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: 669RZ

Calculation Name: 4BG5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4BG5

Chain ID: A

ChEMBL ID:

UniProt ID: O50954

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 OptH
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 201
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2388680.176208
FMO2-HF: Nuclear repulsion 2306537.930082
FMO2-HF: Total energy -82142.246127
FMO2-MP2: Total energy -82382.179988


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:21:ILE)


Summations of interaction energy for fragment #1(A:21:ILE)
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.
-19.006-10.5724.313-3.579-9.1680.003
Interaction energy analysis for fragmet #1(A:21:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.006 / q_NPA : -0.001
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].
3A23LYS10.9370.9773.416-10.913-7.9530.099-1.344-1.7150.009
4A24LEU00.0630.0232.665-3.139-1.6840.578-0.406-1.6270.000
5A25PHE00.0080.0033.538-1.501-0.5070.063-0.274-0.783-0.002
6A26GLU-1-0.899-0.9496.3440.8980.8980.0000.0000.0000.000
7A27ILE0-0.007-0.0096.540-0.109-0.1090.0000.0000.0000.000
8A28LEU00.0020.0138.380-0.088-0.0880.0000.0000.0000.000
9A29ALA0-0.029-0.01910.271-0.007-0.0070.0000.0000.0000.000
10A30ARG10.8570.93610.949-0.715-0.7150.0000.0000.0000.000
11A31GLU-1-0.854-0.95713.1400.3120.3120.0000.0000.0000.000
12A32MET00.0230.01413.756-0.041-0.0410.0000.0000.0000.000
13A33THR0-0.086-0.02415.678-0.029-0.0290.0000.0000.0000.000
14A34ILE00.005-0.00516.917-0.012-0.0120.0000.0000.0000.000
15A35ILE00.0560.02517.790-0.008-0.0080.0000.0000.0000.000
16A36LYS10.9380.97020.1690.0690.0690.0000.0000.0000.000
17A37LYS10.9240.95821.919-0.125-0.1250.0000.0000.0000.000
18A38GLU-1-0.878-0.95122.5250.0970.0970.0000.0000.0000.000
19A39LYS10.8400.92321.9740.0440.0440.0000.0000.0000.000
20A40LEU0-0.026-0.00525.919-0.006-0.0060.0000.0000.0000.000
21A41GLN0-0.0080.01628.574-0.002-0.0020.0000.0000.0000.000
22A42THR0-0.0040.00330.667-0.004-0.0040.0000.0000.0000.000
23A43GLU-1-0.785-0.83033.8280.0220.0220.0000.0000.0000.000
24A44ILE00.0070.01235.213-0.004-0.0040.0000.0000.0000.000
25A45PRO00.0590.02038.7630.0000.0000.0000.0000.0000.000
26A46SER0-0.040-0.04541.1230.0000.0000.0000.0000.0000.000
27A47GLN00.0600.01437.5910.0030.0030.0000.0000.0000.000
28A48PHE00.003-0.00734.7260.0020.0020.0000.0000.0000.000
29A49GLY00.0300.02338.4710.0040.0040.0000.0000.0000.000
30A50LEU00.0350.02135.301-0.001-0.0010.0000.0000.0000.000
31A51LYS10.9410.99039.498-0.014-0.0140.0000.0000.0000.000
32A52ASN0-0.031-0.02741.255-0.001-0.0010.0000.0000.0000.000
33A53SER0-0.031-0.05341.0310.0000.0000.0000.0000.0000.000
34A54MET00.0220.02334.606-0.002-0.0020.0000.0000.0000.000
35A55PHE0-0.028-0.03733.883-0.002-0.0020.0000.0000.0000.000
36A56GLU-1-0.931-0.96038.7200.0100.0100.0000.0000.0000.000
37A57LEU0-0.0230.00139.377-0.002-0.0020.0000.0000.0000.000
38A58LEU0-0.048-0.02834.701-0.002-0.0020.0000.0000.0000.000
39A59ASN0-0.010-0.01938.109-0.004-0.0040.0000.0000.0000.000
40A60VAL0-0.0100.02033.1580.0000.0000.0000.0000.0000.000
41A61TYR00.0300.00934.821-0.003-0.0030.0000.0000.0000.000
42A62LYS10.9570.99031.1590.0440.0440.0000.0000.0000.000
43A71LEU00.003-0.01338.1210.0000.0000.0000.0000.0000.000
44A72GLN0-0.004-0.02938.6120.0040.0040.0000.0000.0000.000
45A73GLU-1-0.925-0.93439.180-0.013-0.0130.0000.0000.0000.000
46A74LYS10.9310.97239.583-0.006-0.0060.0000.0000.0000.000
47A75MET0-0.053-0.01333.424-0.002-0.0020.0000.0000.0000.000
48A76ASN00.024-0.00736.872-0.002-0.0020.0000.0000.0000.000
49A77SER0-0.0170.00738.939-0.002-0.0020.0000.0000.0000.000
50A78SER00.041-0.00638.5320.0020.0020.0000.0000.0000.000
51A79LEU00.0270.04135.981-0.003-0.0030.0000.0000.0000.000
52A80ALA00.0540.01132.8380.0030.0030.0000.0000.0000.000
53A81GLU-1-0.875-0.95131.223-0.033-0.0330.0000.0000.0000.000
54A82SER0-0.048-0.01731.3110.0050.0050.0000.0000.0000.000
55A83GLN00.0100.00932.5570.0080.0080.0000.0000.0000.000
56A84LYS10.8940.94825.5260.0470.0470.0000.0000.0000.000
57A85MET00.010-0.00528.4830.0070.0070.0000.0000.0000.000
58A86ARG10.8170.90530.066-0.001-0.0010.0000.0000.0000.000
59A87ARG10.7910.89123.682-0.010-0.0100.0000.0000.0000.000
60A88GLN0-0.006-0.00224.2040.0140.0140.0000.0000.0000.000
61A89PHE00.0630.03226.1490.0130.0130.0000.0000.0000.000
62A90TYR0-0.010-0.01928.4330.0120.0120.0000.0000.0000.000
63A91SER0-0.036-0.03823.6790.0040.0040.0000.0000.0000.000
64A92SER0-0.021-0.00923.8450.0190.0190.0000.0000.0000.000
65A93LEU0-0.004-0.01524.6150.0190.0190.0000.0000.0000.000
66A94SER0-0.034-0.02023.3130.0080.0080.0000.0000.0000.000
67A95TYR0-0.067-0.04825.101-0.005-0.0050.0000.0000.0000.000
68A96ASN0-0.012-0.00828.390-0.013-0.0130.0000.0000.0000.000
69A97THR0-0.011-0.02030.091-0.001-0.0010.0000.0000.0000.000
70A98THR0-0.004-0.00133.469-0.006-0.0060.0000.0000.0000.000
71A99ASP-1-0.718-0.83030.3630.1120.1120.0000.0000.0000.000
72A100ILE0-0.047-0.01530.360-0.004-0.0040.0000.0000.0000.000
73A101PHE0-0.022-0.02034.105-0.007-0.0070.0000.0000.0000.000
74A102ASN0-0.025-0.03036.3150.0020.0020.0000.0000.0000.000
75A103LEU00.0660.03532.780-0.001-0.0010.0000.0000.0000.000
76A104ALA0-0.040-0.00636.641-0.004-0.0040.0000.0000.0000.000
77A105GLU-1-0.952-0.96839.0060.0580.0580.0000.0000.0000.000
78A106ILE00.0330.02037.958-0.004-0.0040.0000.0000.0000.000
79A107VAL00.019-0.00837.175-0.004-0.0040.0000.0000.0000.000
80A108ASN00.0480.05940.327-0.005-0.0050.0000.0000.0000.000
81A109LYS10.8320.92743.575-0.055-0.0550.0000.0000.0000.000
82A110LEU00.0500.00740.026-0.002-0.0020.0000.0000.0000.000
83A111TYR0-0.024-0.01043.452-0.002-0.0020.0000.0000.0000.000
84A112LYS10.8990.96244.921-0.041-0.0410.0000.0000.0000.000
85A113ASP-1-0.856-0.92747.1570.0360.0360.0000.0000.0000.000
86A114PRO00.022-0.01246.3760.0020.0020.0000.0000.0000.000
87A115LYS10.8970.96545.816-0.032-0.0320.0000.0000.0000.000
88A116ALA00.0580.04743.3150.0020.0020.0000.0000.0000.000
89A117HIS0-0.031-0.02442.2600.0000.0000.0000.0000.0000.000
90A118ASP-1-0.896-0.96338.7730.0490.0490.0000.0000.0000.000
91A119THR0-0.015-0.05737.8320.0030.0030.0000.0000.0000.000
92A120ILE00.0050.01436.7590.0040.0040.0000.0000.0000.000
93A121LYS10.9320.97136.091-0.030-0.0300.0000.0000.0000.000
94A122LYS10.8710.95533.246-0.056-0.0560.0000.0000.0000.000
95A123ILE00.0610.03131.8330.0050.0050.0000.0000.0000.000
96A124SER0-0.038-0.02031.6150.0020.0020.0000.0000.0000.000
97A125GLY00.024-0.00229.135-0.007-0.0070.0000.0000.0000.000
98A126GLY00.0760.03826.4520.0060.0060.0000.0000.0000.000
99A127ILE0-0.045-0.01825.5880.0030.0030.0000.0000.0000.000
100A128ARG10.9050.95525.371-0.039-0.0390.0000.0000.0000.000
101A129ILE00.0690.03321.486-0.004-0.0040.0000.0000.0000.000
102A130GLN00.0160.01220.9370.0110.0110.0000.0000.0000.000
103A131GLN0-0.065-0.03720.750-0.012-0.0120.0000.0000.0000.000
104A132GLY00.0840.03020.023-0.019-0.0190.0000.0000.0000.000
105A133PHE00.0320.01214.738-0.016-0.0160.0000.0000.0000.000
106A134GLU-1-0.843-0.94116.104-0.016-0.0160.0000.0000.0000.000
107A135VAL00.0200.02016.859-0.028-0.0280.0000.0000.0000.000
108A136ALA00.0240.01813.588-0.035-0.0350.0000.0000.0000.000
109A137LEU0-0.044-0.03312.090-0.059-0.0590.0000.0000.0000.000
110A138GLU-1-1.006-0.98312.608-0.222-0.2220.0000.0000.0000.000
111A139ASP-1-0.855-0.94913.297-0.279-0.2790.0000.0000.0000.000
112A140LEU0-0.070-0.0216.343-0.109-0.1090.0000.0000.0000.000
113A141ALA0-0.020-0.0298.548-0.223-0.2230.0000.0000.0000.000
114A142ILE0-0.0200.0029.745-0.105-0.1050.0000.0000.0000.000
115A143ASN0-0.026-0.0189.112-0.062-0.0620.0000.0000.0000.000
116A144MET0-0.051-0.0094.183-0.993-0.5800.022-0.076-0.3590.000
117A145ASP-1-0.871-0.9524.482-1.551-1.464-0.001-0.007-0.0790.000
118A146LYS10.9600.9776.5110.4620.4620.0000.0000.0000.000
119A147LEU0-0.034-0.0173.327-0.2980.0610.017-0.071-0.3050.000
120A148LYS10.8950.9442.362-1.3810.4952.571-1.682-2.765-0.004
121A149ALA0-0.0140.0143.2850.5330.0950.0090.623-0.1940.000
122A150ASN0-0.031-0.0206.064-0.142-0.1420.0000.0000.0000.000
123A151ASP-1-0.949-0.9727.017-0.459-0.4590.0000.0000.0000.000
124A152PHE00.0030.0145.2220.1420.1420.0000.0000.0000.000
125A153ASN0-0.013-0.0187.398-0.054-0.0540.0000.0000.0000.000
126A154LYS11.0561.0117.1070.3550.3550.0000.0000.0000.000
127A155ASN0-0.045-0.0188.1760.0700.0700.0000.0000.0000.000
128A156THR00.0210.0209.3250.0670.0670.0000.0000.0000.000
129A157LEU00.0140.0102.303-0.898-0.1700.955-0.342-1.3410.000
130A158GLU-1-0.980-0.9866.6420.8690.8690.0000.0000.0000.000
131A159GLU-1-0.889-0.9507.6270.1910.1910.0000.0000.0000.000
132A160ILE00.0320.0067.6160.0850.0850.0000.0000.0000.000
133A161TYR0-0.038-0.0184.8780.6560.6560.0000.0000.0000.000
134A162ASN00.017-0.0057.2540.2830.2830.0000.0000.0000.000
135A163LEU00.0270.03110.636-0.025-0.0250.0000.0000.0000.000
136A164ILE0-0.005-0.0048.200-0.009-0.0090.0000.0000.0000.000
137A165VAL00.0180.0129.202-0.024-0.0240.0000.0000.0000.000
138A166ASP-1-0.828-0.87011.6150.3800.3800.0000.0000.0000.000
139A167LEU0-0.037-0.01014.011-0.067-0.0670.0000.0000.0000.000
140A168THR0-0.135-0.12411.897-0.003-0.0030.0000.0000.0000.000
141A169LEU0-0.038-0.02915.061-0.025-0.0250.0000.0000.0000.000
142A170ILE00.0210.01417.203-0.041-0.0410.0000.0000.0000.000
143A171LYS10.8740.95518.595-0.198-0.1980.0000.0000.0000.000
144A172LYS10.9290.96117.042-0.449-0.4490.0000.0000.0000.000
145A173GLU-1-0.891-0.94321.0620.2530.2530.0000.0000.0000.000
146A174TRP0-0.0080.00823.264-0.023-0.0230.0000.0000.0000.000
147A175LEU0-0.0080.01423.990-0.014-0.0140.0000.0000.0000.000
148A176SER00.0160.01725.220-0.017-0.0170.0000.0000.0000.000
149A177THR0-0.0170.00526.894-0.015-0.0150.0000.0000.0000.000
150A178ILE0-0.023-0.01628.889-0.013-0.0130.0000.0000.0000.000
151A179GLU-1-0.899-0.94128.6810.1540.1540.0000.0000.0000.000
152A180THR0-0.070-0.06530.412-0.006-0.0060.0000.0000.0000.000
153A181LEU0-0.018-0.00932.996-0.009-0.0090.0000.0000.0000.000
154A182ILE0-0.015-0.02133.464-0.007-0.0070.0000.0000.0000.000
155A183LYS10.9440.99635.788-0.106-0.1060.0000.0000.0000.000
156A184SER0-0.123-0.11837.473-0.004-0.0040.0000.0000.0000.000
157A185SER00.015-0.00638.643-0.006-0.0060.0000.0000.0000.000
158A186ASN0-0.032-0.01940.692-0.002-0.0020.0000.0000.0000.000
159A187ALA0-0.0250.00242.0020.0000.0000.0000.0000.0000.000
160A188THR00.017-0.00143.748-0.002-0.0020.0000.0000.0000.000
161A189LEU00.0380.00547.397-0.001-0.0010.0000.0000.0000.000
162A190GLU-1-0.811-0.92349.9160.0470.0470.0000.0000.0000.000
163A191LEU0-0.0120.00343.106-0.002-0.0020.0000.0000.0000.000
164A192GLN0-0.0240.00745.3340.0030.0030.0000.0000.0000.000
165A193TYR0-0.075-0.03646.865-0.002-0.0020.0000.0000.0000.000
166A194ASN0-0.026-0.01149.984-0.003-0.0030.0000.0000.0000.000
167A195THR0-0.014-0.01245.9560.0020.0020.0000.0000.0000.000
168A196GLU-1-0.931-0.94946.5660.0470.0470.0000.0000.0000.000
169A197LYS10.9740.98347.080-0.050-0.0500.0000.0000.0000.000
170A198LEU0-0.016-0.00241.6400.0040.0040.0000.0000.0000.000
171A199ASN00.0560.03842.0230.0060.0060.0000.0000.0000.000
172A200ASP-1-0.867-0.91441.8340.0590.0590.0000.0000.0000.000
173A201HIS00.0250.06239.8010.0080.0080.0000.0000.0000.000
174A202ILE00.0260.06936.7370.0060.0060.0000.0000.0000.000
175A203GLU-1-0.930-0.98337.4690.0620.0620.0000.0000.0000.000
176A204GLN0-0.030-0.02438.1380.0030.0030.0000.0000.0000.000
177A205THR0-0.101-0.09736.2730.0030.0030.0000.0000.0000.000
178A206TYR00.003-0.01932.6870.0110.0110.0000.0000.0000.000
179A207LYS10.8810.95632.765-0.057-0.0570.0000.0000.0000.000
180A208ASP-1-0.833-0.91633.0460.0910.0910.0000.0000.0000.000
181A209THR00.010-0.00728.4180.0010.0010.0000.0000.0000.000
182A210MET0-0.031-0.00528.3480.0060.0060.0000.0000.0000.000
183A211ILE0-0.011-0.00629.021-0.005-0.0050.0000.0000.0000.000
184A212SER0-0.020-0.00527.2940.0050.0050.0000.0000.0000.000
185A213LEU00.0090.00823.3370.0040.0040.0000.0000.0000.000
186A214CYS0-0.039-0.02323.975-0.001-0.0010.0000.0000.0000.000
187A215LEU00.0260.01125.068-0.007-0.0070.0000.0000.0000.000
188A216LYS10.9891.00120.388-0.268-0.2680.0000.0000.0000.000
189A217SER00.0290.02320.1390.0060.0060.0000.0000.0000.000
190A218GLU-1-1.055-1.01420.4460.0360.0360.0000.0000.0000.000
191A219GLN00.063-0.01221.222-0.019-0.0190.0000.0000.0000.000
192A220THR0-0.0130.01215.5960.0010.0010.0000.0000.0000.000
193A221LEU0-0.0050.02516.968-0.017-0.0170.0000.0000.0000.000
194A222LEU00.0100.01517.641-0.030-0.0300.0000.0000.0000.000
195A223HIS0-0.0130.00416.652-0.012-0.0120.0000.0000.0000.000
196A224LEU00.024-0.00911.214-0.025-0.0250.0000.0000.0000.000
197A225ASP-1-0.881-0.92514.506-0.198-0.1980.0000.0000.0000.000
198A226THR0-0.055-0.03316.352-0.038-0.0380.0000.0000.0000.000
199A227LEU0-0.009-0.01411.870-0.035-0.0350.0000.0000.0000.000
200A228PHE0-0.055-0.0179.001-0.088-0.0880.0000.0000.0000.000
201A229LYS10.7590.88212.9900.1300.1300.0000.0000.0000.000