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: 37N6L

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 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 218
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2378635.888564
FMO2-HF: Nuclear repulsion 2294903.323696
FMO2-HF: Total energy -83732.564868
FMO2-MP2: Total energy -83980.056378


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.
45.84957.9023.055-5.985-9.125-0.042
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 : 0.924 / q_NPA : 0.952
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].
3A4ILE00.0170.0123.735-7.444-5.416-0.013-0.981-1.0340.002
4A5VAL0-0.022-0.0066.3102.1622.1620.0000.0000.0000.000
5A6LEU00.004-0.0168.692-0.115-0.1150.0000.0000.0000.000
6A7PRO0-0.044-0.02712.214-0.118-0.1180.0000.0000.0000.000
7A8GLY00.0390.02314.7480.7650.7650.0000.0000.0000.000
8A9ASP-1-0.859-0.92511.821-20.686-20.6860.0000.0000.0000.000
9A10LEU0-0.048-0.03113.171-0.701-0.7010.0000.0000.0000.000
10A11LEU0-0.051-0.0238.812-1.171-1.1710.0000.0000.0000.000
11A12SER00.0160.00211.010-0.287-0.2870.0000.0000.0000.000
12A13THR00.0280.01213.4461.1461.1460.0000.0000.0000.000
13A14ASN00.0100.00215.0290.4530.4530.0000.0000.0000.000
14A15PRO00.0540.01215.922-1.081-1.0810.0000.0000.0000.000
15A16ARG10.9160.95817.35513.79613.7960.0000.0000.0000.000
16A17ALA00.0330.03412.390-0.068-0.0680.0000.0000.0000.000
17A18ALA0-0.024-0.00112.561-1.776-1.7760.0000.0000.0000.000
18A19GLY00.0520.02911.9270.8390.8390.0000.0000.0000.000
19A20TYR0-0.008-0.00610.4200.3430.3430.0000.0000.0000.000
20A21GLY00.011-0.00511.168-1.687-1.6870.0000.0000.0000.000
21A22THR0-0.028-0.02011.184-0.046-0.0460.0000.0000.0000.000
22A23TYR0-0.021-0.02013.8800.5260.5260.0000.0000.0000.000
23A24VAL00.002-0.00217.028-0.503-0.5030.0000.0000.0000.000
24A25GLU-1-0.900-0.94619.355-12.285-12.2850.0000.0000.0000.000
25A26GLY00.0260.01221.798-0.222-0.2220.0000.0000.0000.000
26A27GLY0-0.035-0.01821.9890.0650.0650.0000.0000.0000.000
27A28LYS10.9400.98318.11013.46213.4620.0000.0000.0000.000
28A29VAL00.0050.00513.1790.2660.2660.0000.0000.0000.000
29A30TYR00.0390.01814.488-0.528-0.5280.0000.0000.0000.000
30A31ALA00.0530.03210.786-0.502-0.5020.0000.0000.0000.000
31A32LYS10.9170.96612.75220.00320.0030.0000.0000.0000.000
32A33ILE0-0.050-0.02111.2381.2131.2130.0000.0000.0000.000
33A34ILE00.0260.02410.418-1.112-1.1120.0000.0000.0000.000
34A35GLY0-0.012-0.0207.8670.2990.2990.0000.0000.0000.000
35A36LEU0-0.030-0.0092.299-2.125-0.4760.854-0.603-1.9000.001
36A37PHE00.0250.0173.581-1.298-0.5840.016-0.166-0.564-0.001
37A38ASP-1-0.915-0.9742.540-92.909-86.3481.896-3.914-4.544-0.045
38A39GLN00.0320.0233.74510.52710.6820.004-0.015-0.1440.000
39A40THR0-0.047-0.0315.582-1.398-1.3980.0000.0000.0000.000
40A41GLU-1-0.907-0.9557.603-18.637-18.6370.0000.0000.0000.000
41A42THR0-0.042-0.00610.4671.9651.9650.0000.0000.0000.000
42A43HIS0-0.050-0.0415.4535.6355.6350.0000.0000.0000.000
43A44VAL00.0040.0118.270-2.830-2.8300.0000.0000.0000.000
44A45ARG10.8990.9456.94034.42934.4290.0000.0000.0000.000
45A46VAL00.0430.0236.836-3.478-3.4780.0000.0000.0000.000
46A47ILE0-0.039-0.0152.9931.3562.3020.298-0.306-0.9390.001
47A48PRO00.0280.0147.449-0.016-0.0160.0000.0000.0000.000
48A49LEU00.0220.0147.894-1.109-1.1090.0000.0000.0000.000
49A50LYS10.9600.96211.15618.57418.5740.0000.0000.0000.000
50A51GLY00.0140.02014.795-0.403-0.4030.0000.0000.0000.000
51A52ARG10.9430.96717.74113.00113.0010.0000.0000.0000.000
52A53TYR00.0400.00816.703-0.211-0.2110.0000.0000.0000.000
53A54THR0-0.021-0.01416.6590.7830.7830.0000.0000.0000.000
54A55PRO0-0.0110.00416.999-1.024-1.0240.0000.0000.0000.000
55A56SER0-0.029-0.00415.347-0.295-0.2950.0000.0000.0000.000
56A57VAL00.041-0.00717.4040.3250.3250.0000.0000.0000.000
57A58GLY00.0010.01017.349-0.800-0.8000.0000.0000.0000.000
58A59ASP-1-0.826-0.90815.915-19.153-19.1530.0000.0000.0000.000
59A60VAL0-0.004-0.00718.1740.9410.9410.0000.0000.0000.000
60A61VAL0-0.017-0.01619.781-0.602-0.6020.0000.0000.0000.000
61A62ILE0-0.028-0.00322.4010.5160.5160.0000.0000.0000.000
62A63GLY00.0310.00325.410-0.263-0.2630.0000.0000.0000.000
63A64ILE0-0.0050.00128.1300.1860.1860.0000.0000.0000.000
64A65ILE0-0.016-0.00831.696-0.135-0.1350.0000.0000.0000.000
65A66ARG10.9650.98433.9409.2109.2100.0000.0000.0000.000
66A67GLU-1-0.929-0.97435.719-7.870-7.8700.0000.0000.0000.000
67A68VAL0-0.0010.00537.667-0.207-0.2070.0000.0000.0000.000
68A69ALA00.0170.01839.7560.1460.1460.0000.0000.0000.000
69A70ALA00.002-0.00841.458-0.012-0.0120.0000.0000.0000.000
70A71ASN00.022-0.00438.6580.1010.1010.0000.0000.0000.000
71A72GLY00.008-0.01536.849-0.231-0.2310.0000.0000.0000.000
72A73TRP00.0020.00234.7530.1010.1010.0000.0000.0000.000
73A74ALA00.0210.03233.704-0.326-0.3260.0000.0000.0000.000
74A75VAL0-0.034-0.02129.0660.1120.1120.0000.0000.0000.000
75A76ASP-1-0.912-0.95429.666-10.799-10.7990.0000.0000.0000.000
76A77ILE00.007-0.01223.098-0.166-0.1660.0000.0000.0000.000
77A78TYR0-0.0230.00623.122-0.589-0.5890.0000.0000.0000.000
78A79SER0-0.014-0.00922.568-0.698-0.6980.0000.0000.0000.000
79A80PRO0-0.054-0.02922.7940.4240.4240.0000.0000.0000.000
80A81TYR0-0.024-0.01221.7280.0100.0100.0000.0000.0000.000
81A82GLN00.0270.01225.9470.1140.1140.0000.0000.0000.000
82A83ALA00.011-0.00126.950-0.295-0.2950.0000.0000.0000.000
83A84PHE0-0.0130.00928.8750.3430.3430.0000.0000.0000.000
84A85LEU0-0.0230.00730.383-0.313-0.3130.0000.0000.0000.000
85A86PRO00.0220.01931.7800.3420.3420.0000.0000.0000.000
86A87VAL00.0820.02234.974-0.108-0.1080.0000.0000.0000.000
87A88SER0-0.031-0.01634.8910.0710.0710.0000.0000.0000.000
88A89GLU-1-0.905-0.92030.729-10.193-10.1930.0000.0000.0000.000
89A90ASN00.0560.02232.618-0.395-0.3950.0000.0000.0000.000
90A91PRO0-0.021-0.01733.7490.2810.2810.0000.0000.0000.000
91A92GLU-1-0.839-0.90836.592-8.213-8.2130.0000.0000.0000.000
92A93MET0-0.049-0.01738.2550.2220.2220.0000.0000.0000.000
93A94LYS10.9460.97840.6266.8486.8480.0000.0000.0000.000
94A95PRO00.0470.00843.4120.0810.0810.0000.0000.0000.000
95A96ASN00.0080.00545.584-0.039-0.0390.0000.0000.0000.000
96A97LYS10.8710.94643.3667.2807.2800.0000.0000.0000.000
97A98LYS10.9861.01145.4156.1916.1910.0000.0000.0000.000
98A99PRO00.0920.02841.289-0.042-0.0420.0000.0000.0000.000
99A100ASN00.0360.01441.448-0.132-0.1320.0000.0000.0000.000
100A101GLU-1-0.918-0.96143.543-6.636-6.6360.0000.0000.0000.000
101A102VAL0-0.135-0.05738.103-0.002-0.0020.0000.0000.0000.000
102A103LEU0-0.060-0.04434.345-0.209-0.2090.0000.0000.0000.000
103A104ASP-1-0.842-0.90838.694-7.381-7.3810.0000.0000.0000.000
104A105ILE0-0.023-0.03338.267-0.255-0.2550.0000.0000.0000.000
105A106GLY0-0.043-0.01336.8140.1470.1470.0000.0000.0000.000
106A107ASP-1-0.847-0.90036.040-8.382-8.3820.0000.0000.0000.000
107A108ALA00.009-0.00131.003-0.274-0.2740.0000.0000.0000.000
108A109ILE0-0.001-0.01029.2930.1930.1930.0000.0000.0000.000
109A110ILE0-0.0130.00825.344-0.417-0.4170.0000.0000.0000.000
110A111ALA00.011-0.01125.6760.3080.3080.0000.0000.0000.000
111A112LYS10.8810.92420.23313.71713.7170.0000.0000.0000.000
112A113VAL0-0.031-0.00620.5930.6580.6580.0000.0000.0000.000
113A114LEU00.0040.01022.302-0.473-0.4730.0000.0000.0000.000
114A115ASN00.007-0.01523.978-0.447-0.4470.0000.0000.0000.000
115A116ILE00.0010.01520.1710.1710.1710.0000.0000.0000.000
116A117ASP-1-0.799-0.88424.211-11.099-11.0990.0000.0000.0000.000
117A118PRO00.0570.00226.008-0.254-0.2540.0000.0000.0000.000
118A119LYS10.9000.97227.1969.2069.2060.0000.0000.0000.000
119A120MET0-0.024-0.00423.598-0.109-0.1090.0000.0000.0000.000
120A121LYS10.9110.95826.6769.8939.8930.0000.0000.0000.000
121A122VAL00.0050.00024.064-0.371-0.3710.0000.0000.0000.000
122A123THR0-0.049-0.02626.5350.5700.5700.0000.0000.0000.000
123A124LEU0-0.008-0.01525.245-0.472-0.4720.0000.0000.0000.000
124A125THR00.005-0.06526.0430.4470.4470.0000.0000.0000.000
125A126MET00.034-0.00427.410-0.426-0.4260.0000.0000.0000.000
126A127LYS10.8620.96629.5599.2409.2400.0000.0000.0000.000
127A128ASP-1-0.851-0.94824.218-12.938-12.9380.0000.0000.0000.000
128A129ARG10.9590.98424.86212.00112.0010.0000.0000.0000.000
129A130ILE0-0.067-0.03122.6190.2090.2090.0000.0000.0000.000
130A131CYS0-0.0530.00725.603-0.091-0.0910.0000.0000.0000.000
131A132ARG10.9790.99927.34010.82110.8210.0000.0000.0000.000
132A133PRO00.0020.02730.361-0.272-0.2720.0000.0000.0000.000
133A134ILE0-0.043-0.04228.622-0.013-0.0130.0000.0000.0000.000
134A135ARG10.8600.93432.8358.4308.4300.0000.0000.0000.000
135A136PHE00.0070.00333.4830.1940.1940.0000.0000.0000.000
136A137GLY00.0070.01132.443-0.286-0.2860.0000.0000.0000.000
137A138ARG10.9390.96831.0289.3309.3300.0000.0000.0000.000
138A139ILE00.008-0.00227.294-0.301-0.3010.0000.0000.0000.000
139A140VAL0-0.0070.00824.6540.2010.2010.0000.0000.0000.000
140A141ALA00.0030.00324.342-0.364-0.3640.0000.0000.0000.000
141A142ILE00.0330.03218.5560.1090.1090.0000.0000.0000.000
142A143ASN00.000-0.00418.396-1.061-1.0610.0000.0000.0000.000
143A144PRO00.1070.04117.311-0.663-0.6630.0000.0000.0000.000
144A145ALA0-0.043-0.01314.314-1.207-1.2070.0000.0000.0000.000
145A146ARG10.8440.92013.71417.26617.2660.0000.0000.0000.000
146A147VAL00.0760.05014.0210.1790.1790.0000.0000.0000.000
147A148PRO0-0.027-0.0239.6470.1440.1440.0000.0000.0000.000
148A149ARG10.8210.91011.45117.89117.8910.0000.0000.0000.000
149A150VAL00.0590.03313.1740.4850.4850.0000.0000.0000.000
150A151ILE0-0.021-0.01013.0250.7250.7250.0000.0000.0000.000
151A152GLY00.0800.03511.8830.5880.5880.0000.0000.0000.000
152A153LYS11.0120.9988.26727.35427.3540.0000.0000.0000.000
153A154LYS10.9610.99310.00125.95925.9590.0000.0000.0000.000
154A155GLY00.0280.00911.7851.5821.5820.0000.0000.0000.000
155A156SER0-0.074-0.08013.3611.2121.2120.0000.0000.0000.000
156A157MET00.0410.05715.3731.1461.1460.0000.0000.0000.000
157A158ILE00.0240.02916.1140.9030.9030.0000.0000.0000.000
158A159LYS10.8750.96416.10918.21518.2150.0000.0000.0000.000
159A160LEU00.0460.07419.9390.7020.7020.0000.0000.0000.000
160A161LEU00.0480.01020.5340.6160.6160.0000.0000.0000.000
161A162LYS10.8700.93920.49214.40714.4070.0000.0000.0000.000
162A163SER0-0.027-0.06123.7440.5200.5200.0000.0000.0000.000
163A164GLU-1-0.808-0.90725.583-10.556-10.5560.0000.0000.0000.000
164A165LEU0-0.049-0.01026.7330.4500.4500.0000.0000.0000.000
165A166ASP-1-0.955-0.97428.735-9.629-9.6290.0000.0000.0000.000
166A167VAL0-0.045-0.00526.7130.3100.3100.0000.0000.0000.000
167A168GLN0-0.041-0.01126.925-0.149-0.1490.0000.0000.0000.000
168A169ILE00.0380.00222.0350.0040.0040.0000.0000.0000.000
169A170VAL0-0.067-0.03121.934-0.421-0.4210.0000.0000.0000.000
170A171VAL00.0250.00417.2400.3050.3050.0000.0000.0000.000
171A172GLY00.0040.02318.874-0.463-0.4630.0000.0000.0000.000
172A173GLN0-0.023-0.02913.934-1.444-1.4440.0000.0000.0000.000
173A174ASN0-0.020-0.02717.296-1.131-1.1310.0000.0000.0000.000
174A175GLY00.0310.01019.3970.2430.2430.0000.0000.0000.000
175A176LEU0-0.0540.00020.3130.4900.4900.0000.0000.0000.000
176A177ILE0-0.024-0.02520.165-0.426-0.4260.0000.0000.0000.000
177A178TRP0-0.0180.00423.6180.3380.3380.0000.0000.0000.000
178A179VAL00.008-0.00525.767-0.346-0.3460.0000.0000.0000.000
179A180ASN0-0.024-0.04128.0130.5330.5330.0000.0000.0000.000
180A181GLY00.0790.03130.642-0.256-0.2560.0000.0000.0000.000
181A182ASP-1-0.809-0.89233.316-8.202-8.2020.0000.0000.0000.000
182A183ARG11.0071.00134.5137.4597.4590.0000.0000.0000.000
183A184ARG10.9290.94635.1697.8547.8540.0000.0000.0000.000
184A185LYS10.9841.00531.7149.0319.0310.0000.0000.0000.000
185A186VAL0-0.042-0.02630.301-0.319-0.3190.0000.0000.0000.000
186A187SER0-0.044-0.01430.246-0.223-0.2230.0000.0000.0000.000
187A188ILE00.0540.02728.841-0.235-0.2350.0000.0000.0000.000
188A189ALA0-0.007-0.00826.273-0.381-0.3810.0000.0000.0000.000
189A190GLU-1-0.935-0.97425.848-10.435-10.4350.0000.0000.0000.000
190A191GLU-1-0.885-0.95026.389-10.091-10.0910.0000.0000.0000.000
191A192ALA00.0220.01124.136-0.264-0.2640.0000.0000.0000.000
192A193ILE0-0.048-0.03021.081-0.718-0.7180.0000.0000.0000.000
193A194TYR00.0440.01321.937-0.610-0.6100.0000.0000.0000.000
194A195LEU00.0060.01823.576-0.267-0.2670.0000.0000.0000.000
195A196ILE0-0.010-0.00517.718-0.588-0.5880.0000.0000.0000.000
196A197GLU-1-0.930-0.97718.702-14.795-14.7950.0000.0000.0000.000
197A198GLN0-0.027-0.02419.925-0.321-0.3210.0000.0000.0000.000
198A199GLU-1-0.948-0.96618.657-14.067-14.0670.0000.0000.0000.000
199A200ALA00.0040.00318.691-0.943-0.9430.0000.0000.0000.000
200A201HIS00.007-0.00317.257-1.215-1.2150.0000.0000.0000.000
201A202THR0-0.052-0.02813.7680.1170.1170.0000.0000.0000.000
202A203GLU-1-0.822-0.89014.812-16.011-16.0110.0000.0000.0000.000
203A204GLY00.0400.01216.358-0.742-0.7420.0000.0000.0000.000
204A205LEU0-0.0030.00016.8600.5540.5540.0000.0000.0000.000
205A206THR0-0.016-0.04416.0870.2760.2760.0000.0000.0000.000
206A207ASP-1-0.872-0.93518.675-13.610-13.6100.0000.0000.0000.000
207A208ARG10.8750.93421.12314.10114.1010.0000.0000.0000.000
208A209VAL0-0.010-0.00320.2120.4860.4860.0000.0000.0000.000
209A210ALA00.0460.02023.2180.4600.4600.0000.0000.0000.000
210A211GLU-1-0.983-0.98925.060-10.306-10.3060.0000.0000.0000.000
211A212PHE0-0.0050.00226.2060.4360.4360.0000.0000.0000.000
212A213ILE00.003-0.01124.4770.4410.4410.0000.0000.0000.000
213A214LYS10.9540.99228.65210.57110.5710.0000.0000.0000.000
214A215ARG10.9590.97030.9199.2339.2330.0000.0000.0000.000
215A216ARG10.8990.94831.1329.3809.3800.0000.0000.0000.000
216A217LYS10.7840.88830.26410.22710.2270.0000.0000.0000.000
217A218ALA0-0.086-0.01434.3180.2240.2240.0000.0000.0000.000
218A219ASP-1-0.964-0.97137.181-7.653-7.6530.0000.0000.0000.000