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: JQVG9

Calculation Name: 3E7D-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3E7D

Chain ID: A

ChEMBL ID:

UniProt ID: Q2YRF5

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 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 202
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2066833.451091
FMO2-HF: Nuclear repulsion 1992956.860927
FMO2-HF: Total energy -73876.590164
FMO2-MP2: Total energy -74092.820156


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:4:TYR)


Summations of interaction energy for fragment #1(A:4:TYR)
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.
-11.926-5.0233.423-3.331-6.994-0.003
Interaction energy analysis for fragmet #1(A:4:TYR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / q_NPA : -0.011
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].
3A6ARG10.9600.9722.504-12.072-5.4823.423-3.294-6.719-0.003
4A7ASP-1-0.827-0.9044.2850.0020.2430.001-0.032-0.2090.000
5A8GLY00.0330.0127.566-0.110-0.1100.0000.0000.0000.000
6A9GLN00.0390.0149.182-0.004-0.0040.0000.0000.0000.000
7A10ALA00.0330.0268.8160.0450.0450.0000.0000.0000.000
8A11ILE0-0.056-0.0324.6140.0470.119-0.001-0.005-0.0660.000
9A12TYR0-0.0080.0138.7400.1700.1700.0000.0000.0000.000
10A13ASP-1-0.833-0.93112.200-0.090-0.0900.0000.0000.0000.000
11A14ARG10.9210.9576.869-0.477-0.4770.0000.0000.0000.000
12A15SER0-0.043-0.02711.4810.0760.0760.0000.0000.0000.000
13A16PHE00.008-0.01012.7220.0540.0540.0000.0000.0000.000
14A17ALA0-0.021-0.00114.3870.0240.0240.0000.0000.0000.000
15A18ILE0-0.015-0.00510.5750.0350.0350.0000.0000.0000.000
16A19ILE00.0000.01015.1760.0080.0080.0000.0000.0000.000
17A20ARG10.7660.84517.8320.0250.0250.0000.0000.0000.000
18A21ALA0-0.051-0.00717.6790.0040.0040.0000.0000.0000.000
19A22GLU-1-0.950-0.97416.0270.1160.1160.0000.0000.0000.000
20A23ALA0-0.016-0.02220.136-0.006-0.0060.0000.0000.0000.000
21A24ASP-1-0.815-0.88022.7200.0370.0370.0000.0000.0000.000
22A25LEU0-0.028-0.03123.910-0.009-0.0090.0000.0000.0000.000
23A26ARG10.8550.91527.694-0.032-0.0320.0000.0000.0000.000
24A27HIS0-0.028-0.00829.7440.0030.0030.0000.0000.0000.000
25A28ILE0-0.016-0.00228.377-0.005-0.0050.0000.0000.0000.000
26A29PRO00.0570.03931.4790.0030.0030.0000.0000.0000.000
27A30ALA00.0590.01731.525-0.003-0.0030.0000.0000.0000.000
28A31ASP-1-0.911-0.95831.031-0.018-0.0180.0000.0000.0000.000
29A32LEU00.022-0.00830.549-0.006-0.0060.0000.0000.0000.000
30A33GLU-1-0.772-0.83324.884-0.018-0.0180.0000.0000.0000.000
31A34LYS10.9980.97524.6970.0280.0280.0000.0000.0000.000
32A35LEU0-0.008-0.00424.238-0.011-0.0110.0000.0000.0000.000
33A36ALA00.0300.01824.959-0.008-0.0080.0000.0000.0000.000
34A37VAL00.0080.00019.935-0.007-0.0070.0000.0000.0000.000
35A38ARG10.8670.92619.4100.1140.1140.0000.0000.0000.000
36A39VAL00.0140.00120.581-0.017-0.0170.0000.0000.0000.000
37A40ILE00.0270.02218.402-0.009-0.0090.0000.0000.0000.000
38A41HIS0-0.043-0.02213.4990.0130.0130.0000.0000.0000.000
39A42ALA0-0.051-0.01516.304-0.026-0.0260.0000.0000.0000.000
40A43CYS0-0.117-0.03818.220-0.008-0.0080.0000.0000.0000.000
41A44GLY00.0190.01916.2330.0000.0000.0000.0000.0000.000
42A45MET0-0.022-0.01416.8610.0200.0200.0000.0000.0000.000
43A46VAL00.1070.05118.543-0.005-0.0050.0000.0000.0000.000
44A47ASP-1-0.850-0.89221.051-0.019-0.0190.0000.0000.0000.000
45A48VAL00.020-0.01423.297-0.001-0.0010.0000.0000.0000.000
46A49ALA0-0.016-0.01524.865-0.001-0.0010.0000.0000.0000.000
47A50ASN0-0.035-0.02026.6040.0050.0050.0000.0000.0000.000
48A51ASP-1-0.855-0.91228.689-0.021-0.0210.0000.0000.0000.000
49A52LEU0-0.076-0.01226.977-0.005-0.0050.0000.0000.0000.000
50A53ALA00.0050.00530.7950.0040.0040.0000.0000.0000.000
51A54PHE0-0.013-0.02932.826-0.005-0.0050.0000.0000.0000.000
52A55SER00.0470.04936.2230.0020.0020.0000.0000.0000.000
53A56GLU-1-0.887-0.95738.109-0.007-0.0070.0000.0000.0000.000
54A57GLY0-0.0050.00337.996-0.001-0.0010.0000.0000.0000.000
55A58ALA00.0070.00035.730-0.002-0.0020.0000.0000.0000.000
56A59GLY00.0490.01933.500-0.004-0.0040.0000.0000.0000.000
57A60LYS10.8380.90534.1460.0110.0110.0000.0000.0000.000
58A61ALA0-0.0100.01136.657-0.001-0.0010.0000.0000.0000.000
59A62GLY00.0580.01434.712-0.001-0.0010.0000.0000.0000.000
60A63ARG10.8850.95828.9490.0340.0340.0000.0000.0000.000
61A64ASN0-0.007-0.02134.2370.0020.0020.0000.0000.0000.000
62A65ALA00.0800.05537.3880.0000.0000.0000.0000.0000.000
63A66LEU0-0.012-0.01031.397-0.001-0.0010.0000.0000.0000.000
64A67LEU0-0.031-0.02234.050-0.001-0.0010.0000.0000.0000.000
65A68ALA0-0.0260.00036.3560.0010.0010.0000.0000.0000.000
66A69GLY00.0300.01937.5880.0010.0010.0000.0000.0000.000
67A70ALA0-0.052-0.00737.538-0.001-0.0010.0000.0000.0000.000
68A71PRO00.0020.00836.563-0.004-0.0040.0000.0000.0000.000
69A72ILE00.021-0.00531.1890.0000.0000.0000.0000.0000.000
70A73LEU0-0.027-0.00934.872-0.003-0.0030.0000.0000.0000.000
71A74CYS0-0.0050.00832.142-0.002-0.0020.0000.0000.0000.000
72A75ASP-1-0.705-0.85733.061-0.063-0.0630.0000.0000.0000.000
73A76ALA0-0.031-0.03030.9870.0000.0000.0000.0000.0000.000
74A77ARG10.9070.96828.1920.0940.0940.0000.0000.0000.000
75A78MET00.0160.00125.598-0.004-0.0040.0000.0000.0000.000
76A79VAL0-0.045-0.00726.150-0.006-0.0060.0000.0000.0000.000
77A80ALA00.0420.00627.625-0.002-0.0020.0000.0000.0000.000
78A81GLU-1-0.903-0.96825.254-0.104-0.1040.0000.0000.0000.000
79A82GLY0-0.0030.01623.286-0.008-0.0080.0000.0000.0000.000
80A83ILE0-0.015-0.01223.486-0.005-0.0050.0000.0000.0000.000
81A84THR0-0.048-0.02621.766-0.006-0.0060.0000.0000.0000.000
82A85ARG11.0250.98824.3450.0760.0760.0000.0000.0000.000
83A86SER00.0080.01323.0730.0050.0050.0000.0000.0000.000
84A87ARG10.8390.92121.7570.0970.0970.0000.0000.0000.000
85A88LEU0-0.064-0.02426.1430.0050.0050.0000.0000.0000.000
86A89PRO0-0.038-0.00329.7500.0010.0010.0000.0000.0000.000
87A90ALA00.0190.00632.2170.0030.0030.0000.0000.0000.000
88A91ASP-1-0.916-0.93533.911-0.042-0.0420.0000.0000.0000.000
89A92ASN0-0.053-0.03433.235-0.002-0.0020.0000.0000.0000.000
90A93ARG10.9520.97333.7730.0400.0400.0000.0000.0000.000
91A94VAL0-0.0090.00030.4980.0010.0010.0000.0000.0000.000
92A95ILE0-0.026-0.01533.848-0.001-0.0010.0000.0000.0000.000
93A96TYR00.013-0.00933.991-0.002-0.0020.0000.0000.0000.000
94A97THR00.0290.00036.119-0.001-0.0010.0000.0000.0000.000
95A98LEU0-0.0130.00735.3860.0010.0010.0000.0000.0000.000
96A99SER0-0.039-0.02936.235-0.001-0.0010.0000.0000.0000.000
97A100ASP-1-0.806-0.85838.588-0.041-0.0410.0000.0000.0000.000
98A101PRO00.008-0.00141.9680.0000.0000.0000.0000.0000.000
99A102SER0-0.053-0.05244.3630.0010.0010.0000.0000.0000.000
100A103VAL00.0400.01242.0430.0010.0010.0000.0000.0000.000
101A104PRO0-0.060-0.04543.6890.0010.0010.0000.0000.0000.000
102A105GLU-1-0.773-0.88145.936-0.034-0.0340.0000.0000.0000.000
103A106LEU0-0.0090.00646.4290.0020.0020.0000.0000.0000.000
104A107ALA0-0.022-0.01545.6020.0010.0010.0000.0000.0000.000
105A108LYS10.8010.88447.6140.0370.0370.0000.0000.0000.000
106A109LYS10.9460.98550.6580.0300.0300.0000.0000.0000.000
107A110ILE0-0.058-0.01947.0720.0010.0010.0000.0000.0000.000
108A111GLY00.0030.02050.6550.0010.0010.0000.0000.0000.000
109A112ASN00.0890.05745.047-0.002-0.0020.0000.0000.0000.000
110A113THR0-0.016-0.00441.543-0.002-0.0020.0000.0000.0000.000
111A114ARG11.0150.98140.8190.0510.0510.0000.0000.0000.000
112A115SER0-0.001-0.00837.0390.0000.0000.0000.0000.0000.000
113A116ALA0-0.0040.01639.6910.0000.0000.0000.0000.0000.000
114A117ALA00.0630.02242.5850.0010.0010.0000.0000.0000.000
115A118ALA0-0.017-0.00240.4580.0010.0010.0000.0000.0000.000
116A119LEU00.0250.01140.0350.0000.0000.0000.0000.0000.000
117A120ASP-1-0.832-0.90243.156-0.030-0.0300.0000.0000.0000.000
118A121LEU0-0.066-0.04543.1400.0010.0010.0000.0000.0000.000
119A122TRP0-0.048-0.03337.4840.0000.0000.0000.0000.0000.000
120A123LEU00.0260.02343.2570.0010.0010.0000.0000.0000.000
121A124PRO0-0.052-0.03045.7790.0010.0010.0000.0000.0000.000
122A125HIS0-0.021-0.01841.7790.0010.0010.0000.0000.0000.000
123A126ILE0-0.0110.00642.312-0.001-0.0010.0000.0000.0000.000
124A127GLU-1-0.901-0.93942.928-0.023-0.0230.0000.0000.0000.000
125A128GLY00.0050.00942.9750.0000.0000.0000.0000.0000.000
126A129SER0-0.090-0.05839.053-0.002-0.0020.0000.0000.0000.000
127A130ILE0-0.0120.00633.3260.0010.0010.0000.0000.0000.000
128A131VAL00.0230.02036.121-0.003-0.0030.0000.0000.0000.000
129A132ALA00.011-0.00231.3530.0000.0000.0000.0000.0000.000
130A133ILE0-0.011-0.01333.431-0.003-0.0030.0000.0000.0000.000
131A134GLY00.0230.00430.0840.0010.0010.0000.0000.0000.000
132A135ASN0-0.130-0.06930.018-0.003-0.0030.0000.0000.0000.000
133A136ALA00.0390.00632.1540.0010.0010.0000.0000.0000.000
134A137PRO00.0440.02335.3820.0020.0020.0000.0000.0000.000
135A138THR0-0.012-0.02537.8520.0020.0020.0000.0000.0000.000
136A139ALA0-0.017-0.00138.0200.0020.0020.0000.0000.0000.000
137A140LEU0-0.012-0.00137.0330.0010.0010.0000.0000.0000.000
138A141PHE00.0440.00840.0760.0020.0020.0000.0000.0000.000
139A142ARG10.8330.92743.1040.0320.0320.0000.0000.0000.000
140A143LEU0-0.001-0.00840.4380.0010.0010.0000.0000.0000.000
141A144PHE00.006-0.00641.3600.0010.0010.0000.0000.0000.000
142A145GLU-1-0.858-0.92146.025-0.027-0.0270.0000.0000.0000.000
143A146LEU0-0.049-0.02145.1070.0010.0010.0000.0000.0000.000
144A147LEU0-0.031-0.02144.0750.0010.0010.0000.0000.0000.000
145A148ASP-1-0.825-0.87848.512-0.020-0.0200.0000.0000.0000.000
146A149ALA0-0.072-0.02851.4530.0010.0010.0000.0000.0000.000
147A150GLY0-0.041-0.02251.9360.0010.0010.0000.0000.0000.000
148A151ALA0-0.051-0.01747.9120.0000.0000.0000.0000.0000.000
149A152PRO00.0150.00847.3520.0010.0010.0000.0000.0000.000
150A153LYS10.9330.96245.6830.0190.0190.0000.0000.0000.000
151A154PRO0-0.023-0.00240.4410.0000.0000.0000.0000.0000.000
152A155ALA0-0.0030.00239.3390.0020.0020.0000.0000.0000.000
153A156LEU0-0.056-0.03433.9110.0010.0010.0000.0000.0000.000
154A157ILE0-0.0030.00937.239-0.003-0.0030.0000.0000.0000.000
155A158ILE0-0.022-0.01230.5610.0010.0010.0000.0000.0000.000
156A159GLY00.0270.00433.881-0.003-0.0030.0000.0000.0000.000
157A160MET0-0.038-0.02828.3930.0000.0000.0000.0000.0000.000
158A161PRO00.0040.02030.174-0.006-0.0060.0000.0000.0000.000
159A162VAL00.0280.01627.6400.0030.0030.0000.0000.0000.000
160A163GLY0-0.002-0.01130.7600.0010.0010.0000.0000.0000.000
161A164PHE0-0.030-0.04230.4960.0040.0040.0000.0000.0000.000
162A165VAL00.0210.00635.2030.0030.0030.0000.0000.0000.000
163A166GLY00.0690.04438.185-0.002-0.0020.0000.0000.0000.000
164A167ALA0-0.016-0.00233.9170.0010.0010.0000.0000.0000.000
165A168ALA00.001-0.00435.6910.0010.0010.0000.0000.0000.000
166A169GLU-1-0.845-0.92936.536-0.030-0.0300.0000.0000.0000.000
167A170SER0-0.041-0.02137.7760.0010.0010.0000.0000.0000.000
168A171LYS10.7920.89731.6470.0460.0460.0000.0000.0000.000
169A172ASP-1-0.857-0.92837.545-0.021-0.0210.0000.0000.0000.000
170A173GLU-1-0.839-0.93139.796-0.019-0.0190.0000.0000.0000.000
171A174LEU0-0.042-0.01337.4880.0010.0010.0000.0000.0000.000
172A175ALA0-0.043-0.03138.7860.0010.0010.0000.0000.0000.000
173A176ALA0-0.044-0.00240.7420.0020.0020.0000.0000.0000.000
174A177ASN00.0220.00044.2310.0020.0020.0000.0000.0000.000
175A178SER00.0000.00042.313-0.001-0.0010.0000.0000.0000.000
176A179ARG10.7410.84244.0280.0210.0210.0000.0000.0000.000
177A180GLY00.003-0.00546.6000.0000.0000.0000.0000.0000.000
178A181VAL0-0.033-0.01141.1790.0000.0000.0000.0000.0000.000
179A182PRO00.0160.02939.4030.0000.0000.0000.0000.0000.000
180A183TYR00.0410.01737.047-0.003-0.0030.0000.0000.0000.000
181A184VAL00.001-0.00931.1770.0020.0020.0000.0000.0000.000
182A185ILE0-0.0140.00532.865-0.004-0.0040.0000.0000.0000.000
183A186VAL00.0120.01027.5630.0010.0010.0000.0000.0000.000
184A187ARG10.8970.94430.7830.0160.0160.0000.0000.0000.000
185A188GLY00.0550.03131.363-0.001-0.0010.0000.0000.0000.000
186A189ARG10.9730.96831.0230.0360.0360.0000.0000.0000.000
187A190ARG10.7740.85724.5960.0290.0290.0000.0000.0000.000
188A191GLY00.0680.02026.7120.0050.0050.0000.0000.0000.000
189A192GLY00.0320.01925.934-0.007-0.0070.0000.0000.0000.000
190A193SER00.001-0.02025.4840.0010.0010.0000.0000.0000.000
191A194ALA00.0360.02320.9110.0010.0010.0000.0000.0000.000
192A195MET00.0300.01923.0120.0010.0010.0000.0000.0000.000
193A196THR00.0520.01924.3570.0060.0060.0000.0000.0000.000
194A197ALA00.0180.01124.0900.0050.0050.0000.0000.0000.000
195A198ALA0-0.047-0.01022.2500.0000.0000.0000.0000.0000.000
196A199ALA00.0510.01323.7560.0040.0040.0000.0000.0000.000
197A200VAL00.0330.01727.1160.0050.0050.0000.0000.0000.000
198A201ASN00.0230.00622.6750.0090.0090.0000.0000.0000.000
199A202ALA0-0.036-0.00424.9740.0010.0010.0000.0000.0000.000
200A203LEU0-0.052-0.02625.8290.0060.0060.0000.0000.0000.000
201A204ALA0-0.0030.01627.5770.0050.0050.0000.0000.0000.000
202A205SER0-0.037-0.01625.6550.0000.0000.0000.0000.0000.000