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: 1N39Z

Calculation Name: 1WDZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1WDZ

Chain ID: A

ChEMBL ID:

UniProt ID: Q9UQB8

Base Structure: X-ray

Registration Date: 2023-09-23

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 231
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2292396.56644
FMO2-HF: Nuclear repulsion 2198970.026913
FMO2-HF: Total energy -93426.539527
FMO2-MP2: Total energy -93697.199845


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:2:SER)


Summations of interaction energy for fragment #1(A:2:SER)
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.
-1.0151.142-0.008-0.789-1.360.002
Interaction energy analysis for fragmet #1(A:2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.028 / q_NPA : 0.007
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].
3A4SER00.009-0.0133.810-0.3730.979-0.011-0.613-0.7280.002
4A5ARG11.0040.9624.7110.6950.762-0.001-0.006-0.0590.000
5A6SER0-0.008-0.0297.0450.2310.2310.0000.0000.0000.000
6A7GLU-1-0.813-0.8814.1333.8184.1340.005-0.099-0.2220.000
7A8GLU-1-0.972-0.9874.154-0.444-0.022-0.001-0.071-0.3510.000
8A9MET00.0020.0106.046-0.485-0.4850.0000.0000.0000.000
9A10HIS00.0460.0519.018-0.347-0.3470.0000.0000.0000.000
10A11ARG10.8620.9226.406-3.585-3.5850.0000.0000.0000.000
11A12LEU00.0070.0129.395-0.285-0.2850.0000.0000.0000.000
12A13THR00.0130.00911.762-0.177-0.1770.0000.0000.0000.000
13A14GLU-1-0.868-0.93411.6221.1731.1730.0000.0000.0000.000
14A15ASN0-0.042-0.02611.209-0.188-0.1880.0000.0000.0000.000
15A16VAL00.0190.03314.562-0.087-0.0870.0000.0000.0000.000
16A17TYR00.007-0.00717.266-0.060-0.0600.0000.0000.0000.000
17A18LYS10.9080.96416.876-0.525-0.5250.0000.0000.0000.000
18A19THR00.0350.01817.618-0.049-0.0490.0000.0000.0000.000
19A20ILE0-0.039-0.02020.146-0.043-0.0430.0000.0000.0000.000
20A21MET0-0.074-0.03321.515-0.034-0.0340.0000.0000.0000.000
21A22GLU-1-0.886-0.95820.3600.3560.3560.0000.0000.0000.000
22A23GLN00.0030.00320.7240.0020.0020.0000.0000.0000.000
23A24PHE0-0.0250.01524.385-0.021-0.0210.0000.0000.0000.000
24A25ASN00.030-0.02426.288-0.028-0.0280.0000.0000.0000.000
25A26PRO0-0.038-0.00126.838-0.016-0.0160.0000.0000.0000.000
26A27SER00.002-0.01827.837-0.016-0.0160.0000.0000.0000.000
27A28LEU0-0.0060.00930.302-0.013-0.0130.0000.0000.0000.000
28A29ARG10.8730.93632.040-0.160-0.1600.0000.0000.0000.000
29A30ASN00.0070.00633.542-0.010-0.0100.0000.0000.0000.000
30A31PHE00.0070.00934.348-0.008-0.0080.0000.0000.0000.000
31A32ILE00.0130.00535.823-0.007-0.0070.0000.0000.0000.000
32A33ALA0-0.0030.00138.057-0.006-0.0060.0000.0000.0000.000
33A34MET0-0.021-0.01338.485-0.008-0.0080.0000.0000.0000.000
34A35GLY00.0240.01240.127-0.005-0.0050.0000.0000.0000.000
35A36LYS10.8720.90141.831-0.084-0.0840.0000.0000.0000.000
36A37ASN0-0.0060.00443.130-0.004-0.0040.0000.0000.0000.000
37A38TYR00.0050.00944.442-0.004-0.0040.0000.0000.0000.000
38A39GLU-1-0.828-0.92645.9570.0590.0590.0000.0000.0000.000
39A40LYS10.8080.88846.879-0.064-0.0640.0000.0000.0000.000
40A41ALA00.0090.01349.515-0.003-0.0030.0000.0000.0000.000
41A42LEU00.0160.00848.717-0.002-0.0020.0000.0000.0000.000
42A43ALA00.0190.00852.064-0.002-0.0020.0000.0000.0000.000
43A44GLY0-0.021-0.01153.884-0.002-0.0020.0000.0000.0000.000
44A45VAL0-0.039-0.02554.665-0.002-0.0020.0000.0000.0000.000
45A46THR0-0.015-0.02356.467-0.002-0.0020.0000.0000.0000.000
46A47TYR0-0.059-0.02558.297-0.001-0.0010.0000.0000.0000.000
47A48ALA00.0120.00460.231-0.001-0.0010.0000.0000.0000.000
48A49ALA0-0.0110.00060.611-0.002-0.0020.0000.0000.0000.000
49A50LYS10.8740.94160.767-0.035-0.0350.0000.0000.0000.000
50A51GLY00.0940.05865.343-0.001-0.0010.0000.0000.0000.000
51A52TYR0-0.035-0.01764.888-0.001-0.0010.0000.0000.0000.000
52A53PHE0-0.011-0.01666.638-0.001-0.0010.0000.0000.0000.000
53A54ASP-1-0.891-0.94868.2510.0230.0230.0000.0000.0000.000
54A55ALA0-0.039-0.01370.555-0.001-0.0010.0000.0000.0000.000
55A56LEU0-0.007-0.00868.459-0.001-0.0010.0000.0000.0000.000
56A57VAL00.0430.01971.866-0.001-0.0010.0000.0000.0000.000
57A58LYS10.8810.95374.323-0.017-0.0170.0000.0000.0000.000
58A59MET0-0.028-0.01975.213-0.001-0.0010.0000.0000.0000.000
59A60GLY00.0300.00776.323-0.001-0.0010.0000.0000.0000.000
60A61GLU-1-0.909-0.95977.7320.0170.0170.0000.0000.0000.000
61A62LEU0-0.044-0.02279.8390.0000.0000.0000.0000.0000.000
62A63ALA00.0050.01480.273-0.001-0.0010.0000.0000.0000.000
63A64SER00.0120.02381.874-0.001-0.0010.0000.0000.0000.000
64A65GLU-1-0.958-0.97383.7080.0140.0140.0000.0000.0000.000
65A66SER0-0.069-0.04285.126-0.001-0.0010.0000.0000.0000.000
66A67GLN0-0.021-0.03287.0700.0000.0000.0000.0000.0000.000
67A68GLY00.019-0.00688.6260.0000.0000.0000.0000.0000.000
68A69SER0-0.014-0.00783.2320.0000.0000.0000.0000.0000.000
69A70LYS10.9330.97282.927-0.011-0.0110.0000.0000.0000.000
70A71GLU-1-0.850-0.91481.9680.0100.0100.0000.0000.0000.000
71A72LEU0-0.017-0.01778.4810.0000.0000.0000.0000.0000.000
72A73GLY00.0170.00977.9380.0010.0010.0000.0000.0000.000
73A74ASP-1-0.885-0.94677.6810.0140.0140.0000.0000.0000.000
74A75VAL0-0.061-0.03173.8360.0010.0010.0000.0000.0000.000
75A76LEU00.0060.00573.2890.0010.0010.0000.0000.0000.000
76A77PHE00.0540.02872.5610.0010.0010.0000.0000.0000.000
77A78GLN00.0020.00571.7300.0010.0010.0000.0000.0000.000
78A79MET0-0.0370.00368.9400.0010.0010.0000.0000.0000.000
79A80ALA00.0300.01467.8700.0010.0010.0000.0000.0000.000
80A81GLU-1-0.802-0.87567.8100.0220.0220.0000.0000.0000.000
81A82VAL0-0.019-0.01564.2300.0010.0010.0000.0000.0000.000
82A83HIS0-0.020-0.00862.5030.0010.0010.0000.0000.0000.000
83A84ARG10.8660.91262.932-0.022-0.0220.0000.0000.0000.000
84A85GLN0-0.091-0.05563.0130.0020.0020.0000.0000.0000.000
85A86ILE00.0170.00358.3730.0010.0010.0000.0000.0000.000
86A87GLN00.0260.00758.4770.0030.0030.0000.0000.0000.000
87A88ASN00.009-0.00558.3650.0020.0020.0000.0000.0000.000
88A89GLN0-0.056-0.02956.1990.0010.0010.0000.0000.0000.000
89A90LEU00.0130.02052.6450.0010.0010.0000.0000.0000.000
90A91GLU-1-0.792-0.88553.3910.0390.0390.0000.0000.0000.000
91A92GLU-1-0.842-0.89053.5030.0420.0420.0000.0000.0000.000
92A93MET0-0.0050.01048.3870.0040.0040.0000.0000.0000.000
93A94LEU00.0340.02148.8540.0040.0040.0000.0000.0000.000
94A95LYS10.8550.90549.012-0.039-0.0390.0000.0000.0000.000
95A96SER0-0.060-0.02247.1330.0030.0030.0000.0000.0000.000
96A97PHE00.013-0.00842.3390.0040.0040.0000.0000.0000.000
97A98HIS00.0350.02244.3230.0050.0050.0000.0000.0000.000
98A99ASN0-0.058-0.06344.8810.0020.0020.0000.0000.0000.000
99A100GLU-1-0.882-0.93343.1480.0600.0600.0000.0000.0000.000
100A101LEU0-0.016-0.01438.0560.0050.0050.0000.0000.0000.000
101A102LEU0-0.0260.00839.8770.0070.0070.0000.0000.0000.000
102A103THR00.0540.02840.4430.0060.0060.0000.0000.0000.000
103A104GLN0-0.050-0.02339.1190.0080.0080.0000.0000.0000.000
104A105LEU0-0.024-0.02634.4900.0080.0080.0000.0000.0000.000
105A106GLU-1-0.812-0.88436.0510.0950.0950.0000.0000.0000.000
106A107GLN00.0080.00737.3340.0050.0050.0000.0000.0000.000
107A108LYS10.8390.94333.767-0.104-0.1040.0000.0000.0000.000
108A109VAL00.0160.00231.8960.0120.0120.0000.0000.0000.000
109A110GLU-1-0.965-0.96632.7660.1320.1320.0000.0000.0000.000
110A111LEU00.023-0.00633.5740.0090.0090.0000.0000.0000.000
111A112ASP-1-0.729-0.81028.6830.2160.2160.0000.0000.0000.000
112A113SER00.0480.00426.9280.0130.0130.0000.0000.0000.000
113A114ARG10.9651.00126.849-0.151-0.1510.0000.0000.0000.000
114A115TYR00.012-0.00228.2330.0110.0110.0000.0000.0000.000
115A116LEU0-0.0030.00823.7180.0190.0190.0000.0000.0000.000
116A117SER00.0080.00023.4770.0450.0450.0000.0000.0000.000
117A118ALA0-0.054-0.02123.7920.0270.0270.0000.0000.0000.000
118A119ALA0-0.011-0.00723.8490.0210.0210.0000.0000.0000.000
119A120LEU00.0230.02016.9680.0240.0240.0000.0000.0000.000
120A121LYS11.0001.00119.725-0.322-0.3220.0000.0000.0000.000
121A122LYS10.8590.92021.090-0.269-0.2690.0000.0000.0000.000
122A123TYR00.024-0.00313.320-0.032-0.0320.0000.0000.0000.000
123A124GLN0-0.043-0.05915.078-0.056-0.0560.0000.0000.0000.000
124A125THR0-0.077-0.05817.3470.0410.0410.0000.0000.0000.000
125A126GLU-1-0.795-0.85119.7320.3400.3400.0000.0000.0000.000
126A127GLN0-0.003-0.01212.138-0.062-0.0620.0000.0000.0000.000
127A128ARG10.9530.99915.479-0.591-0.5910.0000.0000.0000.000
128A129SER0-0.035-0.00516.596-0.035-0.0350.0000.0000.0000.000
129A130LYS10.8530.90617.553-0.349-0.3490.0000.0000.0000.000
130A131GLY00.0410.02514.622-0.029-0.0290.0000.0000.0000.000
131A132ASP-1-0.849-0.92215.3460.5980.5980.0000.0000.0000.000
132A133ALA0-0.089-0.05017.450-0.062-0.0620.0000.0000.0000.000
133A134LEU00.0080.00214.093-0.068-0.0680.0000.0000.0000.000
134A135ASP-1-0.841-0.91113.5980.6700.6700.0000.0000.0000.000
135A136LYS10.8320.89916.587-0.288-0.2880.0000.0000.0000.000
136A137CYM-1-0.784-0.81620.2040.1550.1550.0000.0000.0000.000
137A138GLN00.0340.00514.698-0.031-0.0310.0000.0000.0000.000
138A139ALA0-0.044-0.01519.052-0.045-0.0450.0000.0000.0000.000
139A140GLU-1-0.955-0.98920.3610.1460.1460.0000.0000.0000.000
140A141LEU00.0680.05421.550-0.027-0.0270.0000.0000.0000.000
141A142LYS10.9800.99517.645-0.091-0.0910.0000.0000.0000.000
142A143LYS10.8660.92722.439-0.175-0.1750.0000.0000.0000.000
143A144LEU00.0130.01025.272-0.010-0.0100.0000.0000.0000.000
144A145ARG10.9840.97621.753-0.004-0.0040.0000.0000.0000.000
145A146LYS10.8880.96124.771-0.076-0.0760.0000.0000.0000.000
146A147LYS10.9030.95027.418-0.054-0.0540.0000.0000.0000.000
147A148SER0-0.0350.00029.726-0.002-0.0020.0000.0000.0000.000
148A149GLN00.005-0.00931.435-0.005-0.0050.0000.0000.0000.000
149A150GLY00.0420.01832.904-0.002-0.0020.0000.0000.0000.000
150A151SER0-0.032-0.02034.0830.0050.0050.0000.0000.0000.000
151A152LYS10.9530.97337.3180.0180.0180.0000.0000.0000.000
152A153ASN00.0170.02732.2560.0090.0090.0000.0000.0000.000
153A154PRO00.0240.00836.488-0.001-0.0010.0000.0000.0000.000
154A155GLN00.0390.01336.735-0.003-0.0030.0000.0000.0000.000
155A156LYS10.9650.99036.241-0.050-0.0500.0000.0000.0000.000
156A157TYR0-0.064-0.05328.9030.0080.0080.0000.0000.0000.000
157A158SER00.0740.02032.0980.0040.0040.0000.0000.0000.000
158A159ASP-1-0.840-0.92031.7180.0240.0240.0000.0000.0000.000
159A160LYS10.8480.92629.467-0.089-0.0890.0000.0000.0000.000
160A161GLU-1-0.842-0.90226.6360.0080.0080.0000.0000.0000.000
161A162LEU00.0400.00826.9550.0040.0040.0000.0000.0000.000
162A163GLN00.0380.04227.9630.0110.0110.0000.0000.0000.000
163A164TYR00.000-0.02224.2630.0010.0010.0000.0000.0000.000
164A165ILE0-0.0220.00123.0150.0140.0140.0000.0000.0000.000
165A166ASP-1-0.871-0.91923.0720.0790.0790.0000.0000.0000.000
166A167ALA00.0170.00624.0410.0120.0120.0000.0000.0000.000
167A168ILE0-0.059-0.03918.2640.0280.0280.0000.0000.0000.000
168A169SER0-0.005-0.01419.4280.0180.0180.0000.0000.0000.000
169A170ASN0-0.034-0.01819.9880.0120.0120.0000.0000.0000.000
170A171LYS10.7610.81619.428-0.222-0.2220.0000.0000.0000.000
171A172GLN0-0.054-0.03314.4610.0320.0320.0000.0000.0000.000
172A173GLY00.0600.03215.8420.0380.0380.0000.0000.0000.000
173A174GLU-1-0.878-0.91917.9180.2680.2680.0000.0000.0000.000
174A175LEU0-0.034-0.01113.2880.0240.0240.0000.0000.0000.000
175A176GLU-1-0.821-0.88811.6410.2840.2840.0000.0000.0000.000
176A177ASN0-0.041-0.03114.4070.0100.0100.0000.0000.0000.000
177A178TYR0-0.050-0.04216.9680.0040.0040.0000.0000.0000.000
178A179VAL0-0.0040.00311.272-0.004-0.0040.0000.0000.0000.000
179A180SER0-0.041-0.03314.505-0.022-0.0220.0000.0000.0000.000
180A181ASP-1-0.885-0.92515.2420.1980.1980.0000.0000.0000.000
181A182GLY00.0200.01117.376-0.028-0.0280.0000.0000.0000.000
182A183TYR00.0220.00914.079-0.043-0.0430.0000.0000.0000.000
183A184LYS10.8900.93416.160-0.243-0.2430.0000.0000.0000.000
184A185THR00.0100.00619.185-0.045-0.0450.0000.0000.0000.000
185A186ALA0-0.0030.00317.622-0.025-0.0250.0000.0000.0000.000
186A187LEU00.0380.01216.877-0.032-0.0320.0000.0000.0000.000
187A188THR0-0.043-0.02320.243-0.042-0.0420.0000.0000.0000.000
188A189GLU-1-0.833-0.87622.6020.2030.2030.0000.0000.0000.000
189A190GLU-1-0.936-0.97319.6300.2200.2200.0000.0000.0000.000
190A191ARG10.9610.97623.284-0.117-0.1170.0000.0000.0000.000
191A192ARG10.8430.88725.209-0.204-0.2040.0000.0000.0000.000
192A193ARG10.7360.82126.200-0.222-0.2220.0000.0000.0000.000
193A194PHE00.0330.01323.621-0.014-0.0140.0000.0000.0000.000
194A195CYS0-0.075-0.04128.897-0.014-0.0140.0000.0000.0000.000
195A196PHE00.0460.01931.042-0.008-0.0080.0000.0000.0000.000
196A197LEU0-0.010-0.00231.751-0.006-0.0060.0000.0000.0000.000
197A198VAL00.0210.00832.310-0.008-0.0080.0000.0000.0000.000
198A199GLU-1-0.839-0.90834.3290.0790.0790.0000.0000.0000.000
199A200LYS10.8790.93437.299-0.076-0.0760.0000.0000.0000.000
200A201GLN00.0140.01737.405-0.006-0.0060.0000.0000.0000.000
201A202CYS0-0.048-0.03638.039-0.006-0.0060.0000.0000.0000.000
202A203ALA0-0.0190.00340.812-0.004-0.0040.0000.0000.0000.000
203A204VAL00.0460.02742.690-0.003-0.0030.0000.0000.0000.000
204A205ALA00.0070.00142.640-0.004-0.0040.0000.0000.0000.000
205A206LYS10.9370.96544.586-0.041-0.0410.0000.0000.0000.000
206A207ASN0-0.033-0.03346.711-0.004-0.0040.0000.0000.0000.000
207A208SER00.0240.00947.163-0.003-0.0030.0000.0000.0000.000
208A209ALA0-0.0100.00748.532-0.002-0.0020.0000.0000.0000.000
209A210ALA00.0010.00250.250-0.002-0.0020.0000.0000.0000.000
210A211TYR00.0150.01151.963-0.002-0.0020.0000.0000.0000.000
211A212HIS0-0.015-0.02349.762-0.002-0.0020.0000.0000.0000.000
212A213SER0-0.044-0.02554.022-0.002-0.0020.0000.0000.0000.000
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214A215GLY00.0450.01457.464-0.001-0.0010.0000.0000.0000.000
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