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: 82ZNY

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 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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2149051.990704
FMO2-HF: Nuclear repulsion 2069834.181771
FMO2-HF: Total energy -79217.808932
FMO2-MP2: Total energy -79453.299047


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.
-16.896-16.8610.584-5.071-5.5480.027
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 : 0.000 / q_NPA : -0.007
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].
3A16LEU00.026-0.0013.8520.4201.656-0.003-0.489-0.7450.002
4A17ILE00.0040.0165.6710.0610.0610.0000.0000.0000.000
5A18PRO00.0080.0097.9670.0900.0900.0000.0000.0000.000
6A19VAL0-0.050-0.03910.2970.1000.1000.0000.0000.0000.000
7A20GLY00.0220.01013.063-0.009-0.0090.0000.0000.0000.000
8A21ALA0-0.038-0.00816.583-0.042-0.0420.0000.0000.0000.000
9A22ARG10.8130.90917.481-0.419-0.4190.0000.0000.0000.000
10A23ALA00.0130.01921.113-0.037-0.0370.0000.0000.0000.000
11A24GLU-1-0.773-0.86922.1410.3140.3140.0000.0000.0000.000
12A25VAL00.0330.00826.022-0.023-0.0230.0000.0000.0000.000
13A26GLY00.0260.00228.8270.0210.0210.0000.0000.0000.000
14A27THR00.0170.02130.248-0.006-0.0060.0000.0000.0000.000
15A28THR00.0060.00227.564-0.009-0.0090.0000.0000.0000.000
16A29GLY00.0340.03430.807-0.013-0.0130.0000.0000.0000.000
17A30TYR0-0.019-0.01629.7670.0170.0170.0000.0000.0000.000
18A31GLY00.0320.00427.242-0.017-0.0170.0000.0000.0000.000
19A32GLY00.0020.00123.7180.0220.0220.0000.0000.0000.000
20A33ALA0-0.0100.00618.841-0.030-0.0300.0000.0000.0000.000
21A34LEU00.0030.00816.6110.0430.0430.0000.0000.0000.000
22A35LEU00.0170.00014.0020.0060.0060.0000.0000.0000.000
23A36TRP0-0.016-0.0139.137-0.012-0.0120.0000.0000.0000.000
24A37GLN0-0.046-0.0287.425-0.427-0.4270.0000.0000.0000.000
25A38ALA0-0.0110.0062.925-0.752-0.4570.161-0.125-0.330-0.001
26A39ASN0-0.016-0.0261.806-11.620-13.10610.427-4.447-4.4930.026
27A40PRO00.003-0.0114.769-1.789-1.798-0.001-0.0100.0200.000
28A41TYR0-0.0040.0076.071-1.124-1.1240.0000.0000.0000.000
29A42VAL0-0.0030.0155.259-0.782-0.7820.0000.0000.0000.000
30A43GLY00.0460.0216.9790.5960.5960.0000.0000.0000.000
31A44LEU0-0.051-0.0209.211-0.252-0.2520.0000.0000.0000.000
32A45ALA00.0530.02711.5280.0820.0820.0000.0000.0000.000
33A46LEU0-0.004-0.00115.292-0.073-0.0730.0000.0000.0000.000
34A47GLY00.000-0.01117.7600.0300.0300.0000.0000.0000.000
35A48TYR0-0.0180.01821.369-0.030-0.0300.0000.0000.0000.000
36A49ASN0-0.111-0.07724.7220.0270.0270.0000.0000.0000.000
37A50GLY00.0550.01827.578-0.015-0.0150.0000.0000.0000.000
38A51GLY0-0.004-0.00431.2360.0130.0130.0000.0000.0000.000
39A52ASP-1-0.909-0.94634.7540.0630.0630.0000.0000.0000.000
40A53ILE0-0.075-0.04534.4510.0070.0070.0000.0000.0000.000
41A54SER00.0430.00938.857-0.001-0.0010.0000.0000.0000.000
42A55TRP0-0.090-0.05733.5670.0130.0130.0000.0000.0000.000
43A56SER0-0.057-0.04139.3040.0070.0070.0000.0000.0000.000
44A57ASP-1-0.822-0.86842.7060.0800.0800.0000.0000.0000.000
45A58ASP-1-0.816-0.90046.3970.0710.0710.0000.0000.0000.000
46A59LEU00.0160.00743.877-0.001-0.0010.0000.0000.0000.000
47A60SER0-0.052-0.02347.972-0.003-0.0030.0000.0000.0000.000
48A61ILE00.0170.00045.3710.0040.0040.0000.0000.0000.000
49A62ASN0-0.035-0.02649.951-0.002-0.0020.0000.0000.0000.000
50A63GLY00.0140.00952.875-0.003-0.0030.0000.0000.0000.000
51A64THR0-0.009-0.00850.263-0.005-0.0050.0000.0000.0000.000
52A65LYS10.7670.88050.361-0.064-0.0640.0000.0000.0000.000
53A66TYR0-0.011-0.01244.875-0.004-0.0040.0000.0000.0000.000
54A67ASP-1-0.840-0.91945.8920.0700.0700.0000.0000.0000.000
55A68MET0-0.054-0.03237.548-0.001-0.0010.0000.0000.0000.000
56A69ASP-1-0.832-0.90541.1330.0770.0770.0000.0000.0000.000
57A70MET0-0.080-0.04234.5250.0000.0000.0000.0000.0000.000
58A71ASP-1-0.822-0.88537.2630.0530.0530.0000.0000.0000.000
59A72ASN0-0.052-0.02531.955-0.014-0.0140.0000.0000.0000.000
60A73LYS10.8310.90130.853-0.036-0.0360.0000.0000.0000.000
61A74LEU0-0.0200.01324.690-0.010-0.0100.0000.0000.0000.000
62A75ALA0-0.006-0.01524.2960.0160.0160.0000.0000.0000.000
63A76TYR0-0.043-0.03518.631-0.008-0.0080.0000.0000.0000.000
64A77LEU00.0100.00214.3650.0110.0110.0000.0000.0000.000
65A78ASN0-0.023-0.01915.413-0.002-0.0020.0000.0000.0000.000
66A79ALA00.0250.01910.4940.0270.0270.0000.0000.0000.000
67A80GLU-1-0.819-0.89611.4970.8420.8420.0000.0000.0000.000
68A81ILE0-0.011-0.0129.4010.3270.3270.0000.0000.0000.000
69A82ARG10.8390.91010.824-1.397-1.3970.0000.0000.0000.000
70A83PRO0-0.004-0.01211.4370.3050.3050.0000.0000.0000.000
71A84TRP00.0270.01113.1310.0370.0370.0000.0000.0000.000
72A85GLY00.0380.01910.720-0.084-0.0840.0000.0000.0000.000
73A86ALA0-0.040-0.01910.1310.0440.0440.0000.0000.0000.000
74A87SER0-0.070-0.03411.959-0.225-0.2250.0000.0000.0000.000
75A88THR00.025-0.00315.7520.0170.0170.0000.0000.0000.000
76A89ASN00.0240.02518.372-0.057-0.0570.0000.0000.0000.000
77A90PRO00.0710.02318.7280.0690.0690.0000.0000.0000.000
78A91TRP00.019-0.00719.4630.0380.0380.0000.0000.0000.000
79A92ALA00.0010.01418.209-0.020-0.0200.0000.0000.0000.000
80A93GLN0-0.014-0.01113.359-0.101-0.1010.0000.0000.0000.000
81A94GLY00.0220.01114.9390.1210.1210.0000.0000.0000.000
82A95LEU0-0.045-0.00417.610-0.050-0.0500.0000.0000.0000.000
83A96TYR0-0.080-0.06614.8480.1560.1560.0000.0000.0000.000
84A97VAL0-0.0020.00115.398-0.108-0.1080.0000.0000.0000.000
85A98ALA00.0060.00714.9600.0880.0880.0000.0000.0000.000
86A99ALA00.010-0.00614.724-0.057-0.0570.0000.0000.0000.000
87A100GLY0-0.009-0.01515.074-0.001-0.0010.0000.0000.0000.000
88A101ALA0-0.033-0.00317.183-0.016-0.0160.0000.0000.0000.000
89A102ALA0-0.008-0.01220.3740.0210.0210.0000.0000.0000.000
90A103TYR00.0020.04323.128-0.017-0.0170.0000.0000.0000.000
91A104VAL0-0.041-0.04526.2050.0220.0220.0000.0000.0000.000
92A105ASP-1-0.808-0.88329.0390.0190.0190.0000.0000.0000.000
93A106ASN00.020-0.01130.6010.0050.0050.0000.0000.0000.000
94A107GLN0-0.016-0.00833.796-0.006-0.0060.0000.0000.0000.000
95A108TYR00.0260.00932.7060.0070.0070.0000.0000.0000.000
96A109ASP-1-0.750-0.83639.0450.0390.0390.0000.0000.0000.000
97A110LEU0-0.027-0.02140.4110.0070.0070.0000.0000.0000.000
98A111THR0-0.020-0.02444.276-0.007-0.0070.0000.0000.0000.000
99A112LYS10.9110.97246.261-0.059-0.0590.0000.0000.0000.000
100A113ASN00.0340.03049.287-0.006-0.0060.0000.0000.0000.000
101A114VAL0-0.0090.00552.7790.0030.0030.0000.0000.0000.000
102A115GLY00.0790.04054.635-0.003-0.0030.0000.0000.0000.000
103A116THR0-0.023-0.04157.620-0.001-0.0010.0000.0000.0000.000
104A117ASN0-0.096-0.05560.5960.0010.0010.0000.0000.0000.000
105A118ALA00.0150.04855.6220.0010.0010.0000.0000.0000.000
106A119SER0-0.071-0.06155.530-0.003-0.0030.0000.0000.0000.000
107A120VAL00.0080.00650.2610.0040.0040.0000.0000.0000.000
108A121GLU-1-0.832-0.89449.7190.0500.0500.0000.0000.0000.000
109A122ILE0-0.004-0.01047.9010.0030.0030.0000.0000.0000.000
110A123ASP-1-0.752-0.84847.4940.0290.0290.0000.0000.0000.000
111A124GLY0-0.0030.00648.491-0.003-0.0030.0000.0000.0000.000
112A125ASN0-0.0160.01350.3990.0000.0000.0000.0000.0000.000
113A126ARG10.8400.89552.813-0.046-0.0460.0000.0000.0000.000
114A127PHE00.0230.01953.177-0.002-0.0020.0000.0000.0000.000
115A128ASN0-0.031-0.03456.6670.0020.0020.0000.0000.0000.000
116A129GLY00.0610.04758.741-0.002-0.0020.0000.0000.0000.000
117A130GLY00.0080.01659.594-0.002-0.0020.0000.0000.0000.000
118A131ALA00.022-0.00662.9990.0020.0020.0000.0000.0000.000
119A132ASN0-0.047-0.02663.1640.0000.0000.0000.0000.0000.000
120A133GLY00.0050.03059.0680.0010.0010.0000.0000.0000.000
121A134VAL0-0.056-0.03955.477-0.002-0.0020.0000.0000.0000.000
122A135SER0-0.010-0.02153.8880.0020.0020.0000.0000.0000.000
123A136ILE0-0.040-0.02349.577-0.003-0.0030.0000.0000.0000.000
124A137ALA00.0100.00448.4520.0040.0040.0000.0000.0000.000
125A138GLY00.004-0.01145.749-0.003-0.0030.0000.0000.0000.000
126A139ASN0-0.066-0.02642.5640.0010.0010.0000.0000.0000.000
127A140LEU0-0.007-0.01838.214-0.004-0.0040.0000.0000.0000.000
128A141LYS10.8060.88035.560-0.023-0.0230.0000.0000.0000.000
129A142TYR0-0.023-0.02532.689-0.003-0.0030.0000.0000.0000.000
130A143ASP-1-0.780-0.87233.3610.0130.0130.0000.0000.0000.000
131A144ASN0-0.051-0.04828.499-0.014-0.0140.0000.0000.0000.000
132A145ASP-1-0.875-0.93728.026-0.034-0.0340.0000.0000.0000.000
133A146ILE0-0.065-0.03321.527-0.008-0.0080.0000.0000.0000.000
134A147ALA00.0460.04124.828-0.009-0.0090.0000.0000.0000.000
135A148PRO0-0.018-0.01321.8680.0110.0110.0000.0000.0000.000
136A149TYR0-0.066-0.05919.2670.0100.0100.0000.0000.0000.000
137A150ILE0-0.025-0.01019.1030.0010.0010.0000.0000.0000.000
138A151GLY00.0600.02419.951-0.018-0.0180.0000.0000.0000.000
139A152PHE0-0.047-0.01719.6750.0360.0360.0000.0000.0000.000
140A153GLY00.0540.03419.860-0.044-0.0440.0000.0000.0000.000
141A154PHE0-0.070-0.02919.9020.0560.0560.0000.0000.0000.000
142A155ALA00.0560.02017.658-0.052-0.0520.0000.0000.0000.000
143A156PRO00.0090.01717.5220.1250.1250.0000.0000.0000.000
144A157LYS10.8330.92214.184-1.090-1.0900.0000.0000.0000.000
145A158PHE00.0030.00917.9650.0070.0070.0000.0000.0000.000
146A159SER00.0100.00020.024-0.045-0.0450.0000.0000.0000.000
147A160LYS10.9360.97115.608-0.766-0.7660.0000.0000.0000.000
148A161ASN00.042-0.00117.5400.0950.0950.0000.0000.0000.000
149A162TRP00.0170.02420.153-0.026-0.0260.0000.0000.0000.000
150A163GLY00.0070.00420.2270.0680.0680.0000.0000.0000.000
151A164VAL00.0050.00421.497-0.042-0.0420.0000.0000.0000.000
152A165PHE0-0.043-0.02120.7230.0690.0690.0000.0000.0000.000
153A166GLY00.0480.03322.726-0.049-0.0490.0000.0000.0000.000
154A167GLU-1-0.827-0.88619.6520.4070.4070.0000.0000.0000.000
155A168VAL00.000-0.00423.223-0.034-0.0340.0000.0000.0000.000
156A169GLY00.0390.01223.7480.0250.0250.0000.0000.0000.000
157A170ALA0-0.032-0.00624.526-0.013-0.0130.0000.0000.0000.000
158A171TYR00.0510.02622.9060.0020.0020.0000.0000.0000.000
159A172TYR0-0.031-0.01125.554-0.001-0.0010.0000.0000.0000.000
160A173SER00.001-0.02227.464-0.012-0.0120.0000.0000.0000.000
161A174GLY00.0140.02429.846-0.012-0.0120.0000.0000.0000.000
162A175ASN0-0.056-0.04432.6680.0030.0030.0000.0000.0000.000
163A176PRO0-0.0090.02035.881-0.005-0.0050.0000.0000.0000.000
164A177LYS10.8600.91737.241-0.002-0.0020.0000.0000.0000.000
165A178VAL0-0.004-0.00540.3710.0050.0050.0000.0000.0000.000
166A179SER0-0.039-0.01442.759-0.005-0.0050.0000.0000.0000.000
167A180LEU0-0.038-0.01644.7240.0050.0050.0000.0000.0000.000
168A181ALA00.0110.01248.383-0.003-0.0030.0000.0000.0000.000
169A182SER0-0.008-0.03951.7300.0040.0040.0000.0000.0000.000
170A183ASN00.0060.00854.480-0.002-0.0020.0000.0000.0000.000
171A184ASN00.000-0.01857.580-0.003-0.0030.0000.0000.0000.000
172A185ASP-1-0.761-0.85455.7360.0280.0280.0000.0000.0000.000
173A186ALA0-0.023-0.01158.238-0.001-0.0010.0000.0000.0000.000
174A187LEU0-0.027-0.00358.483-0.001-0.0010.0000.0000.0000.000
175A188ILE0-0.003-0.00859.3990.0000.0000.0000.0000.0000.000
176A189GLY00.0420.02857.5240.0020.0020.0000.0000.0000.000
177A190SER0-0.047-0.03856.637-0.001-0.0010.0000.0000.0000.000
178A191ASP-1-0.850-0.90854.8370.0280.0280.0000.0000.0000.000
179A192GLY0-0.0110.00058.208-0.002-0.0020.0000.0000.0000.000
180A193ARG10.6970.81151.124-0.029-0.0290.0000.0000.0000.000
181A194THR00.007-0.00558.2740.0010.0010.0000.0000.0000.000
182A195LEU00.0310.03053.3210.0000.0000.0000.0000.0000.000
183A196GLY00.0590.02454.1890.0010.0010.0000.0000.0000.000
184A197LYS10.7540.87053.623-0.018-0.0180.0000.0000.0000.000
185A198THR0-0.006-0.01151.183-0.001-0.0010.0000.0000.0000.000
186A199LEU0-0.0030.00549.6090.0010.0010.0000.0000.0000.000
187A200ASP-1-0.721-0.83949.1010.0140.0140.0000.0000.0000.000
188A201ASP-1-0.794-0.87949.1760.0170.0170.0000.0000.0000.000
189A202GLN0-0.049-0.02744.0990.0020.0020.0000.0000.0000.000
190A203GLU-1-0.836-0.92244.7420.0220.0220.0000.0000.0000.000
191A204ARG10.7950.87544.271-0.014-0.0140.0000.0000.0000.000
192A205LYS10.8420.91143.219-0.030-0.0300.0000.0000.0000.000
193A206ILE0-0.0070.00239.4550.0000.0000.0000.0000.0000.000
194A207ALA00.0280.01439.4700.0000.0000.0000.0000.0000.000
195A208ASN0-0.085-0.04940.221-0.009-0.0090.0000.0000.0000.000
196A209ASP-1-0.825-0.91839.0050.0250.0250.0000.0000.0000.000
197A210ASP-1-0.827-0.91634.1290.0040.0040.0000.0000.0000.000
198A211LYS10.7960.89833.936-0.040-0.0400.0000.0000.0000.000
199A212TYR00.000-0.00535.0780.0090.0090.0000.0000.0000.000
200A213LYS10.7950.91932.161-0.002-0.0020.0000.0000.0000.000
201A214TRP0-0.027-0.01325.430-0.002-0.0020.0000.0000.0000.000
202A215LEU00.0210.02829.5960.0000.0000.0000.0000.0000.000
203A216PRO0-0.018-0.01728.7250.0090.0090.0000.0000.0000.000
204A217VAL0-0.006-0.01225.242-0.004-0.0040.0000.0000.0000.000
205A218GLY00.0090.00427.4130.0150.0150.0000.0000.0000.000
206A219LYS10.8180.92222.132-0.260-0.2600.0000.0000.0000.000
207A220VAL00.006-0.00225.7730.0280.0280.0000.0000.0000.000
208A221GLY00.0450.01924.912-0.025-0.0250.0000.0000.0000.000
209A222VAL0-0.060-0.02023.9870.0290.0290.0000.0000.0000.000
210A223ASN00.0120.00018.567-0.036-0.0360.0000.0000.0000.000
211A224PHE00.003-0.01319.735-0.004-0.0040.0000.0000.0000.000
212A225TYR00.003-0.00915.1080.0360.0360.0000.0000.0000.000
213A226TRP0-0.019-0.00316.820-0.003-0.0030.0000.0000.0000.000