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: K3M13

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 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 180
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2027300.149176
FMO2-HF: Nuclear repulsion 1953064.236604
FMO2-HF: Total energy -74235.912572
FMO2-MP2: Total energy -74455.122901


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.
-330.027-335.23951.573-20.412-25.9490.209
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 : -0.784 / q_NPA : -0.880
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].
3A18TYR00.0540.0063.521-8.405-6.616-0.005-0.845-0.9400.001
4A19ALA0-0.024-0.0113.01810.71212.1880.163-0.742-0.897-0.007
5A20TYR00.0300.0164.976-5.930-5.856-0.001-0.004-0.0690.000
6A21VAL0-0.046-0.0188.5671.4011.4010.0000.0000.0000.000
7A22LEU0-0.017-0.0019.305-0.605-0.6050.0000.0000.0000.000
8A23ASP-1-0.763-0.86412.60015.11115.1110.0000.0000.0000.000
9A24PHE0-0.010-0.01714.2150.9640.9640.0000.0000.0000.000
10A25MET00.0120.02416.103-0.971-0.9710.0000.0000.0000.000
11A26PRO00.009-0.00219.3390.0420.0420.0000.0000.0000.000
12A27TYR0-0.002-0.00621.646-0.260-0.2600.0000.0000.0000.000
13A28GLY0-0.006-0.00519.167-0.225-0.2250.0000.0000.0000.000
14A29HIS00.001-0.02615.874-0.835-0.8350.0000.0000.0000.000
15A30PRO00.0210.01220.883-0.385-0.3850.0000.0000.0000.000
16A31ASP-1-0.882-0.94423.94311.57311.5730.0000.0000.0000.000
17A32ASP-1-0.830-0.89122.78912.29112.2910.0000.0000.0000.000
18A33LYS10.9610.96924.635-10.953-10.9530.0000.0000.0000.000
19A34ARG10.7540.87420.257-13.403-13.4030.0000.0000.0000.000
20A35PRO00.0400.01327.5630.0420.0420.0000.0000.0000.000
21A36ILE00.0820.03427.6400.3220.3220.0000.0000.0000.000
22A37HIS00.0230.01526.8430.4360.4360.0000.0000.0000.000
23A38ARG10.9130.95125.408-10.726-10.7260.0000.0000.0000.000
24A39ARG10.8050.92822.966-10.890-10.8900.0000.0000.0000.000
25A40GLU-1-0.816-0.90717.55914.89014.8900.0000.0000.0000.000
26A41PRO00.0050.01818.5360.1550.1550.0000.0000.0000.000
27A42LEU0-0.014-0.00915.0420.6200.6200.0000.0000.0000.000
28A43ALA00.0260.01112.440-0.570-0.5700.0000.0000.0000.000
29A44GLN0-0.029-0.01010.5240.7680.7680.0000.0000.0000.000
30A45VAL00.0160.0045.802-0.929-0.9290.0000.0000.0000.000
31A46VAL00.0190.0145.5031.1411.1410.0000.0000.0000.000
32A47GLY0-0.016-0.0132.187-4.659-5.3174.849-2.537-1.6550.009
33A48GLU-1-0.799-0.8883.17242.18440.8560.6392.154-1.4650.003
34A49ARG10.9010.9661.977-67.571-68.0006.489-2.580-3.4800.037
35A50ASN0-0.030-0.0381.817-43.932-47.96417.190-6.356-6.8010.079
36A51PHE00.0260.0123.345-8.281-7.4820.442-0.046-1.1950.004
37A52THR0-0.068-0.0521.742-46.369-50.35719.740-8.531-7.2220.082
38A53LEU00.0110.0193.701-3.852-3.1470.029-0.298-0.4360.002
39A54LEU0-0.024-0.0163.214-1.582-1.0990.036-0.091-0.4270.000
40A55GLU-1-0.745-0.8276.77717.16117.1610.0000.0000.0000.000
41A56VAL00.001-0.0077.8430.5640.5640.0000.0000.0000.000
42A57SER00.0190.01410.828-0.876-0.8760.0000.0000.0000.000
43A58ILE0-0.0100.00412.9640.8720.8720.0000.0000.0000.000
44A59ARG10.7620.84815.443-15.969-15.9690.0000.0000.0000.000
45A60LYS10.9830.97217.824-11.894-11.8940.0000.0000.0000.000
46A61GLY00.0340.02421.5080.0110.0110.0000.0000.0000.000
47A62LYS10.8780.93917.728-14.344-14.3440.0000.0000.0000.000
48A63GLN0-0.034-0.02619.562-0.319-0.3190.0000.0000.0000.000
49A64PRO0-0.007-0.00114.433-0.110-0.1100.0000.0000.0000.000
50A65LEU00.0130.01616.370-0.620-0.6200.0000.0000.0000.000
51A66VAL00.003-0.01015.0381.3431.3430.0000.0000.0000.000
52A67MET0-0.017-0.00912.979-0.104-0.1040.0000.0000.0000.000
53A68ASP-1-0.833-0.90012.99718.71818.7180.0000.0000.0000.000
54A69ARG10.8010.8777.959-28.275-28.2750.0000.0000.0000.000
55A70VAL0-0.008-0.0027.796-1.706-1.7060.0000.0000.0000.000
56A71TYR00.0120.0067.1512.6442.6440.0000.0000.0000.000
57A72ILE0-0.057-0.0422.377-1.853-2.0102.003-0.534-1.312-0.001
58A73GLY00.0470.0306.2210.0350.0350.0000.0000.0000.000
59A74LYS10.8920.9366.275-27.389-27.3890.0000.0000.0000.000
60A75GLY00.0590.0519.895-1.366-1.3660.0000.0000.0000.000
61A76GLU-1-0.826-0.89312.40014.84014.8400.0000.0000.0000.000
62A77ARG10.8320.9258.108-22.257-22.2570.0000.0000.0000.000
63A78ASP-1-0.855-0.91013.01215.98715.9870.0000.0000.0000.000
64A79VAL0-0.006-0.00412.786-0.852-0.8520.0000.0000.0000.000
65A80VAL00.0380.0228.914-0.745-0.7450.0000.0000.0000.000
66A81TYR0-0.011-0.00811.979-0.262-0.2620.0000.0000.0000.000
67A82LYS10.8810.93111.527-16.286-16.2860.0000.0000.0000.000
68A83ILE00.0490.0305.1050.0400.0400.0000.0000.0000.000
69A84LYS10.7610.8709.176-17.723-17.7230.0000.0000.0000.000
70A85ARG10.8790.91610.281-19.695-19.6950.0000.0000.0000.000
71A86ARG10.9700.9955.055-44.178-44.124-0.001-0.002-0.0500.000
72A87LEU0-0.053-0.0178.231-2.868-2.8680.0000.0000.0000.000
73A88ARG10.8050.8689.665-15.637-15.6370.0000.0000.0000.000
74A89TYR00.051-0.00212.402-0.908-0.9080.0000.0000.0000.000
75A90GLU-1-0.857-0.93413.76815.97615.9760.0000.0000.0000.000
76A91ASP-1-0.777-0.85113.41218.70318.7030.0000.0000.0000.000
77A92LEU0-0.0260.00310.561-0.012-0.0120.0000.0000.0000.000
78A93THR00.003-0.03614.553-1.016-1.0160.0000.0000.0000.000
79A94PRO00.019-0.00617.2630.6150.6150.0000.0000.0000.000
80A95ALA00.0470.05118.4390.0280.0280.0000.0000.0000.000
81A96ALA00.0510.01813.1860.5250.5250.0000.0000.0000.000
82A97LYS10.7440.85514.401-15.832-15.8320.0000.0000.0000.000
83A98THR0-0.020-0.01116.304-0.027-0.0270.0000.0000.0000.000
84A99GLU-1-0.851-0.93915.55616.87916.8790.0000.0000.0000.000
85A100LEU0-0.041-0.0059.6880.9460.9460.0000.0000.0000.000
86A101PRO0-0.018-0.02412.8911.6171.6170.0000.0000.0000.000
87A102TYR00.0360.02615.0120.4060.4060.0000.0000.0000.000
88A103VAL00.0330.01110.1830.4420.4420.0000.0000.0000.000
89A104ILE0-0.039-0.0189.4381.6391.6390.0000.0000.0000.000
90A105GLU-1-0.867-0.93411.30317.73917.7390.0000.0000.0000.000
91A106HIS00.0280.01412.891-0.662-0.6620.0000.0000.0000.000
92A107ILE00.0030.0096.962-0.121-0.1210.0000.0000.0000.000
93A108ILE0-0.071-0.03410.528-0.357-0.3570.0000.0000.0000.000
94A109LYS10.8040.88412.099-18.281-18.2810.0000.0000.0000.000
95A110GLN0-0.069-0.02411.633-2.050-2.0500.0000.0000.0000.000
96A111ASP-1-0.880-0.95110.91225.96625.9660.0000.0000.0000.000
97A112GLU-1-0.766-0.87612.94516.59316.5930.0000.0000.0000.000
98A113LYS10.8720.94215.789-15.873-15.8730.0000.0000.0000.000
99A114LYS10.8580.91212.039-22.465-22.4650.0000.0000.0000.000
100A115TYR00.0170.0128.2950.5820.5820.0000.0000.0000.000
101A116VAL0-0.013-0.01314.870-1.022-1.0220.0000.0000.0000.000
102A117ASP-1-0.814-0.90616.85917.02617.0260.0000.0000.0000.000
103A118PHE0-0.016-0.00215.991-0.618-0.6180.0000.0000.0000.000
104A119PHE00.0190.00418.090-0.805-0.8050.0000.0000.0000.000
105A120ASN0-0.053-0.03521.251-1.146-1.1460.0000.0000.0000.000
106A121LYS10.8190.91320.914-14.548-14.5480.0000.0000.0000.000
107A122ALA00.0420.02220.718-0.579-0.5790.0000.0000.0000.000
108A123ASP-1-0.756-0.83620.93115.52015.5200.0000.0000.0000.000
109A124SER00.013-0.01021.017-0.782-0.7820.0000.0000.0000.000
110A125ILE0-0.021-0.01822.9450.2350.2350.0000.0000.0000.000
111A126THR0-0.041-0.01222.0720.1700.1700.0000.0000.0000.000
112A127THR00.0310.00624.515-0.496-0.4960.0000.0000.0000.000
113A128ARG10.9030.96027.952-9.794-9.7940.0000.0000.0000.000
114A129MET0-0.0190.00122.953-0.414-0.4140.0000.0000.0000.000
115A130HIS00.021-0.02824.056-0.286-0.2860.0000.0000.0000.000
116A131GLN00.0420.03719.4170.3930.3930.0000.0000.0000.000
117A132LEU00.0080.00419.9790.5610.5610.0000.0000.0000.000
118A133GLU-1-0.783-0.89721.64012.12012.1200.0000.0000.0000.000
119A134LEU0-0.0310.00217.641-0.039-0.0390.0000.0000.0000.000
120A135LEU00.0010.01016.8440.9880.9880.0000.0000.0000.000
121A136PRO0-0.021-0.02117.927-0.989-0.9890.0000.0000.0000.000
122A137GLY00.0190.01020.7920.1090.1090.0000.0000.0000.000
123A138VAL0-0.040-0.01322.870-0.573-0.5730.0000.0000.0000.000
124A139GLY00.0740.03024.6850.2080.2080.0000.0000.0000.000
125A140LYS10.8220.88327.295-11.524-11.5240.0000.0000.0000.000
126A141LYS10.9950.99530.189-9.667-9.6670.0000.0000.0000.000
127A142MET00.0130.02626.737-0.136-0.1360.0000.0000.0000.000
128A143MET0-0.0110.01926.1410.2410.2410.0000.0000.0000.000
129A144TRP00.0350.01027.4270.1110.1110.0000.0000.0000.000
130A145ALA00.0060.01430.193-0.141-0.1410.0000.0000.0000.000
131A146ILE0-0.003-0.00524.009-0.038-0.0380.0000.0000.0000.000
132A147ILE0-0.015-0.01327.1440.0180.0180.0000.0000.0000.000
133A148GLU-1-0.797-0.89529.2179.3259.3250.0000.0000.0000.000
134A149GLU-1-0.803-0.88230.0349.7849.7840.0000.0000.0000.000
135A150ARG10.7670.87123.927-13.483-13.4830.0000.0000.0000.000
136A151LYS10.7810.87729.171-9.562-9.5620.0000.0000.0000.000
137A152LYS10.8280.92032.523-9.566-9.5660.0000.0000.0000.000
138A153ARG10.8730.90928.577-11.127-11.1270.0000.0000.0000.000
139A154PRO00.0260.02725.4620.1300.1300.0000.0000.0000.000
140A155PHE0-0.032-0.01623.648-0.249-0.2490.0000.0000.0000.000
141A156GLU-1-0.815-0.91823.17114.29014.2900.0000.0000.0000.000
142A157SER00.0370.02821.5910.1650.1650.0000.0000.0000.000
143A158PHE00.004-0.02715.537-0.418-0.4180.0000.0000.0000.000
144A159GLU-1-0.780-0.85621.72212.01612.0160.0000.0000.0000.000
145A160ASP-1-0.731-0.83925.20111.13811.1380.0000.0000.0000.000
146A161ILE0-0.022-0.01521.491-0.388-0.3880.0000.0000.0000.000
147A162ALA0-0.014-0.01325.162-0.411-0.4110.0000.0000.0000.000
148A163GLN0-0.026-0.00926.828-0.676-0.6760.0000.0000.0000.000
149A164ARG10.6980.85828.401-11.711-11.7110.0000.0000.0000.000
150A165VAL0-0.016-0.01527.178-0.403-0.4030.0000.0000.0000.000
151A166LYS10.8780.92229.867-9.524-9.5240.0000.0000.0000.000
152A167GLY00.0250.01631.537-0.128-0.1280.0000.0000.0000.000
153A168ILE0-0.051-0.02224.1370.1510.1510.0000.0000.0000.000
154A169GLN0-0.0020.00323.139-0.160-0.1600.0000.0000.0000.000
155A170ARG10.8310.86422.392-13.359-13.3590.0000.0000.0000.000
156A171PRO00.0260.02020.2220.5420.5420.0000.0000.0000.000
157A172GLU-1-0.722-0.84917.22416.37816.3780.0000.0000.0000.000
158A173LYS11.0141.01216.806-14.346-14.3460.0000.0000.0000.000
159A174LEU0-0.0490.00318.1660.4380.4380.0000.0000.0000.000
160A175ILE00.0260.02013.0750.4780.4780.0000.0000.0000.000
161A176VAL00.0270.01613.3591.5831.5830.0000.0000.0000.000
162A177SER0-0.049-0.04913.9300.5180.5180.0000.0000.0000.000
163A178ARG10.7830.87113.511-21.171-21.1710.0000.0000.0000.000
164A179ILE00.0220.0248.5240.1550.1550.0000.0000.0000.000
165A180ILE00.012-0.00310.8920.8730.8730.0000.0000.0000.000
166A181TYR0-0.0060.01113.031-0.460-0.4600.0000.0000.0000.000
167A182GLU-1-0.747-0.83810.64827.23827.2380.0000.0000.0000.000
168A183ILE0-0.022-0.0097.955-0.340-0.3400.0000.0000.0000.000
169A184LYS10.8500.94110.558-19.658-19.6580.0000.0000.0000.000
170A185ASN0-0.066-0.01813.629-2.407-2.4070.0000.0000.0000.000
171A186PRO00.0650.02811.8390.4770.4770.0000.0000.0000.000
172A187GLN00.0550.03113.1271.3491.3490.0000.0000.0000.000
173A188THR0-0.045-0.02014.349-1.069-1.0690.0000.0000.0000.000
174A189LYS10.9580.98115.611-13.969-13.9690.0000.0000.0000.000
175A190TYR00.012-0.00215.713-0.287-0.2870.0000.0000.0000.000
176A191LYS10.8010.88210.058-24.810-24.8100.0000.0000.0000.000
177A192LEU0-0.005-0.00511.2171.0171.0170.0000.0000.0000.000
178A193PHE00.008-0.0079.012-0.314-0.3140.0000.0000.0000.000
179A194THR0-0.009-0.0225.8724.5524.5520.0000.0000.0000.000
180A195ALA0-0.034-0.0026.2704.0114.0110.0000.0000.0000.000