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: 3QMYL

Calculation Name: 4BSZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4BSZ

Chain ID: A

ChEMBL ID:

UniProt ID: P05750

Base Structure: X-ray

Registration Date: 2023-03-14

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 187
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1571585.071942
FMO2-HF: Nuclear repulsion 1499313.849588
FMO2-HF: Total energy -72271.222354
FMO2-MP2: Total energy -72481.9541


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:12:VAL)


Summations of interaction energy for fragment #1(A:12:VAL)
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.
-6.173-0.3661.019-2.642-4.184-0.01
Interaction energy analysis for fragmet #1(A:12:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / q_NPA : -0.004
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].
3A14ASP-1-0.785-0.9072.695-5.950-2.5220.549-1.854-2.124-0.008
4A15GLY00.001-0.0125.3820.4300.499-0.001-0.002-0.0650.000
5A16VAL0-0.005-0.0037.6690.2720.2720.0000.0000.0000.000
6A17PHE00.0420.0256.8950.2340.2340.0000.0000.0000.000
7A18TYR0-0.015-0.0093.484-0.0040.2910.006-0.049-0.2520.000
8A19ALA0-0.0160.0008.6930.1710.1710.0000.0000.0000.000
9A20GLU-1-0.773-0.87511.942-0.526-0.5260.0000.0000.0000.000
10A21LEU0-0.048-0.0239.1290.1170.1170.0000.0000.0000.000
11A22ASN0-0.0030.01112.6820.1100.1100.0000.0000.0000.000
12A23GLU-1-0.953-0.95814.393-0.314-0.3140.0000.0000.0000.000
13A24PHE0-0.042-0.03016.2110.0380.0380.0000.0000.0000.000
14A25PHE00.0540.00512.9730.0360.0360.0000.0000.0000.000
15A26THR0-0.033-0.01617.9220.0330.0330.0000.0000.0000.000
16A27ARG10.9050.95320.0600.1810.1810.0000.0000.0000.000
17A28GLU-1-0.932-0.95220.640-0.096-0.0960.0000.0000.0000.000
18A29LEU0-0.068-0.03818.6220.0200.0200.0000.0000.0000.000
19A30ALA00.0170.02622.5560.0060.0060.0000.0000.0000.000
20A31GLU-1-0.871-0.94125.037-0.055-0.0550.0000.0000.0000.000
21A32GLU-1-0.866-0.92923.186-0.037-0.0370.0000.0000.0000.000
22A33GLY0-0.015-0.00623.3550.0110.0110.0000.0000.0000.000
23A34TYR00.025-0.00614.7260.0180.0180.0000.0000.0000.000
24A35SER0-0.058-0.03017.3550.0000.0000.0000.0000.0000.000
25A36GLY00.011-0.00614.203-0.024-0.0240.0000.0000.0000.000
26A37VAL0-0.037-0.0119.6200.0270.0270.0000.0000.0000.000
27A38GLU-1-0.878-0.9117.0100.5200.5200.0000.0000.0000.000
28A39VAL00.009-0.0074.948-0.103-0.1030.0000.0000.0000.000
29A40ARG10.8360.9143.596-1.294-0.5720.019-0.258-0.483-0.001
30A41VAL00.0140.0052.656-2.023-0.9230.447-0.474-1.073-0.001
31A42THR0-0.008-0.0024.3131.2281.421-0.001-0.005-0.1870.000
32A43PRO00.044-0.0037.411-0.370-0.3700.0000.0000.0000.000
33A44THR0-0.033-0.0139.537-0.106-0.1060.0000.0000.0000.000
34A45LYS10.8990.9659.523-0.328-0.3280.0000.0000.0000.000
35A46THR0-0.022-0.0056.5090.1200.1200.0000.0000.0000.000
36A47GLU-1-0.858-0.9197.5060.7650.7650.0000.0000.0000.000
37A48VAL00.0270.0027.9130.0380.0380.0000.0000.0000.000
38A49ILE0-0.0110.0109.667-0.009-0.0090.0000.0000.0000.000
39A50ILE00.0370.01711.679-0.045-0.0450.0000.0000.0000.000
40A51ARG10.8560.92810.741-0.139-0.1390.0000.0000.0000.000
41A52ALA00.0560.03316.039-0.031-0.0310.0000.0000.0000.000
42A53THR0-0.008-0.00819.7150.0200.0200.0000.0000.0000.000
43A54ARG10.7510.85523.0070.0190.0190.0000.0000.0000.000
44A55THR00.0390.01520.345-0.009-0.0090.0000.0000.0000.000
45A56GLN00.0240.00122.9940.0000.0000.0000.0000.0000.000
46A57ASP-1-0.802-0.89425.7620.0030.0030.0000.0000.0000.000
47A58VAL00.0100.00519.482-0.005-0.0050.0000.0000.0000.000
48A59LEU0-0.010-0.01320.692-0.002-0.0020.0000.0000.0000.000
49A60GLY00.0040.00623.464-0.005-0.0050.0000.0000.0000.000
50A61GLU-1-0.925-0.98427.0060.0320.0320.0000.0000.0000.000
51A62ASN0-0.048-0.02028.1090.0030.0030.0000.0000.0000.000
52A63GLY00.0460.03024.2550.0010.0010.0000.0000.0000.000
53A64ARG10.8250.90924.6860.0170.0170.0000.0000.0000.000
54A65ARG10.7650.87723.2040.0490.0490.0000.0000.0000.000
55A66ILE00.0650.03318.555-0.013-0.0130.0000.0000.0000.000
56A67ASN00.0140.00620.590-0.008-0.0080.0000.0000.0000.000
57A68GLU-1-0.816-0.87622.232-0.059-0.0590.0000.0000.0000.000
58A69LEU00.0280.01418.987-0.020-0.0200.0000.0000.0000.000
59A70THR00.003-0.02216.601-0.023-0.0230.0000.0000.0000.000
60A71LEU0-0.024-0.00618.016-0.024-0.0240.0000.0000.0000.000
61A72LEU0-0.018-0.00620.664-0.024-0.0240.0000.0000.0000.000
62A73VAL00.0090.00514.408-0.030-0.0300.0000.0000.0000.000
63A74GLN00.0060.00216.663-0.029-0.0290.0000.0000.0000.000
64A75LYS10.9280.96617.6550.1280.1280.0000.0000.0000.000
65A76ARG10.7800.88616.5500.4120.4120.0000.0000.0000.000
66A77PHE0-0.006-0.02013.665-0.020-0.0200.0000.0000.0000.000
67A78LYS10.8990.96214.6990.2440.2440.0000.0000.0000.000
68A79TYR00.0640.0468.292-0.027-0.0270.0000.0000.0000.000
69A80ALA0-0.004-0.00115.0210.0440.0440.0000.0000.0000.000
70A81PRO00.0280.01016.2870.0100.0100.0000.0000.0000.000
71A82GLY00.0330.03117.2840.0120.0120.0000.0000.0000.000
72A83THR0-0.077-0.06612.2480.0270.0270.0000.0000.0000.000
73A84ILE0-0.0010.00410.4220.0080.0080.0000.0000.0000.000
74A85VAL0-0.028-0.00512.322-0.001-0.0010.0000.0000.0000.000
75A86LEU00.0050.00812.8940.0150.0150.0000.0000.0000.000
76A87TYR0-0.025-0.01212.539-0.018-0.0180.0000.0000.0000.000
77A88ALA00.012-0.00315.327-0.038-0.0380.0000.0000.0000.000
78A89GLU-1-0.907-0.95513.7450.3270.3270.0000.0000.0000.000
79A90ARG10.9120.96017.445-0.100-0.1000.0000.0000.0000.000
80A91VAL00.0040.00616.3950.0190.0190.0000.0000.0000.000
81A92GLN0-0.036-0.02119.764-0.021-0.0210.0000.0000.0000.000
82A93ASP-1-0.784-0.89720.777-0.025-0.0250.0000.0000.0000.000
83A94ARG10.9850.98217.9690.0160.0160.0000.0000.0000.000
84A95GLY00.0090.00521.5870.0030.0030.0000.0000.0000.000
85A96LEU00.003-0.00424.5570.0010.0010.0000.0000.0000.000
86A97SER0-0.033-0.00223.7640.0080.0080.0000.0000.0000.000
87A98ALA00.0350.00325.838-0.003-0.0030.0000.0000.0000.000
88A99VAL00.0220.00524.429-0.002-0.0020.0000.0000.0000.000
89A100ALA00.0270.01521.5030.0010.0010.0000.0000.0000.000
90A101GLN00.008-0.01922.766-0.011-0.0110.0000.0000.0000.000
91A102ALA00.0030.01525.511-0.005-0.0050.0000.0000.0000.000
92A103GLU-1-0.790-0.87221.6590.0480.0480.0000.0000.0000.000
93A104SER0-0.026-0.00122.501-0.009-0.0090.0000.0000.0000.000
94A105MET0-0.038-0.02223.441-0.009-0.0090.0000.0000.0000.000
95A106LYS10.8610.91224.058-0.054-0.0540.0000.0000.0000.000
96A107PHE00.0150.01219.594-0.002-0.0020.0000.0000.0000.000
97A108LYS10.8930.93523.1320.0410.0410.0000.0000.0000.000
98A109LEU0-0.020-0.01325.817-0.003-0.0030.0000.0000.0000.000
99A110LEU0-0.042-0.01225.5220.0000.0000.0000.0000.0000.000
100A111ASN0-0.056-0.02922.764-0.003-0.0030.0000.0000.0000.000
101A112GLY00.0170.02426.246-0.008-0.0080.0000.0000.0000.000
102A113LEU0-0.0330.00126.940-0.005-0.0050.0000.0000.0000.000
103A114ALA0-0.001-0.01029.8290.0060.0060.0000.0000.0000.000
104A115ILE00.0970.02932.281-0.003-0.0030.0000.0000.0000.000
105A116ARG10.9440.97933.2780.0310.0310.0000.0000.0000.000
106A117ARG10.9590.98130.9740.0560.0560.0000.0000.0000.000
107A118ALA00.0170.01528.839-0.005-0.0050.0000.0000.0000.000
108A119ALA00.0260.00329.309-0.002-0.0020.0000.0000.0000.000
109A120TYR0-0.001-0.00331.4290.0000.0000.0000.0000.0000.000
110A121GLY00.0200.02327.626-0.003-0.0030.0000.0000.0000.000
111A122VAL0-0.010-0.01126.038-0.004-0.0040.0000.0000.0000.000
112A123VAL00.0380.00727.9310.0000.0000.0000.0000.0000.000
113A124ARG10.7960.87127.3950.0930.0930.0000.0000.0000.000
114A125TYR00.0160.01021.2140.0020.0020.0000.0000.0000.000
115A126VAL00.0010.00826.3200.0000.0000.0000.0000.0000.000
116A127MET0-0.042-0.01828.2280.0030.0030.0000.0000.0000.000
117A128GLU-1-0.836-0.87426.020-0.097-0.0970.0000.0000.0000.000
118A129SER0-0.034-0.03024.870-0.005-0.0050.0000.0000.0000.000
119A130GLY00.0060.01626.5800.0050.0050.0000.0000.0000.000
120A131ALA0-0.033-0.00629.9940.0060.0060.0000.0000.0000.000
121A132LYS10.9500.96731.8350.0130.0130.0000.0000.0000.000
122A133GLY00.0300.00034.757-0.002-0.0020.0000.0000.0000.000
123A134CYS0-0.064-0.01331.4540.0020.0020.0000.0000.0000.000
124A135GLU-1-0.878-0.94734.202-0.007-0.0070.0000.0000.0000.000
125A136VAL0-0.023-0.00931.4530.0030.0030.0000.0000.0000.000
126A137VAL00.017-0.00534.308-0.002-0.0020.0000.0000.0000.000
127A138VAL0-0.0050.01333.5000.0030.0030.0000.0000.0000.000
128A139SER00.0210.00036.214-0.001-0.0010.0000.0000.0000.000
129A140GLY00.0310.01838.0080.0020.0020.0000.0000.0000.000
130A141LYS10.8940.94540.458-0.011-0.0110.0000.0000.0000.000
131A142LEU0-0.0010.00938.032-0.001-0.0010.0000.0000.0000.000
132A143ARG10.8060.87140.9420.0100.0100.0000.0000.0000.000
133A144ALA00.0170.01544.0810.0020.0020.0000.0000.0000.000
134A145ALA00.0250.00447.007-0.001-0.0010.0000.0000.0000.000
135A146ARG10.9890.99149.8460.0040.0040.0000.0000.0000.000
136A147ALA00.0320.03452.4150.0010.0010.0000.0000.0000.000
137A148LYS11.0150.99048.927-0.009-0.0090.0000.0000.0000.000
138A149ALA00.006-0.00847.7540.0010.0010.0000.0000.0000.000
139A150MET00.0060.02248.3020.0010.0010.0000.0000.0000.000
140A151LYS10.8670.93043.191-0.012-0.0120.0000.0000.0000.000
141A152PHE00.012-0.00642.876-0.001-0.0010.0000.0000.0000.000
142A153ALA00.039-0.00140.7760.0020.0020.0000.0000.0000.000
143A154ASP-1-0.815-0.84038.639-0.014-0.0140.0000.0000.0000.000
144A155GLY00.0340.01038.3790.0010.0010.0000.0000.0000.000
145A156PHE0-0.041-0.03935.763-0.004-0.0040.0000.0000.0000.000
146A157LEU00.0420.02036.7820.0010.0010.0000.0000.0000.000
147A158ILE0-0.014-0.00134.894-0.003-0.0030.0000.0000.0000.000
148A159HIS0-0.016-0.00837.7460.0030.0030.0000.0000.0000.000
149A160SER00.0280.01338.7980.0010.0010.0000.0000.0000.000
150A161GLY00.0070.01641.1950.0000.0000.0000.0000.0000.000
151A162GLN0-0.039-0.03144.687-0.001-0.0010.0000.0000.0000.000
152A163PRO00.1000.03048.1080.0010.0010.0000.0000.0000.000
153A164VAL00.0150.00451.1430.0010.0010.0000.0000.0000.000
154A165ASN0-0.028-0.02847.4760.0010.0010.0000.0000.0000.000
155A166ASP-1-0.878-0.91150.692-0.005-0.0050.0000.0000.0000.000
156A167PHE0-0.071-0.05052.9200.0000.0000.0000.0000.0000.000
157A168ILE0-0.060-0.01350.8300.0010.0010.0000.0000.0000.000
158A169ASP-1-0.770-0.82554.5150.0020.0020.0000.0000.0000.000
159A170THR0-0.081-0.06152.2940.0010.0010.0000.0000.0000.000
160A171ALA00.0330.02655.6180.0000.0000.0000.0000.0000.000
161A172THR00.001-0.01553.4350.0010.0010.0000.0000.0000.000
162A173ARG10.9020.94956.845-0.011-0.0110.0000.0000.0000.000
163A174HIS00.0450.02755.4950.0000.0000.0000.0000.0000.000
164A175VAL00.0110.00359.133-0.001-0.0010.0000.0000.0000.000
165A176LEU00.0250.01860.9770.0010.0010.0000.0000.0000.000
166A177MET00.0110.00662.172-0.001-0.0010.0000.0000.0000.000
167A178ARG10.9760.97263.448-0.019-0.0190.0000.0000.0000.000
168A179GLN00.0010.00159.1370.0000.0000.0000.0000.0000.000
169A180GLY00.0600.03958.8000.0010.0010.0000.0000.0000.000
170A181VAL0-0.049-0.02457.263-0.001-0.0010.0000.0000.0000.000
171A182LEU00.0070.01456.7560.0010.0010.0000.0000.0000.000
172A183GLY00.0210.01854.840-0.001-0.0010.0000.0000.0000.000
173A184ILE0-0.004-0.00455.9130.0000.0000.0000.0000.0000.000
174A185LYS10.9220.95250.693-0.015-0.0150.0000.0000.0000.000
175A186VAL00.0130.00955.3510.0000.0000.0000.0000.0000.000
176A187LYS10.9590.96848.432-0.012-0.0120.0000.0000.0000.000
177A188ILE00.0350.02155.5400.0000.0000.0000.0000.0000.000
178A189MET00.0010.00852.0180.0000.0000.0000.0000.0000.000
179A190ARG10.8210.87856.7780.0000.0000.0000.0000.0000.000
180A191ASP-1-0.777-0.89158.625-0.003-0.0030.0000.0000.0000.000
181A192PRO00.0660.02457.2650.0000.0000.0000.0000.0000.000
182A193ALA0-0.070-0.03360.364-0.001-0.0010.0000.0000.0000.000
183A194LYS10.8610.91662.9800.0010.0010.0000.0000.0000.000
184A195SER0-0.025-0.00962.7490.0000.0000.0000.0000.0000.000
185A196ARG10.9310.98261.7210.0070.0070.0000.0000.0000.000
186A197THR00.0350.00764.6680.0010.0010.0000.0000.0000.000
187A198GLY0-0.0210.01267.403-0.001-0.0010.0000.0000.0000.000