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: G6341

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 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 196
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2096677.08354
FMO2-HF: Nuclear repulsion 2019367.817539
FMO2-HF: Total energy -77309.266001
FMO2-MP2: Total energy -77531.130797


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.
-0.6091.6060.096-0.941-1.370.003
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 : 0.019 / q_NPA : 0.009
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].
3A469PHE00.0300.0023.890-0.1251.247-0.012-0.701-0.6590.003
4A470ILE0-0.006-0.0036.4060.1910.1910.0000.0000.0000.000
5A471MET00.0110.0248.7780.1210.1210.0000.0000.0000.000
6A472PRO0-0.007-0.00812.1000.0030.0030.0000.0000.0000.000
7A473ILE0-0.021-0.00415.1350.0150.0150.0000.0000.0000.000
8A474ALA00.0210.02218.4060.0250.0250.0000.0000.0000.000
9A475SER0-0.023-0.02620.4660.0260.0260.0000.0000.0000.000
10A476LYS10.8150.90521.9670.1770.1770.0000.0000.0000.000
11A477TYR0-0.029-0.01124.4590.0160.0160.0000.0000.0000.000
12A478LYS10.8010.88326.7980.1680.1680.0000.0000.0000.000
13A479ASP-1-0.816-0.91329.292-0.118-0.1180.0000.0000.0000.000
14A480LEU0-0.0250.00229.404-0.010-0.0100.0000.0000.0000.000
15A481GLY00.0190.02427.948-0.007-0.0070.0000.0000.0000.000
16A482THR0-0.017-0.03824.1470.0180.0180.0000.0000.0000.000
17A483ILE00.0010.01522.463-0.017-0.0170.0000.0000.0000.000
18A484LEU0-0.014-0.01019.3380.0110.0110.0000.0000.0000.000
19A485GLU-1-0.816-0.90218.513-0.192-0.1920.0000.0000.0000.000
20A486GLY00.0520.03416.8640.0010.0010.0000.0000.0000.000
21A487LYS10.8450.92412.8910.1100.1100.0000.0000.0000.000
22A488ILE0-0.034-0.0058.008-0.070-0.0700.0000.0000.0000.000
23A489GLU-1-0.824-0.9069.316-0.025-0.0250.0000.0000.0000.000
24A490ALA0-0.034-0.0274.1080.1920.308-0.001-0.013-0.1020.000
25A491GLY00.0220.0192.938-0.899-0.6030.099-0.156-0.2390.000
26A492SER0-0.021-0.0183.7240.4470.5800.0070.014-0.1550.000
27A493ILE0-0.0080.0097.122-0.264-0.2640.0000.0000.0000.000
28A494LYS10.9540.97110.5240.5470.5470.0000.0000.0000.000
29A495LYS10.8640.91113.7140.2090.2090.0000.0000.0000.000
30A496ASN0-0.084-0.05617.0890.0020.0020.0000.0000.0000.000
31A497SER0-0.0130.00013.339-0.043-0.0430.0000.0000.0000.000
32A498ASN0-0.037-0.02215.3690.0610.0610.0000.0000.0000.000
33A499VAL0-0.033-0.01612.450-0.135-0.1350.0000.0000.0000.000
34A500LEU0-0.027-0.01513.4370.0840.0840.0000.0000.0000.000
35A501VAL00.007-0.00814.562-0.050-0.0500.0000.0000.0000.000
36A502MET0-0.0200.02213.5110.0480.0480.0000.0000.0000.000
37A503PRO00.053-0.00716.4250.0080.0080.0000.0000.0000.000
38A504ILE0-0.041-0.01218.559-0.005-0.0050.0000.0000.0000.000
39A505ASN0-0.036-0.02217.376-0.009-0.0090.0000.0000.0000.000
40A506GLN00.0620.04918.918-0.022-0.0220.0000.0000.0000.000
41A507THR0-0.062-0.04417.552-0.076-0.0760.0000.0000.0000.000
42A508LEU0-0.027-0.00118.2480.0490.0490.0000.0000.0000.000
43A509GLU-1-0.747-0.84318.032-0.367-0.3670.0000.0000.0000.000
44A510VAL00.0270.00014.8650.0390.0390.0000.0000.0000.000
45A511THR0-0.088-0.04918.0720.0120.0120.0000.0000.0000.000
46A512ALA00.0170.00920.2660.0210.0210.0000.0000.0000.000
47A513ILE00.0110.00915.223-0.031-0.0310.0000.0000.0000.000
48A514TYR0-0.054-0.03618.5440.0150.0150.0000.0000.0000.000
49A515ASP-1-0.804-0.90018.889-0.132-0.1320.0000.0000.0000.000
50A516GLU-1-0.922-0.97519.663-0.073-0.0730.0000.0000.0000.000
51A517ALA0-0.059-0.01922.0220.0110.0110.0000.0000.0000.000
52A518ASP-1-0.883-0.92024.032-0.097-0.0970.0000.0000.0000.000
53A519GLU-1-0.912-0.94123.381-0.108-0.1080.0000.0000.0000.000
54A520GLU-1-0.863-0.90321.565-0.221-0.2210.0000.0000.0000.000
55A521ILE0-0.002-0.00116.1670.0110.0110.0000.0000.0000.000
56A522SER0-0.035-0.02916.358-0.015-0.0150.0000.0000.0000.000
57A523SER0-0.067-0.05312.549-0.044-0.0440.0000.0000.0000.000
58A524SER00.0030.01212.1130.0640.0640.0000.0000.0000.000
59A525ILE0-0.034-0.0338.343-0.166-0.1660.0000.0000.0000.000
60A526CYS0-0.053-0.0276.3750.1020.1020.0000.0000.0000.000
61A527GLY0-0.018-0.0078.2530.1280.1280.0000.0000.0000.000
62A528ASP-1-0.790-0.87311.746-0.183-0.1830.0000.0000.0000.000
63A529GLN0-0.006-0.00613.715-0.042-0.0420.0000.0000.0000.000
64A530VAL0-0.039-0.02613.937-0.003-0.0030.0000.0000.0000.000
65A531ARG10.8030.86616.9310.1300.1300.0000.0000.0000.000
66A532LEU00.001-0.00214.432-0.008-0.0080.0000.0000.0000.000
67A533ARG10.8820.93318.8880.1860.1860.0000.0000.0000.000
68A534VAL0-0.048-0.01719.050-0.024-0.0240.0000.0000.0000.000
69A535ARG10.8410.89621.7480.2860.2860.0000.0000.0000.000
70A536GLY00.0370.00422.762-0.031-0.0310.0000.0000.0000.000
71A537ASP-1-0.819-0.87724.842-0.195-0.1950.0000.0000.0000.000
72A538ASP-1-0.742-0.86224.305-0.228-0.2280.0000.0000.0000.000
73A539SER0-0.076-0.05925.3580.0070.0070.0000.0000.0000.000
74A540ASP-1-0.807-0.90425.388-0.189-0.1890.0000.0000.0000.000
75A541VAL0-0.052-0.01021.074-0.004-0.0040.0000.0000.0000.000
76A542GLN00.0090.00623.0540.0230.0230.0000.0000.0000.000
77A543THR0-0.022-0.02721.874-0.023-0.0230.0000.0000.0000.000
78A544GLY0-0.017-0.00820.0100.0120.0120.0000.0000.0000.000
79A545TYR0-0.045-0.03918.657-0.014-0.0140.0000.0000.0000.000
80A546VAL0-0.042-0.03012.3150.0050.0050.0000.0000.0000.000
81A547LEU00.0180.02713.785-0.035-0.0350.0000.0000.0000.000
82A548THR0-0.011-0.0088.763-0.097-0.0970.0000.0000.0000.000
83A549SER00.0270.0137.5080.1020.1020.0000.0000.0000.000
84A550THR00.0290.0119.5930.0760.0760.0000.0000.0000.000
85A551LYS10.8160.8988.5051.0841.0840.0000.0000.0000.000
86A552ASN00.0020.0025.469-0.070-0.0700.0000.0000.0000.000
87A553PRO00.0230.0207.286-0.432-0.4320.0000.0000.0000.000
88A554VAL00.0200.0029.4340.0580.0580.0000.0000.0000.000
89A555HIS0-0.048-0.05310.0160.0720.0720.0000.0000.0000.000
90A556ALA00.003-0.01213.0320.0150.0150.0000.0000.0000.000
91A557THR0-0.0030.00316.5640.0070.0070.0000.0000.0000.000
92A558THR00.0300.03019.8240.0000.0000.0000.0000.0000.000
93A559ARG10.8440.91122.1800.0740.0740.0000.0000.0000.000
94A560PHE00.0290.00619.790-0.001-0.0010.0000.0000.0000.000
95A561ILE0-0.002-0.00120.8790.0090.0090.0000.0000.0000.000
96A562ALA00.0500.01920.6830.0120.0120.0000.0000.0000.000
97A563GLN0-0.055-0.02322.0830.0060.0060.0000.0000.0000.000
98A564ILE00.0320.00923.528-0.001-0.0010.0000.0000.0000.000
99A565ALA0-0.048-0.02626.2930.0050.0050.0000.0000.0000.000
100A566ILE0-0.0040.00628.683-0.005-0.0050.0000.0000.0000.000
101A567LEU0-0.015-0.01329.2610.0050.0050.0000.0000.0000.000
102A568GLU-1-0.803-0.88332.9680.0170.0170.0000.0000.0000.000
103A569LEU00.0330.01334.325-0.004-0.0040.0000.0000.0000.000
104A570PRO0-0.009-0.01236.5320.0020.0020.0000.0000.0000.000
105A571SER0-0.019-0.00839.6170.0000.0000.0000.0000.0000.000
106A572ILE0-0.021-0.00439.2680.0040.0040.0000.0000.0000.000
107A573LEU00.0000.02732.379-0.002-0.0020.0000.0000.0000.000
108A574THR00.028-0.01236.4470.0040.0040.0000.0000.0000.000
109A575THR0-0.012-0.02334.122-0.001-0.0010.0000.0000.0000.000
110A576GLY00.0130.02234.269-0.003-0.0030.0000.0000.0000.000
111A577TYR0-0.096-0.07332.700-0.002-0.0020.0000.0000.0000.000
112A578SER00.014-0.04532.0560.0000.0000.0000.0000.0000.000
113A579CYS0-0.090-0.02230.3640.0060.0060.0000.0000.0000.000
114A580VAL00.0810.04527.680-0.004-0.0040.0000.0000.0000.000
115A581MET0-0.030-0.00521.0280.0080.0080.0000.0000.0000.000
116A582HIS0-0.002-0.01223.363-0.014-0.0140.0000.0000.0000.000
117A583ILE0-0.035-0.02117.1930.0210.0210.0000.0000.0000.000
118A584HIS00.0300.00215.5570.0180.0180.0000.0000.0000.000
119A585THR00.0180.00117.7990.0180.0180.0000.0000.0000.000
120A586ALA0-0.0190.00719.0640.0000.0000.0000.0000.0000.000
121A587VAL0-0.053-0.03520.8060.0210.0210.0000.0000.0000.000
122A588GLU-1-0.779-0.86123.845-0.120-0.1200.0000.0000.0000.000
123A589GLU-1-0.879-0.90425.717-0.035-0.0350.0000.0000.0000.000
124A590VAL0-0.046-0.04025.068-0.005-0.0050.0000.0000.0000.000
125A591SER00.0380.03227.8770.0090.0090.0000.0000.0000.000
126A592PHE0-0.005-0.02628.8180.0030.0030.0000.0000.0000.000
127A593ALA00.0600.04428.7540.0040.0040.0000.0000.0000.000
128A594LYS10.8160.87729.2110.0120.0120.0000.0000.0000.000
129A595LEU00.0270.03229.9570.0050.0050.0000.0000.0000.000
130A596LEU0-0.047-0.01526.8750.0010.0010.0000.0000.0000.000
131A597HIS0-0.077-0.07028.5100.0060.0060.0000.0000.0000.000
132A598LYS10.9140.95030.926-0.056-0.0560.0000.0000.0000.000
133A599LEU0-0.036-0.01427.0870.0070.0070.0000.0000.0000.000
134A600ASP-1-0.846-0.90331.6110.0580.0580.0000.0000.0000.000
135A601LYS10.9920.98631.814-0.060-0.0600.0000.0000.0000.000
136A602THR00.0300.00930.7370.0050.0050.0000.0000.0000.000
137A603ASN00.0000.00825.860-0.006-0.0060.0000.0000.0000.000
138A604ARG10.9971.00628.601-0.080-0.0800.0000.0000.0000.000
139A605LYS11.0261.01326.076-0.110-0.1100.0000.0000.0000.000
140A606SER00.0170.02131.0920.0000.0000.0000.0000.0000.000
141A607LYS10.9740.99333.932-0.059-0.0590.0000.0000.0000.000
142A608LYS10.9180.93135.770-0.045-0.0450.0000.0000.0000.000
143A609PRO00.0770.07334.3610.0050.0050.0000.0000.0000.000
144A610PRO0-0.079-0.02733.726-0.001-0.0010.0000.0000.0000.000
145A611MET00.0160.00536.383-0.002-0.0020.0000.0000.0000.000
146A612PHE00.0260.01237.565-0.003-0.0030.0000.0000.0000.000
147A613ALA0-0.011-0.01534.2610.0050.0050.0000.0000.0000.000
148A614THR00.037-0.00136.131-0.003-0.0030.0000.0000.0000.000
149A615LYS10.8800.91335.694-0.016-0.0160.0000.0000.0000.000
150A616GLY0-0.0070.00734.3220.0020.0020.0000.0000.0000.000
151A617MET0-0.092-0.01433.8200.0060.0060.0000.0000.0000.000
152A618LYS10.8480.91228.697-0.095-0.0950.0000.0000.0000.000
153A619ILE0-0.005-0.01229.127-0.001-0.0010.0000.0000.0000.000
154A620ILE0-0.020-0.01924.0590.0080.0080.0000.0000.0000.000
155A621ALA00.0100.00026.262-0.003-0.0030.0000.0000.0000.000
156A622GLU-1-0.811-0.89325.437-0.004-0.0040.0000.0000.0000.000
157A623LEU0-0.045-0.02424.6610.0020.0020.0000.0000.0000.000
158A624GLU-1-0.808-0.89525.100-0.050-0.0500.0000.0000.0000.000
159A625THR0-0.024-0.01923.4020.0090.0090.0000.0000.0000.000
160A626GLN0-0.0140.00126.232-0.001-0.0010.0000.0000.0000.000
161A627THR0-0.017-0.02224.648-0.003-0.0030.0000.0000.0000.000
162A628PRO0-0.044-0.02021.1080.0060.0060.0000.0000.0000.000
163A629VAL00.0440.02419.062-0.016-0.0160.0000.0000.0000.000
164A630CYS0-0.013-0.00914.3820.0010.0010.0000.0000.0000.000
165A631MET0-0.0360.00014.3210.0520.0520.0000.0000.0000.000
166A632GLU-1-0.772-0.8729.086-0.402-0.4020.0000.0000.0000.000
167A633ARG10.7300.81911.846-0.359-0.3590.0000.0000.0000.000
168A634PHE0-0.036-0.03512.0680.0530.0530.0000.0000.0000.000
169A635GLU-1-0.930-0.96413.2450.4290.4290.0000.0000.0000.000
170A636ASP-1-0.798-0.8448.1490.6150.6150.0000.0000.0000.000
171A637TYR00.0500.0083.906-0.0590.2390.003-0.085-0.2150.000
172A638GLN00.0390.0189.431-0.180-0.1800.0000.0000.0000.000
173A639TYR0-0.052-0.02612.453-0.030-0.0300.0000.0000.0000.000
174A640MET00.0470.03710.110-0.031-0.0310.0000.0000.0000.000
175A641GLY00.0600.03512.954-0.026-0.0260.0000.0000.0000.000
176A642ARG10.8260.90115.013-0.105-0.1050.0000.0000.0000.000
177A643PHE00.0640.03517.986-0.020-0.0200.0000.0000.0000.000
178A644THR0-0.086-0.04321.1010.0170.0170.0000.0000.0000.000
179A645LEU00.0400.01324.850-0.009-0.0090.0000.0000.0000.000
180A646ARG10.8910.93727.6290.0310.0310.0000.0000.0000.000
181A647ASP-1-0.783-0.85830.683-0.019-0.0190.0000.0000.0000.000
182A648GLN00.0250.00330.5390.0010.0010.0000.0000.0000.000
183A649GLY00.0000.02334.214-0.002-0.0020.0000.0000.0000.000
184A650THR0-0.034-0.03234.6700.0030.0030.0000.0000.0000.000
185A651THR0-0.007-0.00128.503-0.006-0.0060.0000.0000.0000.000
186A652VAL00.0150.01931.4150.0070.0070.0000.0000.0000.000
187A653ALA0-0.023-0.00828.8510.0060.0060.0000.0000.0000.000
188A654VAL00.0310.02024.672-0.006-0.0060.0000.0000.0000.000
189A655GLY0-0.014-0.01623.2880.0050.0050.0000.0000.0000.000
190A656LYS10.9010.97018.453-0.160-0.1600.0000.0000.0000.000
191A657VAL00.0350.03916.2490.0120.0120.0000.0000.0000.000
192A658VAL0-0.066-0.04316.8870.0310.0310.0000.0000.0000.000
193A659LYS10.9080.94917.341-0.014-0.0140.0000.0000.0000.000
194A660ILE00.0950.06214.082-0.001-0.0010.0000.0000.0000.000
195A661LEU0-0.101-0.04917.3810.0230.0230.0000.0000.0000.000
196A662ASP-1-0.878-0.92018.168-0.134-0.1340.0000.0000.0000.000