FMODB

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

Last updated: 2025-10-06

All entries: 70436

Number of unique PDB entries: 28101

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FMODB ID: 4QK7N

Calculation Name: 1J08-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

PDB ID: 1J08

Chain ID: A

ChEMBL ID:

UniProt ID: O57917

Base Structure: X-ray

Registration Date: 2025-10-03

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 223
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2910872.797172
FMO2-HF: Nuclear repulsion 2820766.887965
FMO2-HF: Total energy -90105.909207
FMO2-MP2: Total energy -90366.622985


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:GLY)


Summations of interaction energy for fragment #1(A:2:GLY)
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.
-256.232-248.38110.302-10.067-8.088-0.126
Interaction energy analysis for fragmet #1(A:2:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.733 / q_NPA : 0.857
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].
3A4ILE00.0070.0192.99412.52614.0780.039-0.716-0.876-0.002
4A5SER0-0.012-0.0333.117-11.087-9.9740.091-0.582-0.622-0.005
8A9LYS10.8270.9043.26258.92559.0810.002-0.045-0.1140.000
41A43GLN0-0.040-0.0312.1337.1638.2551.029-1.020-1.101-0.011
45A47GLU-1-0.720-0.8531.877-131.578-127.6409.141-7.704-5.375-0.108
5A6GLU-1-0.829-0.9375.345-46.064-46.0640.0000.0000.0000.000
6A7GLU-1-0.986-0.9867.227-19.099-19.0990.0000.0000.0000.000
7A8ASP-1-0.793-0.8737.919-28.689-28.6890.0000.0000.0000.000
9A10ARG10.8490.9508.92025.39225.3920.0000.0000.0000.000
10A11ILE00.1160.05812.4181.0371.0370.0000.0000.0000.000
11A12ILE00.008-0.0019.3701.0621.0620.0000.0000.0000.000
12A13LYS10.8530.93511.22424.86224.8620.0000.0000.0000.000
13A14GLU-1-0.949-0.97914.570-16.488-16.4880.0000.0000.0000.000
14A15GLU-1-0.884-0.92216.852-13.955-13.9550.0000.0000.0000.000
15A16PHE0-0.046-0.01515.9100.7570.7570.0000.0000.0000.000
16A17PHE00.025-0.02512.3390.7910.7910.0000.0000.0000.000
17A18SER0-0.068-0.03417.4670.5690.5690.0000.0000.0000.000
18A19LYS10.8300.90720.11414.72414.7240.0000.0000.0000.000
19A20MET0-0.045-0.00218.4330.0770.0770.0000.0000.0000.000
20A21VAL0-0.049-0.01522.2310.2520.2520.0000.0000.0000.000
21A22ASN0-0.056-0.02825.3030.2250.2250.0000.0000.0000.000
22A23PRO00.0360.03321.829-0.557-0.5570.0000.0000.0000.000
23A24VAL0-0.027-0.01118.9410.5090.5090.0000.0000.0000.000
24A25LYS10.8730.93018.72113.72713.7270.0000.0000.0000.000
25A26LEU0-0.0010.00713.8820.6430.6430.0000.0000.0000.000
26A27ILE0-0.0010.00417.217-0.676-0.6760.0000.0000.0000.000
27A28VAL0-0.005-0.01414.6730.2730.2730.0000.0000.0000.000
28A29PHE00.0220.01917.960-0.059-0.0590.0000.0000.0000.000
29A30ILE00.028-0.01714.818-0.488-0.4880.0000.0000.0000.000
30A31GLY00.0470.02519.2920.5890.5890.0000.0000.0000.000
31A32LYS10.8590.91820.52213.13413.1340.0000.0000.0000.000
32A33GLU-1-0.914-0.94622.675-12.352-12.3520.0000.0000.0000.000
33A34HIS10.8210.88121.92712.15512.1550.0000.0000.0000.000
34A35CYS00.0630.05312.557-2.289-2.2890.0000.0000.0000.000
35A36GLN00.0150.00716.948-0.766-0.7660.0000.0000.0000.000
36A37TYR00.0000.00613.087-0.963-0.9630.0000.0000.0000.000
37A39ASP-1-0.878-0.9399.866-25.321-25.3210.0000.0000.0000.000
38A40GLN0-0.006-0.0047.845-1.795-1.7950.0000.0000.0000.000
39A41LEU00.0450.0188.567-2.297-2.2970.0000.0000.0000.000
40A42LYS10.8730.93110.44823.18023.1800.0000.0000.0000.000
42A44LEU0-0.0050.0056.109-4.127-4.1270.0000.0000.0000.000
43A45VAL00.009-0.0027.8390.9270.9270.0000.0000.0000.000
44A46GLN0-0.050-0.0037.3432.5182.5180.0000.0000.0000.000
46A48LEU0-0.006-0.0026.5852.0192.0190.0000.0000.0000.000
47A49SER00.014-0.0159.8322.8892.8890.0000.0000.0000.000
48A50GLU-1-0.931-0.9526.937-40.001-40.0010.0000.0000.0000.000
49A51LEU0-0.122-0.0507.9101.0761.0760.0000.0000.0000.000
50A52THR00.024-0.01411.6611.7071.7070.0000.0000.0000.000
51A53ASP-1-0.841-0.90215.459-15.544-15.5440.0000.0000.0000.000
52A54LYS10.8560.93018.27914.86114.8610.0000.0000.0000.000
53A55LEU0-0.011-0.00213.4950.4470.4470.0000.0000.0000.000
54A56SER0-0.0100.00515.389-0.469-0.4690.0000.0000.0000.000
55A57TYR00.022-0.00211.233-0.112-0.1120.0000.0000.0000.000
56A58GLU-1-0.859-0.91815.593-14.147-14.1470.0000.0000.0000.000
57A59ILE0-0.046-0.01513.092-0.213-0.2130.0000.0000.0000.000
58A60VAL00.0070.01917.0280.5790.5790.0000.0000.0000.000
59A61ASP-1-0.844-0.92720.687-14.087-14.0870.0000.0000.0000.000
60A62PHE00.0220.00522.0220.7760.7760.0000.0000.0000.000
61A63ASP-1-0.848-0.92924.309-12.264-12.2640.0000.0000.0000.000
62A64THR0-0.082-0.03925.2250.6130.6130.0000.0000.0000.000
63A65PRO0-0.006-0.01327.583-0.011-0.0110.0000.0000.0000.000
64A66GLU-1-0.882-0.94227.520-10.397-10.3970.0000.0000.0000.000
65A67GLY00.0180.00525.396-0.081-0.0810.0000.0000.0000.000
66A68LYS10.8550.93026.14411.11311.1130.0000.0000.0000.000
67A69GLU-1-0.807-0.88229.017-9.456-9.4560.0000.0000.0000.000
68A70LEU00.004-0.01324.3780.1050.1050.0000.0000.0000.000
69A71ALA0-0.025-0.01026.346-0.102-0.1020.0000.0000.0000.000
70A72GLU-1-0.944-0.96627.480-9.101-9.1010.0000.0000.0000.000
71A73LYS10.7930.88129.5089.9359.9350.0000.0000.0000.000
72A74TYR0-0.067-0.05225.9280.0040.0040.0000.0000.0000.000
73A75ARG10.8110.89227.7449.9069.9060.0000.0000.0000.000
74A76ILE0-0.036-0.00723.814-0.144-0.1440.0000.0000.0000.000
75A77ASP-1-0.763-0.85127.205-10.849-10.8490.0000.0000.0000.000
76A78ARG10.8040.89925.09211.40211.4020.0000.0000.0000.000
77A79ALA00.0040.02521.143-0.339-0.3390.0000.0000.0000.000
78A80PRO00.0210.00817.9060.2950.2950.0000.0000.0000.000
79A81ALA00.0090.00819.7820.3560.3560.0000.0000.0000.000
80A82THR0-0.020-0.00116.597-0.691-0.6910.0000.0000.0000.000
81A83THR0-0.004-0.00119.1610.5170.5170.0000.0000.0000.000
82A84ILE0-0.009-0.00318.870-0.623-0.6230.0000.0000.0000.000
83A85THR0-0.041-0.02621.0980.8230.8230.0000.0000.0000.000
84A86GLN0-0.005-0.01822.523-0.222-0.2220.0000.0000.0000.000
85A87ASP-1-0.929-0.97623.932-11.963-11.9630.0000.0000.0000.000
86A88GLY00.0220.03124.0660.2970.2970.0000.0000.0000.000
87A89LYS10.8890.96725.22410.43710.4370.0000.0000.0000.000
88A90ASP-1-0.784-0.90326.702-11.792-11.7920.0000.0000.0000.000
89A91PHE00.011-0.02126.3420.4390.4390.0000.0000.0000.000
90A92GLY00.0360.03427.9590.1180.1180.0000.0000.0000.000
91A93VAL0-0.026-0.01522.4770.0430.0430.0000.0000.0000.000
92A94ARG10.7720.86122.38411.22611.2260.0000.0000.0000.000
93A95TYR0-0.014-0.05418.8440.1420.1420.0000.0000.0000.000
94A96PHE0-0.028-0.00519.927-0.470-0.4700.0000.0000.0000.000
95A97GLY00.0470.02718.1930.3660.3660.0000.0000.0000.000
96A98ILE0-0.060-0.03811.017-0.700-0.7000.0000.0000.0000.000
97A99PRO0-0.0080.00813.5480.8190.8190.0000.0000.0000.000
98A100ALA00.015-0.00113.386-1.547-1.5470.0000.0000.0000.000
99A101GLY0-0.016-0.01713.9831.5371.5370.0000.0000.0000.000
100A102HIS00.005-0.00815.858-0.651-0.6510.0000.0000.0000.000
101A103GLU-1-0.824-0.93717.914-14.708-14.7080.0000.0000.0000.000
102A104PHE0-0.0180.0059.648-0.410-0.4100.0000.0000.0000.000
103A105ALA00.0190.00915.005-0.172-0.1720.0000.0000.0000.000
104A106ALA00.0380.02117.1530.3410.3410.0000.0000.0000.000
105A107PHE00.0380.00813.7470.3280.3280.0000.0000.0000.000
106A108LEU0-0.002-0.00112.2680.1170.1170.0000.0000.0000.000
107A109GLU-1-0.860-0.92716.372-13.477-13.4770.0000.0000.0000.000
108A110ASP-1-0.756-0.83920.119-13.361-13.3610.0000.0000.0000.000
109A111ILE0-0.0030.00715.3010.5260.5260.0000.0000.0000.000
110A112VAL0-0.0020.00618.9150.5410.5410.0000.0000.0000.000
111A113ASP-1-0.791-0.88821.355-11.888-11.8880.0000.0000.0000.000
112A114VAL00.0010.00122.7740.6070.6070.0000.0000.0000.000
113A115SER0-0.004-0.00421.7400.4890.4890.0000.0000.0000.000
114A116LYS10.8380.91423.84212.67112.6710.0000.0000.0000.000
115A117GLY00.0040.01126.9690.4190.4190.0000.0000.0000.000
116A118ASP-1-0.910-0.96328.361-9.385-9.3850.0000.0000.0000.000
117A119THR0-0.047-0.03628.308-0.408-0.4080.0000.0000.0000.000
118A120ASP-1-0.831-0.89329.481-10.533-10.5330.0000.0000.0000.000
119A121LEU0-0.0200.00731.6100.2650.2650.0000.0000.0000.000
120A122MET0-0.022-0.01234.1200.2970.2970.0000.0000.0000.000
121A123GLN0-0.008-0.00837.815-0.186-0.1860.0000.0000.0000.000
122A124ASP-1-0.815-0.89340.167-7.479-7.4790.0000.0000.0000.000
123A125SER0-0.001-0.04637.4580.1580.1580.0000.0000.0000.000
124A126LYS10.8060.91933.5819.2829.2820.0000.0000.0000.000
125A127GLU-1-0.941-0.96138.139-7.314-7.3140.0000.0000.0000.000
126A128GLU-1-0.834-0.92041.246-7.124-7.1240.0000.0000.0000.000
127A129VAL0-0.0020.00135.3400.0360.0360.0000.0000.0000.000
128A130SER0-0.013-0.02038.786-0.115-0.1150.0000.0000.0000.000
129A131LYS10.7740.87940.3667.2027.2020.0000.0000.0000.000
130A132ILE0-0.0430.00138.4060.1340.1340.0000.0000.0000.000
131A133ASP-1-0.850-0.94939.923-7.792-7.7920.0000.0000.0000.000
132A134LYS10.8340.92741.5277.1947.1940.0000.0000.0000.000
133A135ASP-1-0.861-0.92037.068-8.564-8.5640.0000.0000.0000.000
134A136VAL0-0.013-0.01735.2510.1540.1540.0000.0000.0000.000
135A137ARG10.7770.86528.09310.54010.5400.0000.0000.0000.000
136A138ILE0-0.002-0.00431.0760.2650.2650.0000.0000.0000.000
137A139LEU00.0070.01529.113-0.425-0.4250.0000.0000.0000.000
138A140ILE0-0.022-0.02326.6520.3400.3400.0000.0000.0000.000
139A141PHE00.0340.02526.072-0.579-0.5790.0000.0000.0000.000
140A142VAL0-0.003-0.02421.9460.3460.3460.0000.0000.0000.000
141A143THR00.0610.02621.914-0.182-0.1820.0000.0000.0000.000
142A144PRO00.0200.01017.0380.2420.2420.0000.0000.0000.000
143A145THR0-0.011-0.01619.152-0.320-0.3200.0000.0000.0000.000
144A146CYS0-0.0850.01821.4491.1111.1110.0000.0000.0000.000
145A147PRO00.0110.00123.191-0.260-0.2600.0000.0000.0000.000
146A148TYR00.012-0.01224.2320.0700.0700.0000.0000.0000.000
147A150PRO00.0990.04721.1950.3190.3190.0000.0000.0000.000
148A151LEU0-0.012-0.00323.5370.2110.2110.0000.0000.0000.000
149A152ALA0-0.0020.00027.0060.3290.3290.0000.0000.0000.000
150A153VAL00.0060.00922.5160.3380.3380.0000.0000.0000.000
151A154ARG10.7140.81822.24313.53913.5390.0000.0000.0000.000
152A155MET0-0.0320.01325.8710.3430.3430.0000.0000.0000.000
153A156ALA00.0270.01728.4410.2400.2400.0000.0000.0000.000
154A157HIS10.7750.87822.63313.64513.6450.0000.0000.0000.000
155A158LYS10.8740.92126.71811.49111.4910.0000.0000.0000.000
156A159PHE00.014-0.01229.3810.2870.2870.0000.0000.0000.000
157A160ALA00.0270.02728.8080.2730.2730.0000.0000.0000.000
158A161ILE00.0150.01625.7390.1780.1780.0000.0000.0000.000
159A162GLU-1-0.734-0.83930.180-9.352-9.3520.0000.0000.0000.000
160A163ASN00.011-0.00833.7240.1440.1440.0000.0000.0000.000
161A164THR0-0.030-0.02330.6010.2350.2350.0000.0000.0000.000
162A165LYS10.7380.85533.0329.6829.6820.0000.0000.0000.000
163A166ALA0-0.056-0.01934.7310.2180.2180.0000.0000.0000.000
164A167GLY0-0.030-0.01536.8500.2590.2590.0000.0000.0000.000
165A168LYS10.8460.93937.6157.8237.8230.0000.0000.0000.000
166A169GLY00.0130.00833.569-0.053-0.0530.0000.0000.0000.000
167A170LYS10.8540.93333.8508.0128.0120.0000.0000.0000.000
168A171ILE0-0.036-0.00132.1000.0400.0400.0000.0000.0000.000
169A172LEU0-0.010-0.00229.357-0.305-0.3050.0000.0000.0000.000
170A173GLY00.0210.01028.1450.2480.2480.0000.0000.0000.000
171A174ASP-1-0.762-0.84925.585-12.163-12.1630.0000.0000.0000.000
172A175MET0-0.0270.01018.9370.3570.3570.0000.0000.0000.000
173A176VAL00.0190.00023.291-0.333-0.3330.0000.0000.0000.000
174A177GLU-1-0.769-0.89418.527-15.280-15.2800.0000.0000.0000.000
175A178ALA00.0210.00021.7100.2130.2130.0000.0000.0000.000
176A179ILE0-0.061-0.03720.5080.4060.4060.0000.0000.0000.000
177A180GLU-1-0.860-0.93517.284-18.621-18.6210.0000.0000.0000.000
178A181TYR0-0.042-0.05521.3890.6350.6350.0000.0000.0000.000
179A182PRO00.0370.03424.6750.4370.4370.0000.0000.0000.000
180A183GLU-1-0.777-0.87727.402-11.381-11.3810.0000.0000.0000.000
181A184TRP0-0.049-0.03025.7200.2540.2540.0000.0000.0000.000
182A185ALA00.0280.00327.9730.2330.2330.0000.0000.0000.000
183A186ASP-1-0.896-0.95430.066-9.953-9.9530.0000.0000.0000.000
184A187GLN0-0.062-0.02133.0650.1280.1280.0000.0000.0000.000
185A188TYR0-0.079-0.06132.5310.2320.2320.0000.0000.0000.000
186A189ASN0-0.082-0.04634.8480.1620.1620.0000.0000.0000.000
187A190VAL0-0.028-0.00929.0470.0830.0830.0000.0000.0000.000
188A191MET0-0.0250.00832.072-0.119-0.1190.0000.0000.0000.000
189A192ALA0-0.035-0.00731.631-0.311-0.3110.0000.0000.0000.000
190A193VAL0-0.009-0.00226.621-0.137-0.1370.0000.0000.0000.000
191A194PRO0-0.017-0.02527.612-0.004-0.0040.0000.0000.0000.000
192A195LYS10.8660.94029.0589.6479.6470.0000.0000.0000.000
193A196ILE0-0.043-0.01630.599-0.328-0.3280.0000.0000.0000.000
194A197VAL0-0.022-0.01132.6290.3850.3850.0000.0000.0000.000
195A198ILE0-0.0090.00133.655-0.254-0.2540.0000.0000.0000.000
196A199GLN0-0.031-0.03034.4740.1160.1160.0000.0000.0000.000
197A200VAL00.005-0.01037.183-0.117-0.1170.0000.0000.0000.000
198A201ASN0-0.043-0.03839.5800.0340.0340.0000.0000.0000.000
199A202GLY00.0210.01737.7490.0940.0940.0000.0000.0000.000
200A203GLU-1-0.915-0.94138.832-7.270-7.2700.0000.0000.0000.000
201A204ASP-1-0.792-0.88737.152-8.868-8.8680.0000.0000.0000.000
202A205LYS10.8300.93539.6167.4907.4900.0000.0000.0000.000
203A206VAL0-0.006-0.00439.2180.1710.1710.0000.0000.0000.000
204A207GLN00.0170.00637.053-0.373-0.3730.0000.0000.0000.000
205A208PHE0-0.036-0.01634.1260.2890.2890.0000.0000.0000.000
206A209GLU-1-0.844-0.92533.954-9.502-9.5020.0000.0000.0000.000
207A210GLY00.0130.00632.2520.2530.2530.0000.0000.0000.000
208A211ALA0-0.020-0.02429.7750.0040.0040.0000.0000.0000.000
209A212TYR0-0.033-0.00931.7480.3000.3000.0000.0000.0000.000
210A213PRO00.0310.00433.796-0.198-0.1980.0000.0000.0000.000
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