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

tag_button

FMODB ID: LZJG9

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 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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1744010.3785
FMO2-HF: Nuclear repulsion 1671389.440173
FMO2-HF: Total energy -72620.938327
FMO2-MP2: Total energy -72827.569564


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.
-30.628-23.24712.422-10.283-9.523-0.072
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 : 0.016 / q_NPA : 0.008
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].
3K7LYS10.8840.9283.365-3.456-1.050-0.006-1.296-1.1040.004
4K8ALA0-0.004-0.0091.996-2.877-2.0802.523-1.569-1.7520.012
5K9ILE00.0440.0303.795-1.084-0.7650.002-0.077-0.2440.000
6K10GLU-1-0.832-0.9245.5200.1280.1280.0000.0000.0000.000
7K11ILE0-0.080-0.0436.7400.0090.0090.0000.0000.0000.000
8K12TRP00.0010.0017.362-0.023-0.0230.0000.0000.0000.000
9K13LYS10.9070.9488.9340.4350.4350.0000.0000.0000.000
10K14ILE00.0060.00311.4530.0350.0350.0000.0000.0000.000
11K15ARG10.8840.9359.629-0.076-0.0760.0000.0000.0000.000
12K16ARG10.8040.87213.2340.2970.2970.0000.0000.0000.000
13K17LEU0-0.0250.01015.1380.0090.0090.0000.0000.0000.000
14K18VAL0-0.040-0.01817.2420.0200.0200.0000.0000.0000.000
15K19LYS10.8370.91516.6340.2060.2060.0000.0000.0000.000
16K33THR0-0.019-0.02326.497-0.003-0.0030.0000.0000.0000.000
17K34LEU00.0160.01628.4850.0070.0070.0000.0000.0000.000
18K35ILE00.0320.00323.1350.0010.0010.0000.0000.0000.000
19K36ILE0-0.042-0.00625.554-0.003-0.0030.0000.0000.0000.000
20K37PRO0-0.0020.00324.5010.0200.0200.0000.0000.0000.000
21K45TYR00.010-0.01430.775-0.002-0.0020.0000.0000.0000.000
22K46SER00.0150.00234.164-0.001-0.0010.0000.0000.0000.000
23K47ASN0-0.021-0.01337.016-0.004-0.0040.0000.0000.0000.000
24K48MET0-0.0210.00534.9520.0010.0010.0000.0000.0000.000
25K49LEU00.0270.01635.270-0.001-0.0010.0000.0000.0000.000
26K50ALA0-0.0050.00639.638-0.003-0.0030.0000.0000.0000.000
27K51GLU-1-0.945-0.97943.3950.0160.0160.0000.0000.0000.000
28K52GLU-1-0.953-0.97038.9520.0230.0230.0000.0000.0000.000
29K74SER00.019-0.00131.0430.0020.0020.0000.0000.0000.000
30K75THR00.034-0.00630.777-0.001-0.0010.0000.0000.0000.000
31K76ARG10.8600.92232.774-0.014-0.0140.0000.0000.0000.000
32K77GLU-1-0.918-0.94234.6270.0020.0020.0000.0000.0000.000
33K78ARG10.7720.86525.912-0.013-0.0130.0000.0000.0000.000
34K79LEU00.0070.01628.1010.0010.0010.0000.0000.0000.000
35K89GLY00.0690.03620.8880.0090.0090.0000.0000.0000.000
36K90LEU0-0.073-0.03622.091-0.005-0.0050.0000.0000.0000.000
37K91VAL00.0140.01720.039-0.004-0.0040.0000.0000.0000.000
38K92ILE00.0180.00122.761-0.017-0.0170.0000.0000.0000.000
39K110ASP-1-0.825-0.88421.6760.0160.0160.0000.0000.0000.000
40K111PHE0-0.065-0.03616.9780.0040.0040.0000.0000.0000.000
41K130THR00.0380.01722.3600.0000.0000.0000.0000.0000.000
42K131GLU-1-0.895-0.98321.5460.0750.0750.0000.0000.0000.000
43K132ALA0-0.0200.00021.2490.0240.0240.0000.0000.0000.000
44K133LEU00.0080.00416.8910.0230.0230.0000.0000.0000.000
45K134ALA0-0.028-0.00616.5410.0230.0230.0000.0000.0000.000
46K135GLU-1-0.937-0.97616.9530.2510.2510.0000.0000.0000.000
47K136LEU00.0230.02714.4130.0530.0530.0000.0000.0000.000
48K137LEU0-0.115-0.04212.0240.1230.1230.0000.0000.0000.000
49K274ASN00.0750.02513.523-0.056-0.0560.0000.0000.0000.000
50K275VAL0-0.028-0.0219.535-0.070-0.0700.0000.0000.0000.000
51K276LYS10.9300.9568.056-0.432-0.4320.0000.0000.0000.000
52K277TYR00.0600.0387.764-0.147-0.1470.0000.0000.0000.000
53K278VAL0-0.028-0.0169.176-0.115-0.1150.0000.0000.0000.000
54K279GLN00.0340.0203.4210.9811.2420.002-0.051-0.2130.000
55K280GLU-1-0.745-0.8366.807-0.895-0.8950.0000.0000.0000.000
56K281LYS10.9020.9578.1290.1740.1740.0000.0000.0000.000
57K282LYS10.8960.9527.368-0.056-0.0560.0000.0000.0000.000
58K283LEU0-0.024-0.0064.9910.0970.0970.0000.0000.0000.000
59K284ILE00.0310.0238.6730.0410.0410.0000.0000.0000.000
60K285GLN0-0.049-0.02711.6640.0830.0830.0000.0000.0000.000
61K286ARG10.7870.8937.6600.8660.8660.0000.0000.0000.000
62K287PHE0-0.016-0.01212.2480.0190.0190.0000.0000.0000.000
63K288PHE00.013-0.00613.6180.0470.0470.0000.0000.0000.000
64K289ASP-1-0.827-0.91116.059-0.230-0.2300.0000.0000.0000.000
65K290GLU-1-0.811-0.85215.693-0.285-0.2850.0000.0000.0000.000
66K291ILE0-0.0050.00518.3980.0240.0240.0000.0000.0000.000
67K292SER0-0.079-0.05719.8740.0260.0260.0000.0000.0000.000
68K293LEU0-0.092-0.04021.2590.0280.0280.0000.0000.0000.000
69K294ASP-1-0.880-0.92823.112-0.200-0.2000.0000.0000.0000.000
70K295SER0-0.048-0.04919.3390.0130.0130.0000.0000.0000.000
71K296GLY00.0550.04022.5330.0110.0110.0000.0000.0000.000
72K297LYS10.7750.85717.2360.2910.2910.0000.0000.0000.000
73K298TYR0-0.067-0.04217.003-0.064-0.0640.0000.0000.0000.000
74K299CYS00.0780.06016.8140.0390.0390.0000.0000.0000.000
75K300PHE0-0.082-0.02116.242-0.082-0.0820.0000.0000.0000.000
76K301GLY00.1130.03818.9990.0220.0220.0000.0000.0000.000
77K302VAL0-0.030-0.01519.042-0.026-0.0260.0000.0000.0000.000
78K303VAL00.0420.03420.022-0.019-0.0190.0000.0000.0000.000
79K304ASP-1-0.770-0.87620.710-0.313-0.3130.0000.0000.0000.000
80K305THR0-0.018-0.04214.571-0.024-0.0240.0000.0000.0000.000
81K306MET0-0.076-0.03415.058-0.036-0.0360.0000.0000.0000.000
82K307ASN00.0210.00518.7810.0010.0010.0000.0000.0000.000
83K308ALA00.0240.00817.6280.0120.0120.0000.0000.0000.000
84K309LEU0-0.113-0.05013.437-0.032-0.0320.0000.0000.0000.000
85K310GLN0-0.099-0.05316.7750.0020.0020.0000.0000.0000.000
86K311GLU-1-0.874-0.92520.203-0.191-0.1910.0000.0000.0000.000
87K312GLY0-0.047-0.02120.363-0.014-0.0140.0000.0000.0000.000
88K313ALA00.0190.00014.872-0.003-0.0030.0000.0000.0000.000
89K314VAL00.0100.01912.0810.0070.0070.0000.0000.0000.000
90K315GLU-1-0.893-0.9289.639-0.611-0.6110.0000.0000.0000.000
91K316THR0-0.006-0.0406.540-0.135-0.1350.0000.0000.0000.000
92K317LEU0-0.0250.0058.0840.1200.1200.0000.0000.0000.000
93K318LEU0-0.004-0.0127.393-0.502-0.5020.0000.0000.0000.000
94K319CYS00.0020.0008.8100.3310.3310.0000.0000.0000.000
95K320PHE00.0300.0149.852-0.173-0.1730.0000.0000.0000.000
96K321ALA00.0140.00910.3400.0160.0160.0000.0000.0000.000
97K322ASP-1-0.892-0.93011.719-0.296-0.2960.0000.0000.0000.000
98K323LEU0-0.023-0.02614.6920.0500.0500.0000.0000.0000.000
99K324ASP-1-0.832-0.88516.456-0.229-0.2290.0000.0000.0000.000
100K325MET00.0280.01718.5970.0200.0200.0000.0000.0000.000
101K326ILE0-0.056-0.01019.683-0.029-0.0290.0000.0000.0000.000
102K327ARG10.9280.97319.4110.3320.3320.0000.0000.0000.000
103K328TYR00.010-0.02022.7390.0090.0090.0000.0000.0000.000
104K339ILE0-0.0060.00123.0910.0000.0000.0000.0000.0000.000
105K340THR0-0.032-0.02126.5700.0000.0000.0000.0000.0000.000
106K341TYR00.026-0.01119.848-0.024-0.0240.0000.0000.0000.000
107K342MET0-0.0090.01824.1470.0190.0190.0000.0000.0000.000
108K343THR0-0.017-0.04623.183-0.024-0.0240.0000.0000.0000.000
109K344LYS10.7560.86423.5190.2340.2340.0000.0000.0000.000
110K345GLU-1-0.779-0.86127.300-0.205-0.2050.0000.0000.0000.000
111K346GLN0-0.032-0.01927.948-0.001-0.0010.0000.0000.0000.000
112K347GLU-1-0.922-0.96331.198-0.140-0.1400.0000.0000.0000.000
113K348GLU-1-0.969-0.98934.365-0.117-0.1170.0000.0000.0000.000
114K349LYS10.7950.89034.3700.1190.1190.0000.0000.0000.000
115K350ASP-1-0.869-0.91434.922-0.108-0.1080.0000.0000.0000.000
116K351SER00.0040.00332.8490.0030.0030.0000.0000.0000.000
117K369SER0-0.008-0.01024.7620.0000.0000.0000.0000.0000.000
118K370SER00.0250.02225.2420.0010.0010.0000.0000.0000.000
119K371MET0-0.043-0.00519.017-0.003-0.0030.0000.0000.0000.000
120K372LEU00.0690.03417.711-0.004-0.0040.0000.0000.0000.000
121K373LEU0-0.002-0.01115.726-0.021-0.0210.0000.0000.0000.000
122K374SER00.0270.00013.145-0.076-0.0760.0000.0000.0000.000
123K375GLU-1-0.830-0.88912.763-0.422-0.4220.0000.0000.0000.000
124K376TRP00.016-0.01714.501-0.019-0.0190.0000.0000.0000.000
125K377LEU00.0160.01211.4470.0060.0060.0000.0000.0000.000
126K378ALA0-0.018-0.0079.929-0.083-0.0830.0000.0000.0000.000
127K379GLU-1-0.857-0.91910.986-0.421-0.4210.0000.0000.0000.000
128K380HIS10.8270.89212.9940.4380.4380.0000.0000.0000.000
129K381TYR00.0350.0166.726-0.150-0.1500.0000.0000.0000.000
130K382LYS10.8290.9027.6360.5330.5330.0000.0000.0000.000
131K383ASP-1-0.884-0.91911.763-0.278-0.2780.0000.0000.0000.000
132K384TYR00.0100.00813.9190.0390.0390.0000.0000.0000.000
133K385GLY0-0.0060.00212.580-0.008-0.0080.0000.0000.0000.000
134K386ALA00.0110.0369.0720.0130.0130.0000.0000.0000.000
135K387ASN0-0.081-0.0535.3780.1640.1640.0000.0000.0000.000
136K388LEU00.0300.0165.9870.1280.1280.0000.0000.0000.000
137K389GLU-1-0.873-0.9542.175-23.474-19.9589.902-7.268-6.151-0.088
138K390PHE0-0.027-0.0114.3071.0931.175-0.001-0.022-0.0590.000
139K391VAL0-0.032-0.0115.990-0.151-0.1510.0000.0000.0000.000
140K392SER0-0.030-0.0458.7290.1900.1900.0000.0000.0000.000
141K393ASP-1-0.814-0.87611.998-0.359-0.3590.0000.0000.0000.000
142K394ARG10.8360.89713.8770.3100.3100.0000.0000.0000.000
143K395SER0-0.051-0.04512.7010.0550.0550.0000.0000.0000.000
144K396GLN0-0.0050.00715.239-0.040-0.0400.0000.0000.0000.000
145K397GLU-1-0.734-0.89814.027-0.291-0.2910.0000.0000.0000.000
146K398GLY00.0800.04013.693-0.046-0.0460.0000.0000.0000.000
147K399MET0-0.063-0.03914.408-0.002-0.0020.0000.0000.0000.000
148K400GLN0-0.047-0.03218.0850.0150.0150.0000.0000.0000.000
149K401PHE0-0.0120.00512.6070.0010.0010.0000.0000.0000.000
150K402VAL00.008-0.00815.4290.0010.0010.0000.0000.0000.000
151K403LYS10.8840.93617.7270.2280.2280.0000.0000.0000.000
152K404GLY0-0.012-0.00120.4990.0330.0330.0000.0000.0000.000
153K405PHE0-0.008-0.00417.9410.0070.0070.0000.0000.0000.000
154K406GLY00.0420.02819.197-0.015-0.0150.0000.0000.0000.000
155K407GLY0-0.053-0.01715.748-0.001-0.0010.0000.0000.0000.000
156K408ILE0-0.014-0.02613.423-0.099-0.0990.0000.0000.0000.000
157K409GLY00.0290.01713.0770.0970.0970.0000.0000.0000.000
158K410ALA0-0.027-0.01811.833-0.174-0.1740.0000.0000.0000.000
159K411VAL00.0300.03511.1480.0860.0860.0000.0000.0000.000
160K412MET00.0300.02013.240-0.043-0.0430.0000.0000.0000.000
161K413ARG10.7980.88811.6480.4380.4380.0000.0000.0000.000
162K414TYR0-0.047-0.02416.1890.0360.0360.0000.0000.0000.000
163K415GLN0-0.015-0.01619.832-0.016-0.0160.0000.0000.0000.000
164K416LEU0-0.024-0.02220.0590.0140.0140.0000.0000.0000.000
165K417ASP-1-0.831-0.90223.762-0.188-0.1880.0000.0000.0000.000
166K418LEU0-0.048-0.01621.947-0.012-0.0120.0000.0000.0000.000
167K419SER0-0.017-0.01425.8110.0060.0060.0000.0000.0000.000
168K420MET0-0.079-0.04425.701-0.004-0.0040.0000.0000.0000.000
169K421LEU0-0.049-0.04627.319-0.013-0.0130.0000.0000.0000.000
170K422ASP-1-0.878-0.94230.435-0.165-0.1650.0000.0000.0000.000
171K423PRO0-0.093-0.03732.309-0.002-0.0020.0000.0000.0000.000
172K424GLU-1-0.921-0.95233.060-0.147-0.1470.0000.0000.0000.000
173K425SER0-0.050-0.02434.763-0.005-0.0050.0000.0000.0000.000
174K426ASP-1-0.886-0.92037.406-0.107-0.1070.0000.0000.0000.000
175K427GLU-1-1.076-1.04338.789-0.100-0.1000.0000.0000.0000.000