FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 2L24R

Calculation Name: 3BG1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3BG1

Chain ID: A

ChEMBL ID:

UniProt ID: P49687

Base Structure: X-ray

Registration Date: 2023-09-26

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 291
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4097116.117399
FMO2-HF: Nuclear repulsion 3982605.866356
FMO2-HF: Total energy -114510.251043
FMO2-MP2: Total energy -114841.997765


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:14:ASP)


Summations of interaction energy for fragment #1(A:14:ASP)
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.
64.00869.0910.136-2.338-2.880.015
Interaction energy analysis for fragmet #1(A:14:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.963 / q_NPA : -0.986
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].
3A16ILE0-0.033-0.0293.8243.0315.134-0.022-0.959-1.1220.003
4A17HIS0-0.0150.0026.4232.0362.0360.0000.0000.0000.000
5A18ASP-1-0.869-0.9459.30818.63218.6320.0000.0000.0000.000
6A19ALA0-0.010-0.01911.5351.6501.6500.0000.0000.0000.000
7A20GLN00.0320.03113.430-0.773-0.7730.0000.0000.0000.000
8A21MET0-0.051-0.03117.1250.0360.0360.0000.0000.0000.000
9A22ASP-1-0.854-0.90219.42413.06913.0690.0000.0000.0000.000
10A23TYR00.0360.00421.932-0.338-0.3380.0000.0000.0000.000
11A24TYR0-0.057-0.05425.349-0.087-0.0870.0000.0000.0000.000
12A25GLY0-0.0090.00223.491-0.101-0.1010.0000.0000.0000.000
13A26THR0-0.026-0.00623.102-0.246-0.2460.0000.0000.0000.000
14A27ARG10.8600.91319.114-13.246-13.2460.0000.0000.0000.000
15A28LEU00.010-0.01013.673-0.389-0.3890.0000.0000.0000.000
16A29ALA0-0.0050.01914.6821.0761.0760.0000.0000.0000.000
17A30THR0-0.019-0.0258.4730.4600.4600.0000.0000.0000.000
18A31CYS0-0.058-0.0068.970-0.739-0.7390.0000.0000.0000.000
19A32SER00.0690.0034.008-0.245-0.113-0.001-0.032-0.0990.000
20A33SER00.018-0.0102.956-10.812-8.8660.143-1.076-1.0120.010
21A34ASP-1-0.856-0.8993.44247.00147.8750.017-0.269-0.6210.002
22A35ARG10.8320.9165.159-35.880-35.852-0.001-0.002-0.0260.000
23A36SER0-0.037-0.0117.278-4.284-4.2840.0000.0000.0000.000
24A37VAL0-0.026-0.0088.7271.8191.8190.0000.0000.0000.000
25A38LYS10.9220.9805.449-42.854-42.8540.0000.0000.0000.000
26A39ILE00.0490.02011.660-0.008-0.0080.0000.0000.0000.000
27A40PHE0-0.018-0.0169.471-0.308-0.3080.0000.0000.0000.000
28A41ASP-1-0.849-0.93315.45613.39113.3910.0000.0000.0000.000
29A42VAL0-0.0080.00317.7750.3570.3570.0000.0000.0000.000
30A43ARG10.9921.00120.075-12.262-12.2620.0000.0000.0000.000
31A44ASN0-0.050-0.04123.542-0.280-0.2800.0000.0000.0000.000
32A45GLY00.0180.01221.354-0.201-0.2010.0000.0000.0000.000
33A46GLY0-0.038-0.01119.2300.5960.5960.0000.0000.0000.000
34A47GLN0-0.009-0.00712.3850.0430.0430.0000.0000.0000.000
35A48ILE0-0.015-0.01016.3650.0610.0610.0000.0000.0000.000
36A49LEU0-0.057-0.00811.744-0.350-0.3500.0000.0000.0000.000
37A50ILE0-0.004-0.00214.907-0.940-0.9400.0000.0000.0000.000
38A51ALA00.0160.00015.443-0.746-0.7460.0000.0000.0000.000
39A52ASP-1-0.893-0.9629.96729.61229.6120.0000.0000.0000.000
40A53LEU00.0240.01713.168-0.527-0.5270.0000.0000.0000.000
41A54ARG11.0011.0039.129-27.013-27.0130.0000.0000.0000.000
42A55GLY0-0.021-0.02113.456-1.609-1.6090.0000.0000.0000.000
43A56HIS10.8160.93312.406-22.192-22.1920.0000.0000.0000.000
44A57GLU-1-0.912-0.96612.56519.20419.2040.0000.0000.0000.000
45A58GLY0-0.018-0.01411.3560.5930.5930.0000.0000.0000.000
46A59PRO00.0050.0257.608-0.003-0.0030.0000.0000.0000.000
47A60VAL00.0160.0189.168-3.733-3.7330.0000.0000.0000.000
48A61TRP0-0.037-0.0109.3272.6042.6040.0000.0000.0000.000
49A62GLN00.1570.12012.4900.4930.4930.0000.0000.0000.000
50A63VAL0-0.042-0.05013.6910.1020.1020.0000.0000.0000.000
51A64ALA00.0190.02616.380-0.380-0.3800.0000.0000.0000.000
52A65TRP00.0190.00918.061-0.290-0.2900.0000.0000.0000.000
53A66ALA0-0.0250.00021.883-0.401-0.4010.0000.0000.0000.000
54A67HIS00.1030.04725.4120.1730.1730.0000.0000.0000.000
55A68PRO00.0650.02227.474-0.207-0.2070.0000.0000.0000.000
56A69MET0-0.105-0.03329.335-0.317-0.3170.0000.0000.0000.000
57A70TYR0-0.093-0.05629.639-0.335-0.3350.0000.0000.0000.000
58A71GLY0-0.049-0.01529.7840.1710.1710.0000.0000.0000.000
59A72ASN0-0.027-0.01824.6640.0540.0540.0000.0000.0000.000
60A73ILE0-0.019-0.00923.9160.2330.2330.0000.0000.0000.000
61A74LEU00.0220.01816.3470.1450.1450.0000.0000.0000.000
62A75ALA0-0.0060.00220.036-0.001-0.0010.0000.0000.0000.000
63A76SER00.0460.02314.8000.3550.3550.0000.0000.0000.000
64A77CYS00.0100.01916.415-0.634-0.6340.0000.0000.0000.000
65A78SER0-0.024-0.04412.5061.3771.3770.0000.0000.0000.000
66A79TYR0-0.012-0.00912.716-2.001-2.0010.0000.0000.0000.000
67A80ASP-1-0.843-0.94514.55418.74018.7400.0000.0000.0000.000
68A81ARG10.8860.95716.323-17.328-17.3280.0000.0000.0000.000
69A82LYS10.9310.98518.360-16.407-16.4070.0000.0000.0000.000
70A83VAL0-0.0050.01618.3011.0811.0810.0000.0000.0000.000
71A84ILE0-0.074-0.04416.989-0.749-0.7490.0000.0000.0000.000
72A85ILE00.0280.02219.9840.3910.3910.0000.0000.0000.000
73A86TRP0-0.009-0.03616.083-0.490-0.4900.0000.0000.0000.000
74A87ARG10.9410.99021.679-10.794-10.7940.0000.0000.0000.000
75A88GLU-1-0.744-0.88323.49913.20613.2060.0000.0000.0000.000
76A89GLU-1-0.950-0.96825.53210.10810.1080.0000.0000.0000.000
77A90ASN0-0.042-0.02428.679-0.086-0.0860.0000.0000.0000.000
78A91GLY00.0180.02724.715-0.068-0.0680.0000.0000.0000.000
79A92THR0-0.032-0.03023.7760.6230.6230.0000.0000.0000.000
80A93TRP0-0.046-0.01820.1640.0920.0920.0000.0000.0000.000
81A94GLU-1-0.934-0.94821.13412.61212.6120.0000.0000.0000.000
82A95LYS10.9010.94621.276-14.587-14.5870.0000.0000.0000.000
83A96SER0-0.030-0.00823.061-0.469-0.4690.0000.0000.0000.000
84A97HIS00.0260.00525.066-0.528-0.5280.0000.0000.0000.000
85A98GLU-1-0.940-0.97921.41115.31815.3180.0000.0000.0000.000
86A99HIS0-0.009-0.00423.185-0.547-0.5470.0000.0000.0000.000
87A100ALA00.0400.01523.1490.6390.6390.0000.0000.0000.000
88A101GLY0-0.0030.01324.142-0.315-0.3150.0000.0000.0000.000
89A102HIS0-0.086-0.06123.265-0.208-0.2080.0000.0000.0000.000
90A103ASP-1-0.848-0.91623.80312.28612.2860.0000.0000.0000.000
91A104SER0-0.075-0.04320.7710.5280.5280.0000.0000.0000.000
92A105SER0-0.048-0.02216.0810.3060.3060.0000.0000.0000.000
93A106VAL0-0.003-0.01517.453-0.834-0.8340.0000.0000.0000.000
94A107ASN0-0.0100.00216.3260.4290.4290.0000.0000.0000.000
95A108SER0-0.018-0.06216.9110.4850.4850.0000.0000.0000.000
96A109VAL00.006-0.01319.124-0.612-0.6120.0000.0000.0000.000
97A110CYS00.0290.02321.3570.1740.1740.0000.0000.0000.000
98A111TRP00.008-0.00722.646-0.528-0.5280.0000.0000.0000.000
99A112ALA0-0.015-0.01326.473-0.079-0.0790.0000.0000.0000.000
100A113PRO0-0.022-0.02130.1180.0280.0280.0000.0000.0000.000
101A114HIS00.0440.00331.592-0.160-0.1600.0000.0000.0000.000
102A115ASP-1-0.869-0.91832.7778.5948.5940.0000.0000.0000.000
103A116TYR0-0.090-0.04933.991-0.291-0.2910.0000.0000.0000.000
104A117GLY0-0.0050.01334.757-0.186-0.1860.0000.0000.0000.000
105A118LEU0-0.038-0.00928.1270.2030.2030.0000.0000.0000.000
106A119ILE0-0.006-0.01230.4460.1100.1100.0000.0000.0000.000
107A120LEU0-0.022-0.00422.9510.2360.2360.0000.0000.0000.000
108A121ALA0-0.016-0.00426.233-0.250-0.2500.0000.0000.0000.000
109A122CYS0-0.019-0.00722.5670.7640.7640.0000.0000.0000.000
110A123GLY00.0650.02822.447-0.684-0.6840.0000.0000.0000.000
111A124SER0-0.016-0.00121.1580.9150.9150.0000.0000.0000.000
112A125SER00.0310.00619.1550.0560.0560.0000.0000.0000.000
113A126ASP-1-0.861-0.94821.29412.76112.7610.0000.0000.0000.000
114A127GLY00.0190.02724.444-0.507-0.5070.0000.0000.0000.000
115A128ALA0-0.045-0.00525.819-0.628-0.6280.0000.0000.0000.000
116A129ILE00.053-0.00626.1270.4290.4290.0000.0000.0000.000
117A130SER0-0.046-0.00425.950-0.439-0.4390.0000.0000.0000.000
118A131LEU00.0280.00727.7080.2610.2610.0000.0000.0000.000
119A132LEU0-0.0250.00325.898-0.382-0.3820.0000.0000.0000.000
120A133THR00.0030.01229.7120.0390.0390.0000.0000.0000.000
121A134TYR00.0180.00531.2920.1290.1290.0000.0000.0000.000
122A135THR00.0090.00333.060-0.340-0.3400.0000.0000.0000.000
123A136GLY0-0.038-0.02135.6700.0840.0840.0000.0000.0000.000
124A137GLU-1-0.849-0.92235.8468.8038.8030.0000.0000.0000.000
125A138GLY0-0.039-0.00432.2510.2440.2440.0000.0000.0000.000
126A139GLN0-0.058-0.05532.6900.0620.0620.0000.0000.0000.000
127A140TRP00.021-0.00328.5500.1140.1140.0000.0000.0000.000
128A141GLU-1-0.950-0.94832.5378.6998.6990.0000.0000.0000.000
129A142VAL0-0.041-0.04129.2130.3200.3200.0000.0000.0000.000
130A143LYS10.9210.98532.385-9.088-9.0880.0000.0000.0000.000
131A144LYS10.9180.96328.645-10.903-10.9030.0000.0000.0000.000
132A145ILE00.0020.00630.855-0.384-0.3840.0000.0000.0000.000
133A146ASN0-0.034-0.03530.4560.5850.5850.0000.0000.0000.000
134A147ASN00.0020.00130.465-0.145-0.1450.0000.0000.0000.000
135A148ALA00.0410.03328.807-0.286-0.2860.0000.0000.0000.000
136A149HIS10.7420.86026.803-11.819-11.8190.0000.0000.0000.000
137A150THR0-0.024-0.02028.7030.0020.0020.0000.0000.0000.000
138A151ILE0-0.012-0.01623.502-0.121-0.1210.0000.0000.0000.000
139A152GLY00.0770.05922.9280.4830.4830.0000.0000.0000.000
140A153CYS0-0.128-0.06722.543-0.436-0.4360.0000.0000.0000.000
141A154ASN0-0.066-0.04418.9901.1491.1490.0000.0000.0000.000
142A155ALA00.0190.02419.6220.6070.6070.0000.0000.0000.000
143A156VAL00.012-0.00522.084-0.694-0.6940.0000.0000.0000.000
144A157SER00.0210.05023.9580.1630.1630.0000.0000.0000.000
145A158TRP00.027-0.00526.355-0.691-0.6910.0000.0000.0000.000
146A159ALA0-0.013-0.00529.4890.0590.0590.0000.0000.0000.000
147A160PRO0-0.039-0.01832.713-0.001-0.0010.0000.0000.0000.000
148A161ALA00.0450.01033.958-0.212-0.2120.0000.0000.0000.000
149A162VAL0-0.0060.01236.154-0.113-0.1130.0000.0000.0000.000
150A163VAL00.0110.00239.672-0.021-0.0210.0000.0000.0000.000
151A164PRO0-0.0190.01842.800-0.058-0.0580.0000.0000.0000.000
152A165GLY00.032-0.00245.740-0.185-0.1850.0000.0000.0000.000
153A166SER0-0.019-0.01047.1010.0340.0340.0000.0000.0000.000
154A167LEU0-0.014-0.02548.402-0.165-0.1650.0000.0000.0000.000
155A168ILE0-0.038-0.01246.630-0.113-0.1130.0000.0000.0000.000
156A169ASP-1-0.892-0.94546.7706.9566.9560.0000.0000.0000.000
157A170HIS0-0.050-0.03049.171-0.179-0.1790.0000.0000.0000.000
158A171PRO0-0.0120.01452.0240.0500.0500.0000.0000.0000.000
159A172SER0-0.045-0.03752.881-0.058-0.0580.0000.0000.0000.000
160A173GLY00.0240.01851.8620.0660.0660.0000.0000.0000.000
161A174GLN0-0.026-0.02548.2910.1440.1440.0000.0000.0000.000
162A175LYS10.9781.00941.089-7.764-7.7640.0000.0000.0000.000
163A176PRO00.0320.00143.2240.0130.0130.0000.0000.0000.000
164A177ASN00.0190.02443.1480.2850.2850.0000.0000.0000.000
165A178TYR00.019-0.00839.225-0.060-0.0600.0000.0000.0000.000
166A179ILE00.0050.00639.7170.0160.0160.0000.0000.0000.000
167A180LYS10.8650.91236.480-8.481-8.4810.0000.0000.0000.000
168A181ARG10.9770.99235.251-8.253-8.2530.0000.0000.0000.000
169A182PHE0-0.031-0.02429.0470.1300.1300.0000.0000.0000.000
170A183ALA0-0.0140.02629.281-0.113-0.1130.0000.0000.0000.000
171A184SER00.0720.01626.4010.3470.3470.0000.0000.0000.000
172A185GLY00.0870.04125.263-0.418-0.4180.0000.0000.0000.000
173A186GLY00.0250.00323.5480.3520.3520.0000.0000.0000.000
174A187CYS0-0.0080.00621.295-0.004-0.0040.0000.0000.0000.000
175A188ASP-1-0.837-0.92324.22111.09711.0970.0000.0000.0000.000
176A189ASN00.0070.01326.780-0.009-0.0090.0000.0000.0000.000
177A190LEU0-0.047-0.01728.056-0.247-0.2470.0000.0000.0000.000
178A191ILE0-0.004-0.02027.8370.4500.4500.0000.0000.0000.000
179A192LYS10.7980.91529.695-10.253-10.2530.0000.0000.0000.000
180A193LEU00.0150.01130.9850.3410.3410.0000.0000.0000.000
181A194TRP0-0.024-0.01730.840-0.186-0.1860.0000.0000.0000.000
182A195LYS10.9730.97634.570-7.712-7.7120.0000.0000.0000.000
183A196GLU-1-0.835-0.91337.1618.7248.7240.0000.0000.0000.000
184A197GLU-1-0.976-0.97038.5007.3577.3570.0000.0000.0000.000
185A198GLU-1-0.902-0.97341.8977.3437.3430.0000.0000.0000.000
186A199ASP-1-0.953-0.96043.2927.4717.4710.0000.0000.0000.000
187A200GLY00.0050.00041.235-0.015-0.0150.0000.0000.0000.000
188A201GLN0-0.099-0.04538.2330.1490.1490.0000.0000.0000.000
189A202TRP00.0460.01234.879-0.075-0.0750.0000.0000.0000.000
190A203LYS10.8970.95336.983-7.696-7.6960.0000.0000.0000.000
191A204GLU-1-0.862-0.94734.8199.2639.2630.0000.0000.0000.000
192A205GLU-1-0.933-0.96436.5468.1278.1270.0000.0000.0000.000
193A206GLN00.0140.00036.706-0.258-0.2580.0000.0000.0000.000
194A207LYS10.9250.97534.345-8.651-8.6510.0000.0000.0000.000
195A208LEU00.0250.00832.421-0.242-0.2420.0000.0000.0000.000
196A209GLU-1-0.936-0.97432.0099.2239.2230.0000.0000.0000.000
197A210ALA00.0250.01731.866-0.237-0.2370.0000.0000.0000.000
198A211HIS0-0.0530.03827.279-0.057-0.0570.0000.0000.0000.000
199A212SER0-0.018-0.02728.262-0.242-0.2420.0000.0000.0000.000
200A213ASP-1-0.903-0.91924.00813.12413.1240.0000.0000.0000.000
201A214TRP00.016-0.03118.0050.4170.4170.0000.0000.0000.000
202A215VAL0-0.048-0.00223.1330.1270.1270.0000.0000.0000.000
203A216ARG10.8570.91915.810-18.047-18.0470.0000.0000.0000.000
204A217ASP-1-0.786-0.92019.51916.21816.2180.0000.0000.0000.000
205A218VAL0-0.041-0.04121.387-0.688-0.6880.0000.0000.0000.000
206A219ALA0-0.0020.00624.1410.0690.0690.0000.0000.0000.000
207A220TRP00.008-0.00925.966-0.472-0.4720.0000.0000.0000.000
208A221ALA0-0.012-0.00329.4210.0260.0260.0000.0000.0000.000
209A222PRO00.0050.00929.562-0.237-0.2370.0000.0000.0000.000
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