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: G6YK1

Calculation Name: 4U4H-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4U4H

Chain ID: A

ChEMBL ID:

UniProt ID: P10205

Base Structure: X-ray

Registration Date: 2023-06-22

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 201
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2219039.835959
FMO2-HF: Nuclear repulsion 2140096.165904
FMO2-HF: Total energy -78943.670055
FMO2-MP2: Total energy -79171.390693


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:-10:MET)


Summations of interaction energy for fragment #1(A:-10: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.
-1.2921.114-0.013-1.253-1.140.004
Interaction energy analysis for fragmet #1(A:-10:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.006 / q_NPA : 0.000
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].
3A-8SER0-0.027-0.0213.874-0.2442.162-0.013-1.253-1.1400.004
4A-7HIS00.0330.0096.473-0.336-0.3360.0000.0000.0000.000
5A-6PRO00.0550.0218.7930.1120.1120.0000.0000.0000.000
6A-5GLN0-0.042-0.00611.9400.0500.0500.0000.0000.0000.000
7A-4PHE0-0.032-0.02511.5960.0790.0790.0000.0000.0000.000
8A-3GLU-1-0.890-0.89910.299-0.475-0.4750.0000.0000.0000.000
9A-2LYS10.7730.86714.3460.1750.1750.0000.0000.0000.000
10A-1GLY00.0380.02717.5750.0350.0350.0000.0000.0000.000
11A0SER0-0.004-0.01019.056-0.018-0.0180.0000.0000.0000.000
12A1MET0-0.053-0.02221.1030.0000.0000.0000.0000.0000.000
13A2GLU-1-0.788-0.88720.1130.1420.1420.0000.0000.0000.000
14A3LEU0-0.0120.00324.4600.0010.0010.0000.0000.0000.000
15A4SER0-0.0130.00127.2310.0040.0040.0000.0000.0000.000
16A5TYR0-0.035-0.03126.890-0.008-0.0080.0000.0000.0000.000
17A6ALA0-0.041-0.01929.9410.0080.0080.0000.0000.0000.000
18A7THR0-0.018-0.00832.2320.0020.0020.0000.0000.0000.000
19A8THR0-0.014-0.02031.2010.0010.0010.0000.0000.0000.000
20A9MET0-0.0360.00833.6400.0020.0020.0000.0000.0000.000
21A10HIS00.0520.02233.081-0.004-0.0040.0000.0000.0000.000
22A11TYR0-0.058-0.04637.8110.0000.0000.0000.0000.0000.000
23A12ARG10.8550.92940.072-0.014-0.0140.0000.0000.0000.000
24A13ASP-1-0.870-0.92639.0190.0110.0110.0000.0000.0000.000
25A14VAL0-0.0090.01635.477-0.002-0.0020.0000.0000.0000.000
26A15VAL0-0.026-0.01231.3780.0040.0040.0000.0000.0000.000
27A16PHE00.016-0.00433.519-0.002-0.0020.0000.0000.0000.000
28A17TYR0-0.010-0.01428.6670.0040.0040.0000.0000.0000.000
29A18VAL0-0.006-0.00232.649-0.004-0.0040.0000.0000.0000.000
30A19THR00.030-0.01033.4890.0070.0070.0000.0000.0000.000
31A20THR00.0510.00333.527-0.002-0.0020.0000.0000.0000.000
32A21ASP-1-0.858-0.93535.7760.0450.0450.0000.0000.0000.000
33A22ARG10.7890.90238.120-0.052-0.0520.0000.0000.0000.000
34A23ASN00.0090.00539.300-0.005-0.0050.0000.0000.0000.000
35A24ARG10.8610.91735.369-0.025-0.0250.0000.0000.0000.000
36A25ALA00.0110.01935.7610.0060.0060.0000.0000.0000.000
37A26TYR00.0100.00431.530-0.007-0.0070.0000.0000.0000.000
38A27PHE00.0370.01032.4670.0040.0040.0000.0000.0000.000
39A28VAL00.0110.01527.770-0.003-0.0030.0000.0000.0000.000
40A29CYS0-0.017-0.01230.6030.0010.0010.0000.0000.0000.000
41A30GLY00.0910.04230.586-0.003-0.0030.0000.0000.0000.000
42A31GLY0-0.005-0.00226.718-0.007-0.0070.0000.0000.0000.000
43A32CYS0-0.157-0.07026.954-0.003-0.0030.0000.0000.0000.000
44A33VAL00.0210.00127.7210.0060.0060.0000.0000.0000.000
45A34TYR00.0400.00030.620-0.002-0.0020.0000.0000.0000.000
46A35SER0-0.016-0.02233.8180.0080.0080.0000.0000.0000.000
47A36VAL00.0030.00735.774-0.004-0.0040.0000.0000.0000.000
48A37GLY00.0220.00639.0520.0040.0040.0000.0000.0000.000
49A38ARG10.8210.89641.204-0.034-0.0340.0000.0000.0000.000
50A39PRO0-0.0030.01043.966-0.001-0.0010.0000.0000.0000.000
51A40CYS0-0.012-0.01847.4390.0020.0020.0000.0000.0000.000
52A41ALA00.012-0.00650.015-0.002-0.0020.0000.0000.0000.000
53A42SER0-0.035-0.02152.803-0.001-0.0010.0000.0000.0000.000
54A43GLN00.0080.02351.261-0.002-0.0020.0000.0000.0000.000
55A44PRO00.013-0.00847.5350.0020.0020.0000.0000.0000.000
56A45GLY00.0260.02944.6330.0010.0010.0000.0000.0000.000
57A46GLU-1-0.885-0.92740.2730.0170.0170.0000.0000.0000.000
58A47ILE00.0010.01140.0930.0020.0020.0000.0000.0000.000
59A48ALA0-0.012-0.00536.412-0.002-0.0020.0000.0000.0000.000
60A49LYS10.7980.89933.7680.0280.0280.0000.0000.0000.000
61A50PHE00.012-0.00429.1090.0000.0000.0000.0000.0000.000
62A51GLY00.0340.01426.8590.0010.0010.0000.0000.0000.000
63A52LEU00.0030.00922.671-0.001-0.0010.0000.0000.0000.000
64A53VAL0-0.042-0.01726.9990.0060.0060.0000.0000.0000.000
65A54VAL00.0100.00328.470-0.010-0.0100.0000.0000.0000.000
66A55ARG10.8010.85830.1440.0730.0730.0000.0000.0000.000
67A56GLY0-0.009-0.01331.3990.0050.0050.0000.0000.0000.000
68A57THR0-0.001-0.02030.493-0.007-0.0070.0000.0000.0000.000
69A58GLY0-0.0060.00030.534-0.013-0.0130.0000.0000.0000.000
70A59PRO0-0.026-0.01630.2320.0060.0060.0000.0000.0000.000
71A60ASP-1-0.901-0.94232.246-0.074-0.0740.0000.0000.0000.000
72A61ASP-1-0.808-0.86434.571-0.097-0.0970.0000.0000.0000.000
73A62ARG10.8610.90334.4800.0720.0720.0000.0000.0000.000
74A63VAL00.0030.00534.4260.0050.0050.0000.0000.0000.000
75A64VAL00.0280.02530.7800.0030.0030.0000.0000.0000.000
76A65ALA00.0180.01034.0790.0040.0040.0000.0000.0000.000
77A66ASN0-0.035-0.03735.7520.0080.0080.0000.0000.0000.000
78A67TYR0-0.016-0.01935.2650.0040.0040.0000.0000.0000.000
79A68VAL00.0840.04333.8490.0040.0040.0000.0000.0000.000
80A69ARG10.8630.91037.1980.0560.0560.0000.0000.0000.000
81A70SER0-0.067-0.02740.4670.0040.0040.0000.0000.0000.000
82A71GLU-1-0.804-0.87038.194-0.060-0.0600.0000.0000.0000.000
83A72LEU00.0060.00538.0320.0030.0030.0000.0000.0000.000
84A73ARG10.8360.89941.5050.0490.0490.0000.0000.0000.000
85A74GLN0-0.057-0.03942.7550.0030.0030.0000.0000.0000.000
86A75ARG10.7790.87237.8100.0610.0610.0000.0000.0000.000
87A76GLY0-0.0010.01444.2290.0020.0020.0000.0000.0000.000
88A77LEU0-0.079-0.03541.0780.0020.0020.0000.0000.0000.000
89A86ASP-1-0.868-0.94439.855-0.038-0.0380.0000.0000.0000.000
90A87GLU-1-0.808-0.86233.663-0.059-0.0590.0000.0000.0000.000
91A88VAL0-0.0080.00933.6290.0040.0040.0000.0000.0000.000
92A89PHE00.0340.00630.843-0.006-0.0060.0000.0000.0000.000
93A90LEU00.0380.01525.448-0.002-0.0020.0000.0000.0000.000
94A91ASP-1-0.714-0.82430.152-0.032-0.0320.0000.0000.0000.000
95A92SER0-0.040-0.03132.9460.0020.0020.0000.0000.0000.000
96A93VAL0-0.003-0.00130.166-0.002-0.0020.0000.0000.0000.000
97A94CYS0-0.0530.00631.279-0.002-0.0020.0000.0000.0000.000
98A95LEU0-0.0160.00833.2470.0000.0000.0000.0000.0000.000
99A96LEU0-0.034-0.01034.6990.0010.0010.0000.0000.0000.000
100A97ASN0-0.081-0.05531.6900.0010.0010.0000.0000.0000.000
101A98PRO00.0210.00235.2560.0040.0040.0000.0000.0000.000
102A99ASN0-0.074-0.03033.6610.0070.0070.0000.0000.0000.000
103A100VAL0-0.050-0.01634.4570.0040.0040.0000.0000.0000.000
104A101SER0-0.097-0.05637.750-0.001-0.0010.0000.0000.0000.000
105A102SER0-0.051-0.04239.7550.0020.0020.0000.0000.0000.000
106A103GLU-1-0.781-0.90037.221-0.022-0.0220.0000.0000.0000.000
107A104LEU0-0.009-0.01536.9730.0020.0020.0000.0000.0000.000
108A105ASP-1-0.783-0.85737.518-0.019-0.0190.0000.0000.0000.000
109A106VAL00.0070.00432.570-0.002-0.0020.0000.0000.0000.000
110A107ILE00.0350.01132.7950.0010.0010.0000.0000.0000.000
111A108ASN0-0.067-0.04631.2880.0020.0020.0000.0000.0000.000
112A109THR00.0000.01928.4210.0030.0030.0000.0000.0000.000
113A110ASN0-0.054-0.04123.9460.0070.0070.0000.0000.0000.000
114A111ASP-1-0.849-0.89922.645-0.051-0.0510.0000.0000.0000.000
115A112VAL00.017-0.01225.4660.0070.0070.0000.0000.0000.000
116A113GLU-1-0.829-0.89526.462-0.085-0.0850.0000.0000.0000.000
117A114VAL0-0.026-0.01627.8770.0090.0090.0000.0000.0000.000
118A115LEU00.0170.00829.203-0.011-0.0110.0000.0000.0000.000
119A116ASP-1-0.812-0.86931.778-0.089-0.0890.0000.0000.0000.000
120A117GLU-1-0.794-0.94030.867-0.123-0.1230.0000.0000.0000.000
121A118CYS0-0.0600.00031.129-0.011-0.0110.0000.0000.0000.000
122A119LEU00.009-0.00930.312-0.007-0.0070.0000.0000.0000.000
123A120ALA00.0180.01227.326-0.008-0.0080.0000.0000.0000.000
124A121GLU-1-0.880-0.94826.958-0.172-0.1720.0000.0000.0000.000
125A122TYR0-0.018-0.02728.110-0.011-0.0110.0000.0000.0000.000
126A123CYS0-0.088-0.03225.196-0.004-0.0040.0000.0000.0000.000
127A124THR00.0160.00222.692-0.014-0.0140.0000.0000.0000.000
128A125SER0-0.059-0.02823.669-0.022-0.0220.0000.0000.0000.000
129A126LEU0-0.006-0.00422.330-0.007-0.0070.0000.0000.0000.000
130A127ARG10.9240.98726.4560.1630.1630.0000.0000.0000.000
131A128THR0-0.041-0.02825.345-0.020-0.0200.0000.0000.0000.000
132A129SER00.0290.04327.5160.0080.0080.0000.0000.0000.000
133A130PRO0-0.034-0.01527.633-0.013-0.0130.0000.0000.0000.000
134A131GLY00.0690.01628.0250.0110.0110.0000.0000.0000.000
135A132VAL0-0.064-0.02923.225-0.015-0.0150.0000.0000.0000.000
136A133LEU00.0150.02021.6920.0170.0170.0000.0000.0000.000
137A134ILE0-0.021-0.01222.193-0.026-0.0260.0000.0000.0000.000
138A135SER00.019-0.02219.5550.0150.0150.0000.0000.0000.000
139A136GLY00.013-0.00319.865-0.021-0.0210.0000.0000.0000.000
140A137LEU0-0.048-0.01021.5720.0120.0120.0000.0000.0000.000
141A138ARG10.8640.90114.424-0.149-0.1490.0000.0000.0000.000
142A139VAL00.0300.01621.2760.0090.0090.0000.0000.0000.000
143A140ARG10.7130.83017.727-0.152-0.1520.0000.0000.0000.000
144A141ALA00.0190.00421.5190.0020.0020.0000.0000.0000.000
145A142GLN0-0.021-0.01521.483-0.015-0.0150.0000.0000.0000.000
146A143ASP-1-0.818-0.90520.1240.2050.2050.0000.0000.0000.000
147A144ARG10.8090.92323.413-0.138-0.1380.0000.0000.0000.000
148A145ILE00.0100.00422.521-0.009-0.0090.0000.0000.0000.000
149A146ILE0-0.028-0.00823.8680.0030.0030.0000.0000.0000.000
150A147GLU-1-0.752-0.83417.5200.1150.1150.0000.0000.0000.000
151A148LEU00.0020.00322.131-0.014-0.0140.0000.0000.0000.000
152A149PHE00.014-0.00115.7140.0040.0040.0000.0000.0000.000
153A150GLU-1-0.818-0.90420.436-0.126-0.1260.0000.0000.0000.000
154A151HIS0-0.040-0.02215.989-0.069-0.0690.0000.0000.0000.000
155A152PRO00.0050.00218.0810.0060.0060.0000.0000.0000.000
156A153THR00.014-0.00115.654-0.064-0.0640.0000.0000.0000.000
157A154ILE0-0.013-0.00617.6210.0400.0400.0000.0000.0000.000
158A155VAL00.0060.00317.355-0.047-0.0470.0000.0000.0000.000
159A156ASN00.0100.00619.9890.0430.0430.0000.0000.0000.000
160A157VAL00.0120.00522.517-0.001-0.0010.0000.0000.0000.000
161A158SER0-0.031-0.01324.9420.0170.0170.0000.0000.0000.000
162A159SER0-0.057-0.03622.8680.0010.0010.0000.0000.0000.000
163A160HIS00.001-0.00518.802-0.025-0.0250.0000.0000.0000.000
164A161PHE0-0.020-0.00117.682-0.037-0.0370.0000.0000.0000.000
165A162VAL0-0.0040.00213.8610.0360.0360.0000.0000.0000.000
166A163TYR00.004-0.00216.804-0.036-0.0360.0000.0000.0000.000
167A164THR0-0.013-0.01316.214-0.013-0.0130.0000.0000.0000.000
168A165PRO0-0.0030.00118.1150.0270.0270.0000.0000.0000.000
169A166SER0-0.008-0.00921.164-0.024-0.0240.0000.0000.0000.000
170A167PRO00.013-0.00822.8930.0170.0170.0000.0000.0000.000
171A168TYR0-0.032-0.01124.8130.0110.0110.0000.0000.0000.000
172A169VAL0-0.0100.01526.7140.0160.0160.0000.0000.0000.000
173A170PHE00.0120.00524.2070.0150.0150.0000.0000.0000.000
174A171ALA00.0040.00125.588-0.005-0.0050.0000.0000.0000.000
175A172LEU00.0060.01022.8150.0040.0040.0000.0000.0000.000
176A173ALA0-0.020-0.00726.8850.0000.0000.0000.0000.0000.000
177A174GLN00.013-0.01430.1960.0080.0080.0000.0000.0000.000
178A175ALA0-0.0150.00332.796-0.002-0.0020.0000.0000.0000.000
179A176HIS00.0200.00336.3710.0020.0020.0000.0000.0000.000
180A177LEU0-0.015-0.01238.233-0.004-0.0040.0000.0000.0000.000
181A178PRO0-0.022-0.01041.8370.0030.0030.0000.0000.0000.000
182A179ARG10.8270.87444.0860.0100.0100.0000.0000.0000.000
183A180LEU00.0170.01539.166-0.001-0.0010.0000.0000.0000.000
184A181PRO00.0500.03139.0940.0000.0000.0000.0000.0000.000
185A182SER00.0210.00142.4030.0020.0020.0000.0000.0000.000
186A183SER0-0.075-0.05041.4630.0030.0030.0000.0000.0000.000
187A184LEU00.0490.01437.8940.0020.0020.0000.0000.0000.000
188A185GLU-1-0.799-0.86541.830-0.002-0.0020.0000.0000.0000.000
189A186ALA00.0150.01444.8160.0030.0030.0000.0000.0000.000
190A187LEU00.0010.00639.7740.0020.0020.0000.0000.0000.000
191A188VAL00.0370.00740.2890.0030.0030.0000.0000.0000.000
192A189SER0-0.059-0.03142.8990.0020.0020.0000.0000.0000.000
193A190GLY00.0630.04146.6930.0000.0000.0000.0000.0000.000
194A191LEU0-0.0410.00339.3010.0020.0020.0000.0000.0000.000
195A192PHE0-0.007-0.04040.1720.0030.0030.0000.0000.0000.000
196A193ASP-1-0.909-0.93944.5560.0210.0210.0000.0000.0000.000
197A194GLY0-0.038-0.00845.2300.0010.0010.0000.0000.0000.000
198A195ILE0-0.022-0.00939.9890.0040.0040.0000.0000.0000.000
199A196PRO00.0020.01142.495-0.002-0.0020.0000.0000.0000.000
200A197ALA00.0490.01743.6640.0010.0010.0000.0000.0000.000
201A198PRO0-0.0270.01943.3240.0030.0030.0000.0000.0000.000