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: L7L19

Calculation Name: 2BA0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2BA0

Chain ID: A

ChEMBL ID:

UniProt ID: O29757

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 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 218
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2377721.708293
FMO2-HF: Nuclear repulsion 2293987.55035
FMO2-HF: Total energy -83734.157943
FMO2-MP2: Total energy -83981.500572


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:2:ARG)


Summations of interaction energy for fragment #1(A:2:ARG)
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.
22.39131.63314.105-9.802-13.545-0.09
Interaction energy analysis for fragmet #1(A:2:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.909 / q_NPA : 0.955
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].
3A4ILE00.0080.0043.611-7.424-4.371-0.009-1.593-1.4510.005
4A5VAL0-0.029-0.0096.1521.9991.9990.0000.0000.0000.000
5A6LEU00.007-0.0198.603-0.070-0.0700.0000.0000.0000.000
6A7PRO0-0.039-0.02312.124-0.159-0.1590.0000.0000.0000.000
7A8GLY00.0360.01614.6970.7690.7690.0000.0000.0000.000
8A9ASP-1-0.846-0.90911.425-21.629-21.6290.0000.0000.0000.000
9A10LEU0-0.062-0.04013.118-0.684-0.6840.0000.0000.0000.000
10A11LEU0-0.056-0.0208.715-1.219-1.2190.0000.0000.0000.000
11A12SER00.0350.00010.992-0.295-0.2950.0000.0000.0000.000
12A13THR00.0290.01213.4191.1161.1160.0000.0000.0000.000
13A14ASN00.0000.00215.1020.3790.3790.0000.0000.0000.000
14A15PRO00.0580.01115.976-1.045-1.0450.0000.0000.0000.000
15A16ARG10.9160.96217.39013.61213.6120.0000.0000.0000.000
16A17ALA00.0320.03212.594-0.082-0.0820.0000.0000.0000.000
17A18ALA0-0.028-0.00412.540-1.752-1.7520.0000.0000.0000.000
18A19GLY00.0560.03311.8080.9150.9150.0000.0000.0000.000
19A20TYR0-0.044-0.04010.4660.2710.2710.0000.0000.0000.000
20A21GLY00.0240.00410.804-1.731-1.7310.0000.0000.0000.000
21A22THR0-0.023-0.00710.8460.0740.0740.0000.0000.0000.000
22A23TYR0-0.030-0.01413.4920.5280.5280.0000.0000.0000.000
23A24VAL00.0090.00316.748-0.502-0.5020.0000.0000.0000.000
24A25GLU-1-0.884-0.94319.107-12.519-12.5190.0000.0000.0000.000
25A26GLY00.0340.01721.640-0.223-0.2230.0000.0000.0000.000
26A27GLY0-0.038-0.02021.9150.0660.0660.0000.0000.0000.000
27A28LYS10.9540.99018.16013.40913.4090.0000.0000.0000.000
28A29VAL0-0.009-0.00113.0240.2430.2430.0000.0000.0000.000
29A30TYR00.0520.02214.409-0.623-0.6230.0000.0000.0000.000
30A31ALA00.0600.03710.909-0.474-0.4740.0000.0000.0000.000
31A32LYS10.8730.93012.76920.16020.1600.0000.0000.0000.000
32A33ILE0-0.039-0.01711.3461.2111.2110.0000.0000.0000.000
33A34ILE00.0260.02310.473-1.111-1.1110.0000.0000.0000.000
34A35GLY0-0.010-0.0137.7800.3360.3360.0000.0000.0000.000
35A36LEU0-0.024-0.0052.355-2.461-0.7431.472-0.692-2.4980.001
36A37PHE00.0160.0123.544-1.475-0.6900.018-0.182-0.621-0.001
37A38ASP-1-0.848-0.9341.873-113.507-110.89811.957-6.991-7.575-0.095
38A39GLN00.0250.0193.58110.16710.3090.009-0.012-0.140-0.001
39A40THR0-0.032-0.0265.600-1.082-1.0820.0000.0000.0000.000
40A41GLU-1-0.906-0.9507.886-18.519-18.5190.0000.0000.0000.000
41A42THR0-0.034-0.00910.6951.5441.5440.0000.0000.0000.000
42A43HIS0-0.044-0.0215.3666.2246.2240.0000.0000.0000.000
43A44VAL00.0030.0068.395-2.641-2.6410.0000.0000.0000.000
44A45ARG10.8590.9166.67833.40033.4000.0000.0000.0000.000
45A46VAL00.0420.0226.404-3.504-3.5040.0000.0000.0000.000
46A47ILE0-0.038-0.0112.9531.5862.5210.658-0.332-1.2600.001
47A48PRO00.0260.0177.004-0.012-0.0120.0000.0000.0000.000
48A49LEU00.0190.0087.800-1.088-1.0880.0000.0000.0000.000
49A50LYS10.9510.96411.06018.62818.6280.0000.0000.0000.000
50A51GLY00.0240.02114.702-0.399-0.3990.0000.0000.0000.000
51A52ARG10.9490.97017.67513.02413.0240.0000.0000.0000.000
52A53TYR00.005-0.03916.750-0.197-0.1970.0000.0000.0000.000
53A54THR0-0.0020.00016.4800.5830.5830.0000.0000.0000.000
54A55PRO0-0.0070.01517.024-1.023-1.0230.0000.0000.0000.000
55A56SER0-0.049-0.02315.149-0.273-0.2730.0000.0000.0000.000
56A57VAL00.035-0.00817.3160.3250.3250.0000.0000.0000.000
57A58GLY00.0000.00917.222-0.805-0.8050.0000.0000.0000.000
58A59ASP-1-0.798-0.85315.925-18.891-18.8910.0000.0000.0000.000
59A60VAL00.004-0.00718.3150.9250.9250.0000.0000.0000.000
60A61VAL0-0.014-0.01319.826-0.625-0.6250.0000.0000.0000.000
61A62ILE0-0.025-0.00322.4380.5280.5280.0000.0000.0000.000
62A63GLY00.0300.00525.400-0.261-0.2610.0000.0000.0000.000
63A64ILE0-0.015-0.00528.1450.1870.1870.0000.0000.0000.000
64A65ILE0-0.013-0.00831.698-0.130-0.1300.0000.0000.0000.000
65A66ARG10.9150.95233.3859.4919.4910.0000.0000.0000.000
66A67GLU-1-0.926-0.97035.771-7.903-7.9030.0000.0000.0000.000
67A68VAL0-0.0050.00237.768-0.206-0.2060.0000.0000.0000.000
68A69ALA00.0210.01839.7410.1440.1440.0000.0000.0000.000
69A70ALA00.007-0.00441.543-0.012-0.0120.0000.0000.0000.000
70A71ASN00.021-0.00438.3290.1090.1090.0000.0000.0000.000
71A72GLY00.001-0.01136.849-0.231-0.2310.0000.0000.0000.000
72A73TRP0-0.007-0.00134.9470.1060.1060.0000.0000.0000.000
73A74ALA00.0320.03633.810-0.327-0.3270.0000.0000.0000.000
74A75VAL0-0.028-0.01829.3300.1070.1070.0000.0000.0000.000
75A76ASP-1-0.864-0.93329.572-10.764-10.7640.0000.0000.0000.000
76A77ILE00.021-0.00523.253-0.148-0.1480.0000.0000.0000.000
77A78TYR0-0.0300.01122.808-0.449-0.4490.0000.0000.0000.000
78A79SER0-0.018-0.01022.639-0.716-0.7160.0000.0000.0000.000
79A80PRO0-0.049-0.02522.9050.4260.4260.0000.0000.0000.000
80A81TYR0-0.0090.00321.4760.0010.0010.0000.0000.0000.000
81A82GLN00.0230.01025.9500.1440.1440.0000.0000.0000.000
82A83ALA00.010-0.00527.027-0.291-0.2910.0000.0000.0000.000
83A84PHE0-0.0130.00328.9110.3330.3330.0000.0000.0000.000
84A85LEU0-0.0090.01030.703-0.315-0.3150.0000.0000.0000.000
85A86PRO00.0230.02031.8050.3290.3290.0000.0000.0000.000
86A87VAL00.0760.02034.894-0.106-0.1060.0000.0000.0000.000
87A88SER0-0.028-0.01134.6930.0610.0610.0000.0000.0000.000
88A89GLU-1-0.859-0.90630.700-10.023-10.0230.0000.0000.0000.000
89A90ASN00.0520.02732.668-0.355-0.3550.0000.0000.0000.000
90A91PRO00.002-0.00633.8610.2630.2630.0000.0000.0000.000
91A92GLU-1-0.800-0.85336.600-8.207-8.2070.0000.0000.0000.000
92A93MET0-0.036-0.00938.3410.2010.2010.0000.0000.0000.000
93A94LYS10.9520.98440.7356.7626.7620.0000.0000.0000.000
94A95PRO00.0450.00743.2430.0930.0930.0000.0000.0000.000
95A96ASN0-0.0010.00145.619-0.037-0.0370.0000.0000.0000.000
96A97LYS10.8220.91943.3377.3037.3030.0000.0000.0000.000
97A98LYS10.9240.96045.5396.2906.2900.0000.0000.0000.000
98A99PRO00.0870.02341.278-0.040-0.0400.0000.0000.0000.000
99A100ASN00.0310.01441.533-0.108-0.1080.0000.0000.0000.000
100A101GLU-1-0.842-0.91143.615-6.585-6.5850.0000.0000.0000.000
101A102VAL0-0.109-0.04838.3240.0220.0220.0000.0000.0000.000
102A103LEU0-0.037-0.01834.888-0.202-0.2020.0000.0000.0000.000
103A104ASP-1-0.813-0.90138.743-7.354-7.3540.0000.0000.0000.000
104A105ILE0-0.036-0.03538.287-0.253-0.2530.0000.0000.0000.000
105A106GLY0-0.037-0.01036.7900.1510.1510.0000.0000.0000.000
106A107ASP-1-0.853-0.90535.824-8.430-8.4300.0000.0000.0000.000
107A108ALA0-0.013-0.01630.946-0.274-0.2740.0000.0000.0000.000
108A109ILE0-0.006-0.00329.5160.1950.1950.0000.0000.0000.000
109A110ILE0-0.025-0.00325.171-0.424-0.4240.0000.0000.0000.000
110A111ALA00.016-0.01225.7380.3140.3140.0000.0000.0000.000
111A112LYS10.8540.89720.88813.26213.2620.0000.0000.0000.000
112A113VAL0-0.033-0.00720.6490.6590.6590.0000.0000.0000.000
113A114LEU0-0.0020.01122.146-0.452-0.4520.0000.0000.0000.000
114A115ASN00.012-0.01223.960-0.509-0.5090.0000.0000.0000.000
115A116ILE00.0010.01320.1680.1820.1820.0000.0000.0000.000
116A117ASP-1-0.810-0.88824.227-10.834-10.8340.0000.0000.0000.000
117A118PRO00.0800.01826.105-0.284-0.2840.0000.0000.0000.000
118A119LYS10.9030.96727.3179.2139.2130.0000.0000.0000.000
119A120MET0-0.026-0.00923.724-0.125-0.1250.0000.0000.0000.000
120A121LYS10.8590.93526.69310.11710.1170.0000.0000.0000.000
121A122VAL00.008-0.00123.953-0.365-0.3650.0000.0000.0000.000
122A123THR0-0.039-0.01926.4520.5570.5570.0000.0000.0000.000
123A124LEU00.006-0.01025.216-0.461-0.4610.0000.0000.0000.000
124A125THR00.016-0.03626.0450.4510.4510.0000.0000.0000.000
125A126MET00.026-0.00327.531-0.431-0.4310.0000.0000.0000.000
126A127LYS10.7970.91629.6819.4029.4020.0000.0000.0000.000
127A128ASP-1-0.815-0.92824.520-13.047-13.0470.0000.0000.0000.000
128A129ARG10.9680.98824.98911.83311.8330.0000.0000.0000.000
129A130ILE0-0.050-0.01722.4730.2430.2430.0000.0000.0000.000
130A131CYS0-0.0060.03525.626-0.073-0.0730.0000.0000.0000.000
131A132ARG10.8990.96526.95211.07011.0700.0000.0000.0000.000
132A133PRO00.0290.02530.367-0.280-0.2800.0000.0000.0000.000
133A134ILE0-0.064-0.04728.335-0.024-0.0240.0000.0000.0000.000
134A135ARG10.8070.86832.7808.4608.4600.0000.0000.0000.000
135A136PHE00.0130.01033.6570.1920.1920.0000.0000.0000.000
136A137GLY00.0100.01232.291-0.288-0.2880.0000.0000.0000.000
137A138ARG10.8580.90830.9549.3819.3810.0000.0000.0000.000
138A139ILE0-0.001-0.00927.205-0.310-0.3100.0000.0000.0000.000
139A140VAL0-0.0060.00524.6540.2070.2070.0000.0000.0000.000
140A141ALA00.0020.00624.213-0.367-0.3670.0000.0000.0000.000
141A142ILE00.0190.02318.5640.1210.1210.0000.0000.0000.000
142A143ASN0-0.028-0.03318.558-1.007-1.0070.0000.0000.0000.000
143A144PRO00.1110.04117.209-0.643-0.6430.0000.0000.0000.000
144A145ALA0-0.050-0.00714.273-1.210-1.2100.0000.0000.0000.000
145A146ARG10.8260.91413.61716.57816.5780.0000.0000.0000.000
146A147VAL00.0570.03614.0420.1950.1950.0000.0000.0000.000
147A148PRO0-0.015-0.0199.5820.1750.1750.0000.0000.0000.000
148A149ARG10.7720.89011.37217.55617.5560.0000.0000.0000.000
149A150VAL00.0500.02313.0620.5350.5350.0000.0000.0000.000
150A151ILE0-0.0150.00412.7180.7830.7830.0000.0000.0000.000
151A152GLY00.0670.03111.7940.6130.6130.0000.0000.0000.000
152A153LYS11.0020.9928.15926.43826.4380.0000.0000.0000.000
153A154LYS10.9830.9909.71325.80125.8010.0000.0000.0000.000
154A155GLY00.0420.02311.5331.6651.6650.0000.0000.0000.000
155A156SER0-0.068-0.05613.2401.2671.2670.0000.0000.0000.000
156A157MET00.0340.05015.1701.2151.2150.0000.0000.0000.000
157A158ILE00.0390.02316.3550.9600.9600.0000.0000.0000.000
158A159LYS10.8630.94515.65118.11818.1180.0000.0000.0000.000
159A160LEU00.0290.05819.7080.7110.7110.0000.0000.0000.000
160A161LEU00.0420.00320.7750.6120.6120.0000.0000.0000.000
161A162LYS10.8400.93220.46814.32414.3240.0000.0000.0000.000
162A163SER0-0.030-0.05023.4990.5280.5280.0000.0000.0000.000
163A164GLU-1-0.799-0.88025.354-10.495-10.4950.0000.0000.0000.000
164A165LEU0-0.023-0.00126.6680.4030.4030.0000.0000.0000.000
165A166ASP-1-0.910-0.94428.430-9.455-9.4550.0000.0000.0000.000
166A167VAL0-0.030-0.00226.5010.3060.3060.0000.0000.0000.000
167A168GLN0-0.050-0.02326.699-0.321-0.3210.0000.0000.0000.000
168A169ILE00.0390.00221.941-0.029-0.0290.0000.0000.0000.000
169A170VAL0-0.045-0.03121.794-0.457-0.4570.0000.0000.0000.000
170A171VAL00.0190.00417.0590.3010.3010.0000.0000.0000.000
171A172GLY00.0200.03018.805-0.466-0.4660.0000.0000.0000.000
172A173GLN0-0.031-0.03213.999-1.567-1.5670.0000.0000.0000.000
173A174ASN0-0.016-0.02917.270-0.892-0.8920.0000.0000.0000.000
174A175GLY00.0230.00519.3290.2340.2340.0000.0000.0000.000
175A176LEU0-0.063-0.00220.2110.4940.4940.0000.0000.0000.000
176A177ILE0-0.022-0.02519.954-0.423-0.4230.0000.0000.0000.000
177A178TRP0-0.0030.00923.4750.3340.3340.0000.0000.0000.000
178A179VAL0-0.004-0.01425.456-0.360-0.3600.0000.0000.0000.000
179A180ASN0-0.006-0.01927.8220.5470.5470.0000.0000.0000.000
180A181GLY00.0660.02730.432-0.258-0.2580.0000.0000.0000.000
181A182ASP-1-0.775-0.88033.095-8.193-8.1930.0000.0000.0000.000
182A183ARG11.0011.00434.2427.4437.4430.0000.0000.0000.000
183A184ARG10.9100.94134.9917.8357.8350.0000.0000.0000.000
184A185LYS10.9050.94931.4529.1549.1540.0000.0000.0000.000
185A186VAL0-0.044-0.02930.224-0.349-0.3490.0000.0000.0000.000
186A187SER00.0290.02130.084-0.185-0.1850.0000.0000.0000.000
187A188ILE0-0.0020.00428.696-0.242-0.2420.0000.0000.0000.000
188A189ALA00.0030.00026.084-0.388-0.3880.0000.0000.0000.000
189A190GLU-1-0.846-0.90825.762-10.351-10.3510.0000.0000.0000.000
190A191GLU-1-0.807-0.88326.285-10.028-10.0280.0000.0000.0000.000
191A192ALA00.0260.01224.044-0.267-0.2670.0000.0000.0000.000
192A193ILE0-0.040-0.02421.306-0.716-0.7160.0000.0000.0000.000
193A194TYR00.0390.01221.813-0.612-0.6120.0000.0000.0000.000
194A195LEU00.0110.02123.411-0.306-0.3060.0000.0000.0000.000
195A196ILE0-0.011-0.00417.526-0.577-0.5770.0000.0000.0000.000
196A197GLU-1-0.864-0.93118.517-15.022-15.0220.0000.0000.0000.000
197A198GLN0-0.010-0.01419.743-0.391-0.3910.0000.0000.0000.000
198A199GLU-1-0.876-0.91218.563-14.086-14.0860.0000.0000.0000.000
199A200ALA00.0140.00618.442-0.988-0.9880.0000.0000.0000.000
200A201HIS00.0090.00317.256-1.270-1.2700.0000.0000.0000.000
201A202THR0-0.060-0.03813.4280.1650.1650.0000.0000.0000.000
202A203GLU-1-0.806-0.88514.517-16.103-16.1030.0000.0000.0000.000
203A204GLY00.0500.02616.074-0.740-0.7400.0000.0000.0000.000
204A205LEU0-0.021-0.01116.6140.5760.5760.0000.0000.0000.000
205A206THR0-0.006-0.03915.8260.3000.3000.0000.0000.0000.000
206A207ASP-1-0.863-0.93218.490-13.937-13.9370.0000.0000.0000.000
207A208ARG10.7940.87220.60014.42114.4210.0000.0000.0000.000
208A209VAL0-0.001-0.00120.1700.5040.5040.0000.0000.0000.000
209A210ALA00.0430.02223.0400.4530.4530.0000.0000.0000.000
210A211GLU-1-0.888-0.92624.901-10.097-10.0970.0000.0000.0000.000
211A212PHE0-0.0120.00026.0540.4270.4270.0000.0000.0000.000
212A213ILE00.015-0.01124.5740.4360.4360.0000.0000.0000.000
213A214LYS10.8630.93628.51010.68210.6820.0000.0000.0000.000
214A215ARG10.9590.97030.7639.2529.2520.0000.0000.0000.000
215A216ARG10.7560.83931.0319.3689.3680.0000.0000.0000.000
216A217LYS10.7620.86029.94210.27710.2770.0000.0000.0000.000
217A218ALA0-0.082-0.01434.1900.2280.2280.0000.0000.0000.000
218A219ASP-1-0.910-0.93436.999-7.751-7.7510.0000.0000.0000.000