FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: VRLL1

Calculation Name: 2X9Q-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2X9Q

Chain ID: A

ChEMBL ID:

UniProt ID: P9WPF9

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:

Apendix: None


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 236
LigandResidueName
LigandFragmentNumber 0
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2962933.759857
FMO2-HF: Nuclear repulsion 2869780.835044
FMO2-HF: Total energy -93152.924813
FMO2-MP2: Total energy -93422.209693


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:49:DPN)


Summations of interaction energy for fragment #1(A:49:DPN)
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.
-6.315-3.1931.444-1.678-2.888-0.009
Interaction energy analysis for fragmet #1(A:49:DPN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.022 / q_NPA : -0.018
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].
3A51LEU00.0720.0352.506-4.982-2.2771.440-1.621-2.524-0.009
4A52GLY0-0.0270.0045.1800.1050.250-0.001-0.007-0.1370.000
5A53ARG10.9370.9446.1110.1380.1380.0000.0000.0000.000
6A54ARG10.8850.9388.3900.0170.0170.0000.0000.0000.000
7A55ILE0-0.013-0.0113.485-0.2310.0410.005-0.050-0.2270.000
8A56PRO00.0210.0388.1060.0480.0480.0000.0000.0000.000
9A57GLU-1-0.953-0.9729.8830.8000.8000.0000.0000.0000.000
10A58ALA0-0.054-0.04611.718-0.068-0.0680.0000.0000.0000.000
11A59THR00.0080.01414.173-0.036-0.0360.0000.0000.0000.000
12A60ALA00.0230.00617.8780.0090.0090.0000.0000.0000.000
13A61GLN00.0360.02620.483-0.013-0.0130.0000.0000.0000.000
14A62GLU-1-0.863-0.93822.9100.1580.1580.0000.0000.0000.000
15A63GLY00.000-0.00123.924-0.006-0.0060.0000.0000.0000.000
16A64PHE0-0.065-0.03119.1960.0030.0030.0000.0000.0000.000
17A65LEU00.0080.01915.2430.0080.0080.0000.0000.0000.000
18A66VAL00.002-0.00516.0280.0240.0240.0000.0000.0000.000
19A67ARG10.9200.9406.576-1.786-1.7860.0000.0000.0000.000
20A68PRO00.0140.01612.0090.0410.0410.0000.0000.0000.000
21A69PHE0-0.009-0.0066.3970.1470.1470.0000.0000.0000.000
22A70THR0-0.064-0.1279.739-0.013-0.0130.0000.0000.0000.000
23A71GLN00.0650.01311.7980.0420.0420.0000.0000.0000.000
24A72GLN00.0380.01813.978-0.025-0.0250.0000.0000.0000.000
25A73CYM-1-0.743-0.75614.3440.0960.0960.0000.0000.0000.000
26A74GLN00.009-0.00415.5280.0390.0390.0000.0000.0000.000
27A75ILE0-0.027-0.00817.326-0.003-0.0030.0000.0000.0000.000
28A76ILE00.0100.01019.1630.0010.0010.0000.0000.0000.000
29A77HIS0-0.071-0.04018.6140.0160.0160.0000.0000.0000.000
30A78THR0-0.069-0.04820.6880.0010.0010.0000.0000.0000.000
31A79GLU-1-0.934-0.95123.2630.0370.0370.0000.0000.0000.000
32A80GLY00.0010.02124.396-0.004-0.0040.0000.0000.0000.000
33A81ASP-1-0.804-0.86825.9000.0370.0370.0000.0000.0000.000
34A82HIS0-0.020-0.03725.290-0.001-0.0010.0000.0000.0000.000
35A83ALA00.0340.03222.0780.0090.0090.0000.0000.0000.000
36A84VAL0-0.0060.00621.264-0.010-0.0100.0000.0000.0000.000
37A85ILE00.0110.01320.6240.0180.0180.0000.0000.0000.000
38A86GLY00.0560.03420.113-0.015-0.0150.0000.0000.0000.000
39A87VAL0-0.052-0.04320.8460.0150.0150.0000.0000.0000.000
40A88SER00.0440.03220.150-0.005-0.0050.0000.0000.0000.000
41A89PRO00.0340.01422.5400.0070.0070.0000.0000.0000.000
42A90GLY0-0.041-0.03424.527-0.002-0.0020.0000.0000.0000.000
43A91ASN00.0240.02518.8830.0060.0060.0000.0000.0000.000
44A92SER0-0.022-0.03023.2510.0060.0060.0000.0000.0000.000
45A93TYR00.0850.04718.5380.0030.0030.0000.0000.0000.000
46A94PHE00.0540.03319.5640.0060.0060.0000.0000.0000.000
47A95SER0-0.0040.00424.331-0.014-0.0140.0000.0000.0000.000
48A96ARG10.9150.93327.368-0.057-0.0570.0000.0000.0000.000
49A97GLN0-0.041-0.02328.459-0.008-0.0080.0000.0000.0000.000
50A98ARG10.9511.00321.541-0.155-0.1550.0000.0000.0000.000
51A99LEU0-0.003-0.01325.0400.0050.0050.0000.0000.0000.000
52A100ARG10.9250.94326.748-0.073-0.0730.0000.0000.0000.000
53A101ASP-1-0.797-0.88225.3740.1240.1240.0000.0000.0000.000
54A102LEU0-0.023-0.01920.6360.0030.0030.0000.0000.0000.000
55A103GLY00.0310.02024.6820.0000.0000.0000.0000.0000.000
56A104LEU0-0.045-0.02527.789-0.005-0.0050.0000.0000.0000.000
57A105TRP00.0020.01519.873-0.003-0.0030.0000.0000.0000.000
58A106GLY00.0520.00924.9910.0010.0010.0000.0000.0000.000
59A107LEU0-0.025-0.02225.867-0.005-0.0050.0000.0000.0000.000
60A108THR0-0.062-0.03027.575-0.009-0.0090.0000.0000.0000.000
61A109ASN0-0.103-0.06024.3290.0010.0010.0000.0000.0000.000
62A110PHE0-0.0070.01121.1610.0050.0050.0000.0000.0000.000
63A111ASP-1-0.857-0.90727.2980.0510.0510.0000.0000.0000.000
64A112ARG10.7990.90028.951-0.037-0.0370.0000.0000.0000.000
65A113VAL0-0.012-0.00625.4230.0070.0070.0000.0000.0000.000
66A114ASP-1-0.756-0.85526.1760.0310.0310.0000.0000.0000.000
67A115PHE0-0.010-0.00724.8220.0070.0070.0000.0000.0000.000
68A116VAL00.0100.00124.186-0.008-0.0080.0000.0000.0000.000
69A117TYR0-0.0220.00524.1910.0030.0030.0000.0000.0000.000
70A118THR0-0.018-0.03722.058-0.003-0.0030.0000.0000.0000.000
71A119ASP-1-0.843-0.91325.1730.0070.0070.0000.0000.0000.000
72A120VAL00.0140.00625.894-0.002-0.0020.0000.0000.0000.000
73A121HIS00.0710.03525.1010.0010.0010.0000.0000.0000.000
74A122VAL0-0.0040.01025.860-0.001-0.0010.0000.0000.0000.000
75A123ALA0-0.049-0.03927.2510.0000.0000.0000.0000.0000.000
76A124GLU-1-0.792-0.90127.803-0.023-0.0230.0000.0000.0000.000
77A125SER00.0170.00524.051-0.006-0.0060.0000.0000.0000.000
78A126TYR0-0.069-0.03625.4850.0020.0020.0000.0000.0000.000
79A127GLU-1-0.870-0.93928.183-0.025-0.0250.0000.0000.0000.000
80A128ALA0-0.0310.01125.760-0.002-0.0020.0000.0000.0000.000
81A129LEU0-0.075-0.03522.885-0.004-0.0040.0000.0000.0000.000
82A130GLY00.0040.00526.9520.0020.0020.0000.0000.0000.000
83A131ASP-1-0.846-0.88630.630-0.004-0.0040.0000.0000.0000.000
84A132SER00.0330.00632.750-0.002-0.0020.0000.0000.0000.000
85A133ALA00.1330.05734.8410.0020.0020.0000.0000.0000.000
86A134ILE0-0.049-0.02535.9320.0020.0020.0000.0000.0000.000
87A135GLU-1-0.766-0.84534.6850.0040.0040.0000.0000.0000.000
88A136ALA00.0130.01131.6350.0030.0030.0000.0000.0000.000
89A137ARG11.0191.00332.5670.0090.0090.0000.0000.0000.000
90A138ARG10.7780.85134.796-0.003-0.0030.0000.0000.0000.000
91A139LYS10.7730.86330.5910.0050.0050.0000.0000.0000.000
92A140ALA00.0740.04430.4490.0040.0040.0000.0000.0000.000
93A141VAL0-0.013-0.00631.4540.0040.0040.0000.0000.0000.000
94A142LYS10.8890.94632.203-0.017-0.0170.0000.0000.0000.000
95A143ASN0-0.018-0.02828.2590.0060.0060.0000.0000.0000.000
96A144ILE00.0440.03429.2890.0060.0060.0000.0000.0000.000
97A145ARG10.8980.94530.992-0.010-0.0100.0000.0000.0000.000
98A146GLY00.0330.02332.2490.0020.0020.0000.0000.0000.000
99A147VAL0-0.014-0.00926.2170.0040.0040.0000.0000.0000.000
100A148ARG11.0101.00629.633-0.014-0.0140.0000.0000.0000.000
101A149ALA0-0.0100.01631.9110.0020.0020.0000.0000.0000.000
102A150LYS10.8410.91527.943-0.059-0.0590.0000.0000.0000.000
103A151ILE00.0150.02027.0390.0030.0030.0000.0000.0000.000
104A152THR00.009-0.00930.6780.0000.0000.0000.0000.0000.000
105A153THR0-0.071-0.04234.198-0.001-0.0010.0000.0000.0000.000
106A154THR0-0.035-0.03129.5780.0020.0020.0000.0000.0000.000
107A155VAL00.0380.02031.3520.0020.0020.0000.0000.0000.000
108A156ASN0-0.025-0.00733.662-0.001-0.0010.0000.0000.0000.000
109A157GLU-1-0.847-0.92235.1750.0590.0590.0000.0000.0000.000
110A158LEU0-0.078-0.03430.8890.0010.0010.0000.0000.0000.000
111A159ASP-1-0.759-0.86834.6430.0480.0480.0000.0000.0000.000
112A160PRO0-0.046-0.01236.520-0.003-0.0030.0000.0000.0000.000
113A161ALA0-0.037-0.02739.841-0.003-0.0030.0000.0000.0000.000
114A162GLY0-0.0100.01136.642-0.002-0.0020.0000.0000.0000.000
115A163ALA0-0.057-0.02037.216-0.002-0.0020.0000.0000.0000.000
116A164ARG10.7870.85331.017-0.065-0.0650.0000.0000.0000.000
117A165LEU0-0.0230.00429.0710.0030.0030.0000.0000.0000.000
118A166CYS0-0.019-0.00630.650-0.006-0.0060.0000.0000.0000.000
119A167VAL0-0.036-0.02729.4900.0050.0050.0000.0000.0000.000
120A168ARG10.8030.89929.311-0.027-0.0270.0000.0000.0000.000
121A169PRO0-0.039-0.01328.8760.0040.0040.0000.0000.0000.000
122A170MET00.0400.01522.535-0.003-0.0030.0000.0000.0000.000
123A171SER0-0.080-0.07627.532-0.004-0.0040.0000.0000.0000.000
124A172GLU-1-0.826-0.91030.6640.0120.0120.0000.0000.0000.000
125A173PHE00.0350.00626.927-0.001-0.0010.0000.0000.0000.000
126A174GLN0-0.0120.00730.455-0.006-0.0060.0000.0000.0000.000
127A175SER0-0.085-0.03032.066-0.003-0.0030.0000.0000.0000.000
128A176ASN0-0.002-0.00331.284-0.003-0.0030.0000.0000.0000.000
129A177GLU-1-0.915-0.96832.335-0.022-0.0220.0000.0000.0000.000
130A178ALA00.1130.06329.536-0.003-0.0030.0000.0000.0000.000
131A179TYR0-0.047-0.04625.516-0.006-0.0060.0000.0000.0000.000
132A180ARG10.8800.91828.0670.0150.0150.0000.0000.0000.000
133A181GLU-1-0.959-0.96230.161-0.038-0.0380.0000.0000.0000.000
134A182LEU0-0.009-0.00824.111-0.007-0.0070.0000.0000.0000.000
135A183HIS00.0090.00325.206-0.009-0.0090.0000.0000.0000.000
136A184ALA0-0.011-0.00526.397-0.007-0.0070.0000.0000.0000.000
137A185ASP-1-0.786-0.84424.972-0.091-0.0910.0000.0000.0000.000
138A186LEU00.0130.00820.478-0.010-0.0100.0000.0000.0000.000
139A187LEU00.001-0.02224.007-0.010-0.0100.0000.0000.0000.000
140A188THR0-0.063-0.02926.115-0.002-0.0020.0000.0000.0000.000
141A189ARG10.8260.87322.8710.1000.1000.0000.0000.0000.000
142A190LEU00.0010.00419.975-0.009-0.0090.0000.0000.0000.000
143A191LYS10.7690.89123.7990.0730.0730.0000.0000.0000.000
144A192ASP-1-0.841-0.94327.410-0.081-0.0810.0000.0000.0000.000
145A193ASP-1-0.856-0.89822.717-0.161-0.1610.0000.0000.0000.000
146A194GLU-1-0.964-1.00023.056-0.133-0.1330.0000.0000.0000.000
147A195ASP-1-0.884-0.93019.836-0.191-0.1910.0000.0000.0000.000
148A196MET0-0.051-0.02618.431-0.022-0.0220.0000.0000.0000.000
149A197ARG10.9200.95418.2570.1100.1100.0000.0000.0000.000
150A198ALA0-0.0030.00218.644-0.006-0.0060.0000.0000.0000.000
151A199VAL0-0.011-0.00612.843-0.022-0.0220.0000.0000.0000.000
152A200CYS0-0.015-0.00614.072-0.030-0.0300.0000.0000.0000.000
153A201GLN0-0.016-0.01215.4030.0070.0070.0000.0000.0000.000
154A202ASP-1-0.808-0.86311.912-0.403-0.4030.0000.0000.0000.000
155A203LEU0-0.0030.0019.229-0.023-0.0230.0000.0000.0000.000
156A204VAL00.0030.00011.9520.0150.0150.0000.0000.0000.000
157A205ARG10.8350.88814.7000.2050.2050.0000.0000.0000.000
158A206ARG10.7720.8508.9290.4330.4330.0000.0000.0000.000
159A207PHE00.0740.03811.3750.0400.0400.0000.0000.0000.000
160A208LEU00.0220.00812.1680.0470.0470.0000.0000.0000.000
161A209SER0-0.102-0.04212.3690.0170.0170.0000.0000.0000.000
162A210THR0-0.056-0.03510.0080.0270.0270.0000.0000.0000.000
163A211LYS10.8770.93913.4200.0220.0220.0000.0000.0000.000
164A212VAL0-0.0060.01716.679-0.001-0.0010.0000.0000.0000.000
165A213GLY0-0.004-0.02419.9590.0090.0090.0000.0000.0000.000
166A214PRO0-0.0060.01220.950-0.002-0.0020.0000.0000.0000.000
167A215ARG10.9200.95313.3700.1340.1340.0000.0000.0000.000
168A216GLN0-0.024-0.01820.029-0.003-0.0030.0000.0000.0000.000
169A217GLY0-0.0140.00319.979-0.001-0.0010.0000.0000.0000.000
170A218ALA0-0.005-0.00819.7800.0120.0120.0000.0000.0000.000
171A219THR00.0180.00921.509-0.005-0.0050.0000.0000.0000.000
172A220ALA00.0720.01723.263-0.005-0.0050.0000.0000.0000.000
173A221THR00.0100.00824.540-0.004-0.0040.0000.0000.0000.000
174A222GLN00.018-0.00922.075-0.006-0.0060.0000.0000.0000.000
175A223GLU-1-0.818-0.87419.225-0.154-0.1540.0000.0000.0000.000
176A224GLN0-0.029-0.01821.028-0.010-0.0100.0000.0000.0000.000
177A225VAL00.0380.01423.6230.0030.0030.0000.0000.0000.000
178A226CYS0-0.058-0.02417.9620.0040.0040.0000.0000.0000.000
179A227MET00.0180.01418.0090.0010.0010.0000.0000.0000.000
180A228ASP-1-0.834-0.90320.473-0.064-0.0640.0000.0000.0000.000
181A229TYR0-0.120-0.07519.2120.0100.0100.0000.0000.0000.000
182A230ILE0-0.013-0.02015.3560.0070.0070.0000.0000.0000.000
183A231CYS0-0.043-0.02819.0990.0010.0010.0000.0000.0000.000
184A232ALA00.0300.02021.5350.0060.0060.0000.0000.0000.000
185A233GLU-1-0.799-0.87318.7670.0150.0150.0000.0000.0000.000
186A234ALA00.0050.00118.9770.0080.0080.0000.0000.0000.000
187A235PRO00.0080.01119.9730.0030.0030.0000.0000.0000.000
188A236LEU00.0620.02921.5920.0020.0020.0000.0000.0000.000
189A237PHE0-0.063-0.01615.5170.0140.0140.0000.0000.0000.000
190A238LEU0-0.0100.02317.988-0.006-0.0060.0000.0000.0000.000
191A239ASP-1-0.810-0.93620.351-0.022-0.0220.0000.0000.0000.000
192A240THR00.0380.01522.2320.0010.0010.0000.0000.0000.000
193A241PRO0-0.058-0.01023.7380.0010.0010.0000.0000.0000.000
194A242ALA00.0060.00326.8500.0010.0010.0000.0000.0000.000
195A243ILE0-0.082-0.02125.2590.0010.0010.0000.0000.0000.000
196A244LEU0-0.050-0.04126.9520.0020.0020.0000.0000.0000.000
197A245GLY00.0180.03130.0140.0030.0030.0000.0000.0000.000
198A246VAL0-0.072-0.02526.9080.0030.0030.0000.0000.0000.000
199A247PRO00.0130.00328.868-0.006-0.0060.0000.0000.0000.000
200A248SER0-0.046-0.05823.772-0.005-0.0050.0000.0000.0000.000
201A249SER0-0.001-0.02222.7680.0060.0060.0000.0000.0000.000
202A250LEU00.0050.00616.750-0.003-0.0030.0000.0000.0000.000
203A251ASN0-0.028-0.02617.2200.0180.0180.0000.0000.0000.000
204A252CYS0-0.0130.00116.1680.0390.0390.0000.0000.0000.000
205A253TYR0-0.033-0.04914.067-0.031-0.0310.0000.0000.0000.000
206A254HIS0-0.0010.02514.2160.0660.0660.0000.0000.0000.000
207A255GLN0-0.019-0.00710.814-0.004-0.0040.0000.0000.0000.000
208A256SER00.0200.0087.0940.0510.0510.0000.0000.0000.000
209A257LEU00.0080.0089.390-0.096-0.0960.0000.0000.0000.000
210A258PRO0-0.010-0.0109.801-0.046-0.0460.0000.0000.0000.000
211A259LEU00.0840.02810.248-0.086-0.0860.0000.0000.0000.000
212A260ALA0-0.0200.0018.803-0.017-0.0170.0000.0000.0000.000
213A261GLU-1-0.937-0.9756.164-1.284-1.2840.0000.0000.0000.000
214A262MET0-0.026-0.0058.978-0.004-0.0040.0000.0000.0000.000
215A263LEU0-0.009-0.01112.7000.0220.0220.0000.0000.0000.000
216A264TYR0-0.006-0.02511.6790.0430.0430.0000.0000.0000.000
217A265ALA00.0090.03211.755-0.020-0.0200.0000.0000.0000.000
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