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: QNVMY

Calculation Name: 2AHE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2AHE

Chain ID: A

ChEMBL ID:

UniProt ID: Q9Y696

Base Structure: X-ray

Registration Date: 2023-09-27

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 228
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2823262.832947
FMO2-HF: Nuclear repulsion 2732682.446875
FMO2-HF: Total energy -90580.386072
FMO2-MP2: Total energy -90844.973768


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.
-155.265-167.73655.388-22.854-20.0620.241
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 : -0.739 / q_NPA : -0.841
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].
3A18LEU00.0250.0163.4483.4895.2480.017-0.903-0.8730.002
4A19ILE0-0.012-0.0105.685-2.799-2.7990.0000.0000.0000.000
5A20GLU-1-0.814-0.8637.57520.62920.6290.0000.0000.0000.000
6A21LEU0-0.035-0.01610.899-0.897-0.8970.0000.0000.0000.000
7A22PHE00.0200.01813.697-0.705-0.7050.0000.0000.0000.000
8A23VAL00.002-0.02316.855-0.380-0.3800.0000.0000.0000.000
9A24LYS10.8890.92919.549-11.938-11.9380.0000.0000.0000.000
10A25ALA00.0320.02423.1640.2390.2390.0000.0000.0000.000
11A26GLY00.0130.00624.748-0.292-0.2920.0000.0000.0000.000
12A27SER0-0.107-0.09427.430-0.300-0.3000.0000.0000.0000.000
13A28ASP-1-0.811-0.89427.92711.18711.1870.0000.0000.0000.000
14A29GLY0-0.0190.00028.420-0.170-0.1700.0000.0000.0000.000
15A30GLU-1-0.857-0.91725.12911.73311.7330.0000.0000.0000.000
16A31SER0-0.046-0.04123.4330.7340.7340.0000.0000.0000.000
17A32ILE00.0420.01018.024-0.018-0.0180.0000.0000.0000.000
18A33GLY00.0310.02422.386-0.406-0.4060.0000.0000.0000.000
19A34ASN0-0.057-0.04024.0490.7270.7270.0000.0000.0000.000
20A35CYS0-0.0030.00823.037-0.345-0.3450.0000.0000.0000.000
21A36PRO00.0370.03022.4330.6390.6390.0000.0000.0000.000
22A37PHE00.000-0.01321.2810.5190.5190.0000.0000.0000.000
23A38SER00.0640.01018.6570.7300.7300.0000.0000.0000.000
24A39GLN0-0.006-0.01917.2910.3480.3480.0000.0000.0000.000
25A40ARG10.8080.88517.069-14.689-14.6890.0000.0000.0000.000
26A41LEU00.0260.00713.9940.8640.8640.0000.0000.0000.000
27A42PHE00.0500.02712.6361.8121.8120.0000.0000.0000.000
28A43MET0-0.047-0.00912.5391.1261.1260.0000.0000.0000.000
29A44ILE0-0.004-0.00311.3601.1651.1650.0000.0000.0000.000
30A45LEU00.0020.0017.7281.9701.9700.0000.0000.0000.000
31A46TRP00.0200.0077.8804.0704.0700.0000.0000.0000.000
32A47LEU0-0.035-0.0309.6111.3601.3600.0000.0000.0000.000
33A48LYS10.7120.8417.002-31.749-31.7490.0000.0000.0000.000
34A49GLY0-0.0220.0006.5604.1074.1070.0000.0000.0000.000
35A50VAL0-0.056-0.0082.5243.2105.4643.376-2.355-3.2750.029
36A51VAL0-0.007-0.0171.772-25.162-30.29013.429-3.848-4.4520.043
37A52PHE0-0.059-0.0333.811-4.115-3.7950.007-0.070-0.2560.002
38A53SER0-0.013-0.0077.194-1.085-1.0850.0000.0000.0000.000
39A54VAL0-0.019-0.02710.7460.2180.2180.0000.0000.0000.000
40A55THR0-0.001-0.00614.050-0.986-0.9860.0000.0000.0000.000
41A56THR0-0.051-0.03317.091-0.007-0.0070.0000.0000.0000.000
42A57VAL00.0070.00220.498-0.310-0.3100.0000.0000.0000.000
43A58ASP-1-0.749-0.85623.10610.34010.3400.0000.0000.0000.000
44A59LEU0-0.026-0.02925.777-0.179-0.1790.0000.0000.0000.000
45A60LYS10.7850.88728.684-10.557-10.5570.0000.0000.0000.000
46A61ARG10.7590.86128.704-10.774-10.7740.0000.0000.0000.000
47A62LYS10.8290.93723.968-12.005-12.0050.0000.0000.0000.000
48A63PRO00.0430.03023.803-0.311-0.3110.0000.0000.0000.000
49A64ALA00.0260.00725.6980.1770.1770.0000.0000.0000.000
50A65ASP-1-0.867-0.94022.40712.48212.4820.0000.0000.0000.000
51A66LEU00.0680.02319.3800.2960.2960.0000.0000.0000.000
52A67GLN0-0.0170.00222.3830.4760.4760.0000.0000.0000.000
53A68ASN0-0.027-0.02224.603-0.364-0.3640.0000.0000.0000.000
54A69LEU0-0.0310.00116.8310.0250.0250.0000.0000.0000.000
55A70ALA00.000-0.00720.1690.3830.3830.0000.0000.0000.000
56A71PRO00.0250.01922.214-0.281-0.2810.0000.0000.0000.000
57A72GLY0-0.036-0.02126.0690.0210.0210.0000.0000.0000.000
58A73THR0-0.0130.00221.663-0.288-0.2880.0000.0000.0000.000
59A74HIS0-0.022-0.01524.594-0.421-0.4210.0000.0000.0000.000
60A75PRO0-0.0200.03421.1130.3320.3320.0000.0000.0000.000
61A76PRO0-0.072-0.05218.268-0.667-0.6670.0000.0000.0000.000
62A77PHE0-0.018-0.02217.603-0.526-0.5260.0000.0000.0000.000
63A78ILE00.0280.00811.5530.4250.4250.0000.0000.0000.000
64A79THR0-0.0050.00512.057-0.974-0.9740.0000.0000.0000.000
65A80PHE00.0380.0026.8911.8761.8760.0000.0000.0000.000
66A81ASN0-0.003-0.0176.957-0.135-0.1350.0000.0000.0000.000
67A82SER00.014-0.0019.605-1.134-1.1340.0000.0000.0000.000
68A83GLU-1-0.825-0.87312.64217.22917.2290.0000.0000.0000.000
69A84VAL00.004-0.00114.0241.1541.1540.0000.0000.0000.000
70A85LYS10.7930.89612.437-20.443-20.4430.0000.0000.0000.000
71A86THR00.033-0.00516.8970.0720.0720.0000.0000.0000.000
72A87ASP-1-0.786-0.88819.77314.28114.2810.0000.0000.0000.000
73A88VAL00.0050.00418.7830.6930.6930.0000.0000.0000.000
74A89ASN0-0.014-0.02018.5690.8870.8870.0000.0000.0000.000
75A90LYS10.8270.89518.965-13.997-13.9970.0000.0000.0000.000
76A91ILE0-0.0210.00513.9080.8420.8420.0000.0000.0000.000
77A92GLU-1-0.802-0.90114.39018.73018.7300.0000.0000.0000.000
78A93GLU-1-0.840-0.90115.24316.32516.3250.0000.0000.0000.000
79A94PHE00.0460.02210.5340.9670.9670.0000.0000.0000.000
80A95LEU00.008-0.0069.1911.9761.9760.0000.0000.0000.000
81A96GLU-1-0.745-0.82910.63026.19726.1970.0000.0000.0000.000
82A97GLU-1-0.984-0.98612.42920.80120.8010.0000.0000.0000.000
83A98VAL0-0.002-0.0057.4980.6630.6630.0000.0000.0000.000
84A99LEU0-0.0290.0004.9753.8753.8750.0000.0000.0000.000
85A100CYS0-0.0050.0067.873-1.423-1.4230.0000.0000.0000.000
86A101PRO00.0060.0109.0642.8442.8440.0000.0000.0000.000
87A102PRO0-0.024-0.02311.012-0.829-0.8290.0000.0000.0000.000
88A103LYS10.8150.9041.740-137.805-141.38717.153-7.628-5.9430.090
89A104TYR0-0.004-0.0301.610-24.143-32.23721.406-8.050-5.2630.075
90A105LEU00.0190.0107.888-4.574-4.5740.0000.0000.0000.000
91A106LYS10.8810.94611.323-16.764-16.7640.0000.0000.0000.000
92A107LEU00.011-0.00111.823-1.066-1.0660.0000.0000.0000.000
93A108SER0-0.043-0.05915.330-1.681-1.6810.0000.0000.0000.000
94A109PRO0-0.073-0.02318.4770.1010.1010.0000.0000.0000.000
95A110LYS10.7900.87821.437-14.799-14.7990.0000.0000.0000.000
96A111HIS0-0.019-0.01723.810-0.784-0.7840.0000.0000.0000.000
97A112PRO00.0190.00526.3440.3240.3240.0000.0000.0000.000
98A113GLU-1-0.838-0.92927.70410.61910.6190.0000.0000.0000.000
99A114SER0-0.045-0.02125.174-0.285-0.2850.0000.0000.0000.000
100A115ASN0-0.031-0.02823.3040.8240.8240.0000.0000.0000.000
101A116THR0-0.027-0.01825.948-0.021-0.0210.0000.0000.0000.000
102A117ALA00.0260.01928.935-0.393-0.3930.0000.0000.0000.000
103A118GLY00.0260.00329.2740.2940.2940.0000.0000.0000.000
104A119MET00.0040.01625.1440.0040.0040.0000.0000.0000.000
105A120ASP-1-0.843-0.91230.3649.2239.2230.0000.0000.0000.000
106A121ILE00.0110.01231.987-0.283-0.2830.0000.0000.0000.000
107A122PHE00.0360.01329.883-0.240-0.2400.0000.0000.0000.000
108A123ALA00.0240.02632.795-0.155-0.1550.0000.0000.0000.000
109A124LYS10.9140.96535.588-8.349-8.3490.0000.0000.0000.000
110A125PHE00.0390.02832.729-0.276-0.2760.0000.0000.0000.000
111A126SER00.007-0.00934.338-0.131-0.1310.0000.0000.0000.000
112A127ALA0-0.037-0.01936.794-0.175-0.1750.0000.0000.0000.000
113A128TYR0-0.064-0.06939.590-0.140-0.1400.0000.0000.0000.000
114A129ILE00.0140.01436.755-0.208-0.2080.0000.0000.0000.000
115A130LYS10.9530.97737.634-8.457-8.4570.0000.0000.0000.000
116A131ASN0-0.036-0.01441.354-0.248-0.2480.0000.0000.0000.000
117A132SER00.0340.01344.8390.0260.0260.0000.0000.0000.000
118A133ARG10.8430.89147.863-6.177-6.1770.0000.0000.0000.000
119A134PRO00.0380.01249.7940.1120.1120.0000.0000.0000.000
120A135GLU-1-0.786-0.86551.3606.0666.0660.0000.0000.0000.000
121A136ALA00.0120.00948.5660.0080.0080.0000.0000.0000.000
122A137ASN00.007-0.00145.9230.2330.2330.0000.0000.0000.000
123A138GLU-1-0.800-0.88346.5486.7366.7360.0000.0000.0000.000
124A139ALA00.0360.01147.5680.1000.1000.0000.0000.0000.000
125A140LEU0-0.038-0.01543.1170.1520.1520.0000.0000.0000.000
126A141GLU-1-0.800-0.85442.7997.4117.4110.0000.0000.0000.000
127A142ARG10.8400.89843.023-6.858-6.8580.0000.0000.0000.000
128A143GLY0-0.025-0.00943.0110.1020.1020.0000.0000.0000.000
129A144LEU00.003-0.00436.4270.1830.1830.0000.0000.0000.000
130A145LEU00.0280.01538.7230.2310.2310.0000.0000.0000.000
131A146LYS10.9911.00240.181-7.241-7.2410.0000.0000.0000.000
132A147THR0-0.092-0.05636.2500.0860.0860.0000.0000.0000.000
133A148LEU00.009-0.00934.2840.2310.2310.0000.0000.0000.000
134A149GLN0-0.048-0.03436.0630.0920.0920.0000.0000.0000.000
135A150LYS10.9080.95135.986-8.693-8.6930.0000.0000.0000.000
136A151LEU0-0.0240.00429.5090.1510.1510.0000.0000.0000.000
137A152ASP-1-0.784-0.89133.0039.3369.3360.0000.0000.0000.000
138A153GLU-1-0.829-0.91535.2318.3088.3080.0000.0000.0000.000
139A154TYR0-0.016-0.01328.195-0.124-0.1240.0000.0000.0000.000
140A155LEU0-0.0060.00328.3190.2080.2080.0000.0000.0000.000
141A156ASN0-0.014-0.00232.0010.3150.3150.0000.0000.0000.000
142A157SER0-0.019-0.01635.201-0.270-0.2700.0000.0000.0000.000
143A158PRO0-0.067-0.04533.8230.3580.3580.0000.0000.0000.000
144A159LEU0-0.0180.01927.664-0.175-0.1750.0000.0000.0000.000
145A174SER0-0.022-0.00732.0640.1170.1170.0000.0000.0000.000
146A175THR00.014-0.00732.6310.0420.0420.0000.0000.0000.000
147A176ARG10.7560.89527.711-11.051-11.0510.0000.0000.0000.000
148A177LYS10.9760.99723.995-13.819-13.8190.0000.0000.0000.000
149A178PHE00.020-0.00621.7290.1090.1090.0000.0000.0000.000
150A179LEU00.0200.01024.077-0.459-0.4590.0000.0000.0000.000
151A180ASP-1-0.685-0.81822.82413.55913.5590.0000.0000.0000.000
152A181GLY0-0.004-0.00124.1060.0680.0680.0000.0000.0000.000
153A182ASN0-0.005-0.01723.590-0.580-0.5800.0000.0000.0000.000
154A183GLU-1-0.791-0.87818.26115.72715.7270.0000.0000.0000.000
155A184MET0-0.055-0.00917.343-0.700-0.7000.0000.0000.0000.000
156A185THR00.015-0.02117.1650.8740.8740.0000.0000.0000.000
157A186LEU00.0560.01915.194-0.182-0.1820.0000.0000.0000.000
158A187ALA00.0280.01918.283-0.473-0.4730.0000.0000.0000.000
159A188ASP-1-0.748-0.84720.11114.28414.2840.0000.0000.0000.000
160A189CYS0-0.006-0.00616.616-0.016-0.0160.0000.0000.0000.000
161A190ASN0-0.010-0.00419.081-0.994-0.9940.0000.0000.0000.000
162A191LEU0-0.0210.00321.856-0.695-0.6950.0000.0000.0000.000
163A192LEU00.0270.02121.507-0.574-0.5740.0000.0000.0000.000
164A193PRO00.0530.02821.020-0.642-0.6420.0000.0000.0000.000
165A194LYS10.7560.86423.917-13.281-13.2810.0000.0000.0000.000
166A195LEU00.0110.00427.093-0.530-0.5300.0000.0000.0000.000
167A196HIS00.0640.04525.802-0.660-0.6600.0000.0000.0000.000
168A197ILE00.002-0.00126.496-0.459-0.4590.0000.0000.0000.000
169A198VAL0-0.048-0.02629.847-0.424-0.4240.0000.0000.0000.000
170A199LYS10.8460.93229.645-11.002-11.0020.0000.0000.0000.000
171A200VAL0-0.023-0.00230.576-0.354-0.3540.0000.0000.0000.000
172A201VAL0-0.022-0.00832.828-0.370-0.3700.0000.0000.0000.000
173A202ALA00.0260.00535.399-0.327-0.3270.0000.0000.0000.000
174A203LYS10.8400.92236.947-8.187-8.1870.0000.0000.0000.000
175A204LYS10.8430.90937.403-8.680-8.6800.0000.0000.0000.000
176A205TYR0-0.076-0.06636.922-0.332-0.3320.0000.0000.0000.000
177A206ARG10.7500.87041.129-7.651-7.6510.0000.0000.0000.000
178A207ASN0-0.025-0.00142.061-0.038-0.0380.0000.0000.0000.000
179A208PHE00.0130.01437.680-0.043-0.0430.0000.0000.0000.000
180A209ASP-1-0.821-0.89538.8568.1738.1730.0000.0000.0000.000
181A210ILE00.0150.00033.724-0.121-0.1210.0000.0000.0000.000
182A211PRO00.0200.00637.9140.0330.0330.0000.0000.0000.000
183A212LYS10.9600.99238.841-7.131-7.1310.0000.0000.0000.000
184A213GLU-1-0.861-0.95639.4387.6827.6820.0000.0000.0000.000
185A214MET0-0.0630.00236.6590.0720.0720.0000.0000.0000.000
186A215THR00.045-0.00136.0140.3290.3290.0000.0000.0000.000
187A216GLY00.0180.01933.5780.2200.2200.0000.0000.0000.000
188A217ILE0-0.017-0.02331.5730.4430.4430.0000.0000.0000.000
189A218TRP0-0.041-0.02531.1490.4850.4850.0000.0000.0000.000
190A219ARG10.7910.91230.141-10.312-10.3120.0000.0000.0000.000
191A220TYR0-0.013-0.02524.0820.2730.2730.0000.0000.0000.000
192A221LEU0-0.003-0.01026.6980.5110.5110.0000.0000.0000.000
193A222THR0-0.041-0.02427.3450.2230.2230.0000.0000.0000.000
194A223ASN0-0.035-0.02924.9930.0470.0470.0000.0000.0000.000
195A224ALA00.0230.02822.8120.6220.6220.0000.0000.0000.000
196A225TYR0-0.049-0.05622.6870.3360.3360.0000.0000.0000.000
197A226SER0-0.080-0.03624.131-0.214-0.2140.0000.0000.0000.000
198A227ARG10.8140.87216.053-18.345-18.3450.0000.0000.0000.000
199A228ASP-1-0.793-0.87416.70116.88516.8850.0000.0000.0000.000
200A229GLU-1-0.775-0.85713.65620.45320.4530.0000.0000.0000.000
201A230PHE0-0.029-0.01515.946-0.101-0.1010.0000.0000.0000.000
202A231THR00.0410.00419.351-0.313-0.3130.0000.0000.0000.000
203A232ASN0-0.068-0.03117.105-1.453-1.4530.0000.0000.0000.000
204A233THR0-0.034-0.02415.3340.0090.0090.0000.0000.0000.000
205A234CYS0-0.077-0.01418.326-0.453-0.4530.0000.0000.0000.000
206A235PRO0-0.0010.02122.115-0.155-0.1550.0000.0000.0000.000
207A236SER00.0490.00524.393-0.446-0.4460.0000.0000.0000.000
208A237ASP-1-0.762-0.90527.34110.60310.6030.0000.0000.0000.000
209A238LYS10.9740.98130.411-9.404-9.4040.0000.0000.0000.000
210A239GLU-1-0.768-0.85127.37110.54910.5490.0000.0000.0000.000
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