.0000.0000.0000.000
207A330LYS10.8640.94247.3735.8735.8730.0000.0000.0000.000
208A331GLY00.0130.02545.8830.0570.0570.0000.0000.0000.000
209A332VAL0-0.073-0.02846.846-0.028-0.0280.0000.0000.0000.000
210A333ILE0-0.028-0.01044.784-0.024-0.0240.0000.0000.0000.000
211A334GLN00.0180.00438.951-0.093-0.0930.0000.0000.0000.000
212A335THR0-0.026-0.00637.069-0.138-0.1380.0000.0000.0000.000