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: 6GNGZ

Calculation Name: 4Q20-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4Q20

Chain ID: A

ChEMBL ID:

UniProt ID: Q9RQQ9

Base Structure: X-ray

Registration Date: 2023-09-26

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 233
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2556712.552959
FMO2-HF: Nuclear repulsion 2469410.233048
FMO2-HF: Total energy -87302.319911
FMO2-MP2: Total energy -87559.464624


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:526:ALA)


Summations of interaction energy for fragment #1(A:526: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.
-26.356-17.9314.025-5.682-6.767-0.008
Interaction energy analysis for fragmet #1(A:526:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.033 / 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].
3A528ALA00.0360.0113.151-0.7140.7710.017-0.648-0.8530.001
4A529ASP-1-0.844-0.9262.367-11.212-7.9012.751-2.773-3.290-0.036
5A530ARG10.9130.9482.540-15.687-12.1791.258-2.255-2.5110.027
6A531SER0-0.0210.0005.3340.4910.612-0.001-0.006-0.1130.000
7A532ALA00.0310.0117.7100.3030.3030.0000.0000.0000.000
8A533ALA00.0150.0157.7940.2340.2340.0000.0000.0000.000
9A534LEU0-0.013-0.0069.4900.1910.1910.0000.0000.0000.000
10A535ALA0-0.008-0.00511.5950.0870.0870.0000.0000.0000.000
11A536GLU-1-0.844-0.92112.707-0.353-0.3530.0000.0000.0000.000
12A537ALA00.0220.01113.7160.0610.0610.0000.0000.0000.000
13A538GLU-1-0.815-0.89615.497-0.077-0.0770.0000.0000.0000.000
14A539ARG10.8080.90117.2820.3130.3130.0000.0000.0000.000
15A540LEU00.0620.03217.6690.0250.0250.0000.0000.0000.000
16A541LYS10.8660.95320.0090.0990.0990.0000.0000.0000.000
17A542ARG10.8170.86719.0060.2010.2010.0000.0000.0000.000
18A543ASP-1-0.850-0.90923.099-0.178-0.1780.0000.0000.0000.000
19A544PHE00.0080.01924.4730.0110.0110.0000.0000.0000.000
20A545VAL0-0.002-0.01125.8090.0100.0100.0000.0000.0000.000
21A546GLY0-0.002-0.00327.4230.0080.0080.0000.0000.0000.000
22A547ASN0-0.030-0.02427.8030.0080.0080.0000.0000.0000.000
23A548VAL00.0580.02930.3420.0060.0060.0000.0000.0000.000
24A549SER0-0.0010.00031.7430.0060.0060.0000.0000.0000.000
25A550TYR0-0.038-0.01433.4120.0040.0040.0000.0000.0000.000
26A551GLU-1-0.820-0.90935.079-0.058-0.0580.0000.0000.0000.000
27A552LEU0-0.0230.00035.1410.0050.0050.0000.0000.0000.000
28A553ARG10.9180.93633.8480.0590.0590.0000.0000.0000.000
29A554THR00.0080.01238.8740.0020.0020.0000.0000.0000.000
30A555PRO0-0.004-0.00340.8610.0020.0020.0000.0000.0000.000
31A556LEU00.0180.01241.7490.0030.0030.0000.0000.0000.000
32A557THR0-0.007-0.00742.9950.0020.0020.0000.0000.0000.000
33A558THR0-0.026-0.00845.5630.0010.0010.0000.0000.0000.000
34A559ILE0-0.0020.00545.8960.0020.0020.0000.0000.0000.000
35A560ILE00.0140.02946.8030.0020.0020.0000.0000.0000.000
36A561GLY00.0430.02549.5920.0010.0010.0000.0000.0000.000
37A562TYR0-0.019-0.02551.5290.0010.0010.0000.0000.0000.000
38A563SER0-0.041-0.04351.9360.0020.0020.0000.0000.0000.000
39A564GLU-1-0.783-0.87352.372-0.018-0.0180.0000.0000.0000.000
40A565LEU0-0.084-0.04255.5140.0010.0010.0000.0000.0000.000
41A566LEU0-0.081-0.04556.7660.0010.0010.0000.0000.0000.000
42A567GLU-1-0.959-0.96457.459-0.011-0.0110.0000.0000.0000.000
43A568ARG10.7910.89155.6550.0190.0190.0000.0000.0000.000
44A569ALA0-0.036-0.03262.260-0.001-0.0010.0000.0000.0000.000
45A570ASP-1-0.901-0.93364.291-0.012-0.0120.0000.0000.0000.000
46A571GLY0-0.034-0.02667.5050.0000.0000.0000.0000.0000.000
47A572ILE00.0350.00864.9110.0000.0000.0000.0000.0000.000
48A573SER0-0.044-0.00765.539-0.001-0.0010.0000.0000.0000.000
49A574GLU-1-0.729-0.85565.299-0.018-0.0180.0000.0000.0000.000
50A575ARG10.9040.96661.6700.0170.0170.0000.0000.0000.000
51A576GLY00.0580.03061.532-0.001-0.0010.0000.0000.0000.000
52A577ARG10.8590.89860.6550.0160.0160.0000.0000.0000.000
53A578ASN0-0.013-0.02559.286-0.001-0.0010.0000.0000.0000.000
54A579HIS00.0140.01756.899-0.001-0.0010.0000.0000.0000.000
55A580VAL00.0370.02055.750-0.001-0.0010.0000.0000.0000.000
56A581ALA0-0.042-0.01655.3550.0000.0000.0000.0000.0000.000
57A582ALA00.0370.02952.947-0.001-0.0010.0000.0000.0000.000
58A583VAL0-0.002-0.00351.412-0.001-0.0010.0000.0000.0000.000
59A584ARG10.7950.85250.6610.0240.0240.0000.0000.0000.000
60A585ALA00.0310.03350.5240.0000.0000.0000.0000.0000.000
61A586ALA0-0.026-0.00747.126-0.002-0.0020.0000.0000.0000.000
62A587ALA00.018-0.00445.867-0.001-0.0010.0000.0000.0000.000
63A588THR0-0.019-0.02746.0360.0010.0010.0000.0000.0000.000
64A589GLN0-0.042-0.02642.920-0.003-0.0030.0000.0000.0000.000
65A590LEU00.0040.02040.301-0.002-0.0020.0000.0000.0000.000
66A591ALA0-0.015-0.01341.094-0.001-0.0010.0000.0000.0000.000
67A592ARG10.9140.94841.8290.0330.0330.0000.0000.0000.000
68A593SER00.0220.00437.7200.0000.0000.0000.0000.0000.000
69A594ILE0-0.048-0.03337.080-0.002-0.0020.0000.0000.0000.000
70A595ASP-1-0.901-0.94837.202-0.021-0.0210.0000.0000.0000.000
71A596ASP-1-0.834-0.90936.614-0.044-0.0440.0000.0000.0000.000
72A597VAL0-0.059-0.03232.571-0.003-0.0030.0000.0000.0000.000
73A598LEU0-0.025-0.00732.8310.0000.0000.0000.0000.0000.000
74A599ASP-1-0.728-0.84634.477-0.023-0.0230.0000.0000.0000.000
75A600MET0-0.043-0.01730.846-0.003-0.0030.0000.0000.0000.000
76A601ALA00.0020.00729.734-0.003-0.0030.0000.0000.0000.000
77A602GLN00.0160.00430.2900.0020.0020.0000.0000.0000.000
78A603ILE0-0.007-0.01231.7450.0020.0020.0000.0000.0000.000
79A604ASP-1-0.806-0.85827.106-0.076-0.0760.0000.0000.0000.000
80A605ALA0-0.058-0.01627.627-0.002-0.0020.0000.0000.0000.000
81A606GLY0-0.034-0.01128.9730.0060.0060.0000.0000.0000.000
82A607GLU-1-0.980-0.99631.5380.0060.0060.0000.0000.0000.000
83A608MET0-0.090-0.03034.0980.0010.0010.0000.0000.0000.000
84A609ALA0-0.017-0.00736.810-0.003-0.0030.0000.0000.0000.000
85A610LEU0-0.023-0.01339.4670.0010.0010.0000.0000.0000.000
86A611GLU-1-0.963-0.97542.589-0.007-0.0070.0000.0000.0000.000
87A612ILE0-0.067-0.03644.441-0.001-0.0010.0000.0000.0000.000
88A613GLU-1-0.920-0.96347.986-0.012-0.0120.0000.0000.0000.000
89A614ASP-1-0.934-0.98351.748-0.017-0.0170.0000.0000.0000.000
90A615ILE0-0.015-0.00250.8630.0000.0000.0000.0000.0000.000
91A616ARG10.8780.94254.3110.0160.0160.0000.0000.0000.000
92A617VAL00.0410.01253.8060.0000.0000.0000.0000.0000.000
93A618SER00.0620.01155.7390.0000.0000.0000.0000.0000.000
94A619ASP-1-0.861-0.92757.428-0.018-0.0180.0000.0000.0000.000
95A620LEU00.0290.02850.3470.0000.0000.0000.0000.0000.000
96A621LEU0-0.026-0.02453.093-0.001-0.0010.0000.0000.0000.000
97A622LEU00.0010.00155.212-0.001-0.0010.0000.0000.0000.000
98A623ASN0-0.043-0.03554.7180.0000.0000.0000.0000.0000.000
99A624ALA0-0.002-0.00251.6750.0000.0000.0000.0000.0000.000
100A625GLN0-0.046-0.02553.2610.0000.0000.0000.0000.0000.000
101A626GLU-1-0.904-0.94956.110-0.018-0.0180.0000.0000.0000.000
102A627ARG10.7920.87250.4520.0250.0250.0000.0000.0000.000
103A628ALA0-0.0030.00652.0350.0000.0000.0000.0000.0000.000
104A629LEU00.0150.01153.710-0.001-0.0010.0000.0000.0000.000
105A630LYS10.9590.96656.2270.0180.0180.0000.0000.0000.000
106A631ASP-1-0.750-0.85552.087-0.027-0.0270.0000.0000.0000.000
107A632ALA00.0120.02154.215-0.001-0.0010.0000.0000.0000.000
108A633GLN0-0.021-0.00955.8790.0000.0000.0000.0000.0000.000
109A634LEU0-0.061-0.02053.7520.0000.0000.0000.0000.0000.000
110A635GLY00.0110.00954.8410.0000.0000.0000.0000.0000.000
111A636GLY0-0.007-0.00255.751-0.001-0.0010.0000.0000.0000.000
112A637VAL0-0.033-0.00854.461-0.001-0.0010.0000.0000.0000.000
113A638THR0-0.033-0.01257.7580.0020.0020.0000.0000.0000.000
114A639LEU00.0060.00153.855-0.001-0.0010.0000.0000.0000.000
115A640ALA0-0.031-0.01057.6210.0020.0020.0000.0000.0000.000
116A641VAL00.0180.00657.186-0.001-0.0010.0000.0000.0000.000
117A642GLU-1-0.884-0.93958.325-0.030-0.0300.0000.0000.0000.000
118A643CYS0-0.052-0.03358.085-0.001-0.0010.0000.0000.0000.000
119A644GLU-1-0.888-0.91959.809-0.024-0.0240.0000.0000.0000.000
120A645GLU-1-0.924-0.98061.500-0.020-0.0200.0000.0000.0000.000
121A646ASP-1-0.977-0.98461.673-0.024-0.0240.0000.0000.0000.000
122A647VAL0-0.0030.00356.523-0.001-0.0010.0000.0000.0000.000
123A648GLY00.0180.01058.0400.0000.0000.0000.0000.0000.000
124A649LEU0-0.034-0.02856.7880.0000.0000.0000.0000.0000.000
125A650ILE00.0070.00750.205-0.001-0.0010.0000.0000.0000.000
126A651ARG10.8990.95750.6730.0180.0180.0000.0000.0000.000
127A652GLY00.002-0.00547.375-0.002-0.0020.0000.0000.0000.000
128A653ASP-1-0.762-0.87244.424-0.019-0.0190.0000.0000.0000.000
129A654GLY00.1110.03347.006-0.002-0.0020.0000.0000.0000.000
130A655LYS10.9060.95442.5860.0180.0180.0000.0000.0000.000
131A656ARG10.8150.88039.7630.0230.0230.0000.0000.0000.000
132A657LEU00.0350.03144.349-0.003-0.0030.0000.0000.0000.000
133A658ALA0-0.011-0.00646.693-0.002-0.0020.0000.0000.0000.000
134A659GLN00.0050.00540.8080.0000.0000.0000.0000.0000.000
135A660THR0-0.007-0.00943.020-0.004-0.0040.0000.0000.0000.000
136A661LEU00.0160.00044.360-0.003-0.0030.0000.0000.0000.000
137A662ASP-1-0.813-0.87046.638-0.029-0.0290.0000.0000.0000.000
138A663HIS10.7220.83940.6140.0410.0410.0000.0000.0000.000
139A664LEU00.0100.00643.553-0.003-0.0030.0000.0000.0000.000
140A665VAL00.0560.02245.823-0.001-0.0010.0000.0000.0000.000
141A666GLU-1-0.844-0.90546.016-0.036-0.0360.0000.0000.0000.000
142A667ASN0-0.050-0.02342.822-0.003-0.0030.0000.0000.0000.000
143A668ALA00.0340.02645.286-0.001-0.0010.0000.0000.0000.000
144A669LEU0-0.015-0.01048.5500.0000.0000.0000.0000.0000.000
145A670ARG10.8990.94943.1150.0480.0480.0000.0000.0000.000
146A671GLN0-0.026-0.00744.796-0.005-0.0050.0000.0000.0000.000
147A672THR0-0.003-0.01948.3380.0000.0000.0000.0000.0000.000
148A673PRO0-0.057-0.00852.1880.0010.0010.0000.0000.0000.000
149A674PRO00.0260.00854.5320.0010.0010.0000.0000.0000.000
150A675GLY0-0.040-0.02757.8100.0000.0000.0000.0000.0000.000
151A676GLY0-0.033-0.00356.7880.0000.0000.0000.0000.0000.000
152A677ARG10.8610.90256.8670.0330.0330.0000.0000.0000.000
153A678VAL00.0220.01152.100-0.002-0.0020.0000.0000.0000.000
154A679THR0-0.022-0.01654.2970.0020.0020.0000.0000.0000.000
155A680LEU0-0.0110.01152.619-0.002-0.0020.0000.0000.0000.000
156A681SER00.0360.01153.7720.0020.0020.0000.0000.0000.000
157A682ALA00.010-0.00253.522-0.001-0.0010.0000.0000.0000.000
158A683ARG10.9520.98053.9560.0390.0390.0000.0000.0000.000
159A684ARG10.8400.91354.3190.0240.0240.0000.0000.0000.000
160A685ALA0-0.020-0.02154.6730.0010.0010.0000.0000.0000.000
161A686LEU0-0.049-0.03352.812-0.001-0.0010.0000.0000.0000.000
162A687GLY00.0300.02952.161-0.002-0.0020.0000.0000.0000.000
163A688GLU-1-0.837-0.89248.370-0.046-0.0460.0000.0000.0000.000
164A689VAL0-0.002-0.00950.5400.0010.0010.0000.0000.0000.000
165A690ARG10.7920.87849.6620.0430.0430.0000.0000.0000.000
166A691LEU00.002-0.00348.6270.0020.0020.0000.0000.0000.000
167A692ASP-1-0.797-0.86148.963-0.047-0.0470.0000.0000.0000.000
168A693VAL00.006-0.00348.4400.0020.0020.0000.0000.0000.000
169A694SER0-0.0090.00049.406-0.002-0.0020.0000.0000.0000.000
170A695ASP-1-0.790-0.90848.823-0.049-0.0490.0000.0000.0000.000
171A696THR00.0020.00652.352-0.001-0.0010.0000.0000.0000.000
172A697GLY0-0.022-0.02351.1210.0010.0010.0000.0000.0000.000
173A698ARG10.7980.89444.1970.0660.0660.0000.0000.0000.000
174A699GLY00.0210.02647.6040.0000.0000.0000.0000.0000.000
175A700VAL0-0.021-0.02341.133-0.002-0.0020.0000.0000.0000.000
176A701PRO0-0.025-0.00740.6780.0000.0000.0000.0000.0000.000
177A702PHE00.0700.01138.722-0.004-0.0040.0000.0000.0000.000
178A703HIS00.0060.00235.908-0.001-0.0010.0000.0000.0000.000
179A704VAL0-0.011-0.01335.832-0.006-0.0060.0000.0000.0000.000
180A705GLN0-0.065-0.03537.193-0.001-0.0010.0000.0000.0000.000
181A706ALA0-0.013-0.00134.7020.0030.0030.0000.0000.0000.000
182A707HIS0-0.050-0.02129.860-0.005-0.0050.0000.0000.0000.000
183A708ILE0-0.0010.00434.1610.0010.0010.0000.0000.0000.000
184A709PHE0-0.027-0.02535.4420.0040.0040.0000.0000.0000.000
185A710ASP-1-0.874-0.91930.496-0.129-0.1290.0000.0000.0000.000
186A711ARG10.7380.80528.2140.0930.0930.0000.0000.0000.000
187A712PHE0-0.053-0.03028.837-0.009-0.0090.0000.0000.0000.000
188A713VAL00.0170.04431.685-0.008-0.0080.0000.0000.0000.000
189A714GLY00.008-0.01433.3450.0080.0080.0000.0000.0000.000
190A715ARG10.8360.90535.0420.0750.0750.0000.0000.0000.000
191A716ASP-1-0.806-0.87038.847-0.072-0.0720.0000.0000.0000.000
192A717ARG10.8420.93141.3570.0520.0520.0000.0000.0000.000
193A718GLY00.0440.00841.9460.0040.0040.0000.0000.0000.000
194A719GLY0-0.0220.00238.235-0.002-0.0020.0000.0000.0000.000
195A720PRO00.0020.00537.1800.0040.0040.0000.0000.0000.000
196A721GLY00.0400.02635.1980.0030.0030.0000.0000.0000.000
197A722LEU00.0400.00731.113-0.007-0.0070.0000.0000.0000.000
198A723GLY00.0360.01935.1120.0010.0010.0000.0000.0000.000
199A724LEU0-0.019-0.02137.7220.0020.0020.0000.0000.0000.000
200A725ALA00.0140.01732.972-0.001-0.0010.0000.0000.0000.000
201A726LEU00.0020.00735.0700.0000.0000.0000.0000.0000.000
202A727VAL0-0.007-0.00636.9630.0030.0030.0000.0000.0000.000
203A728LYS10.8960.96132.7810.0960.0960.0000.0000.0000.000
204A729ALA00.0260.01634.2630.0010.0010.0000.0000.0000.000
205A730LEU00.0170.00336.0280.0040.0040.0000.0000.0000.000
206A731VAL0-0.0060.00139.4190.0030.0030.0000.0000.0000.000
207A732GLU-1-0.899-0.96535.030-0.076-0.0760.0000.0000.0000.000
208A733LEU0-0.048-0.00536.0900.0010.0010.0000.0000.0000.000
209A734HIS0-0.049-0.03038.7840.0060.0060.0000.0000.0000.000
210A735GLY0-0.0230.00140.6970.0020.0020.0000.0000.0000.000
211A736GLY0-0.003-0.00441.672-0.001-0.0010.0000.0000.0000.000
212A737TRP0-0.009-0.01040.072-0.005-0.0050.0000.0000.0000.000
213A738VAL00.0000.00339.1400.0040.0040.0000.0000.0000.000
214A739ALA0-0.026-0.01640.812-0.004-0.0040.0000.0000.0000.000
215A740LEU0-0.010-0.00841.4030.0030.0030.0000.0000.0000.000
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