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: 176GZ

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 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 201
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2216417.124037
FMO2-HF: Nuclear repulsion 2137473.644069
FMO2-HF: Total energy -78943.479968
FMO2-MP2: Total energy -79171.162579


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.
-1.3161.197-0.019-1.239-1.2550.005
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 : -0.005 / q_NPA : 0.001
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-8SER0-0.028-0.0073.817-0.5371.976-0.019-1.239-1.2550.005
4A-7HIS00.0220.0035.922-0.231-0.2310.0000.0000.0000.000
5A-6PRO00.0830.0398.3700.0850.0850.0000.0000.0000.000
6A-5GLN0-0.043-0.02011.5730.0530.0530.0000.0000.0000.000
7A-4PHE0-0.039-0.02211.2520.0760.0760.0000.0000.0000.000
8A-3GLU-1-0.894-0.92610.233-0.386-0.3860.0000.0000.0000.000
9A-2LYS10.7750.88314.2120.1680.1680.0000.0000.0000.000
10A-1GLY00.0440.03117.1490.0340.0340.0000.0000.0000.000
11A0SER0-0.002-0.01518.879-0.017-0.0170.0000.0000.0000.000
12A1MET0-0.065-0.01920.8380.0030.0030.0000.0000.0000.000
13A2GLU-1-0.829-0.91220.1340.1700.1700.0000.0000.0000.000
14A3LEU0-0.040-0.01124.345-0.004-0.0040.0000.0000.0000.000
15A4SER00.0240.02026.9880.0060.0060.0000.0000.0000.000
16A5TYR0-0.037-0.03226.400-0.009-0.0090.0000.0000.0000.000
17A6ALA0-0.053-0.02029.6610.0090.0090.0000.0000.0000.000
18A7THR0-0.019-0.01331.9410.0030.0030.0000.0000.0000.000
19A8THR00.0020.00130.7590.0010.0010.0000.0000.0000.000
20A9MET0-0.046-0.01133.2100.0000.0000.0000.0000.0000.000
21A10HIS00.0500.02932.855-0.004-0.0040.0000.0000.0000.000
22A11TYR0-0.064-0.05837.548-0.001-0.0010.0000.0000.0000.000
23A12ARG10.8800.94039.772-0.021-0.0210.0000.0000.0000.000
24A13ASP-1-0.876-0.92938.5560.0210.0210.0000.0000.0000.000
25A14VAL0-0.0160.01335.202-0.001-0.0010.0000.0000.0000.000
26A15VAL0-0.029-0.01830.9290.0040.0040.0000.0000.0000.000
27A16PHE00.013-0.00733.023-0.001-0.0010.0000.0000.0000.000
28A17TYR0-0.017-0.01728.2370.0050.0050.0000.0000.0000.000
29A18VAL00.0260.01732.326-0.004-0.0040.0000.0000.0000.000
30A19THR0-0.001-0.00432.9510.0070.0070.0000.0000.0000.000
31A20THR00.0550.00233.156-0.002-0.0020.0000.0000.0000.000
32A21ASP-1-0.877-0.94935.4190.0530.0530.0000.0000.0000.000
33A22ARG10.8030.91537.733-0.062-0.0620.0000.0000.0000.000
34A23ASN00.0050.00038.820-0.006-0.0060.0000.0000.0000.000
35A24ARG10.8980.94734.571-0.037-0.0370.0000.0000.0000.000
36A25ALA00.0220.01635.6600.0060.0060.0000.0000.0000.000
37A26TYR00.005-0.00431.305-0.007-0.0070.0000.0000.0000.000
38A27PHE00.0310.01632.2870.0040.0040.0000.0000.0000.000
39A28VAL00.0270.02027.606-0.003-0.0030.0000.0000.0000.000
40A29CYS0-0.0070.00130.6130.0000.0000.0000.0000.0000.000
41A30GLY00.0850.03930.949-0.003-0.0030.0000.0000.0000.000
42A31GLY00.0000.00626.822-0.007-0.0070.0000.0000.0000.000
43A32CYS0-0.158-0.06626.765-0.001-0.0010.0000.0000.0000.000
44A33VAL00.015-0.00327.5790.0060.0060.0000.0000.0000.000
45A34TYR00.0490.00430.419-0.003-0.0030.0000.0000.0000.000
46A35SER0-0.028-0.02433.8590.0090.0090.0000.0000.0000.000
47A36VAL00.0140.00635.601-0.004-0.0040.0000.0000.0000.000
48A37GLY00.0150.00339.0270.0050.0050.0000.0000.0000.000
49A38ARG10.8140.89540.929-0.042-0.0420.0000.0000.0000.000
50A39PRO0-0.0010.00943.707-0.001-0.0010.0000.0000.0000.000
51A40CYS0-0.004-0.00647.0610.0020.0020.0000.0000.0000.000
52A41ALA00.019-0.00949.417-0.002-0.0020.0000.0000.0000.000
53A42SER0-0.028-0.01752.097-0.001-0.0010.0000.0000.0000.000
54A43GLN00.0020.02151.116-0.002-0.0020.0000.0000.0000.000
55A44PRO0-0.001-0.01347.4680.0020.0020.0000.0000.0000.000
56A45GLY00.0190.01944.1970.0000.0000.0000.0000.0000.000
57A46GLU-1-0.905-0.94040.0790.0250.0250.0000.0000.0000.000
58A47ILE0-0.0020.00139.3610.0030.0030.0000.0000.0000.000
59A48ALA0-0.017-0.00335.916-0.002-0.0020.0000.0000.0000.000
60A49LYS10.7960.89733.7290.0170.0170.0000.0000.0000.000
61A50PHE00.010-0.00928.930-0.001-0.0010.0000.0000.0000.000
62A51GLY00.0310.01026.9240.0020.0020.0000.0000.0000.000
63A52LEU00.0000.01222.617-0.001-0.0010.0000.0000.0000.000
64A53VAL0-0.034-0.01127.0270.0040.0040.0000.0000.0000.000
65A54VAL00.0140.00328.578-0.010-0.0100.0000.0000.0000.000
66A55ARG10.8010.84630.4840.0600.0600.0000.0000.0000.000
67A56GLY00.0380.01831.7350.0030.0030.0000.0000.0000.000
68A57THR0-0.0030.00030.296-0.006-0.0060.0000.0000.0000.000
69A58GLY0-0.0120.00030.204-0.013-0.0130.0000.0000.0000.000
70A59PRO0-0.032-0.02130.0710.0050.0050.0000.0000.0000.000
71A60ASP-1-0.910-0.95431.921-0.066-0.0660.0000.0000.0000.000
72A61ASP-1-0.802-0.88234.439-0.090-0.0900.0000.0000.0000.000
73A62ARG10.8590.90434.2560.0640.0640.0000.0000.0000.000
74A63VAL00.0040.00534.4900.0050.0050.0000.0000.0000.000
75A64VAL00.0290.02930.7450.0020.0020.0000.0000.0000.000
76A65ALA00.000-0.00134.0310.0050.0050.0000.0000.0000.000
77A66ASN0-0.042-0.05035.6330.0080.0080.0000.0000.0000.000
78A67TYR0-0.010-0.00335.2920.0040.0040.0000.0000.0000.000
79A68VAL00.0780.03133.6780.0040.0040.0000.0000.0000.000
80A69ARG10.8680.92536.9810.0500.0500.0000.0000.0000.000
81A70SER0-0.074-0.03640.2130.0040.0040.0000.0000.0000.000
82A71GLU-1-0.790-0.87438.223-0.054-0.0540.0000.0000.0000.000
83A72LEU0-0.009-0.00537.7910.0030.0030.0000.0000.0000.000
84A73ARG10.8840.93541.4260.0430.0430.0000.0000.0000.000
85A74GLN0-0.074-0.03842.8350.0030.0030.0000.0000.0000.000
86A75ARG10.7950.88837.9810.0520.0520.0000.0000.0000.000
87A76GLY0-0.0210.00544.4610.0020.0020.0000.0000.0000.000
88A77LEU0-0.053-0.02241.2550.0030.0030.0000.0000.0000.000
89A86ASP-1-0.918-0.96539.618-0.026-0.0260.0000.0000.0000.000
90A87GLU-1-0.766-0.85433.605-0.048-0.0480.0000.0000.0000.000
91A88VAL0-0.0150.00133.7160.0040.0040.0000.0000.0000.000
92A89PHE00.0150.00030.733-0.005-0.0050.0000.0000.0000.000
93A90LEU00.0610.01625.574-0.002-0.0020.0000.0000.0000.000
94A91ASP-1-0.713-0.82530.246-0.021-0.0210.0000.0000.0000.000
95A92SER0-0.030-0.02432.8240.0010.0010.0000.0000.0000.000
96A93VAL0-0.006-0.00530.291-0.002-0.0020.0000.0000.0000.000
97A94CYS0-0.0500.00331.389-0.002-0.0020.0000.0000.0000.000
98A95LEU0-0.0050.00833.1900.0000.0000.0000.0000.0000.000
99A96LEU0-0.047-0.00834.3560.0000.0000.0000.0000.0000.000
100A97ASN0-0.057-0.03431.8290.0010.0010.0000.0000.0000.000
101A98PRO00.0290.01235.4440.0040.0040.0000.0000.0000.000
102A99ASN0-0.083-0.04534.4870.0060.0060.0000.0000.0000.000
103A100VAL0-0.053-0.01634.3380.0040.0040.0000.0000.0000.000
104A101SER0-0.078-0.04437.674-0.002-0.0020.0000.0000.0000.000
105A102SER0-0.051-0.03739.7890.0020.0020.0000.0000.0000.000
106A103GLU-1-0.792-0.91437.189-0.013-0.0130.0000.0000.0000.000
107A104LEU0-0.012-0.00736.9370.0030.0030.0000.0000.0000.000
108A105ASP-1-0.788-0.87537.384-0.009-0.0090.0000.0000.0000.000
109A106VAL00.0020.00832.4530.0000.0000.0000.0000.0000.000
110A107ILE00.0330.00932.6930.0020.0020.0000.0000.0000.000
111A108ASN0-0.086-0.06830.8250.0040.0040.0000.0000.0000.000
112A109THR0-0.0040.01828.5470.0030.0030.0000.0000.0000.000
113A110ASN0-0.033-0.02823.9390.0020.0020.0000.0000.0000.000
114A111ASP-1-0.860-0.89822.405-0.031-0.0310.0000.0000.0000.000
115A112VAL00.016-0.01025.2640.0060.0060.0000.0000.0000.000
116A113GLU-1-0.851-0.90826.379-0.076-0.0760.0000.0000.0000.000
117A114VAL0-0.029-0.01827.8290.0080.0080.0000.0000.0000.000
118A115LEU00.0200.00129.216-0.010-0.0100.0000.0000.0000.000
119A116ASP-1-0.821-0.87531.821-0.082-0.0820.0000.0000.0000.000
120A117GLU-1-0.798-0.94431.193-0.114-0.1140.0000.0000.0000.000
121A118CYS0-0.0540.00031.423-0.011-0.0110.0000.0000.0000.000
122A119LEU00.012-0.00530.522-0.006-0.0060.0000.0000.0000.000
123A120ALA00.0100.00227.546-0.007-0.0070.0000.0000.0000.000
124A121GLU-1-0.894-0.94927.200-0.160-0.1600.0000.0000.0000.000
125A122TYR0-0.026-0.02728.298-0.012-0.0120.0000.0000.0000.000
126A123CYS0-0.059-0.02625.246-0.002-0.0020.0000.0000.0000.000
127A124THR0-0.033-0.01422.953-0.015-0.0150.0000.0000.0000.000
128A125SER0-0.039-0.02423.929-0.021-0.0210.0000.0000.0000.000
129A126LEU0-0.030-0.01422.529-0.010-0.0100.0000.0000.0000.000
130A127ARG10.9590.98726.7020.1600.1600.0000.0000.0000.000
131A128THR0-0.058-0.02825.577-0.020-0.0200.0000.0000.0000.000
132A129SER00.0250.04827.7390.0080.0080.0000.0000.0000.000
133A130PRO0-0.035-0.02227.518-0.012-0.0120.0000.0000.0000.000
134A131GLY00.0730.02127.8800.0100.0100.0000.0000.0000.000
135A132VAL0-0.062-0.02923.350-0.014-0.0140.0000.0000.0000.000
136A133LEU00.0060.00721.8230.0170.0170.0000.0000.0000.000
137A134ILE0-0.022-0.01722.010-0.022-0.0220.0000.0000.0000.000
138A135SER00.011-0.02819.4370.0140.0140.0000.0000.0000.000
139A136GLY00.0220.00319.784-0.018-0.0180.0000.0000.0000.000
140A137LEU0-0.058-0.01021.3510.0140.0140.0000.0000.0000.000
141A138ARG10.8700.91613.948-0.201-0.2010.0000.0000.0000.000
142A139VAL00.0280.01520.9030.0060.0060.0000.0000.0000.000
143A140ARG10.7280.83517.880-0.200-0.2000.0000.0000.0000.000
144A141ALA00.0190.00221.3390.0020.0020.0000.0000.0000.000
145A142GLN0-0.020-0.01821.137-0.019-0.0190.0000.0000.0000.000
146A143ASP-1-0.838-0.91219.3810.2620.2620.0000.0000.0000.000
147A144ARG10.8320.93622.885-0.157-0.1570.0000.0000.0000.000
148A145ILE00.0120.00722.143-0.010-0.0100.0000.0000.0000.000
149A146ILE0-0.034-0.00923.3090.0050.0050.0000.0000.0000.000
150A147GLU-1-0.733-0.84117.4540.1670.1670.0000.0000.0000.000
151A148LEU0-0.005-0.00421.834-0.013-0.0130.0000.0000.0000.000
152A149PHE00.016-0.01015.5130.0030.0030.0000.0000.0000.000
153A150GLU-1-0.819-0.91520.002-0.110-0.1100.0000.0000.0000.000
154A151HIS0-0.027-0.00915.953-0.068-0.0680.0000.0000.0000.000
155A152PRO0-0.0050.00317.7630.0050.0050.0000.0000.0000.000
156A153THR0-0.001-0.01715.761-0.060-0.0600.0000.0000.0000.000
157A154ILE0-0.0100.00117.7140.0370.0370.0000.0000.0000.000
158A155VAL00.0190.01517.343-0.045-0.0450.0000.0000.0000.000
159A156ASN0-0.0050.00620.0140.0420.0420.0000.0000.0000.000
160A157VAL00.0130.00522.386-0.001-0.0010.0000.0000.0000.000
161A158SER0-0.053-0.01324.8370.0110.0110.0000.0000.0000.000
162A159SER0-0.014-0.02822.693-0.001-0.0010.0000.0000.0000.000
163A160HIS00.000-0.00218.729-0.020-0.0200.0000.0000.0000.000
164A161PHE0-0.031-0.00917.684-0.035-0.0350.0000.0000.0000.000
165A162VAL00.0090.00613.8590.0350.0350.0000.0000.0000.000
166A163TYR00.005-0.00216.834-0.038-0.0380.0000.0000.0000.000
167A164THR0-0.025-0.01916.390-0.008-0.0080.0000.0000.0000.000
168A165PRO0-0.0010.00618.1600.0250.0250.0000.0000.0000.000
169A166SER00.0090.01721.230-0.020-0.0200.0000.0000.0000.000
170A167PRO00.001-0.01722.5440.0170.0170.0000.0000.0000.000
171A168TYR0-0.039-0.02724.4350.0110.0110.0000.0000.0000.000
172A169VAL0-0.0030.03226.5100.0150.0150.0000.0000.0000.000
173A170PHE00.0170.00324.1010.0150.0150.0000.0000.0000.000
174A171ALA0-0.0030.00125.709-0.004-0.0040.0000.0000.0000.000
175A172LEU00.0060.01022.4490.0030.0030.0000.0000.0000.000
176A173ALA0-0.021-0.00526.6390.0000.0000.0000.0000.0000.000
177A174GLN00.016-0.01530.1310.0090.0090.0000.0000.0000.000
178A175ALA0-0.0170.00532.655-0.003-0.0030.0000.0000.0000.000
179A176HIS00.0200.00636.1750.0030.0030.0000.0000.0000.000
180A177LEU0-0.018-0.01737.707-0.004-0.0040.0000.0000.0000.000
181A178PRO0-0.018-0.00841.3300.0030.0030.0000.0000.0000.000
182A179ARG10.8280.87243.6040.0030.0030.0000.0000.0000.000
183A180LEU00.0100.01738.968-0.001-0.0010.0000.0000.0000.000
184A181PRO00.0570.03338.905-0.001-0.0010.0000.0000.0000.000
185A182SER00.0290.00442.2150.0020.0020.0000.0000.0000.000
186A183SER0-0.075-0.04341.5190.0030.0030.0000.0000.0000.000
187A184LEU00.0490.01137.5810.0020.0020.0000.0000.0000.000
188A185GLU-1-0.816-0.86841.6940.0060.0060.0000.0000.0000.000
189A186ALA00.015-0.00244.5240.0030.0030.0000.0000.0000.000
190A187LEU00.0020.01039.1540.0020.0020.0000.0000.0000.000
191A188VAL00.0280.00240.2090.0030.0030.0000.0000.0000.000
192A189SER0-0.037-0.00742.9020.0010.0010.0000.0000.0000.000
193A190GLY00.0470.03546.3520.0010.0010.0000.0000.0000.000
194A191LEU0-0.0220.01139.3450.0020.0020.0000.0000.0000.000
195A192PHE0-0.009-0.04340.1120.0030.0030.0000.0000.0000.000
196A193ASP-1-0.900-0.93344.4800.0280.0280.0000.0000.0000.000
197A194GLY0-0.046-0.01144.8510.0010.0010.0000.0000.0000.000
198A195ILE0-0.046-0.02039.7920.0040.0040.0000.0000.0000.000
199A196PRO00.0260.02042.433-0.002-0.0020.0000.0000.0000.000
200A197ALA00.0250.00543.5390.0010.0010.0000.0000.0000.000
201A198PRO00.0040.03342.6620.0030.0030.0000.0000.0000.000