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: 6677Z

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 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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1902734.559671
FMO2-HF: Nuclear repulsion 1828335.806887
FMO2-HF: Total energy -74398.752785
FMO2-MP2: Total energy -74615.915569


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.
-2.9870.6460.973-1.733-2.8720.005
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 : 0.061 / q_NPA : 0.022
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].
3A168LEU00.026-0.0073.837-5.838-3.5930.021-1.080-1.1870.006
4A169LEU0-0.023-0.0022.564-1.741-0.6010.953-0.626-1.466-0.001
5A170ARG10.8140.8894.9830.3190.429-0.001-0.009-0.1000.000
6A171THR00.0060.0157.4360.8370.8370.0000.0000.0000.000
7A172ILE0-0.044-0.0029.655-0.286-0.2860.0000.0000.0000.000
8A173THR00.020-0.01212.7530.1390.1390.0000.0000.0000.000
9A174ALA0-0.011-0.01013.968-0.138-0.1380.0000.0000.0000.000
10A175ASP-1-0.885-0.94316.8980.5350.5350.0000.0000.0000.000
11A176LYS10.8930.95814.441-0.406-0.4060.0000.0000.0000.000
12A177MET0-0.032-0.00718.807-0.013-0.0130.0000.0000.0000.000
13A178ILE0-0.012-0.01818.821-0.038-0.0380.0000.0000.0000.000
14A179PRO0-0.0020.02722.2180.0050.0050.0000.0000.0000.000
15A180ALA00.011-0.00925.527-0.014-0.0140.0000.0000.0000.000
16A181PHE00.0260.02627.8170.0010.0010.0000.0000.0000.000
17A182LEU0-0.018-0.00731.3680.0020.0020.0000.0000.0000.000
18A183ILE0-0.015-0.01532.120-0.012-0.0120.0000.0000.0000.000
19A184THR0-0.063-0.02435.197-0.006-0.0060.0000.0000.0000.000
20A185PRO00.0400.02636.6270.0080.0080.0000.0000.0000.000
21A186ILE00.0120.00334.4180.0050.0050.0000.0000.0000.000
22A187SER0-0.031-0.01138.968-0.004-0.0040.0000.0000.0000.000
23A188SER00.0460.03541.5330.0030.0030.0000.0000.0000.000
24A189GLN00.003-0.00543.0670.0060.0060.0000.0000.0000.000
25A190ILE0-0.014-0.01241.8420.0050.0050.0000.0000.0000.000
26A191ALA00.0360.03838.8180.0050.0050.0000.0000.0000.000
27A192GLY00.011-0.00238.057-0.008-0.0080.0000.0000.0000.000
28A193LYS10.9230.96933.204-0.117-0.1170.0000.0000.0000.000
29A194VAL00.0250.01431.720-0.011-0.0110.0000.0000.0000.000
30A195ILE0-0.005-0.00330.5390.0110.0110.0000.0000.0000.000
31A196ALA00.0370.03228.550-0.010-0.0100.0000.0000.0000.000
32A197GLN00.0130.01727.984-0.002-0.0020.0000.0000.0000.000
33A198VAL00.0120.01121.9190.0020.0020.0000.0000.0000.000
34A199GLU-1-0.812-0.89325.4070.0610.0610.0000.0000.0000.000
35A200SER0-0.036-0.03422.137-0.018-0.0180.0000.0000.0000.000
36A201ASP-1-0.847-0.92218.609-0.046-0.0460.0000.0000.0000.000
37A202ILE0-0.035-0.00615.8490.0210.0210.0000.0000.0000.000
38A203PHE00.010-0.00413.133-0.020-0.0200.0000.0000.0000.000
39A204ALA0-0.006-0.0088.6690.1600.1600.0000.0000.0000.000
40A205HIS0-0.0230.0068.585-0.123-0.1230.0000.0000.0000.000
41A206MET00.0200.0184.7840.0200.1580.000-0.018-0.1190.000
42A207GLY00.0060.0037.318-0.360-0.3600.0000.0000.0000.000
43A208LYS10.9600.9578.4440.7960.7960.0000.0000.0000.000
44A209ALA00.0170.0249.7540.0650.0650.0000.0000.0000.000
45A210VAL00.0190.01011.4890.1170.1170.0000.0000.0000.000
46A211LEU0-0.063-0.01110.419-0.027-0.0270.0000.0000.0000.000
47A212ILE00.0090.00214.4180.0320.0320.0000.0000.0000.000
48A213PRO00.0250.01918.091-0.008-0.0080.0000.0000.0000.000
49A214LYS10.9580.99620.2820.0520.0520.0000.0000.0000.000
50A215GLY0-0.021-0.01023.414-0.017-0.0170.0000.0000.0000.000
51A216SER0-0.029-0.03622.283-0.001-0.0010.0000.0000.0000.000
52A217LYS10.8870.94424.733-0.053-0.0530.0000.0000.0000.000
53A218VAL00.0020.00224.2190.0130.0130.0000.0000.0000.000
54A219ILE0-0.005-0.00926.402-0.016-0.0160.0000.0000.0000.000
55A220GLY00.0500.02127.6420.0310.0310.0000.0000.0000.000
56A221TYR0-0.064-0.02929.712-0.033-0.0330.0000.0000.0000.000
57A222TYR00.0110.00532.0660.0180.0180.0000.0000.0000.000
58A223SER00.009-0.00634.621-0.009-0.0090.0000.0000.0000.000
59A224ASN00.0280.01336.9310.0040.0040.0000.0000.0000.000
60A225ASN0-0.039-0.01437.348-0.014-0.0140.0000.0000.0000.000
61A226ASN00.040-0.00140.1320.0060.0060.0000.0000.0000.000
62A227LYS10.9460.98041.502-0.169-0.1690.0000.0000.0000.000
63A228MET0-0.042-0.02344.2270.0000.0000.0000.0000.0000.000
64A229GLY00.0640.05847.009-0.001-0.0010.0000.0000.0000.000
65A230GLU-1-1.013-1.00340.8690.1770.1770.0000.0000.0000.000
66A231TYR00.004-0.00438.4830.0010.0010.0000.0000.0000.000
67A232ARG10.8990.92833.922-0.243-0.2430.0000.0000.0000.000
68A233LEU0-0.037-0.00434.688-0.006-0.0060.0000.0000.0000.000
69A234ASP-1-0.858-0.90132.1720.2720.2720.0000.0000.0000.000
70A235ILE00.022-0.00829.802-0.016-0.0160.0000.0000.0000.000
71A236VAL0-0.0050.00726.4700.0270.0270.0000.0000.0000.000
72A237TRP00.006-0.02624.798-0.032-0.0320.0000.0000.0000.000
73A238SER0-0.024-0.00224.5270.0290.0290.0000.0000.0000.000
74A239ARG10.9850.98323.140-0.156-0.1560.0000.0000.0000.000
75A240ILE00.0250.02219.707-0.022-0.0220.0000.0000.0000.000
76A241ILE0-0.040-0.00622.257-0.002-0.0020.0000.0000.0000.000
77A242THR00.0380.01219.267-0.009-0.0090.0000.0000.0000.000
78A243PRO00.0190.00422.7240.0000.0000.0000.0000.0000.000
79A244HIS00.0060.00122.1700.0100.0100.0000.0000.0000.000
80A245GLY00.0030.01824.096-0.005-0.0050.0000.0000.0000.000
81A246ILE0-0.066-0.02017.1870.0060.0060.0000.0000.0000.000
82A247ASN0-0.026-0.03021.4130.0310.0310.0000.0000.0000.000
83A248ILE00.0290.01316.9400.0130.0130.0000.0000.0000.000
84A249MET0-0.022-0.01819.539-0.010-0.0100.0000.0000.0000.000
85A250LEU0-0.020-0.01018.9970.0690.0690.0000.0000.0000.000
86A251THR0-0.030-0.04021.0060.0430.0430.0000.0000.0000.000
87A252ASN0-0.007-0.00622.761-0.006-0.0060.0000.0000.0000.000
88A253ALA00.0690.04425.834-0.011-0.0110.0000.0000.0000.000
89A261TYR00.0330.00536.2100.0000.0000.0000.0000.0000.000
90A262ASN00.0490.00736.7290.0180.0180.0000.0000.0000.000
91A263GLY00.0290.02237.2640.0090.0090.0000.0000.0000.000
92A264LEU0-0.017-0.00632.6590.0110.0110.0000.0000.0000.000
93A265VAL00.0280.00832.3220.0190.0190.0000.0000.0000.000
94A266GLY00.0300.02232.1650.0190.0190.0000.0000.0000.000
95A267GLU-1-0.871-0.94131.5450.2980.2980.0000.0000.0000.000
96A268LEU0-0.080-0.03428.1410.0280.0280.0000.0000.0000.000
97A269ILE0-0.017-0.00827.7010.0380.0380.0000.0000.0000.000
98A270GLU-1-0.900-0.94628.4100.3200.3200.0000.0000.0000.000
99A271ARG10.8880.94226.193-0.324-0.3240.0000.0000.0000.000
100A272ASN0-0.066-0.03723.9820.0640.0640.0000.0000.0000.000
101A273PHE0-0.003-0.00623.7820.0590.0590.0000.0000.0000.000
102A274GLN0-0.0030.00225.7120.0270.0270.0000.0000.0000.000
103A275ARG10.8710.95120.012-0.596-0.5960.0000.0000.0000.000
104A276TYR0-0.002-0.02017.4880.0860.0860.0000.0000.0000.000
105A277GLY00.0590.05121.0710.0330.0330.0000.0000.0000.000
106A278VAL0-0.063-0.04221.880-0.018-0.0180.0000.0000.0000.000
107A279PRO00.0220.02524.3500.0020.0020.0000.0000.0000.000
108A280LEU00.0330.00725.626-0.011-0.0110.0000.0000.0000.000
109A281LEU00.0030.00819.8290.0300.0300.0000.0000.0000.000
110A282LEU0-0.043-0.01720.3070.0530.0530.0000.0000.0000.000
111A283SER00.020-0.00423.178-0.045-0.0450.0000.0000.0000.000
112A284THR0-0.020-0.01225.902-0.006-0.0060.0000.0000.0000.000
113A285LEU00.0470.01926.284-0.011-0.0110.0000.0000.0000.000
114A286THR0-0.021-0.01329.714-0.009-0.0090.0000.0000.0000.000
115A287ASN0-0.010-0.00129.8260.0030.0030.0000.0000.0000.000
116A288GLY00.0650.03731.970-0.013-0.0130.0000.0000.0000.000
117A289LEU0-0.009-0.00834.075-0.004-0.0040.0000.0000.0000.000
118A290LEU00.0390.01237.208-0.006-0.0060.0000.0000.0000.000
119A291ILE0-0.022-0.00939.1540.0020.0020.0000.0000.0000.000
120A292GLY0-0.045-0.00842.398-0.006-0.0060.0000.0000.0000.000
121A293ILE00.004-0.00844.6530.0050.0050.0000.0000.0000.000
122A294THR00.0270.03047.867-0.004-0.0040.0000.0000.0000.000
123A295SER0-0.001-0.02050.7290.0060.0060.0000.0000.0000.000
124A296ALA00.0190.02053.021-0.003-0.0030.0000.0000.0000.000
125A310PHE0-0.015-0.02569.0270.0000.0000.0000.0000.0000.000
126A311GLY00.0350.03470.0610.0010.0010.0000.0000.0000.000
127A312ASP-1-0.833-0.92565.6150.0640.0640.0000.0000.0000.000
128A313TYR0-0.040-0.03863.0040.0010.0010.0000.0000.0000.000
129A314LEU00.0110.01167.6950.0010.0010.0000.0000.0000.000
130A315LEU00.0370.01769.9620.0000.0000.0000.0000.0000.000
131A316MET00.0230.01763.7800.0000.0000.0000.0000.0000.000
132A317GLN00.021-0.00269.0890.0000.0000.0000.0000.0000.000
133A318LEU00.0110.00071.1980.0000.0000.0000.0000.0000.000
134A319MET0-0.0420.00470.4600.0000.0000.0000.0000.0000.000
135A320ARG10.8690.91765.578-0.072-0.0720.0000.0000.0000.000
136A321GLN0-0.006-0.02566.3050.0020.0020.0000.0000.0000.000
137A322SER00.0080.02770.439-0.001-0.0010.0000.0000.0000.000
138A323GLY00.0450.03274.201-0.001-0.0010.0000.0000.0000.000
139A324MET0-0.019-0.00466.1590.0020.0020.0000.0000.0000.000
140A325GLY00.0190.01770.132-0.001-0.0010.0000.0000.0000.000
141A326ILE00.0810.01269.1710.0020.0020.0000.0000.0000.000
142A327ASN00.0330.01465.8920.0000.0000.0000.0000.0000.000
143A328GLN00.0100.00263.6420.0040.0040.0000.0000.0000.000
144A329VAL00.0150.02064.7850.0020.0020.0000.0000.0000.000
145A330VAL00.0210.02064.0290.0020.0020.0000.0000.0000.000
146A331ASN0-0.025-0.03160.9020.0040.0040.0000.0000.0000.000
147A332GLN0-0.0280.00058.7620.0040.0040.0000.0000.0000.000
148A333ILE00.0270.01260.1300.0030.0030.0000.0000.0000.000
149A334LEU0-0.012-0.01258.9110.0020.0020.0000.0000.0000.000
150A335ARG10.9040.94655.992-0.088-0.0880.0000.0000.0000.000
151A336ASP-1-0.835-0.93255.3050.0950.0950.0000.0000.0000.000
152A337LYS10.8740.94756.143-0.073-0.0730.0000.0000.0000.000
153A338SER0-0.081-0.02551.5390.0020.0020.0000.0000.0000.000
154A339LYS10.9330.97851.133-0.102-0.1020.0000.0000.0000.000
155A340ILE0-0.009-0.00850.8030.0050.0050.0000.0000.0000.000
156A341ALA00.0270.01647.0060.0000.0000.0000.0000.0000.000
157A342PRO0-0.0160.00547.387-0.003-0.0030.0000.0000.0000.000
158A343ILE0-0.010-0.01146.9180.0060.0060.0000.0000.0000.000
159A344VAL0-0.019-0.01542.196-0.003-0.0030.0000.0000.0000.000
160A345VAL0-0.010-0.02242.6740.0040.0040.0000.0000.0000.000
161A346ILE00.0010.00436.622-0.002-0.0020.0000.0000.0000.000
162A347ARG10.9460.96639.363-0.085-0.0850.0000.0000.0000.000
163A348GLU-1-0.845-0.90937.5440.0920.0920.0000.0000.0000.000
164A349GLY0-0.027-0.02336.452-0.007-0.0070.0000.0000.0000.000
165A350SER0-0.076-0.04835.760-0.001-0.0010.0000.0000.0000.000
166A351ARG10.8430.88731.386-0.076-0.0760.0000.0000.0000.000
167A352VAL0-0.038-0.02128.2830.0060.0060.0000.0000.0000.000
168A353PHE00.0060.00525.487-0.008-0.0080.0000.0000.0000.000
169A354ILE0-0.010-0.00623.1650.0130.0130.0000.0000.0000.000
170A355SER00.0520.02521.8640.0030.0030.0000.0000.0000.000
171A356PRO0-0.020-0.00717.612-0.002-0.0020.0000.0000.0000.000
172A357ASN00.0310.03319.810-0.005-0.0050.0000.0000.0000.000
173A358THR0-0.012-0.01115.5430.0000.0000.0000.0000.0000.000
174A359ASP-1-0.774-0.88510.2732.2132.2130.0000.0000.0000.000
175A360ILE0-0.050-0.02213.3560.0290.0290.0000.0000.0000.000
176A361PHE0-0.043-0.0256.1220.1800.1800.0000.0000.0000.000
177A362PHE00.0400.01210.325-0.197-0.1970.0000.0000.0000.000
178A363PRO00.0920.0559.731-0.270-0.2700.0000.0000.0000.000
179A364ILE0-0.020-0.0198.000-0.126-0.1260.0000.0000.0000.000
180A365PRO0-0.025-0.00311.5400.0730.0730.0000.0000.0000.000
181A366ARG10.8590.91315.356-0.005-0.0050.0000.0000.0000.000
182A367GLU-1-0.793-0.88517.571-0.001-0.0010.0000.0000.0000.000
183A368ASN0-0.048-0.03320.2740.0050.0050.0000.0000.0000.000
184A369GLU-1-0.895-0.93219.5540.2350.2350.0000.0000.0000.000
185A370VAL0-0.022-0.01614.240-0.012-0.0120.0000.0000.0000.000
186A371ILE00.0130.00816.0360.0030.0030.0000.0000.0000.000
187A372ALA0-0.024-0.00514.4660.0920.0920.0000.0000.0000.000
188A373GLU-1-0.902-0.95210.8941.8491.8490.0000.0000.0000.000
189A374PHE0-0.010-0.00812.9430.1380.1380.0000.0000.0000.000
190A375LEU0-0.009-0.0048.9290.0260.0260.0000.0000.0000.000
191A376LYS10.8910.95612.436-0.963-0.9630.0000.0000.0000.000