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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

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FMODB ID: 3JJZL

Calculation Name: 4R3O-K-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4R3O

Chain ID: K

ChEMBL ID:

UniProt ID: P25786

Base Structure: X-ray

Registration Date: 2023-09-21

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 199
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2330921.214106
FMO2-HF: Nuclear repulsion 2250886.306067
FMO2-HF: Total energy -80034.908039
FMO2-MP2: Total energy -80266.554345


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(K:1:MET)


Summations of interaction energy for fragment #1(K: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.
-2.69-2.55415.459-3.124-12.47-0.008
Interaction energy analysis for fragmet #1(K:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.001 / q_NPA : 0.024
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].
3K3TYR0-0.047-0.0442.691-4.050-1.5951.299-1.305-2.450-0.006
4K4LEU0-0.010-0.0035.2790.4170.505-0.001-0.005-0.0820.000
5K5ILE00.001-0.0028.005-0.040-0.0400.0000.0000.0000.000
6K6GLY00.0190.01211.0670.0640.0640.0000.0000.0000.000
7K7ILE00.001-0.01314.4420.0030.0030.0000.0000.0000.000
8K8GLN0-0.010-0.00517.7260.0190.0190.0000.0000.0000.000
9K9GLY00.0280.03020.842-0.001-0.0010.0000.0000.0000.000
10K10PRO0-0.029-0.02624.2580.0080.0080.0000.0000.0000.000
11K11ASP-1-0.836-0.92127.509-0.143-0.1430.0000.0000.0000.000
12K12TYR0-0.043-0.04522.191-0.006-0.0060.0000.0000.0000.000
13K13VAL0-0.030-0.01018.458-0.007-0.0070.0000.0000.0000.000
14K14LEU0-0.0250.00117.8910.0050.0050.0000.0000.0000.000
15K15VAL00.014-0.00914.486-0.018-0.0180.0000.0000.0000.000
16K16ALA00.0210.00113.3300.0250.0250.0000.0000.0000.000
17K17SER00.0250.0109.7470.0140.0140.0000.0000.0000.000
18K18ASP-1-0.772-0.8705.528-3.018-3.0180.0000.0000.0000.000
19K19ARG10.8680.9358.3620.6970.6970.0000.0000.0000.000
20K20VAL0-0.031-0.0124.4890.2690.371-0.001-0.006-0.0950.000
21K21ALA00.0000.0035.510-0.321-0.3210.0000.0000.0000.000
22K22ALA0-0.024-0.0143.627-0.1260.0170.002-0.025-0.1190.000
23K23SER00.0270.0115.7090.2900.2900.0000.0000.0000.000
24K24ASN0-0.005-0.0108.165-0.109-0.1090.0000.0000.0000.000
25K25ILE00.0210.0158.1110.3990.3990.0000.0000.0000.000
26K26VAL0-0.027-0.0039.325-0.165-0.1650.0000.0000.0000.000
27K27GLN0-0.010-0.0177.3620.2120.2120.0000.0000.0000.000
28K28MET0-0.046-0.0228.297-0.014-0.0140.0000.0000.0000.000
29K29LYS10.8170.9009.1590.1230.1230.0000.0000.0000.000
30K30ASP-1-0.873-0.9358.877-0.436-0.4360.0000.0000.0000.000
31K31ASP-1-0.793-0.89310.811-0.269-0.2690.0000.0000.0000.000
32K32HIS0-0.029-0.0147.8750.0560.0560.0000.0000.0000.000
33K33ASP-1-0.781-0.89111.241-0.439-0.4390.0000.0000.0000.000
34K34LYS10.8440.9205.6621.6881.6880.0000.0000.0000.000
35K35MET0-0.072-0.01111.6960.0960.0960.0000.0000.0000.000
36K36PHE00.0160.01413.3800.0350.0350.0000.0000.0000.000
37K37LYS10.8940.95517.5550.1620.1620.0000.0000.0000.000
38K38MET00.0350.02619.4210.0300.0300.0000.0000.0000.000
39K39SER0-0.050-0.02222.4280.0150.0150.0000.0000.0000.000
40K40GLU-1-0.854-0.91924.726-0.079-0.0790.0000.0000.0000.000
41K41LYS10.8820.94025.1320.0700.0700.0000.0000.0000.000
42K42ILE0-0.008-0.00220.429-0.007-0.0070.0000.0000.0000.000
43K43LEU00.0050.00317.1300.0050.0050.0000.0000.0000.000
44K44LEU0-0.014-0.01714.595-0.004-0.0040.0000.0000.0000.000
45K45LEU0-0.007-0.00410.8080.0010.0010.0000.0000.0000.000
46K46CYS0-0.039-0.01210.4980.0470.0470.0000.0000.0000.000
47K47VAL00.0180.0034.188-0.323-0.1560.001-0.027-0.1410.000
48K48GLY0-0.027-0.0205.483-0.228-0.164-0.001-0.007-0.0560.000
49K49GLU-1-0.861-0.9126.4041.2471.334-0.001-0.002-0.0840.000
50K50ALA0-0.037-0.0318.752-0.131-0.1310.0000.0000.0000.000
51K51GLY0-0.009-0.00610.390-0.106-0.1060.0000.0000.0000.000
52K52ASP-1-0.820-0.92011.8010.4700.4700.0000.0000.0000.000
53K53THR00.0230.0038.791-0.171-0.1710.0000.0000.0000.000
54K54VAL00.0290.01212.088-0.100-0.1000.0000.0000.0000.000
55K55GLN0-0.0150.00315.070-0.058-0.0580.0000.0000.0000.000
56K56PHE00.0270.01615.059-0.044-0.0440.0000.0000.0000.000
57K57ALA00.0070.00114.746-0.042-0.0420.0000.0000.0000.000
58K58GLU-1-0.836-0.91416.7810.0340.0340.0000.0000.0000.000
59K59TYR0-0.026-0.00419.901-0.021-0.0210.0000.0000.0000.000
60K60ILE0-0.0030.00118.652-0.021-0.0210.0000.0000.0000.000
61K61GLN0-0.007-0.00220.5430.0000.0000.0000.0000.0000.000
62K62LYS10.8200.88122.219-0.045-0.0450.0000.0000.0000.000
63K63ASN0-0.052-0.03224.523-0.009-0.0090.0000.0000.0000.000
64K64VAL0-0.0150.00423.058-0.005-0.0050.0000.0000.0000.000
65K65GLN0-0.025-0.02725.907-0.004-0.0040.0000.0000.0000.000
66K66LEU0-0.0040.00728.156-0.002-0.0020.0000.0000.0000.000
67K67TYR0-0.017-0.01029.2580.0000.0000.0000.0000.0000.000
68K68LYS10.8330.90629.4150.0450.0450.0000.0000.0000.000
69K69MET0-0.040-0.02331.860-0.003-0.0030.0000.0000.0000.000
70K70ARG10.8860.95333.392-0.011-0.0110.0000.0000.0000.000
71K71ASN0-0.033-0.01533.2640.0030.0030.0000.0000.0000.000
72K72GLY0-0.0070.01935.735-0.001-0.0010.0000.0000.0000.000
73K73TYR0-0.0020.00133.532-0.004-0.0040.0000.0000.0000.000
74K74GLU-1-0.755-0.89428.752-0.059-0.0590.0000.0000.0000.000
75K75LEU0-0.010-0.00126.1310.0000.0000.0000.0000.0000.000
76K76SER00.0820.04327.453-0.006-0.0060.0000.0000.0000.000
77K77PRO00.0900.02622.4890.0070.0070.0000.0000.0000.000
78K78THR00.0340.02522.526-0.002-0.0020.0000.0000.0000.000
79K79ALA00.0140.01924.0320.0080.0080.0000.0000.0000.000
80K80ALA00.0250.01322.2750.0110.0110.0000.0000.0000.000
81K81ALA00.0140.00919.6600.0140.0140.0000.0000.0000.000
82K82ASN0-0.028-0.04520.2230.0190.0190.0000.0000.0000.000
83K83PHE00.0190.03022.8430.0140.0140.0000.0000.0000.000
84K84THR00.0120.00817.5830.0230.0230.0000.0000.0000.000
85K85ARG10.9490.96018.572-0.010-0.0100.0000.0000.0000.000
86K86ARG10.8170.89619.562-0.034-0.0340.0000.0000.0000.000
87K87ASN0-0.010-0.02420.9610.0170.0170.0000.0000.0000.000
88K88LEU00.0300.01913.9620.0060.0060.0000.0000.0000.000
89K89ALA0-0.039-0.02318.5580.0190.0190.0000.0000.0000.000
90K90ASP-1-0.874-0.92520.6030.0770.0770.0000.0000.0000.000
91K91CYS0-0.051-0.01819.6300.0020.0020.0000.0000.0000.000
92K92LEU00.0040.03217.0780.0200.0200.0000.0000.0000.000
93K93ARG10.9350.95819.889-0.093-0.0930.0000.0000.0000.000
94K94SER0-0.026-0.01121.598-0.011-0.0110.0000.0000.0000.000
95K95ARG10.9710.96922.074-0.177-0.1770.0000.0000.0000.000
96K96THR0-0.060-0.03419.9680.0110.0110.0000.0000.0000.000
97K97PRO0-0.0010.02716.717-0.013-0.0130.0000.0000.0000.000
98K98TYR00.015-0.00514.4680.0220.0220.0000.0000.0000.000
99K99HIS00.0140.0019.728-0.002-0.0020.0000.0000.0000.000
100K100VAL0-0.038-0.0179.4950.1870.1870.0000.0000.0000.000
101K101ASN00.0000.0045.695-0.248-0.2480.0000.0000.0000.000
102K102LEU0-0.007-0.0248.732-0.017-0.0170.0000.0000.0000.000
103K103LEU0-0.0030.00010.146-0.044-0.0440.0000.0000.0000.000
104K104LEU0-0.045-0.00912.6820.0300.0300.0000.0000.0000.000
105K105ALA00.0240.02016.363-0.009-0.0090.0000.0000.0000.000
106K106GLY00.004-0.02118.3920.0210.0210.0000.0000.0000.000
107K107TYR0-0.0050.00522.141-0.012-0.0120.0000.0000.0000.000
108K108ASP-1-0.871-0.95325.658-0.063-0.0630.0000.0000.0000.000
109K109GLU-1-0.856-0.91228.626-0.086-0.0860.0000.0000.0000.000
110K110HIS0-0.067-0.02431.7090.0010.0010.0000.0000.0000.000
111K111GLU-1-0.951-0.98128.649-0.075-0.0750.0000.0000.0000.000
112K112GLY0-0.0030.02328.570-0.007-0.0070.0000.0000.0000.000
113K113PRO0-0.036-0.00523.7320.0020.0020.0000.0000.0000.000
114K114ALA0-0.045-0.03422.1900.0050.0050.0000.0000.0000.000
115K115LEU00.0340.02014.745-0.012-0.0120.0000.0000.0000.000
116K116TYR0-0.041-0.03817.0060.0110.0110.0000.0000.0000.000
117K117TYR00.0170.0178.9640.0270.0270.0000.0000.0000.000
118K118MET0-0.025-0.00812.3640.0290.0290.0000.0000.0000.000
119K119ASP-1-0.812-0.91110.7430.1100.1100.0000.0000.0000.000
120K120TYR00.0570.0279.9940.0310.0310.0000.0000.0000.000
121K121LEU0-0.073-0.02111.8960.0010.0010.0000.0000.0000.000
122K122ALA0-0.023-0.00414.572-0.025-0.0250.0000.0000.0000.000
123K123ALA0-0.028-0.00615.519-0.017-0.0170.0000.0000.0000.000
124K124LEU0-0.017-0.01215.755-0.014-0.0140.0000.0000.0000.000
125K125ALA0-0.001-0.00316.4160.0030.0030.0000.0000.0000.000
126K126LYS10.9180.97617.2670.1100.1100.0000.0000.0000.000
127K127ALA0-0.002-0.00116.6240.0040.0040.0000.0000.0000.000
128K128PRO00.0070.02118.769-0.002-0.0020.0000.0000.0000.000
129K129PHE00.010-0.01115.458-0.013-0.0130.0000.0000.0000.000
130K130ALA0-0.0220.00212.3580.0230.0230.0000.0000.0000.000
131K131ALA00.0220.0018.689-0.042-0.0420.0000.0000.0000.000
132K132HIS00.0110.0125.1990.0510.0510.0000.0000.0000.000
133K133GLY00.0570.0212.053-0.353-1.4244.057-1.952-1.0340.008
134K134TYR0-0.008-0.0222.2080.576-0.6353.9911.980-4.760-0.011
135K135GLY00.0570.0254.0340.2820.4720.003-0.040-0.1540.000
136K136ALA00.0450.0326.1300.3660.3660.0000.0000.0000.000
137K137PHE0-0.019-0.0076.0240.1940.1940.0000.0000.0000.000
138K138LEU0-0.036-0.0099.3580.1410.1410.0000.0000.0000.000
139K139THR0-0.033-0.0209.7400.0630.0630.0000.0000.0000.000
140K140LEU00.0220.01110.6500.0850.0850.0000.0000.0000.000
141K141SER00.0670.04613.5450.0400.0400.0000.0000.0000.000
142K142ILE00.0020.00315.1640.0540.0540.0000.0000.0000.000
143K143LEU00.002-0.00913.9430.0420.0420.0000.0000.0000.000
144K144ASP-1-0.855-0.94517.401-0.287-0.2870.0000.0000.0000.000
145K145ARG10.8120.91819.6120.2500.2500.0000.0000.0000.000
146K146TYR0-0.072-0.05120.6660.0400.0400.0000.0000.0000.000
147K147TYR0-0.0080.00120.3270.0140.0140.0000.0000.0000.000
148K148THR0-0.023-0.01522.4180.0160.0160.0000.0000.0000.000
149K149PRO00.0630.01225.219-0.007-0.0070.0000.0000.0000.000
150K150THR0-0.026-0.00526.2240.0030.0030.0000.0000.0000.000
151K151ILE0-0.0400.00522.5260.0060.0060.0000.0000.0000.000
152K152SER00.026-0.00126.264-0.004-0.0040.0000.0000.0000.000
153K153ARG10.9210.93124.3950.1520.1520.0000.0000.0000.000
154K154GLU-1-0.828-0.89324.152-0.210-0.2100.0000.0000.0000.000
155K155ARG10.8620.90224.6970.1840.1840.0000.0000.0000.000
156K156ALA0-0.0040.01421.104-0.023-0.0230.0000.0000.0000.000
157K157VAL00.0310.00820.173-0.045-0.0450.0000.0000.0000.000
158K158GLU-1-0.853-0.89420.172-0.285-0.2850.0000.0000.0000.000
159K159LEU0-0.016-0.01118.511-0.023-0.0230.0000.0000.0000.000
160K160LEU00.0340.01514.095-0.046-0.0460.0000.0000.0000.000
161K161ARG10.9550.97315.7560.2840.2840.0000.0000.0000.000
162K162LYS10.9180.96017.1830.2660.2660.0000.0000.0000.000
163K163CYS0-0.043-0.01113.032-0.005-0.0050.0000.0000.0000.000
164K164LEU00.0190.00511.468-0.098-0.0980.0000.0000.0000.000
165K165GLU-1-0.918-0.96712.732-0.479-0.4790.0000.0000.0000.000
166K166GLU-1-0.877-0.94913.675-0.473-0.4730.0000.0000.0000.000
167K167LEU0-0.091-0.0398.128-0.038-0.0380.0000.0000.0000.000
168K168GLN0-0.048-0.02810.2070.0700.0700.0000.0000.0000.000
169K169LYS10.8790.96412.1650.4270.4270.0000.0000.0000.000
170K170ARG10.9070.94712.8830.4200.4200.0000.0000.0000.000
171K171PHE0-0.0060.0023.298-0.3330.1550.015-0.090-0.4130.000
172K172ILE00.0460.0167.0010.0510.0510.0000.0000.0000.000
173K173LEU0-0.054-0.0121.9820.095-1.6026.090-1.553-2.8390.001
174K174ASN00.0150.0055.351-0.391-0.350-0.0010.000-0.0390.000
175K175LEU00.0030.0003.566-0.0590.2310.006-0.092-0.2040.000
176K176PRO00.0520.0407.2430.1550.1550.0000.0000.0000.000
177K177THR00.021-0.00310.2940.1120.1120.0000.0000.0000.000
178K178PHE00.0100.0008.524-0.243-0.2430.0000.0000.0000.000
179K179SER00.0250.02012.4180.1270.1270.0000.0000.0000.000
180K180VAL0-0.008-0.00814.491-0.066-0.0660.0000.0000.0000.000
181K181ARG10.7930.87316.6220.3330.3330.0000.0000.0000.000
182K182ILE0-0.016-0.00718.962-0.023-0.0230.0000.0000.0000.000
183K183ILE0-0.0150.00219.7830.0210.0210.0000.0000.0000.000
184K184ASP-1-0.756-0.86623.357-0.151-0.1510.0000.0000.0000.000
185K185LYS10.8410.90426.7980.0900.0900.0000.0000.0000.000
186K186ASN0-0.093-0.05729.7420.0160.0160.0000.0000.0000.000
187K187GLY00.0220.02727.1850.0060.0060.0000.0000.0000.000
188K188ILE0-0.063-0.04021.723-0.014-0.0140.0000.0000.0000.000
189K189HIS0-0.010-0.00323.8900.0100.0100.0000.0000.0000.000
190K190ASP-1-0.838-0.91521.580-0.249-0.2490.0000.0000.0000.000
191K191LEU0-0.048-0.02421.0040.0160.0160.0000.0000.0000.000
192K192ASP-1-0.901-0.94620.526-0.255-0.2550.0000.0000.0000.000
193K193ASN0-0.028-0.02416.075-0.067-0.0670.0000.0000.0000.000
194K194ILE0-0.0070.00715.5110.0360.0360.0000.0000.0000.000
195K195SER0-0.015-0.01614.719-0.076-0.0760.0000.0000.0000.000
196K196PHE0-0.001-0.00113.2220.0460.0460.0000.0000.0000.000
197K197PRO0-0.005-0.01015.558-0.011-0.0110.0000.0000.0000.000
198K198LYS10.8590.94910.5100.7390.7390.0000.0000.0000.000
199K199GLN00.0040.01014.9220.0050.0050.0000.0000.0000.000