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: N1G2Q

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 OptAll
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 -2325065.038991
FMO2-HF: Nuclear repulsion 2236543.727846
FMO2-HF: Total energy -88521.311144
FMO2-MP2: Total energy -88778.8561


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.
-6.686-6.1037.682-4.436-3.83-0.033
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 : 0.033 / q_NPA : 0.016
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].
3A112LEU00.0460.0453.8690.3911.687-0.004-0.659-0.6330.003
4A113GLY0-0.025-0.0046.3740.5490.5490.0000.0000.0000.000
5A114SER0-0.020-0.0509.3240.1000.1000.0000.0000.0000.000
6A115MET0-0.027-0.01912.7120.1050.1050.0000.0000.0000.000
7A116GLN00.0320.00416.2760.0040.0040.0000.0000.0000.000
8A117LYS10.8420.92718.2620.3460.3460.0000.0000.0000.000
9A118ASN0-0.062-0.03915.2790.1010.1010.0000.0000.0000.000
10A119PHE00.0670.00514.988-0.042-0.0420.0000.0000.0000.000
11A120ALA00.0320.02918.9700.0170.0170.0000.0000.0000.000
12A121TYR0-0.051-0.04120.8160.0090.0090.0000.0000.0000.000
13A122LEU00.013-0.00218.0800.0330.0330.0000.0000.0000.000
14A123GLY0-0.0010.01622.0520.0140.0140.0000.0000.0000.000
15A124LYS10.9080.94523.0480.2430.2430.0000.0000.0000.000
16A125ILE0-0.0300.00424.0760.0240.0240.0000.0000.0000.000
17A126LYS10.9100.94924.9130.1880.1880.0000.0000.0000.000
18A127PRO00.0410.02622.130-0.003-0.0030.0000.0000.0000.000
19A128GLN00.0200.01923.692-0.010-0.0100.0000.0000.0000.000
20A129GLN00.0160.00326.2530.0040.0040.0000.0000.0000.000
21A130LEU0-0.0050.00119.8430.0010.0010.0000.0000.0000.000
22A131ALA00.0200.00121.811-0.017-0.0170.0000.0000.0000.000
23A132ASP-1-0.944-0.96522.833-0.223-0.2230.0000.0000.0000.000
24A133PHE0-0.036-0.02123.974-0.001-0.0010.0000.0000.0000.000
25A134ILE0-0.054-0.03518.505-0.012-0.0120.0000.0000.0000.000
26A135ILE00.0140.01521.017-0.029-0.0290.0000.0000.0000.000
27A136ASN0-0.034-0.02122.6550.0160.0160.0000.0000.0000.000
28A137GLU-1-0.899-0.93518.856-0.389-0.3890.0000.0000.0000.000
29A138HIS00.0210.01513.767-0.055-0.0550.0000.0000.0000.000
30A139PRO00.0750.02413.520-0.063-0.0630.0000.0000.0000.000
31A140GLN00.0040.0018.7670.0870.0870.0000.0000.0000.000
32A141THR0-0.018-0.01311.793-0.173-0.1730.0000.0000.0000.000
33A142ILE00.0190.01414.562-0.054-0.0540.0000.0000.0000.000
34A143ALA00.0280.0199.283-0.016-0.0160.0000.0000.0000.000
35A144LEU0-0.030-0.01410.392-0.145-0.1450.0000.0000.0000.000
36A145ILE0-0.023-0.00711.7600.0260.0260.0000.0000.0000.000
37A146LEU00.021-0.00412.8230.0390.0390.0000.0000.0000.000
38A147ALA0-0.015-0.0039.5860.0430.0430.0000.0000.0000.000
39A148HIS0-0.0450.00411.4400.0160.0160.0000.0000.0000.000
40A149MET0-0.056-0.01214.4050.1340.1340.0000.0000.0000.000
41A150GLU-1-0.918-0.95615.218-0.411-0.4110.0000.0000.0000.000
42A151ALA00.0200.00115.2090.0080.0080.0000.0000.0000.000
43A152PRO00.0170.00816.5790.0030.0030.0000.0000.0000.000
44A153ASN00.0560.02920.1230.0200.0200.0000.0000.0000.000
45A154ALA00.0240.02915.0150.0060.0060.0000.0000.0000.000
46A155ALA00.0240.00717.174-0.002-0.0020.0000.0000.0000.000
47A156GLU-1-0.810-0.90118.218-0.239-0.2390.0000.0000.0000.000
48A157THR0-0.021-0.02218.6590.0220.0220.0000.0000.0000.000
49A158LEU00.005-0.00514.4030.0160.0160.0000.0000.0000.000
50A159SER0-0.076-0.05318.2920.0360.0360.0000.0000.0000.000
51A160TYR0-0.049-0.05321.2680.0350.0350.0000.0000.0000.000
52A161PHE00.0060.01919.3330.0080.0080.0000.0000.0000.000
53A162PRO00.0610.02121.4100.0150.0150.0000.0000.0000.000
54A163ASP-1-0.842-0.93019.752-0.234-0.2340.0000.0000.0000.000
55A164GLU-1-0.948-0.96218.304-0.189-0.1890.0000.0000.0000.000
56A165MET00.0160.00817.182-0.018-0.0180.0000.0000.0000.000
57A166LYS10.7820.89415.5550.1830.1830.0000.0000.0000.000
58A167ALA00.0170.03014.083-0.078-0.0780.0000.0000.0000.000
59A168GLU-1-0.816-0.90112.260-0.560-0.5600.0000.0000.0000.000
60A169ILE0-0.025-0.01511.106-0.162-0.1620.0000.0000.0000.000
61A170SER0-0.014-0.02010.099-0.267-0.2670.0000.0000.0000.000
62A171ILE0-0.031-0.0127.998-0.289-0.2890.0000.0000.0000.000
63A172ARG10.8340.8956.4400.4510.4510.0000.0000.0000.000
64A173MET0-0.012-0.0106.432-0.520-0.5200.0000.0000.0000.000
65A174ALA0-0.030-0.0074.256-1.013-0.788-0.001-0.183-0.0410.000
66A175ASN0-0.049-0.0231.942-6.119-7.1027.680-3.737-2.960-0.036
67A176LEU00.0100.0283.3842.1362.1610.0080.162-0.1960.000
68A177GLY00.0140.0135.0240.5950.5950.0000.0000.0000.000
69A178GLU-1-0.896-0.9904.310-2.779-2.759-0.001-0.0190.0000.000
70A179ILE0-0.088-0.0147.6170.4040.4040.0000.0000.0000.000
71A180SER00.0200.00210.5890.0050.0050.0000.0000.0000.000
72A181PRO00.0960.03013.399-0.030-0.0300.0000.0000.0000.000
73A182GLN00.0300.01715.135-0.038-0.0380.0000.0000.0000.000
74A183VAL0-0.028-0.00714.9170.0410.0410.0000.0000.0000.000
75A184VAL00.0500.03311.9550.0350.0350.0000.0000.0000.000
76A185LYS10.9931.00114.9930.3530.3530.0000.0000.0000.000
77A186ARG10.9340.97618.5240.4000.4000.0000.0000.0000.000
78A187VAL00.0280.01016.0030.0410.0410.0000.0000.0000.000
79A188SER00.0520.04717.9210.0250.0250.0000.0000.0000.000
80A189THR0-0.030-0.02019.3140.0420.0420.0000.0000.0000.000
81A190VAL0-0.024-0.01121.9300.0320.0320.0000.0000.0000.000
82A191LEU00.0200.01119.3720.0280.0280.0000.0000.0000.000
83A192GLU-1-0.852-0.92422.639-0.318-0.3180.0000.0000.0000.000
84A193ASN0-0.040-0.03424.6750.0380.0380.0000.0000.0000.000
85A194LYS10.8610.93223.5440.3460.3460.0000.0000.0000.000
86A195LEU00.0100.01022.8320.0120.0120.0000.0000.0000.000
87A196GLU-1-0.827-0.90227.211-0.208-0.2080.0000.0000.0000.000
88A197SER0-0.059-0.03230.5560.0150.0150.0000.0000.0000.000
89A198LEU0-0.068-0.03527.1580.0090.0090.0000.0000.0000.000
90A199THR0-0.019-0.00327.518-0.005-0.0050.0000.0000.0000.000
91A200SER0-0.036-0.01830.0280.0130.0130.0000.0000.0000.000
92A201TYR0-0.036-0.01333.2440.0080.0080.0000.0000.0000.000
93A202LYS10.8170.89034.9770.1180.1180.0000.0000.0000.000
94A203ILE00.0090.00434.887-0.001-0.0010.0000.0000.0000.000
95A204GLU-1-0.856-0.90438.563-0.106-0.1060.0000.0000.0000.000
96A205VAL00.000-0.01237.350-0.006-0.0060.0000.0000.0000.000
97A206GLY00.0060.01140.4150.0050.0050.0000.0000.0000.000
98A207GLY00.0460.01142.8080.0000.0000.0000.0000.0000.000
99A208LEU00.008-0.00345.707-0.002-0.0020.0000.0000.0000.000
100A209ARG10.9920.96543.6830.0840.0840.0000.0000.0000.000
101A210ALA00.0200.03141.357-0.001-0.0010.0000.0000.0000.000
102A211VAL0-0.001-0.00242.331-0.001-0.0010.0000.0000.0000.000
103A212ALA00.0170.01044.7630.0010.0010.0000.0000.0000.000
104A213GLU-1-0.787-0.88939.717-0.092-0.0920.0000.0000.0000.000
105A214ILE0-0.019-0.01139.468-0.001-0.0010.0000.0000.0000.000
106A215PHE0-0.025-0.03741.2900.0020.0020.0000.0000.0000.000
107A216ASN0-0.038-0.03042.3730.0070.0070.0000.0000.0000.000
108A217ARG10.8260.91336.0950.1000.1000.0000.0000.0000.000
109A218LEU0-0.0390.00639.7340.0010.0010.0000.0000.0000.000
110A219GLY00.0470.02842.2380.0020.0020.0000.0000.0000.000
111A220GLN00.0750.02243.8830.0030.0030.0000.0000.0000.000
112A221LYS10.9600.97647.2940.0410.0410.0000.0000.0000.000
113A222SER00.0630.03345.3400.0010.0010.0000.0000.0000.000
114A223ALA00.0470.04746.2260.0000.0000.0000.0000.0000.000
115A224LYS10.9290.96247.8280.0440.0440.0000.0000.0000.000
116A225THR00.004-0.01250.0770.0020.0020.0000.0000.0000.000
117A226THR0-0.063-0.03647.6580.0010.0010.0000.0000.0000.000
118A227LEU00.0030.00250.4930.0000.0000.0000.0000.0000.000
119A228ALA00.0140.01252.5810.0010.0010.0000.0000.0000.000
120A229ARG10.9470.96952.2550.0490.0490.0000.0000.0000.000
121A230ILE00.0190.02450.0340.0000.0000.0000.0000.0000.000
122A231GLU-1-0.803-0.89454.593-0.045-0.0450.0000.0000.0000.000
123A232SER0-0.119-0.05957.6710.0020.0020.0000.0000.0000.000
124A233VAL0-0.046-0.02257.0010.0010.0010.0000.0000.0000.000
125A234ASP-1-0.795-0.91256.965-0.051-0.0510.0000.0000.0000.000
126A235ASN00.0260.00757.373-0.002-0.0020.0000.0000.0000.000
127A236LYS10.9180.97258.7260.0450.0450.0000.0000.0000.000
128A237LEU00.0200.01251.317-0.001-0.0010.0000.0000.0000.000
129A238ALA0-0.0010.00453.754-0.002-0.0020.0000.0000.0000.000
130A239GLY00.0130.00154.380-0.001-0.0010.0000.0000.0000.000
131A240ALA00.002-0.00453.838-0.001-0.0010.0000.0000.0000.000
132A241ILE0-0.031-0.02748.607-0.002-0.0020.0000.0000.0000.000
133A242LYS10.8040.88450.2960.0460.0460.0000.0000.0000.000
134A243GLU-1-0.841-0.90851.634-0.051-0.0510.0000.0000.0000.000
135A244MET0-0.069-0.00747.542-0.003-0.0030.0000.0000.0000.000
136A245MET0-0.061-0.02146.416-0.002-0.0020.0000.0000.0000.000
137A246PHE00.0220.03246.775-0.001-0.0010.0000.0000.0000.000
138A247THR0-0.010-0.03943.224-0.002-0.0020.0000.0000.0000.000
139A248PHE00.0710.00644.9720.0040.0040.0000.0000.0000.000
140A249GLU-1-0.693-0.81741.410-0.070-0.0700.0000.0000.0000.000
141A250ASP-1-0.809-0.86244.745-0.061-0.0610.0000.0000.0000.000
142A251ILE0-0.0040.00447.1700.0040.0040.0000.0000.0000.000
143A252VAL0-0.011-0.00745.1630.0030.0030.0000.0000.0000.000
144A253LYS10.8150.89145.2350.0600.0600.0000.0000.0000.000
145A254LEU00.0090.03450.0770.0020.0020.0000.0000.0000.000
146A255ASP-1-0.778-0.87753.390-0.033-0.0330.0000.0000.0000.000
147A256ASN00.018-0.02254.167-0.003-0.0030.0000.0000.0000.000
148A257PHE0-0.019-0.01856.5960.0000.0000.0000.0000.0000.000
149A258ALA00.0600.02256.9230.0000.0000.0000.0000.0000.000
150A259ILE0-0.032-0.00852.537-0.001-0.0010.0000.0000.0000.000
151A260ARG10.8680.94356.1490.0300.0300.0000.0000.0000.000
152A261GLU-1-0.791-0.87959.383-0.032-0.0320.0000.0000.0000.000
153A262ILE00.0140.01454.229-0.001-0.0010.0000.0000.0000.000
154A263LEU0-0.038-0.01654.728-0.001-0.0010.0000.0000.0000.000
155A264LYS10.7520.86158.1430.0310.0310.0000.0000.0000.000
156A265VAL0-0.0200.00260.2020.0010.0010.0000.0000.0000.000
157A266ALA00.0130.01055.498-0.001-0.0010.0000.0000.0000.000
158A267ASP-1-0.779-0.87857.414-0.044-0.0440.0000.0000.0000.000
159A268LYS10.8360.90454.9340.0400.0400.0000.0000.0000.000
160A269LYS10.9290.94753.2110.0440.0440.0000.0000.0000.000
161A270ASP-1-0.800-0.87451.789-0.061-0.0610.0000.0000.0000.000
162A271LEU0-0.003-0.00550.508-0.003-0.0030.0000.0000.0000.000
163A272SER0-0.023-0.05149.297-0.003-0.0030.0000.0000.0000.000
164A273LEU00.0180.00245.931-0.003-0.0030.0000.0000.0000.000
165A274ALA0-0.023-0.01945.799-0.004-0.0040.0000.0000.0000.000
166A275LEU00.007-0.00545.094-0.003-0.0030.0000.0000.0000.000
167A276LYS10.7930.90042.4680.0740.0740.0000.0000.0000.000
168A277THR0-0.042-0.02138.607-0.004-0.0040.0000.0000.0000.000
169A278SER0-0.035-0.02139.643-0.003-0.0030.0000.0000.0000.000
170A279THR0-0.060-0.05339.1670.0000.0000.0000.0000.0000.000
171A280LYS10.8630.91140.4480.0500.0500.0000.0000.0000.000
172A281ASP-1-0.871-0.93041.348-0.054-0.0540.0000.0000.0000.000
173A282LEU00.007-0.00344.0860.0040.0040.0000.0000.0000.000
174A283THR0-0.003-0.00944.0420.0020.0020.0000.0000.0000.000
175A284ASP-1-0.792-0.89345.991-0.043-0.0430.0000.0000.0000.000
176A285LYS10.7980.92148.0080.0440.0440.0000.0000.0000.000
177A286PHE00.0470.01549.2760.0030.0030.0000.0000.0000.000
178A287LEU00.0130.01048.3280.0020.0020.0000.0000.0000.000
179A288ASN0-0.077-0.05150.1390.0040.0040.0000.0000.0000.000
180A289ASN0-0.055-0.02753.7100.0040.0040.0000.0000.0000.000
181A290MET0-0.0200.01252.8270.0000.0000.0000.0000.0000.000
182A291SER00.0130.00757.5170.0010.0010.0000.0000.0000.000
183A292SER00.0540.01456.702-0.001-0.0010.0000.0000.0000.000
184A293ARG10.8660.91556.4610.0280.0280.0000.0000.0000.000
185A294ALA0-0.002-0.00257.572-0.001-0.0010.0000.0000.0000.000
186A295ALA00.0300.00153.145-0.002-0.0020.0000.0000.0000.000
187A296GLU-1-0.828-0.89052.592-0.033-0.0330.0000.0000.0000.000
188A297GLN00.0370.01152.7300.0000.0000.0000.0000.0000.000
189A298PHE0-0.0110.01049.619-0.002-0.0020.0000.0000.0000.000
190A299VAL00.0090.00147.339-0.003-0.0030.0000.0000.0000.000
191A300GLU-1-0.925-0.96348.570-0.043-0.0430.0000.0000.0000.000
192A301GLU-1-0.898-0.93150.018-0.052-0.0520.0000.0000.0000.000
193A302MET0-0.013-0.00945.005-0.002-0.0020.0000.0000.0000.000
194A303GLN0-0.041-0.00145.193-0.004-0.0040.0000.0000.0000.000
195A304TYR0-0.013-0.02346.023-0.004-0.0040.0000.0000.0000.000
196A305LEU0-0.047-0.00846.588-0.002-0.0020.0000.0000.0000.000
197A306GLY0-0.0130.01043.924-0.003-0.0030.0000.0000.0000.000
198A307ALA0-0.037-0.01339.589-0.002-0.0020.0000.0000.0000.000
199A308VAL00.0290.01541.1270.0020.0020.0000.0000.0000.000
200A309LYS10.8870.93940.1880.0910.0910.0000.0000.0000.000
201A310ILE00.0780.03235.8610.0040.0040.0000.0000.0000.000
202A311LYS10.9090.96740.4590.0950.0950.0000.0000.0000.000
203A312ASP-1-0.836-0.92842.883-0.086-0.0860.0000.0000.0000.000
204A313VAL00.0210.01742.4210.0050.0050.0000.0000.0000.000
205A314ASP-1-0.865-0.94042.309-0.095-0.0950.0000.0000.0000.000
206A315VAL0-0.095-0.05045.1070.0030.0030.0000.0000.0000.000
207A316ALA00.0240.02148.0720.0030.0030.0000.0000.0000.000
208A317GLN00.001-0.01542.9130.0020.0020.0000.0000.0000.000
209A318ARG10.8320.93947.9350.0690.0690.0000.0000.0000.000
210A319LYS10.8950.93750.1840.0610.0610.0000.0000.0000.000
211A320ILE0-0.023-0.00751.0980.0030.0030.0000.0000.0000.000
212A321ILE0-0.062-0.02247.7930.0020.0020.0000.0000.0000.000
213A322GLU-1-0.888-0.95452.431-0.056-0.0560.0000.0000.0000.000
214A323ILE0-0.034-0.00655.5580.0030.0030.0000.0000.0000.000
215A324VAL00.003-0.00153.1450.0020.0020.0000.0000.0000.000
216A325GLN0-0.046-0.05153.5100.0010.0010.0000.0000.0000.000
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218A327LEU00.010-0.00558.6390.0020.0020.0000.0000.0000.000
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