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: ZYLLN

Calculation Name: 2BHV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2BHV

Chain ID: A

ChEMBL ID:

UniProt ID: O24883

Base Structure: X-ray

Registration Date: 2023-03-13

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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1904118.590507
FMO2-HF: Nuclear repulsion 1829719.039436
FMO2-HF: Total energy -74399.551071
FMO2-MP2: Total energy -74616.652956


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:166:ASN)


Summations of interaction energy for fragment #1(A:166: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.
-2.2041.6380.524-1.688-2.6780.004
Interaction energy analysis for fragmet #1(A:166:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.067 / q_NPA : 0.027
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].
3A168LEU00.0270.0143.832-5.622-3.4390.033-1.058-1.1580.006
4A169LEU0-0.015-0.0102.661-1.299-0.0070.481-0.543-1.230-0.001
5A170ARG10.8170.8955.1700.0980.207-0.001-0.007-0.1010.000
6A171THR0-0.0010.0057.1600.9730.9730.0000.0000.0000.000
7A172ILE0-0.026-0.0039.459-0.343-0.3430.0000.0000.0000.000
8A173THR00.021-0.01812.2610.1390.1390.0000.0000.0000.000
9A174ALA00.0080.00113.502-0.100-0.1000.0000.0000.0000.000
10A175ASP-1-0.867-0.91416.3060.4860.4860.0000.0000.0000.000
11A176LYS10.8440.92313.489-0.419-0.4190.0000.0000.0000.000
12A177MET0-0.023-0.00518.291-0.006-0.0060.0000.0000.0000.000
13A178ILE00.0050.00419.136-0.043-0.0430.0000.0000.0000.000
14A179PRO0-0.0170.01122.1150.0020.0020.0000.0000.0000.000
15A180ALA00.009-0.01225.314-0.009-0.0090.0000.0000.0000.000
16A181PHE00.0130.01827.721-0.003-0.0030.0000.0000.0000.000
17A182LEU00.0000.00231.2580.0070.0070.0000.0000.0000.000
18A183ILE0-0.041-0.03331.805-0.014-0.0140.0000.0000.0000.000
19A184THR0-0.067-0.02635.033-0.005-0.0050.0000.0000.0000.000
20A185PRO00.0420.02736.5060.0080.0080.0000.0000.0000.000
21A186ILE0-0.003-0.00234.3860.0080.0080.0000.0000.0000.000
22A187SER0-0.038-0.01638.856-0.007-0.0070.0000.0000.0000.000
23A188SER00.0020.00341.8120.0030.0030.0000.0000.0000.000
24A189GLN00.0570.02042.8500.0070.0070.0000.0000.0000.000
25A190ILE0-0.0150.00341.8150.0040.0040.0000.0000.0000.000
26A191ALA00.0280.02538.6400.0050.0050.0000.0000.0000.000
27A192GLY00.001-0.00237.530-0.009-0.0090.0000.0000.0000.000
28A193LYS10.9200.96733.409-0.142-0.1420.0000.0000.0000.000
29A194VAL00.0220.01531.736-0.013-0.0130.0000.0000.0000.000
30A195ILE0-0.009-0.01230.6790.0140.0140.0000.0000.0000.000
31A196ALA00.0240.02428.766-0.010-0.0100.0000.0000.0000.000
32A197GLN00.0160.01927.8050.0010.0010.0000.0000.0000.000
33A198VAL00.0380.02921.939-0.001-0.0010.0000.0000.0000.000
34A199GLU-1-0.804-0.87225.4200.0660.0660.0000.0000.0000.000
35A200SER0-0.034-0.02522.000-0.024-0.0240.0000.0000.0000.000
36A201ASP-1-0.820-0.90918.837-0.007-0.0070.0000.0000.0000.000
37A202ILE00.0020.01015.894-0.012-0.0120.0000.0000.0000.000
38A203PHE00.010-0.00413.3310.0000.0000.0000.0000.0000.000
39A204ALA00.0110.0148.7810.1450.1450.0000.0000.0000.000
40A205HIS0-0.0090.0218.114-0.024-0.0240.0000.0000.0000.000
41A206MET00.0100.0054.241-0.431-0.1730.011-0.080-0.189-0.001
42A207GLY00.0150.0097.381-0.258-0.2580.0000.0000.0000.000
43A208LYS10.9440.9538.3220.8300.8300.0000.0000.0000.000
44A209ALA00.0410.0339.8390.0760.0760.0000.0000.0000.000
45A210VAL00.0150.01311.5410.1180.1180.0000.0000.0000.000
46A211LEU0-0.074-0.02510.547-0.029-0.0290.0000.0000.0000.000
47A212ILE00.0090.00114.7030.0480.0480.0000.0000.0000.000
48A213PRO00.0160.01518.244-0.013-0.0130.0000.0000.0000.000
49A214LYS10.9040.96220.5400.0280.0280.0000.0000.0000.000
50A215GLY0-0.020-0.01423.726-0.015-0.0150.0000.0000.0000.000
51A216SER0-0.044-0.04622.2490.0020.0020.0000.0000.0000.000
52A217LYS10.8830.93924.632-0.084-0.0840.0000.0000.0000.000
53A218VAL00.0060.00424.2200.0190.0190.0000.0000.0000.000
54A219ILE0-0.006-0.00626.439-0.024-0.0240.0000.0000.0000.000
55A220GLY00.0520.02627.5380.0330.0330.0000.0000.0000.000
56A221TYR0-0.052-0.01729.629-0.033-0.0330.0000.0000.0000.000
57A222TYR00.0130.00031.6110.0210.0210.0000.0000.0000.000
58A223SER0-0.017-0.02134.219-0.010-0.0100.0000.0000.0000.000
59A224ASN00.036-0.00136.7000.0040.0040.0000.0000.0000.000
60A225ASN0-0.0150.01436.724-0.019-0.0190.0000.0000.0000.000
61A226ASN00.022-0.01139.6120.0050.0050.0000.0000.0000.000
62A227LYS10.9550.98541.115-0.176-0.1760.0000.0000.0000.000
63A228MET0-0.056-0.02643.802-0.003-0.0030.0000.0000.0000.000
64A229GLY00.0550.04646.729-0.004-0.0040.0000.0000.0000.000
65A230GLU-1-0.985-0.98440.7350.1820.1820.0000.0000.0000.000
66A231TYR0-0.017-0.01938.7220.0010.0010.0000.0000.0000.000
67A232ARG10.8900.93033.593-0.249-0.2490.0000.0000.0000.000
68A233LEU0-0.033-0.00534.303-0.008-0.0080.0000.0000.0000.000
69A234ASP-1-0.853-0.89832.4220.2790.2790.0000.0000.0000.000
70A235ILE00.017-0.01629.501-0.016-0.0160.0000.0000.0000.000
71A236VAL00.0040.00825.8300.0270.0270.0000.0000.0000.000
72A237TRP00.004-0.02424.647-0.030-0.0300.0000.0000.0000.000
73A238SER00.0160.01424.4210.0360.0360.0000.0000.0000.000
74A239ARG10.9360.95423.060-0.201-0.2010.0000.0000.0000.000
75A240ILE00.0160.01819.650-0.028-0.0280.0000.0000.0000.000
76A241ILE0-0.033-0.01222.8460.0050.0050.0000.0000.0000.000
77A242THR00.0260.01519.556-0.013-0.0130.0000.0000.0000.000
78A243PRO00.0160.00122.9910.0000.0000.0000.0000.0000.000
79A244HIS00.0090.00722.3610.0080.0080.0000.0000.0000.000
80A245GLY00.0190.01524.485-0.004-0.0040.0000.0000.0000.000
81A246ILE0-0.045-0.01017.4950.0130.0130.0000.0000.0000.000
82A247ASN0-0.027-0.01821.7550.0210.0210.0000.0000.0000.000
83A248ILE00.0260.00516.9450.0150.0150.0000.0000.0000.000
84A249MET0-0.006-0.00719.769-0.014-0.0140.0000.0000.0000.000
85A250LEU0-0.019-0.00718.8700.0820.0820.0000.0000.0000.000
86A251THR0-0.027-0.02320.9270.0320.0320.0000.0000.0000.000
87A252ASN00.0300.02622.490-0.011-0.0110.0000.0000.0000.000
88A253ALA00.0270.00925.635-0.029-0.0290.0000.0000.0000.000
89A261TYR00.0490.01735.798-0.001-0.0010.0000.0000.0000.000
90A262ASN00.0530.01436.3960.0210.0210.0000.0000.0000.000
91A263GLY00.0160.01836.7200.0100.0100.0000.0000.0000.000
92A264LEU00.0060.01131.9350.0110.0110.0000.0000.0000.000
93A265VAL00.007-0.00332.1720.0210.0210.0000.0000.0000.000
94A266GLY00.0230.01431.8020.0200.0200.0000.0000.0000.000
95A267GLU-1-0.793-0.88831.0610.3350.3350.0000.0000.0000.000
96A268LEU0-0.103-0.05527.7530.0290.0290.0000.0000.0000.000
97A269ILE0-0.006-0.00227.3280.0380.0380.0000.0000.0000.000
98A270GLU-1-0.890-0.94028.0080.3420.3420.0000.0000.0000.000
99A271ARG10.8370.90526.066-0.348-0.3480.0000.0000.0000.000
100A272ASN0-0.036-0.02823.3960.0770.0770.0000.0000.0000.000
101A273PHE0-0.013-0.00823.4750.0560.0560.0000.0000.0000.000
102A274GLN0-0.026-0.02525.0660.0370.0370.0000.0000.0000.000
103A275ARG10.8780.95619.724-0.674-0.6740.0000.0000.0000.000
104A276TYR0-0.008-0.01517.1190.1070.1070.0000.0000.0000.000
105A277GLY00.0530.04020.8690.0300.0300.0000.0000.0000.000
106A278VAL0-0.040-0.03221.770-0.028-0.0280.0000.0000.0000.000
107A279PRO00.0030.01624.1880.0160.0160.0000.0000.0000.000
108A280LEU00.0170.00225.298-0.013-0.0130.0000.0000.0000.000
109A281LEU00.0030.01419.6580.0250.0250.0000.0000.0000.000
110A282LEU0-0.033-0.01319.8310.0530.0530.0000.0000.0000.000
111A283SER00.0220.00022.822-0.051-0.0510.0000.0000.0000.000
112A284THR0-0.025-0.00925.508-0.003-0.0030.0000.0000.0000.000
113A285LEU00.0290.01326.348-0.011-0.0110.0000.0000.0000.000
114A286THR0-0.004-0.01829.686-0.008-0.0080.0000.0000.0000.000
115A287ASN0-0.0070.00729.334-0.002-0.0020.0000.0000.0000.000
116A288GLY00.0380.02131.787-0.014-0.0140.0000.0000.0000.000
117A289LEU0-0.0010.00333.754-0.004-0.0040.0000.0000.0000.000
118A290LEU00.0670.03436.956-0.006-0.0060.0000.0000.0000.000
119A291ILE0-0.015-0.00538.9290.0000.0000.0000.0000.0000.000
120A292GLY0-0.023-0.00941.936-0.009-0.0090.0000.0000.0000.000
121A293ILE0-0.010-0.00844.7300.0060.0060.0000.0000.0000.000
122A294THR00.0020.00847.799-0.006-0.0060.0000.0000.0000.000
123A295SER00.008-0.00950.7070.0050.0050.0000.0000.0000.000
124A296ALA00.0270.02852.339-0.002-0.0020.0000.0000.0000.000
125A310PHE0-0.043-0.03368.3770.0000.0000.0000.0000.0000.000
126A311GLY00.0330.02670.1390.0000.0000.0000.0000.0000.000
127A312ASP-1-0.780-0.88365.5720.0650.0650.0000.0000.0000.000
128A313TYR0-0.053-0.05863.0890.0020.0020.0000.0000.0000.000
129A314LEU00.0350.01867.5400.0010.0010.0000.0000.0000.000
130A315LEU00.0550.03369.487-0.001-0.0010.0000.0000.0000.000
131A316MET00.0080.01263.4600.0010.0010.0000.0000.0000.000
132A317GLN0-0.015-0.01868.5040.0000.0000.0000.0000.0000.000
133A318LEU00.000-0.00170.6330.0000.0000.0000.0000.0000.000
134A319MET0-0.038-0.00770.3530.0000.0000.0000.0000.0000.000
135A320ARG10.9120.93365.251-0.073-0.0730.0000.0000.0000.000
136A321GLN0-0.004-0.01365.5380.0010.0010.0000.0000.0000.000
137A322SER00.0280.01370.151-0.001-0.0010.0000.0000.0000.000
138A323GLY00.0160.02972.812-0.002-0.0020.0000.0000.0000.000
139A324MET0-0.058-0.01365.4040.0010.0010.0000.0000.0000.000
140A325GLY00.0470.02670.268-0.001-0.0010.0000.0000.0000.000
141A326ILE00.0610.00968.9080.0020.0020.0000.0000.0000.000
142A327ASN00.0400.01765.9620.0010.0010.0000.0000.0000.000
143A328GLN00.0470.03462.9220.0040.0040.0000.0000.0000.000
144A329VAL00.0170.01464.0810.0030.0030.0000.0000.0000.000
145A330VAL00.0330.02363.7800.0020.0020.0000.0000.0000.000
146A331ASN0-0.025-0.03260.5450.0040.0040.0000.0000.0000.000
147A332GLN0-0.037-0.00858.4760.0030.0030.0000.0000.0000.000
148A333ILE00.0130.00859.7500.0030.0030.0000.0000.0000.000
149A334LEU0-0.032-0.01658.3750.0020.0020.0000.0000.0000.000
150A335ARG10.8790.92255.633-0.085-0.0850.0000.0000.0000.000
151A336ASP-1-0.829-0.91154.9770.0960.0960.0000.0000.0000.000
152A337LYS10.8800.94155.638-0.073-0.0730.0000.0000.0000.000
153A338SER0-0.063-0.03251.7860.0030.0030.0000.0000.0000.000
154A339LYS10.9240.96750.920-0.103-0.1030.0000.0000.0000.000
155A340ILE0-0.021-0.00550.6690.0040.0040.0000.0000.0000.000
156A341ALA00.0200.01146.411-0.002-0.0020.0000.0000.0000.000
157A342PRO0-0.0050.00247.218-0.003-0.0030.0000.0000.0000.000
158A343ILE0-0.006-0.00546.9520.0070.0070.0000.0000.0000.000
159A344VAL0-0.004-0.00542.102-0.004-0.0040.0000.0000.0000.000
160A345VAL00.006-0.01642.5650.0050.0050.0000.0000.0000.000
161A346ILE0-0.0120.00536.500-0.005-0.0050.0000.0000.0000.000
162A347ARG10.9100.95139.722-0.093-0.0930.0000.0000.0000.000
163A348GLU-1-0.818-0.90037.3790.1050.1050.0000.0000.0000.000
164A349GLY0-0.021-0.02036.288-0.006-0.0060.0000.0000.0000.000
165A350SER0-0.075-0.05035.589-0.003-0.0030.0000.0000.0000.000
166A351ARG10.8270.88231.279-0.078-0.0780.0000.0000.0000.000
167A352VAL0-0.032-0.02428.0630.0050.0050.0000.0000.0000.000
168A353PHE00.0190.01125.269-0.010-0.0100.0000.0000.0000.000
169A354ILE0-0.017-0.01123.1370.0090.0090.0000.0000.0000.000
170A355SER00.027-0.01821.823-0.001-0.0010.0000.0000.0000.000
171A356PRO0-0.026-0.00417.2060.0060.0060.0000.0000.0000.000
172A357ASN00.0340.04119.0720.0100.0100.0000.0000.0000.000
173A358THR0-0.016-0.02715.274-0.020-0.0200.0000.0000.0000.000
174A359ASP-1-0.800-0.8909.7252.4982.4980.0000.0000.0000.000
175A360ILE00.0000.00612.7090.0690.0690.0000.0000.0000.000
176A361PHE0-0.029-0.0126.2390.2550.2550.0000.0000.0000.000
177A362PHE00.0330.00810.058-0.286-0.2860.0000.0000.0000.000
178A363PRO00.0760.0499.688-0.255-0.2550.0000.0000.0000.000
179A364ILE0-0.016-0.0118.419-0.199-0.1990.0000.0000.0000.000
180A365PRO0-0.031-0.01011.8600.0660.0660.0000.0000.0000.000
181A366ARG10.8330.88315.702-0.135-0.1350.0000.0000.0000.000
182A367GLU-1-0.773-0.85818.0960.0930.0930.0000.0000.0000.000
183A368ASN0-0.031-0.01520.820-0.006-0.0060.0000.0000.0000.000
184A369GLU-1-0.916-0.94819.7950.3340.3340.0000.0000.0000.000
185A370VAL0-0.011-0.01014.391-0.011-0.0110.0000.0000.0000.000
186A371ILE00.0090.00515.965-0.029-0.0290.0000.0000.0000.000
187A372ALA0-0.013-0.00314.7040.1050.1050.0000.0000.0000.000
188A373GLU-1-0.893-0.95410.4922.1422.1420.0000.0000.0000.000
189A374PHE0-0.013-0.01212.2030.2220.2220.0000.0000.0000.000
190A375LEU0-0.017-0.0128.6900.1120.1120.0000.0000.0000.000
191A376LYS10.8850.95312.346-1.056-1.0560.0000.0000.0000.000