FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: N9R3Q

Calculation Name: 4E3Z-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4E3Z

Chain ID: A

ChEMBL ID:

UniProt ID: Q2K3F6

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 231
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2537578.016124
FMO2-HF: Nuclear repulsion 2452884.735453
FMO2-HF: Total energy -84693.280671
FMO2-MP2: Total energy -84937.764377


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:SER)


Summations of interaction energy for fragment #1(A:2: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.
-4.1310.4010.883-2.213-3.2010.004
Interaction energy analysis for fragmet #1(A:2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.007 / q_NPA : -0.015
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].
3A4THR0-0.026-0.0122.464-3.2950.0940.821-1.861-2.3490.003
4A5PRO00.0170.0154.1831.2771.4060.000-0.014-0.1150.000
5A6VAL00.0160.0076.5040.4900.4900.0000.0000.0000.000
6A7VAL0-0.0050.0038.974-0.441-0.4410.0000.0000.0000.000
7A8LEU00.0120.01912.7560.1030.1030.0000.0000.0000.000
8A9VAL0-0.009-0.01615.213-0.108-0.1080.0000.0000.0000.000
9A10THR00.0480.01718.3130.0020.0020.0000.0000.0000.000
10A11GLY00.005-0.01021.416-0.026-0.0260.0000.0000.0000.000
11A12GLY00.009-0.00820.408-0.022-0.0220.0000.0000.0000.000
12A13SER00.0180.00421.4740.0010.0010.0000.0000.0000.000
13A14ARG10.9810.98023.671-0.276-0.2760.0000.0000.0000.000
14A15GLY00.0080.01225.8590.0060.0060.0000.0000.0000.000
15A16ILE00.0720.01724.7970.0160.0160.0000.0000.0000.000
16A17GLY00.0670.04022.5880.0190.0190.0000.0000.0000.000
17A18ALA00.0220.02220.9700.0500.0500.0000.0000.0000.000
18A19ALA0-0.027-0.02421.0330.0320.0320.0000.0000.0000.000
19A20VAL00.004-0.00218.3810.0090.0090.0000.0000.0000.000
20A21CYS0-0.0420.00016.7360.0560.0560.0000.0000.0000.000
21A22ARG10.8560.91716.150-0.311-0.3110.0000.0000.0000.000
22A23LEU0-0.030-0.00217.1120.0240.0240.0000.0000.0000.000
23A24ALA00.006-0.00914.116-0.015-0.0150.0000.0000.0000.000
24A25ALA00.0570.03412.1570.0590.0590.0000.0000.0000.000
25A26ARG10.9200.97812.694-0.376-0.3760.0000.0000.0000.000
26A27GLN0-0.062-0.04014.254-0.087-0.0870.0000.0000.0000.000
27A28GLY00.0080.00810.129-0.093-0.0930.0000.0000.0000.000
28A29TRP0-0.066-0.0378.4030.2660.2660.0000.0000.0000.000
29A30ARG10.9210.9763.509-7.890-7.1190.064-0.286-0.5490.001
30A31VAL0-0.036-0.0258.681-0.257-0.2570.0000.0000.0000.000
31A32GLY00.0310.02012.1230.0430.0430.0000.0000.0000.000
32A33VAL0-0.014-0.02614.010-0.140-0.1400.0000.0000.0000.000
33A34ASN00.012-0.00417.344-0.059-0.0590.0000.0000.0000.000
34A35TYR0-0.032-0.00920.022-0.030-0.0300.0000.0000.0000.000
35A36ALA00.0240.00823.4390.0030.0030.0000.0000.0000.000
36A37ALA00.004-0.00226.450-0.011-0.0110.0000.0000.0000.000
37A38ASN0-0.012-0.01127.5000.0070.0070.0000.0000.0000.000
38A39ARG10.8830.90818.691-0.532-0.5320.0000.0000.0000.000
39A40GLU-1-0.900-0.93923.6240.3030.3030.0000.0000.0000.000
40A41ALA0-0.033-0.02024.7390.0130.0130.0000.0000.0000.000
41A42ALA00.008-0.00920.7770.0140.0140.0000.0000.0000.000
42A43ASP-1-0.767-0.85020.0000.5850.5850.0000.0000.0000.000
43A44ALA00.0160.02220.4510.0210.0210.0000.0000.0000.000
44A45VAL0-0.069-0.03418.6500.0010.0010.0000.0000.0000.000
45A46VAL0-0.029-0.03015.0630.0350.0350.0000.0000.0000.000
46A47ALA00.0320.03116.5900.0510.0510.0000.0000.0000.000
47A48ALA0-0.0080.00218.667-0.008-0.0080.0000.0000.0000.000
48A49ILE0-0.039-0.01113.505-0.018-0.0180.0000.0000.0000.000
49A50THR00.0240.02112.9470.0260.0260.0000.0000.0000.000
50A51GLU-1-0.917-0.95614.8630.4470.4470.0000.0000.0000.000
51A52SER0-0.144-0.07616.662-0.077-0.0770.0000.0000.0000.000
52A53GLY0-0.046-0.02813.815-0.041-0.0410.0000.0000.0000.000
53A54GLY0-0.035-0.01611.3350.0790.0790.0000.0000.0000.000
54A55GLU-1-0.916-0.9636.7382.5292.5290.0000.0000.0000.000
55A56ALA0-0.001-0.0219.9390.0600.0600.0000.0000.0000.000
56A57VAL00.0230.02211.062-0.060-0.0600.0000.0000.0000.000
57A58ALA0-0.0200.01013.829-0.034-0.0340.0000.0000.0000.000
58A59ILE0-0.059-0.03014.2210.0070.0070.0000.0000.0000.000
59A60PRO00.0210.01918.415-0.035-0.0350.0000.0000.0000.000
60A61GLY00.020-0.00221.4640.0180.0180.0000.0000.0000.000
61A62ASP-1-0.856-0.94023.8300.2620.2620.0000.0000.0000.000
62A63VAL0-0.005-0.02723.980-0.003-0.0030.0000.0000.0000.000
63A64GLY0-0.022-0.00126.519-0.017-0.0170.0000.0000.0000.000
64A65ASN0-0.050-0.03228.351-0.034-0.0340.0000.0000.0000.000
65A66ALA00.0450.01727.0980.0190.0190.0000.0000.0000.000
66A67ALA0-0.003-0.00325.8930.0140.0140.0000.0000.0000.000
67A68ASP-1-0.776-0.88124.5480.3170.3170.0000.0000.0000.000
68A69ILE0-0.0100.01622.0010.0450.0450.0000.0000.0000.000
69A70ALA00.0530.02620.7920.0410.0410.0000.0000.0000.000
70A71ALA0-0.0140.00619.7540.0370.0370.0000.0000.0000.000
71A72MET0-0.006-0.00118.1530.0660.0660.0000.0000.0000.000
72A73PHE00.023-0.00716.0400.1010.1010.0000.0000.0000.000
73A74SER0-0.002-0.00214.8360.0510.0510.0000.0000.0000.000
74A75ALA0-0.089-0.03814.6380.0570.0570.0000.0000.0000.000
75A76VAL00.0190.00711.0590.1500.1500.0000.0000.0000.000
76A77ASP-1-0.826-0.87910.3650.8530.8530.0000.0000.0000.000
77A78ARG10.9070.9379.995-0.484-0.4840.0000.0000.0000.000
78A79GLN0-0.031-0.00210.2100.1550.1550.0000.0000.0000.000
79A80PHE0-0.011-0.0196.4670.4640.4640.0000.0000.0000.000
80A81GLY0-0.0070.0095.1490.7600.826-0.0010.000-0.0640.000
81A82ARG10.8070.8854.529-0.237-0.060-0.001-0.052-0.1240.000
82A83LEU0-0.034-0.0237.8250.3130.3130.0000.0000.0000.000
83A84ASP-1-0.768-0.8498.4740.7180.7180.0000.0000.0000.000
84A85GLY00.0230.00811.725-0.145-0.1450.0000.0000.0000.000
85A86LEU0-0.040-0.00514.5820.1010.1010.0000.0000.0000.000
86A87VAL00.008-0.00117.400-0.066-0.0660.0000.0000.0000.000
87A88ASN0-0.026-0.02620.0450.0470.0470.0000.0000.0000.000
88A89ASN0-0.037-0.04622.910-0.056-0.0560.0000.0000.0000.000
89A90ALA0-0.044-0.00324.460-0.022-0.0220.0000.0000.0000.000
90A91GLY00.0210.00526.258-0.010-0.0100.0000.0000.0000.000
91A92ILE0-0.075-0.02829.9350.0040.0040.0000.0000.0000.000
92A93VAL00.0340.00433.435-0.006-0.0060.0000.0000.0000.000
93A94ASP-1-0.821-0.90736.7290.1410.1410.0000.0000.0000.000
94A95TYR0-0.012-0.00640.090-0.002-0.0020.0000.0000.0000.000
95A96PRO0-0.048-0.02843.261-0.001-0.0010.0000.0000.0000.000
96A97GLN00.0420.02945.7220.0030.0030.0000.0000.0000.000
97A98ARG10.7860.85347.461-0.068-0.0680.0000.0000.0000.000
98A99VAL00.044-0.00747.0930.0020.0020.0000.0000.0000.000
99A100ASP-1-0.850-0.88249.1510.0710.0710.0000.0000.0000.000
100A101GLU-1-0.842-0.91350.5030.0790.0790.0000.0000.0000.000
101A102MET0-0.126-0.03445.0500.0040.0040.0000.0000.0000.000
102A103SER0-0.001-0.01946.193-0.001-0.0010.0000.0000.0000.000
103A104VAL00.0620.01244.4570.0040.0040.0000.0000.0000.000
104A105GLU-1-0.869-0.91542.7620.1040.1040.0000.0000.0000.000
105A106ARG10.7780.86441.151-0.107-0.1070.0000.0000.0000.000
106A107ILE00.008-0.00240.2950.0080.0080.0000.0000.0000.000
107A108GLU-1-0.798-0.86537.3980.1490.1490.0000.0000.0000.000
108A109ARG10.9500.96435.851-0.153-0.1530.0000.0000.0000.000
109A110MET0-0.0430.00235.3830.0160.0160.0000.0000.0000.000
110A111LEU0-0.021-0.02235.1180.0080.0080.0000.0000.0000.000
111A112ARG10.7660.85632.702-0.158-0.1580.0000.0000.0000.000
112A113VAL00.005-0.01130.2140.0130.0130.0000.0000.0000.000
113A114ASN0-0.027-0.01029.8130.0280.0280.0000.0000.0000.000
114A115VAL00.0060.01230.2800.0060.0060.0000.0000.0000.000
115A116THR00.0140.00129.7210.0060.0060.0000.0000.0000.000
116A117GLY00.0790.05727.5470.0080.0080.0000.0000.0000.000
117A118SER0-0.014-0.01325.4010.0320.0320.0000.0000.0000.000
118A119ILE0-0.021-0.01525.1070.0090.0090.0000.0000.0000.000
119A120LEU0-0.023-0.01525.3260.0010.0010.0000.0000.0000.000
120A121CYS0-0.022-0.00721.2440.0220.0220.0000.0000.0000.000
121A122ALA00.013-0.00820.5210.0260.0260.0000.0000.0000.000
122A123ALA00.0140.00921.197-0.004-0.0040.0000.0000.0000.000
123A124GLU-1-0.818-0.86418.6840.2750.2750.0000.0000.0000.000
124A125ALA00.0170.01216.6470.0180.0180.0000.0000.0000.000
125A126VAL00.006-0.00316.890-0.010-0.0100.0000.0000.0000.000
126A127ARG10.8060.87218.674-0.247-0.2470.0000.0000.0000.000
127A128ARG10.7530.84113.434-0.479-0.4790.0000.0000.0000.000
128A129MET0-0.0240.01013.657-0.012-0.0120.0000.0000.0000.000
129A130SER0-0.020-0.03115.196-0.075-0.0750.0000.0000.0000.000
130A131ARG10.8760.92615.9600.0960.0960.0000.0000.0000.000
131A132LEU0-0.046-0.00918.665-0.030-0.0300.0000.0000.0000.000
132A133TYR0-0.056-0.03518.215-0.005-0.0050.0000.0000.0000.000
133A134SER0-0.050-0.01914.620-0.004-0.0040.0000.0000.0000.000
134A135GLY00.0820.06613.372-0.023-0.0230.0000.0000.0000.000
135A136GLN0-0.022-0.04011.662-0.089-0.0890.0000.0000.0000.000
136A137GLY0-0.0270.00313.784-0.025-0.0250.0000.0000.0000.000
137A138GLY00.030-0.00613.9100.0470.0470.0000.0000.0000.000
138A139ALA0-0.055-0.02215.476-0.060-0.0600.0000.0000.0000.000
139A140ILE00.0270.02017.3590.0720.0720.0000.0000.0000.000
140A141VAL0-0.037-0.02220.082-0.043-0.0430.0000.0000.0000.000
141A142ASN00.005-0.00322.4510.0490.0490.0000.0000.0000.000
142A143VAL00.0360.02924.897-0.015-0.0150.0000.0000.0000.000
143A144SER00.009-0.02227.425-0.005-0.0050.0000.0000.0000.000
144A145SER00.022-0.01131.0590.0030.0030.0000.0000.0000.000
145A146MET0-0.0130.00133.892-0.006-0.0060.0000.0000.0000.000
146A147ALA0-0.0080.00436.942-0.009-0.0090.0000.0000.0000.000
147A148ALA0-0.0030.01335.926-0.006-0.0060.0000.0000.0000.000
148A149ILE0-0.052-0.01737.713-0.006-0.0060.0000.0000.0000.000
149A150LEU0-0.037-0.02940.274-0.005-0.0050.0000.0000.0000.000
150A151GLY00.0390.01841.778-0.005-0.0050.0000.0000.0000.000
151A152SER0-0.035-0.02740.6540.0010.0010.0000.0000.0000.000
152A153ALA00.0870.03743.7610.0000.0000.0000.0000.0000.000
153A154THR0-0.061-0.03547.4630.0000.0000.0000.0000.0000.000
154A155GLN0-0.0300.00743.238-0.002-0.0020.0000.0000.0000.000
155A156TYR00.0720.01439.8010.0030.0030.0000.0000.0000.000
156A157VAL00.0310.01741.6420.0050.0050.0000.0000.0000.000
157A158ASP-1-0.733-0.84741.1700.1200.1200.0000.0000.0000.000
158A159TYR00.0340.01633.8910.0070.0070.0000.0000.0000.000
159A160ALA0-0.0100.00637.3690.0060.0060.0000.0000.0000.000
160A161ALA00.005-0.00438.3440.0010.0010.0000.0000.0000.000
161A162SER0-0.026-0.01635.2450.0050.0050.0000.0000.0000.000
162A163LYS10.8840.93130.084-0.197-0.1970.0000.0000.0000.000
163A164ALA00.0150.00834.1280.0010.0010.0000.0000.0000.000
164A165ALA00.0040.00834.780-0.003-0.0030.0000.0000.0000.000
165A166ILE00.0020.00128.7740.0000.0000.0000.0000.0000.000
166A167ASP-1-0.746-0.82130.7190.1320.1320.0000.0000.0000.000
167A168THR00.003-0.01032.284-0.007-0.0070.0000.0000.0000.000
168A169PHE00.0080.01626.076-0.007-0.0070.0000.0000.0000.000
169A170THR0-0.014-0.01527.0800.0070.0070.0000.0000.0000.000
170A171ILE0-0.040-0.00928.467-0.006-0.0060.0000.0000.0000.000
171A172GLY0-0.026-0.01730.718-0.010-0.0100.0000.0000.0000.000
172A173LEU00.0420.02523.750-0.005-0.0050.0000.0000.0000.000
173A174ALA0-0.0110.00425.889-0.006-0.0060.0000.0000.0000.000
174A175ARG10.8680.91526.966-0.070-0.0700.0000.0000.0000.000
175A176GLU-1-0.959-0.96127.4070.0790.0790.0000.0000.0000.000
176A177VAL00.0340.01722.626-0.007-0.0070.0000.0000.0000.000
177A178ALA0-0.026-0.00923.216-0.007-0.0070.0000.0000.0000.000
178A179ALA0-0.041-0.02723.969-0.012-0.0120.0000.0000.0000.000
179A180GLU-1-0.847-0.88321.4980.0270.0270.0000.0000.0000.000
180A181GLY0-0.030-0.02119.171-0.007-0.0070.0000.0000.0000.000
181A182ILE0-0.0100.01618.0020.0200.0200.0000.0000.0000.000
182A183ARG10.7850.90318.475-0.169-0.1690.0000.0000.0000.000
183A184VAL00.0440.02121.2930.0330.0330.0000.0000.0000.000
184A185ASN0-0.018-0.00923.313-0.042-0.0420.0000.0000.0000.000
185A186ALA00.0370.01925.2800.0220.0220.0000.0000.0000.000
186A187VAL00.0430.02625.978-0.015-0.0150.0000.0000.0000.000
187A188ARG10.7960.87628.628-0.111-0.1110.0000.0000.0000.000
188A189PRO00.0320.02229.393-0.011-0.0110.0000.0000.0000.000
189A190GLY0-0.003-0.01332.169-0.008-0.0080.0000.0000.0000.000
190A191ILE0-0.039-0.01935.2280.0060.0060.0000.0000.0000.000
191A192ILE0-0.026-0.00430.483-0.002-0.0020.0000.0000.0000.000
192A193GLU-1-0.951-0.97032.2390.1960.1960.0000.0000.0000.000
193A212SER00.0220.01044.8660.0030.0030.0000.0000.0000.000
194A213VAL00.0110.00139.407-0.001-0.0010.0000.0000.0000.000
195A214PRO00.0390.03241.554-0.001-0.0010.0000.0000.0000.000
196A215MET0-0.0010.00935.949-0.002-0.0020.0000.0000.0000.000
197A216GLN0-0.078-0.04140.8300.0020.0020.0000.0000.0000.000
198A217ARG10.7740.86233.773-0.131-0.1310.0000.0000.0000.000
199A218ALA0-0.0080.00436.6440.0000.0000.0000.0000.0000.000
200A219GLY00.002-0.00633.412-0.003-0.0030.0000.0000.0000.000
201A220MET00.0360.01029.7990.0030.0030.0000.0000.0000.000
202A221PRO00.021-0.00127.1910.0030.0030.0000.0000.0000.000
203A222GLU-1-0.787-0.90924.5980.2930.2930.0000.0000.0000.000
204A223GLU-1-0.718-0.79825.4130.1540.1540.0000.0000.0000.000
205A224VAL0-0.049-0.03126.350-0.007-0.0070.0000.0000.0000.000
206A225ALA0-0.001-0.00421.8380.0040.0040.0000.0000.0000.000
207A226ASP-1-0.846-0.92522.0360.2560.2560.0000.0000.0000.000
208A227ALA0-0.048-0.01923.066-0.007-0.0070.0000.0000.0000.000
209A228ILE0-0.0120.00020.275-0.008-0.0080.0000.0000.0000.000
210A229LEU00.016-0.01015.9700.0100.0100.0000.0000.0000.000
211A230TYR0-0.024-0.00719.027-0.008-0.0080.0000.0000.0000.000
212A231LEU0-0.027-0.00920.919-0.018-0.0180.0000.0000.0000.000
213A232LEU00.0260.01416.070-0.024-0.0240.0000.0000.0000.000
214A233SER0-0.076-0.02316.3990.0050.0050.0000.0000.0000.000
215A234PRO00.034-0.01014.967-0.029-0.0290.0000.0000.0000.000
216A235SER0-0.0020.00417.894-0.038-0.0380.0000.0000.0000.000
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