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: GQKL1

Calculation Name: 1BU2-A-Xray308

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1BU2

Chain ID: A

ChEMBL ID:

UniProt ID: Q01043

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 229
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2885763.191312
FMO2-HF: Nuclear repulsion 2794298.534409
FMO2-HF: Total energy -91464.656903
FMO2-MP2: Total energy -91728.112826


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:22:ARG )


Summations of interaction energy for fragment #1(A:22:ARG )
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.
-69.71-62.6746.524-4.239-9.32-0.018
Interaction energy analysis for fragmet #1(A:22:ARG )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.980 / q_NPA : 0.980
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].
3A24LEU 00.0520.0192.053-5.397-1.6594.938-3.058-5.618-0.008
4A25ASN 00.0190.0192.7461.3563.3180.388-0.515-1.835-0.005
5A26ASN 00.0230.0014.7173.0113.0730.000-0.018-0.0430.000
6A27LEU 00.0020.0116.3482.8492.8490.0000.0000.0000.000
7A28LYS 10.9240.9465.16237.68237.6820.0000.0000.0000.000
8A29LEU 00.0130.0038.2383.0093.0090.0000.0000.0000.000
9A30ARG 10.9360.98010.64824.36024.3600.0000.0000.0000.000
10A31GLU -1-0.745-0.88310.004-27.032-27.0320.0000.0000.0000.000
11A32LEU 0-0.052-0.03611.8281.4931.4930.0000.0000.0000.000
12A33LEU 0-0.055-0.01814.5391.3161.3160.0000.0000.0000.000
13A34LEU 00.0140.01915.0830.9400.9400.0000.0000.0000.000
14A35PRO 00.0050.00418.257-0.070-0.0700.0000.0000.0000.000
15A36LYS 10.8700.93116.60017.02017.0200.0000.0000.0000.000
16A37PHE 00.0300.01021.5450.4660.4660.0000.0000.0000.000
17A38THR 0-0.041-0.01024.2870.1780.1780.0000.0000.0000.000
18A39SER 00.0210.00525.7740.2060.2060.0000.0000.0000.000
19A40LEU 0-0.028-0.01525.0740.1990.1990.0000.0000.0000.000
20A41TRP 0-0.025-0.03728.5790.4590.4590.0000.0000.0000.000
21A42GLU -1-0.860-0.92731.370-9.210-9.2100.0000.0000.0000.000
22A43ILE 0-0.080-0.03233.1890.2860.2860.0000.0000.0000.000
23A44GLN 0-0.057-0.03234.2300.4450.4450.0000.0000.0000.000
24A45THR 0-0.0120.00036.8920.1400.1400.0000.0000.0000.000
25A46GLU -1-0.836-0.92540.552-7.161-7.1610.0000.0000.0000.000
26A47VAL 0-0.092-0.03936.3940.0150.0150.0000.0000.0000.000
27A48THR 00.0830.02336.037-0.040-0.0400.0000.0000.0000.000
28A49VAL 00.0410.01430.517-0.092-0.0920.0000.0000.0000.000
29A50ASP -1-0.844-0.91932.580-8.604-8.6040.0000.0000.0000.000
30A51ASN 00.0750.02935.0820.1370.1370.0000.0000.0000.000
31A52ARG 10.8670.92325.15411.42711.4270.0000.0000.0000.000
32A53THR 00.0190.01030.835-0.221-0.2210.0000.0000.0000.000
33A54ILE 00.0160.03831.885-0.086-0.0860.0000.0000.0000.000
34A55LEU 00.0190.00732.826-0.030-0.0300.0000.0000.0000.000
35A56LEU 0-0.013-0.02026.649-0.090-0.0900.0000.0000.0000.000
36A57THR 0-0.005-0.01329.913-0.344-0.3440.0000.0000.0000.000
37A58TRP 00.0080.02931.904-0.126-0.1260.0000.0000.0000.000
38A59MET 0-0.103-0.03429.0490.0130.0130.0000.0000.0000.000
39A60HIS 0-0.0120.00826.243-0.003-0.0030.0000.0000.0000.000
40A61LEU 00.0770.04329.704-0.067-0.0670.0000.0000.0000.000
41A62LEU 0-0.0300.00432.2750.1170.1170.0000.0000.0000.000
42A63CYS 0-0.073-0.05927.190-0.074-0.0740.0000.0000.0000.000
43A64GLU -1-0.925-0.95626.803-11.242-11.2420.0000.0000.0000.000
44A65SER 0-0.069-0.03929.8890.2180.2180.0000.0000.0000.000
45A66PHE 0-0.116-0.06730.6300.2820.2820.0000.0000.0000.000
46A67GLU -1-0.974-0.97128.089-9.530-9.5300.0000.0000.0000.000
47A68LEU 0-0.068-0.02726.013-0.165-0.1650.0000.0000.0000.000
48A69ASP -1-0.859-0.94620.581-12.916-12.9160.0000.0000.0000.000
49A70LYS 10.9340.94719.09013.01113.0110.0000.0000.0000.000
50A71SER 00.011-0.01217.802-0.321-0.3210.0000.0000.0000.000
51A72VAL 0-0.001-0.00319.656-0.088-0.0880.0000.0000.0000.000
52A73PHE 00.0930.04223.2410.0590.0590.0000.0000.0000.000
53A74PRO 0-0.0130.00019.7680.0150.0150.0000.0000.0000.000
54A75LEU 0-0.0190.00620.654-0.159-0.1590.0000.0000.0000.000
55A76SER 0-0.015-0.01722.1490.3760.3760.0000.0000.0000.000
56A77VAL 00.0470.03023.3950.3320.3320.0000.0000.0000.000
57A78SER 00.0000.00221.3950.2160.2160.0000.0000.0000.000
58A79ILE 0-0.047-0.02823.4130.2210.2210.0000.0000.0000.000
59A80LEU 00.0560.01426.1850.3530.3530.0000.0000.0000.000
60A81ASP -1-0.782-0.86225.505-11.314-11.3140.0000.0000.0000.000
61A82ARG 10.8430.94022.36813.16713.1670.0000.0000.0000.000
62A83TYR 00.0160.02027.5380.3810.3810.0000.0000.0000.000
63A84LEU 00.010-0.00330.8530.3280.3280.0000.0000.0000.000
64A85CYS 0-0.081-0.03228.9390.0840.0840.0000.0000.0000.000
65A86LYS 10.8910.93529.89510.35510.3550.0000.0000.0000.000
66A87LYS 10.9480.98833.6088.6338.6330.0000.0000.0000.000
67A88GLN 00.0250.01035.959-0.163-0.1630.0000.0000.0000.000
68A89GLY 00.0480.03337.8250.0520.0520.0000.0000.0000.000
69A90THR 0-0.0120.02038.7230.1220.1220.0000.0000.0000.000
70A91LYS 10.9110.93740.2777.5737.5730.0000.0000.0000.000
71A92LYS 10.8350.90841.3136.9226.9220.0000.0000.0000.000
72A93THR 0-0.022-0.03840.528-0.011-0.0110.0000.0000.0000.000
73A94LEU 00.0280.02935.566-0.145-0.1450.0000.0000.0000.000
74A95GLN 00.1040.05436.007-0.112-0.1120.0000.0000.0000.000
75A96LYS 10.9470.99636.9867.4677.4670.0000.0000.0000.000
76A97ILE 0-0.019-0.02033.476-0.199-0.1990.0000.0000.0000.000
77A98GLY 00.0660.00732.401-0.285-0.2850.0000.0000.0000.000
78A99ALA 00.0460.02132.177-0.263-0.2630.0000.0000.0000.000
79A100ALA 0-0.028-0.01232.764-0.149-0.1490.0000.0000.0000.000
80A101CYS 0-0.077-0.02128.689-0.262-0.2620.0000.0000.0000.000
81A102VAL 00.0430.02128.122-0.439-0.4390.0000.0000.0000.000
82A103LEU 0-0.054-0.00828.320-0.164-0.1640.0000.0000.0000.000
83A104ILE 0-0.008-0.02126.735-0.209-0.2090.0000.0000.0000.000
84A105GLY 00.0370.01124.636-0.283-0.2830.0000.0000.0000.000
85A106SER 0-0.009-0.01323.888-0.301-0.3010.0000.0000.0000.000
86A107LYS 10.8160.85025.2349.1469.1460.0000.0000.0000.000
87A108ILE 0-0.0280.00321.467-0.053-0.0530.0000.0000.0000.000
88A109ARG 10.8000.92915.65315.82615.8260.0000.0000.0000.000
89A110THR 00.0010.00220.4410.0030.0030.0000.0000.0000.000
90A111VAL 00.0530.02222.4060.1960.1960.0000.0000.0000.000
91A112LYS 10.8730.93123.75410.08310.0830.0000.0000.0000.000
92A113PRO 00.0280.04526.0100.1750.1750.0000.0000.0000.000
93A114MET 00.0140.02727.8960.4580.4580.0000.0000.0000.000
94A115THR 00.010-0.00330.8720.0090.0090.0000.0000.0000.000
95A116VAL 00.0400.01833.9690.0010.0010.0000.0000.0000.000
96A117SER 00.003-0.01436.3850.1150.1150.0000.0000.0000.000
97A118LYS 10.9340.97632.0868.9158.9150.0000.0000.0000.000
98A119LEU 00.0950.04133.188-0.018-0.0180.0000.0000.0000.000
99A120THR 0-0.0010.01436.2390.0560.0560.0000.0000.0000.000
100A121TYR 0-0.014-0.01639.9240.1190.1190.0000.0000.0000.000
101A122LEU 0-0.029-0.00736.1970.0930.0930.0000.0000.0000.000
102A123SER 0-0.051-0.02837.8150.0300.0300.0000.0000.0000.000
103A124CYS 0-0.032-0.03139.6970.1400.1400.0000.0000.0000.000
104A125ASP -1-0.922-0.96543.408-6.742-6.7420.0000.0000.0000.000
105A126CYS 0-0.0230.02641.0150.0670.0670.0000.0000.0000.000
106A127PHE 00.001-0.01438.5030.0000.0000.0000.0000.0000.000
107A128THR 0-0.0080.00443.1470.0060.0060.0000.0000.0000.000
108A129ASN 0-0.015-0.01541.125-0.110-0.1100.0000.0000.0000.000
109A130LEU 00.0470.00841.087-0.133-0.1330.0000.0000.0000.000
110A131GLU -1-0.874-0.94442.308-7.116-7.1160.0000.0000.0000.000
111A132LEU 00.0310.01236.274-0.157-0.1570.0000.0000.0000.000
112A133ILE 0-0.0190.01537.560-0.198-0.1980.0000.0000.0000.000
113A134ASN 0-0.025-0.03237.884-0.126-0.1260.0000.0000.0000.000
114A135GLN 0-0.0070.00936.1160.0620.0620.0000.0000.0000.000
115A136GLU -1-0.799-0.90032.421-9.292-9.2920.0000.0000.0000.000
116A137LYS 10.9440.96133.8587.6647.6640.0000.0000.0000.000
117A138ASP -1-0.882-0.92434.867-8.129-8.1290.0000.0000.0000.000
118A139ILE 0-0.019-0.01630.245-0.167-0.1670.0000.0000.0000.000
119A140LEU 0-0.0170.00129.321-0.317-0.3170.0000.0000.0000.000
120A141GLU -1-0.923-0.96230.901-8.418-8.4180.0000.0000.0000.000
121A142ALA 0-0.080-0.04132.666-0.136-0.1360.0000.0000.0000.000
122A143LEU 0-0.081-0.05026.374-0.170-0.1700.0000.0000.0000.000
123A144LYS 10.8790.93127.7339.4459.4450.0000.0000.0000.000
124A145TRP 0-0.015-0.02028.157-0.194-0.1940.0000.0000.0000.000
125A146ASP -1-0.911-0.92222.422-13.654-13.6540.0000.0000.0000.000
126A147THR 0-0.069-0.06123.943-0.016-0.0160.0000.0000.0000.000
127A148GLU -1-0.813-0.89817.596-15.827-15.8270.0000.0000.0000.000
128A149ALA 0-0.062-0.03717.6950.0450.0450.0000.0000.0000.000
129A150VAL 0-0.057-0.01311.448-0.373-0.3730.0000.0000.0000.000
130A151LEU 0-0.014-0.01614.6570.6580.6580.0000.0000.0000.000
131A152ALA 00.0500.02213.599-1.233-1.2330.0000.0000.0000.000
132A153THR 00.0140.00413.572-1.151-1.1510.0000.0000.0000.000
133A154ASP -1-0.872-0.92611.464-19.942-19.9420.0000.0000.0000.000
134A155PHE 0-0.025-0.0317.097-2.876-2.8760.0000.0000.0000.000
135A156LEU 00.0310.0239.778-2.058-2.0580.0000.0000.0000.000
136A157ILE 00.0610.0348.473-1.044-1.0440.0000.0000.0000.000
137A158PRO 0-0.059-0.0375.674-1.499-1.4990.0000.0000.0000.000
138A159LEU 0-0.034-0.0295.569-5.930-5.9300.0000.0000.0000.000
139A160CYS 00.0080.0147.9121.0861.0860.0000.0000.0000.000
140A161ASN 0-0.0090.0035.470-2.136-2.1360.0000.0000.0000.000
141A162ALA 00.0010.0094.990-0.038-0.0380.0000.0000.0000.000
142A163LEU 0-0.016-0.0176.877-0.521-0.5210.0000.0000.0000.000
143A164LYS 10.8860.9559.95024.41424.4140.0000.0000.0000.000
144A165ILE 0-0.002-0.00411.8272.0712.0710.0000.0000.0000.000
145A166PRO 00.0180.00912.962-0.928-0.9280.0000.0000.0000.000
146A167GLU -1-0.936-0.96712.664-18.029-18.0290.0000.0000.0000.000
147A168ASP -1-0.911-0.95915.133-13.935-13.9350.0000.0000.0000.000
148A169LEU 0-0.028-0.02617.6500.5970.5970.0000.0000.0000.000
149A170TRP 00.0150.0029.225-0.482-0.4820.0000.0000.0000.000
150A171PRO 0-0.006-0.00216.139-0.060-0.0600.0000.0000.0000.000
151A172GLN 00.0320.01518.8470.3800.3800.0000.0000.0000.000
152A173LEU 00.0070.01315.1510.1520.1520.0000.0000.0000.000
153A174TYR 00.005-0.01414.468-0.219-0.2190.0000.0000.0000.000
154A175GLU -1-0.824-0.88617.357-12.458-12.4580.0000.0000.0000.000
155A176ALA 00.0700.05721.0670.2320.2320.0000.0000.0000.000
156A177ALA 00.0340.04416.6930.0930.0930.0000.0000.0000.000
157A178SER 0-0.023-0.04018.280-0.345-0.3450.0000.0000.0000.000
158A179THR 00.023-0.00519.8770.3730.3730.0000.0000.0000.000
159A180THR 0-0.032-0.03020.2170.5960.5960.0000.0000.0000.000
160A181ILE 00.020-0.00415.7100.2420.2420.0000.0000.0000.000
161A182CYS 0-0.095-0.04719.9780.2540.2540.0000.0000.0000.000
162A183LYS 10.9991.00922.68111.38311.3830.0000.0000.0000.000
163A184ALA 0-0.002-0.00421.2810.3260.3260.0000.0000.0000.000
164A185LEU 0-0.092-0.05519.4280.0820.0820.0000.0000.0000.000
165A186ILE 0-0.0090.00922.9680.2010.2010.0000.0000.0000.000
166A187GLN 00.0510.03425.3390.4460.4460.0000.0000.0000.000
167A188PRO 0-0.067-0.03625.051-0.532-0.5320.0000.0000.0000.000
168A189ASN 00.002-0.00223.992-0.206-0.2060.0000.0000.0000.000
169A190ILE 00.0730.00419.000-0.489-0.4890.0000.0000.0000.000
170A191ALA 0-0.0400.01220.024-0.720-0.7200.0000.0000.0000.000
171A192LEU 0-0.011-0.02020.9170.2640.2640.0000.0000.0000.000
172A193LEU 0-0.0620.00016.416-0.556-0.5560.0000.0000.0000.000
173A194SER 0-0.0280.00711.747-0.499-0.4990.0000.0000.0000.000
174A195PRO 00.042-0.01112.2630.0480.0480.0000.0000.0000.000
175A196GLY 00.0830.0229.641-0.144-0.1440.0000.0000.0000.000
176A197LEU 0-0.018-0.01810.398-0.081-0.0810.0000.0000.0000.000
177A198ILE 00.0000.02112.2540.3190.3190.0000.0000.0000.000
178A199CYS 00.0020.00611.3870.7530.7530.0000.0000.0000.000
179A200ALA 0-0.0210.01710.3670.0150.0150.0000.0000.0000.000
180A201GLY 00.025-0.00812.1231.0241.0240.0000.0000.0000.000
181A202GLY 00.0390.02315.6391.1011.1010.0000.0000.0000.000
182A203LEU 00.0220.01511.6730.6460.6460.0000.0000.0000.000
183A204LEU 0-0.071-0.04413.5530.5440.5440.0000.0000.0000.000
184A205THR 0-0.050-0.04916.4640.9630.9630.0000.0000.0000.000
185A206THR 00.0590.02918.6290.8730.8730.0000.0000.0000.000
186A207ILE 0-0.012-0.01016.5790.4140.4140.0000.0000.0000.000
187A208GLU -1-0.954-0.96419.525-12.531-12.5310.0000.0000.0000.000
188A209THR 0-0.046-0.04221.7690.3740.3740.0000.0000.0000.000
189A210ASP -1-0.918-0.93023.126-11.693-11.6930.0000.0000.0000.000
190A211ASN 0-0.049-0.01722.039-1.048-1.0480.0000.0000.0000.000
191A212THR 00.0040.00821.8730.2620.2620.0000.0000.0000.000
192A213ASN 0-0.029-0.02818.7290.2740.2740.0000.0000.0000.000
193A214CYS 00.0160.02521.2870.2890.2890.0000.0000.0000.000
194A215ARG 11.0220.99517.87614.74814.7480.0000.0000.0000.000
195A216PRO 0-0.002-0.00516.447-0.536-0.5360.0000.0000.0000.000
196A217TRP 00.0330.01012.437-1.229-1.2290.0000.0000.0000.000
197A218THR 0-0.084-0.03611.893-1.614-1.6140.0000.0000.0000.000
198A219CYS 0-0.020-0.00212.2600.1920.1920.0000.0000.0000.000
199A220TYR 00.0010.0068.774-0.102-0.1020.0000.0000.0000.000
200A221LEU 00.039-0.0087.463-4.344-4.3440.0000.0000.0000.000
201A222GLU -1-0.843-0.9177.047-27.273-27.2730.0000.0000.0000.000
202A223ASP -1-0.835-0.9075.119-35.716-35.7160.0000.0000.0000.000
203A224LEU 0-0.147-0.0782.556-14.722-13.5731.197-0.670-1.676-0.004
204A225SER 0-0.104-0.0573.643-0.579-0.4540.0010.022-0.148-0.001
205A226SER 0-0.045-0.0165.4733.6303.6300.0000.0000.0000.000
206A227ILE 0-0.017-0.0017.4333.5073.5070.0000.0000.0000.000
207A228LEU 00.0230.04210.823-0.450-0.4500.0000.0000.0000.000
208A229ASN 00.010-0.01213.478-0.007-0.0070.0000.0000.0000.000
209A230PHE 00.040-0.00714.5570.6920.6920.0000.0000.0000.000
210A231SER 00.0220.00211.763-0.552-0.5520.0000.0000.0000.000
211A232THR 0-0.049-0.00813.8310.3470.3470.0000.0000.0000.000
212A233ASN 00.026-0.00317.2250.7590.7590.0000.0000.0000.000
213A234THR 00.0350.03413.8410.8950.8950.0000.0000.0000.000
214A235VAL 00.0330.03516.0230.4860.4860.0000.0000.0000.000
215A236ARG 10.8660.93018.35913.95113.9510.0000.0000.0000.000
216A237THR 00.0300.02219.6100.3390.3390.0000.0000.0000.000
217A238VAL 0-0.0210.00117.4270.3210.3210.0000.0000.0000.000
218A239LYS 10.8680.90820.65412.95912.9590.0000.0000.0000.000
219A240ASP -1-0.882-0.89922.926-10.703-10.7030.0000.0000.0000.000
220A241GLN 0-0.019-0.04923.5820.0150.0150.0000.0000.0000.000
221A242VAL 0-0.017-0.01823.4950.3600.3600.0000.0000.0000.000
222A243SER 0-0.111-0.04325.5690.2590.2590.0000.0000.0000.000
223A244GLU -1-0.916-0.95428.316-9.461-9.4610.0000.0000.0000.000
224A245ALA 0-0.049-0.02729.2980.0690.0690.0000.0000.0000.000
225A246PHE 0-0.007-0.00131.1510.2660.2660.0000.0000.0000.000
226A247SER 00.005-0.01134.9460.0430.0430.0000.0000.0000.000
227A248LEU 0-0.064-0.03935.9620.1420.1420.0000.0000.0000.000
228A249TYR 0-0.070-0.02834.9180.2130.2130.0000.0000.0000.000
229A250ASP -2-1.818-1.90636.638-16.213-16.2130.0000.0000.0000.000