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: 1713Z

Calculation Name: 3E20-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3E20

Chain ID: A

ChEMBL ID:

UniProt ID: P79063

Base Structure: X-ray

Registration Date: 2023-09-20

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 196
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2098483.971802
FMO2-HF: Nuclear repulsion 2021175.752437
FMO2-HF: Total energy -77308.219366
FMO2-MP2: Total energy -77530.123398


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:467:ALA)


Summations of interaction energy for fragment #1(A:467: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.
-0.3441.9420.014-0.976-1.3250.005
Interaction energy analysis for fragmet #1(A:467:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : 0.004
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].
3A469PHE00.015-0.0133.811-0.1671.456-0.019-0.803-0.8010.005
4A470ILE00.0170.0145.9670.1570.1570.0000.0000.0000.000
5A471MET00.0020.0168.4560.1620.1620.0000.0000.0000.000
6A472PRO00.005-0.00211.882-0.010-0.0100.0000.0000.0000.000
7A473ILE0-0.046-0.01314.7890.0250.0250.0000.0000.0000.000
8A474ALA00.0600.02917.9130.0190.0190.0000.0000.0000.000
9A475SER0-0.050-0.03820.3970.0220.0220.0000.0000.0000.000
10A476LYS10.7970.90222.2220.1580.1580.0000.0000.0000.000
11A477TYR0-0.033-0.00424.5090.0120.0120.0000.0000.0000.000
12A478LYS10.8340.89426.8650.1540.1540.0000.0000.0000.000
13A479ASP-1-0.854-0.94329.352-0.097-0.0970.0000.0000.0000.000
14A480LEU0-0.0040.01430.066-0.005-0.0050.0000.0000.0000.000
15A481GLY00.0090.00327.657-0.005-0.0050.0000.0000.0000.000
16A482THR0-0.042-0.04524.2000.0150.0150.0000.0000.0000.000
17A483ILE00.0050.00522.559-0.017-0.0170.0000.0000.0000.000
18A484LEU0-0.023-0.00519.0530.0100.0100.0000.0000.0000.000
19A485GLU-1-0.833-0.90319.049-0.139-0.1390.0000.0000.0000.000
20A486GLY00.0740.02916.6730.0000.0000.0000.0000.0000.000
21A487LYS10.8560.92713.7320.0010.0010.0000.0000.0000.000
22A488ILE0-0.055-0.0118.419-0.027-0.0270.0000.0000.0000.000
23A489GLU-1-0.819-0.8939.5340.1050.1050.0000.0000.0000.000
24A490ALA0-0.020-0.0204.2440.2150.300-0.001-0.007-0.0770.000
25A491GLY00.0060.0173.172-0.810-0.6510.031-0.071-0.1200.000
26A492SER0-0.009-0.0144.0280.2870.4100.001-0.017-0.1070.000
27A493ILE0-0.0080.0057.088-0.266-0.2660.0000.0000.0000.000
28A494LYS10.9720.98010.3020.4990.4990.0000.0000.0000.000
29A495LYS10.8200.90213.1060.1890.1890.0000.0000.0000.000
30A496ASN0-0.078-0.04916.7650.0090.0090.0000.0000.0000.000
31A497SER0-0.009-0.00213.184-0.051-0.0510.0000.0000.0000.000
32A498ASN0-0.019-0.02014.6010.0770.0770.0000.0000.0000.000
33A499VAL0-0.028-0.00212.191-0.138-0.1380.0000.0000.0000.000
34A500LEU0-0.042-0.03513.2370.0630.0630.0000.0000.0000.000
35A501VAL0-0.001-0.01314.238-0.037-0.0370.0000.0000.0000.000
36A502MET0-0.0360.02913.3790.0380.0380.0000.0000.0000.000
37A503PRO00.069-0.01716.2520.0150.0150.0000.0000.0000.000
38A504ILE0-0.048-0.02518.163-0.010-0.0100.0000.0000.0000.000
39A505ASN0-0.008-0.01017.234-0.021-0.0210.0000.0000.0000.000
40A506GLN00.0390.04718.831-0.008-0.0080.0000.0000.0000.000
41A507THR0-0.044-0.01717.416-0.072-0.0720.0000.0000.0000.000
42A508LEU0-0.033-0.00517.9620.0460.0460.0000.0000.0000.000
43A509GLU-1-0.772-0.86917.898-0.344-0.3440.0000.0000.0000.000
44A510VAL00.0020.00114.8970.0350.0350.0000.0000.0000.000
45A511THR0-0.061-0.03918.0300.0030.0030.0000.0000.0000.000
46A512ALA00.0280.00619.4100.0240.0240.0000.0000.0000.000
47A513ILE0-0.0080.00514.952-0.027-0.0270.0000.0000.0000.000
48A514TYR0-0.022-0.01418.3190.0140.0140.0000.0000.0000.000
49A515ASP-1-0.793-0.90118.934-0.089-0.0890.0000.0000.0000.000
50A516GLU-1-0.899-0.96019.851-0.027-0.0270.0000.0000.0000.000
51A517ALA0-0.064-0.01822.1300.0070.0070.0000.0000.0000.000
52A518ASP-1-0.900-0.92723.697-0.074-0.0740.0000.0000.0000.000
53A519GLU-1-0.927-0.95123.329-0.079-0.0790.0000.0000.0000.000
54A520GLU-1-0.861-0.91621.137-0.194-0.1940.0000.0000.0000.000
55A521ILE0-0.0040.00015.9440.0090.0090.0000.0000.0000.000
56A522SER0-0.035-0.02316.204-0.016-0.0160.0000.0000.0000.000
57A523SER0-0.066-0.06211.992-0.055-0.0550.0000.0000.0000.000
58A524SER00.0030.01512.1540.0520.0520.0000.0000.0000.000
59A525ILE0-0.030-0.0168.454-0.140-0.1400.0000.0000.0000.000
60A526CYS0-0.008-0.0146.9370.0560.0560.0000.0000.0000.000
61A527GLY0-0.063-0.0408.7990.0810.0810.0000.0000.0000.000
62A528ASP-1-0.803-0.87811.844-0.089-0.0890.0000.0000.0000.000
63A529GLN0-0.014-0.01013.851-0.021-0.0210.0000.0000.0000.000
64A530VAL0-0.025-0.00914.390-0.004-0.0040.0000.0000.0000.000
65A531ARG10.8020.86617.1880.1000.1000.0000.0000.0000.000
66A532LEU0-0.029-0.02414.257-0.016-0.0160.0000.0000.0000.000
67A533ARG10.9500.99218.8520.1660.1660.0000.0000.0000.000
68A534VAL0-0.043-0.02418.707-0.025-0.0250.0000.0000.0000.000
69A535ARG10.8440.90421.3360.2640.2640.0000.0000.0000.000
70A536GLY00.0270.00222.583-0.028-0.0280.0000.0000.0000.000
71A537ASP-1-0.826-0.90624.846-0.185-0.1850.0000.0000.0000.000
72A538ASP-1-0.732-0.85823.808-0.211-0.2110.0000.0000.0000.000
73A539SER0-0.096-0.05325.0180.0070.0070.0000.0000.0000.000
74A540ASP-1-0.845-0.93324.788-0.170-0.1700.0000.0000.0000.000
75A541VAL0-0.077-0.02920.582-0.004-0.0040.0000.0000.0000.000
76A542GLN00.0360.02622.3980.0250.0250.0000.0000.0000.000
77A543THR0-0.071-0.04821.516-0.022-0.0220.0000.0000.0000.000
78A544GLY00.0300.01019.8940.0150.0150.0000.0000.0000.000
79A545TYR0-0.027-0.01718.197-0.009-0.0090.0000.0000.0000.000
80A546VAL0-0.022-0.02111.7710.0080.0080.0000.0000.0000.000
81A547LEU00.0050.02413.429-0.039-0.0390.0000.0000.0000.000
82A548THR0-0.006-0.0018.419-0.103-0.1030.0000.0000.0000.000
83A549SER00.0320.0247.617-0.035-0.0350.0000.0000.0000.000
84A550THR00.0430.0129.5350.0080.0080.0000.0000.0000.000
85A551LYS10.8300.9108.1261.1601.1600.0000.0000.0000.000
86A552ASN0-0.002-0.0075.355-0.096-0.0960.0000.0000.0000.000
87A553PRO00.0120.0127.154-0.287-0.2870.0000.0000.0000.000
88A554VAL00.0290.0019.1530.0770.0770.0000.0000.0000.000
89A555HIS0-0.052-0.0509.0580.0380.0380.0000.0000.0000.000
90A556ALA0-0.005-0.01612.4180.0290.0290.0000.0000.0000.000
91A557THR00.0090.01216.1140.0100.0100.0000.0000.0000.000
92A558THR00.0250.02519.2010.0020.0020.0000.0000.0000.000
93A559ARG10.8530.93721.8920.0620.0620.0000.0000.0000.000
94A560PHE00.0200.00219.6160.0010.0010.0000.0000.0000.000
95A561ILE0-0.0010.01320.7990.0080.0080.0000.0000.0000.000
96A562ALA00.0550.02120.6940.0150.0150.0000.0000.0000.000
97A563GLN0-0.067-0.03222.1910.0020.0020.0000.0000.0000.000
98A564ILE00.0270.00423.7390.0010.0010.0000.0000.0000.000
99A565ALA0-0.058-0.01826.3740.0000.0000.0000.0000.0000.000
100A566ILE00.0150.01328.472-0.004-0.0040.0000.0000.0000.000
101A567LEU0-0.062-0.04329.1630.0040.0040.0000.0000.0000.000
102A568GLU-1-0.801-0.89432.8600.0310.0310.0000.0000.0000.000
103A569LEU00.039-0.01833.651-0.003-0.0030.0000.0000.0000.000
104A570PRO0-0.0090.04136.7190.0010.0010.0000.0000.0000.000
105A571SER0-0.026-0.02939.8590.0000.0000.0000.0000.0000.000
106A572ILE0-0.0020.01839.3480.0030.0030.0000.0000.0000.000
107A573LEU0-0.0040.01432.349-0.002-0.0020.0000.0000.0000.000
108A574THR0-0.005-0.03336.1920.0040.0040.0000.0000.0000.000
109A575THR0-0.012-0.02633.837-0.002-0.0020.0000.0000.0000.000
110A576GLY00.0480.04933.941-0.002-0.0020.0000.0000.0000.000
111A577TYR0-0.106-0.08232.215-0.001-0.0010.0000.0000.0000.000
112A578SER00.0710.00232.0210.0000.0000.0000.0000.0000.000
113A579CYS0-0.114-0.04030.0690.0070.0070.0000.0000.0000.000
114A580VAL00.0810.05227.563-0.005-0.0050.0000.0000.0000.000
115A581MET0-0.044-0.01020.9900.0090.0090.0000.0000.0000.000
116A582HIS0-0.004-0.00423.021-0.014-0.0140.0000.0000.0000.000
117A583ILE0-0.024-0.02316.8630.0200.0200.0000.0000.0000.000
118A584HIS00.009-0.02415.2390.0200.0200.0000.0000.0000.000
119A585THR00.0010.02617.3040.0130.0130.0000.0000.0000.000
120A586ALA0-0.0110.00919.049-0.003-0.0030.0000.0000.0000.000
121A587VAL0-0.050-0.04420.7970.0200.0200.0000.0000.0000.000
122A588GLU-1-0.844-0.91223.573-0.102-0.1020.0000.0000.0000.000
123A589GLU-1-0.882-0.90525.457-0.020-0.0200.0000.0000.0000.000
124A590VAL0-0.047-0.04525.083-0.005-0.0050.0000.0000.0000.000
125A591SER00.0340.03427.7990.0070.0070.0000.0000.0000.000
126A592PHE0-0.061-0.05528.9760.0030.0030.0000.0000.0000.000
127A593ALA00.0570.03528.693-0.002-0.0020.0000.0000.0000.000
128A594LYS10.8240.87828.8800.0040.0040.0000.0000.0000.000
129A595LEU00.0230.02029.8910.0050.0050.0000.0000.0000.000
130A596LEU0-0.013-0.00526.4210.0000.0000.0000.0000.0000.000
131A597HIS0-0.075-0.05828.1380.0050.0050.0000.0000.0000.000
132A598LYS10.9250.95431.245-0.064-0.0640.0000.0000.0000.000
133A599LEU0-0.042-0.01227.2670.0080.0080.0000.0000.0000.000
134A600ASP-1-0.848-0.91131.8310.0670.0670.0000.0000.0000.000
135A601LYS10.9930.99832.490-0.071-0.0710.0000.0000.0000.000
136A602THR00.0250.01630.7920.0070.0070.0000.0000.0000.000
137A603ASN0-0.003-0.01925.731-0.009-0.0090.0000.0000.0000.000
138A604ARG10.9911.00528.650-0.086-0.0860.0000.0000.0000.000
139A605LYS11.0131.00125.351-0.126-0.1260.0000.0000.0000.000
140A606SER00.0170.02330.825-0.003-0.0030.0000.0000.0000.000
141A607LYS10.9790.97633.455-0.058-0.0580.0000.0000.0000.000
142A608LYS10.9390.97635.077-0.046-0.0460.0000.0000.0000.000
143A609PRO00.0540.04033.9280.0040.0040.0000.0000.0000.000
144A610PRO0-0.036-0.02033.695-0.002-0.0020.0000.0000.0000.000
145A611MET0-0.0110.00636.642-0.002-0.0020.0000.0000.0000.000
146A612PHE00.0180.00537.715-0.003-0.0030.0000.0000.0000.000
147A613ALA00.002-0.01234.2970.0050.0050.0000.0000.0000.000
148A614THR00.022-0.01036.136-0.004-0.0040.0000.0000.0000.000
149A615LYS10.8890.92235.647-0.030-0.0300.0000.0000.0000.000
150A616GLY00.0000.01033.9980.0010.0010.0000.0000.0000.000
151A617MET0-0.0670.00333.8380.0030.0030.0000.0000.0000.000
152A618LYS10.8430.91728.770-0.108-0.1080.0000.0000.0000.000
153A619ILE0-0.001-0.00829.069-0.002-0.0020.0000.0000.0000.000
154A620ILE0-0.017-0.01023.9770.0080.0080.0000.0000.0000.000
155A621ALA00.0190.00826.699-0.003-0.0030.0000.0000.0000.000
156A622GLU-1-0.836-0.90425.2150.0060.0060.0000.0000.0000.000
157A623LEU0-0.019-0.00524.4520.0000.0000.0000.0000.0000.000
158A624GLU-1-0.798-0.89524.795-0.039-0.0390.0000.0000.0000.000
159A625THR0-0.007-0.01823.3170.0070.0070.0000.0000.0000.000
160A626GLN00.0010.00526.151-0.002-0.0020.0000.0000.0000.000
161A627THR00.0090.00024.752-0.003-0.0030.0000.0000.0000.000
162A628PRO0-0.035-0.01920.4220.0060.0060.0000.0000.0000.000
163A629VAL00.0600.03418.482-0.009-0.0090.0000.0000.0000.000
164A630CYS0-0.037-0.01713.7630.0040.0040.0000.0000.0000.000
165A631MET0-0.031-0.00214.0480.0540.0540.0000.0000.0000.000
166A632GLU-1-0.774-0.8778.982-0.336-0.3360.0000.0000.0000.000
167A633ARG10.7590.83911.396-0.398-0.3980.0000.0000.0000.000
168A634PHE0-0.024-0.01612.1960.0770.0770.0000.0000.0000.000
169A635GLU-1-0.971-0.97713.4800.4600.4600.0000.0000.0000.000
170A636ASP-1-0.816-0.8668.4130.6820.6820.0000.0000.0000.000
171A637TYR00.0530.0123.9200.1810.4770.002-0.078-0.2200.000
172A638GLN00.0380.0069.632-0.198-0.1980.0000.0000.0000.000
173A639TYR0-0.002-0.01312.081-0.051-0.0510.0000.0000.0000.000
174A640MET00.0200.0309.910-0.038-0.0380.0000.0000.0000.000
175A641GLY00.0610.03312.809-0.028-0.0280.0000.0000.0000.000
176A642ARG10.8440.91615.073-0.194-0.1940.0000.0000.0000.000
177A643PHE00.0940.05618.036-0.018-0.0180.0000.0000.0000.000
178A644THR0-0.097-0.04220.8820.0130.0130.0000.0000.0000.000
179A645LEU00.035-0.00124.560-0.009-0.0090.0000.0000.0000.000
180A646ARG10.9090.94027.4950.0050.0050.0000.0000.0000.000
181A647ASP-1-0.789-0.85030.523-0.005-0.0050.0000.0000.0000.000
182A648GLN00.042-0.01130.2010.0030.0030.0000.0000.0000.000
183A649GLY0-0.0170.02933.739-0.001-0.0010.0000.0000.0000.000
184A650THR0-0.032-0.03534.2650.0020.0020.0000.0000.0000.000
185A651THR0-0.011-0.01328.459-0.005-0.0050.0000.0000.0000.000
186A652VAL00.0160.02730.9500.0060.0060.0000.0000.0000.000
187A653ALA0-0.0090.00028.4720.0060.0060.0000.0000.0000.000
188A654VAL00.0210.02824.217-0.004-0.0040.0000.0000.0000.000
189A655GLY0-0.012-0.01623.0880.0010.0010.0000.0000.0000.000
190A656LYS10.9090.96518.333-0.184-0.1840.0000.0000.0000.000
191A657VAL00.0350.04116.0300.0060.0060.0000.0000.0000.000
192A658VAL0-0.076-0.05717.0110.0390.0390.0000.0000.0000.000
193A659LYS10.9180.95316.913-0.026-0.0260.0000.0000.0000.000
194A660ILE00.0820.05413.7940.0000.0000.0000.0000.0000.000
195A661LEU0-0.106-0.05617.0860.0100.0100.0000.0000.0000.000
196A662ASP-1-0.883-0.93317.630-0.129-0.1290.0000.0000.0000.000