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

tag_button

FMODB ID: GNKJ1

Calculation Name: 5BNF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5BNF

Chain ID: A

ChEMBL ID:

UniProt ID: F1S5D9

Base Structure: X-ray

Registration Date: 2023-06-20

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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2690515.744735
FMO2-HF: Nuclear repulsion 2600509.329003
FMO2-HF: Total energy -90006.415731
FMO2-MP2: Total energy -90264.151611


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:54:TRP)


Summations of interaction energy for fragment #1(A:54:TRP)
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.
-31.043-12.78718.096-10.145-26.207-0.011
Interaction energy analysis for fragmet #1(A:54:TRP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / q_NPA : -0.011
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].
3A56GLY00.0030.0142.761-1.6411.1670.076-1.401-1.4840.001
4A57LYS10.8580.9294.229-0.940-0.825-0.001-0.030-0.0840.000
5A58GLY00.0500.0375.740-0.297-0.2970.0000.0000.0000.000
6A59SER0-0.037-0.0376.5880.9390.9390.0000.0000.0000.000
7A60THR0-0.034-0.0249.0120.0810.0810.0000.0000.0000.000
8A61VAL00.0590.01912.622-0.015-0.0150.0000.0000.0000.000
9A62ASP-1-0.830-0.91514.685-0.604-0.6040.0000.0000.0000.000
10A63PHE00.0090.00814.1620.0790.0790.0000.0000.0000.000
11A64GLN00.0550.00515.6010.0820.0820.0000.0000.0000.000
12A65GLU-1-0.935-0.96418.538-0.399-0.3990.0000.0000.0000.000
13A66ILE0-0.069-0.03017.4470.0730.0730.0000.0000.0000.000
14A67ILE00.0260.01418.0660.0640.0640.0000.0000.0000.000
15A68LEU0-0.022-0.00520.9700.0450.0450.0000.0000.0000.000
16A69ARG10.9690.98623.1700.3930.3930.0000.0000.0000.000
17A70ARG10.8280.93119.3240.3620.3620.0000.0000.0000.000
18A71CYS00.0590.02324.7710.0300.0300.0000.0000.0000.000
19A72TYR00.014-0.01826.4410.0200.0200.0000.0000.0000.000
20A73THR0-0.038-0.03228.5470.0170.0170.0000.0000.0000.000
21A74TYR00.008-0.02628.0190.0160.0160.0000.0000.0000.000
22A75ILE0-0.011-0.01429.9480.0110.0110.0000.0000.0000.000
23A76ARG10.9060.96332.4340.1930.1930.0000.0000.0000.000
24A77VAL0-0.040-0.00933.4050.0060.0060.0000.0000.0000.000
25A78VAL0-0.059-0.01229.7910.0080.0080.0000.0000.0000.000
26A79GLN0-0.058-0.05032.8450.0140.0140.0000.0000.0000.000
27A80PRO00.0140.01634.701-0.005-0.0050.0000.0000.0000.000
28A81GLU-1-0.876-0.92737.121-0.092-0.0920.0000.0000.0000.000
29A82LEU0-0.035-0.01430.9140.0040.0040.0000.0000.0000.000
30A83GLY00.0150.00433.799-0.011-0.0110.0000.0000.0000.000
31A84ASP-1-0.865-0.90135.340-0.117-0.1170.0000.0000.0000.000
32A85ARG10.7450.86030.0890.1160.1160.0000.0000.0000.000
33A86ASP-1-0.773-0.89030.210-0.223-0.2230.0000.0000.0000.000
34A88GLN00.0390.03724.015-0.038-0.0380.0000.0000.0000.000
35A89LYS10.8920.92325.2170.1710.1710.0000.0000.0000.000
36A90ILE0-0.0020.01022.995-0.015-0.0150.0000.0000.0000.000
37A91LYS10.9320.96520.8800.3960.3960.0000.0000.0000.000
38A92LYS10.8010.89620.1760.3700.3700.0000.0000.0000.000
39A93ALA00.0210.00720.048-0.029-0.0290.0000.0000.0000.000
40A94PHE0-0.013-0.01315.787-0.008-0.0080.0000.0000.0000.000
41A95THR0-0.007-0.01615.728-0.051-0.0510.0000.0000.0000.000
42A96ASP-1-0.804-0.88615.107-0.513-0.5130.0000.0000.0000.000
43A97ALA0-0.0110.01015.9370.0040.0040.0000.0000.0000.000
44A98PHE0-0.020-0.01610.1820.0470.0470.0000.0000.0000.000
45A99ILE00.0260.02210.677-0.219-0.2190.0000.0000.0000.000
46A100SER0-0.066-0.02811.0290.1790.1790.0000.0000.0000.000
47A101LYS10.7970.89510.1970.4070.4070.0000.0000.0000.000
48A102ASP-1-0.798-0.9144.873-1.742-1.615-0.001-0.004-0.1210.000
49A103PRO0-0.043-0.0112.493-0.8330.6450.933-0.607-1.8040.003
50A104CYS00.0160.0083.4390.3202.3491.334-0.768-2.5950.007
51A105SER0-0.033-0.0105.707-0.148-0.1480.0000.0000.0000.000
52A106ALA0-0.0150.0168.872-0.086-0.0860.0000.0000.0000.000
53A107ARG10.8180.87211.1300.0920.0920.0000.0000.0000.000
54A108GLU-1-0.757-0.86714.6990.0500.0500.0000.0000.0000.000
55A109GLU-1-0.728-0.86918.1000.0270.0270.0000.0000.0000.000
56A110ASP-1-0.864-0.90513.838-0.173-0.1730.0000.0000.0000.000
57A111TYR0-0.021-0.04413.703-0.113-0.1130.0000.0000.0000.000
58A112ASP-1-0.865-0.92219.219-0.053-0.0530.0000.0000.0000.000
59A113LEU0-0.049-0.03122.3300.0010.0010.0000.0000.0000.000
60A114LEU00.0150.00319.2280.0020.0020.0000.0000.0000.000
61A115MET00.009-0.00120.5260.0080.0080.0000.0000.0000.000
62A116LYS10.9360.98124.4480.1090.1090.0000.0000.0000.000
63A117LEU0-0.038-0.02125.0910.0050.0050.0000.0000.0000.000
64A118GLY00.033-0.00426.081-0.001-0.0010.0000.0000.0000.000
65A119HIS0-0.0180.01927.0980.0090.0090.0000.0000.0000.000
66A120GLN00.036-0.00729.509-0.011-0.0110.0000.0000.0000.000
67A121THR0-0.015-0.00330.9410.0080.0080.0000.0000.0000.000
68A122VAL0-0.0270.00030.988-0.004-0.0040.0000.0000.0000.000
69A123PRO00.0260.00833.8570.0060.0060.0000.0000.0000.000
70A124CYS00.019-0.00333.1350.0050.0050.0000.0000.0000.000
71A125ASP-1-0.849-0.92338.389-0.012-0.0120.0000.0000.0000.000
72A126LYS10.8020.90135.9170.0250.0250.0000.0000.0000.000
73A127THR00.0360.02630.750-0.004-0.0040.0000.0000.0000.000
74A128VAL0-0.054-0.02930.3180.0080.0080.0000.0000.0000.000
75A129PHE00.0360.01026.230-0.004-0.0040.0000.0000.0000.000
76A130TRP0-0.055-0.04219.9140.0110.0110.0000.0000.0000.000
77A131SER00.0360.02224.0670.0120.0120.0000.0000.0000.000
78A132LYS10.9230.96119.695-0.046-0.0460.0000.0000.0000.000
79A133THR0-0.041-0.04823.161-0.008-0.0080.0000.0000.0000.000
80A134LYS10.8730.95819.9230.1080.1080.0000.0000.0000.000
81A135GLU-1-0.861-0.91020.725-0.086-0.0860.0000.0000.0000.000
82A145LYS10.9940.98635.0150.0760.0760.0000.0000.0000.000
83A146GLY00.0110.00336.4970.0050.0050.0000.0000.0000.000
84A147LEU0-0.058-0.02434.0030.0060.0060.0000.0000.0000.000
85A148PHE00.0190.00330.828-0.005-0.0050.0000.0000.0000.000
86A149THR00.004-0.01426.6640.0090.0090.0000.0000.0000.000
87A150LEU00.0450.02721.115-0.010-0.0100.0000.0000.0000.000
88A151GLU-1-0.765-0.88621.852-0.069-0.0690.0000.0000.0000.000
89A152ASN0-0.0380.01224.315-0.008-0.0080.0000.0000.0000.000
90A153THR00.0120.01825.270-0.006-0.0060.0000.0000.0000.000
91A154LEU00.0120.01226.030-0.015-0.0150.0000.0000.0000.000
92A155LEU00.006-0.01022.343-0.023-0.0230.0000.0000.0000.000
93A156GLY00.0400.02521.377-0.018-0.0180.0000.0000.0000.000
94A157TYR00.0150.01421.397-0.033-0.0330.0000.0000.0000.000
95A158ILE0-0.075-0.04920.819-0.029-0.0290.0000.0000.0000.000
96A159ALA00.0260.01417.318-0.050-0.0500.0000.0000.0000.000
97A160ASP-1-0.880-0.94516.906-0.234-0.2340.0000.0000.0000.000
98A161ASP-1-0.895-0.94915.715-0.400-0.4000.0000.0000.0000.000
99A162LEU0-0.054-0.00414.252-0.096-0.0960.0000.0000.0000.000
100A163SER0-0.066-0.0438.7870.0900.0900.0000.0000.0000.000
101A164TRP00.007-0.0019.544-0.145-0.1450.0000.0000.0000.000
102A165CYS0-0.049-0.0092.897-4.809-1.9710.878-1.258-2.458-0.007
103A166GLY00.0680.0477.585-0.262-0.2620.0000.0000.0000.000
104A167LYS10.8430.9054.9433.6353.6350.0000.0000.0000.000
105A168VAL00.0400.0236.7390.5240.5240.0000.0000.0000.000
106A169GLY0-0.0060.0059.320-0.019-0.0190.0000.0000.0000.000
107A170SER0-0.040-0.0189.8240.1730.1730.0000.0000.0000.000
108A171SER00.018-0.00811.6700.0310.0310.0000.0000.0000.000
109A172GLU-1-0.990-0.98712.635-0.894-0.8940.0000.0000.0000.000
110A173ILE0-0.014-0.00410.147-0.229-0.2290.0000.0000.0000.000
111A174ASN0-0.007-0.0283.3221.3991.6920.006-0.049-0.2500.000
112A175LEU00.006-0.0046.427-0.463-0.4630.0000.0000.0000.000
113A176GLU-1-0.836-0.8854.398-6.187-5.990-0.001-0.019-0.1760.000
114A177SER00.0220.0052.305-6.989-4.4563.337-2.378-3.493-0.020
115A179PRO00.0090.0132.183-5.812-2.2038.773-3.157-9.2260.012
116A180ASP-1-0.798-0.9112.9820.381-0.7520.0981.722-0.6860.001
117A181ARG10.9220.9505.6610.2050.2050.0000.0000.0000.000
118A182ARG10.8870.9387.716-0.898-0.8980.0000.0000.0000.000
119A183ASN0-0.015-0.0072.550-4.516-1.1542.664-2.196-3.830-0.008
120A185ASN00.0080.0015.893-0.203-0.2030.0000.0000.0000.000
121A186SER0-0.033-0.0277.793-0.087-0.0870.0000.0000.0000.000
122A187ASN00.0430.0416.994-0.593-0.5930.0000.0000.0000.000
123A188PHE00.0610.0098.220-0.269-0.2690.0000.0000.0000.000
124A189VAL00.0200.0469.349-0.073-0.0730.0000.0000.0000.000
125A190SER0-0.009-0.0239.824-0.040-0.0400.0000.0000.0000.000
126A191VAL0-0.0170.01312.068-0.070-0.0700.0000.0000.0000.000
127A192PHE00.0030.01214.329-0.052-0.0520.0000.0000.0000.000
128A193TRP00.0280.01913.9950.0040.0040.0000.0000.0000.000
129A194ASN0-0.064-0.04415.181-0.007-0.0070.0000.0000.0000.000
130A195LEU0-0.0060.01818.235-0.014-0.0140.0000.0000.0000.000
131A196LEU00.0130.00719.859-0.010-0.0100.0000.0000.0000.000
132A197SER0-0.012-0.03220.973-0.005-0.0050.0000.0000.0000.000
133A198LYS10.7730.88521.887-0.097-0.0970.0000.0000.0000.000
134A199ARG10.7900.86123.676-0.029-0.0290.0000.0000.0000.000
135A200PHE00.0020.00625.542-0.008-0.0080.0000.0000.0000.000
136A201ALA0-0.002-0.01026.854-0.003-0.0030.0000.0000.0000.000
137A202GLU-1-0.801-0.86726.8050.0360.0360.0000.0000.0000.000
138A203ASN0-0.036-0.04129.514-0.009-0.0090.0000.0000.0000.000
139A204ALA00.0380.04331.383-0.005-0.0050.0000.0000.0000.000
140A206GLY00.0040.01836.939-0.004-0.0040.0000.0000.0000.000
141A207MET0-0.089-0.04138.8850.0070.0070.0000.0000.0000.000
142A208VAL00.0660.02333.425-0.004-0.0040.0000.0000.0000.000
143A209GLN00.0270.00433.7540.0070.0070.0000.0000.0000.000
144A210VAL00.0050.00628.708-0.002-0.0020.0000.0000.0000.000
145A211PHE0-0.0090.00629.9100.0010.0010.0000.0000.0000.000
146A212LEU00.011-0.01028.7580.0050.0050.0000.0000.0000.000
147A213ASN00.0540.04226.846-0.013-0.0130.0000.0000.0000.000
148A214GLY00.0740.03029.7340.0110.0110.0000.0000.0000.000
149A215SER0-0.007-0.02029.9640.0050.0050.0000.0000.0000.000
150A216ILE0-0.039-0.02725.9540.0060.0060.0000.0000.0000.000
151A217SER0-0.024-0.03329.487-0.004-0.0040.0000.0000.0000.000
152A218ASN0-0.015-0.00727.5530.0000.0000.0000.0000.0000.000
153A219ALA0-0.0110.01127.6990.0050.0050.0000.0000.0000.000
154A220PHE0-0.025-0.00527.864-0.005-0.0050.0000.0000.0000.000
155A221ASP-1-0.730-0.85122.2170.2270.2270.0000.0000.0000.000
156A222LYS10.8690.94124.814-0.158-0.1580.0000.0000.0000.000
157A223THR0-0.060-0.03819.5040.0220.0220.0000.0000.0000.000
158A224SER0-0.005-0.02519.8380.0190.0190.0000.0000.0000.000
159A225THR00.027-0.00618.5610.0190.0190.0000.0000.0000.000
160A226PHE00.0730.04220.910-0.005-0.0050.0000.0000.0000.000
161A227GLY0-0.005-0.01124.441-0.006-0.0060.0000.0000.0000.000
162A228ARG10.8230.93517.841-0.296-0.2960.0000.0000.0000.000
163A229VAL0-0.019-0.01120.5220.0110.0110.0000.0000.0000.000
164A230GLU-1-0.818-0.88723.7960.0450.0450.0000.0000.0000.000
165A231VAL00.0210.00426.237-0.011-0.0110.0000.0000.0000.000
166A232HIS0-0.017-0.02025.948-0.016-0.0160.0000.0000.0000.000
167A233SER0-0.009-0.01326.352-0.005-0.0050.0000.0000.0000.000
168A234LEU0-0.051-0.00628.949-0.012-0.0120.0000.0000.0000.000
169A235GLN00.0690.04431.7240.0060.0060.0000.0000.0000.000
170A236PRO00.0440.01734.823-0.006-0.0060.0000.0000.0000.000
171A237SER0-0.031-0.00738.041-0.003-0.0030.0000.0000.0000.000
172A238LYS10.7780.88034.355-0.007-0.0070.0000.0000.0000.000
173A239VAL0-0.0120.01334.397-0.005-0.0050.0000.0000.0000.000
174A240HIS00.0710.06637.8090.0090.0090.0000.0000.0000.000
175A241THR0-0.030-0.04339.5340.0050.0050.0000.0000.0000.000
176A242LEU00.0030.01332.419-0.002-0.0020.0000.0000.0000.000
177A243LYS10.8270.90036.370-0.014-0.0140.0000.0000.0000.000
178A244ALA00.0170.00934.147-0.001-0.0010.0000.0000.0000.000
179A245TRP0-0.035-0.03433.970-0.002-0.0020.0000.0000.0000.000
180A246VAL00.0240.00933.4460.0010.0010.0000.0000.0000.000
181A247ILE0-0.020-0.01032.325-0.005-0.0050.0000.0000.0000.000
182A248HIS0-0.039-0.03333.6620.0060.0060.0000.0000.0000.000
183A249ASP-1-0.836-0.92733.2580.0070.0070.0000.0000.0000.000
184A250SER0-0.026-0.02836.3620.0040.0040.0000.0000.0000.000
185A251GLY00.0000.01738.5920.0000.0000.0000.0000.0000.000
186A252LYS10.8190.89535.078-0.050-0.0500.0000.0000.0000.000
187A253THR00.0390.02537.9960.0010.0010.0000.0000.0000.000
188A254PRO00.0400.03136.4490.0030.0030.0000.0000.0000.000
189A255ARG10.8660.92931.709-0.094-0.0940.0000.0000.0000.000
190A256ASP-1-0.766-0.86732.5380.0970.0970.0000.0000.0000.000
191A257THR0-0.027-0.02134.658-0.008-0.0080.0000.0000.0000.000
192A258CYS0-0.017-0.00836.7300.0060.0060.0000.0000.0000.000
193A259SER0-0.027-0.00138.515-0.001-0.0010.0000.0000.0000.000
194A260GLY00.0060.02536.2730.0030.0030.0000.0000.0000.000
195A261SER00.005-0.01534.485-0.002-0.0020.0000.0000.0000.000
196A262SER00.0110.00629.939-0.003-0.0030.0000.0000.0000.000
197A263ILE00.0550.00432.3730.0010.0010.0000.0000.0000.000
198A264ASN00.0250.01334.250-0.009-0.0090.0000.0000.0000.000
199A265GLU-1-0.842-0.92329.9820.1470.1470.0000.0000.0000.000
200A266LEU0-0.040-0.00130.9600.0000.0000.0000.0000.0000.000
201A267GLN00.0170.01533.167-0.009-0.0090.0000.0000.0000.000
202A268LEU00.001-0.01135.604-0.004-0.0040.0000.0000.0000.000
203A269ILE0-0.0190.00129.811-0.001-0.0010.0000.0000.0000.000
204A270LEU0-0.024-0.00133.823-0.004-0.0040.0000.0000.0000.000
205A271ARG10.9280.94336.280-0.057-0.0570.0000.0000.0000.000
206A272GLY00.0090.01837.066-0.003-0.0030.0000.0000.0000.000
207A273LYS10.7720.87031.644-0.074-0.0740.0000.0000.0000.000
208A274ASN0-0.045-0.02338.095-0.006-0.0060.0000.0000.0000.000
209A275ILE0-0.0230.00635.827-0.005-0.0050.0000.0000.0000.000
210A276LYS10.8390.92139.779-0.025-0.0250.0000.0000.0000.000
211A277PHE00.0650.01235.3580.0000.0000.0000.0000.0000.000
212A278THR0-0.029-0.00339.165-0.004-0.0040.0000.0000.0000.000
213A280GLN00.0300.02538.402-0.003-0.0030.0000.0000.0000.000
214A281GLU-1-0.737-0.85838.0130.0450.0450.0000.0000.0000.000
215A282ASN0-0.045-0.02737.883-0.007-0.0070.0000.0000.0000.000
216A283TYR00.0500.03037.342-0.001-0.0010.0000.0000.0000.000
217A284ARG10.9230.97335.2630.0090.0090.0000.0000.0000.000