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: ZNVLN

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 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 228
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2811256.077361
FMO2-HF: Nuclear repulsion 2720677.577804
FMO2-HF: Total energy -90578.499556
FMO2-MP2: Total energy -90843.04503


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.
-95.752-82.40314.896-13.011-15.2340.147
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 : -0.836 / q_NPA : -0.935
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].
3A18LEU00.0410.0213.3543.4855.7260.041-1.146-1.1360.003
4A19ILE0-0.009-0.0115.304-3.261-3.2610.0000.0000.0000.000
5A20GLU-1-0.831-0.8807.56120.94020.9400.0000.0000.0000.000
6A21LEU0-0.035-0.01411.062-1.168-1.1680.0000.0000.0000.000
7A22PHE0-0.0070.00513.409-0.769-0.7690.0000.0000.0000.000
8A23VAL00.019-0.01117.054-0.450-0.4500.0000.0000.0000.000
9A24LYS10.9260.95719.635-11.818-11.8180.0000.0000.0000.000
10A25ALA00.0360.03323.3250.2910.2910.0000.0000.0000.000
11A26GLY0-0.024-0.03024.885-0.368-0.3680.0000.0000.0000.000
12A27SER0-0.155-0.12727.440-0.203-0.2030.0000.0000.0000.000
13A28ASP-1-0.833-0.90427.92811.10811.1080.0000.0000.0000.000
14A29GLY0-0.032-0.01828.356-0.073-0.0730.0000.0000.0000.000
15A30GLU-1-0.924-0.96324.91312.21312.2130.0000.0000.0000.000
16A31SER0-0.068-0.02923.3010.7910.7910.0000.0000.0000.000
17A32ILE00.0510.01618.0760.0790.0790.0000.0000.0000.000
18A33GLY00.0290.01522.588-0.489-0.4890.0000.0000.0000.000
19A34ASN0-0.015-0.01724.3200.5380.5380.0000.0000.0000.000
20A35CYS0-0.068-0.02623.369-0.093-0.0930.0000.0000.0000.000
21A36PRO00.0350.02523.0160.5800.5800.0000.0000.0000.000
22A37PHE0-0.012-0.01821.4800.4240.4240.0000.0000.0000.000
23A38SER00.1040.01618.9140.7450.7450.0000.0000.0000.000
24A39GLN0-0.017-0.00417.7950.3060.3060.0000.0000.0000.000
25A40ARG10.9060.95917.699-14.345-14.3450.0000.0000.0000.000
26A41LEU0-0.004-0.00814.5050.8810.8810.0000.0000.0000.000
27A42PHE00.0410.02112.9441.6541.6540.0000.0000.0000.000
28A43MET0-0.031-0.01412.9491.2791.2790.0000.0000.0000.000
29A44ILE00.0060.00811.5221.1971.1970.0000.0000.0000.000
30A45LEU00.0010.0008.0521.9161.9160.0000.0000.0000.000
31A46TRP00.0000.0078.2964.0814.0810.0000.0000.0000.000
32A47LEU0-0.036-0.0349.4561.9181.9180.0000.0000.0000.000
33A48LYS10.6880.8296.739-29.616-29.6160.0000.0000.0000.000
34A49GLY0-0.0010.0125.9744.2264.2260.0000.0000.0000.000
35A50VAL0-0.068-0.0072.6435.1339.0252.105-2.561-3.4350.029
36A51VAL00.003-0.0121.971-29.663-28.6466.389-3.190-4.2160.050
37A52PHE0-0.055-0.0333.934-4.970-4.7430.005-0.109-0.1230.001
38A53SER00.0170.0237.375-0.994-0.9940.0000.0000.0000.000
39A54VAL0-0.011-0.02010.819-0.132-0.1320.0000.0000.0000.000
40A55THR0-0.009-0.01614.170-0.658-0.6580.0000.0000.0000.000
41A56THR0-0.062-0.03017.480-0.034-0.0340.0000.0000.0000.000
42A57VAL00.0110.00220.653-0.350-0.3500.0000.0000.0000.000
43A58ASP-1-0.801-0.91023.22710.37910.3790.0000.0000.0000.000
44A59LEU0-0.077-0.06125.479-0.241-0.2410.0000.0000.0000.000
45A60LYS10.9030.95428.584-10.190-10.1900.0000.0000.0000.000
46A61ARG10.9240.97030.181-10.132-10.1320.0000.0000.0000.000
47A62LYS10.8990.98123.413-12.106-12.1060.0000.0000.0000.000
48A63PRO00.0450.03324.409-0.393-0.3930.0000.0000.0000.000
49A64ALA00.022-0.00426.1580.1910.1910.0000.0000.0000.000
50A65ASP-1-0.850-0.93322.70612.71512.7150.0000.0000.0000.000
51A66LEU00.0450.01720.0570.2870.2870.0000.0000.0000.000
52A67GLN0-0.031-0.01522.9230.3640.3640.0000.0000.0000.000
53A68ASN0-0.022-0.02024.804-0.289-0.2890.0000.0000.0000.000
54A69LEU0-0.0070.01917.123-0.017-0.0170.0000.0000.0000.000
55A70ALA00.0020.00520.1970.2450.2450.0000.0000.0000.000
56A71PRO00.0140.01422.147-0.235-0.2350.0000.0000.0000.000
57A72GLY0-0.034-0.02225.928-0.038-0.0380.0000.0000.0000.000
58A73THR0-0.057-0.03022.0540.0400.0400.0000.0000.0000.000
59A74HIS0-0.033-0.02924.015-0.161-0.1610.0000.0000.0000.000
60A75PRO0-0.0070.03020.8660.3330.3330.0000.0000.0000.000
61A76PRO0-0.080-0.04617.984-0.662-0.6620.0000.0000.0000.000
62A77PHE0-0.033-0.03216.881-0.460-0.4600.0000.0000.0000.000
63A78ILE00.0320.01210.7020.5250.5250.0000.0000.0000.000
64A79THR00.0070.00512.264-0.930-0.9300.0000.0000.0000.000
65A80PHE00.0380.0066.7442.0942.0940.0000.0000.0000.000
66A81ASN00.007-0.0106.392-0.460-0.4600.0000.0000.0000.000
67A82SER0-0.007-0.0079.541-1.166-1.1660.0000.0000.0000.000
68A83GLU-1-0.939-0.93812.58615.61115.6110.0000.0000.0000.000
69A84VAL0-0.006-0.00613.6481.1121.1120.0000.0000.0000.000
70A85LYS10.9120.96812.510-19.168-19.1680.0000.0000.0000.000
71A86THR00.023-0.00716.2360.2910.2910.0000.0000.0000.000
72A87ASP-1-0.843-0.92519.06513.64713.6470.0000.0000.0000.000
73A88VAL00.023-0.00418.5890.5580.5580.0000.0000.0000.000
74A89ASN00.0300.00518.3940.9960.9960.0000.0000.0000.000
75A90LYS10.9700.99718.900-12.995-12.9950.0000.0000.0000.000
76A91ILE0-0.035-0.00613.4090.7450.7450.0000.0000.0000.000
77A92GLU-1-0.864-0.94814.03118.37118.3710.0000.0000.0000.000
78A93GLU-1-0.969-0.98714.94316.05316.0530.0000.0000.0000.000
79A94PHE00.0090.00710.1040.5780.5780.0000.0000.0000.000
80A95LEU00.006-0.0088.8091.5631.5630.0000.0000.0000.000
81A96GLU-1-0.735-0.84510.69924.85724.8570.0000.0000.0000.000
82A97GLU-1-1.002-0.99412.68519.59219.5920.0000.0000.0000.000
83A98VAL0-0.018-0.0127.6240.5820.5820.0000.0000.0000.000
84A99LEU0-0.0400.0025.3542.7142.7140.0000.0000.0000.000
85A100CYS00.0070.0108.287-1.321-1.3210.0000.0000.0000.000
86A101PRO0-0.0130.0079.5492.1732.1730.0000.0000.0000.000
87A102PRO0-0.014-0.03111.223-0.886-0.8860.0000.0000.0000.000
88A103LYS10.9170.9702.331-82.114-80.4751.105-1.098-1.6470.011
89A104TYR00.0030.0002.075-18.510-14.1775.251-4.907-4.6770.053
90A105LEU00.0280.0167.770-4.223-4.2230.0000.0000.0000.000
91A106LYS10.9820.99310.963-16.439-16.4390.0000.0000.0000.000
92A107LEU0-0.018-0.01411.632-0.901-0.9010.0000.0000.0000.000
93A108SER0-0.065-0.05614.953-1.398-1.3980.0000.0000.0000.000
94A109PRO0-0.073-0.02718.187-0.010-0.0100.0000.0000.0000.000
95A110LYS10.9050.94420.675-14.798-14.7980.0000.0000.0000.000
96A111HIS0-0.021-0.00923.425-0.782-0.7820.0000.0000.0000.000
97A112PRO00.0270.01126.0630.2650.2650.0000.0000.0000.000
98A113GLU-1-0.872-0.94427.36410.06110.0610.0000.0000.0000.000
99A114SER0-0.063-0.04524.747-0.259-0.2590.0000.0000.0000.000
100A115ASN00.019-0.00123.1560.7110.7110.0000.0000.0000.000
101A116THR0-0.030-0.00325.7730.0190.0190.0000.0000.0000.000
102A117ALA00.0470.02728.561-0.354-0.3540.0000.0000.0000.000
103A118GLY00.007-0.00628.7900.3410.3410.0000.0000.0000.000
104A119MET0-0.054-0.02026.2770.0700.0700.0000.0000.0000.000
105A120ASP-1-0.911-0.95530.4279.2309.2300.0000.0000.0000.000
106A121ILE00.0030.00631.807-0.288-0.2880.0000.0000.0000.000
107A122PHE00.0140.00530.560-0.253-0.2530.0000.0000.0000.000
108A123ALA00.0430.01433.118-0.217-0.2170.0000.0000.0000.000
109A124LYS10.9160.96635.968-8.218-8.2180.0000.0000.0000.000
110A125PHE00.0550.03433.705-0.244-0.2440.0000.0000.0000.000
111A126SER0-0.008-0.00834.955-0.126-0.1260.0000.0000.0000.000
112A127ALA0-0.014-0.01437.493-0.180-0.1800.0000.0000.0000.000
113A128TYR0-0.054-0.03540.030-0.148-0.1480.0000.0000.0000.000
114A129ILE0-0.0090.00337.340-0.193-0.1930.0000.0000.0000.000
115A130LYS10.9540.97538.220-8.382-8.3820.0000.0000.0000.000
116A131ASN0-0.020-0.00742.147-0.253-0.2530.0000.0000.0000.000
117A132SER00.016-0.00545.643-0.025-0.0250.0000.0000.0000.000
118A133ARG10.8740.92848.383-6.109-6.1090.0000.0000.0000.000
119A134PRO00.0490.01850.6580.1060.1060.0000.0000.0000.000
120A135GLU-1-0.829-0.90952.1595.9735.9730.0000.0000.0000.000
121A136ALA0-0.0020.00349.322-0.005-0.0050.0000.0000.0000.000
122A137ASN00.001-0.00246.6130.2520.2520.0000.0000.0000.000
123A138GLU-1-0.853-0.93047.1396.8106.8100.0000.0000.0000.000
124A139ALA00.0130.01247.8430.0940.0940.0000.0000.0000.000
125A140LEU0-0.067-0.04243.9350.1530.1530.0000.0000.0000.000
126A141GLU-1-0.846-0.91743.1987.4247.4240.0000.0000.0000.000
127A142ARG10.9470.97843.179-6.822-6.8220.0000.0000.0000.000
128A143GLY0-0.064-0.02643.0280.0980.0980.0000.0000.0000.000
129A144LEU00.0190.00436.6690.1900.1900.0000.0000.0000.000
130A145LEU00.0440.01838.9380.2100.2100.0000.0000.0000.000
131A146LYS10.9720.99440.208-7.299-7.2990.0000.0000.0000.000
132A147THR0-0.083-0.04536.2000.1350.1350.0000.0000.0000.000
133A148LEU00.0240.00634.5030.2260.2260.0000.0000.0000.000
134A149GLN0-0.044-0.03736.1020.0890.0890.0000.0000.0000.000
135A150LYS10.9760.99236.299-8.375-8.3750.0000.0000.0000.000
136A151LEU00.0000.01429.6950.1300.1300.0000.0000.0000.000
137A152ASP-1-0.814-0.92033.0719.1699.1690.0000.0000.0000.000
138A153GLU-1-0.841-0.92235.0978.1818.1810.0000.0000.0000.000
139A154TYR0-0.023-0.01327.779-0.106-0.1060.0000.0000.0000.000
140A155LEU0-0.014-0.00228.2850.1820.1820.0000.0000.0000.000
141A156ASN00.0180.00331.7860.3470.3470.0000.0000.0000.000
142A157SER0-0.034-0.00234.515-0.325-0.3250.0000.0000.0000.000
143A158PRO0-0.050-0.02133.1160.3710.3710.0000.0000.0000.000
144A159LEU0-0.0110.01127.101-0.221-0.2210.0000.0000.0000.000
145A174SER0-0.006-0.00931.2360.1000.1000.0000.0000.0000.000
146A175THR0-0.031-0.01631.888-0.037-0.0370.0000.0000.0000.000
147A176ARG10.7730.90426.869-10.952-10.9520.0000.0000.0000.000
148A177LYS10.9700.98922.467-14.263-14.2630.0000.0000.0000.000
149A178PHE0-0.008-0.01120.8610.0590.0590.0000.0000.0000.000
150A179LEU00.0150.00523.981-0.513-0.5130.0000.0000.0000.000
151A180ASP-1-0.697-0.84022.23813.25913.2590.0000.0000.0000.000
152A181GLY00.0130.00023.966-0.152-0.1520.0000.0000.0000.000
153A182ASN0-0.015-0.01922.994-0.341-0.3410.0000.0000.0000.000
154A183GLU-1-0.900-0.94317.44416.25916.2590.0000.0000.0000.000
155A184MET0-0.071-0.01716.714-0.571-0.5710.0000.0000.0000.000
156A185THR00.0130.00316.7140.7130.7130.0000.0000.0000.000
157A186LEU00.0390.00314.838-0.135-0.1350.0000.0000.0000.000
158A187ALA00.0300.01218.087-0.447-0.4470.0000.0000.0000.000
159A188ASP-1-0.758-0.86519.83714.22514.2250.0000.0000.0000.000
160A189CYS00.0070.01916.5070.0620.0620.0000.0000.0000.000
161A190ASN00.0110.02419.188-0.780-0.7800.0000.0000.0000.000
162A191LEU00.012-0.00722.100-0.474-0.4740.0000.0000.0000.000
163A192LEU00.0220.02121.414-0.548-0.5480.0000.0000.0000.000
164A193PRO00.0460.02921.386-0.639-0.6390.0000.0000.0000.000
165A194LYS10.7970.89324.354-12.904-12.9040.0000.0000.0000.000
166A195LEU00.011-0.00227.465-0.509-0.5090.0000.0000.0000.000
167A196HIS00.1440.13326.752-0.529-0.5290.0000.0000.0000.000
168A197ILE0-0.0100.00227.003-0.457-0.4570.0000.0000.0000.000
169A198VAL0-0.043-0.01830.200-0.433-0.4330.0000.0000.0000.000
170A199LYS10.9090.95830.800-10.810-10.8100.0000.0000.0000.000
171A200VAL00.0120.01130.590-0.357-0.3570.0000.0000.0000.000
172A201VAL0-0.008-0.00432.973-0.387-0.3870.0000.0000.0000.000
173A202ALA00.004-0.00535.549-0.328-0.3280.0000.0000.0000.000
174A203LYS10.8790.95637.190-8.292-8.2920.0000.0000.0000.000
175A204LYS10.9030.96337.457-8.535-8.5350.0000.0000.0000.000
176A205TYR0-0.122-0.10736.915-0.399-0.3990.0000.0000.0000.000
177A206ARG10.7720.88841.338-7.656-7.6560.0000.0000.0000.000
178A207ASN0-0.0230.00742.537-0.015-0.0150.0000.0000.0000.000
179A208PHE00.0020.00938.110-0.076-0.0760.0000.0000.0000.000
180A209ASP-1-0.845-0.91739.0938.2738.2730.0000.0000.0000.000
181A210ILE00.015-0.00433.789-0.109-0.1090.0000.0000.0000.000
182A211PRO00.0330.00538.0680.0330.0330.0000.0000.0000.000
183A212LYS10.9971.00739.000-7.238-7.2380.0000.0000.0000.000
184A213GLU-1-0.922-0.98039.5437.6087.6080.0000.0000.0000.000
185A214MET0-0.0650.00136.8940.0550.0550.0000.0000.0000.000
186A215THR00.031-0.00236.2440.3370.3370.0000.0000.0000.000
187A216GLY00.0290.02233.5980.2460.2460.0000.0000.0000.000
188A217ILE0-0.014-0.02631.7480.4290.4290.0000.0000.0000.000
189A218TRP0-0.037-0.01331.1690.5300.5300.0000.0000.0000.000
190A219ARG10.7960.91929.783-10.289-10.2890.0000.0000.0000.000
191A220TYR0-0.023-0.03723.8350.2910.2910.0000.0000.0000.000
192A221LEU00.011-0.00326.7130.5090.5090.0000.0000.0000.000
193A222THR0-0.046-0.02527.3790.2680.2680.0000.0000.0000.000
194A223ASN0-0.032-0.02624.8910.1920.1920.0000.0000.0000.000
195A224ALA00.0460.03222.9080.5730.5730.0000.0000.0000.000
196A225TYR0-0.067-0.10922.9720.2650.2650.0000.0000.0000.000
197A226SER0-0.097-0.04224.184-0.041-0.0410.0000.0000.0000.000
198A227ARG10.8250.90116.125-18.103-18.1030.0000.0000.0000.000
199A228ASP-1-0.819-0.89917.13517.22017.2200.0000.0000.0000.000
200A229GLU-1-0.812-0.90514.12720.59820.5980.0000.0000.0000.000
201A230PHE0-0.028-0.01916.585-0.191-0.1910.0000.0000.0000.000
202A231THR00.0390.00519.996-0.247-0.2470.0000.0000.0000.000
203A232ASN0-0.015-0.00817.051-1.292-1.2920.0000.0000.0000.000
204A233THR0-0.034-0.01316.061-0.235-0.2350.0000.0000.0000.000
205A234CYS0-0.076-0.01618.851-0.461-0.4610.0000.0000.0000.000
206A235PRO00.0090.01622.671-0.123-0.1230.0000.0000.0000.000
207A236SER00.0060.00024.907-0.396-0.3960.0000.0000.0000.000
208A237ASP-1-0.829-0.93327.86910.42810.4280.0000.0000.0000.000
209A238LYS10.9480.96730.997-9.418-9.4180.0000.0000.0000.000
210A239GLU-1-0.760-0.82527.94310.38810.3880.0000.0000.0000.000
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