FMODB

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

Last updated: 2025-07-23

All entries: 44592

Number of unique PDB entries: 7794

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FMODB ID: 3753L

Calculation Name: 4H6J-A-Xray540

Preferred Name: Aryl hydrocarbon receptor nuclear translocator

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4H6J

Chain ID: A

ChEMBL ID: CHEMBL5618

UniProt ID: P27540

Base Structure: X-ray

Registration Date: 2025-07-10

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 204
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -871896.588834
FMO2-HF: Nuclear repulsion 827464.513762
FMO2-HF: Total energy -44432.075072
FMO2-MP2: Total energy -44557.450422


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:238:ASP)


Summations of interaction energy for fragment #1(A:238:ASP)
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.
-12.852-7.2070.69-3.155-3.1810.031
Interaction energy analysis for fragmet #1(A:238:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.050 / q_NPA : 0.021
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].
4A239SER0-0.0490.0753.7251.1721.455-0.001-0.116-0.1650.000
5A240LYS00.043-0.1062.945-1.3200.7580.032-1.067-1.0430.004
6A240LYS10.8601.0624.047-0.152-0.051-0.001-0.019-0.0810.000
7A241THR00.102-0.0614.130-1.527-1.2280.008-0.071-0.2360.001
8A241THR0-0.0790.0532.703-7.697-5.1610.613-1.701-1.4480.025
9A242PHE00.048-0.0795.107-0.894-0.893-0.002-0.0080.0080.000
10A242PHE0-0.0540.0978.786-0.181-0.1810.0000.0000.0000.000
11A243LEU00.089-0.1188.1370.1090.1090.0000.0000.0000.000
12A243LEU0-0.0650.1108.2270.0130.0130.0000.0000.0000.000
13A244SER00.016-0.06410.349-0.178-0.1780.0000.0000.0000.000
14A244SER0-0.0030.06814.1240.0660.0660.0000.0000.0000.000
15A245GLU00.098-0.13314.0720.0920.0920.0000.0000.0000.000
16A245GLU-1-0.992-0.79916.9270.5690.5690.0000.0000.0000.000
17A246HIS00.043-0.09317.321-0.033-0.0330.0000.0000.0000.000
18A246HIS0-0.0770.11017.3060.1090.1090.0000.0000.0000.000
19A247SER00.112-0.03420.5580.0030.0030.0000.0000.0000.000
20A247SER0-0.0620.03125.255-0.004-0.0040.0000.0000.0000.000
21A248LEU00.064-0.11523.6970.0370.0370.0000.0000.0000.000
22A248LEU0-0.0800.10524.832-0.006-0.0060.0000.0000.0000.000
23A249ASP00.015-0.12525.8150.0030.0030.0000.0000.0000.000
24A249ASP-1-0.869-0.78326.3880.3620.3620.0000.0000.0000.000
25A250MET00.073-0.10922.264-0.014-0.0140.0000.0000.0000.000
26A250MET0-0.1100.08918.8170.0030.0030.0000.0000.0000.000
27A251LYS00.101-0.08922.1010.0430.0430.0000.0000.0000.000
28A251LYS10.8751.05724.913-0.311-0.3110.0000.0000.0000.000
29A252PHE00.025-0.11620.0290.0190.0190.0000.0000.0000.000
30A252PHE0-0.0730.11316.0440.0190.0190.0000.0000.0000.000
31A253SER00.044-0.09020.126-0.062-0.0620.0000.0000.0000.000
32A253SER0-0.0610.04720.8570.0080.0080.0000.0000.0000.000
33A254TYR00.064-0.12417.415-0.068-0.0680.0000.0000.0000.000
34A254TYR0-0.0650.10212.8840.0400.0400.0000.0000.0000.000
35A255CYS00.103-0.12514.5010.0910.0910.0000.0000.0000.000
36A255CYS0-0.1390.12113.5020.0210.0210.0000.0000.0000.000
37A256ASP00.151-0.05710.430-0.206-0.2060.0000.0000.0000.000
38A256ASP-1-0.904-0.8018.2451.9981.9980.0000.0000.0000.000
39A257GLU00.123-0.12511.7560.0770.0770.0000.0000.0000.000
40A257GLU-1-0.981-0.82212.0910.2500.2500.0000.0000.0000.000
41A258ARG00.008-0.1227.890-0.292-0.2920.0000.0000.0000.000
42A258ARG10.7881.0203.219-4.591-4.2440.041-0.173-0.2160.001
43A259ILE00.063-0.1259.3450.0320.0320.0000.0000.0000.000
44A259ILE0-0.0720.10012.2770.0150.0150.0000.0000.0000.000
45A260THR00.001-0.10811.795-0.040-0.0400.0000.0000.0000.000
46A260THR0-0.0050.08913.9800.0000.0000.0000.0000.0000.000
47A261GLU00.012-0.12411.199-0.021-0.0210.0000.0000.0000.000
48A261GLU-1-1.020-0.8559.335-0.741-0.7410.0000.0000.0000.000
49A262LEU0-0.003-0.12310.561-0.200-0.2000.0000.0000.0000.000
50A262LEU0-0.0860.1037.2110.0690.0690.0000.0000.0000.000
51A263MET00.001-0.15011.590-0.054-0.0540.0000.0000.0000.000
52A263MET0-0.0760.11112.3300.0010.0010.0000.0000.0000.000
53A264GLY0-0.005-0.11215.031-0.043-0.0430.0000.0000.0000.000
54A265TYR00.048-0.02016.855-0.070-0.0700.0000.0000.0000.000
55A265TYR0-0.1130.04617.030-0.016-0.0160.0000.0000.0000.000
56A266GLU00.116-0.07816.4720.0570.0570.0000.0000.0000.000
57A266GLU-1-0.978-0.82918.4470.2060.2060.0000.0000.0000.000
58A267PRO00.020-0.09615.1320.0130.0130.0000.0000.0000.000
59A268GLU00.088-0.05117.7750.0300.0300.0000.0000.0000.000
60A268GLU-1-0.988-0.83121.1100.2220.2220.0000.0000.0000.000
61A269GLU0-0.028-0.14020.971-0.020-0.0200.0000.0000.0000.000
62A269GLU-1-0.916-0.82721.0740.2670.2670.0000.0000.0000.000
63A270LEU00.018-0.12419.734-0.038-0.0380.0000.0000.0000.000
64A270LEU0-0.0620.11917.1080.0110.0110.0000.0000.0000.000
65A271LEU00.083-0.12921.1870.0260.0260.0000.0000.0000.000
66A271LEU0-0.0980.14120.379-0.005-0.0050.0000.0000.0000.000
67A272GLY0-0.042-0.11422.454-0.040-0.0400.0000.0000.0000.000
68A273ARG00.021-0.05423.851-0.031-0.0310.0000.0000.0000.000
69A273ARG10.8961.11723.594-0.289-0.2890.0000.0000.0000.000
70A274SER00.141-0.03623.2070.0460.0460.0000.0000.0000.000
71A274SER0-0.0240.06225.3450.0080.0080.0000.0000.0000.000
72A275ILE00.079-0.09520.136-0.039-0.0390.0000.0000.0000.000
73A275ILE0-0.0620.12416.9840.0100.0100.0000.0000.0000.000
74A276TYR00.068-0.11121.3330.0210.0210.0000.0000.0000.000
75A276TYR0-0.1310.03223.770-0.012-0.0120.0000.0000.0000.000
76A277GLU00.010-0.15323.898-0.019-0.0190.0000.0000.0000.000
77A277GLU-1-1.011-0.84324.5350.3070.3070.0000.0000.0000.000
78A278TYR00.046-0.08720.735-0.044-0.0440.0000.0000.0000.000
79A278TYR0-0.0960.08220.0630.0100.0100.0000.0000.0000.000
80A279TYR00.058-0.11420.7670.0190.0190.0000.0000.0000.000
81A279TYR00.0010.12518.195-0.016-0.0160.0000.0000.0000.000
82A280HIS00.148-0.04321.543-0.039-0.0390.0000.0000.0000.000
83A280HIS0-0.1220.07622.0210.0030.0030.0000.0000.0000.000
84A281ALA00.141-0.08023.4750.0230.0230.0000.0000.0000.000
85A281ALA0-0.0950.09928.260-0.006-0.0060.0000.0000.0000.000
86A282LEU0-0.005-0.13526.006-0.005-0.0050.0000.0000.0000.000
87A282LEU0-0.0840.08625.547-0.004-0.0040.0000.0000.0000.000
88A283ASP00.020-0.12122.321-0.022-0.0220.0000.0000.0000.000
89A283ASP-1-0.846-0.79021.4250.4320.4320.0000.0000.0000.000
90A284SER00.048-0.09023.7120.0370.0370.0000.0000.0000.000
91A284SER00.0110.09425.599-0.009-0.0090.0000.0000.0000.000
92A285ASP00.108-0.09925.4170.0230.0230.0000.0000.0000.000
93A285ASP-1-1.023-0.83928.3350.2550.2550.0000.0000.0000.000
94A286HIS00.052-0.09724.695-0.007-0.0070.0000.0000.0000.000
95A286HIS0-0.0880.07920.276-0.002-0.0020.0000.0000.0000.000
96A287LEU00.063-0.12222.0700.0100.0100.0000.0000.0000.000
97A287LEU0-0.0720.12519.0660.0120.0120.0000.0000.0000.000
98A288THR00.091-0.07522.7960.0300.0300.0000.0000.0000.000
99A288THR0-0.0550.07626.668-0.006-0.0060.0000.0000.0000.000
100A289LYS00.054-0.12125.906-0.003-0.0030.0000.0000.0000.000
101A289LYS10.7551.05226.299-0.301-0.3010.0000.0000.0000.000
102A290THR00.034-0.09522.004-0.028-0.0280.0000.0000.0000.000
103A290THR0-0.0240.07819.9750.0140.0140.0000.0000.0000.000
104A291HIS00.089-0.09422.9040.0180.0180.0000.0000.0000.000
105A291HIS0-0.0260.13819.255-0.048-0.0480.0000.0000.0000.000
106A292HIS00.086-0.07323.6840.0000.0000.0000.0000.0000.000
107A292HIS0-0.1150.06728.0060.0000.0000.0000.0000.0000.000
108A293ASP00.092-0.11125.755-0.017-0.0170.0000.0000.0000.000
109A293ASP-1-0.972-0.84124.7510.3400.3400.0000.0000.0000.000
110A294MET00.121-0.11722.791-0.018-0.0180.0000.0000.0000.000
111A294MET0-0.0850.13220.9810.0360.0360.0000.0000.0000.000
112A295PHE00.009-0.12623.5070.0170.0170.0000.0000.0000.000
113A295PHE0-0.0860.10725.725-0.002-0.0020.0000.0000.0000.000
114A296THR00.024-0.08126.282-0.015-0.0150.0000.0000.0000.000
115A296THR0-0.0600.05527.963-0.011-0.0110.0000.0000.0000.000
116A297LYS0-0.025-0.11224.229-0.027-0.0270.0000.0000.0000.000
117A297LYS10.8921.07123.600-0.381-0.3810.0000.0000.0000.000
118A298GLY00.009-0.07923.112-0.005-0.0050.0000.0000.0000.000
119A299GLN00.143-0.02018.9460.0350.0350.0000.0000.0000.000
120A299GLN0-0.1300.08916.102-0.036-0.0360.0000.0000.0000.000
121A300VAL0-0.076-0.13918.342-0.059-0.0590.0000.0000.0000.000
122A300VAL0-0.0450.12318.932-0.008-0.0080.0000.0000.0000.000
123A301THR00.050-0.09915.8670.0980.0980.0000.0000.0000.000
124A301THR0-0.0250.08814.2490.0310.0310.0000.0000.0000.000
125A302THR0-0.011-0.10316.020-0.113-0.1130.0000.0000.0000.000
126A302THR0-0.0450.05215.9970.0550.0550.0000.0000.0000.000
127A303GLY0-0.004-0.05316.073-0.098-0.0980.0000.0000.0000.000
128A304GLN00.1250.04015.6180.0920.0920.0000.0000.0000.000
129A304GLN0-0.1070.06714.5630.0080.0080.0000.0000.0000.000
130A305TYR00.063-0.09816.198-0.090-0.0900.0000.0000.0000.000
131A305TYR0-0.1130.06414.579-0.036-0.0360.0000.0000.0000.000
132A306ARG00.137-0.08716.5770.0860.0860.0000.0000.0000.000
133A306ARG10.7871.03518.577-0.317-0.3170.0000.0000.0000.000
134A307MET00.150-0.09417.021-0.044-0.0440.0000.0000.0000.000
135A307MET0-0.0840.11516.0600.0550.0550.0000.0000.0000.000
136A308LEU00.054-0.13818.0580.0000.0000.0000.0000.0000.000
137A308LEU0-0.1260.11221.729-0.008-0.0080.0000.0000.0000.000
138A309ALA00.135-0.08118.0450.0560.0560.0000.0000.0000.000
139A309ALA0-0.0730.12317.193-0.004-0.0040.0000.0000.0000.000
140A310LYS00.122-0.08318.794-0.033-0.0330.0000.0000.0000.000
141A310LYS10.8021.05820.036-0.202-0.2020.0000.0000.0000.000
142A311ARG0-0.039-0.14920.223-0.029-0.0290.0000.0000.0000.000
143A311ARG10.8971.07121.337-0.107-0.1070.0000.0000.0000.000
144A312GLY00.004-0.09219.9840.0150.0150.0000.0000.0000.000
145A313GLY0-0.0030.01021.119-0.014-0.0140.0000.0000.0000.000
146A314TYR00.0710.01519.2580.0210.0210.0000.0000.0000.000
147A314TYR0-0.0740.07119.356-0.013-0.0130.0000.0000.0000.000
148A315VAL00.081-0.11714.625-0.091-0.0910.0000.0000.0000.000
149A315VAL0-0.0470.14312.5290.0040.0040.0000.0000.0000.000
150A316TRP00.120-0.08414.5950.0270.0270.0000.0000.0000.000
151A316TRP0-0.1250.06314.226-0.025-0.0250.0000.0000.0000.000
152A317VAL00.066-0.11311.8820.0780.0780.0000.0000.0000.000
153A317VAL0-0.0270.12211.3720.0010.0010.0000.0000.0000.000
154A318GLU00.085-0.10411.323-0.255-0.2550.0000.0000.0000.000
155A318GLU-1-0.946-0.79411.3611.0001.0000.0000.0000.0000.000
156A319THR00.008-0.09511.0440.4180.4180.0000.0000.0000.000
157A319THR0-0.0610.06513.142-0.056-0.0560.0000.0000.0000.000
158A320GLN00.149-0.09112.025-0.259-0.2590.0000.0000.0000.000
159A320GLN0-0.1050.11311.9440.0270.0270.0000.0000.0000.000
160A321ALA00.091-0.10413.5730.1790.1790.0000.0000.0000.000
161A321ALA0-0.0440.11317.049-0.023-0.0230.0000.0000.0000.000
162A322THR0-0.013-0.10716.356-0.086-0.0860.0000.0000.0000.000
163A322THR0-0.0230.08715.410-0.017-0.0170.0000.0000.0000.000
164A323VAL00.106-0.09717.9270.0400.0400.0000.0000.0000.000
165A323VAL0-0.0620.12221.906-0.008-0.0080.0000.0000.0000.000
166A324ILE00.047-0.12421.400-0.011-0.0110.0000.0000.0000.000
167A324ILE0-0.0630.12918.448-0.006-0.0060.0000.0000.0000.000
168A325TYR00.068-0.10622.239-0.014-0.0140.0000.0000.0000.000
169A325TYR0-0.0330.11224.0760.0040.0040.0000.0000.0000.000
170A326ASN00.152-0.08525.9390.0050.0050.0000.0000.0000.000
171A326ASN0-0.1150.08129.259-0.011-0.0110.0000.0000.0000.000
172A327THR00.016-0.04328.637-0.002-0.0020.0000.0000.0000.000
173A327THR0-0.0380.04227.908-0.003-0.0030.0000.0000.0000.000
174A328LYS00.112-0.03530.104-0.006-0.0060.0000.0000.0000.000
175A328LYS10.8211.00331.042-0.219-0.2190.0000.0000.0000.000
176A329ASN00.081-0.05833.017-0.011-0.0110.0000.0000.0000.000
177A329ASN0-0.0360.09932.3590.0130.0130.0000.0000.0000.000
178A330SER0-0.013-0.04930.155-0.002-0.0020.0000.0000.0000.000
179A330SER0-0.0070.03330.848-0.005-0.0050.0000.0000.0000.000
180A331GLN00.043-0.11330.4330.0090.0090.0000.0000.0000.000
181A331GLN0-0.0860.09131.448-0.010-0.0100.0000.0000.0000.000
182A332PRO00.003-0.09826.2090.0070.0070.0000.0000.0000.000
183A333GLN00.1040.00725.606-0.026-0.0260.0000.0000.0000.000
184A333GLN0-0.1270.07624.862-0.021-0.0210.0000.0000.0000.000
185A334CYS00.000-0.11922.343-0.029-0.0290.0000.0000.0000.000
186A334CYS0-0.0900.09120.9630.0030.0030.0000.0000.0000.000
187A335ILE00.064-0.12620.096-0.021-0.0210.0000.0000.0000.000
188A335ILE0-0.0420.13218.2610.0010.0010.0000.0000.0000.000
189A336VAL00.129-0.07416.170-0.009-0.0090.0000.0000.0000.000
190A336VAL0-0.0780.10314.0910.0010.0010.0000.0000.0000.000
191A337CYS00.045-0.13913.904-0.034-0.0340.0000.0000.0000.000
192A337CYS0-0.1150.09813.802-0.069-0.0690.0000.0000.0000.000
193A338VAL00.112-0.0919.6100.0360.0360.0000.0000.0000.000
194A338VAL0-0.0740.1177.7420.0990.0990.0000.0000.0000.000
195A339ASN00.073-0.0919.468-0.139-0.1390.0000.0000.0000.000
196A339ASN0-0.0580.10410.211-0.284-0.2840.0000.0000.0000.000
197A340TYR00.101-0.0766.9470.8690.8690.0000.0000.0000.000
198A340TYR0-0.1300.0546.0880.1230.1230.0000.0000.0000.000
199A341VAL00.107-0.1247.470-0.603-0.6030.0000.0000.0000.000
200A341VAL0-0.1060.1307.444-0.087-0.0870.0000.0000.0000.000
201A342VAL0-0.023-0.1648.0600.0960.0960.0000.0000.0000.000
202A342VAL0-0.0200.1579.684-0.030-0.0300.0000.0000.0000.000
203A343SER0-0.123-0.16010.557-0.269-0.2690.0000.0000.0000.000
204A343SER00.0470.04813.8500.0140.0140.0000.0000.0000.000