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

tag_button

FMODB ID: MN4NZ

Calculation Name: 4XVW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4XVW

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-09-23

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 222
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2502175.634135
FMO2-HF: Nuclear repulsion 2416326.983722
FMO2-HF: Total energy -85848.650413
FMO2-MP2: Total energy -86100.058685


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:ALA)


Summations of interaction energy for fragment #1(A:3:ALA)
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.
1.773-1.3596.8170.088-3.772-0.018
Interaction energy analysis for fragmet #1(A:3:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.018 / q_NPA : -0.022
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].
3A5LEU00.0250.0131.9093.972-0.4015.9520.857-2.435-0.007
4A6ASN00.0330.0192.597-2.714-1.6300.867-0.763-1.187-0.011
5A7ALA00.0910.0255.1990.2460.289-0.001-0.001-0.0410.000
6A8ALA0-0.042-0.0167.0580.1160.1160.0000.0000.0000.000
7A9GLN00.0910.0387.178-0.055-0.0550.0000.0000.0000.000
8A10GLU-1-0.822-0.8894.935-0.460-0.346-0.001-0.005-0.1090.000
9A11LYS10.9070.9537.6980.1450.1450.0000.0000.0000.000
10A12GLU-1-0.932-0.95911.1390.0950.0950.0000.0000.0000.000
11A13VAL00.0210.0088.7980.0130.0130.0000.0000.0000.000
12A14ARG10.7990.8717.9560.1440.1440.0000.0000.0000.000
13A15ALA0-0.0110.01012.766-0.012-0.0120.0000.0000.0000.000
14A16LEU00.0360.00913.5290.0040.0040.0000.0000.0000.000
15A17VAL0-0.0070.01514.6040.0030.0030.0000.0000.0000.000
16A18ARG10.8420.90416.747-0.054-0.0540.0000.0000.0000.000
17A19ASP-1-0.802-0.89819.4640.0550.0550.0000.0000.0000.000
18A20THR0-0.0170.00718.5210.0020.0020.0000.0000.0000.000
19A21LEU00.000-0.00120.199-0.006-0.0060.0000.0000.0000.000
20A22VAL0-0.067-0.03023.044-0.010-0.0100.0000.0000.0000.000
21A23SER0-0.082-0.05823.656-0.004-0.0040.0000.0000.0000.000
22A24ASN0-0.038-0.04625.1120.0010.0010.0000.0000.0000.000
23A25PRO00.0300.01225.7130.0080.0080.0000.0000.0000.000
24A26GLU-1-0.852-0.90327.8310.0900.0900.0000.0000.0000.000
25A27ILE00.0390.02222.1140.0040.0040.0000.0000.0000.000
26A28LEU0-0.054-0.02124.1140.0070.0070.0000.0000.0000.000
27A29GLU-1-0.938-0.97625.9030.0770.0770.0000.0000.0000.000
28A30GLU-1-0.914-0.94925.9280.1480.1480.0000.0000.0000.000
29A31ALA0-0.006-0.00923.5250.0030.0030.0000.0000.0000.000
30A32ILE0-0.040-0.01825.305-0.002-0.0020.0000.0000.0000.000
31A33MET0-0.004-0.00428.141-0.003-0.0030.0000.0000.0000.000
32A34ALA00.0440.04026.033-0.002-0.0020.0000.0000.0000.000
33A35LEU0-0.032-0.01524.130-0.001-0.0010.0000.0000.0000.000
34A36GLN0-0.014-0.02327.233-0.006-0.0060.0000.0000.0000.000
35A37THR0-0.0120.00129.921-0.007-0.0070.0000.0000.0000.000
36A38LYS10.8850.93623.344-0.144-0.1440.0000.0000.0000.000
37A39LYS10.8130.90028.764-0.079-0.0790.0000.0000.0000.000
38A40ALA00.0400.02330.916-0.005-0.0050.0000.0000.0000.000
39A41ASP-1-0.858-0.93530.3280.1050.1050.0000.0000.0000.000
40A42GLU-1-0.796-0.88527.0920.1070.1070.0000.0000.0000.000
41A43GLN0-0.065-0.03031.866-0.002-0.0020.0000.0000.0000.000
42A44GLN0-0.075-0.03935.104-0.008-0.0080.0000.0000.0000.000
43A45ALA00.0050.02032.9850.0010.0010.0000.0000.0000.000
44A46GLN0-0.016-0.01435.083-0.007-0.0070.0000.0000.0000.000
45A47PHE00.0690.03436.4230.0020.0020.0000.0000.0000.000
46A48ARG10.8770.90636.387-0.047-0.0470.0000.0000.0000.000
47A49GLN00.0090.00933.3020.0010.0010.0000.0000.0000.000
48A50ALA00.0270.04232.0720.0050.0050.0000.0000.0000.000
49A51LEU0-0.043-0.01831.9260.0020.0020.0000.0000.0000.000
50A52ALA0-0.023-0.01433.249-0.001-0.0010.0000.0000.0000.000
51A53SER0-0.061-0.04628.9900.0030.0030.0000.0000.0000.000
52A54GLU-1-0.838-0.92826.4580.1180.1180.0000.0000.0000.000
53A55HIS0-0.026-0.02028.834-0.011-0.0110.0000.0000.0000.000
54A56ASP-1-0.843-0.91625.4180.0790.0790.0000.0000.0000.000
55A57ALA0-0.002-0.00124.931-0.006-0.0060.0000.0000.0000.000
56A58LEU0-0.060-0.03126.048-0.008-0.0080.0000.0000.0000.000
57A59TYR0-0.047-0.04529.409-0.007-0.0070.0000.0000.0000.000
58A60ASN0-0.051-0.03026.107-0.007-0.0070.0000.0000.0000.000
59A61ASP-1-0.752-0.85623.1430.0490.0490.0000.0000.0000.000
60A62ALA00.0050.00222.391-0.008-0.0080.0000.0000.0000.000
61A63ALA0-0.077-0.03221.315-0.012-0.0120.0000.0000.0000.000
62A64SER0-0.015-0.03123.408-0.003-0.0030.0000.0000.0000.000
63A65PRO0-0.015-0.01027.045-0.001-0.0010.0000.0000.0000.000
64A66ARG10.8720.94129.870-0.012-0.0120.0000.0000.0000.000
65A67ILE00.0170.02732.888-0.004-0.0040.0000.0000.0000.000
66A68GLY00.1010.04336.5560.0030.0030.0000.0000.0000.000
67A69ALA0-0.0080.00636.687-0.002-0.0020.0000.0000.0000.000
68A70LYS10.9560.96131.8270.0140.0140.0000.0000.0000.000
69A71ASP-1-0.854-0.92333.8940.0160.0160.0000.0000.0000.000
70A72ALA00.0140.02836.311-0.002-0.0020.0000.0000.0000.000
71A73LYS10.8010.89337.446-0.010-0.0100.0000.0000.0000.000
72A74LEU0-0.0040.01439.6390.0030.0030.0000.0000.0000.000
73A75VAL00.0140.00434.019-0.003-0.0030.0000.0000.0000.000
74A76LEU00.0020.01137.3600.0030.0030.0000.0000.0000.000
75A77VAL00.0190.01032.001-0.001-0.0010.0000.0000.0000.000
76A78SER0-0.005-0.00435.0470.0010.0010.0000.0000.0000.000
77A79PHE00.0210.01730.610-0.002-0.0020.0000.0000.0000.000
78A80THR0-0.011-0.02734.155-0.003-0.0030.0000.0000.0000.000
79A81ASP-1-0.727-0.86534.2180.0220.0220.0000.0000.0000.000
80A82TYR00.025-0.02132.176-0.001-0.0010.0000.0000.0000.000
81A83ASN00.008-0.00936.560-0.005-0.0050.0000.0000.0000.000
82A84CYS0-0.089-0.02039.2220.0000.0000.0000.0000.0000.000
83A85PRO00.0380.00041.098-0.001-0.0010.0000.0000.0000.000
84A86TYR00.0070.00443.962-0.002-0.0020.0000.0000.0000.000
85A87CYS00.0110.03739.6060.0010.0010.0000.0000.0000.000
86A88LYS10.8430.90440.267-0.005-0.0050.0000.0000.0000.000
87A89ARG10.8150.90543.518-0.012-0.0120.0000.0000.0000.000
88A90PHE00.0300.02041.9830.0000.0000.0000.0000.0000.000
89A91ASP-1-0.789-0.88938.7170.0070.0070.0000.0000.0000.000
90A92PRO00.0570.01741.7700.0000.0000.0000.0000.0000.000
91A93LEU0-0.057-0.01844.422-0.001-0.0010.0000.0000.0000.000
92A94LEU00.0220.00739.6750.0010.0010.0000.0000.0000.000
93A95GLU-1-0.863-0.92040.378-0.001-0.0010.0000.0000.0000.000
94A96LYS10.8370.93842.725-0.006-0.0060.0000.0000.0000.000
95A97ILE00.0070.01143.7770.0000.0000.0000.0000.0000.000
96A98THR0-0.083-0.05439.8200.0000.0000.0000.0000.0000.000
97A99GLU-1-0.929-0.95643.004-0.003-0.0030.0000.0000.0000.000
98A100GLN0-0.050-0.03745.819-0.001-0.0010.0000.0000.0000.000
99A101TYR0-0.075-0.06146.0910.0010.0010.0000.0000.0000.000
100A102PRO00.0660.03743.6100.0010.0010.0000.0000.0000.000
101A103ASP-1-0.960-0.97742.0290.0100.0100.0000.0000.0000.000
102A104VAL0-0.042-0.02641.1040.0030.0030.0000.0000.0000.000
103A105ALA0-0.026-0.01036.387-0.003-0.0030.0000.0000.0000.000
104A106VAL00.002-0.00836.7040.0030.0030.0000.0000.0000.000
105A107ILE0-0.0090.01130.286-0.004-0.0040.0000.0000.0000.000
106A108ILE0-0.024-0.01132.2380.0030.0030.0000.0000.0000.000
107A109LYS10.8270.91826.612-0.051-0.0510.0000.0000.0000.000
108A110PRO0-0.0080.00029.1740.0020.0020.0000.0000.0000.000
109A111LEU00.0200.01129.7210.0060.0060.0000.0000.0000.000
110A112PRO00.000-0.01428.963-0.005-0.0050.0000.0000.0000.000
111A113PHE0-0.014-0.00531.626-0.001-0.0010.0000.0000.0000.000
112A114LYS10.8770.93434.861-0.023-0.0230.0000.0000.0000.000
113A115GLY00.0440.02834.968-0.002-0.0020.0000.0000.0000.000
114A116GLU-1-0.849-0.93130.7550.0030.0030.0000.0000.0000.000
115A117SER00.0680.02231.6010.0000.0000.0000.0000.0000.000
116A118SER0-0.040-0.01933.495-0.003-0.0030.0000.0000.0000.000
117A119ALA00.0280.01828.2550.0000.0000.0000.0000.0000.000
118A120LYS10.8650.95326.3760.0130.0130.0000.0000.0000.000
119A121ALA00.0240.00529.578-0.004-0.0040.0000.0000.0000.000
120A122SER0-0.010-0.02628.399-0.001-0.0010.0000.0000.0000.000
121A123GLN00.0240.00922.463-0.001-0.0010.0000.0000.0000.000
122A124ALA00.0160.02025.781-0.007-0.0070.0000.0000.0000.000
123A125VAL00.0060.00527.718-0.005-0.0050.0000.0000.0000.000
124A126LEU00.004-0.00324.571-0.002-0.0020.0000.0000.0000.000
125A127SER0-0.043-0.02823.379-0.003-0.0030.0000.0000.0000.000
126A128VAL0-0.009-0.00524.375-0.007-0.0070.0000.0000.0000.000
127A129TRP00.0140.01325.291-0.007-0.0070.0000.0000.0000.000
128A130LYS10.8450.93219.300-0.002-0.0020.0000.0000.0000.000
129A131GLU-1-0.878-0.91822.534-0.099-0.0990.0000.0000.0000.000
130A132ASP-1-0.804-0.91824.577-0.042-0.0420.0000.0000.0000.000
131A133PRO0-0.020-0.01127.0340.0050.0050.0000.0000.0000.000
132A134LYS10.8680.94029.7840.0350.0350.0000.0000.0000.000
133A135ALA00.0280.00731.8260.0040.0040.0000.0000.0000.000
134A136PHE00.0000.00130.4080.0020.0020.0000.0000.0000.000
135A137LEU00.0250.02932.3170.0020.0020.0000.0000.0000.000
136A138ALA00.0500.02235.8320.0020.0020.0000.0000.0000.000
137A139LEU0-0.025-0.00531.5490.0010.0010.0000.0000.0000.000
138A140HIS00.0250.01734.1640.0020.0020.0000.0000.0000.000
139A141GLN00.010-0.02235.6870.0000.0000.0000.0000.0000.000
140A142ARG10.8590.94738.4360.0180.0180.0000.0000.0000.000
141A143LEU0-0.015-0.00933.5890.0010.0010.0000.0000.0000.000
142A144MET0-0.0290.00637.6510.0030.0030.0000.0000.0000.000
143A145GLN0-0.008-0.02139.8280.0010.0010.0000.0000.0000.000
144A146LYS10.8540.95140.1710.0030.0030.0000.0000.0000.000
145A147LYS10.9861.00442.898-0.001-0.0010.0000.0000.0000.000
146A148THR0-0.033-0.03444.649-0.002-0.0020.0000.0000.0000.000
147A149MET00.0060.01838.0650.0000.0000.0000.0000.0000.000
148A150LEU00.000-0.00435.967-0.002-0.0020.0000.0000.0000.000
149A151ASP-1-0.797-0.87236.299-0.007-0.0070.0000.0000.0000.000
150A152ASN00.005-0.01331.021-0.003-0.0030.0000.0000.0000.000
151A153ALA00.0870.05434.108-0.003-0.0030.0000.0000.0000.000
152A154SER0-0.037-0.05136.878-0.001-0.0010.0000.0000.0000.000
153A155ILE0-0.061-0.02431.7790.0000.0000.0000.0000.0000.000
154A156GLU-1-0.919-0.97332.114-0.032-0.0320.0000.0000.0000.000
155A157ASP-1-0.906-0.94734.460-0.022-0.0220.0000.0000.0000.000
156A158ALA0-0.058-0.03736.634-0.001-0.0010.0000.0000.0000.000
157A159MET00.0220.01328.8100.0000.0000.0000.0000.0000.000
158A160LYS10.9931.00333.5410.0440.0440.0000.0000.0000.000
159A161SER0-0.0430.00236.1240.0000.0000.0000.0000.0000.000
160A162THR0-0.049-0.05035.4780.0020.0020.0000.0000.0000.000
161A163ASN0-0.042-0.02434.887-0.002-0.0020.0000.0000.0000.000
162A164THR00.0620.03030.734-0.004-0.0040.0000.0000.0000.000
163A165SER0-0.023-0.01729.790-0.003-0.0030.0000.0000.0000.000
164A166LYS10.8070.90424.0850.0900.0900.0000.0000.0000.000
165A167ILE0-0.029-0.01124.786-0.009-0.0090.0000.0000.0000.000
166A168LYS10.8290.91418.9210.0750.0750.0000.0000.0000.000
167A169LEU00.0400.00722.7850.0010.0010.0000.0000.0000.000
168A170THR00.0030.00519.0070.0000.0000.0000.0000.0000.000
169A171ASP-1-0.797-0.89317.001-0.045-0.0450.0000.0000.0000.000
170A172ASP-1-0.800-0.89914.5910.0300.0300.0000.0000.0000.000
171A173SER0-0.079-0.03917.6870.0150.0150.0000.0000.0000.000
172A174LEU00.0250.00420.6930.0080.0080.0000.0000.0000.000
173A175LYS10.8370.91513.714-0.063-0.0630.0000.0000.0000.000
174A176THR00.0750.03719.6710.0050.0050.0000.0000.0000.000
175A177LEU0-0.0050.01122.1940.0040.0040.0000.0000.0000.000
176A178GLN00.0250.00722.0010.0030.0030.0000.0000.0000.000
177A179ASN0-0.009-0.00820.386-0.001-0.0010.0000.0000.0000.000
178A180ASN00.0220.00023.9590.0040.0040.0000.0000.0000.000
179A181LEU0-0.025-0.00926.992-0.002-0.0020.0000.0000.0000.000
180A182GLU-1-0.848-0.91423.1070.1330.1330.0000.0000.0000.000
181A183LEU00.0080.00626.327-0.001-0.0010.0000.0000.0000.000
182A184SER0-0.083-0.05629.384-0.004-0.0040.0000.0000.0000.000
183A185ARG10.7950.88426.359-0.092-0.0920.0000.0000.0000.000
184A186LYS10.8640.93625.372-0.119-0.1190.0000.0000.0000.000
185A187LEU0-0.038-0.01532.366-0.002-0.0020.0000.0000.0000.000
186A188GLY00.0230.01935.049-0.004-0.0040.0000.0000.0000.000
187A189ILE0-0.062-0.02734.696-0.005-0.0050.0000.0000.0000.000
188A190GLN0-0.0070.00036.6590.0030.0030.0000.0000.0000.000
189A191GLY0-0.016-0.01339.027-0.003-0.0030.0000.0000.0000.000
190A192THR0-0.033-0.00137.1040.0010.0010.0000.0000.0000.000
191A193PRO00.035-0.01439.178-0.002-0.0020.0000.0000.0000.000
192A194ALA00.0110.00837.9580.0010.0010.0000.0000.0000.000
193A195THR0-0.0020.00637.6950.0000.0000.0000.0000.0000.000
194A196VAL00.0280.02234.9440.0000.0000.0000.0000.0000.000
195A197ILE0-0.011-0.02238.305-0.003-0.0030.0000.0000.0000.000
196A198GLY00.0310.02239.605-0.001-0.0010.0000.0000.0000.000
197A199ASP-1-0.820-0.89039.0410.0480.0480.0000.0000.0000.000
198A200THR0-0.029-0.02540.8020.0010.0010.0000.0000.0000.000
199A201ILE0-0.0040.00937.105-0.001-0.0010.0000.0000.0000.000
200A202LEU00.0240.01541.032-0.001-0.0010.0000.0000.0000.000
201A203PRO0-0.014-0.00942.107-0.001-0.0010.0000.0000.0000.000
202A204GLY00.0240.00742.847-0.001-0.0010.0000.0000.0000.000
203A205ALA0-0.058-0.03444.5600.0000.0000.0000.0000.0000.000
204A206VAL0-0.033-0.01546.2870.0000.0000.0000.0000.0000.000
205A207ASP-1-0.845-0.92748.8130.0100.0100.0000.0000.0000.000
206A208TYR0-0.021-0.03148.1300.0010.0010.0000.0000.0000.000
207A209ASP-1-0.835-0.92750.9510.0090.0090.0000.0000.0000.000
208A210GLN0-0.044-0.02751.8000.0010.0010.0000.0000.0000.000
209A211LEU0-0.003-0.00144.7280.0010.0010.0000.0000.0000.000
210A212GLU-1-0.748-0.83248.1110.0090.0090.0000.0000.0000.000
211A213ILE0-0.012-0.01049.9920.0010.0010.0000.0000.0000.000
212A214ILE00.0080.01146.0920.0010.0010.0000.0000.0000.000
213A215VAL00.017-0.00144.2540.0010.0010.0000.0000.0000.000
214A216LYS10.9180.95446.454-0.010-0.0100.0000.0000.0000.000
215A217GLU-1-0.873-0.91549.3170.0230.0230.0000.0000.0000.000
216A218GLN00.0230.01243.8640.0020.0020.0000.0000.0000.000
217A219LEU00.0370.02044.5400.0010.0010.0000.0000.0000.000
218A220ALA0-0.049-0.01646.6140.0000.0000.0000.0000.0000.000
219A221LYS10.7700.86245.380-0.025-0.0250.0000.0000.0000.000
220A222VAL00.0120.01841.9670.0010.0010.0000.0000.0000.000
221A223LYS10.8100.90145.160-0.019-0.0190.0000.0000.0000.000
222A224LYS11.0071.01641.621-0.018-0.0180.0000.0000.0000.000