Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

tag_button

FMODB ID: 89Y5Y

Calculation Name: 4RZ9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4RZ9

Chain ID: A

ChEMBL ID:

UniProt ID: Q8NAV1

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 179
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2107668.790849
FMO2-HF: Nuclear repulsion 2032786.887602
FMO2-HF: Total energy -74881.903247
FMO2-MP2: Total energy -75097.275388


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:1:MET)


Summations of interaction energy for fragment #1(A:1: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.
-27.228-31.25225.857-8.637-13.1950.005
Interaction energy analysis for fragmet #1(A:1: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 : 0.031
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].
3A3ASN00.0250.0182.372-4.270-5.0419.405-3.561-5.072-0.015
4A4ARG10.8730.9101.906-24.205-29.05115.965-4.629-6.4910.025
5A5THR00.0430.0113.5980.2850.4710.0180.002-0.2060.000
6A6VAL00.0030.0267.2480.1050.1050.0000.0000.0000.000
7A7LYS10.9010.9449.905-0.346-0.3460.0000.0000.0000.000
8A8ASP-1-0.881-0.95411.4090.1990.1990.0000.0000.0000.000
9A9ALA0-0.0010.03012.058-0.020-0.0200.0000.0000.0000.000
10A10HIS0-0.039-0.02114.0460.0120.0120.0000.0000.0000.000
11A11SER0-0.037-0.02114.519-0.028-0.0280.0000.0000.0000.000
12A12ILE00.0180.01115.3150.0250.0250.0000.0000.0000.000
13A13HIS00.000-0.00816.322-0.036-0.0360.0000.0000.0000.000
14A14GLY00.0060.01318.079-0.014-0.0140.0000.0000.0000.000
15A15THR0-0.038-0.01712.875-0.033-0.0330.0000.0000.0000.000
16A16ASN00.0310.0306.9490.1650.1650.0000.0000.0000.000
17A17PRO00.1040.05011.140-0.076-0.0760.0000.0000.0000.000
18A18GLN00.0340.0045.2000.1090.1090.0000.0000.0000.000
19A19TYR0-0.131-0.0835.942-0.253-0.2530.0000.0000.0000.000
20A20LEU00.0570.04610.3510.0130.0130.0000.0000.0000.000
21A21VAL00.0160.03010.2780.0370.0370.0000.0000.0000.000
22A22GLU-1-0.719-0.85210.001-1.083-1.0830.0000.0000.0000.000
23A23LYS10.8790.9226.5661.0461.0460.0000.0000.0000.000
24A24ILE0-0.022-0.0207.150-0.190-0.1900.0000.0000.0000.000
25A25ILE00.0260.0149.5360.0610.0610.0000.0000.0000.000
26A26ARG10.8920.9515.1241.8571.8570.0000.0000.0000.000
27A27THR0-0.028-0.0085.1880.0750.0750.0000.0000.0000.000
28A28ARG10.8610.9156.1540.7630.7630.0000.0000.0000.000
29A29ILE00.0120.0098.9860.1240.1240.0000.0000.0000.000
30A30TYR0-0.053-0.0432.698-0.9120.4950.469-0.449-1.426-0.005
31A31GLU-1-0.849-0.9076.921-0.320-0.3200.0000.0000.0000.000
32A32SER0-0.016-0.0138.8660.0150.0150.0000.0000.0000.000
33A33LYS10.8130.87312.1460.0110.0110.0000.0000.0000.000
34A34TYR00.0990.03315.0490.0330.0330.0000.0000.0000.000
35A35TRP00.009-0.0086.941-0.092-0.0920.0000.0000.0000.000
36A36LYS10.8220.8959.950-0.063-0.0630.0000.0000.0000.000
37A37GLU-1-0.833-0.89412.0640.0960.0960.0000.0000.0000.000
38A38GLU-1-0.871-0.92515.5700.0740.0740.0000.0000.0000.000
39A39CYS0-0.040-0.01212.581-0.030-0.0300.0000.0000.0000.000
40A40PHE0-0.032-0.01111.6310.0640.0640.0000.0000.0000.000
41A41GLY0-0.030-0.02611.627-0.041-0.0410.0000.0000.0000.000
42A42LEU0-0.0360.00213.219-0.023-0.0230.0000.0000.0000.000
43A43THR00.0480.01914.092-0.003-0.0030.0000.0000.0000.000
44A44ALA00.0460.01016.422-0.010-0.0100.0000.0000.0000.000
45A45GLU-1-0.906-0.94917.9970.0700.0700.0000.0000.0000.000
46A46LEU00.0240.00518.979-0.005-0.0050.0000.0000.0000.000
47A47VAL0-0.036-0.02116.697-0.001-0.0010.0000.0000.0000.000
48A48VAL00.0300.01419.338-0.011-0.0110.0000.0000.0000.000
49A49ASP-1-0.864-0.93622.5570.0520.0520.0000.0000.0000.000
50A50LYS10.7550.85918.518-0.079-0.0790.0000.0000.0000.000
51A51ALA0-0.011-0.01721.322-0.012-0.0120.0000.0000.0000.000
52A52MET0-0.042-0.01422.674-0.011-0.0110.0000.0000.0000.000
53A53GLU-1-0.865-0.90722.5210.0440.0440.0000.0000.0000.000
54A54LEU0-0.080-0.01820.332-0.009-0.0090.0000.0000.0000.000
55A55ARG10.9330.94924.3070.0140.0140.0000.0000.0000.000
56A56PHE0-0.066-0.05222.0560.0020.0020.0000.0000.0000.000
57A57VAL00.0490.04923.4580.0020.0020.0000.0000.0000.000
58A58GLY00.0420.00021.9180.0020.0020.0000.0000.0000.000
59A59GLY00.0450.02118.0880.0000.0000.0000.0000.0000.000
60A60VAL0-0.064-0.03214.6030.0000.0000.0000.0000.0000.000
61A61TYR00.0210.00617.6490.0130.0130.0000.0000.0000.000
62A62GLY00.0400.02619.405-0.010-0.0100.0000.0000.0000.000
63A63GLY00.0080.00320.449-0.018-0.0180.0000.0000.0000.000
64A64ASN00.0080.00416.4420.0010.0010.0000.0000.0000.000
65A65ILE0-0.0090.00013.151-0.034-0.0340.0000.0000.0000.000
66A66LYS10.9310.97614.4740.1220.1220.0000.0000.0000.000
67A67PRO00.0240.01412.434-0.002-0.0020.0000.0000.0000.000
68A68THR0-0.005-0.00915.2220.0360.0360.0000.0000.0000.000
69A69PRO00.0290.00516.508-0.004-0.0040.0000.0000.0000.000
70A70PHE00.0810.04717.4500.0110.0110.0000.0000.0000.000
71A71LEU00.0050.03413.975-0.002-0.0020.0000.0000.0000.000
72A72CYS0-0.081-0.04312.871-0.019-0.0190.0000.0000.0000.000
73A73LEU00.0480.02413.1110.0300.0300.0000.0000.0000.000
74A74THR00.021-0.00215.3720.0030.0030.0000.0000.0000.000
75A75LEU0-0.041-0.0267.698-0.033-0.0330.0000.0000.0000.000
76A76LYS10.8370.9299.132-0.440-0.4400.0000.0000.0000.000
77A77MET00.0320.02812.0220.0020.0020.0000.0000.0000.000
78A78LEU0-0.022-0.01411.909-0.008-0.0080.0000.0000.0000.000
79A79GLN0-0.083-0.0416.0140.0740.0740.0000.0000.0000.000
80A80ILE0-0.012-0.0269.517-0.006-0.0060.0000.0000.0000.000
81A81GLN0-0.031-0.00212.2100.0360.0360.0000.0000.0000.000
82A82PRO00.0130.01014.9500.0140.0140.0000.0000.0000.000
83A83GLU-1-0.832-0.90918.0460.0330.0330.0000.0000.0000.000
84A84LYS10.8410.89121.3220.0280.0280.0000.0000.0000.000
85A85ASP-1-0.880-0.94523.6880.0120.0120.0000.0000.0000.000
86A86ILE00.0920.05821.224-0.004-0.0040.0000.0000.0000.000
87A87ILE0-0.041-0.01919.972-0.007-0.0070.0000.0000.0000.000
88A88VAL0-0.055-0.02824.015-0.005-0.0050.0000.0000.0000.000
89A89GLU-1-0.899-0.95426.9710.0160.0160.0000.0000.0000.000
90A90PHE0-0.035-0.03621.009-0.003-0.0030.0000.0000.0000.000
91A91ILE0-0.053-0.02625.851-0.003-0.0030.0000.0000.0000.000
92A92LYS10.8960.94928.5540.0250.0250.0000.0000.0000.000
93A93ASN00.0470.02929.659-0.001-0.0010.0000.0000.0000.000
94A94GLU-1-0.913-0.95931.607-0.012-0.0120.0000.0000.0000.000
95A95ASP-1-0.893-0.91232.309-0.001-0.0010.0000.0000.0000.000
96A96PHE0-0.004-0.01128.580-0.003-0.0030.0000.0000.0000.000
97A97LYS10.9350.96229.2730.0240.0240.0000.0000.0000.000
98A98TYR0-0.018-0.00225.378-0.006-0.0060.0000.0000.0000.000
99A99VAL00.0600.05124.721-0.006-0.0060.0000.0000.0000.000
100A100ARG10.8410.91625.2310.0190.0190.0000.0000.0000.000
101A101MET0-0.036-0.01425.590-0.008-0.0080.0000.0000.0000.000
102A102LEU0-0.0130.00318.747-0.012-0.0120.0000.0000.0000.000
103A103GLY00.0400.01421.730-0.010-0.0100.0000.0000.0000.000
104A104ALA0-0.0020.00023.536-0.006-0.0060.0000.0000.0000.000
105A105LEU00.0420.01218.867-0.009-0.0090.0000.0000.0000.000
106A106TYR00.0400.00015.706-0.025-0.0250.0000.0000.0000.000
107A107MET00.0220.02720.092-0.010-0.0100.0000.0000.0000.000
108A108ARG10.8230.90722.9860.1270.1270.0000.0000.0000.000
109A109LEU0-0.046-0.02416.544-0.017-0.0170.0000.0000.0000.000
110A110THR0-0.089-0.06217.108-0.015-0.0150.0000.0000.0000.000
111A111GLY00.0280.02619.8220.0110.0110.0000.0000.0000.000
112A112THR0-0.046-0.05123.557-0.010-0.0100.0000.0000.0000.000
113A113ALA00.0400.00326.137-0.002-0.0020.0000.0000.0000.000
114A114ILE00.0550.02928.4640.0010.0010.0000.0000.0000.000
115A115ASP-1-0.803-0.87726.846-0.041-0.0410.0000.0000.0000.000
116A116CYS0-0.029-0.00726.154-0.002-0.0020.0000.0000.0000.000
117A117TYR00.052-0.00128.3740.0010.0010.0000.0000.0000.000
118A118LYS10.9560.98331.7250.0270.0270.0000.0000.0000.000
119A119TYR0-0.066-0.03929.0020.0060.0060.0000.0000.0000.000
120A120LEU0-0.0020.00726.8750.0030.0030.0000.0000.0000.000
121A121GLU-1-0.748-0.84330.994-0.047-0.0470.0000.0000.0000.000
122A122PRO0-0.043-0.02733.8450.0020.0020.0000.0000.0000.000
123A123LEU0-0.019-0.00530.6410.0030.0030.0000.0000.0000.000
124A124TYR00.000-0.03434.473-0.001-0.0010.0000.0000.0000.000
125A125ASN0-0.078-0.03736.6330.0010.0010.0000.0000.0000.000
126A126ASP-1-0.768-0.84434.570-0.028-0.0280.0000.0000.0000.000
127A127TYR00.0210.01635.826-0.001-0.0010.0000.0000.0000.000
128A128ARG10.7060.82034.0840.0250.0250.0000.0000.0000.000
129A129LYS10.9720.98534.6750.0330.0330.0000.0000.0000.000
130A130ILE0-0.032-0.02028.6650.0050.0050.0000.0000.0000.000
131A131LYS10.8100.94127.5270.0500.0500.0000.0000.0000.000
132A132SER00.0620.02626.690-0.003-0.0030.0000.0000.0000.000
133A133GLN0-0.066-0.05022.5330.0070.0070.0000.0000.0000.000
134A134ASN00.0220.01524.153-0.022-0.0220.0000.0000.0000.000
135A135ARG10.9070.94619.3860.2250.2250.0000.0000.0000.000
136A136ASN0-0.013-0.02122.700-0.013-0.0130.0000.0000.0000.000
137A137GLY0-0.053-0.03623.925-0.002-0.0020.0000.0000.0000.000
138A138GLU-1-0.868-0.92024.891-0.070-0.0700.0000.0000.0000.000
139A139PHE0-0.029-0.03425.189-0.002-0.0020.0000.0000.0000.000
140A140GLU-1-0.837-0.89829.235-0.089-0.0890.0000.0000.0000.000
141A141LEU0-0.082-0.06230.9890.0040.0040.0000.0000.0000.000
142A142MET00.0290.04528.910-0.004-0.0040.0000.0000.0000.000
143A143HIS00.003-0.01333.1480.0050.0050.0000.0000.0000.000
144A144VAL0-0.016-0.02330.913-0.005-0.0050.0000.0000.0000.000
145A145ASP-1-0.824-0.92431.658-0.053-0.0530.0000.0000.0000.000
146A146GLU-1-0.828-0.90732.932-0.065-0.0650.0000.0000.0000.000
147A147PHE0-0.003-0.02123.391-0.008-0.0080.0000.0000.0000.000
148A148ILE0-0.014-0.01528.276-0.008-0.0080.0000.0000.0000.000
149A149ASP-1-0.807-0.87230.111-0.075-0.0750.0000.0000.0000.000
150A150GLU-1-0.874-0.91927.359-0.117-0.1170.0000.0000.0000.000
151A151LEU0-0.072-0.03723.661-0.011-0.0110.0000.0000.0000.000
152A152LEU0-0.035-0.01026.631-0.008-0.0080.0000.0000.0000.000
153A153HIS0-0.099-0.05629.398-0.001-0.0010.0000.0000.0000.000
154A154SER0-0.042-0.02826.6910.0000.0000.0000.0000.0000.000
155A155GLU-1-0.964-0.98124.544-0.162-0.1620.0000.0000.0000.000
156A156ARG10.8240.90017.9550.2500.2500.0000.0000.0000.000
157A157VAL00.0960.06021.2300.0120.0120.0000.0000.0000.000
158A158CYS0-0.048-0.00919.143-0.010-0.0100.0000.0000.0000.000
159A159ASP-1-0.848-0.94117.285-0.254-0.2540.0000.0000.0000.000
160A160ILE0-0.0180.00515.270-0.041-0.0410.0000.0000.0000.000
161A161ILE0-0.022-0.01017.2560.0260.0260.0000.0000.0000.000
162A162LEU00.0190.01718.669-0.018-0.0180.0000.0000.0000.000
163A163PRO0-0.014-0.00118.9670.0040.0040.0000.0000.0000.000
164A164ARG10.9580.96721.5020.1500.1500.0000.0000.0000.000
165A165LEU0-0.0020.02724.9050.0070.0070.0000.0000.0000.000
166A166GLN00.0250.01527.370-0.002-0.0020.0000.0000.0000.000
167A167LYS10.9400.97430.2720.0980.0980.0000.0000.0000.000
168A168ARG10.7920.84433.7550.0460.0460.0000.0000.0000.000
169A169TYR00.0800.04035.6820.0000.0000.0000.0000.0000.000
170A170VAL0-0.0110.00735.1900.0020.0020.0000.0000.0000.000
171A171LEU0-0.043-0.02531.8480.0010.0010.0000.0000.0000.000
172A172GLU-1-0.872-0.92436.315-0.040-0.0400.0000.0000.0000.000
173A173GLU-1-0.950-0.99039.880-0.041-0.0410.0000.0000.0000.000
174A174ALA0-0.059-0.01937.2940.0020.0020.0000.0000.0000.000
175A175GLU-1-0.942-0.97038.393-0.020-0.0200.0000.0000.0000.000
176A176GLN0-0.073-0.04333.700-0.002-0.0020.0000.0000.0000.000
177A177LEU0-0.076-0.04234.212-0.001-0.0010.0000.0000.0000.000
178A178GLU-1-0.899-0.93738.038-0.021-0.0210.0000.0000.0000.000
179A179PRO0-0.0270.00740.925-0.001-0.0010.0000.0000.0000.000