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: R8QL8

Calculation Name: 2BDQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2BDQ

Chain ID: A

ChEMBL ID:

UniProt ID: Q8DYB9

Base Structure: X-ray

Registration Date: 2023-09-22

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 OptH
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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2475418.647206
FMO2-HF: Nuclear repulsion 2393532.763008
FMO2-HF: Total energy -81885.884199
FMO2-MP2: Total energy -82123.824595


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-2.748-0.757-0.005-0.704-1.2830.002
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.032 / q_NPA : -0.014
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].
3A3LEU0-0.040-0.0013.880-1.458-0.003-0.002-0.661-0.7920.002
4A4ARG10.9400.9666.1620.1130.1130.0000.0000.0000.000
5A5GLU-1-0.730-0.8528.6270.4860.4860.0000.0000.0000.000
6A6PHE0-0.009-0.01812.241-0.076-0.0760.0000.0000.0000.000
7A7CYS0-0.083-0.03014.9780.0230.0230.0000.0000.0000.000
8A8ALA00.0190.00418.460-0.032-0.0320.0000.0000.0000.000
9A9GLU-1-0.837-0.90721.0860.0570.0570.0000.0000.0000.000
10A10ASN0-0.033-0.02624.866-0.001-0.0010.0000.0000.0000.000
11A11LEU00.016-0.02223.7660.0060.0060.0000.0000.0000.000
12A12THR0-0.030-0.00524.632-0.001-0.0010.0000.0000.0000.000
13A13ASP-1-0.908-0.95221.4320.0040.0040.0000.0000.0000.000
14A14LEU00.0250.00819.175-0.004-0.0040.0000.0000.0000.000
15A15THR0-0.009-0.00619.6720.0000.0000.0000.0000.0000.000
16A16ARG10.8920.94418.5510.0290.0290.0000.0000.0000.000
17A17LEU0-0.0310.00515.262-0.025-0.0250.0000.0000.0000.000
18A18ASP-1-0.837-0.93512.9560.0030.0030.0000.0000.0000.000
19A19LYS10.9921.00111.507-0.268-0.2680.0000.0000.0000.000
20A20ALA0-0.065-0.0129.1660.1640.1640.0000.0000.0000.000
21A21ILE0-0.081-0.0457.340-0.131-0.1310.0000.0000.0000.000
22A22ILE0-0.038-0.0217.8280.0570.0570.0000.0000.0000.000
23A23SER00.0330.0138.033-0.085-0.0850.0000.0000.0000.000
24A24ARG10.8240.90010.159-0.773-0.7730.0000.0000.0000.000
25A25VAL00.0270.00913.123-0.041-0.0410.0000.0000.0000.000
26A26GLU-1-0.880-0.93516.1290.2240.2240.0000.0000.0000.000
27A27LEU00.006-0.00918.730-0.032-0.0320.0000.0000.0000.000
28A28CYS0-0.048-0.02322.0010.0020.0020.0000.0000.0000.000
29A29ASP-1-0.791-0.89725.0430.0580.0580.0000.0000.0000.000
30A30ASN00.0190.00627.898-0.001-0.0010.0000.0000.0000.000
31A31LEU00.0820.01123.1240.0030.0030.0000.0000.0000.000
32A32ALA0-0.069-0.01327.065-0.003-0.0030.0000.0000.0000.000
33A33VAL0-0.054-0.00329.992-0.003-0.0030.0000.0000.0000.000
34A34GLY0-0.043-0.04226.4380.0060.0060.0000.0000.0000.000
35A35GLY00.0010.01125.6440.0130.0130.0000.0000.0000.000
36A36THR0-0.039-0.02726.8310.0010.0010.0000.0000.0000.000
37A37THR00.0680.02727.6890.0090.0090.0000.0000.0000.000
38A38PRO0-0.0270.01526.090-0.012-0.0120.0000.0000.0000.000
39A39SER00.0610.01929.1740.0030.0030.0000.0000.0000.000
40A40TYR00.0350.00630.4300.0040.0040.0000.0000.0000.000
41A41GLY0-0.004-0.00630.9770.0050.0050.0000.0000.0000.000
42A42VAL00.0000.00426.7720.0020.0020.0000.0000.0000.000
43A43ILE00.0350.01526.1030.0080.0080.0000.0000.0000.000
44A44LYS10.9610.99626.224-0.095-0.0950.0000.0000.0000.000
45A45GLU-1-0.919-0.97227.3330.1000.1000.0000.0000.0000.000
46A46ALA0-0.014-0.00623.1070.0030.0030.0000.0000.0000.000
47A47ASN0-0.005-0.00922.3030.0180.0180.0000.0000.0000.000
48A48GLN00.0120.01922.4240.0190.0190.0000.0000.0000.000
49A49TYR00.0230.00321.221-0.003-0.0030.0000.0000.0000.000
50A50LEU0-0.024-0.03617.740-0.001-0.0010.0000.0000.0000.000
51A51HIS10.8400.90418.416-0.245-0.2450.0000.0000.0000.000
52A52GLU-1-0.961-0.95219.5400.1240.1240.0000.0000.0000.000
53A53LYS10.8080.91917.363-0.098-0.0980.0000.0000.0000.000
54A54GLY0-0.047-0.02615.7060.0150.0150.0000.0000.0000.000
55A55ILE0-0.094-0.03013.6140.0830.0830.0000.0000.0000.000
56A56SER0-0.007-0.00614.154-0.005-0.0050.0000.0000.0000.000
57A57VAL00.000-0.01515.997-0.005-0.0050.0000.0000.0000.000
58A58ALA0-0.040-0.01817.7550.0090.0090.0000.0000.0000.000
59A59VAL00.0440.01719.549-0.020-0.0200.0000.0000.0000.000
60A60MET0-0.043-0.01922.8280.0090.0090.0000.0000.0000.000
61A61ILE0-0.015-0.00224.823-0.011-0.0110.0000.0000.0000.000
62A62ARG10.8270.91627.977-0.098-0.0980.0000.0000.0000.000
63A63PRO00.0310.02130.095-0.005-0.0050.0000.0000.0000.000
64A64ARG10.7830.88632.896-0.085-0.0850.0000.0000.0000.000
65A65GLY00.0520.01832.0830.0060.0060.0000.0000.0000.000
66A66GLY0-0.020-0.00432.536-0.002-0.0020.0000.0000.0000.000
67A67ASN00.009-0.01432.2080.0060.0060.0000.0000.0000.000
68A68PHE00.0530.03327.6780.0030.0030.0000.0000.0000.000
69A69VAL0-0.0030.01332.6020.0050.0050.0000.0000.0000.000
70A70TYR0-0.007-0.01730.756-0.007-0.0070.0000.0000.0000.000
71A71ASN00.0260.03137.3210.0040.0040.0000.0000.0000.000
72A72ASP-1-0.786-0.92039.6780.0800.0800.0000.0000.0000.000
73A73LEU0-0.048-0.01940.7230.0030.0030.0000.0000.0000.000
74A74GLU-1-0.823-0.93536.8810.0780.0780.0000.0000.0000.000
75A75LEU00.0220.01335.3700.0070.0070.0000.0000.0000.000
76A76ARG10.8150.91636.576-0.089-0.0890.0000.0000.0000.000
77A77ILE0-0.037-0.01634.9650.0020.0020.0000.0000.0000.000
78A78MET0-0.023-0.00330.4420.0020.0020.0000.0000.0000.000
79A79GLU-1-0.843-0.92632.6140.1170.1170.0000.0000.0000.000
80A80GLU-1-0.885-0.93234.1830.1030.1030.0000.0000.0000.000
81A81ASP-1-0.908-0.97931.0840.1120.1120.0000.0000.0000.000
82A82ILE0-0.050-0.01328.9730.0090.0090.0000.0000.0000.000
83A83LEU00.0080.00530.1030.0080.0080.0000.0000.0000.000
84A84ARG10.7770.87132.045-0.109-0.1090.0000.0000.0000.000
85A85ALA00.0260.01626.6020.0040.0040.0000.0000.0000.000
86A86VAL00.0100.01127.1550.0140.0140.0000.0000.0000.000
87A87GLU-1-0.836-0.90428.3270.1200.1200.0000.0000.0000.000
88A88LEU0-0.093-0.04228.142-0.005-0.0050.0000.0000.0000.000
89A89GLU-1-0.970-0.98224.9600.1890.1890.0000.0000.0000.000
90A90SER0-0.035-0.02822.9870.0170.0170.0000.0000.0000.000
91A91ASP-1-0.817-0.89118.4140.3690.3690.0000.0000.0000.000
92A92ALA0-0.068-0.04018.7790.0320.0320.0000.0000.0000.000
93A93LEU00.0240.03520.773-0.024-0.0240.0000.0000.0000.000
94A94VAL0-0.016-0.01220.2540.0230.0230.0000.0000.0000.000
95A95LEU00.0420.01823.094-0.025-0.0250.0000.0000.0000.000
96A96GLY00.007-0.01425.3580.0160.0160.0000.0000.0000.000
97A97ILE0-0.0200.00227.728-0.013-0.0130.0000.0000.0000.000
98A98LEU0-0.044-0.02428.6120.0060.0060.0000.0000.0000.000
99A99THR00.0920.04732.539-0.007-0.0070.0000.0000.0000.000
100A100SER0-0.014-0.02235.2620.0000.0000.0000.0000.0000.000
101A101ASN0-0.052-0.03036.5910.0000.0000.0000.0000.0000.000
102A102ASN0-0.017-0.00631.5350.0020.0020.0000.0000.0000.000
103A103HIS00.0250.01631.2150.0110.0110.0000.0000.0000.000
104A104ILE00.0180.00226.583-0.001-0.0010.0000.0000.0000.000
105A105ASP-1-0.864-0.93131.0300.1050.1050.0000.0000.0000.000
106A106THR0-0.005-0.01232.3850.0090.0090.0000.0000.0000.000
107A107GLU-1-0.890-0.93933.4110.1120.1120.0000.0000.0000.000
108A108ALA00.0000.00534.7430.0010.0010.0000.0000.0000.000
109A109ILE0-0.028-0.03128.6720.0050.0050.0000.0000.0000.000
110A110GLU-1-0.946-0.98132.2280.1450.1450.0000.0000.0000.000
111A111GLN0-0.057-0.03233.7790.0000.0000.0000.0000.0000.000
112A112LEU0-0.0060.00231.999-0.002-0.0020.0000.0000.0000.000
113A113LEU0-0.0240.00328.6690.0070.0070.0000.0000.0000.000
114A114PRO0-0.026-0.01831.1050.0080.0080.0000.0000.0000.000
115A115ALA00.0410.02132.9890.0030.0030.0000.0000.0000.000
116A116THR0-0.025-0.00926.5560.0050.0050.0000.0000.0000.000
117A117GLN0-0.050-0.03428.0380.0110.0110.0000.0000.0000.000
118A118GLY0-0.010-0.00126.9180.0050.0050.0000.0000.0000.000
119A119LEU0-0.0270.00923.6050.0260.0260.0000.0000.0000.000
120A120PRO0-0.001-0.00619.1040.0020.0020.0000.0000.0000.000
121A121LEU00.0360.03421.248-0.013-0.0130.0000.0000.0000.000
122A122VAL0-0.031-0.02118.6390.0390.0390.0000.0000.0000.000
123A123PHE00.0460.03020.839-0.032-0.0320.0000.0000.0000.000
124A124HIS00.0520.02621.2210.0240.0240.0000.0000.0000.000
125A125MET00.0290.00519.009-0.002-0.0020.0000.0000.0000.000
126A126ALA00.0000.01922.649-0.016-0.0160.0000.0000.0000.000
127A127PHE00.019-0.00821.550-0.007-0.0070.0000.0000.0000.000
128A128ASP-1-0.793-0.89121.0750.1410.1410.0000.0000.0000.000
129A129VAL0-0.036-0.02123.982-0.014-0.0140.0000.0000.0000.000
130A130ILE0-0.0230.01826.075-0.008-0.0080.0000.0000.0000.000
131A131PRO0-0.0010.01927.262-0.002-0.0020.0000.0000.0000.000
132A132LYS10.9420.95822.978-0.095-0.0950.0000.0000.0000.000
133A133SER0-0.029-0.01226.3550.0060.0060.0000.0000.0000.000
134A134ASP-1-0.841-0.94528.9430.1060.1060.0000.0000.0000.000
135A135GLN0-0.0340.00022.6560.0090.0090.0000.0000.0000.000
136A136LYS10.9760.97622.461-0.147-0.1470.0000.0000.0000.000
137A137LYS10.9200.98924.918-0.123-0.1230.0000.0000.0000.000
138A138SER00.0450.01025.7600.0030.0030.0000.0000.0000.000
139A139ILE00.0140.01320.1210.0080.0080.0000.0000.0000.000
140A140ASP-1-0.778-0.85123.6690.2250.2250.0000.0000.0000.000
141A141GLN00.0240.00125.9240.0080.0080.0000.0000.0000.000
142A142LEU00.0110.01022.9010.0020.0020.0000.0000.0000.000
143A143VAL0-0.039-0.01821.6910.0130.0130.0000.0000.0000.000
144A144ALA0-0.048-0.02524.0690.0030.0030.0000.0000.0000.000
145A145LEU0-0.019-0.00727.027-0.004-0.0040.0000.0000.0000.000
146A146GLY0-0.0100.00924.613-0.002-0.0020.0000.0000.0000.000
147A147PHE0-0.017-0.01121.8720.0150.0150.0000.0000.0000.000
148A148THR0-0.023-0.01716.4110.0230.0230.0000.0000.0000.000
149A149ARG10.9120.94014.311-0.504-0.5040.0000.0000.0000.000
150A150ILE00.0090.01617.188-0.052-0.0520.0000.0000.0000.000
151A151LEU0-0.043-0.00616.3940.0420.0420.0000.0000.0000.000
152A152LEU0-0.021-0.01216.232-0.036-0.0360.0000.0000.0000.000
153A153HIS10.7900.86716.665-0.041-0.0410.0000.0000.0000.000
154A154GLY0-0.014-0.02117.819-0.018-0.0180.0000.0000.0000.000
155A155SER0-0.080-0.06119.252-0.008-0.0080.0000.0000.0000.000
156A156SER00.019-0.00622.6190.0040.0040.0000.0000.0000.000
157A157ASN0-0.0230.00225.5530.0000.0000.0000.0000.0000.000
158A158GLY00.0000.01323.744-0.006-0.0060.0000.0000.0000.000
159A159GLU-1-0.828-0.91022.6950.0140.0140.0000.0000.0000.000
160A160PRO00.0320.01919.5710.0070.0070.0000.0000.0000.000
161A161ILE00.0480.02413.555-0.002-0.0020.0000.0000.0000.000
162A162ILE0-0.026-0.00913.4790.0110.0110.0000.0000.0000.000
163A163GLU-1-0.928-0.97015.732-0.065-0.0650.0000.0000.0000.000
164A164ASN0-0.043-0.01517.1540.0090.0090.0000.0000.0000.000
165A165ILE0-0.006-0.00112.9550.0410.0410.0000.0000.0000.000
166A166LYS10.9330.95115.1030.0120.0120.0000.0000.0000.000
167A167HIS00.0150.01617.6250.0210.0210.0000.0000.0000.000
168A168ILE00.0390.00913.2910.0260.0260.0000.0000.0000.000
169A169LYS10.9250.97712.890-0.111-0.1110.0000.0000.0000.000
170A170ALA00.0090.01614.8170.0340.0340.0000.0000.0000.000
171A171LEU0-0.046-0.02717.3800.0090.0090.0000.0000.0000.000
172A172VAL00.0040.01412.0130.0180.0180.0000.0000.0000.000
173A173GLU-1-0.951-0.98615.3330.2570.2570.0000.0000.0000.000
174A174TYR0-0.107-0.09416.992-0.011-0.0110.0000.0000.0000.000
175A175ALA00.0220.01216.640-0.012-0.0120.0000.0000.0000.000
176A176ASN0-0.033-0.01017.0500.0230.0230.0000.0000.0000.000
177A177ASN0-0.041-0.03113.3230.0740.0740.0000.0000.0000.000
178A178ARG10.7860.89715.914-0.275-0.2750.0000.0000.0000.000
179A179ILE00.0080.00817.457-0.013-0.0130.0000.0000.0000.000
180A180GLU-1-0.868-0.92310.6061.1651.1650.0000.0000.0000.000
181A181ILE00.0290.01713.283-0.084-0.0840.0000.0000.0000.000
182A182MET0-0.094-0.04112.1920.1490.1490.0000.0000.0000.000
183A183VAL00.0330.03010.557-0.086-0.0860.0000.0000.0000.000
184A184GLY00.0680.01413.4120.0050.0050.0000.0000.0000.000
185A185GLY00.0200.01215.989-0.015-0.0150.0000.0000.0000.000
186A186GLY00.015-0.00817.596-0.008-0.0080.0000.0000.0000.000
187A187VAL0-0.0310.00511.548-0.044-0.0440.0000.0000.0000.000
188A188THR00.003-0.01113.4090.0150.0150.0000.0000.0000.000
189A189ALA00.006-0.01310.950-0.046-0.0460.0000.0000.0000.000
190A190GLU-1-0.954-0.97710.820-0.457-0.4570.0000.0000.0000.000
191A191ASN00.0030.00210.748-0.068-0.0680.0000.0000.0000.000
192A192TYR00.0310.0255.3850.0180.0180.0000.0000.0000.000
193A193GLN00.0050.0053.962-0.731-0.5280.000-0.025-0.1790.000
194A194TYR00.0290.0214.997-0.190-0.135-0.001-0.001-0.0530.000
195A195ILE00.040-0.0037.5900.1190.1190.0000.0000.0000.000
196A196CYS0-0.052-0.0024.8210.1880.1880.0000.0000.0000.000
197A197GLN0-0.0170.0024.340-0.0030.122-0.001-0.009-0.1150.000
198A198GLU-1-0.920-0.9545.749-0.072-0.0720.0000.0000.0000.000
199A199THR0-0.119-0.0858.8250.1030.1030.0000.0000.0000.000
200A200GLY00.0220.0168.2840.0000.0000.0000.0000.0000.000
201A201VAL0-0.021-0.0018.7630.2210.2210.0000.0000.0000.000
202A202LYS10.9370.9555.852-1.621-1.468-0.001-0.008-0.1440.000
203A203GLN00.0060.0026.6240.0870.0870.0000.0000.0000.000
204A204ALA00.0180.0129.055-0.177-0.1770.0000.0000.0000.000
205A205HIS10.8350.89910.728-0.212-0.2120.0000.0000.0000.000
206A206GLY00.016-0.01014.153-0.053-0.0530.0000.0000.0000.000
207A207THR00.0290.03016.0770.0010.0010.0000.0000.0000.000
208A208ARG10.9520.97117.1290.0670.0670.0000.0000.0000.000
209A209ILE00.0290.02210.614-0.070-0.0700.0000.0000.0000.000
210A210THR00.0020.00011.238-0.108-0.1080.0000.0000.0000.000