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

tag_button

FMODB ID: J4QK9

Calculation Name: 4J4F-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

PDB ID: 4J4F

Chain ID: A

ChEMBL ID:

UniProt ID: P81180

Base Structure: X-ray

Registration Date: 2025-07-14

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 OptAll
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 192
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -567392.623175
FMO2-HF: Nuclear repulsion 528188.108361
FMO2-HF: Total energy -39204.514814
FMO2-MP2: Total energy -39316.112589


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:1:LEU)


Summations of interaction energy for fragment #1(A:1:LEU)
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.
-23.935-24.6878.488-4.073-3.6620.046
Interaction energy analysis for fragmet #1(A:1:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.103 / q_NPA : -0.008
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].
4A3LYS00.0140.0113.885-0.2490.821-0.011-0.524-0.5340.001
5A3LYS10.8281.0212.142-25.131-26.9538.499-3.549-3.1280.045
6A4PHE00.201-0.0396.3730.2150.2150.0000.0000.0000.000
7A4PHE0-0.0470.0778.589-0.037-0.0370.0000.0000.0000.000
8A5SER00.031-0.0609.0500.0110.0110.0000.0000.0000.000
9A5SER0-0.0340.06010.8280.0340.0340.0000.0000.0000.000
10A6GLN00.041-0.0939.766-0.084-0.0840.0000.0000.0000.000
11A6GLN0-0.0670.0707.4510.5190.5190.0000.0000.0000.000
12A7THR0-0.021-0.07510.9720.0010.0010.0000.0000.0000.000
13A7THR0-0.0340.07010.1350.0380.0380.0000.0000.0000.000
14A8CYS00.033-0.11412.439-0.060-0.0600.0000.0000.0000.000
15A8CYS0-0.1980.20912.762-0.041-0.0410.0000.0000.0000.000
16A9TYR00.131-0.02814.8030.0400.0400.0000.0000.0000.000
17A9TYR0-0.0690.07718.407-0.008-0.0080.0000.0000.0000.000
18A10ASN00.054-0.06218.169-0.022-0.0220.0000.0000.0000.000
19A10ASN0-0.0830.05721.1130.0100.0100.0000.0000.0000.000
20A11SER00.070-0.08816.685-0.023-0.0230.0000.0000.0000.000
21A11SER0-0.0450.04615.8710.0170.0170.0000.0000.0000.000
22A12ALA00.081-0.08418.0120.0210.0210.0000.0000.0000.000
23A12ALA0-0.0670.10721.3270.0020.0020.0000.0000.0000.000
24A13ILE00.048-0.11418.695-0.021-0.0210.0000.0000.0000.000
25A13ILE0-0.0520.10816.396-0.003-0.0030.0000.0000.0000.000
26A14GLN00.093-0.08520.1450.0220.0220.0000.0000.0000.000
27A14GLN0-0.0910.10323.642-0.001-0.0010.0000.0000.0000.000
28A15GLY0-0.014-0.11422.626-0.015-0.0150.0000.0000.0000.000
29A16SER00.0300.00219.9060.0060.0060.0000.0000.0000.000
30A16SER0-0.0280.06319.3680.0120.0120.0000.0000.0000.000
31A17VAL00.066-0.09918.257-0.062-0.0620.0000.0000.0000.000
32A17VAL0-0.1070.10819.1890.0040.0040.0000.0000.0000.000
33A18LEU00.166-0.07315.4890.0570.0570.0000.0000.0000.000
34A18LEU0-0.1190.09612.643-0.016-0.0160.0000.0000.0000.000
35A19THR00.022-0.10616.974-0.026-0.0260.0000.0000.0000.000
36A19THR0-0.0240.09519.5700.0040.0040.0000.0000.0000.000
37A20SER00.063-0.06915.4680.0160.0160.0000.0000.0000.000
38A20SER0-0.0010.07914.4050.0120.0120.0000.0000.0000.000
39A21THR0-0.025-0.07516.955-0.027-0.0270.0000.0000.0000.000
40A21THR0-0.0670.06619.580-0.001-0.0010.0000.0000.0000.000
41A22CYS00.083-0.12514.1400.0400.0400.0000.0000.0000.000
42A23GLU00.170-0.08514.660-0.048-0.0480.0000.0000.0000.000
43A23GLU-1-0.941-0.79514.3320.2970.2970.0000.0000.0000.000
44A24ARG00.023-0.11214.446-0.004-0.0040.0000.0000.0000.000
45A24ARG10.8061.03517.328-0.024-0.0240.0000.0000.0000.000
46A25THR00.034-0.10514.9520.0280.0280.0000.0000.0000.000
47A25THR0-0.0490.06513.317-0.013-0.0130.0000.0000.0000.000
48A26ASN00.022-0.05015.7340.0260.0260.0000.0000.0000.000
49A26ASN0-0.0890.07118.822-0.002-0.0020.0000.0000.0000.000
50A27GLY00.075-0.06718.589-0.009-0.0090.0000.0000.0000.000
51A28GLY0-0.003-0.01120.293-0.022-0.0220.0000.0000.0000.000
52A29TYR00.054-0.00218.6470.0200.0200.0000.0000.0000.000
53A29TYR0-0.1040.05517.325-0.017-0.0170.0000.0000.0000.000
54A30ASN00.139-0.09418.179-0.008-0.0080.0000.0000.0000.000
55A30ASN0-0.1420.07217.3520.0070.0070.0000.0000.0000.000
56A31THR00.026-0.06617.6780.0010.0010.0000.0000.0000.000
57A31THR0-0.0110.08520.3990.0080.0080.0000.0000.0000.000
58A32SER0-0.042-0.07816.5070.0050.0050.0000.0000.0000.000
59A32SER0-0.0070.07615.469-0.017-0.0170.0000.0000.0000.000
60A33SER00.041-0.10817.0120.0120.0120.0000.0000.0000.000
61A33SER0-0.0120.07318.8280.0120.0120.0000.0000.0000.000
62A34ILE00.066-0.07514.1770.0150.0150.0000.0000.0000.000
63A34ILE0-0.0840.09611.672-0.015-0.0150.0000.0000.0000.000
64A35ASP00.098-0.10515.7260.0070.0070.0000.0000.0000.000
65A35ASP-1-0.868-0.76818.399-0.345-0.3450.0000.0000.0000.000
66A36LEU00.080-0.12314.669-0.067-0.0670.0000.0000.0000.000
67A36LEU0-0.0900.10512.850-0.009-0.0090.0000.0000.0000.000
68A37ASN00.145-0.05615.636-0.064-0.0640.0000.0000.0000.000
69A37ASN0-0.1090.05919.9250.0140.0140.0000.0000.0000.000
70A38SER0-0.030-0.09517.0350.0240.0240.0000.0000.0000.000
71A38SER0-0.0410.07916.144-0.025-0.0250.0000.0000.0000.000
72A39VAL00.011-0.10512.4620.0130.0130.0000.0000.0000.000
73A39VAL0-0.0990.08211.486-0.046-0.0460.0000.0000.0000.000
74A40ILE00.110-0.07912.555-0.176-0.1760.0000.0000.0000.000
75A40ILE0-0.0950.07211.9910.0080.0080.0000.0000.0000.000
76A41GLU00.071-0.09114.7170.0520.0520.0000.0000.0000.000
77A41GLU-1-0.917-0.82316.393-0.496-0.4960.0000.0000.0000.000
78A42ASN00.087-0.08917.765-0.015-0.0150.0000.0000.0000.000
79A42ASN0-0.1140.05721.2770.0060.0060.0000.0000.0000.000
80A43VAL00.081-0.09220.1520.0130.0130.0000.0000.0000.000
81A43VAL0-0.0720.10518.783-0.006-0.0060.0000.0000.0000.000
82A44ASP00.023-0.10821.3240.0020.0020.0000.0000.0000.000
83A44ASP-1-0.976-0.83824.053-0.201-0.2010.0000.0000.0000.000
84A45GLY00.035-0.11423.8550.0200.0200.0000.0000.0000.000
85A46SER00.0710.01520.6270.0170.0170.0000.0000.0000.000
86A46SER0-0.0740.07819.825-0.010-0.0100.0000.0000.0000.000
87A47LEU00.099-0.09117.407-0.020-0.0200.0000.0000.0000.000
88A47LEU0-0.0650.10716.5410.0020.0020.0000.0000.0000.000
89A48LYS0-0.051-0.14814.3030.0230.0230.0000.0000.0000.000
90A48LYS10.8631.05314.8920.3400.3400.0000.0000.0000.000
91A49TRP00.113-0.06510.5200.0720.0720.0000.0000.0000.000
92A49TRP0-0.1430.0548.774-0.231-0.2310.0000.0000.0000.000
93A50GLN00.118-0.07811.9940.0310.0310.0000.0000.0000.000
94A50GLN0-0.1180.09913.6120.0000.0000.0000.0000.0000.000
95A51GLY0-0.055-0.13012.481-0.174-0.1740.0000.0000.0000.000
96A52SER00.0170.01014.592-0.062-0.0620.0000.0000.0000.000
97A52SER00.0080.07115.045-0.015-0.0150.0000.0000.0000.000
98A53ASN00.097-0.06916.7140.0210.0210.0000.0000.0000.000
99A53ASN0-0.1310.06420.715-0.001-0.0010.0000.0000.0000.000
100A54PHE00.152-0.06020.451-0.014-0.0140.0000.0000.0000.000
101A54PHE0-0.0430.08221.9050.0040.0040.0000.0000.0000.000
102A55ILE00.038-0.11921.7080.0040.0040.0000.0000.0000.000
103A55ILE0-0.0720.11723.9830.0010.0010.0000.0000.0000.000
104A56GLU00.051-0.13220.8530.0310.0310.0000.0000.0000.000
105A56GLU-1-0.917-0.80820.081-0.402-0.4020.0000.0000.0000.000
106A57THR0-0.045-0.08017.9890.0040.0040.0000.0000.0000.000
107A57THR0-0.0720.03916.3120.0090.0090.0000.0000.0000.000
108A58CYS00.038-0.10619.308-0.023-0.0230.0000.0000.0000.000
109A58CYS0-0.1850.22718.934-0.004-0.0040.0000.0000.0000.000
110A59ARG00.097-0.04722.0470.0040.0040.0000.0000.0000.000
111A59ARG10.7700.98324.1500.2060.2060.0000.0000.0000.000
112A60ASN00.062-0.06725.464-0.006-0.0060.0000.0000.0000.000
113A60ASN0-0.1350.03628.0120.0010.0010.0000.0000.0000.000
114A61THR00.110-0.08028.1650.0090.0090.0000.0000.0000.000
115A61THR0-0.0540.06426.252-0.006-0.0060.0000.0000.0000.000
116A62GLN00.023-0.06828.7070.0040.0040.0000.0000.0000.000
117A62GLN0-0.1130.05230.6440.0110.0110.0000.0000.0000.000
118A63LEU00.159-0.08831.278-0.011-0.0110.0000.0000.0000.000
119A63LEU0-0.0850.11433.8590.0000.0000.0000.0000.0000.000
120A64ALA00.027-0.10833.4200.0050.0050.0000.0000.0000.000
121A64ALA0-0.0830.09432.644-0.001-0.0010.0000.0000.0000.000
122A65GLY0-0.006-0.11434.552-0.001-0.0010.0000.0000.0000.000
123A66SER00.035-0.00637.401-0.001-0.0010.0000.0000.0000.000
124A66SER0-0.0230.08438.1320.0030.0030.0000.0000.0000.000
125A67SER0-0.034-0.10335.5010.0000.0000.0000.0000.0000.000
126A67SER0-0.0130.07635.2070.0020.0020.0000.0000.0000.000
127A68GLU00.104-0.08831.598-0.007-0.0070.0000.0000.0000.000
128A68GLU-1-0.905-0.79830.964-0.120-0.1200.0000.0000.0000.000
129A69LEU00.160-0.05429.1920.0090.0090.0000.0000.0000.000
130A69LEU0-0.1130.09027.065-0.002-0.0020.0000.0000.0000.000
131A70ALA00.072-0.10427.853-0.012-0.0120.0000.0000.0000.000
132A70ALA0-0.0780.08929.3590.0030.0030.0000.0000.0000.000
133A71ALA00.096-0.07425.3680.0100.0100.0000.0000.0000.000
134A71ALA0-0.0530.07924.555-0.005-0.0050.0000.0000.0000.000
135A72GLU00.043-0.10023.5590.0060.0060.0000.0000.0000.000
136A72GLU-1-0.891-0.78623.744-0.176-0.1760.0000.0000.0000.000
137A73CYS00.085-0.14419.8930.0070.0070.0000.0000.0000.000
138A74LYS00.126-0.08417.2150.0250.0250.0000.0000.0000.000
139A74LYS10.7391.01715.1450.4510.4510.0000.0000.0000.000
140A75THR00.039-0.09814.376-0.068-0.0680.0000.0000.0000.000
141A75THR0-0.0930.05013.715-0.011-0.0110.0000.0000.0000.000
142A76ARG00.119-0.0539.5200.0660.0660.0000.0000.0000.000
143A76ARG10.8811.0647.1181.8081.8080.0000.0000.0000.000
144A77ALA00.084-0.10210.527-0.140-0.1400.0000.0000.0000.000
145A77ALA0-0.0600.11211.8850.0220.0220.0000.0000.0000.000
146A78GLN0-0.009-0.11712.1160.0960.0960.0000.0000.0000.000
147A78GLN0-0.0240.12111.5330.1070.1070.0000.0000.0000.000
148A79GLN00.133-0.07514.7140.0230.0230.0000.0000.0000.000
149A79GLN0-0.0260.11617.1920.0050.0050.0000.0000.0000.000
150A80PHE00.060-0.08517.236-0.060-0.0600.0000.0000.0000.000
151A80PHE0-0.0560.08720.8760.0010.0010.0000.0000.0000.000
152A81VAL00.027-0.11719.9860.0330.0330.0000.0000.0000.000
153A81VAL0-0.0500.11418.5880.0000.0000.0000.0000.0000.000
154A82SER00.088-0.07921.087-0.025-0.0250.0000.0000.0000.000
155A82SER0-0.0200.08325.3240.0080.0080.0000.0000.0000.000
156A83THR0-0.028-0.05522.4690.0050.0050.0000.0000.0000.000
157A83THR0-0.0540.04321.3510.0040.0040.0000.0000.0000.000
158A84LYS00.081-0.11223.8510.0040.0040.0000.0000.0000.000
159A84LYS10.7500.99527.0090.1280.1280.0000.0000.0000.000
160A85ILE00.063-0.07925.204-0.007-0.0070.0000.0000.0000.000
161A85ILE0-0.0690.10624.260-0.004-0.0040.0000.0000.0000.000
162A86ASN00.106-0.09727.0240.0030.0030.0000.0000.0000.000
163A86ASN0-0.1100.07230.5220.0030.0030.0000.0000.0000.000
164A87LEU00.069-0.09630.116-0.010-0.0100.0000.0000.0000.000
165A87LEU0-0.0820.09430.086-0.001-0.0010.0000.0000.0000.000
166A88ASP00.132-0.07232.033-0.005-0.0050.0000.0000.0000.000
167A88ASP-1-0.916-0.82735.128-0.106-0.1060.0000.0000.0000.000
168A89ASP00.072-0.11130.5940.0090.0090.0000.0000.0000.000
169A89ASP-1-0.957-0.82629.248-0.147-0.1470.0000.0000.0000.000
170A90HIS0-0.043-0.09330.5920.0020.0020.0000.0000.0000.000
171A90HIS10.8011.01028.0890.1640.1640.0000.0000.0000.000
172A91ILE00.084-0.08632.069-0.002-0.0020.0000.0000.0000.000
173A91ILE0-0.0710.10331.261-0.001-0.0010.0000.0000.0000.000
174A92ALA00.146-0.06634.4470.0040.0040.0000.0000.0000.000
175A92ALA0-0.0590.10137.6830.0010.0010.0000.0000.0000.000
176A93ASN00.135-0.06938.160-0.004-0.0040.0000.0000.0000.000
177A93ASN0-0.1250.06441.8910.0000.0000.0000.0000.0000.000
178A94ILE00.032-0.11841.5660.0050.0050.0000.0000.0000.000
179A94ILE0-0.1270.09740.1960.0000.0000.0000.0000.0000.000
180A95ASP00.085-0.11043.093-0.002-0.0020.0000.0000.0000.000
181A95ASP-1-0.982-0.84047.156-0.068-0.0680.0000.0000.0000.000
182A96GLY00.003-0.11445.4610.0020.0020.0000.0000.0000.000
183A97THR00.010-0.00942.698-0.002-0.0020.0000.0000.0000.000
184A97THR0-0.0420.08040.6780.0000.0000.0000.0000.0000.000
185A98LEU00.050-0.09238.6060.0020.0020.0000.0000.0000.000
186A98LEU0-0.0690.10337.574-0.001-0.0010.0000.0000.0000.000
187A99LYS00.078-0.09936.664-0.004-0.0040.0000.0000.0000.000
188A99LYS10.7400.98636.2380.1210.1210.0000.0000.0000.000
189A100TYR00.125-0.10332.4580.0040.0040.0000.0000.0000.000
190A100TYR0-0.0910.10628.523-0.004-0.0040.0000.0000.0000.000
191A101GLU0-0.170-0.16232.362-0.005-0.0050.0000.0000.0000.000
192A101GLU-1-0.737-0.85235.370-0.114-0.1140.0000.0000.0000.000