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: VQ7K1

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 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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2130460.528744
FMO2-HF: Nuclear repulsion 2047360.601306
FMO2-HF: Total energy -83099.927438
FMO2-MP2: Total energy -83342.495546


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.
-96.585-96.83733.574-12.192-21.13-0.116
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 : 0.875 / q_NPA : 0.915
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].
3A119PHE00.0690.0502.908-5.896-2.8070.175-1.491-1.774-0.009
4A120ALA00.024-0.0015.6183.6833.6830.0000.0000.0000.000
5A121TYR00.005-0.0065.5062.0172.0170.0000.0000.0000.000
6A122LEU00.0160.0039.0831.9961.9960.0000.0000.0000.000
7A123GLY0-0.0220.00411.3911.2801.2800.0000.0000.0000.000
8A124LYS10.8840.93713.47018.47918.4790.0000.0000.0000.000
9A125ILE00.0260.02312.8200.9380.9380.0000.0000.0000.000
10A126LYS10.9660.98616.57312.33612.3360.0000.0000.0000.000
11A127PRO00.0750.03417.704-0.211-0.2110.0000.0000.0000.000
12A128GLN00.0050.01018.7730.0470.0470.0000.0000.0000.000
13A129GLN0-0.030-0.01118.9480.1590.1590.0000.0000.0000.000
14A130LEU00.0170.01113.263-0.217-0.2170.0000.0000.0000.000
15A131ALA00.0080.00117.205-0.489-0.4890.0000.0000.0000.000
16A132ASP-1-0.900-0.97719.369-13.005-13.0050.0000.0000.0000.000
17A133PHE0-0.050-0.01314.8500.2160.2160.0000.0000.0000.000
18A134ILE0-0.035-0.03313.445-0.370-0.3700.0000.0000.0000.000
19A135ILE00.0120.02016.603-0.307-0.3070.0000.0000.0000.000
20A136ASN0-0.032-0.02219.6780.5400.5400.0000.0000.0000.000
21A137GLU-1-0.919-0.93914.529-19.394-19.3940.0000.0000.0000.000
22A138HIS00.0330.01415.803-0.640-0.6400.0000.0000.0000.000
23A139PRO00.1120.04415.137-1.710-1.7100.0000.0000.0000.000
24A140GLN00.0310.02710.7260.7370.7370.0000.0000.0000.000
25A141THR0-0.004-0.00710.747-3.060-3.0600.0000.0000.0000.000
26A142ILE00.0160.01210.713-2.746-2.7460.0000.0000.0000.000
27A143ALA00.0170.01511.086-1.287-1.2870.0000.0000.0000.000
28A144LEU0-0.046-0.0294.526-4.107-4.015-0.001-0.003-0.0880.000
29A145ILE0-0.0110.0016.511-5.936-5.9360.0000.0000.0000.000
30A146LEU00.0380.0038.428-1.410-1.4100.0000.0000.0000.000
31A147ALA0-0.020-0.0016.2840.5170.5170.0000.0000.0000.000
32A148HIS0-0.066-0.0411.963-54.976-54.54411.092-6.101-5.423-0.099
33A149MET0-0.071-0.0136.3132.0442.0440.0000.0000.0000.000
34A150GLU-1-0.883-0.93810.046-22.649-22.6490.0000.0000.0000.000
35A151ALA00.0330.00112.7150.5960.5960.0000.0000.0000.000
36A152PRO00.0180.00314.3840.6420.6420.0000.0000.0000.000
37A153ASN00.0380.01914.7371.3101.3100.0000.0000.0000.000
38A154ALA00.0160.02312.5470.5430.5430.0000.0000.0000.000
39A155ALA0-0.005-0.00414.5460.6500.6500.0000.0000.0000.000
40A156GLU-1-0.797-0.88917.776-14.228-14.2280.0000.0000.0000.000
41A157THR0-0.025-0.01015.5440.4890.4890.0000.0000.0000.000
42A158LEU00.006-0.00516.4290.6120.6120.0000.0000.0000.000
43A159SER0-0.096-0.06018.4160.9460.9460.0000.0000.0000.000
44A160TYR0-0.049-0.04620.8681.0381.0380.0000.0000.0000.000
45A161PHE0-0.0100.00316.8490.3990.3990.0000.0000.0000.000
46A162PRO00.0870.03222.5240.1680.1680.0000.0000.0000.000
47A163ASP-1-0.831-0.91023.338-13.001-13.0010.0000.0000.0000.000
48A164GLU-1-0.943-0.96823.373-12.256-12.2560.0000.0000.0000.000
49A165MET00.0090.01819.134-0.185-0.1850.0000.0000.0000.000
50A166LYS10.8000.87919.14912.76612.7660.0000.0000.0000.000
51A167ALA00.0110.02218.568-1.051-1.0510.0000.0000.0000.000
52A168GLU-1-0.911-0.95419.078-15.834-15.8340.0000.0000.0000.000
53A169ILE0-0.033-0.01714.035-1.155-1.1550.0000.0000.0000.000
54A170SER0-0.032-0.03214.444-1.756-1.7560.0000.0000.0000.000
55A171ILE0-0.032-0.02215.259-0.852-0.8520.0000.0000.0000.000
56A172ARG10.8690.93713.31818.52218.5220.0000.0000.0000.000
57A173MET0-0.006-0.0109.438-1.234-1.2340.0000.0000.0000.000
58A174ALA0-0.041-0.00710.799-1.962-1.9620.0000.0000.0000.000
59A175ASN0-0.102-0.05211.9001.3521.3520.0000.0000.0000.000
60A176LEU00.0690.0477.005-0.487-0.4870.0000.0000.0000.000
61A177GLY0-0.049-0.0126.850-5.438-5.4380.0000.0000.0000.000
62A178GLU-1-0.890-0.9588.589-28.045-28.0450.0000.0000.0000.000
63A179ILE0-0.017-0.0015.9041.7941.7940.0000.0000.0000.000
64A180SER00.0220.0105.970-5.602-5.6020.0000.0000.0000.000
65A181PRO00.0970.0212.877-3.817-2.8200.273-0.263-1.0070.000
66A182GLN0-0.029-0.0132.851-2.716-1.2450.362-0.613-1.221-0.008
67A183VAL00.0040.0025.5541.6921.6920.0000.0000.0000.000
68A184VAL00.0470.0292.081-1.223-1.1905.153-1.469-3.716-0.008
69A185LYS10.9160.9581.63627.61927.24916.251-9.098-6.7820.011
70A186ARG10.9871.0082.46633.31526.4150.0657.236-0.402-0.002
71A187VAL00.0130.0025.8602.4882.4880.0000.0000.0000.000
72A188SER0-0.013-0.0202.7914.4595.2890.205-0.386-0.649-0.001
73A189THR00.0210.0044.5103.9013.975-0.001-0.004-0.0680.000
74A190VAL0-0.036-0.0166.3172.1992.1990.0000.0000.0000.000
75A191LEU00.0100.0078.3551.7821.7820.0000.0000.0000.000
76A192GLU-1-0.920-0.9676.764-23.674-23.6740.0000.0000.0000.000
77A193ASN0-0.067-0.0579.2722.4072.4070.0000.0000.0000.000
78A194LYS10.8320.93712.01719.22419.2240.0000.0000.0000.000
79A195LEU0-0.051-0.03410.8890.6750.6750.0000.0000.0000.000
80A196GLU-1-0.992-0.96414.327-14.190-14.1900.0000.0000.0000.000
81A204GLU-1-0.962-0.98725.488-10.123-10.1230.0000.0000.0000.000
82A205VAL0-0.012-0.01128.493-0.019-0.0190.0000.0000.0000.000
83A206GLY00.0130.02531.3320.0410.0410.0000.0000.0000.000
84A207GLY00.0380.00430.248-0.193-0.1930.0000.0000.0000.000
85A208LEU00.006-0.01129.8710.2600.2600.0000.0000.0000.000
86A209ARG10.9690.96130.9029.5459.5450.0000.0000.0000.000
87A210ALA00.0020.01133.1160.2530.2530.0000.0000.0000.000
88A211VAL00.0160.01635.0250.2890.2890.0000.0000.0000.000
89A212ALA00.0410.02135.9280.2660.2660.0000.0000.0000.000
90A213GLU-1-0.896-0.94935.984-8.266-8.2660.0000.0000.0000.000
91A214ILE0-0.0020.00639.1550.2460.2460.0000.0000.0000.000
92A215PHE0-0.009-0.03540.3880.2230.2230.0000.0000.0000.000
93A216ASN0-0.0020.00739.2750.1840.1840.0000.0000.0000.000
94A217ARG10.7980.89142.9337.1087.1080.0000.0000.0000.000
95A218LEU0-0.0290.01244.4260.1990.1990.0000.0000.0000.000
96A219GLY00.0310.01947.1910.0220.0220.0000.0000.0000.000
97A220GLN00.0930.03348.087-0.119-0.1190.0000.0000.0000.000
98A221LYS10.9490.97548.8715.8525.8520.0000.0000.0000.000
99A222SER00.0420.01749.318-0.071-0.0710.0000.0000.0000.000
100A223ALA00.0690.05244.725-0.082-0.0820.0000.0000.0000.000
101A224LYS10.9320.97144.6416.3946.3940.0000.0000.0000.000
102A225THR0-0.063-0.04646.066-0.015-0.0150.0000.0000.0000.000
103A226THR0-0.015-0.03343.316-0.002-0.0020.0000.0000.0000.000
104A227LEU00.0120.01539.594-0.081-0.0810.0000.0000.0000.000
105A228ALA00.0080.01441.901-0.139-0.1390.0000.0000.0000.000
106A229ARG10.9230.96144.0206.4666.4660.0000.0000.0000.000
107A230ILE00.0060.01838.020-0.024-0.0240.0000.0000.0000.000
108A231GLU-1-0.922-0.96939.304-7.868-7.8680.0000.0000.0000.000
109A232SER0-0.087-0.04940.085-0.054-0.0540.0000.0000.0000.000
110A233VAL0-0.065-0.03438.8570.0300.0300.0000.0000.0000.000
111A234ASP-1-0.874-0.93833.816-9.559-9.5590.0000.0000.0000.000
112A235ASN00.0470.01235.2670.1350.1350.0000.0000.0000.000
113A236LYS10.9130.95926.65011.79311.7930.0000.0000.0000.000
114A237LEU00.0120.02332.619-0.073-0.0730.0000.0000.0000.000
115A238ALA00.0190.01633.9230.0660.0660.0000.0000.0000.000
116A239GLY00.0220.00735.5080.1330.1330.0000.0000.0000.000
117A240ALA00.0080.00731.383-0.017-0.0170.0000.0000.0000.000
118A241ILE0-0.011-0.02633.1740.0230.0230.0000.0000.0000.000
119A242LYS10.9140.94935.8317.9687.9680.0000.0000.0000.000
120A243GLU-1-1.002-1.00232.186-9.735-9.7350.0000.0000.0000.000
121A244MET0-0.0140.01830.013-0.015-0.0150.0000.0000.0000.000
122A245MET0-0.111-0.04735.1300.1420.1420.0000.0000.0000.000
123A246PHE0-0.026-0.01238.826-0.052-0.0520.0000.0000.0000.000
124A247THR0-0.019-0.03440.2100.3080.3080.0000.0000.0000.000
125A248PHE00.002-0.01542.6090.0260.0260.0000.0000.0000.000
126A249GLU-1-0.793-0.89641.487-7.618-7.6180.0000.0000.0000.000
127A250ASP-1-0.783-0.86938.350-8.512-8.5120.0000.0000.0000.000
128A251ILE0-0.031-0.02240.833-0.054-0.0540.0000.0000.0000.000
129A252VAL0-0.025-0.00639.7960.0530.0530.0000.0000.0000.000
130A253LYS10.8340.90635.4688.8728.8720.0000.0000.0000.000
131A254LEU0-0.0030.03039.663-0.051-0.0510.0000.0000.0000.000
132A255ASP-1-0.803-0.90241.978-7.201-7.2010.0000.0000.0000.000
133A256ASN00.029-0.01243.3170.1240.1240.0000.0000.0000.000
134A257PHE00.006-0.00546.3630.1900.1900.0000.0000.0000.000
135A258ALA00.0590.03145.2340.1560.1560.0000.0000.0000.000
136A259ILE0-0.0110.00045.9120.1510.1510.0000.0000.0000.000
137A260ARG10.8740.94348.8656.5296.5290.0000.0000.0000.000
138A261GLU-1-0.824-0.88850.119-5.845-5.8450.0000.0000.0000.000
139A262ILE00.0020.00247.3510.1180.1180.0000.0000.0000.000
140A263LEU0-0.032-0.01751.8860.1440.1440.0000.0000.0000.000
141A264LYS10.7720.87054.3075.9705.9700.0000.0000.0000.000
142A265VAL0-0.038-0.01155.0590.1180.1180.0000.0000.0000.000
143A266ALA0-0.011-0.00254.5540.0740.0740.0000.0000.0000.000
144A267ASP-1-0.789-0.88656.640-5.132-5.1320.0000.0000.0000.000
145A268LYS10.8850.93658.2625.4515.4510.0000.0000.0000.000
146A269LYS10.9230.95159.2975.0155.0150.0000.0000.0000.000
147A270ASP-1-0.813-0.89256.777-5.535-5.5350.0000.0000.0000.000
148A271LEU00.0160.00352.350-0.093-0.0930.0000.0000.0000.000
149A272SER00.0190.01054.748-0.142-0.1420.0000.0000.0000.000
150A273LEU00.020-0.00555.992-0.065-0.0650.0000.0000.0000.000
151A274ALA0-0.034-0.02052.126-0.093-0.0930.0000.0000.0000.000
152A275LEU0-0.003-0.00849.676-0.151-0.1510.0000.0000.0000.000
153A276LYS10.7960.90751.3455.6605.6600.0000.0000.0000.000
154A277THR0-0.031-0.01948.957-0.010-0.0100.0000.0000.0000.000
155A278SER00.0070.01946.869-0.185-0.1850.0000.0000.0000.000
156A279THR00.0530.02341.8000.0920.0920.0000.0000.0000.000
157A280LYS10.8940.92545.2116.8136.8130.0000.0000.0000.000
158A281ASP-1-0.889-0.94342.121-7.653-7.6530.0000.0000.0000.000
159A282LEU0-0.009-0.00744.4840.0690.0690.0000.0000.0000.000
160A283THR00.013-0.00345.9780.1550.1550.0000.0000.0000.000
161A284ASP-1-0.796-0.89347.427-6.513-6.5130.0000.0000.0000.000
162A285LYS10.8170.93242.4137.6917.6910.0000.0000.0000.000
163A286PHE00.0400.00547.8090.0870.0870.0000.0000.0000.000
164A287LEU00.004-0.00151.0520.1080.1080.0000.0000.0000.000
165A288ASN0-0.054-0.04349.3750.1710.1710.0000.0000.0000.000
166A289ASN0-0.077-0.03948.4220.0560.0560.0000.0000.0000.000
167A290MET0-0.0470.00252.6370.1320.1320.0000.0000.0000.000
168A291SER00.0110.00356.293-0.022-0.0220.0000.0000.0000.000
169A292SER00.0730.02058.4180.0030.0030.0000.0000.0000.000
170A293ARG10.9610.98259.3855.0555.0550.0000.0000.0000.000
171A294ALA0-0.054-0.02960.0340.0400.0400.0000.0000.0000.000
172A295ALA00.0350.00656.675-0.004-0.0040.0000.0000.0000.000
173A296GLU-1-0.897-0.95158.397-5.231-5.2310.0000.0000.0000.000
174A297GLN00.0170.02160.855-0.004-0.0040.0000.0000.0000.000
175A298PHE00.0110.01254.8330.0030.0030.0000.0000.0000.000
176A299VAL00.0200.00456.105-0.041-0.0410.0000.0000.0000.000
177A300GLU-1-0.912-0.95458.591-5.040-5.0400.0000.0000.0000.000
178A301GLU-1-0.948-0.98561.020-5.297-5.2970.0000.0000.0000.000
179A302MET0-0.031-0.01253.203-0.017-0.0170.0000.0000.0000.000
180A303GLN0-0.057-0.02258.939-0.003-0.0030.0000.0000.0000.000
181A304TYR0-0.034-0.02160.2510.0560.0560.0000.0000.0000.000
182A305LEU0-0.028-0.00358.9340.0510.0510.0000.0000.0000.000
183A306GLY0-0.0090.01961.0370.0150.0150.0000.0000.0000.000
184A307ALA0-0.019-0.00958.066-0.125-0.1250.0000.0000.0000.000
185A308VAL00.0320.01655.4990.0760.0760.0000.0000.0000.000
186A309LYS10.8040.87356.3485.3865.3860.0000.0000.0000.000
187A310ILE00.0680.02749.8990.0280.0280.0000.0000.0000.000
188A311LYS10.9720.98753.3015.6385.6380.0000.0000.0000.000
189A312ASP-1-0.797-0.87955.146-5.524-5.5240.0000.0000.0000.000
190A313VAL00.0180.01451.5020.0270.0270.0000.0000.0000.000
191A314ASP-1-0.858-0.92950.315-6.543-6.5430.0000.0000.0000.000
192A315VAL0-0.071-0.04852.138-0.026-0.0260.0000.0000.0000.000
193A316ALA00.0030.00954.8550.0300.0300.0000.0000.0000.000
194A317GLN00.007-0.01948.451-0.083-0.0830.0000.0000.0000.000
195A318ARG10.7550.87347.6176.3706.3700.0000.0000.0000.000
196A319LYS10.8430.91251.3365.4705.4700.0000.0000.0000.000
197A320ILE0-0.020-0.00149.5450.0220.0220.0000.0000.0000.000
198A321ILE00.0250.01545.165-0.029-0.0290.0000.0000.0000.000
199A322GLU-1-0.847-0.90748.342-6.105-6.1050.0000.0000.0000.000
200A323ILE0-0.0150.00150.8880.0320.0320.0000.0000.0000.000
201A324VAL00.0110.00745.051-0.001-0.0010.0000.0000.0000.000
202A325GLN00.0130.00545.665-0.094-0.0940.0000.0000.0000.000
203A326SER00.0480.03047.3220.0230.0230.0000.0000.0000.000
204A327LEU0-0.022-0.02648.8230.0340.0340.0000.0000.0000.000
205A328GLN00.0240.00841.492-0.036-0.0360.0000.0000.0000.000
206A329GLU-1-0.897-0.92645.354-6.525-6.5250.0000.0000.0000.000
207A330LYS10.8530.92747.2755.9145.9140.0000.0000.0000.000
208A331GLY00.0180.02845.7650.0570.0570.0000.0000.0000.000
209A332VAL0-0.071-0.02946.717-0.023-0.0230.0000.0000.0000.000
210A333ILE0-0.036-0.01144.855-0.022-0.0220.0000.0000.0000.000
211A334GLN00.0280.00838.931-0.046-0.0460.0000.0000.0000.000
212A335THR0-0.025-0.00536.599-0.146-0.1460.0000.0000.0000.000