Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: VKKY1

Calculation Name: 4Q25-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4Q25

Chain ID: A

ChEMBL ID:

UniProt ID: Q51547

Base Structure: X-ray

Registration Date: 2023-09-27

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 211
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2456694.679417
FMO2-HF: Nuclear repulsion 2372762.240866
FMO2-HF: Total energy -83932.438551
FMO2-MP2: Total energy -84176.830641


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:12:SER)


Summations of interaction energy for fragment #1(A:12: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.
-4.7121.1431.602-3.591-3.866-0.003
Interaction energy analysis for fragmet #1(A:12:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.046 / q_NPA : 0.015
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].
3A14GLN0-0.023-0.0073.735-2.5711.2300.012-2.127-1.6860.005
4A15PHE0-0.0010.0112.377-0.0620.6001.458-0.801-1.318-0.002
5A16ASN0-0.004-0.0293.039-1.0830.3090.132-0.663-0.862-0.006
6A17ALA0-0.0050.0225.9770.2580.2580.0000.0000.0000.000
7A18GLU-1-0.729-0.8317.041-0.558-0.5580.0000.0000.0000.000
8A19LEU0-0.041-0.0197.1880.1410.1410.0000.0000.0000.000
9A20GLU-1-0.806-0.8709.7930.0680.0680.0000.0000.0000.000
10A21ASP-1-0.906-0.94012.203-0.330-0.3300.0000.0000.0000.000
11A22VAL00.0190.01712.2960.0490.0490.0000.0000.0000.000
12A23ARG10.7360.83613.9020.0260.0260.0000.0000.0000.000
13A24SER0-0.052-0.04315.7940.0220.0220.0000.0000.0000.000
14A25HIS0-0.043-0.04316.6070.0140.0140.0000.0000.0000.000
15A26LEU00.0280.02118.7700.0090.0090.0000.0000.0000.000
16A27LEU0-0.0090.00019.5470.0080.0080.0000.0000.0000.000
17A28ALA0-0.030-0.00822.0930.0050.0050.0000.0000.0000.000
18A29MET0-0.048-0.01723.3560.0030.0030.0000.0000.0000.000
19A30GLY00.0390.00624.6450.0050.0050.0000.0000.0000.000
20A31GLY00.0210.01026.3780.0040.0040.0000.0000.0000.000
21A32LEU0-0.050-0.02328.1390.0020.0020.0000.0000.0000.000
22A33VAL00.0340.00928.3790.0020.0020.0000.0000.0000.000
23A34GLU-1-0.819-0.90730.430-0.002-0.0020.0000.0000.0000.000
24A35LYS10.8130.89732.2720.0230.0230.0000.0000.0000.000
25A36GLN0-0.027-0.02933.5890.0020.0020.0000.0000.0000.000
26A37VAL00.0040.00434.2050.0020.0020.0000.0000.0000.000
27A38ASN0-0.024-0.02236.5540.0020.0020.0000.0000.0000.000
28A39ASP-1-0.843-0.90638.362-0.015-0.0150.0000.0000.0000.000
29A40ALA00.0160.00939.7710.0000.0000.0000.0000.0000.000
30A41VAL0-0.028-0.01540.7560.0010.0010.0000.0000.0000.000
31A42ASN0-0.0200.00441.5630.0010.0010.0000.0000.0000.000
32A43ALA00.0090.00844.1160.0000.0000.0000.0000.0000.000
33A44LEU0-0.043-0.02045.7290.0000.0000.0000.0000.0000.000
34A45ILE0-0.105-0.04946.9530.0010.0010.0000.0000.0000.000
35A46ASP-1-0.817-0.92247.229-0.004-0.0040.0000.0000.0000.000
36A47ALA0-0.031-0.01050.122-0.001-0.0010.0000.0000.0000.000
37A48ASP-1-0.817-0.89547.203-0.012-0.0120.0000.0000.0000.000
38A49SER00.034-0.03047.1330.0000.0000.0000.0000.0000.000
39A50GLY0-0.038-0.00646.9720.0000.0000.0000.0000.0000.000
40A51LEU0-0.051-0.02141.373-0.001-0.0010.0000.0000.0000.000
41A52ALA00.008-0.00142.3730.0000.0000.0000.0000.0000.000
42A53GLN0-0.052-0.03442.8470.0020.0020.0000.0000.0000.000
43A54GLN00.0350.01538.959-0.002-0.0020.0000.0000.0000.000
44A55VAL00.0010.00037.856-0.002-0.0020.0000.0000.0000.000
45A56ARG10.8770.93737.2130.0090.0090.0000.0000.0000.000
46A57GLU-1-0.907-0.93237.518-0.019-0.0190.0000.0000.0000.000
47A58ILE0-0.019-0.00632.673-0.003-0.0030.0000.0000.0000.000
48A59ASP-1-0.764-0.85332.709-0.011-0.0110.0000.0000.0000.000
49A60ASP-1-0.925-0.96032.008-0.020-0.0200.0000.0000.0000.000
50A61GLN0-0.056-0.02127.960-0.001-0.0010.0000.0000.0000.000
51A62ILE00.0180.01228.065-0.004-0.0040.0000.0000.0000.000
52A63ASN00.015-0.00127.247-0.001-0.0010.0000.0000.0000.000
53A64GLN0-0.025-0.01624.9740.0060.0060.0000.0000.0000.000
54A65MET0-0.049-0.02923.760-0.005-0.0050.0000.0000.0000.000
55A66GLU-1-0.804-0.91222.566-0.006-0.0060.0000.0000.0000.000
56A67ARG10.8730.93722.3100.0190.0190.0000.0000.0000.000
57A68ASN0-0.0080.00020.7620.0060.0060.0000.0000.0000.000
58A69ILE00.0210.01717.736-0.013-0.0130.0000.0000.0000.000
59A70ASP-1-0.832-0.91517.3240.0120.0120.0000.0000.0000.000
60A71GLU-1-0.952-0.98217.602-0.013-0.0130.0000.0000.0000.000
61A72GLU-1-0.844-0.89913.757-0.175-0.1750.0000.0000.0000.000
62A73CYS0-0.033-0.01713.158-0.008-0.0080.0000.0000.0000.000
63A74VAL0-0.014-0.00613.2200.0330.0330.0000.0000.0000.000
64A75ARG10.8020.88112.6250.1890.1890.0000.0000.0000.000
65A76ILE0-0.0010.0067.8540.0280.0280.0000.0000.0000.000
66A77LEU0-0.017-0.0178.6860.1220.1220.0000.0000.0000.000
67A78ALA0-0.0070.01010.8390.0910.0910.0000.0000.0000.000
68A79ARG10.7230.8346.4240.4050.4050.0000.0000.0000.000
69A80ARG10.9060.9435.121-1.434-1.4340.0000.0000.0000.000
70A81GLN00.0020.0068.321-0.095-0.0950.0000.0000.0000.000
71A82PRO00.0430.0306.8660.1710.1710.0000.0000.0000.000
72A83ALA00.0140.0066.733-0.012-0.0120.0000.0000.0000.000
73A84ALA00.013-0.0128.348-0.070-0.0700.0000.0000.0000.000
74A85SER0-0.005-0.0078.880-0.034-0.0340.0000.0000.0000.000
75A86ASP-1-0.822-0.9136.0440.3350.3350.0000.0000.0000.000
76A87LEU0-0.001-0.0019.541-0.055-0.0550.0000.0000.0000.000
77A88ARG10.8300.92712.109-0.238-0.2380.0000.0000.0000.000
78A89LEU00.0220.03410.870-0.020-0.0200.0000.0000.0000.000
79A90ILE00.0640.02311.175-0.023-0.0230.0000.0000.0000.000
80A91ILE0-0.031-0.00914.126-0.014-0.0140.0000.0000.0000.000
81A92SER0-0.008-0.02616.872-0.010-0.0100.0000.0000.0000.000
82A93ILE00.0010.02414.427-0.008-0.0080.0000.0000.0000.000
83A94SER00.031-0.00417.839-0.001-0.0010.0000.0000.0000.000
84A95LYS10.8840.96119.735-0.082-0.0820.0000.0000.0000.000
85A96SER00.027-0.01720.914-0.008-0.0080.0000.0000.0000.000
86A97VAL00.0250.01021.103-0.005-0.0050.0000.0000.0000.000
87A98ILE0-0.0020.01423.847-0.003-0.0030.0000.0000.0000.000
88A99ASP-1-0.834-0.89926.4410.0300.0300.0000.0000.0000.000
89A100LEU0-0.001-0.01124.254-0.002-0.0020.0000.0000.0000.000
90A101GLU-1-0.813-0.87727.843-0.001-0.0010.0000.0000.0000.000
91A102ARG10.8130.88629.513-0.010-0.0100.0000.0000.0000.000
92A103ILE0-0.028-0.01429.6040.0000.0000.0000.0000.0000.000
93A104GLY00.0660.04332.104-0.001-0.0010.0000.0000.0000.000
94A105ASP-1-0.781-0.90533.6220.0040.0040.0000.0000.0000.000
95A106GLU-1-0.868-0.91435.6890.0100.0100.0000.0000.0000.000
96A107ALA00.0350.01536.4680.0000.0000.0000.0000.0000.000
97A108SER0-0.026-0.03837.5170.0000.0000.0000.0000.0000.000
98A109LYS10.7090.85137.951-0.005-0.0050.0000.0000.0000.000
99A110VAL0-0.012-0.00741.1150.0000.0000.0000.0000.0000.000
100A111ALA00.0370.02041.7230.0000.0000.0000.0000.0000.000
101A112ARG10.9180.95442.6760.0000.0000.0000.0000.0000.000
102A113ARG10.8340.93745.654-0.003-0.0030.0000.0000.0000.000
103A114ALA00.0240.01946.3640.0000.0000.0000.0000.0000.000
104A115ILE00.0110.01546.0770.0000.0000.0000.0000.0000.000
105A116GLN0-0.005-0.00449.5910.0000.0000.0000.0000.0000.000
106A117LEU0-0.028-0.02750.2270.0000.0000.0000.0000.0000.000
107A118CYS0-0.079-0.01651.3160.0000.0000.0000.0000.0000.000
108A119GLU-1-0.987-0.98653.107-0.004-0.0040.0000.0000.0000.000
109A120GLU-1-0.832-0.90255.6230.0010.0010.0000.0000.0000.000
110A121GLY0-0.0090.00756.8820.0000.0000.0000.0000.0000.000
111A122GLU-1-0.912-0.95855.6090.0000.0000.0000.0000.0000.000
112A123SER0-0.003-0.01454.4270.0000.0000.0000.0000.0000.000
113A124PRO0-0.039-0.01756.3140.0000.0000.0000.0000.0000.000
114A125ARG10.7480.83456.149-0.005-0.0050.0000.0000.0000.000
115A126GLY00.0440.02551.9460.0000.0000.0000.0000.0000.000
116A127TYR00.0500.03750.2760.0010.0010.0000.0000.0000.000
117A128VAL0-0.0030.00349.5640.0000.0000.0000.0000.0000.000
118A129GLU-1-0.844-0.93048.6180.0060.0060.0000.0000.0000.000
119A130VAL00.0230.00345.2080.0010.0010.0000.0000.0000.000
120A131ARG10.8280.90844.1510.0020.0020.0000.0000.0000.000
121A132HIS0-0.052-0.02944.243-0.001-0.0010.0000.0000.0000.000
122A133ILE0-0.018-0.01142.0020.0010.0010.0000.0000.0000.000
123A134GLY00.0440.01540.6940.0010.0010.0000.0000.0000.000
124A135SER0-0.031-0.02139.2870.0000.0000.0000.0000.0000.000
125A136GLN0-0.046-0.02938.4200.0020.0020.0000.0000.0000.000
126A137VAL00.004-0.00236.4780.0010.0010.0000.0000.0000.000
127A138GLN0-0.029-0.02634.7840.0010.0010.0000.0000.0000.000
128A139LYS10.7890.87733.577-0.017-0.0170.0000.0000.0000.000
129A140MET0-0.045-0.01032.6270.0010.0010.0000.0000.0000.000
130A141VAL00.0250.01829.5560.0030.0030.0000.0000.0000.000
131A142GLN0-0.024-0.01828.6700.0030.0030.0000.0000.0000.000
132A143GLU-1-0.828-0.89428.0560.0210.0210.0000.0000.0000.000
133A144ALA00.0030.00726.7400.0050.0050.0000.0000.0000.000
134A145LEU0-0.0100.00224.1440.0030.0030.0000.0000.0000.000
135A146ASP-1-0.803-0.88723.2340.0220.0220.0000.0000.0000.000
136A147ALA0-0.020-0.00923.3290.0050.0050.0000.0000.0000.000
137A148PHE0-0.003-0.01116.8040.0130.0130.0000.0000.0000.000
138A149ALA0-0.024-0.01018.9290.0040.0040.0000.0000.0000.000
139A150ARG10.7060.81619.067-0.035-0.0350.0000.0000.0000.000
140A151PHE0-0.038-0.01113.9380.0180.0180.0000.0000.0000.000
141A152ASP-1-0.773-0.85919.4620.0640.0640.0000.0000.0000.000
142A153ALA00.017-0.02122.790-0.005-0.0050.0000.0000.0000.000
143A154ASP-1-0.927-0.95324.3370.0680.0680.0000.0000.0000.000
144A155LEU0-0.025-0.01026.948-0.004-0.0040.0000.0000.0000.000
145A156ALA00.0320.02725.148-0.004-0.0040.0000.0000.0000.000
146A157LEU0-0.028-0.01327.288-0.003-0.0030.0000.0000.0000.000
147A158SER0-0.054-0.03429.702-0.004-0.0040.0000.0000.0000.000
148A159VAL00.0290.01129.874-0.003-0.0030.0000.0000.0000.000
149A160ALA00.016-0.00529.904-0.002-0.0020.0000.0000.0000.000
150A161GLN0-0.086-0.04631.960-0.002-0.0020.0000.0000.0000.000
151A162TYR0-0.041-0.03535.079-0.001-0.0010.0000.0000.0000.000
152A163ASP-1-0.734-0.85434.6290.0250.0250.0000.0000.0000.000
153A164LYS10.9460.96736.708-0.035-0.0350.0000.0000.0000.000
154A165THR0-0.062-0.03639.690-0.001-0.0010.0000.0000.0000.000
155A166VAL00.0630.04038.582-0.001-0.0010.0000.0000.0000.000
156A167ASP-1-0.837-0.89939.9350.0210.0210.0000.0000.0000.000
157A168ARG10.9230.94941.878-0.019-0.0190.0000.0000.0000.000
158A169GLU-1-0.813-0.88044.0350.0130.0130.0000.0000.0000.000
159A170TYR00.0530.04644.131-0.001-0.0010.0000.0000.0000.000
160A171LYS10.7670.86243.116-0.020-0.0200.0000.0000.0000.000
161A172THR0-0.149-0.07848.1100.0000.0000.0000.0000.0000.000
162A173ALA00.0770.03048.841-0.001-0.0010.0000.0000.0000.000
163A174LEU00.0230.00749.097-0.001-0.0010.0000.0000.0000.000
164A175ARG10.8870.94851.406-0.015-0.0150.0000.0000.0000.000
165A176GLU-1-0.799-0.86054.4190.0070.0070.0000.0000.0000.000
166A177LEU00.0040.00551.194-0.001-0.0010.0000.0000.0000.000
167A178VAL00.002-0.01154.0080.0000.0000.0000.0000.0000.000
168A179THR0-0.049-0.05356.5970.0000.0000.0000.0000.0000.000
169A180TYR0-0.006-0.01458.430-0.001-0.0010.0000.0000.0000.000
170A181MET0-0.034-0.01055.097-0.001-0.0010.0000.0000.0000.000
171A182MET0-0.083-0.04060.1770.0000.0000.0000.0000.0000.000
172A183GLU-1-0.857-0.90363.0050.0050.0050.0000.0000.0000.000
173A184ASP-1-0.813-0.90663.2240.0030.0030.0000.0000.0000.000
174A185PRO00.0260.00662.6750.0000.0000.0000.0000.0000.000
175A186ARG10.8620.92462.709-0.003-0.0030.0000.0000.0000.000
176A187ALA00.0220.02459.465-0.001-0.0010.0000.0000.0000.000
177A188ILE0-0.0250.00557.9310.0000.0000.0000.0000.0000.000
178A189SER0-0.048-0.04556.0960.0010.0010.0000.0000.0000.000
179A190ARG10.8960.95054.600-0.001-0.0010.0000.0000.0000.000
180A191VAL00.0230.00353.7700.0000.0000.0000.0000.0000.000
181A192LEU00.000-0.01152.6030.0010.0010.0000.0000.0000.000
182A193ASN0-0.028-0.01850.3080.0010.0010.0000.0000.0000.000
183A194ILE00.0300.02248.9880.0000.0000.0000.0000.0000.000
184A195ILE0-0.024-0.00848.4110.0010.0010.0000.0000.0000.000
185A196TRP0-0.049-0.03646.5170.0010.0010.0000.0000.0000.000
186A197ALA00.0340.02744.5770.0000.0000.0000.0000.0000.000
187A198LEU00.0080.00143.4990.0010.0010.0000.0000.0000.000
188A199ARG10.8330.91640.443-0.016-0.0160.0000.0000.0000.000
189A200SER00.009-0.03140.2370.0010.0010.0000.0000.0000.000
190A201LEU0-0.0050.00038.8220.0000.0000.0000.0000.0000.000
191A202GLU-1-0.783-0.88438.4940.0180.0180.0000.0000.0000.000
192A203ARG10.7090.82434.346-0.016-0.0160.0000.0000.0000.000
193A204ILE00.0140.02133.8030.0010.0010.0000.0000.0000.000
194A205GLY00.0220.01333.5580.0010.0010.0000.0000.0000.000
195A206ASP-1-0.821-0.89233.5740.0280.0280.0000.0000.0000.000
196A207HIS0-0.031-0.02430.4820.0010.0010.0000.0000.0000.000
197A208ALA00.0130.00629.4580.0020.0020.0000.0000.0000.000
198A209ARG10.7150.85629.003-0.029-0.0290.0000.0000.0000.000
199A210ASN0-0.0040.00027.9690.0060.0060.0000.0000.0000.000
200A211ILE00.0120.00323.9150.0060.0060.0000.0000.0000.000
201A212ALA00.0170.01624.2130.0050.0050.0000.0000.0000.000
202A213GLU-1-0.910-0.98325.0410.0550.0550.0000.0000.0000.000
203A214LEU0-0.049-0.02021.4560.0110.0110.0000.0000.0000.000
204A215VAL00.0230.02220.5960.0130.0130.0000.0000.0000.000
205A216ILE0-0.035-0.01120.9650.0140.0140.0000.0000.0000.000
206A217TYR0-0.038-0.01918.2730.0140.0140.0000.0000.0000.000
207A218LEU0-0.016-0.00214.9080.0190.0190.0000.0000.0000.000
208A219VAL00.0070.01016.8960.0280.0280.0000.0000.0000.000
209A220ARG10.9300.95618.640-0.071-0.0710.0000.0000.0000.000
210A221GLY0-0.0140.00018.4670.0050.0050.0000.0000.0000.000
211A222THR0-0.047-0.01819.366-0.007-0.0070.0000.0000.0000.000