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: N99LQ

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 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 179
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2116161.027775
FMO2-HF: Nuclear repulsion 2041278.420396
FMO2-HF: Total energy -74882.607379
FMO2-MP2: Total energy -75097.890973


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.
-12.655-7.1048.104-5.525-8.1310.007
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 : 0.009 / q_NPA : -0.005
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].
3A3ASN00.0370.0312.119-5.678-0.5052.586-3.088-4.670-0.001
4A4ARG10.9170.9732.110-5.665-5.3685.519-2.414-3.4030.008
5A5THR00.016-0.0154.411-0.456-0.375-0.001-0.023-0.0580.000
6A6VAL00.0100.0287.432-0.315-0.3150.0000.0000.0000.000
7A7LYS10.9180.9377.3440.7880.7880.0000.0000.0000.000
8A8ASP-1-0.882-0.9299.948-0.544-0.5440.0000.0000.0000.000
9A9ALA0-0.0160.01812.2010.0810.0810.0000.0000.0000.000
10A10HIS10.8750.94013.9100.1590.1590.0000.0000.0000.000
11A11SER0-0.070-0.03716.1730.0060.0060.0000.0000.0000.000
12A12ILE00.0190.00517.142-0.008-0.0080.0000.0000.0000.000
13A13HIS0-0.002-0.01118.7750.0330.0330.0000.0000.0000.000
14A14GLY0-0.0110.00320.6110.0190.0190.0000.0000.0000.000
15A15THR0-0.025-0.01216.0890.0380.0380.0000.0000.0000.000
16A16ASN00.0390.0448.915-0.124-0.1240.0000.0000.0000.000
17A17PRO00.1310.06912.7640.0640.0640.0000.0000.0000.000
18A18GLN00.019-0.0086.8400.2570.2570.0000.0000.0000.000
19A19TYR0-0.145-0.0859.4320.1520.1520.0000.0000.0000.000
20A20LEU00.0490.04113.932-0.004-0.0040.0000.0000.0000.000
21A21VAL0-0.0050.01314.030-0.014-0.0140.0000.0000.0000.000
22A22GLU-1-0.831-0.92514.4890.4320.4320.0000.0000.0000.000
23A23LYS10.9700.98810.756-0.434-0.4340.0000.0000.0000.000
24A24ILE00.009-0.00911.7330.1200.1200.0000.0000.0000.000
25A25ILE00.0410.02813.4810.0210.0210.0000.0000.0000.000
26A26ARG10.8940.9509.409-0.798-0.7980.0000.0000.0000.000
27A27THR0-0.017-0.0087.9670.1820.1820.0000.0000.0000.000
28A28ARG10.8110.8879.557-0.451-0.4510.0000.0000.0000.000
29A29ILE00.008-0.00110.478-0.045-0.0450.0000.0000.0000.000
30A30TYR0-0.042-0.0255.9950.3860.3860.0000.0000.0000.000
31A31GLU-1-0.831-0.8918.0900.6690.6690.0000.0000.0000.000
32A32SER0-0.034-0.01310.135-0.232-0.2320.0000.0000.0000.000
33A33LYS10.8330.87812.029-0.041-0.0410.0000.0000.0000.000
34A34TYR00.0720.02613.991-0.029-0.0290.0000.0000.0000.000
35A35TRP00.020-0.0166.072-0.071-0.0710.0000.0000.0000.000
36A36LYS10.8100.8928.837-0.737-0.7370.0000.0000.0000.000
37A37GLU-1-0.829-0.88810.446-0.079-0.0790.0000.0000.0000.000
38A38GLU-1-0.842-0.91113.721-0.130-0.1300.0000.0000.0000.000
39A39CYS0-0.059-0.01010.876-0.012-0.0120.0000.0000.0000.000
40A40PHE0-0.0110.0027.235-0.224-0.2240.0000.0000.0000.000
41A41GLY0-0.020-0.0119.3670.0380.0380.0000.0000.0000.000
42A42LEU0-0.0330.00411.1830.0470.0470.0000.0000.0000.000
43A43THR00.0440.00612.695-0.087-0.0870.0000.0000.0000.000
44A44ALA00.0440.00715.2270.0630.0630.0000.0000.0000.000
45A45GLU-1-0.884-0.94417.856-0.225-0.2250.0000.0000.0000.000
46A46LEU0-0.0140.00016.6510.0190.0190.0000.0000.0000.000
47A47VAL0-0.031-0.02316.2400.0310.0310.0000.0000.0000.000
48A48VAL00.0490.01818.6470.0360.0360.0000.0000.0000.000
49A49ASP-1-0.869-0.92721.009-0.154-0.1540.0000.0000.0000.000
50A50LYS10.7840.87717.2620.1300.1300.0000.0000.0000.000
51A51ALA0-0.028-0.03020.3840.0300.0300.0000.0000.0000.000
52A52MET0-0.037-0.01122.1120.0230.0230.0000.0000.0000.000
53A53GLU-1-0.904-0.92922.100-0.067-0.0670.0000.0000.0000.000
54A54LEU0-0.077-0.02320.4350.0210.0210.0000.0000.0000.000
55A55ARG10.9080.94124.1960.0080.0080.0000.0000.0000.000
56A56PHE0-0.052-0.04123.4430.0010.0010.0000.0000.0000.000
57A57VAL00.0240.02724.6020.0000.0000.0000.0000.0000.000
58A58GLY00.0710.01823.7710.0010.0010.0000.0000.0000.000
59A59GLY00.0410.02720.7900.0020.0020.0000.0000.0000.000
60A60VAL0-0.067-0.04417.7620.0140.0140.0000.0000.0000.000
61A61TYR00.0520.02620.602-0.015-0.0150.0000.0000.0000.000
62A62GLY00.0440.01822.0970.0150.0150.0000.0000.0000.000
63A63GLY0-0.008-0.01322.9070.0140.0140.0000.0000.0000.000
64A64ASN0-0.017-0.01417.1980.0270.0270.0000.0000.0000.000
65A65ILE0-0.029-0.01417.1960.0380.0380.0000.0000.0000.000
66A66LYS10.8950.95517.496-0.146-0.1460.0000.0000.0000.000
67A67PRO00.0490.02614.337-0.032-0.0320.0000.0000.0000.000
68A68THR0-0.0030.01317.613-0.022-0.0220.0000.0000.0000.000
69A69PRO00.0500.02117.6860.0230.0230.0000.0000.0000.000
70A70PHE00.0720.04017.851-0.008-0.0080.0000.0000.0000.000
71A71LEU00.0070.02516.354-0.007-0.0070.0000.0000.0000.000
72A72CYS0-0.082-0.04313.7620.0450.0450.0000.0000.0000.000
73A73LEU00.0530.01513.696-0.011-0.0110.0000.0000.0000.000
74A74THR00.0130.00615.848-0.044-0.0440.0000.0000.0000.000
75A75LEU0-0.030-0.01510.174-0.011-0.0110.0000.0000.0000.000
76A76LYS10.8500.9248.0870.6030.6030.0000.0000.0000.000
77A77MET00.0270.02112.253-0.105-0.1050.0000.0000.0000.000
78A78LEU0-0.032-0.01113.628-0.032-0.0320.0000.0000.0000.000
79A79GLN0-0.095-0.0466.3340.4450.4450.0000.0000.0000.000
80A80ILE0-0.002-0.03110.860-0.179-0.1790.0000.0000.0000.000
81A81GLN0-0.0420.00312.666-0.013-0.0130.0000.0000.0000.000
82A82PRO00.0110.00515.862-0.014-0.0140.0000.0000.0000.000
83A83GLU-1-0.851-0.90418.549-0.198-0.1980.0000.0000.0000.000
84A84LYS10.8790.89721.4570.0800.0800.0000.0000.0000.000
85A85ASP-1-0.878-0.94924.291-0.126-0.1260.0000.0000.0000.000
86A86ILE00.1020.06321.1970.0100.0100.0000.0000.0000.000
87A87ILE0-0.052-0.02220.6340.0180.0180.0000.0000.0000.000
88A88VAL0-0.054-0.03724.6550.0170.0170.0000.0000.0000.000
89A89GLU-1-0.890-0.94327.374-0.104-0.1040.0000.0000.0000.000
90A90PHE0-0.070-0.04521.2920.0090.0090.0000.0000.0000.000
91A91ILE0-0.051-0.01827.0580.0110.0110.0000.0000.0000.000
92A92LYS10.9310.95129.4280.0460.0460.0000.0000.0000.000
93A93ASN00.0000.01230.0190.0070.0070.0000.0000.0000.000
94A94GLU-1-0.849-0.91831.995-0.022-0.0220.0000.0000.0000.000
95A95ASP-1-0.890-0.91832.664-0.045-0.0450.0000.0000.0000.000
96A96PHE00.0080.00028.6880.0050.0050.0000.0000.0000.000
97A97LYS10.9010.94429.822-0.001-0.0010.0000.0000.0000.000
98A98TYR0-0.014-0.01925.8640.0050.0050.0000.0000.0000.000
99A99VAL00.0510.03824.9690.0050.0050.0000.0000.0000.000
100A100ARG10.8230.90125.7860.0250.0250.0000.0000.0000.000
101A101MET0-0.075-0.03426.6290.0040.0040.0000.0000.0000.000
102A102LEU00.0010.00719.2980.0090.0090.0000.0000.0000.000
103A103GLY00.0330.01422.7070.0000.0000.0000.0000.0000.000
104A104ALA00.011-0.00224.5140.0010.0010.0000.0000.0000.000
105A105LEU00.0240.00621.4730.0060.0060.0000.0000.0000.000
106A106TYR00.0620.01317.0410.0080.0080.0000.0000.0000.000
107A107MET00.0270.02421.733-0.002-0.0020.0000.0000.0000.000
108A108ARG10.8330.91324.609-0.046-0.0460.0000.0000.0000.000
109A109LEU0-0.067-0.03519.0600.0120.0120.0000.0000.0000.000
110A110THR0-0.060-0.04918.9670.0040.0040.0000.0000.0000.000
111A111GLY00.0180.03021.780-0.009-0.0090.0000.0000.0000.000
112A112THR0-0.034-0.03825.3780.0140.0140.0000.0000.0000.000
113A113ALA00.0160.00128.2990.0000.0000.0000.0000.0000.000
114A114ILE00.0270.01531.309-0.001-0.0010.0000.0000.0000.000
115A115ASP-1-0.787-0.86128.060-0.043-0.0430.0000.0000.0000.000
116A116CYS0-0.028-0.01028.4790.0000.0000.0000.0000.0000.000
117A117TYR00.001-0.00830.6260.0010.0010.0000.0000.0000.000
118A118LYS10.9190.96833.2000.0430.0430.0000.0000.0000.000
119A119TYR0-0.035-0.03330.150-0.002-0.0020.0000.0000.0000.000
120A120LEU00.0060.00628.379-0.001-0.0010.0000.0000.0000.000
121A121GLU-1-0.867-0.92432.5430.0060.0060.0000.0000.0000.000
122A122PRO0-0.038-0.01535.1600.0010.0010.0000.0000.0000.000
123A123LEU0-0.023-0.00631.4160.0000.0000.0000.0000.0000.000
124A124TYR0-0.030-0.04835.7170.0020.0020.0000.0000.0000.000
125A125ASN0-0.094-0.05138.1530.0020.0020.0000.0000.0000.000
126A126ASP-1-0.759-0.83935.053-0.011-0.0110.0000.0000.0000.000
127A127TYR00.0400.01537.4890.0020.0020.0000.0000.0000.000
128A128ARG10.7310.84534.1370.0190.0190.0000.0000.0000.000
129A129LYS10.9150.95136.160-0.011-0.0110.0000.0000.0000.000
130A130ILE0-0.028-0.01230.219-0.006-0.0060.0000.0000.0000.000
131A131LYS10.9510.98030.074-0.019-0.0190.0000.0000.0000.000
132A132SER00.0420.02528.3460.0020.0020.0000.0000.0000.000
133A133GLN0-0.064-0.03124.6420.0050.0050.0000.0000.0000.000
134A134ASN00.0130.00826.3710.0190.0190.0000.0000.0000.000
135A135ARG10.8580.88322.163-0.176-0.1760.0000.0000.0000.000
136A136ASN0-0.059-0.05226.2440.0140.0140.0000.0000.0000.000
137A137GLY0-0.018-0.00126.8910.0000.0000.0000.0000.0000.000
138A138GLU-1-0.890-0.91327.8610.0570.0570.0000.0000.0000.000
139A139PHE0-0.056-0.04726.7880.0030.0030.0000.0000.0000.000
140A140GLU-1-0.834-0.89731.4370.0590.0590.0000.0000.0000.000
141A141LEU0-0.092-0.06432.815-0.002-0.0020.0000.0000.0000.000
142A142MET00.0350.04131.6180.0030.0030.0000.0000.0000.000
143A143HIS00.0370.00535.299-0.005-0.0050.0000.0000.0000.000
144A144VAL0-0.017-0.01632.5330.0040.0040.0000.0000.0000.000
145A145ASP-1-0.837-0.93033.5930.0170.0170.0000.0000.0000.000
146A146GLU-1-0.827-0.90635.2400.0320.0320.0000.0000.0000.000
147A147PHE0-0.002-0.00625.5280.0050.0050.0000.0000.0000.000
148A148ILE0-0.023-0.02130.7380.0030.0030.0000.0000.0000.000
149A149ASP-1-0.769-0.85332.5320.0300.0300.0000.0000.0000.000
150A150GLU-1-0.922-0.96230.5980.0640.0640.0000.0000.0000.000
151A151LEU0-0.067-0.03526.3410.0060.0060.0000.0000.0000.000
152A152LEU0-0.040-0.02029.6930.0020.0020.0000.0000.0000.000
153A153HIS10.7770.87932.385-0.029-0.0290.0000.0000.0000.000
154A154SER00.0190.02930.5730.0010.0010.0000.0000.0000.000
155A155GLU-1-0.936-0.96428.7060.0900.0900.0000.0000.0000.000
156A156ARG10.8800.92824.060-0.135-0.1350.0000.0000.0000.000
157A157VAL00.1120.06724.932-0.007-0.0070.0000.0000.0000.000
158A158CYS0-0.056-0.00622.1130.0080.0080.0000.0000.0000.000
159A159ASP-1-0.829-0.90120.9900.1890.1890.0000.0000.0000.000
160A160ILE0-0.017-0.00718.6790.0340.0340.0000.0000.0000.000
161A161ILE0-0.033-0.02021.239-0.021-0.0210.0000.0000.0000.000
162A162LEU00.0110.01222.5560.0030.0030.0000.0000.0000.000
163A163PRO00.0140.02622.0810.0010.0010.0000.0000.0000.000
164A164ARG10.9570.96524.517-0.076-0.0760.0000.0000.0000.000
165A165LEU00.0620.03927.000-0.003-0.0030.0000.0000.0000.000
166A166GLN00.0070.00927.8170.0030.0030.0000.0000.0000.000
167A167LYS10.9850.97229.697-0.028-0.0280.0000.0000.0000.000
168A168ARG10.9090.96032.349-0.017-0.0170.0000.0000.0000.000
169A169TYR00.0490.00631.7020.0000.0000.0000.0000.0000.000
170A170VAL0-0.046-0.02527.0560.0020.0020.0000.0000.0000.000
171A171LEU00.0300.03227.1800.0000.0000.0000.0000.0000.000
172A172GLU-1-0.929-0.98221.491-0.032-0.0320.0000.0000.0000.000
173A173GLU-1-0.834-0.90020.874-0.165-0.1650.0000.0000.0000.000
174A174ALA0-0.013-0.02023.6770.0080.0080.0000.0000.0000.000
175A175GLU-1-0.939-0.96224.610-0.144-0.1440.0000.0000.0000.000
176A176GLN0-0.086-0.04823.4410.0110.0110.0000.0000.0000.000
177A177LEU00.0150.00627.5010.0080.0080.0000.0000.0000.000
178A178GLU-1-0.929-0.96830.934-0.046-0.0460.0000.0000.0000.000
179A179PRO0-0.063-0.00932.6250.0050.0050.0000.0000.0000.000