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

tag_button

FMODB ID: 1NZ6Z

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 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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2135196.85994
FMO2-HF: Nuclear repulsion 2052096.230583
FMO2-HF: Total energy -83100.629357
FMO2-MP2: Total energy -83343.046399


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.
-101.506-99.89431.209-13.423-19.396-0.124
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 : 0.857 / q_NPA : 0.895
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].
3A119PHE00.0790.0503.548-0.6701.4310.017-0.898-1.220-0.001
4A120ALA00.0180.0076.2973.6093.6090.0000.0000.0000.000
5A121TYR00.0480.0176.1932.5382.5380.0000.0000.0000.000
6A122LEU00.0200.0049.2182.0052.0050.0000.0000.0000.000
7A123GLY0-0.0280.00012.1771.1731.1730.0000.0000.0000.000
8A124LYS10.8770.93414.03118.66618.6660.0000.0000.0000.000
9A125ILE00.0240.02013.8090.9090.9090.0000.0000.0000.000
10A126LYS10.9630.99017.48412.25412.2540.0000.0000.0000.000
11A127PRO00.0420.02217.642-0.203-0.2030.0000.0000.0000.000
12A128GLN00.0030.00218.7700.0740.0740.0000.0000.0000.000
13A129GLN0-0.029-0.01119.6360.1710.1710.0000.0000.0000.000
14A130LEU00.0100.00113.270-0.106-0.1060.0000.0000.0000.000
15A131ALA00.0220.00717.331-0.298-0.2980.0000.0000.0000.000
16A132ASP-1-0.857-0.94019.322-12.633-12.6330.0000.0000.0000.000
17A133PHE0-0.041-0.01015.3880.2800.2800.0000.0000.0000.000
18A134ILE0-0.041-0.04013.677-0.630-0.6300.0000.0000.0000.000
19A135ILE00.0000.00916.830-0.344-0.3440.0000.0000.0000.000
20A136ASN0-0.023-0.01219.4850.7150.7150.0000.0000.0000.000
21A137GLU-1-0.885-0.91614.282-19.284-19.2840.0000.0000.0000.000
22A138HIS00.0310.01915.636-0.452-0.4520.0000.0000.0000.000
23A139PRO00.0730.02015.337-1.630-1.6300.0000.0000.0000.000
24A140GLN00.0340.01911.5700.8430.8430.0000.0000.0000.000
25A141THR0-0.025-0.01310.651-3.026-3.0260.0000.0000.0000.000
26A142ILE00.0180.01110.884-2.572-2.5720.0000.0000.0000.000
27A143ALA00.0300.02011.293-1.332-1.3320.0000.0000.0000.000
28A144LEU0-0.030-0.0175.132-3.645-3.6450.0000.0000.0000.000
29A145ILE0-0.015-0.0016.565-6.432-6.4320.0000.0000.0000.000
30A146LEU00.019-0.0028.485-1.633-1.6330.0000.0000.0000.000
31A147ALA0-0.031-0.0076.2240.5180.5180.0000.0000.0000.000
32A148HIS0-0.047-0.0181.848-60.100-62.92816.194-7.549-5.816-0.109
33A149MET0-0.058-0.0096.1002.2632.2630.0000.0000.0000.000
34A150GLU-1-0.849-0.9289.910-22.491-22.4910.0000.0000.0000.000
35A151ALA00.0210.01312.4490.7880.7880.0000.0000.0000.000
36A152PRO00.011-0.00214.0730.7380.7380.0000.0000.0000.000
37A153ASN00.0300.01514.6480.9930.9930.0000.0000.0000.000
38A154ALA00.0250.02712.2930.4160.4160.0000.0000.0000.000
39A155ALA00.0150.00514.2570.6940.6940.0000.0000.0000.000
40A156GLU-1-0.803-0.89817.611-14.177-14.1770.0000.0000.0000.000
41A157THR0-0.026-0.02215.3630.5300.5300.0000.0000.0000.000
42A158LEU0-0.009-0.00516.4930.5610.5610.0000.0000.0000.000
43A159SER0-0.076-0.05718.2660.9950.9950.0000.0000.0000.000
44A160TYR0-0.035-0.04621.0501.0041.0040.0000.0000.0000.000
45A161PHE00.0150.01817.0360.4220.4220.0000.0000.0000.000
46A162PRO00.0740.02422.6920.1860.1860.0000.0000.0000.000
47A163ASP-1-0.828-0.91023.707-12.987-12.9870.0000.0000.0000.000
48A164GLU-1-0.938-0.95723.729-12.015-12.0150.0000.0000.0000.000
49A165MET00.0050.01119.520-0.216-0.2160.0000.0000.0000.000
50A166LYS10.7590.87719.42512.62212.6220.0000.0000.0000.000
51A167ALA00.0130.02418.945-0.972-0.9720.0000.0000.0000.000
52A168GLU-1-0.811-0.90719.482-16.751-16.7510.0000.0000.0000.000
53A169ILE0-0.005-0.00314.361-1.069-1.0690.0000.0000.0000.000
54A170SER0-0.017-0.02614.701-1.732-1.7320.0000.0000.0000.000
55A171ILE0-0.041-0.02115.564-0.768-0.7680.0000.0000.0000.000
56A172ARG10.7580.87513.59217.80417.8040.0000.0000.0000.000
57A173MET0-0.004-0.0139.599-1.138-1.1380.0000.0000.0000.000
58A174ALA0-0.040-0.00411.172-1.762-1.7620.0000.0000.0000.000
59A175ASN0-0.118-0.05811.8941.3031.3030.0000.0000.0000.000
60A176LEU00.0450.0347.313-0.113-0.1130.0000.0000.0000.000
61A177GLY0-0.025-0.0046.729-6.038-6.0380.0000.0000.0000.000
62A178GLU-1-0.873-0.9488.513-28.221-28.2210.0000.0000.0000.000
63A179ILE0-0.0090.0036.5461.7771.7770.0000.0000.0000.000
64A180SER00.0490.0256.048-5.998-5.9980.0000.0000.0000.000
65A181PRO00.0590.0132.805-3.733-2.6440.246-0.246-1.0890.000
66A182GLN0-0.039-0.0152.798-1.6670.1420.400-0.899-1.310-0.012
67A183VAL00.0210.0075.4510.6990.6990.0000.0000.0000.000
68A184VAL00.0610.0282.282-0.807-0.0802.979-0.981-2.724-0.005
69A185LYS10.9070.9511.92527.99929.39511.127-5.874-6.6480.006
70A186ARG10.9611.0052.73128.89825.8480.1983.167-0.316-0.002
71A187VAL00.0190.0065.8662.1972.1970.0000.0000.0000.000
72A188SER0-0.006-0.0103.3024.5254.8930.048-0.143-0.273-0.001
73A189THR00.006-0.0115.0573.2953.2950.0000.0000.0000.000
74A190VAL0-0.032-0.0126.8762.3302.3300.0000.0000.0000.000
75A191LEU00.0030.0068.4011.6951.6950.0000.0000.0000.000
76A192GLU-1-0.924-0.9776.944-24.561-24.5610.0000.0000.0000.000
77A193ASN0-0.072-0.0529.8572.4362.4360.0000.0000.0000.000
78A194LYS10.8000.90512.50218.81618.8160.0000.0000.0000.000
79A195LEU0-0.049-0.03611.5150.6940.6940.0000.0000.0000.000
80A196GLU-1-0.992-0.96014.844-13.713-13.7130.0000.0000.0000.000
81A204GLU-1-0.935-0.97426.431-10.008-10.0080.0000.0000.0000.000
82A205VAL0-0.039-0.02628.9410.0420.0420.0000.0000.0000.000
83A206GLY00.0310.01932.0660.1800.1800.0000.0000.0000.000
84A207GLY00.0090.00330.907-0.156-0.1560.0000.0000.0000.000
85A208LEU00.013-0.00430.8140.2520.2520.0000.0000.0000.000
86A209ARG10.8670.89931.8489.3149.3140.0000.0000.0000.000
87A210ALA00.0370.02933.6700.2500.2500.0000.0000.0000.000
88A211VAL00.0070.00435.7760.2810.2810.0000.0000.0000.000
89A212ALA00.0260.01636.2570.2550.2550.0000.0000.0000.000
90A213GLU-1-0.801-0.87936.685-8.298-8.2980.0000.0000.0000.000
91A214ILE0-0.022-0.00239.8180.2550.2550.0000.0000.0000.000
92A215PHE00.015-0.02540.8930.2370.2370.0000.0000.0000.000
93A216ASN0-0.0180.00139.6440.1810.1810.0000.0000.0000.000
94A217ARG10.7840.87943.5827.0887.0880.0000.0000.0000.000
95A218LEU0-0.0300.01444.8130.1980.1980.0000.0000.0000.000
96A219GLY00.0450.03047.7120.0110.0110.0000.0000.0000.000
97A220GLN00.0820.03348.865-0.128-0.1280.0000.0000.0000.000
98A221LYS10.9530.98549.4695.8325.8320.0000.0000.0000.000
99A222SER00.0420.02249.899-0.065-0.0650.0000.0000.0000.000
100A223ALA00.0820.06045.328-0.078-0.0780.0000.0000.0000.000
101A224LYS10.9120.95045.2756.4406.4400.0000.0000.0000.000
102A225THR0-0.055-0.05046.356-0.011-0.0110.0000.0000.0000.000
103A226THR0-0.025-0.02943.5830.0100.0100.0000.0000.0000.000
104A227LEU00.0040.00240.216-0.081-0.0810.0000.0000.0000.000
105A228ALA00.0170.01842.113-0.133-0.1330.0000.0000.0000.000
106A229ARG10.9040.95244.0746.4776.4770.0000.0000.0000.000
107A230ILE00.0250.02338.187-0.015-0.0150.0000.0000.0000.000
108A231GLU-1-0.911-0.96739.259-7.907-7.9070.0000.0000.0000.000
109A232SER0-0.074-0.03839.786-0.061-0.0610.0000.0000.0000.000
110A233VAL0-0.073-0.03938.9940.0690.0690.0000.0000.0000.000
111A234ASP-1-0.852-0.92533.520-9.650-9.6500.0000.0000.0000.000
112A235ASN00.0560.01535.8610.0680.0680.0000.0000.0000.000
113A236LYS10.8730.95126.50511.70111.7010.0000.0000.0000.000
114A237LEU0-0.0010.00532.842-0.071-0.0710.0000.0000.0000.000
115A238ALA0-0.004-0.00134.1040.0870.0870.0000.0000.0000.000
116A239GLY00.0140.00335.3930.1410.1410.0000.0000.0000.000
117A240ALA00.0170.00931.7870.0140.0140.0000.0000.0000.000
118A241ILE00.000-0.01233.5700.0350.0350.0000.0000.0000.000
119A242LYS10.8810.93436.5798.1298.1290.0000.0000.0000.000
120A243GLU-1-0.980-0.99032.408-9.862-9.8620.0000.0000.0000.000
121A244MET0-0.0020.02230.2920.0040.0040.0000.0000.0000.000
122A245MET0-0.099-0.05135.4900.1510.1510.0000.0000.0000.000
123A246PHE0-0.024-0.00139.289-0.034-0.0340.0000.0000.0000.000
124A247THR0-0.064-0.06740.5140.2870.2870.0000.0000.0000.000
125A248PHE00.008-0.00743.1770.0220.0220.0000.0000.0000.000
126A249GLU-1-0.789-0.88941.126-7.649-7.6490.0000.0000.0000.000
127A250ASP-1-0.780-0.87538.574-8.572-8.5720.0000.0000.0000.000
128A251ILE0-0.025-0.00741.029-0.046-0.0460.0000.0000.0000.000
129A252VAL0-0.017-0.00939.3580.0590.0590.0000.0000.0000.000
130A253LYS10.8450.91435.5108.9278.9270.0000.0000.0000.000
131A254LEU0-0.0040.03139.637-0.053-0.0530.0000.0000.0000.000
132A255ASP-1-0.790-0.89142.505-7.212-7.2120.0000.0000.0000.000
133A256ASN00.031-0.01543.5900.1220.1220.0000.0000.0000.000
134A257PHE0-0.011-0.01346.7530.1950.1950.0000.0000.0000.000
135A258ALA00.0540.01945.8190.1570.1570.0000.0000.0000.000
136A259ILE0-0.0220.00046.1430.1230.1230.0000.0000.0000.000
137A260ARG10.8620.93649.2586.5706.5700.0000.0000.0000.000
138A261GLU-1-0.834-0.89450.597-5.885-5.8850.0000.0000.0000.000
139A262ILE00.0070.00748.0270.1080.1080.0000.0000.0000.000
140A263LEU0-0.025-0.00952.5210.1390.1390.0000.0000.0000.000
141A264LYS10.7750.87354.6036.0026.0020.0000.0000.0000.000
142A265VAL0-0.032-0.00755.4920.1130.1130.0000.0000.0000.000
143A266ALA00.0140.01155.0550.0680.0680.0000.0000.0000.000
144A267ASP-1-0.792-0.88357.151-5.144-5.1440.0000.0000.0000.000
145A268LYS10.8430.91758.5445.4375.4370.0000.0000.0000.000
146A269LYS10.9350.95359.0555.0155.0150.0000.0000.0000.000
147A270ASP-1-0.797-0.88457.190-5.574-5.5740.0000.0000.0000.000
148A271LEU00.0110.00152.247-0.093-0.0930.0000.0000.0000.000
149A272SER00.0190.00454.400-0.142-0.1420.0000.0000.0000.000
150A273LEU00.008-0.01055.608-0.070-0.0700.0000.0000.0000.000
151A274ALA0-0.033-0.02052.020-0.083-0.0830.0000.0000.0000.000
152A275LEU00.008-0.00549.517-0.151-0.1510.0000.0000.0000.000
153A276LYS10.7960.90251.2305.6615.6610.0000.0000.0000.000
154A277THR0-0.026-0.01148.9510.0130.0130.0000.0000.0000.000
155A278SER00.0010.01346.713-0.191-0.1910.0000.0000.0000.000
156A279THR0-0.010-0.02941.8770.0930.0930.0000.0000.0000.000
157A280LYS10.8880.92045.3266.8126.8120.0000.0000.0000.000
158A281ASP-1-0.838-0.89641.941-7.645-7.6450.0000.0000.0000.000
159A282LEU0-0.003-0.00144.5040.0680.0680.0000.0000.0000.000
160A283THR00.0150.00145.9460.1580.1580.0000.0000.0000.000
161A284ASP-1-0.796-0.89147.446-6.503-6.5030.0000.0000.0000.000
162A285LYS10.8200.92142.2057.7187.7180.0000.0000.0000.000
163A286PHE00.0520.01747.7020.0680.0680.0000.0000.0000.000
164A287LEU00.0050.00450.8650.1070.1070.0000.0000.0000.000
165A288ASN0-0.068-0.05149.6670.1740.1740.0000.0000.0000.000
166A289ASN0-0.055-0.02748.0110.0120.0120.0000.0000.0000.000
167A290MET0-0.0420.00352.3350.1200.1200.0000.0000.0000.000
168A291SER00.0080.00455.975-0.035-0.0350.0000.0000.0000.000
169A292SER00.0540.01958.354-0.002-0.0020.0000.0000.0000.000
170A293ARG10.9570.97159.2785.0235.0230.0000.0000.0000.000
171A294ALA0-0.049-0.01759.8320.0580.0580.0000.0000.0000.000
172A295ALA00.0410.00856.251-0.011-0.0110.0000.0000.0000.000
173A296GLU-1-0.904-0.96658.034-5.285-5.2850.0000.0000.0000.000
174A297GLN00.0020.00860.4470.0150.0150.0000.0000.0000.000
175A298PHE00.0040.00854.4930.0110.0110.0000.0000.0000.000
176A299VAL00.0070.00356.027-0.052-0.0520.0000.0000.0000.000
177A300GLU-1-0.884-0.93958.540-5.008-5.0080.0000.0000.0000.000
178A301GLU-1-0.922-0.97060.610-5.312-5.3120.0000.0000.0000.000
179A302MET0-0.020-0.01152.850-0.014-0.0140.0000.0000.0000.000
180A303GLN0-0.060-0.02358.552-0.001-0.0010.0000.0000.0000.000
181A304TYR0-0.023-0.01160.2570.0600.0600.0000.0000.0000.000
182A305LEU0-0.039-0.01758.8550.0510.0510.0000.0000.0000.000
183A306GLY0-0.0050.01660.998-0.020-0.0200.0000.0000.0000.000
184A307ALA0-0.033-0.01058.217-0.127-0.1270.0000.0000.0000.000
185A308VAL00.0200.01155.7000.0870.0870.0000.0000.0000.000
186A309LYS10.8090.87956.3715.3595.3590.0000.0000.0000.000
187A310ILE00.0570.02249.8830.0280.0280.0000.0000.0000.000
188A311LYS10.9920.99053.2905.7005.7000.0000.0000.0000.000
189A312ASP-1-0.816-0.88355.050-5.507-5.5070.0000.0000.0000.000
190A313VAL00.0050.01351.5320.0430.0430.0000.0000.0000.000
191A314ASP-1-0.847-0.92950.555-6.485-6.4850.0000.0000.0000.000
192A315VAL0-0.073-0.04252.277-0.038-0.0380.0000.0000.0000.000
193A316ALA00.0120.01254.9990.0100.0100.0000.0000.0000.000
194A317GLN00.002-0.01848.343-0.097-0.0970.0000.0000.0000.000
195A318ARG10.7460.86848.1896.3956.3950.0000.0000.0000.000
196A319LYS10.8470.91251.7245.4875.4870.0000.0000.0000.000
197A320ILE00.0010.00550.0530.0120.0120.0000.0000.0000.000
198A321ILE00.0210.01545.527-0.054-0.0540.0000.0000.0000.000
199A322GLU-1-0.853-0.91448.765-6.139-6.1390.0000.0000.0000.000
200A323ILE0-0.017-0.00351.2800.0200.0200.0000.0000.0000.000
201A324VAL00.0160.00845.424-0.007-0.0070.0000.0000.0000.000
202A325GLN00.0070.00346.478-0.101-0.1010.0000.0000.0000.000
203A326SER00.0400.00647.8170.0150.0150.0000.0000.0000.000
204A327LEU0-0.049-0.01749.1710.0880.0880.0000.0000.0000.000
205A328GLN00.011-0.00142.159-0.148-0.1480.0000.0000.0000.000
206A329GLU-1-0.835-0.91146.075-6.460-6.4600.0000.0000.0000.000
207A330LYS10.8360.92448.0396.0216.0210.0000.0000.0000.000
208A331GLY00.0070.01446.0760.0560.0560.0000.0000.0000.000
209A332VAL0-0.046-0.01447.096-0.026-0.0260.0000.0000.0000.000
210A333ILE0-0.027-0.00645.418-0.009-0.0090.0000.0000.0000.000
211A334GLN00.0150.00639.6330.0230.0230.0000.0000.0000.000
212A335THR0-0.0140.00537.188-0.125-0.1250.0000.0000.0000.000