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: LNGQ9

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 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 -2554039.453552
FMO2-HF: Nuclear repulsion 2466508.058607
FMO2-HF: Total energy -87531.394945
FMO2-MP2: Total energy -87777.663692


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.
6.157.539-0.014-0.743-0.6320.001
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 : -0.005 / q_NPA : -0.019
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].
3A3CYS00.0500.0363.9141.3502.739-0.014-0.743-0.6320.001
4A4SER0-0.003-0.0187.410-0.417-0.4170.0000.0000.0000.000
5A5SER00.015-0.0109.7510.1200.1200.0000.0000.0000.000
6A6THR0-0.060-0.02811.9780.0340.0340.0000.0000.0000.000
7A7ALA0-0.0180.00713.8430.0320.0320.0000.0000.0000.000
8A8LEU00.0020.00715.5410.0220.0220.0000.0000.0000.000
9A9SER00.0460.01918.920-0.001-0.0010.0000.0000.0000.000
10A10CYS0-0.058-0.03920.065-0.025-0.0250.0000.0000.0000.000
11A11SER00.0340.00920.509-0.030-0.0300.0000.0000.0000.000
12A12ASN0-0.012-0.02521.0310.0270.0270.0000.0000.0000.000
13A13SER0-0.052-0.02117.365-0.017-0.0170.0000.0000.0000.000
14A14ALA0-0.0190.00216.180-0.007-0.0070.0000.0000.0000.000
15A15ASN0-0.024-0.03011.8140.1090.1090.0000.0000.0000.000
16A16SER0-0.001-0.02114.0460.0190.0190.0000.0000.0000.000
17A17ASP-1-0.827-0.8919.7801.3461.3460.0000.0000.0000.000
18A18THR00.0150.00512.765-0.006-0.0060.0000.0000.0000.000
19A19CYS0-0.077-0.01511.0400.0580.0580.0000.0000.0000.000
20A21SER0-0.027-0.01111.444-0.215-0.2150.0000.0000.0000.000
21A22PRO0-0.0040.01315.0880.0310.0310.0000.0000.0000.000
22A23GLU-1-0.861-0.93218.1210.2350.2350.0000.0000.0000.000
23A24TYR0-0.082-0.03520.493-0.054-0.0540.0000.0000.0000.000
24A25GLY00.0340.01521.583-0.002-0.0020.0000.0000.0000.000
25A26LEU00.0130.02222.461-0.024-0.0240.0000.0000.0000.000
26A27VAL0-0.005-0.00822.8170.0160.0160.0000.0000.0000.000
27A28VAL00.0020.00926.225-0.017-0.0170.0000.0000.0000.000
28A29LEU00.0110.00227.2850.0130.0130.0000.0000.0000.000
29A30ASN0-0.010-0.00529.721-0.016-0.0160.0000.0000.0000.000
30A31MET00.0230.00532.1050.0070.0070.0000.0000.0000.000
31A32GLN0-0.013-0.00235.013-0.002-0.0020.0000.0000.0000.000
32A33TRP0-0.052-0.04438.7270.0000.0000.0000.0000.0000.000
33A34ALA00.0380.02641.731-0.002-0.0020.0000.0000.0000.000
34A35PRO00.0420.00343.6890.0010.0010.0000.0000.0000.000
35A36GLY0-0.013-0.00346.2290.0020.0020.0000.0000.0000.000
36A37TYR0-0.066-0.02140.8750.0030.0030.0000.0000.0000.000
37A38GLY00.0780.03739.171-0.001-0.0010.0000.0000.0000.000
38A39PRO0-0.020-0.01338.001-0.003-0.0030.0000.0000.0000.000
39A40ASP-1-0.808-0.88440.9780.0310.0310.0000.0000.0000.000
40A41ASN0-0.040-0.01539.0910.0010.0010.0000.0000.0000.000
41A42ALA0-0.015-0.01136.258-0.002-0.0020.0000.0000.0000.000
42A43PHE00.0620.03836.0920.0010.0010.0000.0000.0000.000
43A44THR0-0.0160.00435.4530.0010.0010.0000.0000.0000.000
44A45LEU0-0.037-0.02428.799-0.003-0.0030.0000.0000.0000.000
45A46HIS0-0.053-0.01733.301-0.003-0.0030.0000.0000.0000.000
46A47GLY0-0.013-0.01830.2650.0080.0080.0000.0000.0000.000
47A48LEU0-0.0130.01023.163-0.012-0.0120.0000.0000.0000.000
48A49TRP0-0.050-0.03226.9820.0140.0140.0000.0000.0000.000
49A50PRO00.0140.02524.044-0.013-0.0130.0000.0000.0000.000
50A51ASP-1-0.800-0.92226.0430.1270.1270.0000.0000.0000.000
51A52LYS10.8710.91224.811-0.192-0.1920.0000.0000.0000.000
52A54SER0-0.032-0.00727.560-0.008-0.0080.0000.0000.0000.000
53A55GLY00.0360.01030.554-0.008-0.0080.0000.0000.0000.000
54A56ALA0-0.092-0.03031.963-0.001-0.0010.0000.0000.0000.000
55A57TYR0-0.007-0.01130.9680.0060.0060.0000.0000.0000.000
56A58ALA00.0440.02928.1270.0040.0040.0000.0000.0000.000
57A59PRO0-0.027-0.01628.710-0.013-0.0130.0000.0000.0000.000
58A60SER00.0090.00431.6590.0080.0080.0000.0000.0000.000
59A61GLY0-0.049-0.02833.480-0.006-0.0060.0000.0000.0000.000
60A62GLY0-0.0140.00229.4600.0040.0040.0000.0000.0000.000
61A63CYS0-0.095-0.04423.6440.0010.0010.0000.0000.0000.000
62A64ASP-1-0.721-0.85324.2680.3430.3430.0000.0000.0000.000
63A65SER0-0.035-0.02826.619-0.006-0.0060.0000.0000.0000.000
64A66ASN0-0.093-0.04626.419-0.026-0.0260.0000.0000.0000.000
65A67ARG10.8200.90520.735-0.416-0.4160.0000.0000.0000.000
66A68ALA0-0.0080.01926.801-0.007-0.0070.0000.0000.0000.000
67A69SER00.005-0.00529.702-0.002-0.0020.0000.0000.0000.000
68A70SER00.000-0.00931.683-0.007-0.0070.0000.0000.0000.000
69A71SER0-0.018-0.00733.051-0.011-0.0110.0000.0000.0000.000
70A72ILE00.0920.06728.1650.0020.0020.0000.0000.0000.000
71A73ALA0-0.010-0.01230.8230.0010.0010.0000.0000.0000.000
72A74SER0-0.088-0.04733.071-0.005-0.0050.0000.0000.0000.000
73A75VAL00.0800.04926.676-0.001-0.0010.0000.0000.0000.000
74A76ILE00.0530.02626.8310.0050.0050.0000.0000.0000.000
75A77LYS10.8400.92828.384-0.118-0.1180.0000.0000.0000.000
76A78SER0-0.077-0.04529.683-0.004-0.0040.0000.0000.0000.000
77A79LYS10.7980.90320.715-0.358-0.3580.0000.0000.0000.000
78A80ASP-1-0.743-0.86425.0110.1460.1460.0000.0000.0000.000
79A81SER0-0.010-0.00427.072-0.006-0.0060.0000.0000.0000.000
80A82SER0-0.032-0.03527.571-0.016-0.0160.0000.0000.0000.000
81A83LEU00.0200.03124.547-0.014-0.0140.0000.0000.0000.000
82A84TYR00.0380.01128.180-0.008-0.0080.0000.0000.0000.000
83A85ASN0-0.017-0.02731.207-0.009-0.0090.0000.0000.0000.000
84A86SER0-0.011-0.01529.931-0.012-0.0120.0000.0000.0000.000
85A87MET00.0100.00129.266-0.003-0.0030.0000.0000.0000.000
86A88LEU0-0.076-0.03332.400-0.004-0.0040.0000.0000.0000.000
87A89THR0-0.061-0.01234.978-0.007-0.0070.0000.0000.0000.000
88A90TYR0-0.010-0.02832.633-0.008-0.0080.0000.0000.0000.000
89A91TRP00.0030.00727.4100.0020.0020.0000.0000.0000.000
90A92PRO0-0.0140.01434.0870.0060.0060.0000.0000.0000.000
91A93SER00.009-0.00637.550-0.003-0.0030.0000.0000.0000.000
92A94ASN00.015-0.00339.270-0.003-0.0030.0000.0000.0000.000
93A95GLN0-0.035-0.02042.112-0.003-0.0030.0000.0000.0000.000
94A96GLY00.0090.01843.0570.0000.0000.0000.0000.0000.000
95A97ASN0-0.031-0.02440.1890.0060.0060.0000.0000.0000.000
96A98ASN00.0840.03036.3670.0010.0010.0000.0000.0000.000
97A99ASN00.0100.00635.1960.0120.0120.0000.0000.0000.000
98A100VAL00.0040.01235.2960.0090.0090.0000.0000.0000.000
99A101PHE00.0040.01735.9630.0070.0070.0000.0000.0000.000
100A102TRP00.046-0.00431.4100.0080.0080.0000.0000.0000.000
101A103SER0-0.016-0.01731.2550.0150.0150.0000.0000.0000.000
102A104HIS00.0370.04432.0750.0140.0140.0000.0000.0000.000
103A105GLU-1-0.756-0.88230.7330.1320.1320.0000.0000.0000.000
104A106TRP0-0.005-0.02022.282-0.006-0.0060.0000.0000.0000.000
105A107SER0-0.006-0.02327.7510.0160.0160.0000.0000.0000.000
106A108LYS10.8560.93329.435-0.131-0.1310.0000.0000.0000.000
107A109HIS10.7990.90827.608-0.154-0.1540.0000.0000.0000.000
108A110GLY00.0680.03824.2110.0110.0110.0000.0000.0000.000
109A111THR0-0.036-0.02723.0490.0240.0240.0000.0000.0000.000
110A113VAL0-0.022-0.00818.955-0.007-0.0070.0000.0000.0000.000
111A114SER0-0.003-0.01917.1030.0030.0030.0000.0000.0000.000
112A115THR0-0.022-0.00614.2990.0510.0510.0000.0000.0000.000
113A116TYR0-0.054-0.02314.5220.0360.0360.0000.0000.0000.000
114A117ASP-1-0.823-0.92416.6750.4920.4920.0000.0000.0000.000
115A118PRO00.000-0.01215.6770.0940.0940.0000.0000.0000.000
116A119ASP-1-0.895-0.93814.4270.8190.8190.0000.0000.0000.000
117A121TYR0-0.087-0.07010.6740.1580.1580.0000.0000.0000.000
118A122ASP-1-0.906-0.9438.5741.6061.6060.0000.0000.0000.000
119A123ASN0-0.116-0.08510.722-0.247-0.2470.0000.0000.0000.000
120A124TYR0-0.016-0.01013.793-0.134-0.1340.0000.0000.0000.000
121A125GLU-1-0.861-0.91016.1860.3110.3110.0000.0000.0000.000
122A126GLU-1-0.956-0.98319.6170.2790.2790.0000.0000.0000.000
123A127GLY00.012-0.00922.252-0.030-0.0300.0000.0000.0000.000
124A128GLU-1-0.863-0.94215.4370.5950.5950.0000.0000.0000.000
125A129ASP-1-0.720-0.82518.5290.3870.3870.0000.0000.0000.000
126A130ILE0-0.052-0.02019.519-0.038-0.0380.0000.0000.0000.000
127A131VAL00.002-0.00621.022-0.031-0.0310.0000.0000.0000.000
128A132ASP-1-0.765-0.83415.6810.4370.4370.0000.0000.0000.000
129A133TYR0-0.028-0.02919.309-0.038-0.0380.0000.0000.0000.000
130A134PHE0-0.049-0.04421.782-0.032-0.0320.0000.0000.0000.000
131A135GLN0-0.024-0.02621.405-0.021-0.0210.0000.0000.0000.000
132A136LYS10.8910.95417.348-0.167-0.1670.0000.0000.0000.000
133A137ALA00.006-0.00321.914-0.026-0.0260.0000.0000.0000.000
134A138MET0-0.037-0.01425.348-0.024-0.0240.0000.0000.0000.000
135A139ASP-1-0.838-0.89621.4800.1030.1030.0000.0000.0000.000
136A140LEU0-0.014-0.00522.768-0.022-0.0220.0000.0000.0000.000
137A141ARG10.9080.95425.893-0.079-0.0790.0000.0000.0000.000
138A142SER0-0.107-0.06227.763-0.008-0.0080.0000.0000.0000.000
139A143GLN0-0.056-0.02623.1740.0020.0020.0000.0000.0000.000
140A144TYR0-0.017-0.01424.716-0.015-0.0150.0000.0000.0000.000
141A145ASN00.0260.00830.3130.0050.0050.0000.0000.0000.000
142A146VAL00.0740.03133.559-0.006-0.0060.0000.0000.0000.000
143A147TYR00.0460.03536.295-0.003-0.0030.0000.0000.0000.000
144A148LYS10.8540.94035.6730.0090.0090.0000.0000.0000.000
145A149ALA00.0240.02536.231-0.004-0.0040.0000.0000.0000.000
146A150PHE0-0.0030.00938.167-0.002-0.0020.0000.0000.0000.000
147A151SER00.008-0.01340.926-0.004-0.0040.0000.0000.0000.000
148A152SER0-0.087-0.05339.894-0.002-0.0020.0000.0000.0000.000
149A153ASN0-0.085-0.04440.536-0.006-0.0060.0000.0000.0000.000
150A154GLY0-0.0060.00444.1610.0000.0000.0000.0000.0000.000
151A155ILE0-0.0150.01544.4480.0020.0020.0000.0000.0000.000
152A156THR00.000-0.02044.7980.0000.0000.0000.0000.0000.000
153A157PRO0-0.024-0.00444.8270.0000.0000.0000.0000.0000.000
154A158GLY0-0.053-0.02247.542-0.001-0.0010.0000.0000.0000.000
155A159GLY0-0.0090.00250.703-0.002-0.0020.0000.0000.0000.000
156A160THR0-0.033-0.02251.3920.0020.0020.0000.0000.0000.000
157A161TYR00.0120.00548.701-0.002-0.0020.0000.0000.0000.000
158A162THR0-0.0070.01249.7870.0020.0020.0000.0000.0000.000
159A163ALA00.0510.00446.541-0.001-0.0010.0000.0000.0000.000
160A164THR0-0.048-0.02345.5610.0000.0000.0000.0000.0000.000
161A165GLU-1-0.836-0.91345.7760.0030.0030.0000.0000.0000.000
162A166MET00.0080.00643.689-0.001-0.0010.0000.0000.0000.000
163A167GLN00.0260.00139.260-0.001-0.0010.0000.0000.0000.000
164A168SER0-0.006-0.01340.559-0.002-0.0020.0000.0000.0000.000
165A169ALA0-0.0170.01341.154-0.004-0.0040.0000.0000.0000.000
166A170ILE0-0.017-0.00935.902-0.002-0.0020.0000.0000.0000.000
167A171GLU-1-0.807-0.89336.267-0.005-0.0050.0000.0000.0000.000
168A172SER0-0.071-0.05136.599-0.005-0.0050.0000.0000.0000.000
169A173TYR0-0.0270.00333.351-0.006-0.0060.0000.0000.0000.000
170A174PHE0-0.033-0.03231.003-0.002-0.0020.0000.0000.0000.000
171A175GLY0-0.0120.00631.645-0.002-0.0020.0000.0000.0000.000
172A176ALA0-0.010-0.00332.036-0.002-0.0020.0000.0000.0000.000
173A177LYS10.7880.88134.0620.0030.0030.0000.0000.0000.000
174A178ALA00.0170.00434.8070.0040.0040.0000.0000.0000.000
175A179LYS10.8360.93036.137-0.053-0.0530.0000.0000.0000.000
176A180ILE00.016-0.00538.0510.0020.0020.0000.0000.0000.000
177A181ASP-1-0.765-0.86640.4100.0460.0460.0000.0000.0000.000
178A182CYS0-0.0380.00442.951-0.002-0.0020.0000.0000.0000.000
179A183SER00.0090.01946.3420.0010.0010.0000.0000.0000.000
180A184SER0-0.029-0.03448.261-0.001-0.0010.0000.0000.0000.000
181A185GLY00.0350.02850.289-0.002-0.0020.0000.0000.0000.000
182A186THR0-0.026-0.01448.203-0.002-0.0020.0000.0000.0000.000
183A187LEU0-0.025-0.02942.2150.0020.0020.0000.0000.0000.000
184A188SER0-0.087-0.05643.1990.0000.0000.0000.0000.0000.000
185A189ASP-1-0.848-0.91238.8270.0620.0620.0000.0000.0000.000
186A190VAL00.007-0.00136.088-0.005-0.0050.0000.0000.0000.000
187A191ALA0-0.0150.00133.6740.0060.0060.0000.0000.0000.000
188A192LEU00.0080.01930.744-0.006-0.0060.0000.0000.0000.000
189A193TYR00.0450.00729.4980.0100.0100.0000.0000.0000.000
190A194PHE0-0.017-0.00924.427-0.012-0.0120.0000.0000.0000.000
191A195TYR00.0230.02322.6830.0160.0160.0000.0000.0000.000
192A196VAL00.013-0.00117.161-0.009-0.0090.0000.0000.0000.000
193A197ARG10.9290.97716.5170.1030.1030.0000.0000.0000.000
194A198GLY0-0.002-0.00412.925-0.032-0.0320.0000.0000.0000.000
195A199ARG10.8330.90110.918-0.545-0.5450.0000.0000.0000.000
196A200ASP-1-0.780-0.87813.2440.2770.2770.0000.0000.0000.000
197A201THR0-0.006-0.00515.180-0.041-0.0410.0000.0000.0000.000
198A202TYR00.0150.00117.603-0.003-0.0030.0000.0000.0000.000
199A203VAL0-0.066-0.03520.764-0.029-0.0290.0000.0000.0000.000
200A204ILE0-0.0060.01023.4490.0130.0130.0000.0000.0000.000
201A205THR0-0.018-0.01527.202-0.012-0.0120.0000.0000.0000.000
202A206ASP-1-0.866-0.92629.6550.0060.0060.0000.0000.0000.000
203A207ALA0-0.026-0.01132.9340.0060.0060.0000.0000.0000.000
204A208LEU0-0.034-0.01231.861-0.003-0.0030.0000.0000.0000.000
205A209SER0-0.031-0.02535.6940.0000.0000.0000.0000.0000.000
206A210THR00.0670.03138.3430.0010.0010.0000.0000.0000.000
207A211GLY0-0.056-0.01240.7650.0000.0000.0000.0000.0000.000
208A212SER0-0.032-0.04042.042-0.002-0.0020.0000.0000.0000.000
209A214SER0-0.006-0.02046.484-0.002-0.0020.0000.0000.0000.000
210A215GLY0-0.0010.00949.3710.0000.0000.0000.0000.0000.000
211A216ASP-1-0.932-0.96551.2340.0110.0110.0000.0000.0000.000
212A217VAL0-0.006-0.01546.9240.0020.0020.0000.0000.0000.000
213A218GLU-1-0.905-0.93450.3890.0230.0230.0000.0000.0000.000
214A219TYR00.0300.00542.7340.0040.0040.0000.0000.0000.000
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