FMODB

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

Last updated: 2025-09-03

All entries: 45600

Number of unique PDB entries: 8613

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FMODB ID: NZN6Q

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 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 192
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -568148.216561
FMO2-HF: Nuclear repulsion 528943.908416
FMO2-HF: Total energy -39204.308145
FMO2-MP2: Total energy -39315.929759


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.
-10.508-7.5570.689-1.782-1.8580.01
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 : 0.084 / q_NPA : 0.004
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].
4A3LYS00.0380.0053.8140.1481.547-0.017-0.707-0.6750.002
5A3LYS10.8471.0532.633-12.490-10.9380.706-1.075-1.1830.008
6A4PHE00.189-0.0476.4170.3220.3220.0000.0000.0000.000
7A4PHE0-0.0540.0848.697-0.052-0.0520.0000.0000.0000.000
8A5SER00.051-0.0779.0620.0620.0620.0000.0000.0000.000
9A5SER0-0.0270.07711.129-0.020-0.0200.0000.0000.0000.000
10A6GLN00.011-0.09210.289-0.149-0.1490.0000.0000.0000.000
11A6GLN0-0.0770.0658.5630.3450.3450.0000.0000.0000.000
12A7THR00.008-0.06411.746-0.046-0.0460.0000.0000.0000.000
13A7THR0-0.0340.07611.4110.0960.0960.0000.0000.0000.000
14A8CYS00.041-0.11213.279-0.040-0.0400.0000.0000.0000.000
15A8CYS0-0.2110.19212.804-0.025-0.0250.0000.0000.0000.000
16A9TYR00.117-0.04114.8590.0200.0200.0000.0000.0000.000
17A9TYR0-0.0560.07718.510-0.015-0.0150.0000.0000.0000.000
18A10ASN00.088-0.05518.123-0.020-0.0200.0000.0000.0000.000
19A10ASN0-0.1060.05221.2640.0060.0060.0000.0000.0000.000
20A11SER00.078-0.08417.073-0.014-0.0140.0000.0000.0000.000
21A11SER0-0.0440.03716.1840.0080.0080.0000.0000.0000.000
22A12ALA00.060-0.09218.3200.0090.0090.0000.0000.0000.000
23A12ALA0-0.0690.11121.6020.0020.0020.0000.0000.0000.000
24A13ILE00.072-0.10519.117-0.010-0.0100.0000.0000.0000.000
25A13ILE0-0.0710.11216.400-0.006-0.0060.0000.0000.0000.000
26A14GLN00.087-0.09920.3770.0190.0190.0000.0000.0000.000
27A14GLN0-0.0970.10723.7550.0050.0050.0000.0000.0000.000
28A15GLY0-0.023-0.11522.539-0.009-0.0090.0000.0000.0000.000
29A16SER00.0290.00619.956-0.005-0.0050.0000.0000.0000.000
30A16SER0-0.0170.06619.4240.0150.0150.0000.0000.0000.000
31A17VAL00.051-0.10118.280-0.072-0.0720.0000.0000.0000.000
32A17VAL0-0.1010.10519.3310.0070.0070.0000.0000.0000.000
33A18LEU00.160-0.08515.7340.0500.0500.0000.0000.0000.000
34A18LEU0-0.1390.09612.957-0.017-0.0170.0000.0000.0000.000
35A19THR00.040-0.07417.137-0.012-0.0120.0000.0000.0000.000
36A19THR0-0.0310.08319.966-0.004-0.0040.0000.0000.0000.000
37A20SER00.090-0.05915.729-0.003-0.0030.0000.0000.0000.000
38A20SER00.0020.08414.7440.0120.0120.0000.0000.0000.000
39A21THR00.030-0.07617.172-0.015-0.0150.0000.0000.0000.000
40A21THR0-0.0490.09919.650-0.006-0.0060.0000.0000.0000.000
41A22CYS00.059-0.14814.4670.0270.0270.0000.0000.0000.000
42A23GLU00.171-0.08715.087-0.078-0.0780.0000.0000.0000.000
43A23GLU-1-0.938-0.77914.9010.5710.5710.0000.0000.0000.000
44A24ARG00.025-0.11614.4970.0690.0690.0000.0000.0000.000
45A24ARG10.8431.05917.679-0.231-0.2310.0000.0000.0000.000
46A25THR00.080-0.08015.3040.0260.0260.0000.0000.0000.000
47A25THR0-0.0550.05513.369-0.014-0.0140.0000.0000.0000.000
48A26ASN00.005-0.04915.9180.0280.0280.0000.0000.0000.000
49A26ASN0-0.1220.05918.9080.0320.0320.0000.0000.0000.000
50A27GLY00.089-0.06818.786-0.036-0.0360.0000.0000.0000.000
51A28GLY00.003-0.00620.503-0.033-0.0330.0000.0000.0000.000
52A29TYR00.056-0.00318.8940.0470.0470.0000.0000.0000.000
53A29TYR0-0.1220.05017.569-0.033-0.0330.0000.0000.0000.000
54A30ASN00.129-0.07218.301-0.027-0.0270.0000.0000.0000.000
55A30ASN0-0.1450.05417.677-0.001-0.0010.0000.0000.0000.000
56A31THR00.032-0.09217.9190.0250.0250.0000.0000.0000.000
57A31THR0-0.0290.08820.2910.0030.0030.0000.0000.0000.000
58A32SER0-0.076-0.08216.914-0.002-0.0020.0000.0000.0000.000
59A32SER0-0.0230.06115.753-0.005-0.0050.0000.0000.0000.000
60A33SER00.064-0.10917.5290.0110.0110.0000.0000.0000.000
61A33SER0-0.0340.07319.2900.0110.0110.0000.0000.0000.000
62A34ILE00.069-0.07814.3130.0300.0300.0000.0000.0000.000
63A34ILE0-0.1020.09011.681-0.015-0.0150.0000.0000.0000.000
64A35ASP00.105-0.10815.8610.0000.0000.0000.0000.0000.000
65A35ASP-1-0.873-0.77818.219-0.385-0.3850.0000.0000.0000.000
66A36LEU00.030-0.13214.499-0.067-0.0670.0000.0000.0000.000
67A36LEU0-0.0890.10312.637-0.016-0.0160.0000.0000.0000.000
68A37ASN00.128-0.05815.446-0.088-0.0880.0000.0000.0000.000
69A37ASN0-0.1200.05719.5940.0070.0070.0000.0000.0000.000
70A38SER00.046-0.07116.9310.0120.0120.0000.0000.0000.000
71A38SER0-0.0590.05616.131-0.022-0.0220.0000.0000.0000.000
72A39VAL00.035-0.08212.2510.0260.0260.0000.0000.0000.000
73A39VAL0-0.1030.08111.322-0.051-0.0510.0000.0000.0000.000
74A40ILE00.133-0.06512.599-0.217-0.2170.0000.0000.0000.000
75A40ILE0-0.0930.06912.2660.0060.0060.0000.0000.0000.000
76A41GLU00.059-0.11314.7370.0740.0740.0000.0000.0000.000
77A41GLU-1-0.901-0.80516.361-0.648-0.6480.0000.0000.0000.000
78A42ASN00.110-0.08117.839-0.041-0.0410.0000.0000.0000.000
79A42ASN0-0.1370.06321.672-0.001-0.0010.0000.0000.0000.000
80A43VAL00.074-0.09819.9260.0310.0310.0000.0000.0000.000
81A43VAL0-0.0830.09818.407-0.010-0.0100.0000.0000.0000.000
82A44ASP00.047-0.10621.057-0.010-0.0100.0000.0000.0000.000
83A44ASP-1-0.985-0.83323.516-0.338-0.3380.0000.0000.0000.000
84A45GLY00.026-0.12423.4990.0240.0240.0000.0000.0000.000
85A46SER0-0.016-0.01619.7670.0220.0220.0000.0000.0000.000
86A46SER0-0.0270.04518.722-0.009-0.0090.0000.0000.0000.000
87A47LEU00.089-0.06217.234-0.011-0.0110.0000.0000.0000.000
88A47LEU0-0.0770.10616.408-0.002-0.0020.0000.0000.0000.000
89A48LYS0-0.028-0.15814.240-0.029-0.0290.0000.0000.0000.000
90A48LYS10.9131.09814.8840.5890.5890.0000.0000.0000.000
91A49TRP00.104-0.04910.5920.1050.1050.0000.0000.0000.000
92A49TRP0-0.1710.0428.811-0.246-0.2460.0000.0000.0000.000
93A50GLN00.143-0.09012.0420.0160.0160.0000.0000.0000.000
94A50GLN0-0.1570.09413.7140.0020.0020.0000.0000.0000.000
95A51GLY0-0.056-0.12312.608-0.204-0.2040.0000.0000.0000.000
96A52SER00.0570.03914.5760.0060.0060.0000.0000.0000.000
97A52SER0-0.0620.02714.605-0.033-0.0330.0000.0000.0000.000
98A53ASN00.144-0.07616.1640.0220.0220.0000.0000.0000.000
99A53ASN0-0.1550.06620.041-0.001-0.0010.0000.0000.0000.000
100A54PHE00.127-0.07119.806-0.019-0.0190.0000.0000.0000.000
101A54PHE0-0.0230.09021.5320.0040.0040.0000.0000.0000.000
102A55ILE00.066-0.12021.3720.0020.0020.0000.0000.0000.000
103A55ILE0-0.0690.12723.7350.0010.0010.0000.0000.0000.000
104A56GLU00.063-0.13620.7090.0350.0350.0000.0000.0000.000
105A56GLU-1-0.928-0.81119.650-0.473-0.4730.0000.0000.0000.000
106A57THR0-0.067-0.06817.8040.0250.0250.0000.0000.0000.000
107A57THR0-0.0750.05216.158-0.038-0.0380.0000.0000.0000.000
108A58CYS00.072-0.10219.140-0.041-0.0410.0000.0000.0000.000
109A58CYS0-0.1960.22418.767-0.009-0.0090.0000.0000.0000.000
110A59ARG00.074-0.06021.8260.0110.0110.0000.0000.0000.000
111A59ARG10.7720.97823.9060.2690.2690.0000.0000.0000.000
112A60ASN00.026-0.06625.165-0.010-0.0100.0000.0000.0000.000
113A60ASN0-0.1440.02927.7540.0060.0060.0000.0000.0000.000
114A61THR00.158-0.07228.1420.0040.0040.0000.0000.0000.000
115A61THR0-0.0360.06926.376-0.005-0.0050.0000.0000.0000.000
116A62GLN00.003-0.08228.7070.0110.0110.0000.0000.0000.000
117A62GLN0-0.0990.06030.4120.0140.0140.0000.0000.0000.000
118A63LEU00.145-0.08931.190-0.017-0.0170.0000.0000.0000.000
119A63LEU0-0.0830.12433.6840.0010.0010.0000.0000.0000.000
120A64ALA00.032-0.10733.0200.0110.0110.0000.0000.0000.000
121A64ALA0-0.0930.09132.318-0.002-0.0020.0000.0000.0000.000
122A65GLY0-0.022-0.12134.202-0.002-0.0020.0000.0000.0000.000
123A66SER00.0630.00537.263-0.001-0.0010.0000.0000.0000.000
124A66SER0-0.0120.08538.5640.0030.0030.0000.0000.0000.000
125A67SER0-0.069-0.10335.4100.0020.0020.0000.0000.0000.000
126A67SER0-0.0330.09035.0050.0010.0010.0000.0000.0000.000
127A68GLU00.149-0.10431.524-0.010-0.0100.0000.0000.0000.000
128A68GLU-1-0.900-0.78430.762-0.206-0.2060.0000.0000.0000.000
129A69LEU00.132-0.05629.0300.0160.0160.0000.0000.0000.000
130A69LEU0-0.1250.08326.916-0.002-0.0020.0000.0000.0000.000
131A70ALA00.088-0.09827.840-0.020-0.0200.0000.0000.0000.000
132A70ALA0-0.0860.08529.2500.0040.0040.0000.0000.0000.000
133A71ALA00.083-0.07625.2060.0160.0160.0000.0000.0000.000
134A71ALA0-0.0600.07124.366-0.006-0.0060.0000.0000.0000.000
135A72GLU00.071-0.09123.389-0.002-0.0020.0000.0000.0000.000
136A72GLU-1-0.903-0.78623.513-0.245-0.2450.0000.0000.0000.000
137A73CYS00.090-0.14819.7330.0190.0190.0000.0000.0000.000
138A74LYS00.158-0.07317.0880.0140.0140.0000.0000.0000.000
139A74LYS10.7571.04315.1980.5090.5090.0000.0000.0000.000
140A75THR00.029-0.09414.121-0.077-0.0770.0000.0000.0000.000
141A75THR0-0.0600.06913.674-0.017-0.0170.0000.0000.0000.000
142A76ARG00.104-0.0599.3400.1190.1190.0000.0000.0000.000
143A76ARG10.8961.0706.6292.4962.4960.0000.0000.0000.000
144A77ALA00.087-0.10310.122-0.153-0.1530.0000.0000.0000.000
145A77ALA0-0.0640.10712.2750.0200.0200.0000.0000.0000.000
146A78GLN0-0.050-0.12112.2780.1070.1070.0000.0000.0000.000
147A78GLN0-0.0110.11411.5460.1180.1180.0000.0000.0000.000
148A79GLN00.110-0.09614.7800.0700.0700.0000.0000.0000.000
149A79GLN0-0.0390.11817.0030.0110.0110.0000.0000.0000.000
150A80PHE00.088-0.09017.452-0.074-0.0740.0000.0000.0000.000
151A80PHE0-0.0760.08620.9860.0050.0050.0000.0000.0000.000
152A81VAL00.030-0.12319.9930.0420.0420.0000.0000.0000.000
153A81VAL0-0.0560.11118.562-0.005-0.0050.0000.0000.0000.000
154A82SER00.098-0.07421.048-0.022-0.0220.0000.0000.0000.000
155A82SER0-0.0210.08325.1840.0090.0090.0000.0000.0000.000
156A83THR0-0.003-0.05622.550-0.006-0.0060.0000.0000.0000.000
157A83THR0-0.0610.05421.5670.0030.0030.0000.0000.0000.000
158A84LYS00.069-0.12323.8820.0100.0100.0000.0000.0000.000
159A84LYS10.7691.00527.6020.2070.2070.0000.0000.0000.000
160A85ILE00.077-0.07225.502-0.015-0.0150.0000.0000.0000.000
161A85ILE0-0.0660.11124.311-0.004-0.0040.0000.0000.0000.000
162A86ASN00.122-0.09227.1030.0110.0110.0000.0000.0000.000
163A86ASN0-0.1050.08030.3560.0080.0080.0000.0000.0000.000
164A87LEU00.081-0.10630.379-0.011-0.0110.0000.0000.0000.000
165A87LEU0-0.0850.08729.655-0.001-0.0010.0000.0000.0000.000
166A88ASP00.110-0.07331.746-0.003-0.0030.0000.0000.0000.000
167A88ASP-1-0.934-0.84034.671-0.167-0.1670.0000.0000.0000.000
168A89ASP00.078-0.09130.3590.0130.0130.0000.0000.0000.000
169A89ASP-1-1.003-0.84928.898-0.249-0.2490.0000.0000.0000.000
170A90HIS0-0.028-0.10430.6750.0060.0060.0000.0000.0000.000
171A90HIS10.8101.00628.1670.2520.2520.0000.0000.0000.000
172A91ILE00.090-0.08832.0630.0000.0000.0000.0000.0000.000
173A91ILE0-0.0880.10130.987-0.001-0.0010.0000.0000.0000.000
174A92ALA00.174-0.06134.2070.0040.0040.0000.0000.0000.000
175A92ALA0-0.0590.10237.2030.0010.0010.0000.0000.0000.000
176A93ASN00.130-0.07337.728-0.004-0.0040.0000.0000.0000.000
177A93ASN0-0.1330.06241.5120.0010.0010.0000.0000.0000.000
178A94ILE00.051-0.11941.1370.0050.0050.0000.0000.0000.000
179A94ILE0-0.1260.10139.9580.0000.0000.0000.0000.0000.000
180A95ASP00.084-0.11942.718-0.001-0.0010.0000.0000.0000.000
181A95ASP-1-0.994-0.83546.555-0.099-0.0990.0000.0000.0000.000
182A96GLY0-0.011-0.12245.0940.0030.0030.0000.0000.0000.000
183A97THR00.0180.00042.3710.0000.0000.0000.0000.0000.000
184A97THR0-0.0400.07340.4830.0000.0000.0000.0000.0000.000
185A98LEU00.048-0.08638.0730.0010.0010.0000.0000.0000.000
186A98LEU0-0.0800.09737.055-0.001-0.0010.0000.0000.0000.000
187A99LYS00.077-0.10636.443-0.003-0.0030.0000.0000.0000.000
188A99LYS10.7511.00936.5000.1690.1690.0000.0000.0000.000
189A100TYR00.143-0.09432.2280.0040.0040.0000.0000.0000.000
190A100TYR0-0.1030.10228.085-0.006-0.0060.0000.0000.0000.000
191A101GLU0-0.167-0.15632.588-0.004-0.0040.0000.0000.0000.000
192A101GLU-1-0.747-0.86035.485-0.164-0.1640.0000.0000.0000.000