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: L7NY9

Calculation Name: 2OPT-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2OPT

Chain ID: A

ChEMBL ID:

UniProt ID: Q53901

Base Structure: X-ray

Registration Date: 2023-09-27

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 209
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2090014.056762
FMO2-HF: Nuclear repulsion 2010250.716294
FMO2-HF: Total energy -79763.340468
FMO2-MP2: Total energy -79994.582236


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:27:ALA)


Summations of interaction energy for fragment #1(A:27:ALA)
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.
-0.490.875-0.011-0.649-0.7050
Interaction energy analysis for fragmet #1(A:27:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / q_NPA : -0.018
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].
3A29ALA00.0340.0263.859-0.5300.835-0.011-0.649-0.7050.000
4A30PRO0-0.016-0.0226.2940.4430.4430.0000.0000.0000.000
5A31LEU0-0.0130.0039.800-0.095-0.0950.0000.0000.0000.000
6A32THR00.0400.01211.8460.0240.0240.0000.0000.0000.000
7A33GLN00.026-0.00314.6430.0010.0010.0000.0000.0000.000
8A34ASP-1-0.807-0.88514.922-0.322-0.3220.0000.0000.0000.000
9A35ARG10.8880.9419.9090.4260.4260.0000.0000.0000.000
10A36ILE0-0.012-0.00213.4860.0290.0290.0000.0000.0000.000
11A37VAL00.0470.02715.4990.0210.0210.0000.0000.0000.000
12A38VAL00.0290.01515.0510.0130.0130.0000.0000.0000.000
13A39THR0-0.063-0.04612.9320.0060.0060.0000.0000.0000.000
14A40ALA0-0.034-0.02915.1910.0280.0280.0000.0000.0000.000
15A41LEU00.0430.02718.6440.0150.0150.0000.0000.0000.000
16A42GLY00.0170.01617.2800.0080.0080.0000.0000.0000.000
17A43ILE0-0.045-0.02816.7720.0150.0150.0000.0000.0000.000
18A44LEU0-0.019-0.00419.6560.0100.0100.0000.0000.0000.000
19A45ASP-1-0.786-0.88321.707-0.070-0.0700.0000.0000.0000.000
20A46ALA0-0.038-0.01020.7810.0060.0060.0000.0000.0000.000
21A47GLU-1-0.875-0.92420.0380.0320.0320.0000.0000.0000.000
22A48GLY00.0040.00124.0430.0070.0070.0000.0000.0000.000
23A49LEU00.000-0.00925.0810.0030.0030.0000.0000.0000.000
24A50ASP-1-0.858-0.89626.7170.0040.0040.0000.0000.0000.000
25A51ALA00.0090.01923.2520.0070.0070.0000.0000.0000.000
26A52LEU00.0130.02920.4940.0100.0100.0000.0000.0000.000
27A53SER00.0000.00522.7310.0030.0030.0000.0000.0000.000
28A54MET00.0550.02320.9710.0020.0020.0000.0000.0000.000
29A55ARG10.9180.95819.421-0.113-0.1130.0000.0000.0000.000
30A56ARG10.7820.86516.811-0.024-0.0240.0000.0000.0000.000
31A57LEU00.0600.03415.9540.0090.0090.0000.0000.0000.000
32A58ALA0-0.012-0.00815.106-0.007-0.0070.0000.0000.0000.000
33A59GLN00.002-0.00113.4810.0200.0200.0000.0000.0000.000
34A60GLU-1-0.837-0.92412.6440.1310.1310.0000.0000.0000.000
35A61LEU0-0.0100.00810.676-0.019-0.0190.0000.0000.0000.000
36A62LYS10.7500.8867.781-0.161-0.1610.0000.0000.0000.000
37A63THR00.0110.0169.5760.1270.1270.0000.0000.0000.000
38A64GLY0-0.002-0.00212.015-0.012-0.0120.0000.0000.0000.000
39A65HIS00.032-0.01715.281-0.021-0.0210.0000.0000.0000.000
40A66ALA0-0.0030.01418.437-0.022-0.0220.0000.0000.0000.000
41A67SER00.0370.01213.851-0.013-0.0130.0000.0000.0000.000
42A68LEU00.0240.02316.360-0.034-0.0340.0000.0000.0000.000
43A69TYR00.0100.00417.587-0.018-0.0180.0000.0000.0000.000
44A70ALA0-0.028-0.02219.629-0.010-0.0100.0000.0000.0000.000
45A71HIS0-0.051-0.02215.660-0.041-0.0410.0000.0000.0000.000
46A72VAL0-0.033-0.01919.561-0.015-0.0150.0000.0000.0000.000
47A73GLY00.0610.06622.2400.0030.0030.0000.0000.0000.000
48A74ASN0-0.080-0.09423.7390.0110.0110.0000.0000.0000.000
49A75ARG10.8790.91224.825-0.006-0.0060.0000.0000.0000.000
50A76ASP-1-0.846-0.92025.879-0.015-0.0150.0000.0000.0000.000
51A77GLU-1-0.786-0.85226.536-0.018-0.0180.0000.0000.0000.000
52A78LEU0-0.034-0.02520.130-0.010-0.0100.0000.0000.0000.000
53A79LEU0-0.002-0.01623.968-0.010-0.0100.0000.0000.0000.000
54A80ASP-1-0.813-0.88426.291-0.040-0.0400.0000.0000.0000.000
55A81LEU0-0.036-0.02222.383-0.008-0.0080.0000.0000.0000.000
56A82VAL0-0.057-0.03821.479-0.011-0.0110.0000.0000.0000.000
57A83PHE00.0170.01023.960-0.004-0.0040.0000.0000.0000.000
58A84ASP-1-0.750-0.88226.530-0.089-0.0890.0000.0000.0000.000
59A85ILE0-0.042-0.01219.740-0.006-0.0060.0000.0000.0000.000
60A86VAL00.0380.00824.200-0.008-0.0080.0000.0000.0000.000
61A87LEU00.0030.00325.8970.0030.0030.0000.0000.0000.000
62A88THR0-0.043-0.01124.5750.0000.0000.0000.0000.0000.000
63A89GLU-1-0.861-0.90825.418-0.098-0.0980.0000.0000.0000.000
64A90VAL0-0.080-0.03529.0720.0060.0060.0000.0000.0000.000
65A91GLU-1-0.899-0.94532.568-0.084-0.0840.0000.0000.0000.000
66A92VAL0-0.030-0.01833.9800.0060.0060.0000.0000.0000.000
67A93PRO00.0190.02337.375-0.002-0.0020.0000.0000.0000.000
68A94GLU-1-0.801-0.89639.743-0.059-0.0590.0000.0000.0000.000
69A95PRO0-0.0100.00341.8500.0010.0010.0000.0000.0000.000
70A96GLU-1-0.782-0.84843.988-0.049-0.0490.0000.0000.0000.000
71A97PRO0-0.022-0.02547.5240.0020.0020.0000.0000.0000.000
72A98GLY0-0.025-0.00651.3490.0000.0000.0000.0000.0000.000
73A99ARG10.7290.81242.5980.0480.0480.0000.0000.0000.000
74A100TRP00.0100.00647.8520.0000.0000.0000.0000.0000.000
75A101ALA00.0380.02147.339-0.001-0.0010.0000.0000.0000.000
76A102GLU-1-0.758-0.90146.318-0.036-0.0360.0000.0000.0000.000
77A103GLN0-0.019-0.00943.5120.0000.0000.0000.0000.0000.000
78A104VAL00.0610.02742.591-0.002-0.0020.0000.0000.0000.000
79A105LYS10.8120.91742.9530.0310.0310.0000.0000.0000.000
80A106GLU-1-0.890-0.93039.188-0.055-0.0550.0000.0000.0000.000
81A107MET00.0390.03638.268-0.003-0.0030.0000.0000.0000.000
82A108CYS0-0.045-0.01637.837-0.001-0.0010.0000.0000.0000.000
83A109ARG10.7540.83738.5690.0390.0390.0000.0000.0000.000
84A110SER0-0.028-0.01733.072-0.001-0.0010.0000.0000.0000.000
85A111LEU00.0100.02233.684-0.003-0.0030.0000.0000.0000.000
86A112ARG10.7960.85234.3080.0350.0350.0000.0000.0000.000
87A113ARG10.8880.94631.5980.0630.0630.0000.0000.0000.000
88A114MET00.0230.03428.893-0.002-0.0020.0000.0000.0000.000
89A115PHE00.010-0.01629.713-0.001-0.0010.0000.0000.0000.000
90A116LEU0-0.057-0.02731.1760.0020.0020.0000.0000.0000.000
91A117ALA0-0.058-0.00627.3390.0010.0010.0000.0000.0000.000
92A118HIS10.7590.83523.5030.0810.0810.0000.0000.0000.000
93A119ARG10.9180.99226.2410.0190.0190.0000.0000.0000.000
94A120ASP-1-0.817-0.93027.657-0.017-0.0170.0000.0000.0000.000
95A121LEU00.0250.02327.4880.0020.0020.0000.0000.0000.000
96A122ALA00.0310.01229.8890.0000.0000.0000.0000.0000.000
97A123ARG10.7210.81331.2220.0090.0090.0000.0000.0000.000
98A124ILE0-0.042-0.01527.3510.0030.0030.0000.0000.0000.000
99A125ALA00.0340.00731.7240.0000.0000.0000.0000.0000.000
100A126ILE0-0.052-0.01333.6970.0010.0010.0000.0000.0000.000
101A127ASP-1-0.884-0.92434.503-0.020-0.0200.0000.0000.0000.000
102A128ARG10.7310.83530.4140.0260.0260.0000.0000.0000.000
103A129VAL00.0260.01435.258-0.002-0.0020.0000.0000.0000.000
104A130PRO00.0010.00233.282-0.003-0.0030.0000.0000.0000.000
105A131LEU0-0.027-0.02933.532-0.001-0.0010.0000.0000.0000.000
106A132GLY00.0290.03429.6470.0010.0010.0000.0000.0000.000
107A133PRO0-0.025-0.03026.5930.0020.0020.0000.0000.0000.000
108A134ASN0-0.034-0.02725.549-0.002-0.0020.0000.0000.0000.000
109A135GLY00.0090.00129.7400.0040.0040.0000.0000.0000.000
110A136MET0-0.030-0.01532.5780.0030.0030.0000.0000.0000.000
111A137VAL0-0.0060.00632.3210.0030.0030.0000.0000.0000.000
112A138GLY00.0550.02633.8110.0020.0020.0000.0000.0000.000
113A139MET0-0.0260.00235.3210.0050.0050.0000.0000.0000.000
114A140GLU-1-0.905-0.95138.009-0.046-0.0460.0000.0000.0000.000
115A141ARG10.7480.84635.8310.0690.0690.0000.0000.0000.000
116A142THR00.001-0.01938.7410.0030.0030.0000.0000.0000.000
117A143MET0-0.044-0.01341.1480.0030.0030.0000.0000.0000.000
118A144ASN0-0.034-0.00842.5900.0040.0040.0000.0000.0000.000
119A145LEU00.0210.01342.2040.0020.0020.0000.0000.0000.000
120A146LEU0-0.0050.01744.7510.0020.0020.0000.0000.0000.000
121A147ARG10.9070.93147.0090.0370.0370.0000.0000.0000.000
122A148SER0-0.090-0.05047.5360.0010.0010.0000.0000.0000.000
123A149GLY0-0.010-0.00649.6340.0000.0000.0000.0000.0000.000
124A150GLY0-0.043-0.02251.6410.0010.0010.0000.0000.0000.000
125A151LEU0-0.052-0.01949.5540.0010.0010.0000.0000.0000.000
126A152HIS00.0660.02552.363-0.002-0.0020.0000.0000.0000.000
127A153ASP-1-0.807-0.90851.015-0.031-0.0310.0000.0000.0000.000
128A154GLU-1-0.942-0.96450.347-0.022-0.0220.0000.0000.0000.000
129A155LEU0-0.039-0.00750.9920.0000.0000.0000.0000.0000.000
130A156ALA0-0.006-0.00348.115-0.001-0.0010.0000.0000.0000.000
131A157ALA00.006-0.00746.347-0.001-0.0010.0000.0000.0000.000
132A158TYR00.005-0.00646.0650.0000.0000.0000.0000.0000.000
133A159GLY00.0470.02647.4540.0000.0000.0000.0000.0000.000
134A160GLY00.0300.00443.606-0.001-0.0010.0000.0000.0000.000
135A161ASP-1-0.932-0.94542.637-0.028-0.0280.0000.0000.0000.000
136A162LEU0-0.0020.01143.5450.0000.0000.0000.0000.0000.000
137A163LEU0-0.017-0.01842.7570.0000.0000.0000.0000.0000.000
138A164SER0-0.024-0.02338.8440.0000.0000.0000.0000.0000.000
139A165THR00.0260.02239.7930.0000.0000.0000.0000.0000.000
140A166PHE0-0.033-0.01541.8600.0010.0010.0000.0000.0000.000
141A167VAL0-0.016-0.01537.6980.0010.0010.0000.0000.0000.000
142A168THR0-0.004-0.01736.340-0.001-0.0010.0000.0000.0000.000
143A169ALA0-0.025-0.00438.4290.0010.0010.0000.0000.0000.000
144A170GLU-1-0.795-0.87841.035-0.021-0.0210.0000.0000.0000.000
145A171ALA00.0130.01635.7030.0010.0010.0000.0000.0000.000
146A172LEU00.0200.01936.2210.0010.0010.0000.0000.0000.000
147A173GLU-1-0.823-0.88937.781-0.016-0.0160.0000.0000.0000.000
148A174GLN00.0560.02337.6500.0010.0010.0000.0000.0000.000
149A175SER0-0.052-0.03534.6150.0000.0000.0000.0000.0000.000
150A176SER0-0.084-0.05236.3150.0030.0030.0000.0000.0000.000
151A177ARG10.7000.86338.2450.0200.0200.0000.0000.0000.000
152A188ALA00.0430.02041.8460.0000.0000.0000.0000.0000.000
153A189GLY00.0420.01143.7520.0000.0000.0000.0000.0000.000
154A190VAL00.0390.01746.1780.0000.0000.0000.0000.0000.000
155A191PHE00.0030.00146.8770.0010.0010.0000.0000.0000.000
156A192ALA00.0330.01847.9850.0000.0000.0000.0000.0000.000
157A193ASP-1-0.855-0.94249.733-0.008-0.0080.0000.0000.0000.000
158A194GLN0-0.085-0.03451.6120.0010.0010.0000.0000.0000.000
159A195LEU00.0070.01251.8390.0000.0000.0000.0000.0000.000
160A196HIS00.0000.00553.7270.0000.0000.0000.0000.0000.000
161A197GLY00.0340.00755.4840.0000.0000.0000.0000.0000.000
162A198TYR0-0.0120.00857.2250.0000.0000.0000.0000.0000.000
163A199LEU00.011-0.00456.2960.0000.0000.0000.0000.0000.000
164A200LYS10.9210.96359.5230.0080.0080.0000.0000.0000.000
165A201SER0-0.082-0.06061.2980.0000.0000.0000.0000.0000.000
166A202LEU00.0090.02161.8680.0010.0010.0000.0000.0000.000
167A203PRO00.010-0.00964.6560.0000.0000.0000.0000.0000.000
168A204ALA00.0710.03668.0570.0000.0000.0000.0000.0000.000
169A205THR0-0.040-0.02768.9590.0000.0000.0000.0000.0000.000
170A206SER0-0.057-0.02669.2480.0000.0000.0000.0000.0000.000
171A207PHE00.0280.01264.7100.0000.0000.0000.0000.0000.000
172A208PRO00.0380.03465.4090.0000.0000.0000.0000.0000.000
173A209ASN0-0.005-0.02163.9290.0000.0000.0000.0000.0000.000
174A210LEU00.0310.01760.071-0.001-0.0010.0000.0000.0000.000
175A211VAL00.0050.01160.9760.0000.0000.0000.0000.0000.000
176A212HIS0-0.085-0.03862.5280.0000.0000.0000.0000.0000.000
177A213LEU0-0.004-0.01258.810-0.001-0.0010.0000.0000.0000.000
178A214ALA00.0150.02957.591-0.001-0.0010.0000.0000.0000.000
179A215GLY00.0530.03855.5780.0000.0000.0000.0000.0000.000
180A216PRO0-0.012-0.01354.0760.0000.0000.0000.0000.0000.000
181A217ILE0-0.011-0.00853.001-0.001-0.0010.0000.0000.0000.000
182A218THR0-0.026-0.01751.2520.0000.0000.0000.0000.0000.000
183A219SER0-0.055-0.04349.9640.0000.0000.0000.0000.0000.000
184A220LEU0-0.043-0.01148.477-0.001-0.0010.0000.0000.0000.000
185A221ASP-1-0.820-0.89045.184-0.023-0.0230.0000.0000.0000.000
186A222SER00.0670.00841.5370.0000.0000.0000.0000.0000.000
187A223ASP-1-0.828-0.87141.308-0.035-0.0350.0000.0000.0000.000
188A224ARG10.8020.88943.7700.0230.0230.0000.0000.0000.000
189A225ARG10.7320.82445.6750.0200.0200.0000.0000.0000.000
190A226PHE00.0290.01740.5540.0000.0000.0000.0000.0000.000
191A227GLU-1-0.769-0.88444.465-0.035-0.0350.0000.0000.0000.000
192A228LEU0-0.024-0.00646.8200.0000.0000.0000.0000.0000.000
193A229GLY00.0090.00348.1190.0010.0010.0000.0000.0000.000
194A230LEU00.0150.01843.7340.0000.0000.0000.0000.0000.000
195A231GLU-1-0.850-0.92847.318-0.026-0.0260.0000.0000.0000.000
196A232ILE0-0.035-0.01450.6490.0000.0000.0000.0000.0000.000
197A233ILE00.0130.01147.5740.0010.0010.0000.0000.0000.000
198A234ILE00.0000.00346.5490.0000.0000.0000.0000.0000.000
199A235ALA0-0.025-0.01250.7820.0000.0000.0000.0000.0000.000
200A236GLY00.0000.00253.9770.0010.0010.0000.0000.0000.000
201A237LEU0-0.013-0.01148.5620.0000.0000.0000.0000.0000.000
202A238LEU0-0.001-0.00553.0540.0000.0000.0000.0000.0000.000
203A239ALA0-0.034-0.00855.2870.0000.0000.0000.0000.0000.000
204A240GLY00.0420.02556.7530.0010.0010.0000.0000.0000.000
205A241ALA0-0.005-0.01454.9740.0000.0000.0000.0000.0000.000
206A242GLY0-0.028-0.01057.0670.0000.0000.0000.0000.0000.000
207A243GLU-1-0.985-0.99460.319-0.018-0.0180.0000.0000.0000.000
208A244ALA0-0.045-0.01059.1170.0010.0010.0000.0000.0000.000
209A245ALA0-0.112-0.05160.1160.0010.0010.0000.0000.0000.000