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: MNZLZ

Calculation Name: 4PZ9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4PZ9

Chain ID: A

ChEMBL ID:

UniProt ID: P9WIC7

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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2431980.042994
FMO2-HF: Nuclear repulsion 2351374.342235
FMO2-HF: Total energy -80605.700759
FMO2-MP2: Total energy -80845.001419


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:2:ARG)


Summations of interaction energy for fragment #1(A:2:ARG)
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.
-64.544-55.5499.599-5.664-12.931-0.044
Interaction energy analysis for fragmet #1(A:2:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.960 / q_NPA : 0.985
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].
3A4ARG10.8770.9403.86130.78832.191-0.017-0.640-0.7460.001
4A5ARG10.8440.9156.41821.62421.6240.0000.0000.0000.000
5A6LEU00.0130.0139.4000.3580.3580.0000.0000.0000.000
6A7VAL0-0.013-0.00612.8440.4330.4330.0000.0000.0000.000
7A8MET0-0.019-0.00416.0850.3680.3680.0000.0000.0000.000
8A9LEU00.0090.00919.5380.2450.2450.0000.0000.0000.000
9A10ARG10.8570.92122.5839.5009.5000.0000.0000.0000.000
10A11HIS00.0620.01426.1230.0280.0280.0000.0000.0000.000
11A12GLY00.0300.02328.9370.0190.0190.0000.0000.0000.000
12A13GLN0-0.0140.01631.5780.0570.0570.0000.0000.0000.000
13A14THR00.001-0.01234.9110.0120.0120.0000.0000.0000.000
14A15ASP-1-0.947-0.96337.120-6.753-6.7530.0000.0000.0000.000
15A16TYR0-0.019-0.05039.1690.1500.1500.0000.0000.0000.000
16A17ASN0-0.0020.00939.996-0.273-0.2730.0000.0000.0000.000
17A18VAL00.021-0.00836.1780.0530.0530.0000.0000.0000.000
18A19GLY00.0050.02139.091-0.099-0.0990.0000.0000.0000.000
19A20SER0-0.066-0.05140.6800.1060.1060.0000.0000.0000.000
20A21ARG10.8790.95041.9216.7266.7260.0000.0000.0000.000
21A22MET00.0660.06237.389-0.263-0.2630.0000.0000.0000.000
22A23GLN00.0520.05234.9700.2450.2450.0000.0000.0000.000
23A24GLY00.0640.02934.8600.0630.0630.0000.0000.0000.000
24A25GLN0-0.019-0.01231.721-0.019-0.0190.0000.0000.0000.000
25A26LEU00.0120.02134.9810.0860.0860.0000.0000.0000.000
26A27ASP-1-0.799-0.87235.566-8.276-8.2760.0000.0000.0000.000
27A28THR0-0.055-0.05036.9780.0740.0740.0000.0000.0000.000
28A29GLU-1-0.760-0.87436.587-7.679-7.6790.0000.0000.0000.000
29A30LEU0-0.048-0.00532.381-0.017-0.0170.0000.0000.0000.000
30A31SER00.030-0.00636.7690.1400.1400.0000.0000.0000.000
31A32GLU-1-0.793-0.88537.682-7.308-7.3080.0000.0000.0000.000
32A33LEU0-0.0190.00836.106-0.133-0.1330.0000.0000.0000.000
33A34GLY00.0210.01234.165-0.229-0.2290.0000.0000.0000.000
34A35ARG10.8530.89132.9877.1857.1850.0000.0000.0000.000
35A36THR0-0.015-0.01433.295-0.185-0.1850.0000.0000.0000.000
36A37GLN00.027-0.00331.143-0.222-0.2220.0000.0000.0000.000
37A38ALA00.0100.01428.907-0.309-0.3090.0000.0000.0000.000
38A39VAL00.0160.01128.157-0.304-0.3040.0000.0000.0000.000
39A40ALA0-0.0010.00128.535-0.208-0.2080.0000.0000.0000.000
40A41ALA00.0100.00025.023-0.261-0.2610.0000.0000.0000.000
41A42ALA0-0.0010.01023.982-0.481-0.4810.0000.0000.0000.000
42A43GLU-1-0.798-0.88824.007-10.234-10.2340.0000.0000.0000.000
43A44VAL0-0.042-0.01221.515-0.176-0.1760.0000.0000.0000.000
44A45LEU0-0.030-0.02618.809-0.561-0.5610.0000.0000.0000.000
45A46GLY00.0850.03919.233-0.596-0.5960.0000.0000.0000.000
46A47LYS10.7670.88720.28210.60410.6040.0000.0000.0000.000
47A48ARG10.8760.93413.96214.64914.6490.0000.0000.0000.000
48A49GLN00.022-0.00416.674-0.674-0.6740.0000.0000.0000.000
49A50PRO00.0150.00814.779-0.759-0.7590.0000.0000.0000.000
50A51LEU00.0060.02810.6080.1190.1190.0000.0000.0000.000
51A52LEU00.0110.00114.1320.7140.7140.0000.0000.0000.000
52A53ILE0-0.0030.01016.945-0.218-0.2180.0000.0000.0000.000
53A54VAL0-0.027-0.01518.4400.2930.2930.0000.0000.0000.000
54A55SER0-0.010-0.02421.169-0.110-0.1100.0000.0000.0000.000
55A56SER0-0.015-0.02524.3950.0980.0980.0000.0000.0000.000
56A57ASP-1-0.763-0.86526.989-9.270-9.2700.0000.0000.0000.000
57A58LEU0-0.0300.00030.1230.2580.2580.0000.0000.0000.000
58A59ARG10.8670.90031.3267.3487.3480.0000.0000.0000.000
59A60ARG10.8240.90132.2198.5148.5140.0000.0000.0000.000
60A61ALA0-0.045-0.01527.224-0.136-0.1360.0000.0000.0000.000
61A62TYR00.0410.02628.036-0.297-0.2970.0000.0000.0000.000
62A63ASP-1-0.850-0.93429.116-8.527-8.5270.0000.0000.0000.000
63A64THR0-0.064-0.05826.2890.0000.0000.0000.0000.0000.000
64A65ALA0-0.009-0.00424.871-0.241-0.2410.0000.0000.0000.000
65A66VAL00.0130.00625.616-0.221-0.2210.0000.0000.0000.000
66A67LYS10.7800.88028.0078.5478.5470.0000.0000.0000.000
67A68LEU00.0160.00520.289-0.021-0.0210.0000.0000.0000.000
68A69GLY00.0380.03623.668-0.303-0.3030.0000.0000.0000.000
69A70GLU-1-0.811-0.90124.968-8.780-8.7800.0000.0000.0000.000
70A71ARG10.7600.87723.37110.57010.5700.0000.0000.0000.000
71A72THR0-0.047-0.04220.536-0.278-0.2780.0000.0000.0000.000
72A73GLY00.0060.01922.268-0.292-0.2920.0000.0000.0000.000
73A74LEU0-0.046-0.00318.309-0.004-0.0040.0000.0000.0000.000
74A75VAL00.005-0.00222.8000.3860.3860.0000.0000.0000.000
75A76VAL0-0.0020.00623.068-0.466-0.4660.0000.0000.0000.000
76A77ARG10.9550.98719.55413.31913.3190.0000.0000.0000.000
77A78VAL00.000-0.00323.838-0.018-0.0180.0000.0000.0000.000
78A79ASP-1-0.773-0.87723.137-11.997-11.9970.0000.0000.0000.000
79A80THR00.0150.01325.504-0.125-0.1250.0000.0000.0000.000
80A81ARG10.7320.80921.60712.86212.8620.0000.0000.0000.000
81A82LEU0-0.005-0.00320.719-0.201-0.2010.0000.0000.0000.000
82A83ARG10.7970.87024.8459.0809.0800.0000.0000.0000.000
83A84GLU-1-0.836-0.91027.986-10.042-10.0420.0000.0000.0000.000
84A85THR0-0.020-0.02429.983-0.055-0.0550.0000.0000.0000.000
85A86HIS00.0200.00831.4200.2600.2600.0000.0000.0000.000
86A87LEU0-0.025-0.01834.550-0.050-0.0500.0000.0000.0000.000
87A88GLY00.0120.01237.5570.1650.1650.0000.0000.0000.000
88A89ASP-1-0.844-0.91540.288-6.866-6.8660.0000.0000.0000.000
89A90TRP00.013-0.01539.4730.0580.0580.0000.0000.0000.000
90A91GLN0-0.027-0.00637.383-0.219-0.2190.0000.0000.0000.000
91A92GLY00.0670.03841.3410.1340.1340.0000.0000.0000.000
92A93LEU0-0.0380.00843.9260.1860.1860.0000.0000.0000.000
93A94THR0-0.042-0.06044.082-0.147-0.1470.0000.0000.0000.000
94A95HIS0-0.041-0.04040.268-0.076-0.0760.0000.0000.0000.000
95A96ALA00.0340.01945.0750.0090.0090.0000.0000.0000.000
96A97GLN00.0440.06048.1200.0260.0260.0000.0000.0000.000
97A98ILE00.0720.04242.3960.0290.0290.0000.0000.0000.000
98A99ASP-1-0.839-0.88945.156-6.897-6.8970.0000.0000.0000.000
99A100ALA0-0.033-0.02147.6720.0810.0810.0000.0000.0000.000
100A101ASP-1-0.919-0.96048.636-6.095-6.0950.0000.0000.0000.000
101A102ALA0-0.046-0.03046.0820.0080.0080.0000.0000.0000.000
102A103PRO00.0210.01346.383-0.167-0.1670.0000.0000.0000.000
103A104GLY0-0.0150.00045.052-0.031-0.0310.0000.0000.0000.000
104A105ALA00.0090.00642.707-0.204-0.2040.0000.0000.0000.000
105A106ARG10.8080.86440.5176.9806.9800.0000.0000.0000.000
106A107LEU0-0.027-0.01339.192-0.188-0.1880.0000.0000.0000.000
107A108ALA00.0220.01238.231-0.221-0.2210.0000.0000.0000.000
108A109TRP00.0010.00134.369-0.156-0.1560.0000.0000.0000.000
109A110ARG10.7280.83730.5589.1099.1090.0000.0000.0000.000
110A111GLU-1-0.788-0.86932.881-9.347-9.3470.0000.0000.0000.000
111A112ASP-1-0.819-0.88533.357-9.146-9.1460.0000.0000.0000.000
112A113ALA0-0.033-0.03028.7840.0160.0160.0000.0000.0000.000
113A114THR0-0.062-0.06530.572-0.208-0.2080.0000.0000.0000.000
114A115TRP00.0110.01932.5780.1660.1660.0000.0000.0000.000
115A116ALA00.025-0.00334.717-0.236-0.2360.0000.0000.0000.000
116A117PRO0-0.0330.00636.5830.1980.1980.0000.0000.0000.000
117A118HIS0-0.021-0.03339.265-0.141-0.1410.0000.0000.0000.000
118A119GLY00.0480.02040.6130.0420.0420.0000.0000.0000.000
119A120GLY0-0.070-0.03336.816-0.044-0.0440.0000.0000.0000.000
120A121GLU-1-0.786-0.85130.961-9.764-9.7640.0000.0000.0000.000
121A122SER00.001-0.02131.436-0.019-0.0190.0000.0000.0000.000
122A123ARG10.8270.89227.52110.08810.0880.0000.0000.0000.000
123A124VAL00.0200.00226.781-0.480-0.4800.0000.0000.0000.000
124A125ASP-1-0.800-0.85626.864-10.002-10.0020.0000.0000.0000.000
125A126VAL0-0.0020.00525.724-0.272-0.2720.0000.0000.0000.000
126A127ALA0-0.0050.01122.913-0.408-0.4080.0000.0000.0000.000
127A128ALA0-0.041-0.01422.798-0.560-0.5600.0000.0000.0000.000
128A129ARG10.7160.80124.11010.11710.1170.0000.0000.0000.000
129A130SER0-0.015-0.02821.802-0.400-0.4000.0000.0000.0000.000
130A131ARG10.7520.81716.46116.26316.2630.0000.0000.0000.000
131A132PRO0-0.013-0.00917.780-0.920-0.9200.0000.0000.0000.000
132A133LEU00.0530.04518.141-0.568-0.5680.0000.0000.0000.000
133A134VAL0-0.002-0.00713.058-0.625-0.6250.0000.0000.0000.000
134A135ALA0-0.023-0.01313.461-1.363-1.3630.0000.0000.0000.000
135A136GLU-1-0.818-0.87814.306-14.487-14.4870.0000.0000.0000.000
136A137LEU00.0190.01313.758-0.393-0.3930.0000.0000.0000.000
137A138VAL0-0.073-0.0379.155-1.397-1.3970.0000.0000.0000.000
138A139ALA0-0.035-0.00810.343-1.929-1.9290.0000.0000.0000.000
139A140SER0-0.053-0.06613.0930.0340.0340.0000.0000.0000.000
140A141GLU-1-0.860-0.89211.520-15.970-15.9700.0000.0000.0000.000
141A142PRO0-0.018-0.0269.810-1.815-1.8150.0000.0000.0000.000
142A143GLU-1-0.851-0.9178.376-20.137-20.1370.0000.0000.0000.000
143A144TRP0-0.008-0.0137.786-1.956-1.9560.0000.0000.0000.000
144A145GLY0-0.0100.0003.864-2.402-2.2800.001-0.025-0.0980.000
145A146GLY0-0.029-0.0162.886-10.187-7.7560.392-1.488-1.335-0.014
146A147ALA0-0.045-0.0435.010-0.700-0.654-0.001-0.001-0.0440.000
147A148ASP-1-0.912-0.9446.173-22.008-22.0080.0000.0000.0000.000
148A149GLU-1-0.846-0.9288.120-16.387-16.3870.0000.0000.0000.000
149A150PRO0-0.064-0.0173.3530.0190.2960.009-0.080-0.206-0.001
150A151ASP-1-0.847-0.9065.209-20.169-20.178-0.0010.0000.0100.000
151A152ARG10.8130.8977.87618.11718.1170.0000.0000.0000.000
152A153PRO0-0.058-0.0139.957-0.838-0.8380.0000.0000.0000.000
153A154VAL00.0420.03211.6621.0781.0780.0000.0000.0000.000
154A155VAL0-0.035-0.02813.828-0.063-0.0630.0000.0000.0000.000
155A156LEU00.0250.01717.1710.4870.4870.0000.0000.0000.000
156A157VAL0-0.037-0.01519.5510.1360.1360.0000.0000.0000.000
157A158ALA00.0630.01823.2480.2370.2370.0000.0000.0000.000
158A159HIS00.0140.01725.2820.2790.2790.0000.0000.0000.000
159A160GLY00.0130.01226.274-0.310-0.3100.0000.0000.0000.000
160A161GLY00.0270.02126.740-0.259-0.2590.0000.0000.0000.000
161A162LEU00.0210.01722.255-0.282-0.2820.0000.0000.0000.000
162A163ILE0-0.019-0.00921.374-0.536-0.5360.0000.0000.0000.000
163A164ALA00.0030.01421.929-0.606-0.6060.0000.0000.0000.000
164A165ALA00.0130.00523.208-0.393-0.3930.0000.0000.0000.000
165A166LEU00.0070.00418.111-0.449-0.4490.0000.0000.0000.000
166A167SER00.012-0.01718.198-0.947-0.9470.0000.0000.0000.000
167A168ALA00.009-0.00118.439-0.747-0.7470.0000.0000.0000.000
168A169ALA00.0430.03019.860-0.389-0.3890.0000.0000.0000.000
169A170LEU0-0.058-0.01114.143-0.599-0.5990.0000.0000.0000.000
170A171LEU0-0.056-0.03714.865-1.200-1.2000.0000.0000.0000.000
171A172LYS10.8150.93313.01321.25821.2580.0000.0000.0000.000
172A173LEU00.0170.02418.2610.3540.3540.0000.0000.0000.000
173A174PRO00.0440.02421.1570.2150.2150.0000.0000.0000.000
174A175VAL00.0530.02124.3630.1530.1530.0000.0000.0000.000
175A176ALA00.0240.00826.8650.1910.1910.0000.0000.0000.000
176A177ASN0-0.026-0.02224.9680.0880.0880.0000.0000.0000.000
177A178TRP0-0.011-0.01423.0770.0060.0060.0000.0000.0000.000
178A179PRO00.0020.00526.161-0.120-0.1200.0000.0000.0000.000
179A180ALA0-0.0190.00525.8530.2510.2510.0000.0000.0000.000
180A181LEU0-0.0550.00021.734-0.083-0.0830.0000.0000.0000.000
181A182GLY00.0360.01225.9750.3680.3680.0000.0000.0000.000
182A183GLY00.000-0.00528.089-0.092-0.0920.0000.0000.0000.000
183A184MET0-0.036-0.00623.423-0.342-0.3420.0000.0000.0000.000
184A185GLY00.0360.01427.9980.3380.3380.0000.0000.0000.000
185A186ASN0-0.062-0.03829.028-0.222-0.2220.0000.0000.0000.000
186A187ALA00.0260.01127.5760.0870.0870.0000.0000.0000.000
187A188SER0-0.0210.00725.764-0.083-0.0830.0000.0000.0000.000
188A189TRP00.006-0.01619.4430.0480.0480.0000.0000.0000.000
189A190THR0-0.004-0.00118.7350.2100.2100.0000.0000.0000.000
190A191GLN0-0.084-0.05712.3860.5830.5830.0000.0000.0000.000
191A192LEU00.0070.01113.2580.1730.1730.0000.0000.0000.000
192A193SER00.026-0.0218.304-0.650-0.6500.0000.0000.0000.000
193A194GLY00.0100.0008.3070.1560.1560.0000.0000.0000.000
194A195HIS0-0.0110.0064.483-0.299-0.102-0.001-0.028-0.1680.000
195A196TRP00.0110.0022.243-16.014-11.9569.214-3.248-10.024-0.029
196A197ALA00.014-0.0083.865-0.881-0.4110.003-0.154-0.320-0.001
197A198PRO0-0.048-0.0126.090-3.905-3.9050.0000.0000.0000.000
198A199GLY00.0510.0256.7294.2094.2090.0000.0000.0000.000
199A200SER0-0.084-0.0586.239-6.092-6.0920.0000.0000.0000.000
200A201ASP-1-0.793-0.8588.320-24.689-24.6890.0000.0000.0000.000
201A202PHE00.0530.01410.337-2.001-2.0010.0000.0000.0000.000
202A203GLU-1-0.756-0.84611.683-18.826-18.8260.0000.0000.0000.000
203A204SER0-0.031-0.0429.7860.4190.4190.0000.0000.0000.000
204A205ILE0-0.072-0.0057.221-2.955-2.9550.0000.0000.0000.000
205A206ARG10.9160.9478.00629.73729.7370.0000.0000.0000.000
206A207TRP00.0310.0109.242-1.739-1.7390.0000.0000.0000.000
207A208ARG10.8690.9387.98926.05426.0540.0000.0000.0000.000
208A209LEU00.0190.00412.908-0.080-0.0800.0000.0000.0000.000
209A210ASP-1-0.816-0.87111.904-20.689-20.6890.0000.0000.0000.000
210A211VAL0-0.016-0.01414.9920.7030.7030.0000.0000.0000.000
211A212TRP00.021-0.00118.316-0.407-0.4070.0000.0000.0000.000
212A213ASN00.0160.00621.5120.3680.3680.0000.0000.0000.000
213A214ALA00.0480.04721.6030.3710.3710.0000.0000.0000.000
214A215SER0-0.0010.00423.6050.3380.3380.0000.0000.0000.000