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: 39QZL

Calculation Name: 3E20-K-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3E20

Chain ID: K

ChEMBL ID:

UniProt ID: P79063

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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1743190.962695
FMO2-HF: Nuclear repulsion 1670571.659895
FMO2-HF: Total energy -72619.3028
FMO2-MP2: Total energy -72826.073273


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:5:ALA)


Summations of interaction energy for fragment #1(K:5:ALA)
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.
-30.242-20.8799.424-9.435-9.35-0.034
Interaction energy analysis for fragmet #1(K:5:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.039 / q_NPA : 0.018
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].
3K7LYS10.8950.9183.217-4.844-1.2610.008-1.926-1.6650.009
4K8ALA0-0.040-0.0331.827-4.239-4.5205.305-2.512-2.5120.015
5K9ILE00.0490.0393.348-1.602-1.445-0.0020.222-0.3760.000
6K10GLU-1-0.882-0.9445.0710.1900.322-0.001-0.005-0.1250.000
7K11ILE0-0.094-0.0566.149-0.013-0.0130.0000.0000.0000.000
8K12TRP00.0110.0067.094-0.008-0.0080.0000.0000.0000.000
9K13LYS10.9510.9558.5660.4620.4620.0000.0000.0000.000
10K14ILE00.0170.01810.9620.0460.0460.0000.0000.0000.000
11K15ARG10.9050.9539.313-0.147-0.1470.0000.0000.0000.000
12K16ARG10.8110.88913.0820.3200.3200.0000.0000.0000.000
13K17LEU0-0.0050.02414.9470.0000.0000.0000.0000.0000.000
14K18VAL0-0.039-0.01017.1290.0170.0170.0000.0000.0000.000
15K19LYS10.9420.97716.7560.1520.1520.0000.0000.0000.000
16K33THR0-0.013-0.02525.483-0.003-0.0030.0000.0000.0000.000
17K34LEU00.0050.00926.8370.0050.0050.0000.0000.0000.000
18K35ILE00.0310.01022.2990.0020.0020.0000.0000.0000.000
19K36ILE0-0.031-0.00524.733-0.004-0.0040.0000.0000.0000.000
20K37PRO0-0.0020.00924.0470.0220.0220.0000.0000.0000.000
21K45TYR00.013-0.00830.192-0.001-0.0010.0000.0000.0000.000
22K46SER0-0.002-0.01133.659-0.003-0.0030.0000.0000.0000.000
23K47ASN0-0.016-0.00636.381-0.004-0.0040.0000.0000.0000.000
24K48MET0-0.0180.00234.0860.0000.0000.0000.0000.0000.000
25K49LEU00.0150.01134.956-0.002-0.0020.0000.0000.0000.000
26K50ALA0-0.0110.00339.103-0.004-0.0040.0000.0000.0000.000
27K51GLU-1-0.954-0.98342.8760.0200.0200.0000.0000.0000.000
28K52GLU-1-0.943-0.96638.8160.0360.0360.0000.0000.0000.000
29K74SER00.006-0.00230.8930.0020.0020.0000.0000.0000.000
30K75THR00.056-0.00230.069-0.001-0.0010.0000.0000.0000.000
31K76ARG10.8580.91632.253-0.020-0.0200.0000.0000.0000.000
32K77GLU-1-0.929-0.94934.1920.0030.0030.0000.0000.0000.000
33K78ARG10.8280.92825.571-0.015-0.0150.0000.0000.0000.000
34K79LEU00.0030.00827.181-0.001-0.0010.0000.0000.0000.000
35K89GLY00.0510.02920.3070.0100.0100.0000.0000.0000.000
36K90LEU0-0.068-0.04421.893-0.010-0.0100.0000.0000.0000.000
37K91VAL0-0.0020.00119.401-0.001-0.0010.0000.0000.0000.000
38K92ILE00.0200.01621.986-0.018-0.0180.0000.0000.0000.000
39K110ASP-1-0.853-0.91821.3060.0190.0190.0000.0000.0000.000
40K111PHE0-0.042-0.02216.0620.0010.0010.0000.0000.0000.000
41K130THR00.0420.01622.337-0.001-0.0010.0000.0000.0000.000
42K131GLU-1-0.895-0.98721.3830.1090.1090.0000.0000.0000.000
43K132ALA0-0.0420.00120.9380.0300.0300.0000.0000.0000.000
44K133LEU00.0270.00316.2330.0290.0290.0000.0000.0000.000
45K134ALA0-0.048-0.01816.1900.0310.0310.0000.0000.0000.000
46K135GLU-1-0.948-0.97616.8110.3170.3170.0000.0000.0000.000
47K136LEU0-0.0110.00814.0560.0620.0620.0000.0000.0000.000
48K137LEU0-0.100-0.04010.7700.1230.1230.0000.0000.0000.000
49K274ASN00.0530.02112.964-0.064-0.0640.0000.0000.0000.000
50K275VAL0-0.007-0.0128.704-0.074-0.0740.0000.0000.0000.000
51K276LYS10.9820.9797.149-0.579-0.5790.0000.0000.0000.000
52K277TYR00.0530.0357.564-0.227-0.2270.0000.0000.0000.000
53K278VAL0-0.026-0.0189.235-0.127-0.1270.0000.0000.0000.000
54K279GLN00.0350.0103.5600.6530.8500.001-0.034-0.1640.000
55K280GLU-1-0.743-0.8287.247-0.860-0.8600.0000.0000.0000.000
56K281LYS10.8890.9508.1500.1590.1590.0000.0000.0000.000
57K282LYS10.8930.9467.738-0.090-0.0900.0000.0000.0000.000
58K283LEU0-0.024-0.0095.3230.1260.1260.0000.0000.0000.000
59K284ILE00.0420.0218.5820.0500.0500.0000.0000.0000.000
60K285GLN0-0.011-0.00711.7290.0970.0970.0000.0000.0000.000
61K286ARG10.8300.9277.6811.0531.0530.0000.0000.0000.000
62K287PHE00.000-0.02112.4280.0330.0330.0000.0000.0000.000
63K288PHE00.001-0.00913.9760.0450.0450.0000.0000.0000.000
64K289ASP-1-0.854-0.92316.269-0.257-0.2570.0000.0000.0000.000
65K290GLU-1-0.816-0.85216.029-0.318-0.3180.0000.0000.0000.000
66K291ILE0-0.064-0.02818.6460.0090.0090.0000.0000.0000.000
67K292SER0-0.081-0.04620.3650.0290.0290.0000.0000.0000.000
68K293LEU0-0.090-0.04821.5330.0270.0270.0000.0000.0000.000
69K294ASP-1-0.932-0.94922.744-0.211-0.2110.0000.0000.0000.000
70K295SER0-0.064-0.06219.9990.0110.0110.0000.0000.0000.000
71K296GLY00.0840.04122.1330.0190.0190.0000.0000.0000.000
72K297LYS10.7550.84817.1560.3270.3270.0000.0000.0000.000
73K298TYR0-0.013-0.02817.523-0.044-0.0440.0000.0000.0000.000
74K299CYS00.1030.06617.4290.0420.0420.0000.0000.0000.000
75K300PHE0-0.0520.01116.743-0.090-0.0900.0000.0000.0000.000
76K301GLY00.1400.06418.8630.0300.0300.0000.0000.0000.000
77K302VAL0-0.035-0.00619.160-0.030-0.0300.0000.0000.0000.000
78K303VAL00.0480.02120.236-0.025-0.0250.0000.0000.0000.000
79K304ASP-1-0.804-0.90021.367-0.332-0.3320.0000.0000.0000.000
80K305THR0-0.016-0.03714.948-0.031-0.0310.0000.0000.0000.000
81K306MET0-0.083-0.03915.301-0.039-0.0390.0000.0000.0000.000
82K307ASN00.0490.02419.1400.0030.0030.0000.0000.0000.000
83K308ALA0-0.023-0.00817.9060.0110.0110.0000.0000.0000.000
84K309LEU0-0.118-0.05613.768-0.028-0.0280.0000.0000.0000.000
85K310GLN0-0.100-0.04217.2740.0040.0040.0000.0000.0000.000
86K311GLU-1-0.887-0.94520.635-0.241-0.2410.0000.0000.0000.000
87K312GLY0-0.033-0.00920.039-0.026-0.0260.0000.0000.0000.000
88K313ALA00.0210.00515.498-0.019-0.0190.0000.0000.0000.000
89K314VAL00.0020.01012.4110.0110.0110.0000.0000.0000.000
90K315GLU-1-0.918-0.9389.557-0.882-0.8820.0000.0000.0000.000
91K316THR00.009-0.0306.775-0.252-0.2520.0000.0000.0000.000
92K317LEU0-0.030-0.0098.5520.1580.1580.0000.0000.0000.000
93K318LEU0-0.022-0.0198.037-0.428-0.4280.0000.0000.0000.000
94K319CYS00.0280.0069.2840.2940.2940.0000.0000.0000.000
95K320PHE00.0490.03010.285-0.161-0.1610.0000.0000.0000.000
96K321ALA0-0.015-0.01410.6550.0370.0370.0000.0000.0000.000
97K322ASP-1-0.973-0.98812.063-0.311-0.3110.0000.0000.0000.000
98K323LEU0-0.015-0.01314.9440.0530.0530.0000.0000.0000.000
99K324ASP-1-0.842-0.89416.837-0.243-0.2430.0000.0000.0000.000
100K325MET00.0300.01318.6630.0160.0160.0000.0000.0000.000
101K326ILE0-0.0360.00619.841-0.033-0.0330.0000.0000.0000.000
102K327ARG10.9260.96219.5260.3660.3660.0000.0000.0000.000
103K328TYR00.0450.03122.6930.0080.0080.0000.0000.0000.000
104K339ILE0-0.029-0.01723.1450.0000.0000.0000.0000.0000.000
105K340THR0-0.031-0.02226.597-0.001-0.0010.0000.0000.0000.000
106K341TYR00.015-0.02020.563-0.015-0.0150.0000.0000.0000.000
107K342MET00.0070.01924.5740.0200.0200.0000.0000.0000.000
108K343THR0-0.039-0.05423.365-0.019-0.0190.0000.0000.0000.000
109K344LYS10.7900.87923.4690.2420.2420.0000.0000.0000.000
110K345GLU-1-0.797-0.86027.481-0.217-0.2170.0000.0000.0000.000
111K346GLN0-0.008-0.02327.994-0.002-0.0020.0000.0000.0000.000
112K347GLU-1-0.954-0.97731.608-0.142-0.1420.0000.0000.0000.000
113K348GLU-1-0.987-0.97734.329-0.128-0.1280.0000.0000.0000.000
114K349LYS10.8370.91334.3020.1320.1320.0000.0000.0000.000
115K350ASP-1-0.836-0.91635.726-0.112-0.1120.0000.0000.0000.000
116K351SER0-0.049-0.01633.0400.0070.0070.0000.0000.0000.000
117K369SER0-0.007-0.01624.6380.0040.0040.0000.0000.0000.000
118K370SER0-0.009-0.00625.5930.0040.0040.0000.0000.0000.000
119K371MET0-0.0220.01019.135-0.007-0.0070.0000.0000.0000.000
120K372LEU00.0850.04518.0530.0010.0010.0000.0000.0000.000
121K373LEU00.004-0.01016.053-0.034-0.0340.0000.0000.0000.000
122K374SER00.006-0.00713.693-0.103-0.1030.0000.0000.0000.000
123K375GLU-1-0.862-0.91612.992-0.462-0.4620.0000.0000.0000.000
124K376TRP00.028-0.01414.563-0.028-0.0280.0000.0000.0000.000
125K377LEU00.0260.01611.753-0.005-0.0050.0000.0000.0000.000
126K378ALA0-0.008-0.01010.102-0.112-0.1120.0000.0000.0000.000
127K379GLU-1-0.884-0.93611.107-0.425-0.4250.0000.0000.0000.000
128K380HIS10.8240.90713.6170.5050.5050.0000.0000.0000.000
129K381TYR00.0170.0167.058-0.186-0.1860.0000.0000.0000.000
130K382LYS10.8840.9418.0700.8410.8410.0000.0000.0000.000
131K383ASP-1-0.910-0.93412.094-0.371-0.3710.0000.0000.0000.000
132K384TYR00.0380.00514.1360.0450.0450.0000.0000.0000.000
133K385GLY0-0.050-0.01513.0880.0240.0240.0000.0000.0000.000
134K386ALA0-0.0280.0199.544-0.033-0.0330.0000.0000.0000.000
135K387ASN0-0.081-0.0555.9960.1480.1480.0000.0000.0000.000
136K388LEU00.0340.0155.8350.2800.2800.0000.0000.0000.000
137K389GLU-1-0.892-0.9582.429-19.273-13.7324.114-5.174-4.482-0.058
138K390PHE0-0.029-0.0064.8100.9150.949-0.001-0.006-0.0260.000
139K391VAL0-0.040-0.0236.618-0.164-0.1640.0000.0000.0000.000
140K392SER0-0.020-0.0189.3340.1920.1920.0000.0000.0000.000
141K393ASP-1-0.844-0.92112.134-0.353-0.3530.0000.0000.0000.000
142K394ARG10.8240.90714.1160.3040.3040.0000.0000.0000.000
143K395SER0-0.045-0.04612.6170.0450.0450.0000.0000.0000.000
144K396GLN00.0030.00115.148-0.040-0.0400.0000.0000.0000.000
145K397GLU-1-0.745-0.89714.030-0.297-0.2970.0000.0000.0000.000
146K398GLY00.0640.04114.044-0.032-0.0320.0000.0000.0000.000
147K399MET0-0.018-0.01514.686-0.002-0.0020.0000.0000.0000.000
148K400GLN0-0.037-0.01618.2440.0130.0130.0000.0000.0000.000
149K401PHE0-0.021-0.00513.053-0.006-0.0060.0000.0000.0000.000
150K402VAL00.007-0.00915.913-0.012-0.0120.0000.0000.0000.000
151K403LYS10.8730.93318.1520.2270.2270.0000.0000.0000.000
152K404GLY0-0.0090.00020.5810.0320.0320.0000.0000.0000.000
153K405PHE00.006-0.00218.2770.0070.0070.0000.0000.0000.000
154K406GLY00.0000.00619.075-0.035-0.0350.0000.0000.0000.000
155K407GLY0-0.0100.00816.262-0.003-0.0030.0000.0000.0000.000
156K408ILE0-0.036-0.03814.069-0.083-0.0830.0000.0000.0000.000
157K409GLY0-0.012-0.00713.7070.1060.1060.0000.0000.0000.000
158K410ALA0-0.034-0.01912.475-0.176-0.1760.0000.0000.0000.000
159K411VAL00.0230.04511.3040.1000.1000.0000.0000.0000.000
160K412MET00.0170.01513.303-0.046-0.0460.0000.0000.0000.000
161K413ARG10.9170.96012.0550.5630.5630.0000.0000.0000.000
162K414TYR0-0.038-0.03716.5140.0360.0360.0000.0000.0000.000
163K415GLN0-0.019-0.00520.234-0.016-0.0160.0000.0000.0000.000
164K416LEU0-0.024-0.02820.6490.0120.0120.0000.0000.0000.000
165K417ASP-1-0.923-0.95424.376-0.218-0.2180.0000.0000.0000.000
166K418LEU0-0.0290.00022.272-0.006-0.0060.0000.0000.0000.000
167K419SER00.0550.02826.3020.0220.0220.0000.0000.0000.000
168K420MET0-0.117-0.05126.413-0.007-0.0070.0000.0000.0000.000
169K421LEU00.047-0.00327.620-0.019-0.0190.0000.0000.0000.000
170K422ASP-1-0.939-0.98830.957-0.179-0.1790.0000.0000.0000.000
171K423PRO0-0.101-0.09732.441-0.004-0.0040.0000.0000.0000.000
172K424GLU-1-0.850-0.95333.209-0.169-0.1690.0000.0000.0000.000
173K425SER0-0.1490.08235.443-0.004-0.0040.0000.0000.0000.000
174K426ASP-1-0.864-0.93838.108-0.122-0.1220.0000.0000.0000.000
175K427GLU-1-1.054-1.05339.248-0.117-0.1170.0000.0000.0000.000