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: YNNR2

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 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 211
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2452492.437
FMO2-HF: Nuclear repulsion 2368560.615305
FMO2-HF: Total energy -83931.821695
FMO2-MP2: Total energy -84176.10946


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.
-5.2761.723.204-4.887-5.3150.007
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 : 0.070 / q_NPA : 0.024
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].
3A14GLN0-0.006-0.0283.375-3.4791.5430.012-2.594-2.4410.015
4A15PHE00.004-0.0062.246-0.6750.4093.155-1.935-2.304-0.005
5A16ASN00.033-0.0223.404-0.5370.3530.037-0.358-0.570-0.003
6A17ALA00.0020.0316.1410.2010.2010.0000.0000.0000.000
7A18GLU-1-0.762-0.8546.622-0.337-0.3370.0000.0000.0000.000
8A19LEU0-0.010-0.0077.4740.1310.1310.0000.0000.0000.000
9A20GLU-1-0.798-0.8629.6400.0640.0640.0000.0000.0000.000
10A21ASP-1-0.924-0.96211.823-0.301-0.3010.0000.0000.0000.000
11A22VAL00.0140.01412.0640.0380.0380.0000.0000.0000.000
12A23ARG10.7360.84013.9490.0090.0090.0000.0000.0000.000
13A24SER0-0.051-0.03115.8410.0150.0150.0000.0000.0000.000
14A25HIS0-0.040-0.03716.4410.0060.0060.0000.0000.0000.000
15A26LEU00.0340.02818.5280.0070.0070.0000.0000.0000.000
16A27LEU0-0.025-0.00519.4820.0040.0040.0000.0000.0000.000
17A28ALA0-0.006-0.00321.7410.0040.0040.0000.0000.0000.000
18A29MET0-0.045-0.01423.0500.0030.0030.0000.0000.0000.000
19A30GLY00.032-0.00424.4550.0030.0030.0000.0000.0000.000
20A31GLY00.0170.01026.1620.0030.0030.0000.0000.0000.000
21A32LEU0-0.052-0.03127.7600.0010.0010.0000.0000.0000.000
22A33VAL00.0350.01128.5090.0010.0010.0000.0000.0000.000
23A34GLU-1-0.866-0.92930.4250.0040.0040.0000.0000.0000.000
24A35LYS10.8580.91432.2210.0180.0180.0000.0000.0000.000
25A36GLN0-0.009-0.01933.6550.0010.0010.0000.0000.0000.000
26A37VAL0-0.013-0.00434.4740.0010.0010.0000.0000.0000.000
27A38ASN0-0.044-0.02636.5140.0020.0020.0000.0000.0000.000
28A39ASP-1-0.840-0.90838.182-0.011-0.0110.0000.0000.0000.000
29A40ALA00.0080.01539.4650.0000.0000.0000.0000.0000.000
30A41VAL0-0.006-0.00840.7630.0010.0010.0000.0000.0000.000
31A42ASN00.0030.00541.7690.0020.0020.0000.0000.0000.000
32A43ALA00.0190.02743.8880.0000.0000.0000.0000.0000.000
33A44LEU0-0.022-0.02045.4970.0000.0000.0000.0000.0000.000
34A45ILE0-0.118-0.06446.8650.0000.0000.0000.0000.0000.000
35A46ASP-1-0.915-0.95747.581-0.002-0.0020.0000.0000.0000.000
36A47ALA0-0.032-0.01350.112-0.001-0.0010.0000.0000.0000.000
37A48ASP-1-0.851-0.92047.465-0.009-0.0090.0000.0000.0000.000
38A49SER00.019-0.02847.2660.0000.0000.0000.0000.0000.000
39A50GLY0-0.0130.00546.8940.0000.0000.0000.0000.0000.000
40A51LEU0-0.034-0.01141.507-0.001-0.0010.0000.0000.0000.000
41A52ALA00.007-0.00642.4680.0000.0000.0000.0000.0000.000
42A53GLN0-0.065-0.06042.4280.0020.0020.0000.0000.0000.000
43A54GLN0-0.012-0.00139.035-0.002-0.0020.0000.0000.0000.000
44A55VAL00.0270.01437.936-0.001-0.0010.0000.0000.0000.000
45A56ARG10.8680.92837.4170.0050.0050.0000.0000.0000.000
46A57GLU-1-0.871-0.91137.653-0.016-0.0160.0000.0000.0000.000
47A58ILE0-0.026-0.00732.715-0.003-0.0030.0000.0000.0000.000
48A59ASP-1-0.786-0.90432.785-0.003-0.0030.0000.0000.0000.000
49A60ASP-1-0.922-0.95232.405-0.012-0.0120.0000.0000.0000.000
50A61GLN0-0.072-0.03528.0810.0000.0000.0000.0000.0000.000
51A62ILE00.0150.00728.153-0.004-0.0040.0000.0000.0000.000
52A63ASN0-0.021-0.02527.4250.0000.0000.0000.0000.0000.000
53A64GLN0-0.053-0.02525.0720.0060.0060.0000.0000.0000.000
54A65MET0-0.048-0.02823.770-0.005-0.0050.0000.0000.0000.000
55A66GLU-1-0.837-0.92122.6410.0070.0070.0000.0000.0000.000
56A67ARG10.9180.96522.4650.0120.0120.0000.0000.0000.000
57A68ASN0-0.032-0.01620.6810.0060.0060.0000.0000.0000.000
58A69ILE00.0180.01217.708-0.009-0.0090.0000.0000.0000.000
59A70ASP-1-0.856-0.92417.4730.0430.0430.0000.0000.0000.000
60A71GLU-1-0.958-0.98617.8100.0210.0210.0000.0000.0000.000
61A72GLU-1-0.859-0.91113.549-0.133-0.1330.0000.0000.0000.000
62A73CYS0-0.022-0.02013.1160.0060.0060.0000.0000.0000.000
63A74VAL00.0020.00713.5360.0500.0500.0000.0000.0000.000
64A75ARG10.8330.91012.2830.1590.1590.0000.0000.0000.000
65A76ILE0-0.017-0.0107.8480.0730.0730.0000.0000.0000.000
66A77LEU0-0.023-0.0138.7780.1490.1490.0000.0000.0000.000
67A78ALA0-0.0270.00810.8920.0830.0830.0000.0000.0000.000
68A79ARG10.7350.8426.5230.2350.2350.0000.0000.0000.000
69A80ARG10.9140.9585.462-1.269-1.2690.0000.0000.0000.000
70A81GLN00.0060.0038.357-0.052-0.0520.0000.0000.0000.000
71A82PRO00.0440.0337.1580.1830.1830.0000.0000.0000.000
72A83ALA00.0060.0027.549-0.058-0.0580.0000.0000.0000.000
73A84ALA00.042-0.0039.111-0.058-0.0580.0000.0000.0000.000
74A85SER00.002-0.0049.875-0.034-0.0340.0000.0000.0000.000
75A86ASP-1-0.846-0.9306.7070.4720.4720.0000.0000.0000.000
76A87LEU0-0.028-0.00210.139-0.053-0.0530.0000.0000.0000.000
77A88ARG10.8280.92112.608-0.270-0.2700.0000.0000.0000.000
78A89LEU00.0140.02511.108-0.028-0.0280.0000.0000.0000.000
79A90ILE00.0780.03210.881-0.029-0.0290.0000.0000.0000.000
80A91ILE0-0.032-0.01214.293-0.024-0.0240.0000.0000.0000.000
81A92SER0-0.022-0.03217.144-0.016-0.0160.0000.0000.0000.000
82A93ILE00.0130.02514.516-0.012-0.0120.0000.0000.0000.000
83A94SER00.0150.00518.067-0.008-0.0080.0000.0000.0000.000
84A95LYS10.9110.95419.810-0.110-0.1100.0000.0000.0000.000
85A96SER00.020-0.00420.911-0.009-0.0090.0000.0000.0000.000
86A97VAL00.0400.01021.049-0.007-0.0070.0000.0000.0000.000
87A98ILE00.0070.01723.782-0.005-0.0050.0000.0000.0000.000
88A99ASP-1-0.823-0.89426.4750.0420.0420.0000.0000.0000.000
89A100LEU0-0.007-0.00924.228-0.003-0.0030.0000.0000.0000.000
90A101GLU-1-0.781-0.85827.7310.0090.0090.0000.0000.0000.000
91A102ARG10.8220.89029.397-0.023-0.0230.0000.0000.0000.000
92A103ILE0-0.028-0.01329.740-0.001-0.0010.0000.0000.0000.000
93A104GLY00.0530.02731.831-0.002-0.0020.0000.0000.0000.000
94A105ASP-1-0.764-0.86533.2890.0100.0100.0000.0000.0000.000
95A106GLU-1-0.901-0.94935.5320.0150.0150.0000.0000.0000.000
96A107ALA00.0010.00636.234-0.001-0.0010.0000.0000.0000.000
97A108SER0-0.0070.00337.341-0.002-0.0020.0000.0000.0000.000
98A109LYS10.7380.83538.137-0.012-0.0120.0000.0000.0000.000
99A110VAL0-0.0110.00341.1940.0000.0000.0000.0000.0000.000
100A111ALA00.0430.02741.705-0.001-0.0010.0000.0000.0000.000
101A112ARG10.9100.94743.053-0.004-0.0040.0000.0000.0000.000
102A113ARG10.8300.94145.573-0.007-0.0070.0000.0000.0000.000
103A114ALA00.0300.01646.2740.0000.0000.0000.0000.0000.000
104A115ILE0-0.0050.00345.9440.0000.0000.0000.0000.0000.000
105A116GLN0-0.040-0.02049.5430.0000.0000.0000.0000.0000.000
106A117LEU00.004-0.01450.2160.0000.0000.0000.0000.0000.000
107A118CYS0-0.0590.00451.9520.0000.0000.0000.0000.0000.000
108A119GLU-1-0.996-0.98753.539-0.002-0.0020.0000.0000.0000.000
109A120GLU-1-0.860-0.91055.4400.0040.0040.0000.0000.0000.000
110A121GLY0-0.0250.00257.0310.0000.0000.0000.0000.0000.000
111A122GLU-1-0.925-0.96055.8300.0020.0020.0000.0000.0000.000
112A123SER0-0.021-0.03554.8560.0000.0000.0000.0000.0000.000
113A124PRO0-0.026-0.00456.7610.0000.0000.0000.0000.0000.000
114A125ARG10.8160.88756.157-0.008-0.0080.0000.0000.0000.000
115A126GLY00.0810.04052.6120.0000.0000.0000.0000.0000.000
116A127TYR00.0660.04650.6530.0010.0010.0000.0000.0000.000
117A128VAL0-0.031-0.00649.5870.0000.0000.0000.0000.0000.000
118A129GLU-1-0.837-0.93948.7760.0100.0100.0000.0000.0000.000
119A130VAL00.0110.00445.4910.0010.0010.0000.0000.0000.000
120A131ARG10.8990.94443.936-0.002-0.0020.0000.0000.0000.000
121A132HIS0-0.043-0.02844.179-0.001-0.0010.0000.0000.0000.000
122A133ILE00.0090.00741.9630.0010.0010.0000.0000.0000.000
123A134GLY00.0280.01240.7310.0010.0010.0000.0000.0000.000
124A135SER0-0.046-0.03339.3380.0000.0000.0000.0000.0000.000
125A136GLN0-0.056-0.03938.5460.0020.0020.0000.0000.0000.000
126A137VAL00.0120.00436.2580.0020.0020.0000.0000.0000.000
127A138GLN00.0150.01234.8560.0010.0010.0000.0000.0000.000
128A139LYS10.8200.89833.691-0.022-0.0220.0000.0000.0000.000
129A140MET0-0.032-0.00932.6450.0010.0010.0000.0000.0000.000
130A141VAL00.0180.01429.5880.0030.0030.0000.0000.0000.000
131A142GLN0-0.022-0.01828.8380.0030.0030.0000.0000.0000.000
132A143GLU-1-0.860-0.90428.1380.0280.0280.0000.0000.0000.000
133A144ALA00.0210.01426.9000.0050.0050.0000.0000.0000.000
134A145LEU0-0.0150.00424.1960.0050.0050.0000.0000.0000.000
135A146ASP-1-0.814-0.89823.3740.0310.0310.0000.0000.0000.000
136A147ALA0-0.040-0.02223.5430.0050.0050.0000.0000.0000.000
137A148PHE00.008-0.01916.7930.0130.0130.0000.0000.0000.000
138A149ALA0-0.040-0.01619.0970.0070.0070.0000.0000.0000.000
139A150ARG10.7070.82019.229-0.045-0.0450.0000.0000.0000.000
140A151PHE0-0.038-0.01414.1300.0160.0160.0000.0000.0000.000
141A152ASP-1-0.760-0.85119.5630.0730.0730.0000.0000.0000.000
142A153ALA0-0.020-0.04123.007-0.006-0.0060.0000.0000.0000.000
143A154ASP-1-0.933-0.95624.6150.0770.0770.0000.0000.0000.000
144A155LEU0-0.011-0.00527.018-0.004-0.0040.0000.0000.0000.000
145A156ALA00.0220.02025.364-0.004-0.0040.0000.0000.0000.000
146A157LEU0-0.024-0.00727.534-0.002-0.0020.0000.0000.0000.000
147A158SER0-0.048-0.03129.960-0.004-0.0040.0000.0000.0000.000
148A159VAL00.0490.02329.825-0.003-0.0030.0000.0000.0000.000
149A160ALA00.0200.00130.416-0.003-0.0030.0000.0000.0000.000
150A161GLN0-0.083-0.05132.393-0.003-0.0030.0000.0000.0000.000
151A162TYR0-0.052-0.04135.224-0.002-0.0020.0000.0000.0000.000
152A163ASP-1-0.740-0.85635.0870.0330.0330.0000.0000.0000.000
153A164LYS10.9320.96837.171-0.042-0.0420.0000.0000.0000.000
154A165THR0-0.051-0.02940.027-0.001-0.0010.0000.0000.0000.000
155A166VAL00.0730.04638.814-0.002-0.0020.0000.0000.0000.000
156A167ASP-1-0.796-0.89440.4400.0270.0270.0000.0000.0000.000
157A168ARG10.8310.91342.488-0.024-0.0240.0000.0000.0000.000
158A169GLU-1-0.790-0.87844.2510.0170.0170.0000.0000.0000.000
159A170TYR00.0470.03444.232-0.001-0.0010.0000.0000.0000.000
160A171LYS10.8210.90643.247-0.027-0.0270.0000.0000.0000.000
161A172THR0-0.080-0.04448.6550.0000.0000.0000.0000.0000.000
162A173ALA00.0340.02349.046-0.001-0.0010.0000.0000.0000.000
163A174LEU00.0300.01949.499-0.001-0.0010.0000.0000.0000.000
164A175ARG10.8920.95351.626-0.019-0.0190.0000.0000.0000.000
165A176GLU-1-0.795-0.86954.3790.0100.0100.0000.0000.0000.000
166A177LEU00.008-0.00151.579-0.001-0.0010.0000.0000.0000.000
167A178VAL00.002-0.01154.365-0.001-0.0010.0000.0000.0000.000
168A179THR0-0.060-0.04956.931-0.001-0.0010.0000.0000.0000.000
169A180TYR0-0.002-0.00858.715-0.001-0.0010.0000.0000.0000.000
170A181MET0-0.018-0.00255.471-0.001-0.0010.0000.0000.0000.000
171A182MET0-0.103-0.05060.4300.0000.0000.0000.0000.0000.000
172A183GLU-1-0.942-0.95463.2340.0080.0080.0000.0000.0000.000
173A184ASP-1-0.855-0.93363.4030.0050.0050.0000.0000.0000.000
174A185PRO00.0330.00563.0050.0000.0000.0000.0000.0000.000
175A186ARG10.8790.93862.971-0.005-0.0050.0000.0000.0000.000
176A187ALA00.0030.00660.1020.0000.0000.0000.0000.0000.000
177A188ILE0-0.0120.00858.0820.0000.0000.0000.0000.0000.000
178A189SER0-0.034-0.03456.5750.0010.0010.0000.0000.0000.000
179A190ARG10.9080.96355.023-0.004-0.0040.0000.0000.0000.000
180A191VAL00.007-0.01454.1270.0000.0000.0000.0000.0000.000
181A192LEU0-0.007-0.01352.8840.0010.0010.0000.0000.0000.000
182A193ASN00.001-0.00850.3690.0010.0010.0000.0000.0000.000
183A194ILE00.0440.02749.0350.0000.0000.0000.0000.0000.000
184A195ILE0-0.022-0.00448.4250.0010.0010.0000.0000.0000.000
185A196TRP0-0.050-0.03546.6250.0020.0020.0000.0000.0000.000
186A197ALA00.0330.02244.6280.0010.0010.0000.0000.0000.000
187A198LEU0-0.005-0.00543.6200.0010.0010.0000.0000.0000.000
188A199ARG10.8360.91340.883-0.022-0.0220.0000.0000.0000.000
189A200SER00.013-0.03240.4040.0010.0010.0000.0000.0000.000
190A201LEU0-0.020-0.01139.0710.0010.0010.0000.0000.0000.000
191A202GLU-1-0.802-0.89938.7300.0240.0240.0000.0000.0000.000
192A203ARG10.7330.87134.786-0.025-0.0250.0000.0000.0000.000
193A204ILE00.0050.00534.0810.0020.0020.0000.0000.0000.000
194A205GLY00.0190.01433.7800.0010.0010.0000.0000.0000.000
195A206ASP-1-0.773-0.87034.0270.0340.0340.0000.0000.0000.000
196A207HIS0-0.055-0.05130.5890.0020.0020.0000.0000.0000.000
197A208ALA00.0130.01629.4650.0030.0030.0000.0000.0000.000
198A209ARG10.7520.86129.135-0.037-0.0370.0000.0000.0000.000
199A210ASN0-0.029-0.01728.3110.0060.0060.0000.0000.0000.000
200A211ILE00.0170.00123.9430.0080.0080.0000.0000.0000.000
201A212ALA0-0.0050.00724.4380.0060.0060.0000.0000.0000.000
202A213GLU-1-0.909-0.97325.3200.0680.0680.0000.0000.0000.000
203A214LEU0-0.047-0.02121.7580.0130.0130.0000.0000.0000.000
204A215VAL00.0340.02820.8410.0160.0160.0000.0000.0000.000
205A216ILE0-0.011-0.00321.2560.0130.0130.0000.0000.0000.000
206A217TYR0-0.050-0.03118.6880.0160.0160.0000.0000.0000.000
207A218LEU0-0.0100.00715.5190.0200.0200.0000.0000.0000.000
208A219VAL00.0070.01417.3720.0300.0300.0000.0000.0000.000
209A220ARG10.9200.95619.196-0.086-0.0860.0000.0000.0000.000
210A221GLY0-0.0350.00018.8390.0070.0070.0000.0000.0000.000
211A222THR0-0.024-0.01519.799-0.002-0.0020.0000.0000.0000.000