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: J34G9

Calculation Name: 1EL6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1EL6

Chain ID: A

ChEMBL ID:

UniProt ID: P10929

Base Structure: X-ray

Registration Date: 2023-03-13

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 208
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1889172.090677
FMO2-HF: Nuclear repulsion 1810991.72042
FMO2-HF: Total energy -78180.370257
FMO2-MP2: Total energy -78412.520991


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:12:SER)


Summations of interaction energy for fragment #1(A:12:SER)
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.
-26.289-21.98215.403-9.341-10.37-0.007
Interaction energy analysis for fragmet #1(A:12:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.051 / q_NPA : 0.035
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].
3A14LEU00.0810.0173.805-0.9831.269-0.021-1.249-0.9830.004
4A15ALA00.0390.0465.5190.6450.6450.0000.0000.0000.000
5A16ASP-1-0.791-0.9082.518-4.297-0.5341.629-2.686-2.706-0.028
6A17PHE0-0.082-0.0472.356-0.9800.2181.569-1.017-1.7490.002
7A18LEU0-0.0260.0066.5850.1080.1080.0000.0000.0000.000
8A19GLY00.0520.0269.5270.1200.1200.0000.0000.0000.000
9A20PHE0-0.017-0.00312.507-0.080-0.0800.0000.0000.0000.000
10A21ARG10.9440.96614.5650.1950.1950.0000.0000.0000.000
11A22PRO00.0340.02517.419-0.013-0.0130.0000.0000.0000.000
12A23LYS10.9680.98619.442-0.002-0.0020.0000.0000.0000.000
13A24THR00.021-0.01122.9070.0160.0160.0000.0000.0000.000
14A25GLY0-0.022-0.01925.634-0.007-0.0070.0000.0000.0000.000
15A26ASP-1-0.833-0.90121.6380.0620.0620.0000.0000.0000.000
16A27ILE00.0030.02023.6000.0170.0170.0000.0000.0000.000
17A28ASP-1-0.893-0.94722.7540.0710.0710.0000.0000.0000.000
18A29VAL0-0.0180.01117.7520.0060.0060.0000.0000.0000.000
19A30MET0-0.001-0.01520.6470.0100.0100.0000.0000.0000.000
20A31ASN0-0.042-0.01222.971-0.008-0.0080.0000.0000.0000.000
21A32ARG10.8890.94022.590-0.260-0.2600.0000.0000.0000.000
22A33GLN0-0.027-0.01117.2550.0260.0260.0000.0000.0000.000
23A34SER0-0.036-0.03819.721-0.010-0.0100.0000.0000.0000.000
24A35VAL00.0090.02116.7290.0360.0360.0000.0000.0000.000
25A36GLY0-0.011-0.01713.754-0.051-0.0510.0000.0000.0000.000
26A37SER0-0.096-0.04913.5750.0030.0030.0000.0000.0000.000
27A38VAL0-0.0100.01510.8250.0370.0370.0000.0000.0000.000
28A39THR00.0210.0019.5190.1050.1050.0000.0000.0000.000
29A40ILE00.041-0.00510.3820.1180.1180.0000.0000.0000.000
30A41SER00.0220.0066.0210.3160.3160.0000.0000.0000.000
31A42GLN00.0370.0315.9511.0021.0020.0000.0000.0000.000
32A43LEU00.0010.0157.1940.2140.2140.0000.0000.0000.000
33A44ALA0-0.042-0.0167.779-0.061-0.0610.0000.0000.0000.000
34A45LYS10.8500.9291.802-20.670-23.57612.226-4.389-4.9320.015
35A46GLY00.0010.0086.196-0.453-0.4530.0000.0000.0000.000
36A47PHE0-0.032-0.0167.459-0.437-0.4370.0000.0000.0000.000
37A48TYR00.000-0.0309.3650.1530.1530.0000.0000.0000.000
38A49GLU-1-0.948-0.95411.779-0.038-0.0380.0000.0000.0000.000
39A50PRO0-0.0090.00011.7210.0490.0490.0000.0000.0000.000
40A51ASN0-0.019-0.0308.607-0.128-0.1280.0000.0000.0000.000
41A52ILE00.014-0.0069.5710.0720.0720.0000.0000.0000.000
42A53GLU-1-0.901-0.9395.543-0.687-0.6870.0000.0000.0000.000
43A54SER0-0.036-0.0338.2580.1470.1470.0000.0000.0000.000
44A55ALA00.0590.02210.7980.0200.0200.0000.0000.0000.000
45A56ILE0-0.037-0.02010.6260.0260.0260.0000.0000.0000.000
46A57ASN0-0.024-0.0168.502-0.021-0.0210.0000.0000.0000.000
47A58ASP-1-0.818-0.90612.7260.2770.2770.0000.0000.0000.000
48A59VAL0-0.005-0.01015.997-0.001-0.0010.0000.0000.0000.000
49A60HIS0-0.049-0.01413.4420.0110.0110.0000.0000.0000.000
50A61ASN00.006-0.01715.731-0.001-0.0010.0000.0000.0000.000
51A62PHE0-0.048-0.00918.493-0.001-0.0010.0000.0000.0000.000
52A63SER0-0.097-0.05319.533-0.013-0.0130.0000.0000.0000.000
53A64ILE0-0.0340.00419.238-0.016-0.0160.0000.0000.0000.000
54A65LYS10.9390.96822.284-0.043-0.0430.0000.0000.0000.000
55A66ASP-1-0.832-0.90324.9960.1540.1540.0000.0000.0000.000
56A67VAL0-0.036-0.01125.820-0.019-0.0190.0000.0000.0000.000
57A68GLY00.0210.01728.1860.0090.0090.0000.0000.0000.000
58A69THR0-0.070-0.05429.099-0.005-0.0050.0000.0000.0000.000
59A70ILE0-0.002-0.00231.597-0.008-0.0080.0000.0000.0000.000
60A71ILE0-0.0070.00529.505-0.001-0.0010.0000.0000.0000.000
61A72THR0-0.009-0.00434.0360.0000.0000.0000.0000.0000.000
62A73ASN0-0.0050.01335.593-0.002-0.0020.0000.0000.0000.000
63A74LYS10.9980.97938.5860.0190.0190.0000.0000.0000.000
64A75THR0-0.0150.00137.8750.0010.0010.0000.0000.0000.000
65A76GLY00.0470.03139.817-0.001-0.0010.0000.0000.0000.000
66A77VAL0-0.024-0.01434.6400.0000.0000.0000.0000.0000.000
67A78SER00.0310.01732.5400.0040.0040.0000.0000.0000.000
68A79PRO0-0.021-0.02830.240-0.009-0.0090.0000.0000.0000.000
69A80GLU-1-0.836-0.90428.129-0.023-0.0230.0000.0000.0000.000
70A81GLY0-0.0110.00925.930-0.006-0.0060.0000.0000.0000.000
71A82VAL0-0.028-0.01927.0120.0080.0080.0000.0000.0000.000
72A83SER00.0260.00724.460-0.005-0.0050.0000.0000.0000.000
73A84GLN00.0070.01226.1070.0040.0040.0000.0000.0000.000
74A85THR0-0.022-0.00827.836-0.003-0.0030.0000.0000.0000.000
75A86ASP-1-0.736-0.81728.375-0.218-0.2180.0000.0000.0000.000
76A87TYR00.0330.01831.3990.0100.0100.0000.0000.0000.000
77A88TRP0-0.042-0.02425.185-0.010-0.0100.0000.0000.0000.000
78A89ALA00.0210.00032.5990.0110.0110.0000.0000.0000.000
79A90PHE00.017-0.00530.935-0.014-0.0140.0000.0000.0000.000
80A91SER0-0.020-0.01336.4800.0130.0130.0000.0000.0000.000
81A92GLY00.0480.02838.607-0.008-0.0080.0000.0000.0000.000
82A93THR0-0.023-0.02840.5960.0060.0060.0000.0000.0000.000
83A94VAL0-0.0640.02435.864-0.006-0.0060.0000.0000.0000.000
84A95THR0-0.011-0.04537.6130.0120.0120.0000.0000.0000.000
85A96ASP-1-0.804-0.94635.786-0.213-0.2130.0000.0000.0000.000
86A97ASP-1-0.945-0.94938.332-0.152-0.1520.0000.0000.0000.000
87A98SER0-0.068-0.02237.8010.0050.0050.0000.0000.0000.000
88A99LEU0-0.084-0.03935.4530.0030.0030.0000.0000.0000.000
89A100PRO0-0.0100.01040.0900.0050.0050.0000.0000.0000.000
90A101PRO00.011-0.00441.514-0.006-0.0060.0000.0000.0000.000
91A102GLY00.0270.02741.0680.0060.0060.0000.0000.0000.000
92A103SER0-0.046-0.04437.7950.0010.0010.0000.0000.0000.000
93A104PRO0-0.040-0.01733.776-0.005-0.0050.0000.0000.0000.000
94A105ILE00.0080.00132.076-0.007-0.0070.0000.0000.0000.000
95A106THR0-0.017-0.00925.6250.0000.0000.0000.0000.0000.000
96A107VAL0-0.008-0.00228.981-0.009-0.0090.0000.0000.0000.000
97A108LEU00.0040.00623.052-0.004-0.0040.0000.0000.0000.000
98A109VAL00.0270.02226.0840.0120.0120.0000.0000.0000.000
99A110PHE00.011-0.00524.473-0.011-0.0110.0000.0000.0000.000
100A111GLY0-0.010-0.00221.264-0.028-0.0280.0000.0000.0000.000
101A112LEU0-0.021-0.00721.253-0.030-0.0300.0000.0000.0000.000
102A113PRO00.004-0.00821.4670.0240.0240.0000.0000.0000.000
103A114VAL00.0160.02224.5050.0200.0200.0000.0000.0000.000
104A115SER0-0.028-0.00428.157-0.001-0.0010.0000.0000.0000.000
105A116ALA00.021-0.00630.3300.0150.0150.0000.0000.0000.000
106A117THR00.0470.01433.622-0.002-0.0020.0000.0000.0000.000
107A118THR00.024-0.00736.8370.0050.0050.0000.0000.0000.000
108A119GLY00.0160.00239.0200.0080.0080.0000.0000.0000.000
109A120MET0-0.072-0.00836.4600.0010.0010.0000.0000.0000.000
110A121THR00.0280.01440.331-0.005-0.0050.0000.0000.0000.000
111A122ALA00.0550.02038.459-0.005-0.0050.0000.0000.0000.000
112A123ILE00.0110.01038.031-0.005-0.0050.0000.0000.0000.000
113A124GLU-1-0.869-0.94538.808-0.123-0.1230.0000.0000.0000.000
114A125PHE00.0270.00531.100-0.003-0.0030.0000.0000.0000.000
115A126VAL00.0240.02334.064-0.009-0.0090.0000.0000.0000.000
116A127ALA0-0.018-0.02033.939-0.002-0.0020.0000.0000.0000.000
117A128LYS10.8820.94832.0000.1560.1560.0000.0000.0000.000
118A129VAL00.0150.00829.189-0.012-0.0120.0000.0000.0000.000
119A130ARG10.8790.92129.1660.1210.1210.0000.0000.0000.000
120A131VAL0-0.0160.00228.2470.0030.0030.0000.0000.0000.000
121A132ALA00.0540.03525.415-0.004-0.0040.0000.0000.0000.000
122A133LEU0-0.009-0.00724.610-0.016-0.0160.0000.0000.0000.000
123A134GLN0-0.037-0.01825.0970.0000.0000.0000.0000.0000.000
124A135GLU-1-0.926-0.95923.001-0.234-0.2340.0000.0000.0000.000
125A136ALA0-0.019-0.00520.586-0.014-0.0140.0000.0000.0000.000
126A137ILE0-0.022-0.00920.540-0.003-0.0030.0000.0000.0000.000
127A138ALA0-0.035-0.01421.9920.0140.0140.0000.0000.0000.000
128A139SER0-0.083-0.02117.2960.0000.0000.0000.0000.0000.000
129A140PHE0-0.021-0.01416.882-0.017-0.0170.0000.0000.0000.000
130A141THR00.0120.00215.925-0.060-0.0600.0000.0000.0000.000
131A142ALA00.0020.00417.4790.0110.0110.0000.0000.0000.000
132A143ILE0-0.029-0.03219.1790.0300.0300.0000.0000.0000.000
133A144ASN0-0.015-0.00522.4900.0160.0160.0000.0000.0000.000
134A145SER0-0.030-0.03224.3950.0130.0130.0000.0000.0000.000
135A146TYR00.0200.00927.788-0.012-0.0120.0000.0000.0000.000
136A147LYS10.9230.97230.4120.1120.1120.0000.0000.0000.000
137A148ASP-1-0.814-0.88034.206-0.126-0.1260.0000.0000.0000.000
138A149HIS00.0260.01936.8730.0080.0080.0000.0000.0000.000
139A150PRO0-0.055-0.02938.9630.0030.0030.0000.0000.0000.000
140A151THR0-0.005-0.02142.2540.0040.0040.0000.0000.0000.000
141A152ASP-1-0.845-0.89041.192-0.117-0.1170.0000.0000.0000.000
142A153GLY00.015-0.00440.468-0.004-0.0040.0000.0000.0000.000
143A154SER0-0.104-0.07138.858-0.006-0.0060.0000.0000.0000.000
144A155LYS10.8550.90936.3150.1220.1220.0000.0000.0000.000
145A156LEU0-0.025-0.00731.8810.0070.0070.0000.0000.0000.000
146A157GLU-1-0.932-0.96632.849-0.125-0.1250.0000.0000.0000.000
147A158VAL0-0.005-0.00726.7510.0010.0010.0000.0000.0000.000
148A159THR00.0180.01826.9900.0050.0050.0000.0000.0000.000
149A160TYR0-0.043-0.05022.493-0.013-0.0130.0000.0000.0000.000
150A161LEU0-0.011-0.00518.8030.0230.0230.0000.0000.0000.000
151A162ASP-1-0.838-0.87318.709-0.293-0.2930.0000.0000.0000.000
152A163ASN0-0.057-0.04620.694-0.002-0.0020.0000.0000.0000.000
153A164GLN0-0.058-0.03016.694-0.013-0.0130.0000.0000.0000.000
154A165LYN0-0.0080.03222.4350.0100.0100.0000.0000.0000.000
155A166HIS10.7850.85919.9840.3070.3070.0000.0000.0000.000
156A167VAL00.0520.03924.8960.0210.0210.0000.0000.0000.000
157A168LEU0-0.039-0.02524.050-0.027-0.0270.0000.0000.0000.000
158A169SER0-0.024-0.01227.3540.0220.0220.0000.0000.0000.000
159A170THR00.017-0.00429.416-0.010-0.0100.0000.0000.0000.000
160A171TYR0-0.076-0.03827.952-0.007-0.0070.0000.0000.0000.000
161A172SER00.0300.01432.2980.0140.0140.0000.0000.0000.000
162A173THR0-0.034-0.00929.847-0.008-0.0080.0000.0000.0000.000
163A174TYR00.0600.02830.5060.0000.0000.0000.0000.0000.000
164A175GLY00.0150.02535.0370.0090.0090.0000.0000.0000.000
165A176ILE0-0.041-0.00334.2770.0100.0100.0000.0000.0000.000
166A177THR0-0.028-0.02334.520-0.011-0.0110.0000.0000.0000.000
167A178ILE0-0.015-0.00629.9610.0100.0100.0000.0000.0000.000
168A179SER0-0.006-0.01232.527-0.005-0.0050.0000.0000.0000.000
169A180GLN00.017-0.01027.834-0.002-0.0020.0000.0000.0000.000
170A181GLU-1-0.872-0.92332.009-0.138-0.1380.0000.0000.0000.000
171A182ILE0-0.023-0.00730.0560.0010.0010.0000.0000.0000.000
172A183ILE0-0.036-0.01132.9030.0110.0110.0000.0000.0000.000
173A184SER0-0.017-0.02032.7730.0140.0140.0000.0000.0000.000
174A185GLU-1-0.912-0.96530.731-0.177-0.1770.0000.0000.0000.000
175A186SER0-0.011-0.02326.1540.0090.0090.0000.0000.0000.000
176A187LYS10.8320.91727.5870.0750.0750.0000.0000.0000.000
177A188PRO00.0330.01425.4270.0010.0010.0000.0000.0000.000
178A189GLY00.0390.01224.7740.0120.0120.0000.0000.0000.000
179A190TYR00.0400.01422.310-0.006-0.0060.0000.0000.0000.000
180A191GLY0-0.031-0.01823.6130.0110.0110.0000.0000.0000.000
181A192THR00.0570.03225.289-0.009-0.0090.0000.0000.0000.000
182A193TRP0-0.068-0.05427.3460.0170.0170.0000.0000.0000.000
183A194ASN00.0260.01431.676-0.010-0.0100.0000.0000.0000.000
184A195LEU0-0.050-0.01335.2810.0030.0030.0000.0000.0000.000
185A196LEU0-0.016-0.01337.7790.0010.0010.0000.0000.0000.000
186A197GLY00.0310.01740.3440.0010.0010.0000.0000.0000.000
187A198ALA0-0.035-0.02442.495-0.002-0.0020.0000.0000.0000.000
188A199GLN00.0090.01244.5970.0030.0030.0000.0000.0000.000
189A200THR00.001-0.00346.568-0.003-0.0030.0000.0000.0000.000
190A201VAL0-0.004-0.01347.1830.0030.0030.0000.0000.0000.000
191A202THR00.0090.00949.877-0.003-0.0030.0000.0000.0000.000
192A203LEU0-0.039-0.01047.1160.0020.0020.0000.0000.0000.000
193A204ASP-1-0.855-0.93950.9750.0130.0130.0000.0000.0000.000
194A205ASN0-0.048-0.01053.2530.0000.0000.0000.0000.0000.000
195A206GLN0-0.026-0.01550.406-0.002-0.0020.0000.0000.0000.000
196A207GLN00.0260.00955.4200.0020.0020.0000.0000.0000.000
197A208THR0-0.032-0.01653.3460.0000.0000.0000.0000.0000.000
198A209PRO00.0020.00552.7190.0000.0000.0000.0000.0000.000
199A210THR0-0.016-0.01046.338-0.004-0.0040.0000.0000.0000.000
200A211VAL0-0.0020.00846.1020.0030.0030.0000.0000.0000.000
201A212PHE0-0.038-0.02242.053-0.003-0.0030.0000.0000.0000.000
202A213TYR00.0320.01640.3630.0030.0030.0000.0000.0000.000
203A214HIS10.8370.89138.403-0.019-0.0190.0000.0000.0000.000
204A215PHE00.0450.02234.197-0.001-0.0010.0000.0000.0000.000
205A216GLU-1-0.851-0.93733.4760.0610.0610.0000.0000.0000.000
206A217ARG10.8240.92022.501-0.094-0.0940.0000.0000.0000.000
207A218THR00.0480.00030.4390.0090.0090.0000.0000.0000.000
208A219ALA00.0140.04124.9010.0170.0170.0000.0000.0000.000