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: 3JZKL

Calculation Name: 1BOL-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1BOL

Chain ID: A

ChEMBL ID:

UniProt ID: P08056

Base Structure: X-ray

Registration Date: 2023-09-23

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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2544827.648483
FMO2-HF: Nuclear repulsion 2457297.084606
FMO2-HF: Total energy -87530.563877
FMO2-MP2: Total energy -87776.750031


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:1:SER)


Summations of interaction energy for fragment #1(A:1:SER)
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.
4.8546.71-0.011-1.068-0.7770
Interaction energy analysis for fragmet #1(A:1:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / q_NPA : -0.014
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].
3A3CYS00.0120.0024.0300.1712.027-0.011-1.068-0.7770.000
4A4SER0-0.011-0.0297.583-0.348-0.3480.0000.0000.0000.000
5A5SER00.0540.0159.7420.1940.1940.0000.0000.0000.000
6A6THR0-0.076-0.02812.2960.0380.0380.0000.0000.0000.000
7A7ALA0-0.0090.01414.0170.0490.0490.0000.0000.0000.000
8A8LEU00.0150.01215.7760.0020.0020.0000.0000.0000.000
9A9SER00.0000.00319.0130.0060.0060.0000.0000.0000.000
10A10CYS0-0.014-0.00320.535-0.016-0.0160.0000.0000.0000.000
11A11SER00.0370.00520.920-0.025-0.0250.0000.0000.0000.000
12A12ASN0-0.018-0.02821.6910.0250.0250.0000.0000.0000.000
13A13SER0-0.034-0.01417.856-0.015-0.0150.0000.0000.0000.000
14A14ALA0-0.0160.01816.753-0.028-0.0280.0000.0000.0000.000
15A15ASN0-0.033-0.03211.9040.0930.0930.0000.0000.0000.000
16A16SER00.018-0.02414.5740.0130.0130.0000.0000.0000.000
17A17ASP-1-0.813-0.8689.9811.0701.0700.0000.0000.0000.000
18A18THR00.002-0.00813.206-0.024-0.0240.0000.0000.0000.000
19A19CYS0-0.0550.00811.3400.0750.0750.0000.0000.0000.000
20A21SER0-0.010-0.00611.813-0.175-0.1750.0000.0000.0000.000
21A22PRO0-0.049-0.01415.4530.0460.0460.0000.0000.0000.000
22A23GLU-1-0.913-0.94818.4450.2110.2110.0000.0000.0000.000
23A24TYR0-0.081-0.04520.835-0.043-0.0430.0000.0000.0000.000
24A25GLY00.015-0.01121.911-0.001-0.0010.0000.0000.0000.000
25A26LEU00.0550.05822.934-0.021-0.0210.0000.0000.0000.000
26A27VAL0-0.001-0.00622.7990.0140.0140.0000.0000.0000.000
27A28VAL00.0040.00826.157-0.016-0.0160.0000.0000.0000.000
28A29LEU00.0020.00127.5450.0120.0120.0000.0000.0000.000
29A30ASN0-0.021-0.01529.854-0.012-0.0120.0000.0000.0000.000
30A31MET00.0560.01832.6450.0060.0060.0000.0000.0000.000
31A32GLN00.0290.02035.1940.0000.0000.0000.0000.0000.000
32A33TRP0-0.086-0.04638.845-0.001-0.0010.0000.0000.0000.000
33A34ALA00.0560.02641.7870.0000.0000.0000.0000.0000.000
34A35PRO0-0.030-0.03943.5390.0010.0010.0000.0000.0000.000
35A36GLY00.0140.02546.4100.0020.0020.0000.0000.0000.000
36A37TYR0-0.055-0.02041.1860.0030.0030.0000.0000.0000.000
37A38GLY00.0710.03439.551-0.002-0.0020.0000.0000.0000.000
38A39PRO0-0.033-0.01437.825-0.002-0.0020.0000.0000.0000.000
39A40ASP-1-0.882-0.94341.0000.0140.0140.0000.0000.0000.000
40A41ASN0-0.039-0.02139.4950.0010.0010.0000.0000.0000.000
41A42ALA0-0.033-0.02136.581-0.003-0.0030.0000.0000.0000.000
42A43PHE00.0790.06136.3650.0020.0020.0000.0000.0000.000
43A44THR0-0.011-0.00535.540-0.001-0.0010.0000.0000.0000.000
44A45LEU0-0.071-0.04629.075-0.004-0.0040.0000.0000.0000.000
45A46HIS0-0.0380.00733.6340.0000.0000.0000.0000.0000.000
46A47GLY0-0.009-0.02930.6870.0080.0080.0000.0000.0000.000
47A48LEU0-0.0180.02123.485-0.011-0.0110.0000.0000.0000.000
48A49TRP0-0.058-0.05227.4640.0120.0120.0000.0000.0000.000
49A50PRO00.0090.01524.227-0.013-0.0130.0000.0000.0000.000
50A51ASP-1-0.793-0.90526.2620.0790.0790.0000.0000.0000.000
51A52LYS10.9250.94926.569-0.113-0.1130.0000.0000.0000.000
52A54SER0-0.054-0.01527.925-0.007-0.0070.0000.0000.0000.000
53A55GLY00.0480.00430.516-0.005-0.0050.0000.0000.0000.000
54A56ALA0-0.092-0.02632.1880.0020.0020.0000.0000.0000.000
55A57TYR0-0.013-0.00731.3110.0040.0040.0000.0000.0000.000
56A58ALA00.0630.03928.3300.0020.0020.0000.0000.0000.000
57A59PRO0-0.036-0.03329.132-0.009-0.0090.0000.0000.0000.000
58A60SER00.0030.00631.9440.0050.0050.0000.0000.0000.000
59A61GLY0-0.059-0.02933.836-0.003-0.0030.0000.0000.0000.000
60A62GLY00.0130.00429.6730.0070.0070.0000.0000.0000.000
61A63CYS0-0.136-0.04823.4290.0050.0050.0000.0000.0000.000
62A64ASP-1-0.736-0.87524.0780.3040.3040.0000.0000.0000.000
63A65SER0-0.028-0.02126.925-0.008-0.0080.0000.0000.0000.000
64A66ASN0-0.069-0.03126.791-0.021-0.0210.0000.0000.0000.000
65A67ARG10.8650.92921.104-0.337-0.3370.0000.0000.0000.000
66A68ALA0-0.0100.02126.851-0.008-0.0080.0000.0000.0000.000
67A69SER00.005-0.00829.777-0.001-0.0010.0000.0000.0000.000
68A70SER00.004-0.00131.698-0.006-0.0060.0000.0000.0000.000
69A71SER0-0.043-0.02433.203-0.010-0.0100.0000.0000.0000.000
70A72ILE00.0820.05628.3910.0030.0030.0000.0000.0000.000
71A73ALA00.013-0.00231.0260.0010.0010.0000.0000.0000.000
72A74SER0-0.074-0.04232.979-0.001-0.0010.0000.0000.0000.000
73A75VAL00.0740.05127.0370.0000.0000.0000.0000.0000.000
74A76ILE00.0390.01227.2190.0050.0050.0000.0000.0000.000
75A77LYS10.8510.94128.851-0.099-0.0990.0000.0000.0000.000
76A78SER0-0.070-0.04129.999-0.001-0.0010.0000.0000.0000.000
77A79LYS10.8400.93520.681-0.320-0.3200.0000.0000.0000.000
78A80ASP-1-0.851-0.94725.1360.1240.1240.0000.0000.0000.000
79A81SER00.0310.02727.272-0.009-0.0090.0000.0000.0000.000
80A82SER0-0.006-0.00827.958-0.014-0.0140.0000.0000.0000.000
81A83LEU00.0510.05424.828-0.012-0.0120.0000.0000.0000.000
82A84TYR0-0.008-0.03728.309-0.008-0.0080.0000.0000.0000.000
83A85ASN0-0.013-0.02231.417-0.006-0.0060.0000.0000.0000.000
84A86SER0-0.019-0.00930.129-0.010-0.0100.0000.0000.0000.000
85A87MET00.0270.01629.651-0.004-0.0040.0000.0000.0000.000
86A88LEU0-0.062-0.01732.689-0.004-0.0040.0000.0000.0000.000
87A89THR0-0.049-0.01035.364-0.006-0.0060.0000.0000.0000.000
88A90TYR00.005-0.02832.715-0.007-0.0070.0000.0000.0000.000
89A91TRP00.0160.01727.741-0.001-0.0010.0000.0000.0000.000
90A92PRO0-0.0140.00234.3600.0060.0060.0000.0000.0000.000
91A93SER00.0060.01437.899-0.002-0.0020.0000.0000.0000.000
92A94ASN0-0.004-0.01639.394-0.002-0.0020.0000.0000.0000.000
93A95GLN0-0.018-0.03042.186-0.001-0.0010.0000.0000.0000.000
94A96GLY0-0.0200.01243.3980.0010.0010.0000.0000.0000.000
95A97ASN00.001-0.02040.5350.0050.0050.0000.0000.0000.000
96A98ASN00.0890.04236.7160.0000.0000.0000.0000.0000.000
97A99ASN00.0160.01435.3790.0090.0090.0000.0000.0000.000
98A100VAL0-0.014-0.00235.7390.0070.0070.0000.0000.0000.000
99A101PHE00.0090.02436.2360.0050.0050.0000.0000.0000.000
100A102TRP00.026-0.02031.6840.0070.0070.0000.0000.0000.000
101A103SER00.009-0.00231.5180.0120.0120.0000.0000.0000.000
102A104HIS00.0140.02432.1840.0130.0130.0000.0000.0000.000
103A105GLU-1-0.772-0.90030.5570.0960.0960.0000.0000.0000.000
104A106TRP00.0110.00422.365-0.006-0.0060.0000.0000.0000.000
105A107SER0-0.008-0.02727.8310.0130.0130.0000.0000.0000.000
106A108LYS10.8460.93529.678-0.104-0.1040.0000.0000.0000.000
107A109HIS10.8500.93328.097-0.105-0.1050.0000.0000.0000.000
108A110GLY00.0640.03124.7910.0050.0050.0000.0000.0000.000
109A111THR0-0.040-0.02123.3450.0160.0160.0000.0000.0000.000
110A113VAL0-0.008-0.00118.922-0.015-0.0150.0000.0000.0000.000
111A114SER0-0.009-0.03217.135-0.002-0.0020.0000.0000.0000.000
112A115THR0-0.0060.00014.2760.0530.0530.0000.0000.0000.000
113A116TYR0-0.038-0.02514.5640.0330.0330.0000.0000.0000.000
114A117ASP-1-0.859-0.92716.6840.4730.4730.0000.0000.0000.000
115A118PRO00.013-0.02415.8980.0670.0670.0000.0000.0000.000
116A119ASP-1-0.925-0.94815.1570.7190.7190.0000.0000.0000.000
117A121TYR0-0.098-0.05410.6680.1650.1650.0000.0000.0000.000
118A122ASP-1-0.924-0.9518.5331.5621.5620.0000.0000.0000.000
119A123ASN0-0.120-0.09510.691-0.183-0.1830.0000.0000.0000.000
120A124TYR0-0.008-0.00313.820-0.101-0.1010.0000.0000.0000.000
121A125GLU-1-0.899-0.92216.4810.3090.3090.0000.0000.0000.000
122A126GLU-1-0.927-0.98219.9400.2540.2540.0000.0000.0000.000
123A127GLY0-0.008-0.01622.666-0.024-0.0240.0000.0000.0000.000
124A128GLU-1-0.876-0.95615.6660.5180.5180.0000.0000.0000.000
125A129ASP-1-0.725-0.82418.8210.3160.3160.0000.0000.0000.000
126A130ILE0-0.044-0.02119.721-0.035-0.0350.0000.0000.0000.000
127A131VAL00.007-0.00621.638-0.030-0.0300.0000.0000.0000.000
128A132ASP-1-0.794-0.88116.1200.3080.3080.0000.0000.0000.000
129A133TYR0-0.028-0.01019.782-0.036-0.0360.0000.0000.0000.000
130A134PHE0-0.051-0.04122.102-0.027-0.0270.0000.0000.0000.000
131A135GLN0-0.022-0.02621.589-0.014-0.0140.0000.0000.0000.000
132A136LYS10.8610.93617.415-0.069-0.0690.0000.0000.0000.000
133A137ALA00.017-0.00422.041-0.023-0.0230.0000.0000.0000.000
134A138MET0-0.062-0.02525.593-0.018-0.0180.0000.0000.0000.000
135A139ASP-1-0.856-0.91321.8980.0420.0420.0000.0000.0000.000
136A140LEU0-0.013-0.00322.940-0.018-0.0180.0000.0000.0000.000
137A141ARG10.9230.96526.132-0.039-0.0390.0000.0000.0000.000
138A142SER0-0.078-0.04227.964-0.004-0.0040.0000.0000.0000.000
139A143GLN0-0.0360.00323.5160.0010.0010.0000.0000.0000.000
140A144TYR0-0.038-0.02925.019-0.012-0.0120.0000.0000.0000.000
141A145ASN00.0290.01230.3760.0080.0080.0000.0000.0000.000
142A146VAL00.0630.02933.684-0.005-0.0050.0000.0000.0000.000
143A147TYR00.0490.03036.372-0.001-0.0010.0000.0000.0000.000
144A148LYS10.8610.94535.9500.0340.0340.0000.0000.0000.000
145A149ALA00.0400.01936.387-0.003-0.0030.0000.0000.0000.000
146A150PHE0-0.0050.01338.301-0.002-0.0020.0000.0000.0000.000
147A151SER00.0140.00041.253-0.002-0.0020.0000.0000.0000.000
148A152SER0-0.068-0.02640.316-0.001-0.0010.0000.0000.0000.000
149A153ASN0-0.101-0.06140.604-0.005-0.0050.0000.0000.0000.000
150A154GLY0-0.0010.00744.3660.0010.0010.0000.0000.0000.000
151A155ILE0-0.0160.00444.3510.0020.0020.0000.0000.0000.000
152A156THR00.000-0.01844.813-0.001-0.0010.0000.0000.0000.000
153A157PRO0-0.018-0.01345.1330.0010.0010.0000.0000.0000.000
154A158GLY0-0.053-0.01947.787-0.001-0.0010.0000.0000.0000.000
155A159GLY00.0060.00850.995-0.001-0.0010.0000.0000.0000.000
156A160THR0-0.035-0.02051.4940.0020.0020.0000.0000.0000.000
157A161TYR00.0110.00648.703-0.002-0.0020.0000.0000.0000.000
158A162THR00.0100.00649.8700.0010.0010.0000.0000.0000.000
159A163ALA00.040-0.01346.768-0.001-0.0010.0000.0000.0000.000
160A164THR0-0.030-0.01445.608-0.001-0.0010.0000.0000.0000.000
161A165GLU-1-0.865-0.93245.980-0.013-0.0130.0000.0000.0000.000
162A166MET00.0120.01443.670-0.002-0.0020.0000.0000.0000.000
163A167GLN00.0300.00439.390-0.003-0.0030.0000.0000.0000.000
164A168SER0-0.0070.00540.779-0.004-0.0040.0000.0000.0000.000
165A169ALA0-0.0010.01941.189-0.004-0.0040.0000.0000.0000.000
166A170ILE0-0.0090.00336.067-0.003-0.0030.0000.0000.0000.000
167A171GLU-1-0.804-0.89536.535-0.030-0.0300.0000.0000.0000.000
168A172SER0-0.092-0.05836.709-0.006-0.0060.0000.0000.0000.000
169A173TYR0-0.038-0.00633.570-0.006-0.0060.0000.0000.0000.000
170A174PHE0-0.035-0.04031.162-0.004-0.0040.0000.0000.0000.000
171A175GLY0-0.0190.00831.803-0.006-0.0060.0000.0000.0000.000
172A176ALA0-0.017-0.01232.087-0.003-0.0030.0000.0000.0000.000
173A177LYS10.7960.88534.2130.0270.0270.0000.0000.0000.000
174A178ALA00.0350.01834.9880.0020.0020.0000.0000.0000.000
175A179LYS10.8170.90936.411-0.026-0.0260.0000.0000.0000.000
176A180ILE00.004-0.01338.2790.0030.0030.0000.0000.0000.000
177A181ASP-1-0.770-0.86540.4280.0230.0230.0000.0000.0000.000
178A182CYS0-0.050-0.00143.029-0.002-0.0020.0000.0000.0000.000
179A183SER00.0270.02146.3230.0030.0030.0000.0000.0000.000
180A184SER0-0.076-0.05648.524-0.001-0.0010.0000.0000.0000.000
181A185GLY00.0370.02550.981-0.001-0.0010.0000.0000.0000.000
182A186THR00.0230.02748.468-0.002-0.0020.0000.0000.0000.000
183A187LEU0-0.018-0.02742.1430.0010.0010.0000.0000.0000.000
184A188SER0-0.042-0.03443.1070.0000.0000.0000.0000.0000.000
185A189ASP-1-0.848-0.91738.6190.0370.0370.0000.0000.0000.000
186A190VAL00.0020.00136.238-0.004-0.0040.0000.0000.0000.000
187A191ALA0-0.028-0.00333.7580.0040.0040.0000.0000.0000.000
188A192LEU00.0050.00430.666-0.007-0.0070.0000.0000.0000.000
189A193TYR00.0510.02129.6030.0090.0090.0000.0000.0000.000
190A194PHE0-0.022-0.01924.496-0.011-0.0110.0000.0000.0000.000
191A195TYR00.0250.02022.9320.0150.0150.0000.0000.0000.000
192A196VAL00.0160.01017.185-0.009-0.0090.0000.0000.0000.000
193A197ARG10.9380.97416.7530.1860.1860.0000.0000.0000.000
194A198GLY0-0.028-0.01413.357-0.026-0.0260.0000.0000.0000.000
195A199ARG10.9030.95110.894-0.356-0.3560.0000.0000.0000.000
196A200ASP-1-0.812-0.90913.3460.1540.1540.0000.0000.0000.000
197A201THR00.0140.01915.688-0.013-0.0130.0000.0000.0000.000
198A202TYR0-0.005-0.00818.0830.0020.0020.0000.0000.0000.000
199A203VAL0-0.047-0.02521.131-0.022-0.0220.0000.0000.0000.000
200A204ILE0-0.0030.00423.7730.0120.0120.0000.0000.0000.000
201A205THR0-0.004-0.01027.441-0.013-0.0130.0000.0000.0000.000
202A206ASP-1-0.886-0.93929.734-0.025-0.0250.0000.0000.0000.000
203A207ALA0-0.0190.00333.0410.0050.0050.0000.0000.0000.000
204A208LEU0-0.045-0.01532.139-0.002-0.0020.0000.0000.0000.000
205A209SER0-0.036-0.04135.9400.0020.0020.0000.0000.0000.000
206A210THR00.0610.03238.5900.0000.0000.0000.0000.0000.000
207A211GLY0-0.052-0.00841.0390.0000.0000.0000.0000.0000.000
208A212SER0-0.020-0.03142.308-0.002-0.0020.0000.0000.0000.000
209A214SER0-0.002-0.01646.757-0.002-0.0020.0000.0000.0000.000
210A215GLY0-0.0060.00449.6060.0010.0010.0000.0000.0000.000
211A216ASP-1-0.947-0.97251.064-0.002-0.0020.0000.0000.0000.000
212A217VAL0-0.008-0.00946.9260.0020.0020.0000.0000.0000.000
213A218GLU-1-0.947-0.96550.3750.0090.0090.0000.0000.0000.000
214A219TYR00.0300.01842.8540.0030.0030.0000.0000.0000.000
215A220PRO00.0480.02447.518-0.001-0.0010.0000.0000.0000.000
216A221THR00.0460.01547.640-0.001-0.0010.0000.0000.0000.000
217A222LYS10.7700.88740.582-0.020-0.0200.0000.0000.0000.000