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: 855QY

Calculation Name: 4RZA-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4RZA

Chain ID: A

ChEMBL ID:

UniProt ID: Q8NAV1

Base Structure: X-ray

Registration Date: 2023-06-21

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 OptH
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 -2116553.744192
FMO2-HF: Nuclear repulsion 2041672.035948
FMO2-HF: Total energy -74881.708244
FMO2-MP2: Total energy -75097.019578


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.
-1.055.1430.816-2.516-4.493-0.008
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 : 0.012 / q_NPA : -0.020
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].
3A3ASN00.0460.0402.436-3.0710.9380.690-1.820-2.879-0.004
4A4ARG10.9310.9793.2222.0844.1850.126-0.676-1.551-0.004
5A5THR0-0.014-0.0324.388-0.138-0.0550.000-0.020-0.0630.000
6A6VAL0-0.0120.0197.480-0.365-0.3650.0000.0000.0000.000
7A7LYS10.9210.9357.5150.5640.5640.0000.0000.0000.000
8A8ASP-1-0.859-0.9199.878-0.499-0.4990.0000.0000.0000.000
9A9ALA0-0.0170.01612.2350.0640.0640.0000.0000.0000.000
10A10HIS10.9320.96713.9160.2520.2520.0000.0000.0000.000
11A11SER0-0.086-0.04816.268-0.013-0.0130.0000.0000.0000.000
12A12ILE00.0570.02917.2770.0160.0160.0000.0000.0000.000
13A13HIS0-0.001-0.00818.7970.0100.0100.0000.0000.0000.000
14A14GLY0-0.0070.00420.6890.0090.0090.0000.0000.0000.000
15A15THR0-0.010-0.00516.039-0.012-0.0120.0000.0000.0000.000
16A16ASN00.0410.0439.036-0.013-0.0130.0000.0000.0000.000
17A17PRO00.1280.06912.7420.0580.0580.0000.0000.0000.000
18A18GLN00.030-0.0026.7890.2870.2870.0000.0000.0000.000
19A19TYR0-0.147-0.0809.3130.0490.0490.0000.0000.0000.000
20A20LEU00.0460.03813.9170.0280.0280.0000.0000.0000.000
21A21VAL00.0060.02014.1800.0220.0220.0000.0000.0000.000
22A22GLU-1-0.872-0.94114.8450.0770.0770.0000.0000.0000.000
23A23LYS10.9820.98211.367-0.107-0.1070.0000.0000.0000.000
24A24ILE00.0360.00312.1730.0940.0940.0000.0000.0000.000
25A25ILE00.0560.04513.9140.0460.0460.0000.0000.0000.000
26A26ARG10.9010.9549.670-0.171-0.1710.0000.0000.0000.000
27A27THR0-0.087-0.0438.9130.0960.0960.0000.0000.0000.000
28A28ARG10.9550.9719.992-0.214-0.2140.0000.0000.0000.000
29A29ILE00.003-0.00210.646-0.007-0.0070.0000.0000.0000.000
30A30TYR0-0.064-0.0356.4610.2470.2470.0000.0000.0000.000
31A31GLU-1-0.963-0.9838.3160.6520.6520.0000.0000.0000.000
32A32SER0-0.089-0.04310.485-0.130-0.1300.0000.0000.0000.000
33A33LYS10.8910.91111.976-0.110-0.1100.0000.0000.0000.000
34A34TYR00.0500.02213.972-0.014-0.0140.0000.0000.0000.000
35A35TRP00.011-0.0236.1670.0220.0220.0000.0000.0000.000
36A36LYS10.9010.9378.394-0.702-0.7020.0000.0000.0000.000
37A37GLU-1-0.873-0.91510.4310.0460.0460.0000.0000.0000.000
38A38GLU-1-0.871-0.93613.737-0.060-0.0600.0000.0000.0000.000
39A39CYS0-0.051-0.01311.006-0.021-0.0210.0000.0000.0000.000
40A40PHE0-0.0100.0017.335-0.172-0.1720.0000.0000.0000.000
41A41GLY0-0.022-0.0119.5510.0640.0640.0000.0000.0000.000
42A42LEU0-0.0250.00311.3840.0400.0400.0000.0000.0000.000
43A43THR00.0410.00712.964-0.097-0.0970.0000.0000.0000.000
44A44ALA00.0400.00415.3000.0340.0340.0000.0000.0000.000
45A45GLU-1-0.878-0.94417.754-0.129-0.1290.0000.0000.0000.000
46A46LEU0-0.0210.00116.7620.0180.0180.0000.0000.0000.000
47A47VAL0-0.035-0.02016.4900.0180.0180.0000.0000.0000.000
48A48VAL00.0550.01718.8870.0210.0210.0000.0000.0000.000
49A49ASP-1-0.867-0.93221.175-0.087-0.0870.0000.0000.0000.000
50A50LYS10.8800.94517.2650.0860.0860.0000.0000.0000.000
51A51ALA0-0.032-0.03420.5570.0170.0170.0000.0000.0000.000
52A52MET0-0.047-0.01722.3050.0140.0140.0000.0000.0000.000
53A53GLU-1-0.977-0.96722.501-0.032-0.0320.0000.0000.0000.000
54A54LEU0-0.095-0.02820.5670.0140.0140.0000.0000.0000.000
55A55ARG10.9270.95124.3320.0040.0040.0000.0000.0000.000
56A56PHE0-0.080-0.05823.6970.0040.0040.0000.0000.0000.000
57A57VAL00.0300.03024.730-0.004-0.0040.0000.0000.0000.000
58A58GLY00.0770.02023.8960.0080.0080.0000.0000.0000.000
59A59GLY00.0420.03021.056-0.008-0.0080.0000.0000.0000.000
60A60VAL0-0.087-0.05218.3210.0120.0120.0000.0000.0000.000
61A61TYR00.0210.00921.132-0.007-0.0070.0000.0000.0000.000
62A62GLY00.0440.01722.5610.0150.0150.0000.0000.0000.000
63A63GLY0-0.007-0.01123.3280.0050.0050.0000.0000.0000.000
64A64ASN00.008-0.01018.4630.0180.0180.0000.0000.0000.000
65A65ILE0-0.053-0.01117.2900.0280.0280.0000.0000.0000.000
66A66LYS10.9380.99216.852-0.104-0.1040.0000.0000.0000.000
67A67PRO00.0440.02014.674-0.022-0.0220.0000.0000.0000.000
68A68THR00.0020.00317.873-0.004-0.0040.0000.0000.0000.000
69A69PRO00.0390.01117.7800.0020.0020.0000.0000.0000.000
70A70PHE00.0550.03917.980-0.019-0.0190.0000.0000.0000.000
71A71LEU00.0110.02016.486-0.017-0.0170.0000.0000.0000.000
72A72CYS0-0.079-0.03913.9030.0070.0070.0000.0000.0000.000
73A73LEU00.0510.01513.864-0.046-0.0460.0000.0000.0000.000
74A74THR00.0240.02016.069-0.042-0.0420.0000.0000.0000.000
75A75LEU0-0.038-0.01910.132-0.018-0.0180.0000.0000.0000.000
76A76LYS10.8590.9348.6500.7070.7070.0000.0000.0000.000
77A77MET00.0180.01712.492-0.089-0.0890.0000.0000.0000.000
78A78LEU0-0.029-0.01013.390-0.030-0.0300.0000.0000.0000.000
79A79GLN0-0.091-0.0456.4500.4000.4000.0000.0000.0000.000
80A80ILE0-0.005-0.03210.764-0.172-0.1720.0000.0000.0000.000
81A81GLN0-0.0410.00712.6310.0320.0320.0000.0000.0000.000
82A82PRO00.0020.00015.8410.0060.0060.0000.0000.0000.000
83A83GLU-1-0.867-0.90718.512-0.168-0.1680.0000.0000.0000.000
84A84LYS10.8740.90121.4020.1300.1300.0000.0000.0000.000
85A85ASP-1-0.851-0.94024.275-0.124-0.1240.0000.0000.0000.000
86A86ILE00.1420.08320.9960.0060.0060.0000.0000.0000.000
87A87ILE0-0.071-0.03120.5470.0110.0110.0000.0000.0000.000
88A88VAL0-0.053-0.03824.4980.0160.0160.0000.0000.0000.000
89A89GLU-1-0.883-0.94327.359-0.095-0.0950.0000.0000.0000.000
90A90PHE0-0.066-0.04321.4500.0080.0080.0000.0000.0000.000
91A91ILE0-0.055-0.01627.0300.0110.0110.0000.0000.0000.000
92A92LYS10.9200.94529.4730.0720.0720.0000.0000.0000.000
93A93ASN00.0490.04430.1970.0080.0080.0000.0000.0000.000
94A94GLU-1-0.959-0.98632.244-0.039-0.0390.0000.0000.0000.000
95A95ASP-1-0.911-0.94333.234-0.036-0.0360.0000.0000.0000.000
96A96PHE0-0.041-0.02828.9030.0040.0040.0000.0000.0000.000
97A97LYS10.8980.94730.0320.0170.0170.0000.0000.0000.000
98A98TYR00.0180.01426.0080.0010.0010.0000.0000.0000.000
99A99VAL00.0610.04125.222-0.004-0.0040.0000.0000.0000.000
100A100ARG10.9130.96226.0150.0420.0420.0000.0000.0000.000
101A101MET0-0.073-0.03826.760-0.003-0.0030.0000.0000.0000.000
102A102LEU00.0060.00719.548-0.001-0.0010.0000.0000.0000.000
103A103GLY00.0220.01222.794-0.012-0.0120.0000.0000.0000.000
104A104ALA00.0110.00124.553-0.006-0.0060.0000.0000.0000.000
105A105LEU00.0280.00621.4320.0000.0000.0000.0000.0000.000
106A106TYR00.0650.01516.850-0.015-0.0150.0000.0000.0000.000
107A107MET00.0380.02821.582-0.012-0.0120.0000.0000.0000.000
108A108ARG10.8320.91024.4840.0640.0640.0000.0000.0000.000
109A109LEU0-0.082-0.04318.8780.0030.0030.0000.0000.0000.000
110A110THR0-0.066-0.05318.834-0.008-0.0080.0000.0000.0000.000
111A111GLY00.0390.04021.709-0.006-0.0060.0000.0000.0000.000
112A112THR0-0.036-0.01925.3110.0090.0090.0000.0000.0000.000
113A113ALA00.015-0.00428.2580.0030.0030.0000.0000.0000.000
114A114ILE00.0160.01131.2560.0040.0040.0000.0000.0000.000
115A115ASP-1-0.796-0.88727.536-0.106-0.1060.0000.0000.0000.000
116A116CYS0-0.034-0.01028.2500.0030.0030.0000.0000.0000.000
117A117TYR00.008-0.00430.5260.0030.0030.0000.0000.0000.000
118A118LYS10.9540.98633.1110.0750.0750.0000.0000.0000.000
119A119TYR0-0.055-0.04629.8980.0020.0020.0000.0000.0000.000
120A120LEU0-0.0010.00028.2790.0010.0010.0000.0000.0000.000
121A121GLU-1-0.873-0.92732.400-0.043-0.0430.0000.0000.0000.000
122A122PRO0-0.031-0.01135.0300.0040.0040.0000.0000.0000.000
123A123LEU0-0.036-0.01531.3190.0030.0030.0000.0000.0000.000
124A124TYR0-0.024-0.05035.6960.0010.0010.0000.0000.0000.000
125A125ASN0-0.079-0.04138.1160.0050.0050.0000.0000.0000.000
126A126ASP-1-0.762-0.84635.049-0.033-0.0330.0000.0000.0000.000
127A127TYR00.0460.01237.6840.0020.0020.0000.0000.0000.000
128A128ARG10.7670.87233.7490.0380.0380.0000.0000.0000.000
129A129LYS10.9470.97736.3250.0090.0090.0000.0000.0000.000
130A130ILE0-0.038-0.02230.263-0.002-0.0020.0000.0000.0000.000
131A131LYS10.9590.97330.1420.0020.0020.0000.0000.0000.000
132A132SER00.0400.02428.442-0.003-0.0030.0000.0000.0000.000
133A133GLN0-0.042-0.01224.4210.0040.0040.0000.0000.0000.000
134A134ASN00.0450.02526.6180.0050.0050.0000.0000.0000.000
135A135ARG10.9200.93122.406-0.056-0.0560.0000.0000.0000.000
136A136ASN0-0.014-0.00426.7340.0100.0100.0000.0000.0000.000
137A137GLY0-0.0060.00627.2140.0040.0040.0000.0000.0000.000
138A138GLU-1-0.945-0.96028.2140.0250.0250.0000.0000.0000.000
139A139PHE0-0.050-0.04326.904-0.001-0.0010.0000.0000.0000.000
140A140GLU-1-0.861-0.92231.4820.0110.0110.0000.0000.0000.000
141A141LEU0-0.071-0.05932.900-0.002-0.0020.0000.0000.0000.000
142A142MET00.0410.04731.9140.0020.0020.0000.0000.0000.000
143A143HIS00.001-0.01435.4350.0010.0010.0000.0000.0000.000
144A144VAL0-0.031-0.01932.715-0.001-0.0010.0000.0000.0000.000
145A145ASP-1-0.847-0.93333.779-0.024-0.0240.0000.0000.0000.000
146A146GLU-1-0.823-0.91135.451-0.013-0.0130.0000.0000.0000.000
147A147PHE00.004-0.00225.732-0.001-0.0010.0000.0000.0000.000
148A148ILE0-0.032-0.02930.787-0.004-0.0040.0000.0000.0000.000
149A149ASP-1-0.794-0.86832.491-0.029-0.0290.0000.0000.0000.000
150A150GLU-1-0.939-0.97130.770-0.015-0.0150.0000.0000.0000.000
151A151LEU0-0.071-0.03326.323-0.003-0.0030.0000.0000.0000.000
152A152LEU0-0.041-0.02129.553-0.005-0.0050.0000.0000.0000.000
153A153HIS10.7940.89532.2670.0320.0320.0000.0000.0000.000
154A154SER00.0260.03330.5510.0030.0030.0000.0000.0000.000
155A155GLU-1-0.939-0.96828.990-0.021-0.0210.0000.0000.0000.000
156A156ARG10.8850.93524.625-0.014-0.0140.0000.0000.0000.000
157A157VAL00.1160.06625.1160.0020.0020.0000.0000.0000.000
158A158CYS0-0.0480.00122.209-0.002-0.0020.0000.0000.0000.000
159A159ASP-1-0.877-0.94821.5130.0470.0470.0000.0000.0000.000
160A160ILE0-0.028-0.01418.5980.0110.0110.0000.0000.0000.000
161A161ILE0-0.018-0.01421.528-0.003-0.0030.0000.0000.0000.000
162A162LEU0-0.0060.00222.474-0.012-0.0120.0000.0000.0000.000
163A163PRO00.0120.02622.1340.0050.0050.0000.0000.0000.000
164A164ARG10.9720.96924.4720.0600.0600.0000.0000.0000.000
165A165LEU00.0600.03626.983-0.007-0.0070.0000.0000.0000.000
166A166GLN00.0120.01627.9080.0120.0120.0000.0000.0000.000
167A167LYS10.9710.96629.6930.0490.0490.0000.0000.0000.000
168A168ARG10.8990.94932.3010.0640.0640.0000.0000.0000.000
169A169TYR00.0570.00931.713-0.006-0.0060.0000.0000.0000.000
170A170VAL0-0.050-0.02727.1990.0020.0020.0000.0000.0000.000
171A171LEU00.0280.02927.218-0.001-0.0010.0000.0000.0000.000
172A172GLU-1-0.960-0.99821.683-0.185-0.1850.0000.0000.0000.000
173A173GLU-1-0.913-0.96021.756-0.212-0.2120.0000.0000.0000.000
174A174ALA0-0.027-0.02923.6780.0120.0120.0000.0000.0000.000
175A175GLU-1-0.934-0.95824.841-0.130-0.1300.0000.0000.0000.000
176A176GLN0-0.046-0.00923.6120.0120.0120.0000.0000.0000.000
177A177LEU00.0110.00627.4730.0090.0090.0000.0000.0000.000
178A178GLU-1-0.931-0.96930.932-0.084-0.0840.0000.0000.0000.000
179A179PRO0-0.074-0.01232.5320.0070.0070.0000.0000.0000.000