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: 59K3Z

Calculation Name: 2BHV-A-Xray308

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: 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 196
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1922598.4941
FMO2-HF: Nuclear repulsion 1847707.74708
FMO2-HF: Total energy -74890.74702
FMO2-MP2: Total energy -75109.568277


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:165:ACE )


Summations of interaction energy for fragment #1(A:165:ACE )
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.
0.5761.7460.979-0.912-1.239-0.002
Interaction energy analysis for fragmet #1(A:165:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.034 / q_NPA : 0.008
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].
3A167LYS 10.9730.9923.8401.1592.011-0.005-0.366-0.482-0.001
4A168LEU 00.020-0.0045.3680.2190.2190.0000.0000.0000.000
5A169LEU 0-0.034-0.0012.5610.0110.1390.567-0.263-0.4320.000
6A170ARG 10.8170.8926.1750.3630.3630.0000.0000.0000.000
7A171THR 00.0120.0079.415-0.041-0.0410.0000.0000.0000.000
8A172ILE 0-0.0300.00011.3040.0710.0710.0000.0000.0000.000
9A173THR 0-0.015-0.01413.573-0.024-0.0240.0000.0000.0000.000
10A174ALA 00.0340.01015.081-0.005-0.0050.0000.0000.0000.000
11A175ASP -1-0.893-0.95118.3510.0450.0450.0000.0000.0000.000
12A176LYS 10.9100.96516.147-0.081-0.0810.0000.0000.0000.000
13A177MET 0-0.043-0.01819.723-0.014-0.0140.0000.0000.0000.000
14A178ILE 0-0.013-0.01720.2880.0060.0060.0000.0000.0000.000
15A179PRO 0-0.0100.02423.258-0.006-0.0060.0000.0000.0000.000
16A180ALA 00.021-0.00226.511-0.003-0.0030.0000.0000.0000.000
17A181PHE 00.0280.02628.9080.0020.0020.0000.0000.0000.000
18A182LEU 0-0.015-0.00932.597-0.004-0.0040.0000.0000.0000.000
19A183ILE 0-0.015-0.00933.0940.0010.0010.0000.0000.0000.000
20A184THR 0-0.058-0.01536.558-0.001-0.0010.0000.0000.0000.000
21A185PRO 00.0230.01638.0800.0000.0000.0000.0000.0000.000
22A186ILE 00.0220.00735.985-0.002-0.0020.0000.0000.0000.000
23A187SER 0-0.033-0.02440.5610.0010.0010.0000.0000.0000.000
24A188SER 00.0650.03643.472-0.001-0.0010.0000.0000.0000.000
25A189GLN 0-0.017-0.00745.0610.0000.0000.0000.0000.0000.000
26A190ILE 0-0.031-0.01743.656-0.001-0.0010.0000.0000.0000.000
27A191ALA 00.0300.03741.5780.0000.0000.0000.0000.0000.000
28A192GLY 00.010-0.00840.424-0.001-0.0010.0000.0000.0000.000
29A193LYS 10.9380.97835.5360.0260.0260.0000.0000.0000.000
30A194VAL 00.0190.01433.3940.0020.0020.0000.0000.0000.000
31A195ILE 0-0.004-0.01032.422-0.004-0.0040.0000.0000.0000.000
32A196ALA 00.0370.03029.9350.0030.0030.0000.0000.0000.000
33A197GLN 0-0.013-0.01229.292-0.007-0.0070.0000.0000.0000.000
34A198VAL 00.0040.01023.0700.0040.0040.0000.0000.0000.000
35A199GLU -1-0.841-0.93326.5170.0200.0200.0000.0000.0000.000
36A200SER 0-0.079-0.05723.2890.0060.0060.0000.0000.0000.000
37A201ASP -1-0.813-0.90118.9830.0220.0220.0000.0000.0000.000
38A202ILE 0-0.050-0.01516.8860.0150.0150.0000.0000.0000.000
39A203PHE 0-0.014-0.01813.417-0.016-0.0160.0000.0000.0000.000
40A204ALA 0-0.019-0.0099.854-0.009-0.0090.0000.0000.0000.000
41A205HIS 0-0.010-0.0018.8640.0220.0220.0000.0000.0000.000
42A206MET 00.0160.0152.664-0.391-0.2010.417-0.283-0.325-0.001
43A207GLY 0-0.009-0.0027.505-0.107-0.1070.0000.0000.0000.000
44A208LYS 10.9690.9618.065-0.333-0.3330.0000.0000.0000.000
45A209ALA 00.0130.02110.421-0.039-0.0390.0000.0000.0000.000
46A210VAL 00.0190.01112.0800.0190.0190.0000.0000.0000.000
47A211LEU 0-0.067-0.01211.804-0.029-0.0290.0000.0000.0000.000
48A212ILE 00.0080.00515.701-0.013-0.0130.0000.0000.0000.000
49A213PRO 00.0320.02419.3470.0170.0170.0000.0000.0000.000
50A214LYS 10.9851.02021.276-0.027-0.0270.0000.0000.0000.000
51A215GLY 0-0.039-0.01524.267-0.004-0.0040.0000.0000.0000.000
52A216SER 0-0.036-0.06223.606-0.006-0.0060.0000.0000.0000.000
53A217LYS 10.9170.97226.0930.0220.0220.0000.0000.0000.000
54A218VAL 00.0140.01125.886-0.006-0.0060.0000.0000.0000.000
55A219ILE 0-0.021-0.01728.1650.0050.0050.0000.0000.0000.000
56A220GLY 00.0470.01429.881-0.004-0.0040.0000.0000.0000.000
57A221TYR 0-0.055-0.02832.0290.0010.0010.0000.0000.0000.000
58A222TYR 00.0280.01134.642-0.001-0.0010.0000.0000.0000.000
59A223SER 00.009-0.00737.0690.0000.0000.0000.0000.0000.000
60A224ASN 00.0410.03039.5900.0010.0010.0000.0000.0000.000
61A225ASN 0-0.034-0.01140.9050.0000.0000.0000.0000.0000.000
62A226ASN 00.044-0.00143.1700.0020.0020.0000.0000.0000.000
63A227LYS 10.9520.98444.7590.0080.0080.0000.0000.0000.000
64A228MET 0-0.056-0.02647.1940.0010.0010.0000.0000.0000.000
65A229GLY 00.0580.05549.7460.0000.0000.0000.0000.0000.000
66A230GLU -1-1.011-0.99843.024-0.001-0.0010.0000.0000.0000.000
67A231TYR 0-0.004-0.00639.878-0.001-0.0010.0000.0000.0000.000
68A232ARG 10.9270.95737.7940.0110.0110.0000.0000.0000.000
69A233LEU 0-0.060-0.01636.581-0.001-0.0010.0000.0000.0000.000
70A234ASP -1-0.860-0.91835.060-0.015-0.0150.0000.0000.0000.000
71A235ILE 00.000-0.02031.682-0.001-0.0010.0000.0000.0000.000
72A236VAL 00.0110.01329.751-0.001-0.0010.0000.0000.0000.000
73A237TRP 00.003-0.02626.881-0.002-0.0020.0000.0000.0000.000
74A238SER 0-0.029-0.00227.114-0.006-0.0060.0000.0000.0000.000
75A239ARG 10.9940.99125.6790.0440.0440.0000.0000.0000.000
76A240ILE 00.0200.02021.7680.0100.0100.0000.0000.0000.000
77A241ILE 0-0.0230.00124.648-0.008-0.0080.0000.0000.0000.000
78A242THR 00.0230.00821.1310.0090.0090.0000.0000.0000.000
79A243PRO 00.0210.00624.148-0.002-0.0020.0000.0000.0000.000
80A244HIS 00.0110.00123.8660.0010.0010.0000.0000.0000.000
81A245GLY 0-0.0040.01526.154-0.003-0.0030.0000.0000.0000.000
82A246ILE 0-0.058-0.02219.626-0.005-0.0050.0000.0000.0000.000
83A247ASN 0-0.020-0.03224.0190.0110.0110.0000.0000.0000.000
84A248ILE 00.0200.01119.228-0.012-0.0120.0000.0000.0000.000
85A249MET 0-0.009-0.01222.3830.0180.0180.0000.0000.0000.000
86A250LEU 0-0.022-0.00621.557-0.009-0.0090.0000.0000.0000.000
87A251THR 0-0.023-0.03624.0560.0000.0000.0000.0000.0000.000
88A252ASN 00.017-0.00327.3590.0030.0030.0000.0000.0000.000
89A253ALA 00.0210.00029.7070.0040.0040.0000.0000.0000.000
90A254NME 00.0000.03033.0440.0030.0030.0000.0000.0000.000
91A260ACE 00.0220.00143.2560.0000.0000.0000.0000.0000.000
92A261TYR 00.005-0.01039.020-0.001-0.0010.0000.0000.0000.000
93A262ASN 00.0560.02139.954-0.001-0.0010.0000.0000.0000.000
94A263GLY 00.0250.02340.8100.0000.0000.0000.0000.0000.000
95A264LEU 0-0.007-0.00235.749-0.001-0.0010.0000.0000.0000.000
96A265VAL 00.0260.00835.524-0.003-0.0030.0000.0000.0000.000
97A266GLY 00.0250.01935.839-0.001-0.0010.0000.0000.0000.000
98A267GLU -1-0.848-0.93436.150-0.041-0.0410.0000.0000.0000.000
99A268LEU 0-0.109-0.04731.921-0.005-0.0050.0000.0000.0000.000
100A269ILE 0-0.0010.00331.710-0.004-0.0040.0000.0000.0000.000
101A270GLU -1-0.902-0.94032.427-0.037-0.0370.0000.0000.0000.000
102A271ARG 10.8870.93129.5260.0560.0560.0000.0000.0000.000
103A272ASN 0-0.082-0.04027.852-0.011-0.0110.0000.0000.0000.000
104A273PHE 0-0.005-0.00628.032-0.004-0.0040.0000.0000.0000.000
105A274GLN 0-0.021-0.00830.133-0.001-0.0010.0000.0000.0000.000
106A275ARG 10.8790.95625.0610.0860.0860.0000.0000.0000.000
107A276TYR 00.011-0.01521.851-0.011-0.0110.0000.0000.0000.000
108A277GLY 00.0730.05625.4450.0040.0040.0000.0000.0000.000
109A278VAL 0-0.047-0.03425.0460.0070.0070.0000.0000.0000.000
110A279PRO 00.0090.02028.089-0.004-0.0040.0000.0000.0000.000
111A280LEU 00.027-0.00328.850-0.003-0.0030.0000.0000.0000.000
112A281LEU 00.0110.01323.1080.0030.0030.0000.0000.0000.000
113A282LEU 0-0.037-0.01822.3670.0010.0010.0000.0000.0000.000
114A283SER 00.0200.01525.511-0.001-0.0010.0000.0000.0000.000
115A284THR 0-0.013-0.00927.4080.0000.0000.0000.0000.0000.000
116A285LEU 00.0370.01327.1950.0000.0000.0000.0000.0000.000
117A286THR 00.0100.00030.863-0.001-0.0010.0000.0000.0000.000
118A287ASN 0-0.017-0.00330.6450.0050.0050.0000.0000.0000.000
119A288GLY 00.0460.02932.8150.0010.0010.0000.0000.0000.000
120A289LEU 0-0.007-0.00935.368-0.001-0.0010.0000.0000.0000.000
121A290LEU 00.0280.00438.2580.0010.0010.0000.0000.0000.000
122A291ILE 0-0.013-0.00240.301-0.002-0.0020.0000.0000.0000.000
123A292GLY 0-0.043-0.00743.5630.0010.0010.0000.0000.0000.000
124A293ILE 00.001-0.00946.356-0.001-0.0010.0000.0000.0000.000
125A294THR 00.0110.01649.1500.0000.0000.0000.0000.0000.000
126A295SER 00.015-0.01552.1520.0000.0000.0000.0000.0000.000
127A296ALA 0-0.032-0.01354.8550.0000.0000.0000.0000.0000.000
128A297NME 00.0510.03853.7180.0000.0000.0000.0000.0000.000
129A309ACE 00.018-0.00572.0860.0000.0000.0000.0000.0000.000
130A310PHE 0-0.037-0.02970.1650.0000.0000.0000.0000.0000.000
131A311GLY 00.0370.04272.0810.0000.0000.0000.0000.0000.000
132A312ASP -1-0.829-0.91668.015-0.001-0.0010.0000.0000.0000.000
133A313TYR 0-0.068-0.05765.1660.0000.0000.0000.0000.0000.000
134A314LEU 00.0100.00570.1060.0000.0000.0000.0000.0000.000
135A315LEU 00.0320.01572.8020.0000.0000.0000.0000.0000.000
136A316MET 00.0320.02566.3280.0000.0000.0000.0000.0000.000
137A317GLN 00.023-0.00871.8800.0000.0000.0000.0000.0000.000
138A318LEU 00.0310.00873.8600.0000.0000.0000.0000.0000.000
139A319MET 0-0.0550.00473.3450.0000.0000.0000.0000.0000.000
140A320ARG 10.8590.91168.5040.0040.0040.0000.0000.0000.000
141A321GLN 0-0.012-0.02168.6850.0000.0000.0000.0000.0000.000
142A322SER 00.0180.02773.2510.0000.0000.0000.0000.0000.000
143A323GLY 00.0420.03376.9790.0000.0000.0000.0000.0000.000
144A324MET 0-0.029-0.01768.9620.0000.0000.0000.0000.0000.000
145A325GLY 00.0080.01672.4470.0000.0000.0000.0000.0000.000
146A326ILE 00.0850.00971.4980.0000.0000.0000.0000.0000.000
147A327ASN 00.0390.01167.8480.0000.0000.0000.0000.0000.000
148A328GLN 0-0.020-0.01066.5330.0000.0000.0000.0000.0000.000
149A329VAL 00.0170.02267.2000.0000.0000.0000.0000.0000.000
150A330VAL 00.0270.02265.8970.0000.0000.0000.0000.0000.000
151A331ASN 00.002-0.00863.0720.0000.0000.0000.0000.0000.000
152A332GLN 0-0.0310.00461.6690.0000.0000.0000.0000.0000.000
153A333ILE 00.0230.01162.5830.0000.0000.0000.0000.0000.000
154A334LEU 0-0.006-0.01160.8300.0000.0000.0000.0000.0000.000
155A335ARG 10.9530.96357.6360.0000.0000.0000.0000.0000.000
156A336ASP -1-0.891-0.96357.691-0.003-0.0030.0000.0000.0000.000
157A337LYS 10.9130.96658.639-0.001-0.0010.0000.0000.0000.000
158A338SER 0-0.088-0.02453.6680.0000.0000.0000.0000.0000.000
159A339LYS 10.9430.98353.4930.0030.0030.0000.0000.0000.000
160A340ILE 00.001-0.00753.440-0.001-0.0010.0000.0000.0000.000
161A341ALA 00.0300.01949.2250.0010.0010.0000.0000.0000.000
162A342PRO 0-0.020-0.00149.1410.0000.0000.0000.0000.0000.000
163A343ILE 0-0.005-0.00648.596-0.001-0.0010.0000.0000.0000.000
164A344VAL 0-0.025-0.01943.6050.0010.0010.0000.0000.0000.000
165A345VAL 00.001-0.01644.103-0.001-0.0010.0000.0000.0000.000
166A346ILE 0-0.0070.00037.9670.0020.0020.0000.0000.0000.000
167A347ARG 10.9530.96640.735-0.004-0.0040.0000.0000.0000.000
168A348GLU -1-0.852-0.90838.833-0.002-0.0020.0000.0000.0000.000
169A349GLY 0-0.028-0.02537.5210.0010.0010.0000.0000.0000.000
170A350SER 0-0.084-0.04936.9450.0030.0030.0000.0000.0000.000
171A351ARG 10.8750.92732.136-0.020-0.0200.0000.0000.0000.000
172A352VAL 0-0.041-0.02229.6710.0000.0000.0000.0000.0000.000
173A353PHE 00.0170.01026.1890.0030.0030.0000.0000.0000.000
174A354ILE 0-0.010-0.00724.384-0.003-0.0030.0000.0000.0000.000
175A355SER 00.0440.01923.0960.0070.0070.0000.0000.0000.000
176A356PRO 0-0.018-0.00219.043-0.008-0.0080.0000.0000.0000.000
177A357ASN 00.0150.01321.6640.0150.0150.0000.0000.0000.000
178A358THR 00.0100.00017.9950.0010.0010.0000.0000.0000.000
179A359ASP -1-0.835-0.90513.754-0.009-0.0090.0000.0000.0000.000
180A360ILE 0-0.030-0.01415.595-0.021-0.0210.0000.0000.0000.000
181A361PHE 0-0.033-0.0279.484-0.020-0.0200.0000.0000.0000.000
182A362PHE 00.0360.01012.8960.0240.0240.0000.0000.0000.000
183A363PRO 00.0830.05713.058-0.051-0.0510.0000.0000.0000.000
184A364ILE 0-0.022-0.02711.4860.0430.0430.0000.0000.0000.000
185A365PRO 0-0.0180.00014.8910.0070.0070.0000.0000.0000.000
186A366ARG 10.9630.97618.6210.1790.1790.0000.0000.0000.000
187A367GLU -1-0.916-0.95521.159-0.107-0.1070.0000.0000.0000.000
188A368ASN 0-0.048-0.02923.4760.0030.0030.0000.0000.0000.000
189A369GLU -1-0.876-0.92322.993-0.090-0.0900.0000.0000.0000.000
190A370VAL 0-0.036-0.02717.476-0.018-0.0180.0000.0000.0000.000
191A371ILE 00.0070.00619.9360.0200.0200.0000.0000.0000.000
192A372ALA 0-0.028-0.00817.890-0.025-0.0250.0000.0000.0000.000
193A373GLU -1-0.919-0.96115.680-0.307-0.3070.0000.0000.0000.000
194A374PHE 0-0.025-0.01516.7040.0000.0000.0000.0000.0000.000
195A375LEU 0-0.033-0.02712.965-0.010-0.0100.0000.0000.0000.000
196A376LYS 0-0.0190.01516.552-0.010-0.0100.0000.0000.0000.000