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: 82VNY

Calculation Name: 3USY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3USY

Chain ID: A

ChEMBL ID:

UniProt ID: O25119

Base Structure: X-ray

Registration Date: 2023-06-19

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 227
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2318761.545904
FMO2-HF: Nuclear repulsion 2230240.960301
FMO2-HF: Total energy -88520.585603
FMO2-MP2: Total energy -88778.294303


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:110:GLY)


Summations of interaction energy for fragment #1(A:110: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.
-3.373-12.58821.017-7.589-4.215-0.034
Interaction energy analysis for fragmet #1(A:110:GLY)
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 : 0.013
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].
3A112LEU00.0600.0493.837-0.2741.277-0.006-0.860-0.6850.005
4A113GLY0-0.038-0.0126.5660.5250.5250.0000.0000.0000.000
5A114SER0-0.004-0.0479.5200.0890.0890.0000.0000.0000.000
6A115MET0-0.052-0.03112.7330.1240.1240.0000.0000.0000.000
7A116GLN00.0540.02116.266-0.005-0.0050.0000.0000.0000.000
8A117LYS10.9360.97418.1850.3310.3310.0000.0000.0000.000
9A118ASN0-0.077-0.05115.3760.1070.1070.0000.0000.0000.000
10A119PHE00.0600.01215.371-0.032-0.0320.0000.0000.0000.000
11A120ALA00.0360.03019.2130.0070.0070.0000.0000.0000.000
12A121TYR0-0.060-0.05221.2030.0090.0090.0000.0000.0000.000
13A122LEU00.0180.00218.0750.0320.0320.0000.0000.0000.000
14A123GLY00.0070.01922.0190.0080.0080.0000.0000.0000.000
15A124LYS10.9060.94523.0210.2350.2350.0000.0000.0000.000
16A125ILE0-0.0150.00523.9950.0230.0230.0000.0000.0000.000
17A126LYS10.9010.95324.9240.1900.1900.0000.0000.0000.000
18A127PRO00.0630.02822.246-0.006-0.0060.0000.0000.0000.000
19A128GLN00.0290.01823.788-0.011-0.0110.0000.0000.0000.000
20A129GLN00.010-0.00126.3720.0030.0030.0000.0000.0000.000
21A130LEU00.0240.02019.9820.0020.0020.0000.0000.0000.000
22A131ALA00.0160.00222.101-0.020-0.0200.0000.0000.0000.000
23A132ASP-1-0.957-0.97423.133-0.226-0.2260.0000.0000.0000.000
24A133PHE0-0.043-0.01624.2220.0030.0030.0000.0000.0000.000
25A134ILE0-0.066-0.04918.538-0.008-0.0080.0000.0000.0000.000
26A135ILE00.0420.02821.009-0.033-0.0330.0000.0000.0000.000
27A136ASN0-0.031-0.02322.4600.0070.0070.0000.0000.0000.000
28A137GLU-1-0.929-0.94419.300-0.390-0.3900.0000.0000.0000.000
29A138HIS00.0370.01614.217-0.052-0.0520.0000.0000.0000.000
30A139PRO00.0960.03113.891-0.056-0.0560.0000.0000.0000.000
31A140GLN00.0210.0139.6890.0610.0610.0000.0000.0000.000
32A141THR0-0.024-0.01512.149-0.178-0.1780.0000.0000.0000.000
33A142ILE00.0280.01914.905-0.049-0.0490.0000.0000.0000.000
34A143ALA00.0130.0149.562-0.027-0.0270.0000.0000.0000.000
35A144LEU0-0.039-0.01810.627-0.097-0.0970.0000.0000.0000.000
36A145ILE0-0.011-0.00211.9070.0070.0070.0000.0000.0000.000
37A146LEU00.0240.00113.0300.0490.0490.0000.0000.0000.000
38A147ALA0-0.0020.0009.4410.0410.0410.0000.0000.0000.000
39A148HIS0-0.0440.00411.2490.0560.0560.0000.0000.0000.000
40A149MET0-0.072-0.01514.2810.1350.1350.0000.0000.0000.000
41A150GLU-1-0.922-0.95714.968-0.414-0.4140.0000.0000.0000.000
42A151ALA00.024-0.00614.8680.0110.0110.0000.0000.0000.000
43A152PRO00.0190.01416.1250.0030.0030.0000.0000.0000.000
44A153ASN00.0550.02619.7090.0300.0300.0000.0000.0000.000
45A154ALA00.0210.02214.8620.0100.0100.0000.0000.0000.000
46A155ALA00.006-0.00417.006-0.002-0.0020.0000.0000.0000.000
47A156GLU-1-0.840-0.92117.842-0.233-0.2330.0000.0000.0000.000
48A157THR0-0.014-0.00918.6420.0240.0240.0000.0000.0000.000
49A158LEU00.008-0.00514.3990.0200.0200.0000.0000.0000.000
50A159SER0-0.081-0.05018.3520.0330.0330.0000.0000.0000.000
51A160TYR0-0.060-0.04021.3990.0390.0390.0000.0000.0000.000
52A161PHE0-0.0020.00719.3860.0030.0030.0000.0000.0000.000
53A162PRO00.0660.02221.4920.0150.0150.0000.0000.0000.000
54A163ASP-1-0.840-0.93119.928-0.227-0.2270.0000.0000.0000.000
55A164GLU-1-0.927-0.95018.514-0.199-0.1990.0000.0000.0000.000
56A165MET00.0080.00417.538-0.020-0.0200.0000.0000.0000.000
57A166LYS10.7850.90015.6960.1770.1770.0000.0000.0000.000
58A167ALA00.0050.02614.277-0.060-0.0600.0000.0000.0000.000
59A168GLU-1-0.864-0.94512.559-0.580-0.5800.0000.0000.0000.000
60A169ILE0-0.036-0.02911.782-0.147-0.1470.0000.0000.0000.000
61A170SER0-0.019-0.02410.061-0.277-0.2770.0000.0000.0000.000
62A171ILE0-0.022-0.0088.028-0.305-0.3050.0000.0000.0000.000
63A172ARG10.8630.9236.9240.5360.5360.0000.0000.0000.000
64A173MET0-0.012-0.0106.774-0.434-0.4340.0000.0000.0000.000
65A174ALA0-0.0200.0083.912-1.515-1.0760.000-0.332-0.108-0.001
66A175ASN0-0.038-0.0161.724-1.576-12.63021.017-6.688-3.276-0.038
67A176LEU00.0220.0393.2572.7172.5940.0070.301-0.1850.000
68A177GLY00.0440.0355.6340.3440.3440.0000.0000.0000.000
69A178GLU-1-0.946-1.0154.591-3.412-3.440-0.001-0.0100.0390.000
70A179ILE0-0.085-0.0188.0520.4280.4280.0000.0000.0000.000
71A180SER00.0140.00011.1620.0020.0020.0000.0000.0000.000
72A181PRO00.0980.02813.550-0.043-0.0430.0000.0000.0000.000
73A182GLN00.0200.00615.392-0.041-0.0410.0000.0000.0000.000
74A183VAL0-0.040-0.01615.3560.0360.0360.0000.0000.0000.000
75A184VAL00.0670.04212.3990.0410.0410.0000.0000.0000.000
76A185LYS10.9961.00415.5170.3700.3700.0000.0000.0000.000
77A186ARG10.9510.97918.9550.4270.4270.0000.0000.0000.000
78A187VAL00.0130.00816.4840.0440.0440.0000.0000.0000.000
79A188SER00.0540.03718.5410.0260.0260.0000.0000.0000.000
80A189THR0-0.030-0.01319.8890.0440.0440.0000.0000.0000.000
81A190VAL0-0.020-0.00422.4860.0320.0320.0000.0000.0000.000
82A191LEU00.0150.00719.8060.0270.0270.0000.0000.0000.000
83A192GLU-1-0.927-0.97123.112-0.315-0.3150.0000.0000.0000.000
84A193ASN0-0.023-0.02825.2170.0350.0350.0000.0000.0000.000
85A194LYS10.8620.94124.0850.3540.3540.0000.0000.0000.000
86A195LEU0-0.002-0.00223.2110.0120.0120.0000.0000.0000.000
87A196GLU-1-0.903-0.93027.691-0.212-0.2120.0000.0000.0000.000
88A197SER0-0.037-0.01731.0240.0170.0170.0000.0000.0000.000
89A198LEU0-0.053-0.03927.2340.0110.0110.0000.0000.0000.000
90A199THR0-0.0070.00427.242-0.001-0.0010.0000.0000.0000.000
91A200SER0-0.029-0.00430.0410.0120.0120.0000.0000.0000.000
92A201TYR0-0.016-0.01433.2490.0050.0050.0000.0000.0000.000
93A202LYS10.9060.94935.1250.1240.1240.0000.0000.0000.000
94A203ILE0-0.0030.00834.916-0.001-0.0010.0000.0000.0000.000
95A204GLU-1-0.957-0.97138.512-0.099-0.0990.0000.0000.0000.000
96A205VAL00.000-0.01337.592-0.005-0.0050.0000.0000.0000.000
97A206GLY00.0020.00840.6490.0050.0050.0000.0000.0000.000
98A207GLY00.0560.01943.1120.0000.0000.0000.0000.0000.000
99A208LEU00.002-0.00945.883-0.002-0.0020.0000.0000.0000.000
100A209ARG11.0020.98243.8920.0820.0820.0000.0000.0000.000
101A210ALA00.0240.02841.645-0.001-0.0010.0000.0000.0000.000
102A211VAL00.0150.00742.244-0.002-0.0020.0000.0000.0000.000
103A212ALA00.0160.00944.6220.0010.0010.0000.0000.0000.000
104A213GLU-1-0.935-0.97740.173-0.088-0.0880.0000.0000.0000.000
105A214ILE0-0.043-0.02139.3900.0000.0000.0000.0000.0000.000
106A215PHE0-0.023-0.04041.3960.0030.0030.0000.0000.0000.000
107A216ASN0-0.003-0.01142.5580.0060.0060.0000.0000.0000.000
108A217ARG10.9120.97335.2190.0970.0970.0000.0000.0000.000
109A218LEU0-0.0330.00839.7000.0010.0010.0000.0000.0000.000
110A219GLY00.0350.02242.0380.0030.0030.0000.0000.0000.000
111A220GLN00.1120.04643.8310.0010.0010.0000.0000.0000.000
112A221LYS10.9690.98047.1100.0370.0370.0000.0000.0000.000
113A222SER00.0390.01345.2490.0010.0010.0000.0000.0000.000
114A223ALA00.0450.03846.3010.0000.0000.0000.0000.0000.000
115A224LYS10.9340.96147.9380.0390.0390.0000.0000.0000.000
116A225THR0-0.048-0.03450.0580.0000.0000.0000.0000.0000.000
117A226THR0-0.020-0.02047.5640.0000.0000.0000.0000.0000.000
118A227LEU00.0150.00950.4760.0000.0000.0000.0000.0000.000
119A228ALA00.0110.01852.5430.0010.0010.0000.0000.0000.000
120A229ARG10.9350.96252.1490.0460.0460.0000.0000.0000.000
121A230ILE00.0230.01849.9730.0000.0000.0000.0000.0000.000
122A231GLU-1-0.793-0.88754.595-0.042-0.0420.0000.0000.0000.000
123A232SER0-0.125-0.05957.7710.0010.0010.0000.0000.0000.000
124A233VAL0-0.052-0.02657.0480.0010.0010.0000.0000.0000.000
125A234ASP-1-0.863-0.94956.682-0.051-0.0510.0000.0000.0000.000
126A235ASN00.0320.00757.390-0.002-0.0020.0000.0000.0000.000
127A236LYS10.9370.97958.8380.0440.0440.0000.0000.0000.000
128A237LEU00.0270.02351.633-0.001-0.0010.0000.0000.0000.000
129A238ALA00.0250.01253.716-0.002-0.0020.0000.0000.0000.000
130A239GLY00.0080.00354.2560.0000.0000.0000.0000.0000.000
131A240ALA00.009-0.00153.8490.0000.0000.0000.0000.0000.000
132A241ILE0-0.036-0.03248.651-0.002-0.0020.0000.0000.0000.000
133A242LYS10.8280.89950.1680.0430.0430.0000.0000.0000.000
134A243GLU-1-0.851-0.91551.554-0.048-0.0480.0000.0000.0000.000
135A244MET0-0.096-0.02347.400-0.002-0.0020.0000.0000.0000.000
136A245MET0-0.052-0.01846.525-0.002-0.0020.0000.0000.0000.000
137A246PHE00.0140.03447.1120.0000.0000.0000.0000.0000.000
138A247THR0-0.020-0.04043.435-0.003-0.0030.0000.0000.0000.000
139A248PHE00.0610.00845.0390.0040.0040.0000.0000.0000.000
140A249GLU-1-0.738-0.86241.410-0.065-0.0650.0000.0000.0000.000
141A250ASP-1-0.816-0.87144.659-0.056-0.0560.0000.0000.0000.000
142A251ILE00.0090.00547.1530.0040.0040.0000.0000.0000.000
143A252VAL0-0.0070.00545.1580.0030.0030.0000.0000.0000.000
144A253LYS10.8010.89045.5150.0540.0540.0000.0000.0000.000
145A254LEU0-0.0050.02549.9750.0020.0020.0000.0000.0000.000
146A255ASP-1-0.774-0.89253.280-0.029-0.0290.0000.0000.0000.000
147A256ASN00.031-0.01754.506-0.003-0.0030.0000.0000.0000.000
148A257PHE0-0.019-0.01056.8000.0000.0000.0000.0000.0000.000
149A258ALA00.0650.03756.6980.0000.0000.0000.0000.0000.000
150A259ILE0-0.030-0.00852.448-0.001-0.0010.0000.0000.0000.000
151A260ARG10.9010.94556.1440.0260.0260.0000.0000.0000.000
152A261GLU-1-0.798-0.86959.249-0.029-0.0290.0000.0000.0000.000
153A262ILE0-0.002-0.00154.292-0.001-0.0010.0000.0000.0000.000
154A263LEU0-0.062-0.02954.909-0.001-0.0010.0000.0000.0000.000
155A264LYS10.7600.87058.2880.0280.0280.0000.0000.0000.000
156A265VAL0-0.030-0.00460.3110.0000.0000.0000.0000.0000.000
157A266ALA00.0090.01155.733-0.001-0.0010.0000.0000.0000.000
158A267ASP-1-0.764-0.87957.085-0.042-0.0420.0000.0000.0000.000
159A268LYS10.8630.92054.9660.0370.0370.0000.0000.0000.000
160A269LYS10.9070.94653.2970.0420.0420.0000.0000.0000.000
161A270ASP-1-0.804-0.88151.876-0.057-0.0570.0000.0000.0000.000
162A271LEU0-0.018-0.01250.464-0.003-0.0030.0000.0000.0000.000
163A272SER0-0.014-0.04049.388-0.003-0.0030.0000.0000.0000.000
164A273LEU00.0190.00245.684-0.003-0.0030.0000.0000.0000.000
165A274ALA0-0.023-0.01845.735-0.004-0.0040.0000.0000.0000.000
166A275LEU0-0.004-0.00845.219-0.003-0.0030.0000.0000.0000.000
167A276LYS10.7970.90642.3160.0700.0700.0000.0000.0000.000
168A277THR0-0.041-0.02338.653-0.002-0.0020.0000.0000.0000.000
169A278SER00.0050.01339.870-0.003-0.0030.0000.0000.0000.000
170A279THR0-0.050-0.04638.8290.0010.0010.0000.0000.0000.000
171A280LYS10.8620.90340.3350.0440.0440.0000.0000.0000.000
172A281ASP-1-0.891-0.93941.632-0.044-0.0440.0000.0000.0000.000
173A282LEU00.0000.00343.9940.0040.0040.0000.0000.0000.000
174A283THR00.010-0.00644.0380.0020.0020.0000.0000.0000.000
175A284ASP-1-0.790-0.89245.802-0.038-0.0380.0000.0000.0000.000
176A285LYS10.8060.93048.0640.0380.0380.0000.0000.0000.000
177A286PHE00.0370.00149.3150.0030.0030.0000.0000.0000.000
178A287LEU00.0030.00348.2620.0020.0020.0000.0000.0000.000
179A288ASN0-0.059-0.04650.0500.0040.0040.0000.0000.0000.000
180A289ASN0-0.081-0.03953.4760.0040.0040.0000.0000.0000.000
181A290MET0-0.0360.01053.1190.0000.0000.0000.0000.0000.000
182A291SER00.0160.00557.4540.0010.0010.0000.0000.0000.000
183A292SER00.0690.01756.736-0.001-0.0010.0000.0000.0000.000
184A293ARG10.8590.91656.4430.0250.0250.0000.0000.0000.000
185A294ALA0-0.009-0.01257.408-0.001-0.0010.0000.0000.0000.000
186A295ALA00.0330.00853.214-0.002-0.0020.0000.0000.0000.000
187A296GLU-1-0.830-0.89352.570-0.028-0.0280.0000.0000.0000.000
188A297GLN00.005-0.00452.8760.0000.0000.0000.0000.0000.000
189A298PHE00.0000.00949.608-0.002-0.0020.0000.0000.0000.000
190A299VAL00.0160.00547.235-0.003-0.0030.0000.0000.0000.000
191A300GLU-1-0.915-0.95748.235-0.039-0.0390.0000.0000.0000.000
192A301GLU-1-0.893-0.92949.553-0.050-0.0500.0000.0000.0000.000
193A302MET0-0.019-0.00545.029-0.002-0.0020.0000.0000.0000.000
194A303GLN0-0.041-0.00544.632-0.003-0.0030.0000.0000.0000.000
195A304TYR0-0.021-0.02845.419-0.003-0.0030.0000.0000.0000.000
196A305LEU0-0.0500.00246.139-0.002-0.0020.0000.0000.0000.000
197A306GLY0-0.0110.01443.136-0.003-0.0030.0000.0000.0000.000
198A307ALA0-0.027-0.01838.942-0.001-0.0010.0000.0000.0000.000
199A308VAL00.0380.02140.5760.0020.0020.0000.0000.0000.000
200A309LYS10.8990.94940.0230.0920.0920.0000.0000.0000.000
201A310ILE00.0710.02635.6400.0040.0040.0000.0000.0000.000
202A311LYS10.9440.98640.2580.0910.0910.0000.0000.0000.000
203A312ASP-1-0.866-0.95542.827-0.083-0.0830.0000.0000.0000.000
204A313VAL00.0230.01842.1450.0040.0040.0000.0000.0000.000
205A314ASP-1-0.862-0.93142.095-0.091-0.0910.0000.0000.0000.000
206A315VAL0-0.091-0.06145.0890.0040.0040.0000.0000.0000.000
207A316ALA00.0320.02247.9610.0040.0040.0000.0000.0000.000
208A317GLN00.018-0.00143.1280.0030.0030.0000.0000.0000.000
209A318ARG10.8740.95147.7500.0670.0670.0000.0000.0000.000
210A319LYS10.8850.94150.4090.0580.0580.0000.0000.0000.000
211A320ILE0-0.026-0.00851.1690.0030.0030.0000.0000.0000.000
212A321ILE0-0.048-0.03347.8930.0020.0020.0000.0000.0000.000
213A322GLU-1-0.897-0.95552.509-0.053-0.0530.0000.0000.0000.000
214A323ILE0-0.031-0.00355.6870.0030.0030.0000.0000.0000.000
215A324VAL0-0.011-0.01153.1800.0020.0020.0000.0000.0000.000
216A325GLN0-0.032-0.03654.0150.0010.0010.0000.0000.0000.000
217A326SER0-0.0010.01357.4610.0020.0020.0000.0000.0000.000
218A327LEU00.000-0.02158.6940.0020.0020.0000.0000.0000.000
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