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: R5V38

Calculation Name: 2I5H-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2I5H

Chain ID: A

ChEMBL ID:

UniProt ID: O28741

Base Structure: X-ray

Registration Date: 2023-06-19

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 180
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2022260.676425
FMO2-HF: Nuclear repulsion 1948026.30853
FMO2-HF: Total energy -74234.367895
FMO2-MP2: Total energy -74453.62897


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:16:GLU)


Summations of interaction energy for fragment #1(A:16:GLU)
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.
-304.005-296.77630.129-15.225-22.1280.191
Interaction energy analysis for fragmet #1(A:16:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.804 / q_NPA : -0.927
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].
3A18TYR0-0.005-0.0123.197-10.062-8.2240.008-0.801-1.0450.001
4A19ALA0-0.021-0.0023.19813.77015.0760.089-0.615-0.779-0.005
5A20TYR00.0280.0155.130-6.860-6.782-0.001-0.002-0.0750.000
6A21VAL0-0.041-0.0178.7771.1701.1700.0000.0000.0000.000
7A22LEU0-0.012-0.0059.921-0.630-0.6300.0000.0000.0000.000
8A23ASP-1-0.795-0.89913.08715.30015.3000.0000.0000.0000.000
9A24PHE00.0120.00414.7050.8250.8250.0000.0000.0000.000
10A25MET00.0010.01216.271-1.060-1.0600.0000.0000.0000.000
11A26PRO00.0140.00919.4760.0090.0090.0000.0000.0000.000
12A27TYR00.003-0.01521.616-0.165-0.1650.0000.0000.0000.000
13A28GLY0-0.025-0.00619.450-0.265-0.2650.0000.0000.0000.000
14A29HIS0-0.005-0.03016.298-0.800-0.8000.0000.0000.0000.000
15A30PRO00.0300.01021.240-0.437-0.4370.0000.0000.0000.000
16A31ASP-1-0.894-0.93624.10311.23911.2390.0000.0000.0000.000
17A32ASP-1-0.876-0.91522.97012.19212.1920.0000.0000.0000.000
18A33LYS10.9880.97824.999-10.597-10.5970.0000.0000.0000.000
19A34ARG10.7760.88421.159-13.028-13.0280.0000.0000.0000.000
20A35PRO00.0490.02027.9120.0860.0860.0000.0000.0000.000
21A36ILE00.1090.03427.8930.3210.3210.0000.0000.0000.000
22A37HIS00.0200.02127.0190.3600.3600.0000.0000.0000.000
23A38ARG10.8990.94724.448-10.895-10.8950.0000.0000.0000.000
24A39ARG10.8380.93822.928-10.625-10.6250.0000.0000.0000.000
25A40GLU-1-0.886-0.93417.76514.85714.8570.0000.0000.0000.000
26A41PRO0-0.0030.01218.4500.2080.2080.0000.0000.0000.000
27A42LEU0-0.040-0.02714.9970.6820.6820.0000.0000.0000.000
28A43ALA00.0360.02512.322-0.598-0.5980.0000.0000.0000.000
29A44GLN0-0.0080.01310.8521.0711.0710.0000.0000.0000.000
30A45VAL00.001-0.0096.023-0.616-0.6160.0000.0000.0000.000
31A46VAL00.0170.0075.8520.7720.7720.0000.0000.0000.000
32A47GLY0-0.042-0.0262.389-4.829-5.1815.075-3.084-1.6390.022
33A48GLU-1-0.789-0.9123.31943.74842.5530.3832.256-1.4450.004
34A49ARG10.8880.9632.103-75.308-73.9927.038-3.598-4.7550.053
35A50ASN0-0.006-0.0121.885-29.153-31.44910.201-3.826-4.0790.055
36A51PHE00.0270.0112.856-14.240-13.5000.598-0.019-1.3180.007
37A52THR0-0.074-0.0292.256-36.576-30.4703.334-4.613-4.8270.053
38A53LEU00.0170.0234.220-0.367-0.1330.001-0.089-0.1450.000
39A54LEU0-0.020-0.0173.313-2.655-2.2680.028-0.078-0.3360.000
40A55GLU-1-0.748-0.8497.19417.65417.6540.0000.0000.0000.000
41A56VAL0-0.022-0.0257.7620.2140.2140.0000.0000.0000.000
42A57SER00.0640.03610.860-0.601-0.6010.0000.0000.0000.000
43A58ILE0-0.0150.00012.7461.0731.0730.0000.0000.0000.000
44A59ARG10.9170.96015.241-16.344-16.3440.0000.0000.0000.000
45A60LYS10.9840.96717.579-12.111-12.1110.0000.0000.0000.000
46A61GLY00.0230.01221.1600.1020.1020.0000.0000.0000.000
47A62LYS10.9030.98017.165-14.657-14.6570.0000.0000.0000.000
48A63GLN0-0.014-0.01819.573-0.111-0.1110.0000.0000.0000.000
49A64PRO0-0.022-0.01314.384-0.075-0.0750.0000.0000.0000.000
50A65LEU00.0140.02216.319-0.680-0.6800.0000.0000.0000.000
51A66VAL00.0390.01615.1591.4041.4040.0000.0000.0000.000
52A67MET0-0.030-0.02413.526-0.039-0.0390.0000.0000.0000.000
53A68ASP-1-0.836-0.89813.16519.46819.4680.0000.0000.0000.000
54A69ARG10.8110.9077.982-30.224-30.2240.0000.0000.0000.000
55A70VAL0-0.026-0.0257.470-2.235-2.2350.0000.0000.0000.000
56A71TYR00.0340.0216.8443.4893.4890.0000.0000.0000.000
57A72ILE0-0.061-0.0402.177-2.178-3.1113.375-0.756-1.6850.001
58A73GLY00.0810.0305.6430.3650.3650.0000.0000.0000.000
59A74LYS10.8890.9286.101-26.712-26.7120.0000.0000.0000.000
60A75GLY00.0440.0439.148-1.388-1.3880.0000.0000.0000.000
61A76GLU-1-0.924-0.95912.10415.54515.5450.0000.0000.0000.000
62A77ARG10.7980.9017.787-22.733-22.7330.0000.0000.0000.000
63A78ASP-1-0.834-0.91112.80616.64416.6440.0000.0000.0000.000
64A79VAL0-0.030-0.02612.647-0.937-0.9370.0000.0000.0000.000
65A80VAL00.0400.0218.791-0.838-0.8380.0000.0000.0000.000
66A81TYR0-0.050-0.02611.855-0.723-0.7230.0000.0000.0000.000
67A82LYS10.8980.92911.552-16.472-16.4720.0000.0000.0000.000
68A83ILE00.0360.0315.118-0.118-0.1180.0000.0000.0000.000
69A84LYS10.8080.8979.262-17.645-17.6450.0000.0000.0000.000
70A85ARG10.9050.95010.553-18.720-18.7200.0000.0000.0000.000
71A86ARG10.9831.0006.989-34.668-34.6680.0000.0000.0000.000
72A87LEU0-0.063-0.0268.659-2.368-2.3680.0000.0000.0000.000
73A88ARG10.8650.91310.100-15.153-15.1530.0000.0000.0000.000
74A89TYR00.0770.00612.816-0.786-0.7860.0000.0000.0000.000
75A90GLU-1-0.988-1.01013.98915.60015.6000.0000.0000.0000.000
76A91ASP-1-0.773-0.85313.82017.94017.9400.0000.0000.0000.000
77A92LEU0-0.056-0.01210.9830.1350.1350.0000.0000.0000.000
78A93THR00.021-0.01614.882-0.916-0.9160.0000.0000.0000.000
79A94PRO00.021-0.01117.5650.6140.6140.0000.0000.0000.000
80A95ALA00.0520.03219.0060.1360.1360.0000.0000.0000.000
81A96ALA00.0530.03113.7480.5180.5180.0000.0000.0000.000
82A97LYS10.8350.92515.011-15.442-15.4420.0000.0000.0000.000
83A98THR0-0.039-0.02116.6280.0570.0570.0000.0000.0000.000
84A99GLU-1-0.868-0.94215.63217.33717.3370.0000.0000.0000.000
85A100LEU0-0.056-0.0109.8370.9720.9720.0000.0000.0000.000
86A101PRO0-0.038-0.03312.6531.6221.6220.0000.0000.0000.000
87A102TYR00.0530.03114.7470.1450.1450.0000.0000.0000.000
88A103VAL00.0440.01510.1680.4760.4760.0000.0000.0000.000
89A104ILE0-0.040-0.0209.0311.6231.6230.0000.0000.0000.000
90A105GLU-1-0.947-0.98510.92018.35018.3500.0000.0000.0000.000
91A106HIS00.002-0.00112.281-0.950-0.9500.0000.0000.0000.000
92A107ILE0-0.008-0.0076.9230.0160.0160.0000.0000.0000.000
93A108ILE0-0.041-0.01310.531-0.182-0.1820.0000.0000.0000.000
94A109LYS10.9040.95512.166-18.601-18.6010.0000.0000.0000.000
95A110GLN0-0.0400.00711.509-2.097-2.0970.0000.0000.0000.000
96A111ASP-1-0.889-0.96510.65528.87028.8700.0000.0000.0000.000
97A112GLU-1-0.801-0.90312.81316.61216.6120.0000.0000.0000.000
98A113LYS10.9590.97615.716-16.693-16.6930.0000.0000.0000.000
99A114LYS10.9490.97611.401-26.351-26.3510.0000.0000.0000.000
100A115TYR00.0290.0128.592-0.200-0.2000.0000.0000.0000.000
101A116VAL0-0.071-0.02415.108-1.065-1.0650.0000.0000.0000.000
102A117ASP-1-0.947-0.98716.94316.60016.6000.0000.0000.0000.000
103A118PHE0-0.021-0.00115.725-0.364-0.3640.0000.0000.0000.000
104A119PHE0-0.007-0.00517.791-0.962-0.9620.0000.0000.0000.000
105A120ASN0-0.035-0.02721.007-0.443-0.4430.0000.0000.0000.000
106A121LYS10.8670.91921.622-13.768-13.7680.0000.0000.0000.000
107A122ALA00.0350.03321.046-0.697-0.6970.0000.0000.0000.000
108A123ASP-1-0.759-0.87520.68715.53015.5300.0000.0000.0000.000
109A124SER0-0.066-0.03721.417-0.736-0.7360.0000.0000.0000.000
110A125ILE00.018-0.00123.4510.0610.0610.0000.0000.0000.000
111A126THR0-0.0160.00122.7630.2550.2550.0000.0000.0000.000
112A127THR0-0.024-0.02525.227-0.557-0.5570.0000.0000.0000.000
113A128ARG10.8740.94828.708-9.735-9.7350.0000.0000.0000.000
114A129MET00.0270.02123.381-0.200-0.2000.0000.0000.0000.000
115A130HIS0-0.009-0.01023.770-0.278-0.2780.0000.0000.0000.000
116A131GLN00.0200.01519.0230.6650.6650.0000.0000.0000.000
117A132LEU00.0400.00720.5090.4010.4010.0000.0000.0000.000
118A133GLU-1-0.775-0.88622.19311.82411.8240.0000.0000.0000.000
119A134LEU0-0.078-0.02517.903-0.028-0.0280.0000.0000.0000.000
120A135LEU0-0.031-0.00717.0070.8280.8280.0000.0000.0000.000
121A136PRO00.002-0.00718.223-0.920-0.9200.0000.0000.0000.000
122A137GLY00.0080.00921.1150.1180.1180.0000.0000.0000.000
123A138VAL0-0.020-0.00722.700-0.528-0.5280.0000.0000.0000.000
124A139GLY00.0550.03324.9600.0890.0890.0000.0000.0000.000
125A140LYS10.8800.89827.835-10.913-10.9130.0000.0000.0000.000
126A141LYS10.9970.99430.392-9.641-9.6410.0000.0000.0000.000
127A142MET00.0200.02026.592-0.142-0.1420.0000.0000.0000.000
128A143MET00.0240.02926.6420.1400.1400.0000.0000.0000.000
129A144TRP00.0310.00927.5840.1020.1020.0000.0000.0000.000
130A145ALA00.0010.01630.156-0.160-0.1600.0000.0000.0000.000
131A146ILE0-0.003-0.00424.109-0.046-0.0460.0000.0000.0000.000
132A147ILE0-0.050-0.03127.6410.0490.0490.0000.0000.0000.000
133A148GLU-1-0.933-0.96829.1929.3059.3050.0000.0000.0000.000
134A149GLU-1-0.810-0.88929.9579.9459.9450.0000.0000.0000.000
135A150ARG10.8330.93024.419-13.202-13.2020.0000.0000.0000.000
136A151LYS10.8910.95329.035-9.934-9.9340.0000.0000.0000.000
137A152LYS10.8680.93132.206-9.502-9.5020.0000.0000.0000.000
138A153ARG10.9330.96128.849-11.066-11.0660.0000.0000.0000.000
139A154PRO0-0.0130.02625.9140.2460.2460.0000.0000.0000.000
140A155PHE00.014-0.02023.843-0.138-0.1380.0000.0000.0000.000
141A156GLU-1-0.875-0.94224.11113.72913.7290.0000.0000.0000.000
142A157SER0-0.001-0.00621.6570.1410.1410.0000.0000.0000.000
143A158PHE00.0350.00715.782-0.305-0.3050.0000.0000.0000.000
144A159GLU-1-0.844-0.91122.12311.69811.6980.0000.0000.0000.000
145A160ASP-1-0.725-0.86025.36711.34911.3490.0000.0000.0000.000
146A161ILE0-0.016-0.01321.612-0.445-0.4450.0000.0000.0000.000
147A162ALA0-0.026-0.02625.391-0.339-0.3390.0000.0000.0000.000
148A163GLN0-0.044-0.00526.963-0.671-0.6710.0000.0000.0000.000
149A164ARG10.6890.84028.806-11.775-11.7750.0000.0000.0000.000
150A165VAL0-0.015-0.00826.967-0.390-0.3900.0000.0000.0000.000
151A166LYS10.9060.94129.605-9.572-9.5720.0000.0000.0000.000
152A167GLY0-0.013-0.00931.383-0.016-0.0160.0000.0000.0000.000
153A168ILE0-0.047-0.01124.2480.1290.1290.0000.0000.0000.000
154A169GLN0-0.0010.00023.6230.0940.0940.0000.0000.0000.000
155A170ARG10.8980.91221.944-13.813-13.8130.0000.0000.0000.000
156A171PRO00.0410.02620.0240.3820.3820.0000.0000.0000.000
157A172GLU-1-0.710-0.84717.05816.75716.7570.0000.0000.0000.000
158A173LYS10.9780.99616.612-14.012-14.0120.0000.0000.0000.000
159A174LEU0-0.044-0.01318.1140.4010.4010.0000.0000.0000.000
160A175ILE00.0190.01712.8470.3550.3550.0000.0000.0000.000
161A176VAL00.0160.00813.2281.3591.3590.0000.0000.0000.000
162A177SER0-0.048-0.02713.9870.4560.4560.0000.0000.0000.000
163A178ARG10.8140.90313.879-20.095-20.0950.0000.0000.0000.000
164A179ILE00.0310.0238.721-0.126-0.1260.0000.0000.0000.000
165A180ILE00.0160.00511.2070.7090.7090.0000.0000.0000.000
166A181TYR0-0.042-0.01713.040-0.446-0.4460.0000.0000.0000.000
167A182GLU-1-0.721-0.84411.09925.94325.9430.0000.0000.0000.000
168A183ILE0-0.048-0.0108.216-0.566-0.5660.0000.0000.0000.000
169A184LYS10.8680.93711.136-18.676-18.6760.0000.0000.0000.000
170A185ASN0-0.055-0.01914.545-2.110-2.1100.0000.0000.0000.000
171A186PRO00.0600.02912.8180.2770.2770.0000.0000.0000.000
172A187GLN00.0450.03514.0930.4630.4630.0000.0000.0000.000
173A188THR0-0.0070.01015.067-0.971-0.9710.0000.0000.0000.000
174A189LYS10.9830.98716.733-13.864-13.8640.0000.0000.0000.000
175A190TYR00.004-0.00616.626-0.018-0.0180.0000.0000.0000.000
176A191LYS10.7830.88310.995-22.868-22.8680.0000.0000.0000.000
177A192LEU00.005-0.00512.2190.6040.6040.0000.0000.0000.000
178A193PHE00.008-0.0069.262-0.031-0.0310.0000.0000.0000.000
179A194THR0-0.027-0.0216.5263.7393.7390.0000.0000.0000.000
180A195ALA0-0.045-0.0116.9693.5093.5090.0000.0000.0000.000