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: 851JY

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 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 231
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2536495.618285
FMO2-HF: Nuclear repulsion 2451803.282556
FMO2-HF: Total energy -84692.335729
FMO2-MP2: Total energy -84936.977717


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.
-5.519-1.0051.046-2.239-3.3230.007
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 : -0.004 / q_NPA : -0.016
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].
3A4THR0-0.030-0.0152.465-3.482-0.2760.821-1.773-2.2540.006
4A5PRO00.0240.0214.1931.3571.4910.000-0.014-0.1200.000
5A6VAL00.0200.0126.4960.4940.4940.0000.0000.0000.000
6A7VAL0-0.0070.0038.974-0.450-0.4500.0000.0000.0000.000
7A8LEU00.0090.01812.7560.1040.1040.0000.0000.0000.000
8A9VAL0-0.011-0.01515.240-0.111-0.1110.0000.0000.0000.000
9A10THR00.0400.01018.3130.0020.0020.0000.0000.0000.000
10A11GLY00.012-0.01021.416-0.026-0.0260.0000.0000.0000.000
11A12GLY00.011-0.00620.408-0.023-0.0230.0000.0000.0000.000
12A13SER00.0310.01321.4740.0040.0040.0000.0000.0000.000
13A14ARG10.9480.97423.670-0.288-0.2880.0000.0000.0000.000
14A15GLY00.008-0.00525.8590.0070.0070.0000.0000.0000.000
15A16ILE00.0790.02424.8930.0180.0180.0000.0000.0000.000
16A17GLY00.0610.03922.5880.0190.0190.0000.0000.0000.000
17A18ALA00.0070.01420.9700.0500.0500.0000.0000.0000.000
18A19ALA0-0.031-0.02121.0330.0330.0330.0000.0000.0000.000
19A20VAL00.0260.00718.2260.0080.0080.0000.0000.0000.000
20A21CYS0-0.047-0.00516.7350.0590.0590.0000.0000.0000.000
21A22ARG10.9840.98716.150-0.335-0.3350.0000.0000.0000.000
22A23LEU0-0.030-0.00117.1220.0280.0280.0000.0000.0000.000
23A24ALA00.004-0.00914.070-0.015-0.0150.0000.0000.0000.000
24A25ALA00.0510.03112.1670.0610.0610.0000.0000.0000.000
25A26ARG10.9330.98712.703-0.397-0.3970.0000.0000.0000.000
26A27GLN0-0.065-0.04214.264-0.107-0.1070.0000.0000.0000.000
27A28GLY00.0120.00710.138-0.093-0.0930.0000.0000.0000.000
28A29TRP0-0.056-0.0358.4130.2750.2750.0000.0000.0000.000
29A30ARG10.9140.9683.195-8.567-7.6170.227-0.411-0.7680.001
30A31VAL0-0.034-0.0238.681-0.257-0.2570.0000.0000.0000.000
31A32GLY00.0380.02112.1230.0440.0440.0000.0000.0000.000
32A33VAL0-0.020-0.02614.010-0.142-0.1420.0000.0000.0000.000
33A34ASN00.0090.01117.344-0.069-0.0690.0000.0000.0000.000
34A35TYR0-0.0190.00020.022-0.030-0.0300.0000.0000.0000.000
35A36ALA00.0290.01023.4370.0040.0040.0000.0000.0000.000
36A37ALA00.0060.00026.492-0.010-0.0100.0000.0000.0000.000
37A38ASN0-0.021-0.01627.5260.0070.0070.0000.0000.0000.000
38A39ARG10.9590.96818.941-0.533-0.5330.0000.0000.0000.000
39A40GLU-1-0.876-0.92423.6230.3120.3120.0000.0000.0000.000
40A41ALA0-0.034-0.02324.7380.0140.0140.0000.0000.0000.000
41A42ALA00.013-0.00320.7870.0160.0160.0000.0000.0000.000
42A43ASP-1-0.861-0.92320.0140.5720.5720.0000.0000.0000.000
43A44ALA00.0220.02120.4500.0210.0210.0000.0000.0000.000
44A45VAL0-0.091-0.04418.620-0.001-0.0010.0000.0000.0000.000
45A46VAL0-0.018-0.02315.0980.0370.0370.0000.0000.0000.000
46A47ALA00.0320.02316.5890.0570.0570.0000.0000.0000.000
47A48ALA00.0180.01118.667-0.005-0.0050.0000.0000.0000.000
48A49ILE0-0.045-0.02013.466-0.018-0.0180.0000.0000.0000.000
49A50THR0-0.0150.00213.053-0.007-0.0070.0000.0000.0000.000
50A51GLU-1-0.922-0.95414.8630.4030.4030.0000.0000.0000.000
51A52SER0-0.141-0.06516.762-0.077-0.0770.0000.0000.0000.000
52A53GLY0-0.046-0.02713.815-0.041-0.0410.0000.0000.0000.000
53A54GLY0-0.033-0.01611.3410.0790.0790.0000.0000.0000.000
54A55GLU-1-0.913-0.9626.7672.2592.2590.0000.0000.0000.000
55A56ALA0-0.006-0.0229.9380.0620.0620.0000.0000.0000.000
56A57VAL00.0210.02311.073-0.065-0.0650.0000.0000.0000.000
57A58ALA0-0.0070.01413.827-0.032-0.0320.0000.0000.0000.000
58A59ILE0-0.069-0.03214.1910.0090.0090.0000.0000.0000.000
59A60PRO00.0040.00118.448-0.035-0.0350.0000.0000.0000.000
60A61GLY00.0240.00121.5020.0190.0190.0000.0000.0000.000
61A62ASP-1-0.855-0.92923.8690.2690.2690.0000.0000.0000.000
62A63VAL00.013-0.03323.922-0.004-0.0040.0000.0000.0000.000
63A64GLY0-0.043-0.01526.558-0.018-0.0180.0000.0000.0000.000
64A65ASN0-0.0100.00528.228-0.020-0.0200.0000.0000.0000.000
65A66ALA00.0560.01027.1300.0180.0180.0000.0000.0000.000
66A67ALA00.0010.00125.9200.0130.0130.0000.0000.0000.000
67A68ASP-1-0.800-0.90324.5860.3270.3270.0000.0000.0000.000
68A69ILE0-0.0320.01022.0520.0470.0470.0000.0000.0000.000
69A70ALA00.0600.03320.8210.0430.0430.0000.0000.0000.000
70A71ALA0-0.029-0.01319.7770.0390.0390.0000.0000.0000.000
71A72MET0-0.016-0.00618.2450.0690.0690.0000.0000.0000.000
72A73PHE00.022-0.00815.8490.1030.1030.0000.0000.0000.000
73A74SER00.0150.02114.8600.0580.0580.0000.0000.0000.000
74A75ALA0-0.085-0.04614.6570.0620.0620.0000.0000.0000.000
75A76VAL00.0180.00811.0850.1580.1580.0000.0000.0000.000
76A77ASP-1-0.806-0.85310.3920.8960.8960.0000.0000.0000.000
77A78ARG10.9060.93810.008-0.506-0.5060.0000.0000.0000.000
78A79GLN0-0.037-0.00810.2360.1910.1910.0000.0000.0000.000
79A80PHE0-0.003-0.0126.5060.4790.4790.0000.0000.0000.000
80A81GLY0-0.0220.0005.1740.7760.844-0.0010.000-0.0670.000
81A82ARG10.7980.8804.549-0.622-0.466-0.001-0.041-0.1140.000
82A83LEU0-0.031-0.0237.8420.3220.3220.0000.0000.0000.000
83A84ASP-1-0.766-0.8468.5230.7340.7340.0000.0000.0000.000
84A85GLY00.0200.00711.757-0.150-0.1500.0000.0000.0000.000
85A86LEU0-0.030-0.00714.6240.1030.1030.0000.0000.0000.000
86A87VAL00.0030.00217.442-0.067-0.0670.0000.0000.0000.000
87A88ASN0-0.029-0.02320.0450.0490.0490.0000.0000.0000.000
88A89ASN0-0.029-0.04322.926-0.057-0.0570.0000.0000.0000.000
89A90ALA0-0.048-0.00824.438-0.024-0.0240.0000.0000.0000.000
90A91GLY00.0090.00126.258-0.011-0.0110.0000.0000.0000.000
91A92ILE0-0.084-0.03329.9350.0040.0040.0000.0000.0000.000
92A93VAL00.0300.00233.435-0.006-0.0060.0000.0000.0000.000
93A94ASP-1-0.863-0.94136.7290.1420.1420.0000.0000.0000.000
94A95TYR0-0.027-0.01340.0900.0000.0000.0000.0000.0000.000
95A96PRO0-0.051-0.02143.261-0.002-0.0020.0000.0000.0000.000
96A97GLN00.0670.02245.7220.0030.0030.0000.0000.0000.000
97A98ARG10.8270.90247.461-0.070-0.0700.0000.0000.0000.000
98A99VAL00.039-0.00647.1100.0020.0020.0000.0000.0000.000
99A100ASP-1-0.879-0.92249.1950.0730.0730.0000.0000.0000.000
100A101GLU-1-0.867-0.92950.6780.0810.0810.0000.0000.0000.000
101A102MET0-0.129-0.03644.9590.0040.0040.0000.0000.0000.000
102A103SER00.0380.03245.808-0.002-0.0020.0000.0000.0000.000
103A104VAL00.0650.01244.4760.0040.0040.0000.0000.0000.000
104A105GLU-1-0.916-0.96642.7970.1070.1070.0000.0000.0000.000
105A106ARG10.7790.86741.191-0.111-0.1110.0000.0000.0000.000
106A107ILE00.004-0.00440.3370.0080.0080.0000.0000.0000.000
107A108GLU-1-0.833-0.90837.5400.1510.1510.0000.0000.0000.000
108A109ARG11.0101.00335.294-0.165-0.1650.0000.0000.0000.000
109A110MET0-0.0410.00135.4240.0170.0170.0000.0000.0000.000
110A111LEU0-0.018-0.02035.1450.0090.0090.0000.0000.0000.000
111A112ARG10.7940.90732.692-0.163-0.1630.0000.0000.0000.000
112A113VAL00.000-0.01230.1060.0130.0130.0000.0000.0000.000
113A114ASN0-0.020-0.01729.8540.0280.0280.0000.0000.0000.000
114A115VAL00.0070.00830.3210.0060.0060.0000.0000.0000.000
115A116THR00.002-0.00329.7570.0060.0060.0000.0000.0000.000
116A117GLY00.0780.05527.5820.0080.0080.0000.0000.0000.000
117A118SER00.009-0.00125.4320.0300.0300.0000.0000.0000.000
118A119ILE0-0.029-0.01225.1420.0090.0090.0000.0000.0000.000
119A120LEU0-0.025-0.01725.3550.0010.0010.0000.0000.0000.000
120A121CYS0-0.0060.00221.1990.0240.0240.0000.0000.0000.000
121A122ALA00.005-0.00520.5520.0270.0270.0000.0000.0000.000
122A123ALA00.0060.00121.223-0.004-0.0040.0000.0000.0000.000
123A124GLU-1-0.879-0.94018.7670.3010.3010.0000.0000.0000.000
124A125ALA00.0150.01316.6770.0200.0200.0000.0000.0000.000
125A126VAL00.007-0.00516.910-0.010-0.0100.0000.0000.0000.000
126A127ARG10.8900.94418.686-0.243-0.2430.0000.0000.0000.000
127A128ARG10.7310.82713.484-0.510-0.5100.0000.0000.0000.000
128A129MET0-0.0210.01013.693-0.011-0.0110.0000.0000.0000.000
129A130SER0-0.020-0.01915.218-0.077-0.0770.0000.0000.0000.000
130A131ARG10.9270.95716.2770.1090.1090.0000.0000.0000.000
131A132LEU0-0.059-0.01818.662-0.031-0.0310.0000.0000.0000.000
132A133TYR0-0.049-0.03018.129-0.007-0.0070.0000.0000.0000.000
133A134SER0-0.040-0.01615.2680.0070.0070.0000.0000.0000.000
134A135GLY00.0600.05513.368-0.020-0.0200.0000.0000.0000.000
135A136GLN0-0.039-0.04811.666-0.062-0.0620.0000.0000.0000.000
136A137GLY0-0.033-0.00813.784-0.024-0.0240.0000.0000.0000.000
137A138GLY00.028-0.00813.9270.0510.0510.0000.0000.0000.000
138A139ALA0-0.053-0.02315.500-0.063-0.0630.0000.0000.0000.000
139A140ILE00.0270.02417.3950.0750.0750.0000.0000.0000.000
140A141VAL0-0.034-0.02320.118-0.045-0.0450.0000.0000.0000.000
141A142ASN00.007-0.01322.4510.0520.0520.0000.0000.0000.000
142A143VAL00.0350.02324.886-0.016-0.0160.0000.0000.0000.000
143A144SER00.014-0.02127.425-0.006-0.0060.0000.0000.0000.000
144A145SER00.0320.00031.0590.0030.0030.0000.0000.0000.000
145A146MET0-0.030-0.01233.892-0.008-0.0080.0000.0000.0000.000
146A147ALA0-0.0100.00036.933-0.009-0.0090.0000.0000.0000.000
147A148ALA0-0.0050.01135.945-0.007-0.0070.0000.0000.0000.000
148A149ILE0-0.053-0.01037.785-0.006-0.0060.0000.0000.0000.000
149A150LEU0-0.038-0.03540.274-0.005-0.0050.0000.0000.0000.000
150A151GLY00.0420.01741.786-0.005-0.0050.0000.0000.0000.000
151A152SER0-0.034-0.02741.3300.0030.0030.0000.0000.0000.000
152A153ALA00.0810.03243.7610.0010.0010.0000.0000.0000.000
153A154THR0-0.061-0.03547.4630.0000.0000.0000.0000.0000.000
154A155GLN0-0.0240.01642.896-0.003-0.0030.0000.0000.0000.000
155A156TYR00.0720.00739.5890.0030.0030.0000.0000.0000.000
156A157VAL00.0290.02041.6420.0050.0050.0000.0000.0000.000
157A158ASP-1-0.716-0.83841.0690.1240.1240.0000.0000.0000.000
158A159TYR00.0270.01734.1070.0080.0080.0000.0000.0000.000
159A160ALA0-0.0190.00637.3690.0060.0060.0000.0000.0000.000
160A161ALA00.0060.00138.3440.0010.0010.0000.0000.0000.000
161A162SER0-0.032-0.02435.3100.0050.0050.0000.0000.0000.000
162A163LYS10.8700.93230.250-0.201-0.2010.0000.0000.0000.000
163A164ALA00.0170.00834.1560.0010.0010.0000.0000.0000.000
164A165ALA00.0000.00734.655-0.003-0.0030.0000.0000.0000.000
165A166ILE00.002-0.00128.8300.0000.0000.0000.0000.0000.000
166A167ASP-1-0.746-0.82730.7560.1370.1370.0000.0000.0000.000
167A168THR00.011-0.00732.319-0.007-0.0070.0000.0000.0000.000
168A169PHE00.0130.01625.912-0.007-0.0070.0000.0000.0000.000
169A170THR0-0.017-0.01527.1900.0080.0080.0000.0000.0000.000
170A171ILE0-0.041-0.00628.497-0.006-0.0060.0000.0000.0000.000
171A172GLY0-0.029-0.02030.745-0.010-0.0100.0000.0000.0000.000
172A173LEU00.0500.02823.685-0.005-0.0050.0000.0000.0000.000
173A174ALA0-0.0090.00625.915-0.007-0.0070.0000.0000.0000.000
174A175ARG10.8690.91626.987-0.072-0.0720.0000.0000.0000.000
175A176GLU-1-0.979-0.96827.2720.0820.0820.0000.0000.0000.000
176A177VAL00.0370.02222.711-0.006-0.0060.0000.0000.0000.000
177A178ALA0-0.036-0.01723.231-0.007-0.0070.0000.0000.0000.000
178A179ALA0-0.037-0.02723.981-0.013-0.0130.0000.0000.0000.000
179A180GLU-1-0.830-0.88421.2320.0300.0300.0000.0000.0000.000
180A181GLY0-0.035-0.02119.180-0.006-0.0060.0000.0000.0000.000
181A182ILE0-0.0090.01818.0640.0210.0210.0000.0000.0000.000
182A183ARG10.7900.90918.695-0.168-0.1680.0000.0000.0000.000
183A184VAL00.0410.01921.3230.0340.0340.0000.0000.0000.000
184A185ASN0-0.008-0.00323.287-0.046-0.0460.0000.0000.0000.000
185A186ALA00.0280.01725.2800.0220.0220.0000.0000.0000.000
186A187VAL00.0460.03225.990-0.014-0.0140.0000.0000.0000.000
187A188ARG10.7800.87328.628-0.115-0.1150.0000.0000.0000.000
188A189PRO00.0300.02129.432-0.012-0.0120.0000.0000.0000.000
189A190GLY0-0.012-0.01632.169-0.008-0.0080.0000.0000.0000.000
190A191ILE0-0.035-0.01735.2280.0050.0050.0000.0000.0000.000
191A192ILE0-0.0100.00330.491-0.002-0.0020.0000.0000.0000.000
192A193GLU-1-0.980-0.98432.0530.1810.1810.0000.0000.0000.000
193A212SER00.028-0.00744.9040.0010.0010.0000.0000.0000.000
194A213VAL0-0.036-0.01339.338-0.001-0.0010.0000.0000.0000.000
195A214PRO00.0210.02341.591-0.001-0.0010.0000.0000.0000.000
196A215MET00.0000.00235.848-0.002-0.0020.0000.0000.0000.000
197A216GLN0-0.057-0.02040.8800.0020.0020.0000.0000.0000.000
198A217ARG10.7990.89633.849-0.132-0.1320.0000.0000.0000.000
199A218ALA0-0.0150.00136.6490.0000.0000.0000.0000.0000.000
200A219GLY0-0.005-0.00933.423-0.003-0.0030.0000.0000.0000.000
201A220MET00.0530.02229.7440.0020.0020.0000.0000.0000.000
202A221PRO0-0.007-0.01927.1840.0050.0050.0000.0000.0000.000
203A222GLU-1-0.875-0.95624.9040.2770.2770.0000.0000.0000.000
204A223GLU-1-0.738-0.83325.4240.1590.1590.0000.0000.0000.000
205A224VAL0-0.044-0.02926.323-0.007-0.0070.0000.0000.0000.000
206A225ALA0-0.007-0.00621.7750.0050.0050.0000.0000.0000.000
207A226ASP-1-0.836-0.91722.0470.2600.2600.0000.0000.0000.000
208A227ALA0-0.050-0.02323.077-0.007-0.0070.0000.0000.0000.000
209A228ILE0-0.014-0.00420.287-0.008-0.0080.0000.0000.0000.000
210A229LEU00.010-0.01116.0820.0120.0120.0000.0000.0000.000
211A230TYR0-0.006-0.00119.038-0.007-0.0070.0000.0000.0000.000
212A231LEU0-0.030-0.01720.929-0.019-0.0190.0000.0000.0000.000
213A232LEU00.009-0.00315.658-0.024-0.0240.0000.0000.0000.000
214A233SER0-0.072-0.01016.4110.0030.0030.0000.0000.0000.000
215A234PRO00.025-0.01614.823-0.030-0.0300.0000.0000.0000.000
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