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: GNKY1

Calculation Name: 4RLB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4RLB

Chain ID: A

ChEMBL ID:

UniProt ID: Q5DL42

Base Structure: X-ray

Registration Date: 2023-06-20

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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2146052.534275
FMO2-HF: Nuclear repulsion 2066835.230305
FMO2-HF: Total energy -79217.30397
FMO2-MP2: Total energy -79452.645825


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:14:ASN)


Summations of interaction energy for fragment #1(A:14:ASN)
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.
-14.829-15.57210.359-4.521-5.0950.037
Interaction energy analysis for fragmet #1(A:14:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.012 / q_NPA : -0.011
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].
3A16LEU00.017-0.0073.7460.6082.164-0.018-0.578-0.9590.003
4A17ILE0-0.0180.0025.920-0.041-0.0410.0000.0000.0000.000
5A18PRO0-0.0010.0028.3140.0760.0760.0000.0000.0000.000
6A19VAL0-0.040-0.03210.7120.1070.1070.0000.0000.0000.000
7A20GLY00.0270.01413.467-0.016-0.0160.0000.0000.0000.000
8A21ALA0-0.030-0.00816.991-0.042-0.0420.0000.0000.0000.000
9A22ARG10.8210.90317.382-0.374-0.3740.0000.0000.0000.000
10A23ALA00.0000.02521.580-0.039-0.0390.0000.0000.0000.000
11A24GLU-1-0.757-0.85522.3260.2800.2800.0000.0000.0000.000
12A25VAL00.0560.02226.292-0.022-0.0220.0000.0000.0000.000
13A26GLY00.018-0.00628.8040.0180.0180.0000.0000.0000.000
14A27THR00.0130.01430.182-0.005-0.0050.0000.0000.0000.000
15A28THR0-0.0030.00327.663-0.007-0.0070.0000.0000.0000.000
16A29GLY00.0460.03030.851-0.009-0.0090.0000.0000.0000.000
17A30TYR0-0.040-0.02929.4990.0150.0150.0000.0000.0000.000
18A31GLY00.0290.00527.294-0.018-0.0180.0000.0000.0000.000
19A32GLY0-0.007-0.00323.8110.0250.0250.0000.0000.0000.000
20A33ALA0-0.025-0.00518.856-0.034-0.0340.0000.0000.0000.000
21A34LEU00.0000.00716.8900.0470.0470.0000.0000.0000.000
22A35LEU00.0240.00514.310-0.018-0.0180.0000.0000.0000.000
23A36TRP0-0.024-0.0219.3420.0050.0050.0000.0000.0000.000
24A37GLN0-0.026-0.0158.011-0.474-0.4740.0000.0000.0000.000
25A38ALA0-0.0040.0113.029-0.688-0.4050.084-0.124-0.2440.000
26A39ASN0-0.012-0.0281.813-9.168-11.75210.294-3.815-3.8950.034
27A40PRO0-0.017-0.0154.979-1.717-1.715-0.001-0.0040.0030.000
28A41TYR00.0120.0116.096-1.086-1.0860.0000.0000.0000.000
29A42VAL00.0080.0245.344-0.913-0.9130.0000.0000.0000.000
30A43GLY00.0530.0247.1970.7440.7440.0000.0000.0000.000
31A44LEU0-0.059-0.0269.328-0.336-0.3360.0000.0000.0000.000
32A45ALA00.0560.03411.5760.1120.1120.0000.0000.0000.000
33A46LEU0-0.005-0.00215.288-0.091-0.0910.0000.0000.0000.000
34A47GLY00.0210.00417.6980.0460.0460.0000.0000.0000.000
35A48TYR0-0.0250.01121.309-0.038-0.0380.0000.0000.0000.000
36A49ASN0-0.095-0.07124.7870.0210.0210.0000.0000.0000.000
37A50GLY00.0660.02227.599-0.019-0.0190.0000.0000.0000.000
38A51GLY0-0.006-0.00831.2170.0140.0140.0000.0000.0000.000
39A52ASP-1-0.919-0.95234.6570.0520.0520.0000.0000.0000.000
40A53ILE0-0.085-0.03634.2010.0090.0090.0000.0000.0000.000
41A54SER00.0780.05038.673-0.006-0.0060.0000.0000.0000.000
42A55TRP0-0.096-0.06933.8390.0110.0110.0000.0000.0000.000
43A56SER0-0.061-0.04339.4880.0050.0050.0000.0000.0000.000
44A57ASP-1-0.820-0.88942.8560.0690.0690.0000.0000.0000.000
45A58ASP-1-0.828-0.88846.4340.0580.0580.0000.0000.0000.000
46A59LEU0-0.0070.00543.6890.0010.0010.0000.0000.0000.000
47A60SER0-0.051-0.03247.747-0.004-0.0040.0000.0000.0000.000
48A61ILE00.007-0.01045.3400.0030.0030.0000.0000.0000.000
49A62ASN0-0.041-0.02649.980-0.003-0.0030.0000.0000.0000.000
50A63GLY00.0190.00452.924-0.003-0.0030.0000.0000.0000.000
51A64THR0-0.014-0.00550.084-0.004-0.0040.0000.0000.0000.000
52A65LYS10.8080.89950.157-0.049-0.0490.0000.0000.0000.000
53A66TYR0-0.024-0.01544.912-0.006-0.0060.0000.0000.0000.000
54A67ASP-1-0.830-0.91145.5000.0550.0550.0000.0000.0000.000
55A68MET0-0.086-0.05237.548-0.002-0.0020.0000.0000.0000.000
56A69ASP-1-0.816-0.89441.0660.0610.0610.0000.0000.0000.000
57A70MET0-0.090-0.05734.409-0.004-0.0040.0000.0000.0000.000
58A71ASP-1-0.797-0.87537.1760.0400.0400.0000.0000.0000.000
59A72ASN0-0.091-0.04131.856-0.016-0.0160.0000.0000.0000.000
60A73LYS10.8540.91930.855-0.020-0.0200.0000.0000.0000.000
61A74LEU0-0.0070.01724.741-0.012-0.0120.0000.0000.0000.000
62A75ALA0-0.004-0.00823.7560.0230.0230.0000.0000.0000.000
63A76TYR0-0.050-0.04118.724-0.014-0.0140.0000.0000.0000.000
64A77LEU00.0140.00314.1950.0240.0240.0000.0000.0000.000
65A78ASN0-0.034-0.02515.355-0.013-0.0130.0000.0000.0000.000
66A79ALA00.0240.02210.6840.0610.0610.0000.0000.0000.000
67A80GLU-1-0.831-0.90211.3820.7120.7120.0000.0000.0000.000
68A81ILE0-0.027-0.0309.4740.2320.2320.0000.0000.0000.000
69A82ARG10.8700.92710.984-1.197-1.1970.0000.0000.0000.000
70A83PRO0-0.014-0.00911.6940.1900.1900.0000.0000.0000.000
71A84TRP00.0210.00613.3710.0270.0270.0000.0000.0000.000
72A85GLY00.0450.02311.126-0.047-0.0470.0000.0000.0000.000
73A86ALA0-0.031-0.01610.4180.1860.1860.0000.0000.0000.000
74A87SER0-0.065-0.01812.132-0.185-0.1850.0000.0000.0000.000
75A88THR00.0280.00115.9120.0530.0530.0000.0000.0000.000
76A89ASN00.0140.00618.365-0.046-0.0460.0000.0000.0000.000
77A90PRO00.0580.01719.1630.0560.0560.0000.0000.0000.000
78A91TRP00.005-0.00720.1180.0200.0200.0000.0000.0000.000
79A92ALA00.0210.00818.616-0.021-0.0210.0000.0000.0000.000
80A93GLN0-0.023-0.01213.537-0.076-0.0760.0000.0000.0000.000
81A94GLY00.0020.00215.3430.1070.1070.0000.0000.0000.000
82A95LEU0-0.038-0.00117.834-0.039-0.0390.0000.0000.0000.000
83A96TYR0-0.071-0.05914.8510.1370.1370.0000.0000.0000.000
84A97VAL00.0020.01415.438-0.082-0.0820.0000.0000.0000.000
85A98ALA00.0120.00714.9540.0650.0650.0000.0000.0000.000
86A99ALA00.007-0.01215.020-0.049-0.0490.0000.0000.0000.000
87A100GLY0-0.022-0.02015.176-0.016-0.0160.0000.0000.0000.000
88A101ALA0-0.0190.00117.362-0.014-0.0140.0000.0000.0000.000
89A102ALA0-0.026-0.01520.4050.0190.0190.0000.0000.0000.000
90A103TYR00.0170.04923.235-0.018-0.0180.0000.0000.0000.000
91A104VAL0-0.087-0.07326.1400.0240.0240.0000.0000.0000.000
92A105ASP-1-0.773-0.87028.991-0.013-0.0130.0000.0000.0000.000
93A106ASN00.002-0.01430.5470.0070.0070.0000.0000.0000.000
94A107GLN0-0.0260.00434.016-0.008-0.0080.0000.0000.0000.000
95A108TYR00.021-0.00332.7300.0060.0060.0000.0000.0000.000
96A109ASP-1-0.749-0.84939.2640.0180.0180.0000.0000.0000.000
97A110LEU0-0.037-0.02140.3420.0060.0060.0000.0000.0000.000
98A111THR0-0.008-0.01644.190-0.006-0.0060.0000.0000.0000.000
99A112LYS10.9310.98846.475-0.030-0.0300.0000.0000.0000.000
100A113ASN00.0420.01949.325-0.006-0.0060.0000.0000.0000.000
101A114VAL0-0.027-0.02152.5370.0030.0030.0000.0000.0000.000
102A115GLY00.0620.03554.474-0.002-0.0020.0000.0000.0000.000
103A116THR0-0.008-0.03957.313-0.001-0.0010.0000.0000.0000.000
104A117ASN0-0.108-0.04960.2380.0000.0000.0000.0000.0000.000
105A118ALA00.0080.03255.4880.0010.0010.0000.0000.0000.000
106A119SER0-0.070-0.05555.358-0.003-0.0030.0000.0000.0000.000
107A120VAL00.0260.01750.1470.0030.0030.0000.0000.0000.000
108A121GLU-1-0.827-0.89749.9520.0210.0210.0000.0000.0000.000
109A122ILE0-0.016-0.01247.9710.0020.0020.0000.0000.0000.000
110A123ASP-1-0.769-0.86347.727-0.006-0.0060.0000.0000.0000.000
111A124GLY00.0050.00548.720-0.002-0.0020.0000.0000.0000.000
112A125ASN0-0.0020.02650.8180.0010.0010.0000.0000.0000.000
113A126ARG10.8370.89453.087-0.019-0.0190.0000.0000.0000.000
114A127PHE00.0200.01153.464-0.001-0.0010.0000.0000.0000.000
115A128ASN0-0.033-0.02556.4940.0030.0030.0000.0000.0000.000
116A129GLY00.0420.03258.336-0.002-0.0020.0000.0000.0000.000
117A130GLY00.0130.02259.372-0.001-0.0010.0000.0000.0000.000
118A131ALA00.027-0.00662.7440.0020.0020.0000.0000.0000.000
119A132ASN0-0.052-0.03062.8950.0000.0000.0000.0000.0000.000
120A133GLY00.0360.04058.8770.0010.0010.0000.0000.0000.000
121A134VAL0-0.045-0.02455.485-0.002-0.0020.0000.0000.0000.000
122A135SER0-0.021-0.02453.4600.0020.0020.0000.0000.0000.000
123A136ILE0-0.026-0.02149.367-0.003-0.0030.0000.0000.0000.000
124A137ALA00.0100.00948.3570.0040.0040.0000.0000.0000.000
125A138GLY00.007-0.00945.080-0.004-0.0040.0000.0000.0000.000
126A139ASN0-0.048-0.02142.9760.0000.0000.0000.0000.0000.000
127A140LEU0-0.020-0.02038.200-0.005-0.0050.0000.0000.0000.000
128A141LYS10.8130.88535.6450.0070.0070.0000.0000.0000.000
129A142TYR0-0.024-0.02332.738-0.003-0.0030.0000.0000.0000.000
130A143ASP-1-0.773-0.87532.972-0.017-0.0170.0000.0000.0000.000
131A144ASN0-0.066-0.05528.598-0.019-0.0190.0000.0000.0000.000
132A145ASP-1-0.864-0.92527.883-0.080-0.0800.0000.0000.0000.000
133A146ILE0-0.070-0.03521.413-0.009-0.0090.0000.0000.0000.000
134A147ALA00.0250.02125.214-0.012-0.0120.0000.0000.0000.000
135A148PRO0-0.013-0.00821.9350.0080.0080.0000.0000.0000.000
136A149TYR0-0.057-0.06019.4110.0160.0160.0000.0000.0000.000
137A150ILE0-0.023-0.00719.277-0.019-0.0190.0000.0000.0000.000
138A151GLY00.0570.02219.8380.0020.0020.0000.0000.0000.000
139A152PHE0-0.044-0.01919.6490.0120.0120.0000.0000.0000.000
140A153GLY00.0520.02819.726-0.023-0.0230.0000.0000.0000.000
141A154PHE0-0.057-0.02720.0520.0380.0380.0000.0000.0000.000
142A155ALA00.0360.00617.677-0.029-0.0290.0000.0000.0000.000
143A156PRO0-0.0080.01317.7440.1190.1190.0000.0000.0000.000
144A157LYS10.8930.95914.114-1.208-1.2080.0000.0000.0000.000
145A158PHE00.012-0.00118.193-0.009-0.0090.0000.0000.0000.000
146A159SER00.0110.01019.819-0.029-0.0290.0000.0000.0000.000
147A160LYS10.9200.96315.268-1.058-1.0580.0000.0000.0000.000
148A161ASN00.019-0.00618.0940.0790.0790.0000.0000.0000.000
149A162TRP00.0390.02720.641-0.023-0.0230.0000.0000.0000.000
150A163GLY0-0.017-0.00520.7940.0550.0550.0000.0000.0000.000
151A164VAL00.0200.01821.734-0.034-0.0340.0000.0000.0000.000
152A165PHE0-0.035-0.01420.7330.0630.0630.0000.0000.0000.000
153A166GLY00.0360.02222.626-0.039-0.0390.0000.0000.0000.000
154A167GLU-1-0.844-0.88319.7450.3090.3090.0000.0000.0000.000
155A168VAL00.0000.00123.453-0.024-0.0240.0000.0000.0000.000
156A169GLY00.0430.01423.7520.0120.0120.0000.0000.0000.000
157A170ALA0-0.040-0.01624.381-0.003-0.0030.0000.0000.0000.000
158A171TYR00.0420.01822.974-0.010-0.0100.0000.0000.0000.000
159A172TYR0-0.0250.00325.7400.0060.0060.0000.0000.0000.000
160A173SER0-0.006-0.01827.665-0.013-0.0130.0000.0000.0000.000
161A174GLY00.0210.02229.867-0.009-0.0090.0000.0000.0000.000
162A175ASN0-0.083-0.06032.8140.0010.0010.0000.0000.0000.000
163A176PRO0-0.0040.01836.162-0.004-0.0040.0000.0000.0000.000
164A177LYS10.8680.92037.3980.0280.0280.0000.0000.0000.000
165A178VAL0-0.011-0.01940.6210.0050.0050.0000.0000.0000.000
166A179SER0-0.0190.00342.944-0.003-0.0030.0000.0000.0000.000
167A180LEU0-0.045-0.02044.9200.0050.0050.0000.0000.0000.000
168A181ALA00.0200.01848.405-0.002-0.0020.0000.0000.0000.000
169A182SER0-0.022-0.03851.6110.0040.0040.0000.0000.0000.000
170A183ASN00.0050.00954.396-0.002-0.0020.0000.0000.0000.000
171A184ASN0-0.011-0.02757.459-0.002-0.0020.0000.0000.0000.000
172A185ASP-1-0.770-0.86156.1050.0060.0060.0000.0000.0000.000
173A186ALA0-0.010-0.01058.607-0.001-0.0010.0000.0000.0000.000
174A187LEU0-0.037-0.00658.585-0.001-0.0010.0000.0000.0000.000
175A188ILE0-0.014-0.01559.734-0.001-0.0010.0000.0000.0000.000
176A189GLY00.0410.02957.6860.0020.0020.0000.0000.0000.000
177A190SER0-0.051-0.02756.969-0.001-0.0010.0000.0000.0000.000
178A191ASP-1-0.842-0.91755.1060.0010.0010.0000.0000.0000.000
179A192GLY0-0.002-0.00258.485-0.002-0.0020.0000.0000.0000.000
180A193ARG10.6950.82651.3600.0010.0010.0000.0000.0000.000
181A194THR00.0410.01458.4950.0020.0020.0000.0000.0000.000
182A195LEU00.0360.03453.400-0.001-0.0010.0000.0000.0000.000
183A196GLY00.0500.01554.3870.0000.0000.0000.0000.0000.000
184A197LYS10.8410.92453.9180.0100.0100.0000.0000.0000.000
185A198THR0-0.018-0.02751.436-0.002-0.0020.0000.0000.0000.000
186A199LEU00.0120.00949.6430.0000.0000.0000.0000.0000.000
187A200ASP-1-0.831-0.89149.404-0.015-0.0150.0000.0000.0000.000
188A201ASP-1-0.798-0.89449.398-0.014-0.0140.0000.0000.0000.000
189A202GLN0-0.068-0.03543.8110.0000.0000.0000.0000.0000.000
190A203GLU-1-0.831-0.92044.953-0.009-0.0090.0000.0000.0000.000
191A204ARG10.8180.89544.5740.0160.0160.0000.0000.0000.000
192A205LYS10.8550.90943.2070.0060.0060.0000.0000.0000.000
193A206ILE0-0.0130.00239.619-0.003-0.0030.0000.0000.0000.000
194A207ALA00.0440.02939.569-0.003-0.0030.0000.0000.0000.000
195A208ASN0-0.085-0.05240.117-0.010-0.0100.0000.0000.0000.000
196A209ASP-1-0.841-0.92139.146-0.027-0.0270.0000.0000.0000.000
197A210ASP-1-0.834-0.92334.571-0.063-0.0630.0000.0000.0000.000
198A211LYS10.8080.91334.2520.0100.0100.0000.0000.0000.000
199A212TYR00.003-0.01634.2970.0060.0060.0000.0000.0000.000
200A213LYS10.8250.93432.2060.0610.0610.0000.0000.0000.000
201A214TRP0-0.043-0.01125.407-0.006-0.0060.0000.0000.0000.000
202A215LEU00.0090.01629.5830.0060.0060.0000.0000.0000.000
203A216PRO0-0.012-0.00528.7400.0050.0050.0000.0000.0000.000
204A217VAL0-0.005-0.00925.5400.0000.0000.0000.0000.0000.000
205A218GLY00.0210.00927.2750.0080.0080.0000.0000.0000.000
206A219LYS10.8230.91822.309-0.199-0.1990.0000.0000.0000.000
207A220VAL00.0140.00625.7350.0220.0220.0000.0000.0000.000
208A221GLY00.0430.01425.135-0.022-0.0220.0000.0000.0000.000
209A222VAL0-0.068-0.02924.0950.0270.0270.0000.0000.0000.000
210A223ASN0-0.007-0.01018.804-0.044-0.0440.0000.0000.0000.000
211A224PHE00.009-0.01020.3050.0000.0000.0000.0000.0000.000
212A225TYR0-0.016-0.01915.5670.0360.0360.0000.0000.0000.000
213A226TRP00.0100.01117.2720.0010.0010.0000.0000.0000.000