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

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FMODB ID: LNNG9

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 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 199
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2337470.707154
FMO2-HF: Nuclear repulsion 2257435.51322
FMO2-HF: Total energy -80035.193934
FMO2-MP2: Total energy -80266.890566


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.
-5-1.06111.124-3.842-11.221-0.015
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 : -0.005 / q_NPA : 0.006
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].
3K3TYR0-0.060-0.0562.557-4.481-2.2771.994-1.830-2.369-0.010
4K4LEU0-0.011-0.0015.3120.4710.546-0.001-0.004-0.0700.000
5K5ILE0-0.003-0.0058.193-0.029-0.0290.0000.0000.0000.000
6K6GLY00.0190.01111.3960.0610.0610.0000.0000.0000.000
7K7ILE0-0.013-0.01714.8200.0030.0030.0000.0000.0000.000
8K8GLN00.0150.00618.2770.0200.0200.0000.0000.0000.000
9K9GLY00.0240.02621.236-0.004-0.0040.0000.0000.0000.000
10K10PRO0-0.028-0.01624.7870.0080.0080.0000.0000.0000.000
11K11ASP-1-0.835-0.92027.946-0.168-0.1680.0000.0000.0000.000
12K12TYR0-0.041-0.04122.274-0.004-0.0040.0000.0000.0000.000
13K13VAL0-0.028-0.02218.774-0.005-0.0050.0000.0000.0000.000
14K14LEU0-0.0190.00918.2010.0060.0060.0000.0000.0000.000
15K15VAL00.002-0.01614.595-0.014-0.0140.0000.0000.0000.000
16K16ALA00.007-0.00213.4190.0300.0300.0000.0000.0000.000
17K17SER00.0240.0109.6370.0140.0140.0000.0000.0000.000
18K18ASP-1-0.774-0.8745.977-3.055-3.0550.0000.0000.0000.000
19K19ARG10.8450.9268.9290.6890.6890.0000.0000.0000.000
20K20VAL0-0.030-0.0054.4070.2510.357-0.001-0.007-0.0980.000
21K21ALA00.0210.0195.678-0.263-0.2630.0000.0000.0000.000
22K22ALA0-0.008-0.0163.555-0.216-0.0750.003-0.028-0.1160.000
23K23SER00.0250.0095.6290.4040.4040.0000.0000.0000.000
24K24ASN0-0.002-0.0097.713-0.144-0.1440.0000.0000.0000.000
25K25ILE00.0050.0138.0280.4030.4030.0000.0000.0000.000
26K26VAL0-0.022-0.0058.550-0.254-0.2540.0000.0000.0000.000
27K27GLN0-0.008-0.0117.1350.2280.2280.0000.0000.0000.000
28K28MET0-0.051-0.0308.1110.0900.0900.0000.0000.0000.000
29K29LYS10.8280.9059.0940.2100.2100.0000.0000.0000.000
30K30ASP-1-0.867-0.9338.808-0.576-0.5760.0000.0000.0000.000
31K31ASP-1-0.786-0.88210.775-0.321-0.3210.0000.0000.0000.000
32K32HIS0-0.013-0.0017.5480.0730.0730.0000.0000.0000.000
33K33ASP-1-0.757-0.86911.244-0.506-0.5060.0000.0000.0000.000
34K34LYS10.7840.8966.2041.8301.8300.0000.0000.0000.000
35K35MET0-0.0330.01711.6620.0840.0840.0000.0000.0000.000
36K36PHE00.0440.02112.9800.0350.0350.0000.0000.0000.000
37K37LYS10.8870.94017.1370.2120.2120.0000.0000.0000.000
38K38MET00.0120.01119.3360.0340.0340.0000.0000.0000.000
39K39SER0-0.022-0.01822.3260.0200.0200.0000.0000.0000.000
40K40GLU-1-0.859-0.91324.631-0.098-0.0980.0000.0000.0000.000
41K41LYS10.8680.93925.2690.0850.0850.0000.0000.0000.000
42K42ILE00.001-0.00120.395-0.006-0.0060.0000.0000.0000.000
43K43LEU00.0080.01117.0180.0090.0090.0000.0000.0000.000
44K44LEU0-0.003-0.01214.396-0.004-0.0040.0000.0000.0000.000
45K45LEU0-0.0070.00511.0120.0100.0100.0000.0000.0000.000
46K46CYS0-0.061-0.03110.1520.0320.0320.0000.0000.0000.000
47K47VAL00.0410.0173.630-0.431-0.1740.006-0.054-0.2080.000
48K48GLY0-0.015-0.0135.655-0.202-0.140-0.001-0.006-0.0540.000
49K49GLU-1-0.862-0.9136.4231.7521.7520.0000.0000.0000.000
50K50ALA0-0.014-0.0188.607-0.255-0.2550.0000.0000.0000.000
51K51GLY0-0.0180.00210.115-0.166-0.1660.0000.0000.0000.000
52K52ASP-1-0.822-0.92011.6540.5440.5440.0000.0000.0000.000
53K53THR00.011-0.0158.521-0.194-0.1940.0000.0000.0000.000
54K54VAL00.0240.01411.848-0.124-0.1240.0000.0000.0000.000
55K55GLN0-0.021-0.00814.798-0.064-0.0640.0000.0000.0000.000
56K56PHE00.0230.01214.833-0.044-0.0440.0000.0000.0000.000
57K57ALA00.0110.00314.400-0.045-0.0450.0000.0000.0000.000
58K58GLU-1-0.842-0.91316.4820.0340.0340.0000.0000.0000.000
59K59TYR0-0.031-0.01619.657-0.021-0.0210.0000.0000.0000.000
60K60ILE0-0.0040.00518.487-0.019-0.0190.0000.0000.0000.000
61K61GLN00.006-0.00420.1660.0050.0050.0000.0000.0000.000
62K62LYS10.8030.87421.853-0.035-0.0350.0000.0000.0000.000
63K63ASN0-0.042-0.02224.179-0.008-0.0080.0000.0000.0000.000
64K64VAL0-0.0190.00223.051-0.005-0.0050.0000.0000.0000.000
65K65GLN00.000-0.01225.768-0.005-0.0050.0000.0000.0000.000
66K66LEU0-0.0030.00628.056-0.001-0.0010.0000.0000.0000.000
67K67TYR0-0.041-0.02629.0990.0020.0020.0000.0000.0000.000
68K68LYS10.8140.89429.1140.0580.0580.0000.0000.0000.000
69K69MET0-0.036-0.02431.716-0.003-0.0030.0000.0000.0000.000
70K70ARG10.8800.95233.156-0.008-0.0080.0000.0000.0000.000
71K71ASN0-0.026-0.00733.1600.0040.0040.0000.0000.0000.000
72K72GLY00.0030.01735.710-0.002-0.0020.0000.0000.0000.000
73K73TYR0-0.012-0.00633.343-0.004-0.0040.0000.0000.0000.000
74K74GLU-1-0.739-0.87728.471-0.074-0.0740.0000.0000.0000.000
75K75LEU0-0.018-0.00325.8730.0020.0020.0000.0000.0000.000
76K76SER00.0920.05227.300-0.007-0.0070.0000.0000.0000.000
77K77PRO00.0460.01022.4110.0070.0070.0000.0000.0000.000
78K78THR00.0410.02522.571-0.002-0.0020.0000.0000.0000.000
79K79ALA00.0100.02124.2470.0090.0090.0000.0000.0000.000
80K80ALA00.0130.00722.2040.0120.0120.0000.0000.0000.000
81K81ALA00.0180.01019.5790.0130.0130.0000.0000.0000.000
82K82ASN0-0.011-0.03020.1260.0220.0220.0000.0000.0000.000
83K83PHE00.0110.02422.6840.0160.0160.0000.0000.0000.000
84K84THR00.0180.01017.2550.0280.0280.0000.0000.0000.000
85K85ARG10.9080.93618.6230.0010.0010.0000.0000.0000.000
86K86ARG10.8310.90119.603-0.033-0.0330.0000.0000.0000.000
87K87ASN00.0230.00620.9140.0210.0210.0000.0000.0000.000
88K88LEU00.0360.03014.1050.0130.0130.0000.0000.0000.000
89K89ALA0-0.019-0.02318.5600.0230.0230.0000.0000.0000.000
90K90ASP-1-0.882-0.92420.6700.0830.0830.0000.0000.0000.000
91K91CYS0-0.044-0.02119.4410.0080.0080.0000.0000.0000.000
92K92LEU0-0.0280.01616.6840.0210.0210.0000.0000.0000.000
93K93ARG10.9280.96019.590-0.112-0.1120.0000.0000.0000.000
94K94SER0-0.0060.00021.770-0.010-0.0100.0000.0000.0000.000
95K95ARG10.9360.95422.369-0.214-0.2140.0000.0000.0000.000
96K96THR0-0.058-0.03319.8620.0140.0140.0000.0000.0000.000
97K97PRO00.0100.02516.713-0.021-0.0210.0000.0000.0000.000
98K98TYR00.0160.00114.5340.0230.0230.0000.0000.0000.000
99K99HIS00.009-0.0049.817-0.031-0.0310.0000.0000.0000.000
100K100VAL0-0.049-0.0189.3790.2320.2320.0000.0000.0000.000
101K101ASN0-0.006-0.0046.131-0.226-0.2260.0000.0000.0000.000
102K102LEU00.004-0.0108.064-0.081-0.0810.0000.0000.0000.000
103K103LEU00.0090.00410.379-0.024-0.0240.0000.0000.0000.000
104K104LEU0-0.058-0.00712.8210.0290.0290.0000.0000.0000.000
105K105ALA00.0290.01316.450-0.013-0.0130.0000.0000.0000.000
106K106GLY00.022-0.01218.4740.0170.0170.0000.0000.0000.000
107K107TYR0-0.0120.00122.216-0.010-0.0100.0000.0000.0000.000
108K108ASP-1-0.848-0.93725.842-0.075-0.0750.0000.0000.0000.000
109K109GLU-1-0.851-0.91528.827-0.096-0.0960.0000.0000.0000.000
110K110HIS0-0.074-0.02831.9360.0020.0020.0000.0000.0000.000
111K111GLU-1-0.949-0.98328.475-0.088-0.0880.0000.0000.0000.000
112K112GLY0-0.0030.02528.662-0.008-0.0080.0000.0000.0000.000
113K113PRO0-0.016-0.00224.2220.0000.0000.0000.0000.0000.000
114K114ALA0-0.033-0.03322.5960.0070.0070.0000.0000.0000.000
115K115LEU00.0150.02315.128-0.010-0.0100.0000.0000.0000.000
116K116TYR0-0.019-0.03317.3070.0180.0180.0000.0000.0000.000
117K117TYR00.0110.0079.2800.0230.0230.0000.0000.0000.000
118K118MET0-0.019-0.01012.4930.0410.0410.0000.0000.0000.000
119K119ASP-1-0.844-0.90410.6990.0620.0620.0000.0000.0000.000
120K120TYR00.0570.02410.2690.0420.0420.0000.0000.0000.000
121K121LEU0-0.055-0.02312.1560.0050.0050.0000.0000.0000.000
122K122ALA0-0.0130.00014.938-0.029-0.0290.0000.0000.0000.000
123K123ALA0-0.0060.01115.441-0.019-0.0190.0000.0000.0000.000
124K124LEU0-0.018-0.02315.902-0.005-0.0050.0000.0000.0000.000
125K125ALA00.0020.01017.2860.0090.0090.0000.0000.0000.000
126K126LYS10.8800.96017.8360.1330.1330.0000.0000.0000.000
127K127ALA0-0.008-0.00617.0510.0050.0050.0000.0000.0000.000
128K128PRO00.0060.01719.166-0.002-0.0020.0000.0000.0000.000
129K129PHE00.006-0.01215.917-0.013-0.0130.0000.0000.0000.000
130K130ALA0-0.0110.00012.6650.0310.0310.0000.0000.0000.000
131K131ALA00.0110.0029.268-0.042-0.0420.0000.0000.0000.000
132K132HIS00.005-0.0176.0380.0250.0250.0000.0000.0000.000
133K133GLY00.0560.0412.414-0.921-0.8771.389-0.773-0.6590.003
134K134TYR00.011-0.0152.206-1.082-0.5984.0650.070-4.619-0.008
135K135GLY00.0570.0274.1870.3500.5120.002-0.038-0.1260.000
136K136ALA00.0300.0276.5420.3820.3820.0000.0000.0000.000
137K137PHE0-0.012-0.0096.1800.1930.1930.0000.0000.0000.000
138K138LEU0-0.040-0.0119.0700.1330.1330.0000.0000.0000.000
139K139THR0-0.024-0.02510.0450.0500.0500.0000.0000.0000.000
140K140LEU00.0270.01311.2730.0750.0750.0000.0000.0000.000
141K141SER00.0580.03614.0220.0370.0370.0000.0000.0000.000
142K142ILE0-0.036-0.01715.0760.0540.0540.0000.0000.0000.000
143K143LEU00.000-0.00814.3610.0400.0400.0000.0000.0000.000
144K144ASP-1-0.852-0.94217.676-0.320-0.3200.0000.0000.0000.000
145K145ARG10.8500.93620.0800.2720.2720.0000.0000.0000.000
146K146TYR0-0.077-0.04821.1000.0400.0400.0000.0000.0000.000
147K147TYR00.0070.00420.7600.0130.0130.0000.0000.0000.000
148K148THR0-0.015-0.01322.8310.0180.0180.0000.0000.0000.000
149K149PRO00.0370.00625.549-0.008-0.0080.0000.0000.0000.000
150K150THR0-0.0050.00226.7900.0050.0050.0000.0000.0000.000
151K151ILE0-0.052-0.00222.7660.0060.0060.0000.0000.0000.000
152K152SER00.023-0.00226.319-0.005-0.0050.0000.0000.0000.000
153K153ARG10.8890.91024.5880.1740.1740.0000.0000.0000.000
154K154GLU-1-0.822-0.89624.178-0.236-0.2360.0000.0000.0000.000
155K155ARG10.8650.90924.7580.2010.2010.0000.0000.0000.000
156K156ALA00.0180.02121.126-0.023-0.0230.0000.0000.0000.000
157K157VAL00.0430.01620.214-0.050-0.0500.0000.0000.0000.000
158K158GLU-1-0.848-0.89120.402-0.306-0.3060.0000.0000.0000.000
159K159LEU0-0.049-0.02318.823-0.017-0.0170.0000.0000.0000.000
160K160LEU00.0320.01014.472-0.047-0.0470.0000.0000.0000.000
161K161ARG10.9080.95215.8940.3390.3390.0000.0000.0000.000
162K162LYS10.9170.95117.0260.2780.2780.0000.0000.0000.000
163K163CYS0-0.048-0.00713.317-0.002-0.0020.0000.0000.0000.000
164K164LEU00.0170.00311.627-0.110-0.1100.0000.0000.0000.000
165K165GLU-1-0.884-0.94813.223-0.537-0.5370.0000.0000.0000.000
166K166GLU-1-0.820-0.91614.569-0.466-0.4660.0000.0000.0000.000
167K167LEU0-0.038-0.0148.423-0.024-0.0240.0000.0000.0000.000
168K168GLN0-0.039-0.01710.6900.0390.0390.0000.0000.0000.000
169K169LYS10.8800.96512.7210.4690.4690.0000.0000.0000.000
170K170ARG10.8340.90812.3880.5140.5140.0000.0000.0000.000
171K171PHE00.0030.0093.282-0.2230.2520.015-0.082-0.4090.000
172K172ILE00.0120.0026.7480.0150.0150.0000.0000.0000.000
173K173LEU0-0.023-0.0022.010-0.384-0.6343.653-1.045-2.3580.000
174K174ASN00.0130.0015.443-0.431-0.4310.0000.0000.0000.000
175K175LEU00.0140.0043.8050.1780.3570.000-0.045-0.1350.000
176K176PRO00.0570.0377.3820.1740.1740.0000.0000.0000.000
177K177THR00.009-0.00710.4370.1190.1190.0000.0000.0000.000
178K178PHE00.0020.0019.169-0.267-0.2670.0000.0000.0000.000
179K179SER00.0010.00112.7200.1360.1360.0000.0000.0000.000
180K180VAL0-0.037-0.02814.600-0.077-0.0770.0000.0000.0000.000
181K181ARG10.7920.85716.6890.3900.3900.0000.0000.0000.000
182K182ILE0-0.014-0.00219.015-0.028-0.0280.0000.0000.0000.000
183K183ILE0-0.031-0.00319.7490.0220.0220.0000.0000.0000.000
184K184ASP-1-0.740-0.84323.523-0.172-0.1720.0000.0000.0000.000
185K185LYS10.8450.89926.9790.1010.1010.0000.0000.0000.000
186K186ASN0-0.096-0.05429.9490.0180.0180.0000.0000.0000.000
187K187GLY00.0280.02427.6110.0080.0080.0000.0000.0000.000
188K188ILE0-0.065-0.03721.759-0.016-0.0160.0000.0000.0000.000
189K189HIS0-0.024-0.01523.6770.0130.0130.0000.0000.0000.000
190K190ASP-1-0.825-0.90521.686-0.290-0.2900.0000.0000.0000.000
191K191LEU0-0.034-0.02121.0300.0170.0170.0000.0000.0000.000
192K192ASP-1-0.892-0.94520.700-0.296-0.2960.0000.0000.0000.000
193K193ASN0-0.039-0.01416.477-0.054-0.0540.0000.0000.0000.000
194K194ILE00.0150.01515.6040.0190.0190.0000.0000.0000.000
195K195SER0-0.014-0.02114.818-0.080-0.0800.0000.0000.0000.000
196K196PHE0-0.014-0.00613.2460.0630.0630.0000.0000.0000.000
197K197PRO00.0060.00415.403-0.020-0.0200.0000.0000.0000.000
198K198LYS10.8200.92210.8460.8550.8550.0000.0000.0000.000
199K199GLN00.0030.00814.3580.0030.0030.0000.0000.0000.000