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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

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FMODB ID: PJM99

Calculation Name: 4RZ9-A-Xray13

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: 2018-03-01

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water No
Procedure Auto-FMO protocol ver. 1.20181228
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 179
LigandCharge
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -2103487.145194
FMO2-HF: Nuclear repulsion 2028606.686108
FMO2-HF: Total energy -74880.459086
FMO2-MP2: Total energy -75095.701642


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.
60.53366.76414.443-6.249-14.425-0.064
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 : 1 / q_Mulliken : 0.803 / q_NPA : 0.897
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].
3A3ASN00.0430.0411.9295.0078.0794.933-2.788-5.217-0.016
4A4ARG10.9540.9672.06459.38660.8488.800-3.010-7.253-0.039
5A5THR00.0470.0073.4752.1832.2540.0610.146-0.278-0.001
6A6VAL00.0040.0316.937-2.967-2.9670.0000.0000.0000.000
7A7LYS10.9400.9509.59321.73421.7340.0000.0000.0000.000
8A8ASP-1-0.933-0.96111.397-19.425-19.4250.0000.0000.0000.000
9A9ALA00.0120.02911.3881.0331.0330.0000.0000.0000.000
10A10HIS0-0.011-0.00313.463-0.189-0.1890.0000.0000.0000.000
11A11SER0-0.086-0.04613.744-0.305-0.3050.0000.0000.0000.000
12A12ILE00.0450.02114.5800.8730.8730.0000.0000.0000.000
13A13HIS00.019-0.00115.767-0.522-0.5220.0000.0000.0000.000
14A14GLY0-0.0040.00617.464-0.058-0.0580.0000.0000.0000.000
15A15THR0-0.010-0.00612.071-1.266-1.2660.0000.0000.0000.000
16A16ASN00.0300.0376.2221.2221.2220.0000.0000.0000.000
17A17PRO00.1410.07210.343-0.023-0.0230.0000.0000.0000.000
18A18GLN00.026-0.0024.9381.2101.2100.0000.0000.0000.000
19A19TYR0-0.153-0.0885.323-0.358-0.3580.0000.0000.0000.000
20A20LEU00.0510.0429.5620.7510.7510.0000.0000.0000.000
21A21VAL00.0290.03310.2870.9320.9320.0000.0000.0000.000
22A22GLU-1-0.872-0.9389.938-19.579-19.5790.0000.0000.0000.000
23A23LYS10.9790.9865.57624.92124.9210.0000.0000.0000.000
24A24ILE0-0.025-0.0257.036-1.722-1.7220.0000.0000.0000.000
25A25ILE00.0780.0369.417-0.002-0.0020.0000.0000.0000.000
26A26ARG10.9150.9644.71029.39529.502-0.001-0.003-0.1020.000
27A27THR0-0.074-0.0345.657-1.782-1.7820.0000.0000.0000.000
28A28ARG10.9580.9846.50418.73318.7330.0000.0000.0000.000
29A29ILE00.0170.0129.0490.6040.6040.0000.0000.0000.000
30A30TYR0-0.057-0.0473.007-2.921-1.4020.650-0.594-1.575-0.008
31A31GLU-1-0.951-0.9627.589-21.942-21.9420.0000.0000.0000.000
32A32SER0-0.044-0.03110.2982.0082.0080.0000.0000.0000.000
33A33LYS10.8660.91812.98813.40613.4060.0000.0000.0000.000
34A34TYR00.0910.04014.985-0.085-0.0850.0000.0000.0000.000
35A35TRP00.014-0.0087.0340.2090.2090.0000.0000.0000.000
36A36LYS10.8720.92610.86720.59720.5970.0000.0000.0000.000
37A37GLU-1-0.855-0.93512.705-15.307-15.3070.0000.0000.0000.000
38A38GLU-1-0.841-0.89315.904-13.840-13.8400.0000.0000.0000.000
39A39CYS0-0.033-0.01012.4040.2630.2630.0000.0000.0000.000
40A40PHE0-0.037-0.00811.340-1.278-1.2780.0000.0000.0000.000
41A41GLY0-0.020-0.02211.1660.9430.9430.0000.0000.0000.000
42A42LEU0-0.035-0.01012.7400.6470.6470.0000.0000.0000.000
43A43THR00.0460.03713.433-1.166-1.1660.0000.0000.0000.000
44A44ALA00.0380.00616.0430.3650.3650.0000.0000.0000.000
45A45GLU-1-0.872-0.94917.905-11.881-11.8810.0000.0000.0000.000
46A46LEU0-0.022-0.00118.3570.2280.2280.0000.0000.0000.000
47A47VAL0-0.051-0.02216.5500.0430.0430.0000.0000.0000.000
48A48VAL00.0470.01419.1290.1270.1270.0000.0000.0000.000
49A49ASP-1-0.870-0.93122.050-11.874-11.8740.0000.0000.0000.000
50A50LYS10.8310.89618.20614.23214.2320.0000.0000.0000.000
51A51ALA0-0.014-0.02221.2650.2100.2100.0000.0000.0000.000
52A52MET0-0.044-0.01622.4510.4830.4830.0000.0000.0000.000
53A53GLU-1-0.967-0.96023.625-11.643-11.6430.0000.0000.0000.000
54A54LEU0-0.086-0.03020.2090.0170.0170.0000.0000.0000.000
55A55ARG10.9080.93824.23810.54110.5410.0000.0000.0000.000
56A56PHE0-0.079-0.05522.6420.4220.4220.0000.0000.0000.000
57A57VAL00.0400.03823.472-0.467-0.4670.0000.0000.0000.000
58A58GLY00.0530.00921.9000.3270.3270.0000.0000.0000.000
59A59GLY00.0610.04118.185-0.423-0.4230.0000.0000.0000.000
60A60VAL0-0.083-0.05214.738-0.569-0.5690.0000.0000.0000.000
61A61TYR00.0290.01017.8680.7320.7320.0000.0000.0000.000
62A62GLY00.0290.01919.800-0.403-0.4030.0000.0000.0000.000
63A63GLY00.0080.00120.560-0.327-0.3270.0000.0000.0000.000
64A64ASN0-0.012-0.00417.530-0.032-0.0320.0000.0000.0000.000
65A65ILE0-0.061-0.03113.719-0.787-0.7870.0000.0000.0000.000
66A66LYS10.9570.97615.04312.23212.2320.0000.0000.0000.000
67A67PRO00.0260.01712.8630.5250.5250.0000.0000.0000.000
68A68THR0-0.003-0.00315.7040.1650.1650.0000.0000.0000.000
69A69PRO00.0350.00616.925-0.693-0.6930.0000.0000.0000.000
70A70PHE00.0560.04217.369-0.627-0.6270.0000.0000.0000.000
71A71LEU00.0100.02414.021-0.512-0.5120.0000.0000.0000.000
72A72CYS0-0.069-0.03112.877-1.288-1.2880.0000.0000.0000.000
73A73LEU00.0380.01612.981-1.278-1.2780.0000.0000.0000.000
74A74THR00.0390.02515.152-0.141-0.1410.0000.0000.0000.000
75A75LEU0-0.044-0.0247.614-0.618-0.6180.0000.0000.0000.000
76A76LYS10.8480.9248.93523.52923.5290.0000.0000.0000.000
77A77MET00.0300.01811.648-0.549-0.5490.0000.0000.0000.000
78A78LEU0-0.0180.00011.400-0.266-0.2660.0000.0000.0000.000
79A79GLN0-0.095-0.0485.6801.4491.4490.0000.0000.0000.000
80A80ILE0-0.008-0.0369.542-1.322-1.3220.0000.0000.0000.000
81A81GLN0-0.0410.01212.1040.6580.6580.0000.0000.0000.000
82A82PRO00.0150.01114.8640.2960.2960.0000.0000.0000.000
83A83GLU-1-0.835-0.91018.009-14.015-14.0150.0000.0000.0000.000
84A84LYS10.8470.90321.24811.10911.1090.0000.0000.0000.000
85A85ASP-1-0.900-0.96223.477-11.204-11.2040.0000.0000.0000.000
86A86ILE00.1310.08420.7910.1690.1690.0000.0000.0000.000
87A87ILE0-0.060-0.02419.5390.1410.1410.0000.0000.0000.000
88A88VAL0-0.042-0.03123.5790.3730.3730.0000.0000.0000.000
89A89GLU-1-0.889-0.94526.472-10.531-10.5310.0000.0000.0000.000
90A90PHE0-0.049-0.04720.7260.1440.1440.0000.0000.0000.000
91A91ILE0-0.044-0.01925.5750.2930.2930.0000.0000.0000.000
92A92LYS10.9200.95128.3859.3089.3080.0000.0000.0000.000
93A93ASN00.0330.04228.7080.5040.5040.0000.0000.0000.000
94A94GLU-1-0.917-0.96531.233-8.514-8.5140.0000.0000.0000.000
95A95ASP-1-0.934-0.94432.011-8.631-8.6310.0000.0000.0000.000
96A96PHE0-0.062-0.04528.661-0.030-0.0300.0000.0000.0000.000
97A97LYS10.9360.96929.4428.7228.7220.0000.0000.0000.000
98A98TYR00.0300.01425.272-0.017-0.0170.0000.0000.0000.000
99A99VAL00.0550.04524.703-0.415-0.4150.0000.0000.0000.000
100A100ARG10.9030.95225.1868.7938.7930.0000.0000.0000.000
101A101MET0-0.054-0.02425.706-0.133-0.1330.0000.0000.0000.000
102A102LEU0-0.0040.00218.574-0.279-0.2790.0000.0000.0000.000
103A103GLY00.0140.00121.570-0.481-0.4810.0000.0000.0000.000
104A104ALA00.0250.01123.283-0.148-0.1480.0000.0000.0000.000
105A105LEU00.0310.00718.891-0.096-0.0960.0000.0000.0000.000
106A106TYR00.0500.00915.202-0.798-0.7980.0000.0000.0000.000
107A107MET00.0270.01619.856-0.362-0.3620.0000.0000.0000.000
108A108ARG10.8510.92122.57011.59711.5970.0000.0000.0000.000
109A109LEU0-0.072-0.03716.295-0.159-0.1590.0000.0000.0000.000
110A110THR0-0.069-0.05516.605-0.346-0.3460.0000.0000.0000.000
111A111GLY00.0280.02919.3080.0000.0000.0000.0000.0000.000
112A112THR0-0.002-0.00522.9200.0440.0440.0000.0000.0000.000
113A113ALA00.0510.01125.4820.0640.0640.0000.0000.0000.000
114A114ILE00.0500.02928.0430.1020.1020.0000.0000.0000.000
115A115ASP-1-0.858-0.93526.581-10.333-10.3330.0000.0000.0000.000
116A116CYS0-0.062-0.01925.552-0.052-0.0520.0000.0000.0000.000
117A117TYR00.0420.00027.8930.0970.0970.0000.0000.0000.000
118A118LYS10.9740.99931.3259.1989.1980.0000.0000.0000.000
119A119TYR0-0.074-0.06028.1340.1880.1880.0000.0000.0000.000
120A120LEU0-0.0160.00126.347-0.021-0.0210.0000.0000.0000.000
121A121GLU-1-0.735-0.83730.504-8.241-8.2410.0000.0000.0000.000
122A122PRO0-0.048-0.01333.1990.1990.1990.0000.0000.0000.000
123A123LEU0-0.032-0.02730.0150.1720.1720.0000.0000.0000.000
124A124TYR00.008-0.01134.019-0.029-0.0290.0000.0000.0000.000
125A125ASN0-0.051-0.02036.3990.3210.3210.0000.0000.0000.000
126A126ASP-1-0.791-0.86134.170-8.452-8.4520.0000.0000.0000.000
127A127TYR00.0500.01736.156-0.095-0.0950.0000.0000.0000.000
128A128ARG10.7620.86333.5148.5988.5980.0000.0000.0000.000
129A129LYS10.9840.99635.0647.3867.3860.0000.0000.0000.000
130A130ILE0-0.048-0.02828.782-0.111-0.1110.0000.0000.0000.000
131A131LYS10.9220.96628.9169.7169.7160.0000.0000.0000.000
132A132SER00.0360.01426.611-0.487-0.4870.0000.0000.0000.000
133A133GLN0-0.065-0.03623.110-0.094-0.0940.0000.0000.0000.000
134A134ASN00.0470.02824.150-0.588-0.5880.0000.0000.0000.000
135A135ARG10.9290.97019.36112.42212.4220.0000.0000.0000.000
136A136ASN0-0.009-0.03023.015-0.517-0.5170.0000.0000.0000.000
137A137GLY0-0.042-0.02724.5090.0680.0680.0000.0000.0000.000
138A138GLU-1-0.902-0.93325.372-9.182-9.1820.0000.0000.0000.000
139A139PHE0-0.065-0.04425.946-0.227-0.2270.0000.0000.0000.000
140A140GLU-1-0.868-0.92429.677-8.943-8.9430.0000.0000.0000.000
141A141LEU0-0.085-0.06531.050-0.169-0.1690.0000.0000.0000.000
142A142MET00.0250.03929.345-0.070-0.0700.0000.0000.0000.000
143A143HIS00.0410.01133.337-0.099-0.0990.0000.0000.0000.000
144A144VAL0-0.067-0.04131.303-0.240-0.2400.0000.0000.0000.000
145A145ASP-1-0.837-0.93031.850-8.269-8.2690.0000.0000.0000.000
146A146GLU-1-0.810-0.90632.957-8.310-8.3100.0000.0000.0000.000
147A147PHE0-0.022-0.01423.551-0.327-0.3270.0000.0000.0000.000
148A148ILE0-0.046-0.03128.423-0.363-0.3630.0000.0000.0000.000
149A149ASP-1-0.822-0.90530.032-8.683-8.6830.0000.0000.0000.000
150A150GLU-1-0.944-0.97127.323-10.134-10.1340.0000.0000.0000.000
151A151LEU0-0.088-0.04423.871-0.353-0.3530.0000.0000.0000.000
152A152LEU0-0.031-0.01326.605-0.299-0.2990.0000.0000.0000.000
153A153HIS0-0.063-0.02129.2530.1180.1180.0000.0000.0000.000
154A154SER0-0.028-0.00426.7790.1530.1530.0000.0000.0000.000
155A155GLU-1-0.957-0.98024.286-10.769-10.7690.0000.0000.0000.000
156A156ARG10.8860.93519.80212.17712.1770.0000.0000.0000.000
157A157VAL00.1130.07021.2160.3330.3330.0000.0000.0000.000
158A158CYS0-0.041-0.01219.287-0.427-0.4270.0000.0000.0000.000
159A159ASP-1-0.894-0.95517.375-13.817-13.8170.0000.0000.0000.000
160A160ILE0-0.037-0.01615.185-0.895-0.8950.0000.0000.0000.000
161A161ILE0-0.028-0.01817.1340.7010.7010.0000.0000.0000.000
162A162LEU00.0030.01218.257-0.701-0.7010.0000.0000.0000.000
163A163PRO0-0.0040.00518.2900.2410.2410.0000.0000.0000.000
164A164ARG10.9410.96220.72611.68711.6870.0000.0000.0000.000
165A165LEU00.0280.03624.076-0.247-0.2470.0000.0000.0000.000
166A166GLN0-0.0180.00526.7740.2820.2820.0000.0000.0000.000
167A167LYS10.9790.98429.9939.1769.1760.0000.0000.0000.000
168A168ARG10.8310.86333.1677.9377.9370.0000.0000.0000.000
169A169TYR00.0590.02735.225-0.089-0.0890.0000.0000.0000.000
170A170VAL0-0.019-0.00134.4820.0690.0690.0000.0000.0000.000
171A171LEU0-0.027-0.02331.442-0.045-0.0450.0000.0000.0000.000
172A172GLU-1-0.856-0.91535.714-7.481-7.4810.0000.0000.0000.000
173A173GLU-1-0.950-0.97939.211-7.191-7.1910.0000.0000.0000.000
174A174ALA0-0.085-0.02636.6020.0910.0910.0000.0000.0000.000
175A175GLU-1-0.941-0.97238.266-7.278-7.2780.0000.0000.0000.000
176A176GLN0-0.100-0.05733.145-0.186-0.1860.0000.0000.0000.000
177A177LEU0-0.088-0.05633.725-0.251-0.2510.0000.0000.0000.000
178A178GLU-1-0.948-0.96637.516-7.027-7.0270.0000.0000.0000.000
179A179PRO-1-0.928-0.94440.430-7.110-7.1100.0000.0000.0000.000