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: JQY49

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 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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2545230.52097
FMO2-HF: Nuclear repulsion 2457701.222858
FMO2-HF: Total energy -87529.298112
FMO2-MP2: Total energy -87775.418975


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.
-0.0611.61-0.011-0.987-0.6730
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 : 0.021 / q_NPA : -0.012
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].
3A3CYS0-0.018-0.0134.030-0.8570.814-0.011-0.987-0.6730.000
4A4SER0-0.014-0.0267.6040.0000.0000.0000.0000.0000.000
5A5SER00.0850.0309.7420.1550.1550.0000.0000.0000.000
6A6THR0-0.091-0.03412.2960.0440.0440.0000.0000.0000.000
7A7ALA0-0.0060.01314.0230.0480.0480.0000.0000.0000.000
8A8LEU00.0140.00815.776-0.017-0.0170.0000.0000.0000.000
9A9SER0-0.008-0.01219.0130.0130.0130.0000.0000.0000.000
10A10CYS0-0.0040.00120.3360.0040.0040.0000.0000.0000.000
11A11SER00.0370.01420.8840.0020.0020.0000.0000.0000.000
12A12ASN0-0.027-0.02921.5010.0050.0050.0000.0000.0000.000
13A13SER0-0.029-0.01617.9480.0070.0070.0000.0000.0000.000
14A14ALA0-0.0180.01716.685-0.031-0.0310.0000.0000.0000.000
15A15ASN0-0.015-0.02410.9690.0390.0390.0000.0000.0000.000
16A16SER00.021-0.02514.270-0.017-0.0170.0000.0000.0000.000
17A17ASP-1-0.839-0.8848.883-0.199-0.1990.0000.0000.0000.000
18A18THR00.011-0.00612.386-0.050-0.0500.0000.0000.0000.000
19A19CYS0-0.0410.01310.5690.0070.0070.0000.0000.0000.000
20A21SER0-0.020-0.01211.443-0.026-0.0260.0000.0000.0000.000
21A22PRO0-0.058-0.02315.0490.0260.0260.0000.0000.0000.000
22A23GLU-1-0.923-0.95218.065-0.028-0.0280.0000.0000.0000.000
23A24TYR0-0.068-0.03620.1140.0090.0090.0000.0000.0000.000
24A25GLY00.013-0.01221.630-0.007-0.0070.0000.0000.0000.000
25A26LEU00.0430.06022.614-0.011-0.0110.0000.0000.0000.000
26A27VAL00.0050.00322.8380.0050.0050.0000.0000.0000.000
27A28VAL00.0080.00926.182-0.003-0.0030.0000.0000.0000.000
28A29LEU00.003-0.00327.4640.0020.0020.0000.0000.0000.000
29A30ASN00.000-0.00829.8700.0030.0030.0000.0000.0000.000
30A31MET00.0380.01032.6930.0000.0000.0000.0000.0000.000
31A32GLN00.0600.02935.2050.0020.0020.0000.0000.0000.000
32A33TRP0-0.079-0.04438.856-0.002-0.0020.0000.0000.0000.000
33A34ALA00.0550.02841.7950.0020.0020.0000.0000.0000.000
34A35PRO0-0.031-0.04643.5500.0000.0000.0000.0000.0000.000
35A36GLY00.0150.02846.4330.0010.0010.0000.0000.0000.000
36A37TYR0-0.033-0.00941.1440.0010.0010.0000.0000.0000.000
37A38GLY00.0520.02339.557-0.002-0.0020.0000.0000.0000.000
38A39PRO0-0.038-0.01937.7970.0010.0010.0000.0000.0000.000
39A40ASP-1-0.893-0.95540.995-0.024-0.0240.0000.0000.0000.000
40A41ASN0-0.044-0.02439.9100.0000.0000.0000.0000.0000.000
41A42ALA0-0.023-0.01836.550-0.003-0.0030.0000.0000.0000.000
42A43PHE00.0670.05536.3540.0030.0030.0000.0000.0000.000
43A44THR0-0.021-0.00835.531-0.002-0.0020.0000.0000.0000.000
44A45LEU0-0.025-0.03529.150-0.002-0.0020.0000.0000.0000.000
45A46HIS0-0.0560.00833.6460.0040.0040.0000.0000.0000.000
46A47GLY0-0.018-0.03630.7060.0030.0030.0000.0000.0000.000
47A48LEU0-0.0220.02023.554-0.002-0.0020.0000.0000.0000.000
48A49TRP0-0.065-0.05027.4930.0020.0020.0000.0000.0000.000
49A50PRO00.0090.01124.031-0.003-0.0030.0000.0000.0000.000
50A51ASP-1-0.808-0.90426.144-0.037-0.0370.0000.0000.0000.000
51A52LYS10.9360.95126.1920.0220.0220.0000.0000.0000.000
52A54SER0-0.062-0.02127.436-0.001-0.0010.0000.0000.0000.000
53A55GLY00.0570.00530.0920.0020.0020.0000.0000.0000.000
54A56ALA0-0.084-0.02231.5110.0030.0030.0000.0000.0000.000
55A57TYR0-0.011-0.00830.824-0.001-0.0010.0000.0000.0000.000
56A58ALA00.0570.03927.8080.0020.0020.0000.0000.0000.000
57A59PRO0-0.037-0.03428.4880.0020.0020.0000.0000.0000.000
58A60SER00.0130.00931.3920.0000.0000.0000.0000.0000.000
59A61GLY0-0.063-0.03833.2760.0000.0000.0000.0000.0000.000
60A62GLY00.0240.00829.2190.0020.0020.0000.0000.0000.000
61A63CYS0-0.145-0.05022.9670.0040.0040.0000.0000.0000.000
62A64ASP-1-0.742-0.89223.1290.0130.0130.0000.0000.0000.000
63A65SER0-0.025-0.02326.222-0.001-0.0010.0000.0000.0000.000
64A66ASN0-0.057-0.02626.1350.0010.0010.0000.0000.0000.000
65A67ARG10.8750.94920.9110.0100.0100.0000.0000.0000.000
66A68ALA0-0.0130.02226.429-0.004-0.0040.0000.0000.0000.000
67A69SER0-0.001-0.01229.6570.0030.0030.0000.0000.0000.000
68A70SER00.009-0.00631.598-0.003-0.0030.0000.0000.0000.000
69A71SER0-0.037-0.01833.1840.0000.0000.0000.0000.0000.000
70A72ILE00.0760.05628.5710.0010.0010.0000.0000.0000.000
71A73ALA00.0200.00131.051-0.001-0.0010.0000.0000.0000.000
72A74SER0-0.074-0.05032.9990.0000.0000.0000.0000.0000.000
73A75VAL00.0600.04527.0050.0020.0020.0000.0000.0000.000
74A76ILE00.0420.01027.2520.0010.0010.0000.0000.0000.000
75A77LYS10.8750.93828.8690.0000.0000.0000.0000.0000.000
76A78SER0-0.092-0.03729.7650.0010.0010.0000.0000.0000.000
77A79LYS10.9340.99220.232-0.036-0.0360.0000.0000.0000.000
78A80ASP-1-0.845-0.94025.058-0.013-0.0130.0000.0000.0000.000
79A81SER00.0390.02827.278-0.005-0.0050.0000.0000.0000.000
80A82SER0-0.005-0.00328.025-0.003-0.0030.0000.0000.0000.000
81A83LEU00.0260.03924.692-0.003-0.0030.0000.0000.0000.000
82A84TYR0-0.010-0.04228.312-0.001-0.0010.0000.0000.0000.000
83A85ASN0-0.005-0.01331.4250.0000.0000.0000.0000.0000.000
84A86SER0-0.017-0.00230.125-0.002-0.0020.0000.0000.0000.000
85A87MET00.0070.00429.713-0.002-0.0020.0000.0000.0000.000
86A88LEU0-0.050-0.01432.6970.0000.0000.0000.0000.0000.000
87A89THR0-0.035-0.00135.3810.0010.0010.0000.0000.0000.000
88A90TYR0-0.015-0.04032.763-0.001-0.0010.0000.0000.0000.000
89A91TRP00.0090.02127.875-0.003-0.0030.0000.0000.0000.000
90A92PRO0-0.008-0.00534.3720.0020.0020.0000.0000.0000.000
91A93SER00.0280.03337.912-0.001-0.0010.0000.0000.0000.000
92A94ASN0-0.036-0.02239.4130.0030.0030.0000.0000.0000.000
93A95GLN00.002-0.02442.2030.0020.0020.0000.0000.0000.000
94A96GLY0-0.0260.01243.4320.0010.0010.0000.0000.0000.000
95A97ASN00.014-0.01340.3540.0010.0010.0000.0000.0000.000
96A98ASN00.0740.03736.713-0.002-0.0020.0000.0000.0000.000
97A99ASN00.0140.01235.529-0.001-0.0010.0000.0000.0000.000
98A100VAL0-0.020-0.01235.7700.0000.0000.0000.0000.0000.000
99A101PHE0-0.0010.02236.0010.0000.0000.0000.0000.0000.000
100A102TRP00.038-0.00931.7180.0010.0010.0000.0000.0000.000
101A103SER0-0.007-0.00731.5490.0000.0000.0000.0000.0000.000
102A104HIS0-0.046-0.01132.2210.0020.0020.0000.0000.0000.000
103A105GLU-1-0.812-0.92930.578-0.030-0.0300.0000.0000.0000.000
104A106TRP00.0110.00722.528-0.006-0.0060.0000.0000.0000.000
105A107SER0-0.011-0.02427.7740.0000.0000.0000.0000.0000.000
106A108LYS10.8960.96529.3630.0110.0110.0000.0000.0000.000
107A109HIS10.8890.94827.9680.0310.0310.0000.0000.0000.000
108A110GLY00.0760.04024.828-0.005-0.0050.0000.0000.0000.000
109A111THR0-0.046-0.02623.252-0.006-0.0060.0000.0000.0000.000
110A113VAL00.0030.00418.810-0.007-0.0070.0000.0000.0000.000
111A114SER00.006-0.00816.7830.0030.0030.0000.0000.0000.000
112A115THR0-0.018-0.00214.3140.0130.0130.0000.0000.0000.000
113A116TYR0-0.037-0.02314.560-0.014-0.0140.0000.0000.0000.000
114A117ASP-1-0.848-0.93415.9640.0200.0200.0000.0000.0000.000
115A118PRO0-0.007-0.03215.533-0.009-0.0090.0000.0000.0000.000
116A119ASP-1-0.917-0.94014.2860.0810.0810.0000.0000.0000.000
117A121TYR0-0.109-0.04710.458-0.048-0.0480.0000.0000.0000.000
118A122ASP-1-0.926-0.9688.4710.4490.4490.0000.0000.0000.000
119A123ASN0-0.118-0.08110.5690.0200.0200.0000.0000.0000.000
120A124TYR0-0.0030.00213.852-0.018-0.0180.0000.0000.0000.000
121A125GLU-1-0.943-0.96016.5170.0840.0840.0000.0000.0000.000
122A126GLU-1-0.943-0.98919.9710.0310.0310.0000.0000.0000.000
123A127GLY0-0.035-0.01722.699-0.002-0.0020.0000.0000.0000.000
124A128GLU-1-0.877-0.96115.6480.0530.0530.0000.0000.0000.000
125A129ASP-1-0.738-0.82618.853-0.009-0.0090.0000.0000.0000.000
126A130ILE0-0.050-0.02819.754-0.012-0.0120.0000.0000.0000.000
127A131VAL00.008-0.00621.731-0.007-0.0070.0000.0000.0000.000
128A132ASP-1-0.808-0.89216.137-0.073-0.0730.0000.0000.0000.000
129A133TYR0-0.042-0.01719.800-0.010-0.0100.0000.0000.0000.000
130A134PHE0-0.050-0.03822.124-0.004-0.0040.0000.0000.0000.000
131A135GLN00.012-0.00621.6310.0060.0060.0000.0000.0000.000
132A136LYS10.9170.98217.7750.1580.1580.0000.0000.0000.000
133A137ALA00.028-0.00222.050-0.004-0.0040.0000.0000.0000.000
134A138MET0-0.061-0.02725.6040.0020.0020.0000.0000.0000.000
135A139ASP-1-0.873-0.93222.104-0.083-0.0830.0000.0000.0000.000
136A140LEU0-0.024-0.00322.763-0.002-0.0020.0000.0000.0000.000
137A141ARG10.9540.98626.1320.0520.0520.0000.0000.0000.000
138A142SER0-0.070-0.05028.2380.0050.0050.0000.0000.0000.000
139A143GLN0-0.056-0.00923.8700.0010.0010.0000.0000.0000.000
140A144TYR0-0.042-0.02224.9970.0000.0000.0000.0000.0000.000
141A145ASN00.0260.00830.3700.0080.0080.0000.0000.0000.000
142A146VAL00.0630.02633.6760.0000.0000.0000.0000.0000.000
143A147TYR00.0370.03036.3680.0030.0030.0000.0000.0000.000
144A148LYS10.8770.94335.6610.0560.0560.0000.0000.0000.000
145A149ALA00.0580.02336.4510.0010.0010.0000.0000.0000.000
146A150PHE00.000-0.00338.2900.0010.0010.0000.0000.0000.000
147A151SER00.0010.00940.9900.0010.0010.0000.0000.0000.000
148A152SER0-0.102-0.03940.1950.0010.0010.0000.0000.0000.000
149A153ASN0-0.058-0.03640.7190.0000.0000.0000.0000.0000.000
150A154GLY0-0.0010.00844.3510.0010.0010.0000.0000.0000.000
151A155ILE0-0.0320.00344.3930.0020.0020.0000.0000.0000.000
152A156THR0-0.022-0.03044.804-0.001-0.0010.0000.0000.0000.000
153A157PRO0-0.008-0.02045.1950.0010.0010.0000.0000.0000.000
154A158GLY0-0.045-0.01147.7820.0000.0000.0000.0000.0000.000
155A159GLY00.0060.01050.9950.0010.0010.0000.0000.0000.000
156A160THR0-0.022-0.01051.4940.0000.0000.0000.0000.0000.000
157A161TYR00.0200.00748.6900.0000.0000.0000.0000.0000.000
158A162THR0-0.007-0.00249.7300.0010.0010.0000.0000.0000.000
159A163ALA00.056-0.00146.745-0.002-0.0020.0000.0000.0000.000
160A164THR0-0.022-0.01245.612-0.002-0.0020.0000.0000.0000.000
161A165GLU-1-0.866-0.92845.979-0.032-0.0320.0000.0000.0000.000
162A166MET00.0110.01343.728-0.001-0.0010.0000.0000.0000.000
163A167GLN00.0280.00639.620-0.005-0.0050.0000.0000.0000.000
164A168SER00.0120.00040.778-0.002-0.0020.0000.0000.0000.000
165A169ALA0-0.0150.00441.182-0.003-0.0030.0000.0000.0000.000
166A170ILE0-0.0200.00836.007-0.003-0.0030.0000.0000.0000.000
167A171GLU-1-0.828-0.92136.530-0.052-0.0520.0000.0000.0000.000
168A172SER0-0.083-0.03536.702-0.004-0.0040.0000.0000.0000.000
169A173TYR0-0.052-0.02034.022-0.002-0.0020.0000.0000.0000.000
170A174PHE0-0.041-0.04131.339-0.004-0.0040.0000.0000.0000.000
171A175GLY0-0.0150.00731.796-0.006-0.0060.0000.0000.0000.000
172A176ALA0-0.002-0.00132.112-0.002-0.0020.0000.0000.0000.000
173A177LYS10.8120.89334.2140.0510.0510.0000.0000.0000.000
174A178ALA00.0200.01834.996-0.003-0.0030.0000.0000.0000.000
175A179LYS10.8220.90336.4200.0370.0370.0000.0000.0000.000
176A180ILE00.007-0.01638.2930.0000.0000.0000.0000.0000.000
177A181ASP-1-0.805-0.88840.322-0.031-0.0310.0000.0000.0000.000
178A182CYS0-0.061-0.00343.0450.0010.0010.0000.0000.0000.000
179A183SER00.0050.01546.3390.0010.0010.0000.0000.0000.000
180A184SER0-0.046-0.04948.5420.0000.0000.0000.0000.0000.000
181A185GLY00.0380.02351.0120.0000.0000.0000.0000.0000.000
182A186THR00.0070.02748.3380.0000.0000.0000.0000.0000.000
183A187LEU0-0.009-0.02541.9980.0000.0000.0000.0000.0000.000
184A188SER0-0.038-0.01543.2300.0010.0010.0000.0000.0000.000
185A189ASP-1-0.868-0.95038.590-0.029-0.0290.0000.0000.0000.000
186A190VAL0-0.0120.00136.0250.0000.0000.0000.0000.0000.000
187A191ALA0-0.046-0.01533.790-0.001-0.0010.0000.0000.0000.000
188A192LEU00.0070.00330.7630.0000.0000.0000.0000.0000.000
189A193TYR00.0520.03029.6360.0010.0010.0000.0000.0000.000
190A194PHE0-0.018-0.01924.462-0.004-0.0040.0000.0000.0000.000
191A195TYR00.0300.02522.6570.0090.0090.0000.0000.0000.000
192A196VAL0-0.011-0.00217.201-0.001-0.0010.0000.0000.0000.000
193A197ARG10.9350.96916.6920.2230.2230.0000.0000.0000.000
194A198GLY0-0.019-0.01113.356-0.024-0.0240.0000.0000.0000.000
195A199ARG10.9610.98410.9540.2750.2750.0000.0000.0000.000
196A200ASP-1-0.876-0.95513.366-0.208-0.2080.0000.0000.0000.000
197A201THR00.0070.01715.7440.0240.0240.0000.0000.0000.000
198A202TYR0-0.023-0.01818.082-0.001-0.0010.0000.0000.0000.000
199A203VAL0-0.049-0.02721.209-0.002-0.0020.0000.0000.0000.000
200A204ILE00.0040.00223.7740.0040.0040.0000.0000.0000.000
201A205THR0-0.022-0.00927.445-0.002-0.0020.0000.0000.0000.000
202A206ASP-1-0.847-0.92829.742-0.062-0.0620.0000.0000.0000.000
203A207ALA0-0.0020.00333.0570.0000.0000.0000.0000.0000.000
204A208LEU0-0.062-0.02532.1110.0020.0020.0000.0000.0000.000
205A209SER0-0.025-0.04135.9620.0040.0040.0000.0000.0000.000
206A210THR00.0360.02538.608-0.002-0.0020.0000.0000.0000.000
207A211GLY0-0.0200.00941.055-0.001-0.0010.0000.0000.0000.000
208A212SER0-0.009-0.00842.3270.0010.0010.0000.0000.0000.000
209A214SER0-0.008-0.01546.770-0.001-0.0010.0000.0000.0000.000
210A215GLY00.0040.00349.6190.0010.0010.0000.0000.0000.000
211A216ASP-1-0.941-0.97051.071-0.023-0.0230.0000.0000.0000.000
212A217VAL0-0.031-0.01847.0070.0010.0010.0000.0000.0000.000
213A218GLU-1-0.919-0.94650.382-0.020-0.0200.0000.0000.0000.000
214A219TYR00.0110.00542.439-0.001-0.0010.0000.0000.0000.000
215A220PRO00.0350.02147.2730.0000.0000.0000.0000.0000.000
216A221THR00.0620.02347.641-0.001-0.0010.0000.0000.0000.000
217A222LYS10.7900.90440.5250.0300.0300.0000.0000.0000.000