FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: ZVG8N

Calculation Name: 2D1L-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2D1L

Chain ID: A

ChEMBL ID:

UniProt ID: Q8R1S4

Base Structure: X-ray

Registration Date: 2023-09-23

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 249
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2481486.623202
FMO2-HF: Nuclear repulsion 2381451.834706
FMO2-HF: Total energy -100034.788496
FMO2-MP2: Total energy -100321.228644


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:-2:ALA)


Summations of interaction energy for fragment #1(A:-2:ALA)
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.
-1.1023.1011.647-2.411-3.439-0.004
Interaction energy analysis for fragmet #1(A:-2:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.042 / q_NPA : -0.029
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].
3A0HIS00.013-0.0033.810-1.3260.112-0.023-0.746-0.6690.003
4A1MET00.0390.0176.716-0.042-0.0420.0000.0000.0000.000
5A2GLU-1-0.796-0.9032.4121.7552.5161.400-0.995-1.165-0.003
6A3ALA0-0.0080.0054.452-0.214-0.129-0.001-0.012-0.0720.000
7A4VAL0-0.034-0.0225.9660.0730.0730.0000.0000.0000.000
8A5ILE00.0540.0397.277-0.007-0.0070.0000.0000.0000.000
9A6GLU-1-0.784-0.8765.326-0.291-0.2910.0000.0000.0000.000
10A7LYS10.8420.9198.4650.3660.3660.0000.0000.0000.000
11A8GLU-1-0.830-0.89411.4150.0300.0300.0000.0000.0000.000
12A9CYS0-0.052-0.02610.8420.0120.0120.0000.0000.0000.000
13A10SER0-0.067-0.04011.425-0.020-0.0200.0000.0000.0000.000
14A11ALA0-0.0020.01113.987-0.001-0.0010.0000.0000.0000.000
15A12LEU0-0.014-0.00515.3250.0030.0030.0000.0000.0000.000
16A13GLY00.0210.00916.5810.0020.0020.0000.0000.0000.000
17A14GLY0-0.028-0.02017.801-0.002-0.0020.0000.0000.0000.000
18A15LEU00.0100.01319.7410.0020.0020.0000.0000.0000.000
19A16PHE0-0.003-0.01321.1320.0040.0040.0000.0000.0000.000
20A17GLN0-0.030-0.03021.6020.0020.0020.0000.0000.0000.000
21A18THR0-0.019-0.00623.553-0.002-0.0020.0000.0000.0000.000
22A19ILE00.0300.02425.3390.0020.0020.0000.0000.0000.000
23A20ILE0-0.018-0.00425.6970.0020.0020.0000.0000.0000.000
24A21SER0-0.034-0.02027.513-0.001-0.0010.0000.0000.0000.000
25A22ASP-1-0.896-0.94829.241-0.019-0.0190.0000.0000.0000.000
26A23MET0-0.072-0.02830.0380.0020.0020.0000.0000.0000.000
27A24LYS10.8800.94429.1350.0210.0210.0000.0000.0000.000
28A25GLY00.0020.01533.5500.0000.0000.0000.0000.0000.000
29A26SER0-0.036-0.03335.3180.0010.0010.0000.0000.0000.000
30A27TYR00.0120.00235.1420.0020.0020.0000.0000.0000.000
31A28PRO00.0770.04039.5780.0010.0010.0000.0000.0000.000
32A29VAL00.0050.01141.0840.0010.0010.0000.0000.0000.000
33A30TRP00.0120.00238.9900.0010.0010.0000.0000.0000.000
34A31GLU-1-0.816-0.92943.009-0.010-0.0100.0000.0000.0000.000
35A32ASP-1-0.870-0.90946.043-0.008-0.0080.0000.0000.0000.000
36A33PHE00.009-0.00147.0900.0010.0010.0000.0000.0000.000
37A34ILE00.0500.02246.2510.0010.0010.0000.0000.0000.000
38A35ASN00.0100.01750.0240.0000.0000.0000.0000.0000.000
39A36LYS10.8300.88350.9810.0090.0090.0000.0000.0000.000
40A37ALA00.0250.02552.5440.0000.0000.0000.0000.0000.000
41A38GLY00.0650.03054.1400.0010.0010.0000.0000.0000.000
42A39LYS10.8440.91254.8130.0070.0070.0000.0000.0000.000
43A40LEU00.0250.01657.1650.0000.0000.0000.0000.0000.000
44A41GLN00.007-0.00258.1400.0000.0000.0000.0000.0000.000
45A42SER0-0.013-0.01660.0240.0000.0000.0000.0000.0000.000
46A43GLN0-0.021-0.01862.2000.0000.0000.0000.0000.0000.000
47A44LEU00.0310.03660.8240.0000.0000.0000.0000.0000.000
48A45ARG10.9520.98264.1140.0020.0020.0000.0000.0000.000
49A46THR0-0.010-0.02066.0950.0000.0000.0000.0000.0000.000
50A47THR0-0.006-0.00767.0450.0000.0000.0000.0000.0000.000
51A48VAL00.0170.01767.5480.0000.0000.0000.0000.0000.000
52A49VAL0-0.033-0.01270.1580.0000.0000.0000.0000.0000.000
53A50ALA00.0000.00172.3010.0000.0000.0000.0000.0000.000
54A51ALA00.004-0.00172.3690.0000.0000.0000.0000.0000.000
55A52ALA0-0.003-0.00174.2930.0000.0000.0000.0000.0000.000
56A53ALA0-0.002-0.00276.2240.0000.0000.0000.0000.0000.000
57A54PHE00.0010.00177.1920.0000.0000.0000.0000.0000.000
58A55LEU00.0170.00075.8580.0000.0000.0000.0000.0000.000
59A56ASP-1-0.832-0.89979.7840.0010.0010.0000.0000.0000.000
60A57ALA0-0.055-0.02782.2410.0000.0000.0000.0000.0000.000
61A58PHE0-0.026-0.00881.8620.0000.0000.0000.0000.0000.000
62A59GLN00.007-0.04083.7530.0000.0000.0000.0000.0000.000
63A60LYS10.8890.94684.8930.0000.0000.0000.0000.0000.000
64A61VAL0-0.0140.00587.1260.0000.0000.0000.0000.0000.000
65A62ALA00.0170.01386.7710.0000.0000.0000.0000.0000.000
66A63ASP-1-0.836-0.90488.8680.0010.0010.0000.0000.0000.000
67A64MET0-0.046-0.02091.3270.0000.0000.0000.0000.0000.000
68A65ALA0-0.0050.00491.8550.0000.0000.0000.0000.0000.000
69A66THR00.0210.00091.4760.0000.0000.0000.0000.0000.000
70A67ASN0-0.098-0.05194.1370.0000.0000.0000.0000.0000.000
71A68THR0-0.063-0.02896.9350.0000.0000.0000.0000.0000.000
72A69ARG10.9640.96199.2210.0000.0000.0000.0000.0000.000
73A70GLY00.0430.02799.9300.0000.0000.0000.0000.0000.000
74A71GLY00.0900.04497.4540.0000.0000.0000.0000.0000.000
75A72THR0-0.034-0.01995.4050.0000.0000.0000.0000.0000.000
76A73ARG10.8770.95694.517-0.001-0.0010.0000.0000.0000.000
77A74GLU-1-0.821-0.90893.3830.0020.0020.0000.0000.0000.000
78A75ILE00.0150.01690.1610.0000.0000.0000.0000.0000.000
79A76GLY00.0320.00989.6300.0000.0000.0000.0000.0000.000
80A77SER0-0.036-0.02689.1730.0000.0000.0000.0000.0000.000
81A78ALA00.0170.00986.9600.0000.0000.0000.0000.0000.000
82A79LEU0-0.006-0.00385.2430.0000.0000.0000.0000.0000.000
83A80THR00.0180.01084.3160.0000.0000.0000.0000.0000.000
84A81ARG10.8150.90383.235-0.002-0.0020.0000.0000.0000.000
85A82MET0-0.0060.01379.6390.0000.0000.0000.0000.0000.000
86A83CYS0-0.0250.01079.5500.0000.0000.0000.0000.0000.000
87A84MET0-0.002-0.01879.1580.0000.0000.0000.0000.0000.000
88A85ARG10.8430.92073.842-0.003-0.0030.0000.0000.0000.000
89A86HIS0-0.006-0.03374.8830.0000.0000.0000.0000.0000.000
90A87ARG10.8300.92074.455-0.001-0.0010.0000.0000.0000.000
91A88SER0-0.056-0.03172.4230.0000.0000.0000.0000.0000.000
92A89ILE00.0210.00769.6920.0000.0000.0000.0000.0000.000
93A90GLU-1-0.759-0.87269.5540.0010.0010.0000.0000.0000.000
94A91ALA0-0.026-0.01969.6950.0000.0000.0000.0000.0000.000
95A92LYS10.9130.93866.416-0.004-0.0040.0000.0000.0000.000
96A93LEU00.0130.00864.7880.0000.0000.0000.0000.0000.000
97A94ARG10.8080.88764.949-0.001-0.0010.0000.0000.0000.000
98A95GLN0-0.066-0.03163.7700.0000.0000.0000.0000.0000.000
99A96PHE00.0380.02558.4760.0000.0000.0000.0000.0000.000
100A97SER0-0.024-0.01860.1530.0000.0000.0000.0000.0000.000
101A98SER0-0.005-0.01260.4160.0000.0000.0000.0000.0000.000
102A99ALA00.0620.04357.7000.0000.0000.0000.0000.0000.000
103A100LEU0-0.014-0.00554.9990.0000.0000.0000.0000.0000.000
104A101ILE0-0.041-0.03355.2320.0000.0000.0000.0000.0000.000
105A102ASP-1-0.897-0.95455.1560.0030.0030.0000.0000.0000.000
106A103CYS0-0.080-0.03453.4270.0010.0010.0000.0000.0000.000
107A104LEU0-0.021-0.01449.3300.0000.0000.0000.0000.0000.000
108A105ILE0-0.038-0.01450.4750.0000.0000.0000.0000.0000.000
109A106ASN00.0420.01650.788-0.001-0.0010.0000.0000.0000.000
110A107PRO00.0270.01849.1860.0000.0000.0000.0000.0000.000
111A108LEU00.0020.00344.6490.0000.0000.0000.0000.0000.000
112A109GLN0-0.045-0.03345.856-0.001-0.0010.0000.0000.0000.000
113A110GLU-1-0.918-0.96046.501-0.001-0.0010.0000.0000.0000.000
114A111GLN0-0.063-0.01441.1430.0010.0010.0000.0000.0000.000
115A112MET0-0.051-0.01841.5820.0000.0000.0000.0000.0000.000
116A113GLU-1-0.888-0.95539.670-0.008-0.0080.0000.0000.0000.000
117A114GLU-1-0.792-0.88039.3380.0030.0030.0000.0000.0000.000
118A115TRP00.006-0.00437.4030.0000.0000.0000.0000.0000.000
119A116LYS10.8450.94135.6070.0090.0090.0000.0000.0000.000
120A117LYS10.7800.87134.463-0.003-0.0030.0000.0000.0000.000
121A118VAL00.0120.01433.3800.0000.0000.0000.0000.0000.000
122A119ALA00.0290.01731.2850.0010.0010.0000.0000.0000.000
123A120ASN00.023-0.00129.695-0.003-0.0030.0000.0000.0000.000
124A121GLN0-0.069-0.02828.996-0.005-0.0050.0000.0000.0000.000
125A122LEU00.0180.02326.4160.0020.0020.0000.0000.0000.000
126A123ASP-1-0.854-0.93224.760-0.020-0.0200.0000.0000.0000.000
127A124LYS10.8540.90524.0220.0020.0020.0000.0000.0000.000
128A125ASP-1-0.884-0.93124.0870.0140.0140.0000.0000.0000.000
129A126HIS0-0.037-0.02618.0260.0010.0010.0000.0000.0000.000
130A127ALA00.0500.02819.7330.0000.0000.0000.0000.0000.000
131A128LYS10.8580.93319.127-0.015-0.0150.0000.0000.0000.000
132A129GLU-1-0.778-0.89519.1760.0470.0470.0000.0000.0000.000
133A130TYR00.0790.05412.774-0.005-0.0050.0000.0000.0000.000
134A131LYS10.9350.96214.3880.0460.0460.0000.0000.0000.000
135A132LYS10.7740.87014.596-0.057-0.0570.0000.0000.0000.000
136A133ALA00.0500.03613.0520.0070.0070.0000.0000.0000.000
137A134ARG10.8440.8957.0080.1820.1820.0000.0000.0000.000
138A135GLN0-0.028-0.01110.014-0.056-0.0560.0000.0000.0000.000
139A136GLU-1-0.789-0.87711.5950.1300.1300.0000.0000.0000.000
140A137ILE00.0690.0455.7030.0160.0160.0000.0000.0000.000
141A138LYS10.9050.9676.9670.0130.0130.0000.0000.0000.000
142A139LYS10.8110.8728.661-0.130-0.1300.0000.0000.0000.000
143A140LYS10.8650.9287.979-0.393-0.3930.0000.0000.0000.000
144A141SER00.0190.0044.456-0.223-0.110-0.001-0.008-0.1050.000
145A142SER0-0.080-0.0435.757-0.042-0.0420.0000.0000.0000.000
146A143ASP-1-0.868-0.9409.2190.1110.1110.0000.0000.0000.000
147A144THR00.0300.0035.4720.0770.0770.0000.0000.0000.000
148A145LEU0-0.0020.0088.102-0.027-0.0270.0000.0000.0000.000
149A146LYS10.8240.9029.0040.0100.0100.0000.0000.0000.000
150A147LEU00.0460.01811.011-0.025-0.0250.0000.0000.0000.000
151A148GLN00.0510.0365.518-0.268-0.2680.0000.0000.0000.000
152A149LYS10.9070.96210.8120.1060.1060.0000.0000.0000.000
153A150LYS10.8890.93413.528-0.012-0.0120.0000.0000.0000.000
154A151ALA00.0680.04313.4710.0030.0030.0000.0000.0000.000
155A152LYS10.8220.90612.002-0.015-0.0150.0000.0000.0000.000
156A153LYS10.9670.99616.651-0.004-0.0040.0000.0000.0000.000
157A154VAL00.0170.00718.8120.0130.0130.0000.0000.0000.000
158A155ASP-1-0.884-0.94921.1030.0190.0190.0000.0000.0000.000
159A156ALA0-0.040-0.01723.328-0.002-0.0020.0000.0000.0000.000
160A157GLN00.0320.01023.4260.0140.0140.0000.0000.0000.000
161A158GLY00.0650.05420.0010.0130.0130.0000.0000.0000.000
162A159ARG10.8610.90417.892-0.165-0.1650.0000.0000.0000.000
163A160GLY00.0360.01018.9850.0250.0250.0000.0000.0000.000
164A161ASP-1-0.853-0.91120.5480.1500.1500.0000.0000.0000.000
165A162ILE0-0.051-0.03515.3230.0180.0180.0000.0000.0000.000
166A163GLN0-0.100-0.05811.805-0.042-0.0420.0000.0000.0000.000
167A164PRO00.0900.05314.1560.0720.0720.0000.0000.0000.000
168A165GLN0-0.0010.00614.9800.0500.0500.0000.0000.0000.000
169A166LEU0-0.068-0.0388.5450.0450.0450.0000.0000.0000.000
170A167ASP-1-0.818-0.9059.8100.7500.7500.0000.0000.0000.000
171A168SER00.0110.00110.6970.1690.1690.0000.0000.0000.000
172A169ALA0-0.053-0.0249.3550.0500.0500.0000.0000.0000.000
173A170LEU0-0.012-0.0184.591-0.0060.097-0.001-0.009-0.0930.000
174A171GLN0-0.032-0.0086.5170.5770.5770.0000.0000.0000.000
175A172ASP-1-0.750-0.8569.1870.4610.4610.0000.0000.0000.000
176A173VAL0-0.031-0.0212.685-0.723-0.2710.144-0.161-0.4360.000
177A174ASN00.0020.0056.118-0.270-0.2700.0000.0000.0000.000
178A175ASP-1-0.826-0.9157.1790.3820.3820.0000.0000.0000.000
179A176LYS10.7860.8958.038-0.503-0.5030.0000.0000.0000.000
180A177TYR0-0.020-0.0203.188-1.667-0.4160.129-0.480-0.899-0.004
181A178LEU00.0570.0388.232-0.145-0.1450.0000.0000.0000.000
182A179LEU0-0.014-0.00511.251-0.094-0.0940.0000.0000.0000.000
183A180LEU0-0.041-0.0119.761-0.062-0.0620.0000.0000.0000.000
184A181GLU-1-0.793-0.90811.8150.1550.1550.0000.0000.0000.000
185A182GLU-1-0.874-0.92713.4780.1390.1390.0000.0000.0000.000
186A183THR0-0.096-0.05615.937-0.028-0.0280.0000.0000.0000.000
187A184GLU-1-0.828-0.90914.891-0.008-0.0080.0000.0000.0000.000
188A185LYS10.8580.91416.241-0.168-0.1680.0000.0000.0000.000
189A186GLN0-0.011-0.01319.534-0.019-0.0190.0000.0000.0000.000
190A187ALA0-0.037-0.01520.717-0.007-0.0070.0000.0000.0000.000
191A188VAL00.0680.03220.883-0.006-0.0060.0000.0000.0000.000
192A189ARG10.9310.98323.346-0.058-0.0580.0000.0000.0000.000
193A190LYS10.8870.93023.610-0.046-0.0460.0000.0000.0000.000
194A191ALA00.0300.02526.169-0.003-0.0030.0000.0000.0000.000
195A192LEU00.0360.01826.252-0.002-0.0020.0000.0000.0000.000
196A193ILE0-0.079-0.04329.281-0.001-0.0010.0000.0000.0000.000
197A194GLU-1-0.860-0.92531.0250.0070.0070.0000.0000.0000.000
198A195GLU-1-0.891-0.96231.2730.0000.0000.0000.0000.0000.000
199A196ARG10.9590.97333.429-0.019-0.0190.0000.0000.0000.000
200A197GLY00.0320.01335.2400.0000.0000.0000.0000.0000.000
201A198ARG10.8730.95034.9170.0000.0000.0000.0000.0000.000
202A199PHE00.0450.01336.688-0.001-0.0010.0000.0000.0000.000
203A200CYS0-0.098-0.05138.9480.0010.0010.0000.0000.0000.000
204A201THR0-0.018-0.01340.5720.0000.0000.0000.0000.0000.000
205A202PHE00.0470.02442.8760.0000.0000.0000.0000.0000.000
206A203ILE00.004-0.00243.0850.0000.0000.0000.0000.0000.000
207A204SER0-0.094-0.05745.0610.0000.0000.0000.0000.0000.000
208A205MET00.0020.02545.6150.0000.0000.0000.0000.0000.000
209A206LEU00.0310.01748.9000.0000.0000.0000.0000.0000.000
210A207ARG10.8840.93247.292-0.011-0.0110.0000.0000.0000.000
211A208PRO00.0300.02351.9060.0000.0000.0000.0000.0000.000
212A209VAL0-0.0130.00453.9500.0000.0000.0000.0000.0000.000
213A210ILE00.018-0.00553.3530.0000.0000.0000.0000.0000.000
214A211GLU-1-0.940-0.96656.2690.0070.0070.0000.0000.0000.000
215A212GLU-1-0.858-0.92058.1310.0050.0050.0000.0000.0000.000
216A213GLU-1-0.942-0.96158.1590.0020.0020.0000.0000.0000.000
217A214ILE00.0090.00456.9340.0000.0000.0000.0000.0000.000
218A215SER0-0.026-0.01261.2990.0000.0000.0000.0000.0000.000
219A216MET0-0.038-0.02563.7380.0000.0000.0000.0000.0000.000
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