FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: VRLZ1

Calculation Name: 2QWU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2QWU

Chain ID: A

ChEMBL ID:

UniProt ID: Q5NEC5

Base Structure: X-ray

Registration Date: 2023-06-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 207
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2223887.049741
FMO2-HF: Nuclear repulsion 2144565.4905
FMO2-HF: Total energy -79321.559241
FMO2-MP2: Total energy -79546.424018


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:3:MET)


Summations of interaction energy for fragment #1(A:3:MET)
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.
-17.717-12.8996.339-5.691-5.466-0.049
Interaction energy analysis for fragmet #1(A:3:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.049 / q_NPA : -0.032
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].
3A5GLU-1-0.799-0.8831.976-17.162-12.7986.338-5.613-5.090-0.049
4A6MET0-0.063-0.0195.2570.2580.313-0.001-0.002-0.0520.000
5A7ILE0-0.043-0.0227.4940.3910.3910.0000.0000.0000.000
6A8THR00.0480.0103.855-0.0340.1460.000-0.027-0.1530.000
7A9ARG10.9070.9125.8600.4110.4110.0000.0000.0000.000
8A10GLN0-0.0010.0066.8750.1700.1700.0000.0000.0000.000
9A11GLN00.0520.0548.193-0.255-0.2550.0000.0000.0000.000
10A12VAL0-0.029-0.02110.4970.0200.0200.0000.0000.0000.000
11A13THR0-0.079-0.05211.401-0.003-0.0030.0000.0000.0000.000
12A14SER0-0.044-0.03612.217-0.006-0.0060.0000.0000.0000.000
13A15GLY0-0.0120.00514.896-0.010-0.0100.0000.0000.0000.000
14A16GLU-1-0.902-0.93910.4490.1090.1090.0000.0000.0000.000
15A17THR0-0.031-0.01814.679-0.042-0.0420.0000.0000.0000.000
16A18ILE00.0400.03812.787-0.061-0.0610.0000.0000.0000.000
17A19HIS0-0.003-0.01312.4360.0280.0280.0000.0000.0000.000
18A20VAL00.0630.01212.140-0.142-0.1420.0000.0000.0000.000
19A21ARG10.8540.91213.5120.8030.8030.0000.0000.0000.000
20A22THR00.0350.02013.997-0.118-0.1180.0000.0000.0000.000
21A23ASP-1-0.835-0.90316.547-0.686-0.6860.0000.0000.0000.000
22A24PRO0-0.004-0.01519.1410.0160.0160.0000.0000.0000.000
23A25THR00.0490.03122.5520.0250.0250.0000.0000.0000.000
24A26ALA00.0120.01518.9510.0130.0130.0000.0000.0000.000
25A27CYS0-0.056-0.02620.997-0.010-0.0100.0000.0000.0000.000
26A28ILE00.0320.02323.0610.0260.0260.0000.0000.0000.000
27A29GLY00.0320.01624.010-0.024-0.0240.0000.0000.0000.000
28A30SER0-0.005-0.01023.848-0.013-0.0130.0000.0000.0000.000
29A31HIS0-0.032-0.00719.414-0.047-0.0470.0000.0000.0000.000
30A32PRO00.0370.01115.5590.0220.0220.0000.0000.0000.000
31A33ASN0-0.020-0.00414.696-0.153-0.1530.0000.0000.0000.000
32A34CYS00.0220.01712.3350.0970.0970.0000.0000.0000.000
33A35ARG10.7890.87114.5480.7660.7660.0000.0000.0000.000
34A36MET00.0010.00916.806-0.024-0.0240.0000.0000.0000.000
35A37PHE00.011-0.00319.4770.0320.0320.0000.0000.0000.000
36A38ILE0-0.0220.00523.118-0.009-0.0090.0000.0000.0000.000
37A39ASP-1-0.783-0.87325.744-0.224-0.2240.0000.0000.0000.000
38A40SER0-0.012-0.01328.8160.0210.0210.0000.0000.0000.000
39A41LEU00.0530.01728.705-0.015-0.0150.0000.0000.0000.000
40A42THR0-0.055-0.01531.2730.0160.0160.0000.0000.0000.000
41A43ILE00.0500.01630.764-0.006-0.0060.0000.0000.0000.000
42A44ALA00.0450.02534.4000.0070.0070.0000.0000.0000.000
43A45GLY0-0.015-0.00237.1340.0100.0100.0000.0000.0000.000
44A46GLU-1-0.857-0.91937.771-0.119-0.1190.0000.0000.0000.000
45A47LYS10.9150.95336.1500.1270.1270.0000.0000.0000.000
46A48LEU00.0060.00332.5730.0050.0050.0000.0000.0000.000
47A49ASP-1-0.903-0.95034.949-0.164-0.1640.0000.0000.0000.000
48A50LYS10.7880.88830.6810.2230.2230.0000.0000.0000.000
49A51ASN0-0.024-0.03833.702-0.005-0.0050.0000.0000.0000.000
50A52ILE00.0050.00928.2560.0000.0000.0000.0000.0000.000
51A53VAL00.0010.00730.432-0.005-0.0050.0000.0000.0000.000
52A54ALA0-0.026-0.00725.268-0.012-0.0120.0000.0000.0000.000
53A55ILE00.0060.02123.5340.0160.0160.0000.0000.0000.000
54A56ASP-1-0.745-0.86320.491-0.571-0.5710.0000.0000.0000.000
55A57GLY00.0240.00018.1090.0030.0030.0000.0000.0000.000
56A58GLY0-0.025-0.01619.0510.0290.0290.0000.0000.0000.000
57A59GLU-1-0.926-0.94820.866-0.321-0.3210.0000.0000.0000.000
58A60ASP-1-0.787-0.85424.274-0.288-0.2880.0000.0000.0000.000
59A61VAL00.0540.00326.2840.0200.0200.0000.0000.0000.000
60A62THR0-0.117-0.07728.8490.0230.0230.0000.0000.0000.000
61A63LYS10.8050.87831.1060.2600.2600.0000.0000.0000.000
62A64ALA00.0100.02929.2540.0060.0060.0000.0000.0000.000
63A65ASP-1-0.868-0.91631.408-0.201-0.2010.0000.0000.0000.000
64A66SER0-0.065-0.04733.7470.0070.0070.0000.0000.0000.000
65A67ALA0-0.027-0.01132.495-0.015-0.0150.0000.0000.0000.000
66A68THR00.0290.00727.7950.0110.0110.0000.0000.0000.000
67A69ALA0-0.051-0.03227.255-0.001-0.0010.0000.0000.0000.000
68A70ALA0-0.0040.00829.2470.0140.0140.0000.0000.0000.000
69A71ALA0-0.025-0.01527.5460.0100.0100.0000.0000.0000.000
70A72SER0-0.024-0.02123.273-0.013-0.0130.0000.0000.0000.000
71A73VAL00.000-0.02520.1290.0350.0350.0000.0000.0000.000
72A74ILE0-0.0020.03019.687-0.050-0.0500.0000.0000.0000.000
73A75ARG10.9480.95717.8390.3510.3510.0000.0000.0000.000
74A76MET0-0.0010.00817.3890.0510.0510.0000.0000.0000.000
75A77SER00.0020.01216.762-0.085-0.0850.0000.0000.0000.000
76A78ILE00.005-0.00117.2450.0430.0430.0000.0000.0000.000
77A79THR00.0160.00917.409-0.019-0.0190.0000.0000.0000.000
78A80PRO0-0.021-0.01117.8480.0050.0050.0000.0000.0000.000
79A81GLY00.0230.01820.8310.0150.0150.0000.0000.0000.000
80A82SER0-0.058-0.02924.381-0.003-0.0030.0000.0000.0000.000
81A83ILE0-0.012-0.00426.9790.0020.0020.0000.0000.0000.000
82A84ASN00.0140.00027.483-0.009-0.0090.0000.0000.0000.000
83A85PRO00.0360.03622.7790.0110.0110.0000.0000.0000.000
84A86THR0-0.0340.00123.1190.0110.0110.0000.0000.0000.000
85A87ILE0-0.029-0.02122.063-0.016-0.0160.0000.0000.0000.000
86A88SER0-0.0260.00621.7950.0120.0120.0000.0000.0000.000
87A89ILE0-0.033-0.02321.429-0.036-0.0360.0000.0000.0000.000
88A90THR0-0.006-0.00122.0420.0180.0180.0000.0000.0000.000
89A91LEU00.0220.01022.881-0.035-0.0350.0000.0000.0000.000
90A92GLY00.0320.01825.5380.0100.0100.0000.0000.0000.000
91A93VAL00.0110.00327.210-0.006-0.0060.0000.0000.0000.000
92A94LEU00.0000.01430.6390.0050.0050.0000.0000.0000.000
93A95ILE00.0570.02433.4460.0100.0100.0000.0000.0000.000
94A96LYS10.9140.95336.5570.1380.1380.0000.0000.0000.000
95A97SER00.0380.00039.408-0.003-0.0030.0000.0000.0000.000
96A98ASN00.0170.00840.426-0.003-0.0030.0000.0000.0000.000
97A99VAL00.0230.01438.3290.0040.0040.0000.0000.0000.000
98A100ARG10.8210.88836.0840.1540.1540.0000.0000.0000.000
99A101THR00.0300.01538.078-0.001-0.0010.0000.0000.0000.000
100A102LYS10.7630.86540.8570.1090.1090.0000.0000.0000.000
101A103ILE00.0440.02935.0570.0030.0030.0000.0000.0000.000
102A104GLU-1-0.788-0.86836.426-0.142-0.1420.0000.0000.0000.000
103A105GLU-1-0.793-0.88038.436-0.097-0.0970.0000.0000.0000.000
104A106LYS10.8150.91439.7900.1170.1170.0000.0000.0000.000
105A107VAL00.025-0.01134.9370.0040.0040.0000.0000.0000.000
106A108SER0-0.006-0.00138.0650.0060.0060.0000.0000.0000.000
107A109SER0-0.024-0.02240.1410.0070.0070.0000.0000.0000.000
108A110ILE0-0.015-0.01139.6650.0050.0050.0000.0000.0000.000
109A111LEU0-0.039-0.01035.7490.0040.0040.0000.0000.0000.000
110A112GLN0-0.074-0.04739.1440.0080.0080.0000.0000.0000.000
111A113ALA0-0.047-0.00442.4810.0050.0050.0000.0000.0000.000
112A114SER0-0.033-0.05041.8740.0060.0060.0000.0000.0000.000
113A115ALA00.0310.01936.849-0.005-0.0050.0000.0000.0000.000
114A116THR0-0.011-0.01835.766-0.006-0.0060.0000.0000.0000.000
115A117ASP-1-0.824-0.88036.208-0.088-0.0880.0000.0000.0000.000
116A118MET0-0.070-0.00132.961-0.005-0.0050.0000.0000.0000.000
117A119LYS10.8340.91233.8320.1040.1040.0000.0000.0000.000
118A120ILE00.0100.00129.057-0.002-0.0020.0000.0000.0000.000
119A121LYS10.8040.90030.3080.1640.1640.0000.0000.0000.000
120A122LEU00.0330.00524.154-0.003-0.0030.0000.0000.0000.000
121A123GLY00.0430.03327.9050.0120.0120.0000.0000.0000.000
122A124ASN0-0.040-0.05026.100-0.013-0.0130.0000.0000.0000.000
123A125SER00.0310.01220.9680.0000.0000.0000.0000.0000.000
124A126ASN0-0.029-0.01619.0090.0230.0230.0000.0000.0000.000
125A127LYS10.8430.88919.3120.3500.3500.0000.0000.0000.000
126A128LYS10.7640.88316.9530.4480.4480.0000.0000.0000.000
127A129GLN00.0330.00214.922-0.068-0.0680.0000.0000.0000.000
128A130GLU-1-0.780-0.8918.760-2.233-2.2330.0000.0000.0000.000
129A131TYR0-0.043-0.04812.2180.1020.1020.0000.0000.0000.000
130A132LYS10.7520.8738.7921.3771.3770.0000.0000.0000.000
131A133THR00.005-0.0224.5960.1680.221-0.001-0.004-0.0480.000
132A134ASP-1-0.803-0.8728.066-0.765-0.7650.0000.0000.0000.000
133A135GLU-1-0.894-0.90911.395-0.628-0.6280.0000.0000.0000.000
134A136ALA0-0.0050.01713.0350.1390.1390.0000.0000.0000.000
135A137TRP0-0.0010.00213.280-0.163-0.1630.0000.0000.0000.000
136A138GLY0-0.011-0.01113.7610.0940.0940.0000.0000.0000.000
137A139ILE0-0.052-0.01814.047-0.052-0.0520.0000.0000.0000.000
138A140MET00.0000.02410.875-0.158-0.1580.0000.0000.0000.000
139A141ILE00.059-0.00512.7030.0640.0640.0000.0000.0000.000
140A142ASP-1-0.836-0.86215.914-0.378-0.3780.0000.0000.0000.000
141A143LEU00.005-0.00419.2330.0440.0440.0000.0000.0000.000
142A144SER0-0.039-0.03421.7910.0290.0290.0000.0000.0000.000
143A145ASN0-0.071-0.02724.6670.0260.0260.0000.0000.0000.000
144A146LEU00.0130.02122.5810.0210.0210.0000.0000.0000.000
145A147GLU-1-0.879-0.93926.389-0.137-0.1370.0000.0000.0000.000
146A148LEU0-0.0190.00424.7580.0020.0020.0000.0000.0000.000
147A149TYR00.004-0.01328.9360.0060.0060.0000.0000.0000.000
148A150PRO00.0000.00130.545-0.003-0.0030.0000.0000.0000.000
149A151ILE00.0000.01527.4950.0090.0090.0000.0000.0000.000
150A152SER00.006-0.01231.9790.0110.0110.0000.0000.0000.000
151A153ALA00.0410.00734.568-0.007-0.0070.0000.0000.0000.000
152A154LYS10.9120.95736.1290.0540.0540.0000.0000.0000.000
153A155ALA0-0.0130.00330.8180.0010.0010.0000.0000.0000.000
154A156PHE0-0.008-0.00130.665-0.009-0.0090.0000.0000.0000.000
155A157SER0-0.0010.00429.8180.0100.0100.0000.0000.0000.000
156A158ILE0-0.005-0.01230.281-0.011-0.0110.0000.0000.0000.000
157A159SER0-0.030-0.01830.2130.0090.0090.0000.0000.0000.000
158A160ILE00.0110.00031.033-0.013-0.0130.0000.0000.0000.000
159A161GLU-1-0.867-0.91529.863-0.199-0.1990.0000.0000.0000.000
160A162PRO0-0.048-0.01331.710-0.014-0.0140.0000.0000.0000.000
161A163THR0-0.014-0.03029.058-0.006-0.0060.0000.0000.0000.000
162A164GLU-1-0.772-0.87132.306-0.176-0.1760.0000.0000.0000.000
163A165LEU0-0.037-0.01526.355-0.002-0.0020.0000.0000.0000.000
164A166MET0-0.016-0.00329.323-0.021-0.0210.0000.0000.0000.000
165A167GLY0-0.0220.00131.6950.0110.0110.0000.0000.0000.000
166A168VAL0-0.023-0.01335.151-0.001-0.0010.0000.0000.0000.000
167A169SER0-0.011-0.02837.7290.0020.0020.0000.0000.0000.000
168A170LYS10.9490.95339.0520.1630.1630.0000.0000.0000.000
169A171ASP-1-0.787-0.85640.972-0.149-0.1490.0000.0000.0000.000
170A172GLY0-0.024-0.01141.9670.0050.0050.0000.0000.0000.000
171A173MET0-0.086-0.02637.0620.0000.0000.0000.0000.0000.000
172A174ARG10.8810.90135.0470.1650.1650.0000.0000.0000.000
173A175TYR00.0180.00824.9440.0040.0040.0000.0000.0000.000
174A176HIS0-0.022-0.01031.3840.0100.0100.0000.0000.0000.000
175A177ILE00.0250.01525.657-0.014-0.0140.0000.0000.0000.000
176A178ILE00.004-0.00727.7720.0220.0220.0000.0000.0000.000
177A179SER00.0160.02025.990-0.033-0.0330.0000.0000.0000.000
178A180ILE0-0.015-0.01226.0370.0240.0240.0000.0000.0000.000
179A181ASP-1-0.862-0.94524.582-0.246-0.2460.0000.0000.0000.000
180A182GLY00.0410.02026.4680.0130.0130.0000.0000.0000.000
181A183LEU0-0.028-0.00826.2420.0140.0140.0000.0000.0000.000
182A184THR0-0.005-0.03526.5190.0020.0020.0000.0000.0000.000
183A185THR0-0.013-0.03225.093-0.007-0.0070.0000.0000.0000.000
184A186SER00.0380.02428.2100.0100.0100.0000.0000.0000.000
185A187GLN0-0.036-0.01923.4540.0140.0140.0000.0000.0000.000
186A188GLY00.0520.02525.019-0.010-0.0100.0000.0000.0000.000
187A189SER0-0.018-0.01820.9680.0100.0100.0000.0000.0000.000
188A190LEU00.0460.03218.763-0.005-0.0050.0000.0000.0000.000
189A191PRO0-0.0040.00817.7940.0010.0010.0000.0000.0000.000
190A192VAL00.0280.00412.533-0.030-0.0300.0000.0000.0000.000
191A193CYS0-0.068-0.03610.2000.1650.1650.0000.0000.0000.000
192A194CYS0-0.076-0.0016.0290.0680.0680.0000.0000.0000.000
193A195ALA00.0470.0283.393-0.0990.0670.004-0.044-0.1260.000
194A196ALA00.0520.0485.2800.0820.082-0.001-0.0010.0030.000
195A197SER0-0.064-0.0778.7550.1580.1580.0000.0000.0000.000
196A198THR00.013-0.02811.0040.1060.1060.0000.0000.0000.000
197A199ASP-1-0.874-0.8977.483-0.697-0.6970.0000.0000.0000.000
198A200LYS10.9430.95610.6130.3940.3940.0000.0000.0000.000
199A201GLY00.0020.00213.4180.0990.0990.0000.0000.0000.000
200A202VAL0-0.034-0.01514.905-0.042-0.0420.0000.0000.0000.000
201A203ALA00.0500.04315.2880.0500.0500.0000.0000.0000.000
202A204LYS10.8780.92516.9000.0260.0260.0000.0000.0000.000
203A205ILE0-0.001-0.01219.0230.0060.0060.0000.0000.0000.000
204A206GLY00.0530.02921.5050.0060.0060.0000.0000.0000.000
205A207TYR0-0.011-0.00425.3280.0090.0090.0000.0000.0000.000
206A208ILE0-0.007-0.01024.669-0.014-0.0140.0000.0000.0000.000
207A209ALA0-0.0060.01929.2010.0090.0090.0000.0000.0000.000