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: Q1J9Y

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 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 180
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2023122.759896
FMO2-HF: Nuclear repulsion 1948887.255482
FMO2-HF: Total energy -74235.504414
FMO2-MP2: Total energy -74454.718824


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.
-316.961-315.55239.962-18.773-22.5980.202
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 : -0.807 / q_NPA : -0.903
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].
3A18TYR00.0210.0033.251-9.115-7.1530.004-0.870-1.0960.001
4A19ALA0-0.023-0.0063.20411.94513.1880.078-0.601-0.720-0.005
5A20TYR00.0400.0205.145-6.504-6.435-0.001-0.001-0.0670.000
6A21VAL0-0.047-0.0218.7781.3531.3530.0000.0000.0000.000
7A22LEU0-0.0060.0019.883-0.627-0.6270.0000.0000.0000.000
8A23ASP-1-0.793-0.88713.06115.44215.4420.0000.0000.0000.000
9A24PHE00.0120.00714.6280.8600.8600.0000.0000.0000.000
10A25MET00.0110.01516.293-1.067-1.0670.0000.0000.0000.000
11A26PRO00.0170.01019.3750.0160.0160.0000.0000.0000.000
12A27TYR00.007-0.01221.581-0.151-0.1510.0000.0000.0000.000
13A28GLY0-0.025-0.00619.320-0.247-0.2470.0000.0000.0000.000
14A29HIS0-0.010-0.03616.163-0.833-0.8330.0000.0000.0000.000
15A30PRO00.0280.01321.113-0.436-0.4360.0000.0000.0000.000
16A31ASP-1-0.896-0.94424.00511.48311.4830.0000.0000.0000.000
17A32ASP-1-0.878-0.91423.11712.21712.2170.0000.0000.0000.000
18A33LYS10.9870.97624.855-10.826-10.8260.0000.0000.0000.000
19A34ARG10.8070.90120.854-13.273-13.2730.0000.0000.0000.000
20A35PRO00.0440.01327.9110.0700.0700.0000.0000.0000.000
21A36ILE00.0940.03027.8530.3270.3270.0000.0000.0000.000
22A37HIS00.0210.01926.9980.4000.4000.0000.0000.0000.000
23A38ARG10.9070.94724.944-10.858-10.8580.0000.0000.0000.000
24A39ARG10.8280.94422.921-10.791-10.7910.0000.0000.0000.000
25A40GLU-1-0.851-0.91317.38515.16215.1620.0000.0000.0000.000
26A41PRO00.0160.01718.4560.2040.2040.0000.0000.0000.000
27A42LEU0-0.037-0.02514.9730.6760.6760.0000.0000.0000.000
28A43ALA00.0380.02312.324-0.630-0.6300.0000.0000.0000.000
29A44GLN0-0.025-0.00410.7331.1531.1530.0000.0000.0000.000
30A45VAL0-0.001-0.0135.962-0.711-0.7110.0000.0000.0000.000
31A46VAL00.0290.0125.9411.2111.2110.0000.0000.0000.000
32A47GLY0-0.036-0.0202.479-5.560-5.3303.678-2.506-1.4020.016
33A48GLU-1-0.776-0.8753.46141.06040.4040.2191.500-1.0630.003
34A49ARG10.9090.9722.095-68.695-67.7355.630-2.670-3.9200.042
35A50ASN0-0.019-0.0142.251-30.511-28.4234.399-2.444-4.0430.047
36A51PHE00.0370.0163.066-12.128-11.4780.604-0.028-1.2260.004
37A52THR0-0.094-0.0651.664-47.764-53.71523.372-10.421-7.0000.091
38A53LEU00.0100.0213.755-2.708-2.2850.010-0.137-0.2960.003
39A54LEU0-0.021-0.0153.268-2.680-2.2380.035-0.088-0.3890.000
40A55GLU-1-0.717-0.8067.05817.72117.7210.0000.0000.0000.000
41A56VAL0-0.022-0.0267.6180.2150.2150.0000.0000.0000.000
42A57SER00.0480.03010.840-0.669-0.6690.0000.0000.0000.000
43A58ILE0-0.022-0.00312.6941.0241.0240.0000.0000.0000.000
44A59ARG10.8060.89315.196-16.351-16.3510.0000.0000.0000.000
45A60LYS10.9850.96817.529-12.048-12.0480.0000.0000.0000.000
46A61GLY00.0270.01321.1030.0920.0920.0000.0000.0000.000
47A62LYS10.8810.96317.308-14.950-14.9500.0000.0000.0000.000
48A63GLN0-0.025-0.02319.611-0.190-0.1900.0000.0000.0000.000
49A64PRO0-0.018-0.01114.409-0.091-0.0910.0000.0000.0000.000
50A65LEU00.0040.01016.336-0.651-0.6510.0000.0000.0000.000
51A66VAL00.0300.00515.1801.3641.3640.0000.0000.0000.000
52A67MET0-0.029-0.01713.440-0.066-0.0660.0000.0000.0000.000
53A68ASP-1-0.830-0.88813.17219.05219.0520.0000.0000.0000.000
54A69ARG10.7930.8718.164-29.263-29.2630.0000.0000.0000.000
55A70VAL0-0.025-0.0267.702-2.116-2.1160.0000.0000.0000.000
56A71TYR00.0300.0256.9033.0753.0750.0000.0000.0000.000
57A72ILE0-0.057-0.0442.390-2.418-2.4691.934-0.507-1.3760.000
58A73GLY00.0800.0405.6670.5680.5680.0000.0000.0000.000
59A74LYS10.8810.9245.925-27.428-27.4280.0000.0000.0000.000
60A75GLY00.0460.0459.314-1.392-1.3920.0000.0000.0000.000
61A76GLU-1-0.848-0.92212.23615.17815.1780.0000.0000.0000.000
62A77ARG10.8130.9147.441-23.119-23.1190.0000.0000.0000.000
63A78ASP-1-0.833-0.90612.74316.23616.2360.0000.0000.0000.000
64A79VAL0-0.021-0.01512.703-0.947-0.9470.0000.0000.0000.000
65A80VAL00.0460.0248.738-0.731-0.7310.0000.0000.0000.000
66A81TYR0-0.027-0.01511.801-0.683-0.6830.0000.0000.0000.000
67A82LYS10.9090.94211.533-16.221-16.2210.0000.0000.0000.000
68A83ILE00.0250.0205.127-0.100-0.1000.0000.0000.0000.000
69A84LYS10.7650.8699.253-17.630-17.6300.0000.0000.0000.000
70A85ARG10.8720.92210.548-19.189-19.1890.0000.0000.0000.000
71A86ARG10.9790.9926.533-38.198-38.1980.0000.0000.0000.000
72A87LEU0-0.062-0.0248.538-2.536-2.5360.0000.0000.0000.000
73A88ARG10.8070.86810.014-15.491-15.4910.0000.0000.0000.000
74A89TYR00.0950.01712.738-0.757-0.7570.0000.0000.0000.000
75A90GLU-1-0.882-0.95613.69716.04816.0480.0000.0000.0000.000
76A91ASP-1-0.763-0.84513.70418.37618.3760.0000.0000.0000.000
77A92LEU0-0.0330.00310.821-0.028-0.0280.0000.0000.0000.000
78A93THR00.012-0.02314.805-1.119-1.1190.0000.0000.0000.000
79A94PRO00.031-0.00517.5080.6280.6280.0000.0000.0000.000
80A95ALA00.0460.03418.9800.1440.1440.0000.0000.0000.000
81A96ALA00.0500.02413.6820.5140.5140.0000.0000.0000.000
82A97LYS10.7450.87014.924-16.178-16.1780.0000.0000.0000.000
83A98THR0-0.045-0.02816.4740.0630.0630.0000.0000.0000.000
84A99GLU-1-0.868-0.93815.78517.28817.2880.0000.0000.0000.000
85A100LEU0-0.056-0.0109.6130.9800.9800.0000.0000.0000.000
86A101PRO0-0.027-0.02712.7331.5741.5740.0000.0000.0000.000
87A102TYR00.0370.02114.9050.1760.1760.0000.0000.0000.000
88A103VAL00.0480.01610.3790.3960.3960.0000.0000.0000.000
89A104ILE0-0.044-0.0229.0441.4921.4920.0000.0000.0000.000
90A105GLU-1-0.875-0.93311.14118.00618.0060.0000.0000.0000.000
91A106HIS00.0170.01012.856-0.724-0.7240.0000.0000.0000.000
92A107ILE00.0050.0067.129-0.019-0.0190.0000.0000.0000.000
93A108ILE0-0.042-0.01610.532-0.256-0.2560.0000.0000.0000.000
94A109LYS10.8240.90012.111-18.384-18.3840.0000.0000.0000.000
95A110GLN0-0.082-0.02311.637-2.261-2.2610.0000.0000.0000.000
96A111ASP-1-0.877-0.95910.62127.65727.6570.0000.0000.0000.000
97A112GLU-1-0.773-0.88012.89716.49516.4950.0000.0000.0000.000
98A113LYS10.9060.96015.894-15.720-15.7200.0000.0000.0000.000
99A114LYS10.8800.93611.634-23.002-23.0020.0000.0000.0000.000
100A115TYR00.0270.0098.552-0.070-0.0700.0000.0000.0000.000
101A116VAL0-0.052-0.02615.115-1.032-1.0320.0000.0000.0000.000
102A117ASP-1-0.848-0.92616.85116.93516.9350.0000.0000.0000.000
103A118PHE0-0.058-0.01915.930-0.396-0.3960.0000.0000.0000.000
104A119PHE0-0.0050.00017.993-0.895-0.8950.0000.0000.0000.000
105A120ASN0-0.021-0.01721.245-0.448-0.4480.0000.0000.0000.000
106A121LYS10.8560.91321.265-13.876-13.8760.0000.0000.0000.000
107A122ALA00.0270.01921.376-0.689-0.6890.0000.0000.0000.000
108A123ASP-1-0.740-0.82720.81015.36315.3630.0000.0000.0000.000
109A124SER0-0.035-0.02321.317-0.719-0.7190.0000.0000.0000.000
110A125ILE0-0.006-0.00823.4970.0480.0480.0000.0000.0000.000
111A126THR0-0.036-0.01122.6310.2480.2480.0000.0000.0000.000
112A127THR00.017-0.00725.134-0.551-0.5510.0000.0000.0000.000
113A128ARG10.8640.94928.555-9.724-9.7240.0000.0000.0000.000
114A129MET00.0110.01023.291-0.293-0.2930.0000.0000.0000.000
115A130HIS00.030-0.01924.462-0.217-0.2170.0000.0000.0000.000
116A131GLN00.0450.03019.7770.3680.3680.0000.0000.0000.000
117A132LEU00.0160.01520.4950.4720.4720.0000.0000.0000.000
118A133GLU-1-0.776-0.89022.21211.83511.8350.0000.0000.0000.000
119A134LEU0-0.073-0.02418.1510.0070.0070.0000.0000.0000.000
120A135LEU0-0.0100.00517.0910.8580.8580.0000.0000.0000.000
121A136PRO00.004-0.00518.155-0.921-0.9210.0000.0000.0000.000
122A137GLY00.0080.00721.0560.1050.1050.0000.0000.0000.000
123A138VAL0-0.026-0.00922.656-0.520-0.5200.0000.0000.0000.000
124A139GLY00.0590.03424.9800.1080.1080.0000.0000.0000.000
125A140LYS10.8560.89127.812-11.151-11.1510.0000.0000.0000.000
126A141LYS10.9890.99130.380-9.595-9.5950.0000.0000.0000.000
127A142MET00.0170.02126.797-0.151-0.1510.0000.0000.0000.000
128A143MET00.0140.03126.3800.1520.1520.0000.0000.0000.000
129A144TRP00.0370.00927.6640.0880.0880.0000.0000.0000.000
130A145ALA0-0.0040.01230.409-0.171-0.1710.0000.0000.0000.000
131A146ILE0-0.002-0.00524.271-0.042-0.0420.0000.0000.0000.000
132A147ILE0-0.027-0.01927.4450.0390.0390.0000.0000.0000.000
133A148GLU-1-0.815-0.90429.3659.2999.2990.0000.0000.0000.000
134A149GLU-1-0.824-0.89330.2129.8309.8300.0000.0000.0000.000
135A150ARG10.7830.88324.326-13.248-13.2480.0000.0000.0000.000
136A151LYS10.7880.88529.178-9.588-9.5880.0000.0000.0000.000
137A152LYS10.8530.92732.310-9.405-9.4050.0000.0000.0000.000
138A153ARG10.9110.93328.793-10.975-10.9750.0000.0000.0000.000
139A154PRO00.0180.02325.8030.2260.2260.0000.0000.0000.000
140A155PHE0-0.028-0.02123.807-0.101-0.1010.0000.0000.0000.000
141A156GLU-1-0.826-0.93623.97514.00214.0020.0000.0000.0000.000
142A157SER0-0.0040.00621.6230.1350.1350.0000.0000.0000.000
143A158PHE00.020-0.01215.883-0.295-0.2950.0000.0000.0000.000
144A159GLU-1-0.773-0.85522.10311.84711.8470.0000.0000.0000.000
145A160ASP-1-0.724-0.84925.30511.11611.1160.0000.0000.0000.000
146A161ILE0-0.016-0.01221.889-0.417-0.4170.0000.0000.0000.000
147A162ALA0-0.020-0.02025.598-0.334-0.3340.0000.0000.0000.000
148A163GLN0-0.037-0.00527.211-0.674-0.6740.0000.0000.0000.000
149A164ARG10.7100.86328.629-11.641-11.6410.0000.0000.0000.000
150A165VAL0-0.015-0.01027.365-0.384-0.3840.0000.0000.0000.000
151A166LYS10.9000.93829.847-9.531-9.5310.0000.0000.0000.000
152A167GLY0-0.008-0.00531.566-0.011-0.0110.0000.0000.0000.000
153A168ILE0-0.035-0.01224.4420.1400.1400.0000.0000.0000.000
154A169GLN0-0.009-0.00223.2680.0040.0040.0000.0000.0000.000
155A170ARG10.8300.86522.204-13.563-13.5630.0000.0000.0000.000
156A171PRO00.0370.02320.2690.4440.4440.0000.0000.0000.000
157A172GLU-1-0.718-0.85317.33316.44816.4480.0000.0000.0000.000
158A173LYS10.9931.00516.817-14.134-14.1340.0000.0000.0000.000
159A174LEU0-0.0390.00418.2130.4380.4380.0000.0000.0000.000
160A175ILE00.0230.01513.1590.4330.4330.0000.0000.0000.000
161A176VAL00.0280.01413.3331.4301.4300.0000.0000.0000.000
162A177SER0-0.065-0.05213.9880.4980.4980.0000.0000.0000.000
163A178ARG10.7970.88513.900-20.317-20.3170.0000.0000.0000.000
164A179ILE00.0220.0228.6310.0340.0340.0000.0000.0000.000
165A180ILE00.0200.00411.0230.8480.8480.0000.0000.0000.000
166A181TYR0-0.026-0.00712.883-0.350-0.3500.0000.0000.0000.000
167A182GLU-1-0.741-0.84211.03525.78725.7870.0000.0000.0000.000
168A183ILE0-0.031-0.0067.947-0.512-0.5120.0000.0000.0000.000
169A184LYS10.8640.94210.772-19.261-19.2610.0000.0000.0000.000
170A185ASN0-0.068-0.02514.163-2.152-2.1520.0000.0000.0000.000
171A186PRO00.0710.03312.1580.2870.2870.0000.0000.0000.000
172A187GLN00.0420.02513.6070.8930.8930.0000.0000.0000.000
173A188THR0-0.0260.00014.735-1.046-1.0460.0000.0000.0000.000
174A189LYS10.9660.98416.347-13.947-13.9470.0000.0000.0000.000
175A190TYR0-0.004-0.01216.370-0.064-0.0640.0000.0000.0000.000
176A191LYS10.8050.89510.689-23.513-23.5130.0000.0000.0000.000
177A192LEU0-0.001-0.01112.0660.6000.6000.0000.0000.0000.000
178A193PHE00.001-0.0139.407-0.135-0.1350.0000.0000.0000.000
179A194THR0-0.015-0.0136.3533.6743.6740.0000.0000.0000.000
180A195ALA0-0.037-0.0046.7564.1594.1590.0000.0000.0000.000