FMODB

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

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

tag_button

FMODB ID: 8G6JY

Calculation Name: 1H2S-A-Xray547

Preferred Name:

Target Type:

Ligand Name: retinal | octyl beta-d-glucopyranoside

Ligand 3-letter code: RET | BOG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1H2S

Chain ID: A

ChEMBL ID:

UniProt ID: P42196

Base Structure: X-ray

Registration Date: 2025-09-03

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
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 225
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2562520.357285
FMO2-HF: Nuclear repulsion 2479293.63002
FMO2-HF: Total energy -83226.727265
FMO2-MP2: Total energy -83472.336528


3D Structure Molmil
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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
15.60916.735-0.013-0.491-0.623-0.001
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.885 / q_NPA : 0.926
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].
3A3GLY00.0770.0473.8770.9532.079-0.013-0.491-0.623-0.001
4A4LEU0-0.0190.0005.9394.4364.4360.0000.0000.0000.000
5A5THR00.0760.0357.5371.6771.6770.0000.0000.0000.000
6A6THR00.0070.0157.4542.6122.6120.0000.0000.0000.000
7A7LEU0-0.009-0.0059.8302.6252.6250.0000.0000.0000.000
8A8PHE00.0100.00312.0701.8581.8580.0000.0000.0000.000
9A9TRP00.0570.01611.2192.6122.6120.0000.0000.0000.000
10A10LEU0-0.029-0.00912.7151.4771.4770.0000.0000.0000.000
11A11GLY00.0380.02315.7421.2761.2760.0000.0000.0000.000
12A12ALA00.010-0.00217.5341.0861.0860.0000.0000.0000.000
13A13ILE0-0.010-0.00516.4601.0151.0150.0000.0000.0000.000
14A14GLY00.0210.01319.9410.8510.8510.0000.0000.0000.000
15A15MET0-0.030-0.00121.8601.0191.0190.0000.0000.0000.000
16A16LEU0-0.0130.01221.3300.7570.7570.0000.0000.0000.000
17A17VAL00.0000.00023.8150.6240.6240.0000.0000.0000.000
18A18GLY00.0290.01126.0170.5130.5130.0000.0000.0000.000
19A19THR0-0.003-0.01027.1710.5150.5150.0000.0000.0000.000
20A20LEU0-0.024-0.01127.1290.4620.4620.0000.0000.0000.000
21A21ALA00.0030.01230.2400.4170.4170.0000.0000.0000.000
22A22PHE00.002-0.00730.0160.3710.3710.0000.0000.0000.000
23A23ALA00.0130.00633.4340.3410.3410.0000.0000.0000.000
24A24TRP0-0.020-0.00934.5230.3090.3090.0000.0000.0000.000
25A25ALA0-0.019-0.01136.2060.2770.2770.0000.0000.0000.000
26A26GLY00.0310.00437.8340.2380.2380.0000.0000.0000.000
27A27ARG10.7850.90739.3688.0608.0600.0000.0000.0000.000
28A28ASP-1-0.819-0.92340.986-7.253-7.2530.0000.0000.0000.000
29A29ALA0-0.0430.00642.6130.1630.1630.0000.0000.0000.000
30A30GLY00.1180.06044.6530.0840.0840.0000.0000.0000.000
31A31SER0-0.022-0.03146.787-0.116-0.1160.0000.0000.0000.000
32A32GLY0-0.023-0.00148.200-0.023-0.0230.0000.0000.0000.000
33A33GLU-1-0.760-0.88743.796-7.321-7.3210.0000.0000.0000.000
34A34ARG10.8290.92342.1007.2417.2410.0000.0000.0000.000
35A35ARG11.0000.98841.5186.8196.8190.0000.0000.0000.000
36A36TYR0-0.0250.00540.172-0.168-0.1680.0000.0000.0000.000
37A37TYR00.0330.00337.609-0.323-0.3230.0000.0000.0000.000
38A38VAL0-0.0030.00036.415-0.291-0.2910.0000.0000.0000.000
39A39THR0-0.023-0.02136.116-0.230-0.2300.0000.0000.0000.000
40A40LEU0-0.031-0.00333.542-0.294-0.2940.0000.0000.0000.000
41A41VAL0-0.0040.00131.954-0.390-0.3900.0000.0000.0000.000
42A42GLY00.0010.00731.357-0.327-0.3270.0000.0000.0000.000
43A43ILE0-0.035-0.01929.733-0.387-0.3870.0000.0000.0000.000
44A44SER00.007-0.02527.290-0.279-0.2790.0000.0000.0000.000
45A45GLY00.0320.02126.436-0.555-0.5550.0000.0000.0000.000
46A46ILE0-0.028-0.02126.783-0.412-0.4120.0000.0000.0000.000
47A47ALA00.0490.02424.161-0.457-0.4570.0000.0000.0000.000
48A48ALA0-0.023-0.01322.477-0.841-0.8410.0000.0000.0000.000
49A49VAL0-0.0080.00521.617-0.804-0.8040.0000.0000.0000.000
50A50ALA00.0070.00921.332-0.683-0.6830.0000.0000.0000.000
51A51TYR0-0.044-0.05417.093-1.411-1.4110.0000.0000.0000.000
52A52VAL00.0160.00416.969-1.406-1.4060.0000.0000.0000.000
53A53VAL0-0.030-0.01316.763-0.980-0.9800.0000.0000.0000.000
54A54MET0-0.033-0.00315.236-0.796-0.7960.0000.0000.0000.000
55A55ALA00.0210.00012.836-1.992-1.9920.0000.0000.0000.000
56A56LEU0-0.052-0.02411.952-2.135-2.1350.0000.0000.0000.000
57A57GLY0-0.0160.00511.968-0.242-0.2420.0000.0000.0000.000
58A58VAL0-0.014-0.00412.5760.8090.8090.0000.0000.0000.000
59A59GLY00.020-0.00416.2390.0910.0910.0000.0000.0000.000
60A60TRP0-0.059-0.0458.485-0.814-0.8140.0000.0000.0000.000
61A61VAL00.0410.01015.4310.3240.3240.0000.0000.0000.000
62A62PRO0-0.021-0.01013.8590.0780.0780.0000.0000.0000.000
63A63VAL00.0210.02016.2370.5740.5740.0000.0000.0000.000
64A64ALA00.0300.00118.831-0.370-0.3700.0000.0000.0000.000
65A65GLU-1-0.927-0.95516.726-13.891-13.8910.0000.0000.0000.000
66A66ARG10.8200.92416.01313.74813.7480.0000.0000.0000.000
67A67THR0-0.071-0.04712.551-1.074-1.0740.0000.0000.0000.000
68A68VAL00.0070.02115.486-0.172-0.1720.0000.0000.0000.000
69A69PHE00.010-0.01012.423-0.461-0.4610.0000.0000.0000.000
70A70ALA00.0520.02517.7820.6460.6460.0000.0000.0000.000
71A71PRO00.009-0.00518.7400.6820.6820.0000.0000.0000.000
72A72ARG10.8670.92216.69717.35017.3500.0000.0000.0000.000
73A73TYR00.0140.00821.1510.3250.3250.0000.0000.0000.000
74A74ILE0-0.0060.00224.3640.5620.5620.0000.0000.0000.000
75A75ASP-1-0.782-0.88524.084-12.378-12.3780.0000.0000.0000.000
76A76TRP0-0.002-0.00822.6460.5720.5720.0000.0000.0000.000
77A77ILE0-0.0030.00927.6450.4870.4870.0000.0000.0000.000
78A78LEU0-0.022-0.00228.8470.4540.4540.0000.0000.0000.000
79A79THR0-0.048-0.04727.6460.4110.4110.0000.0000.0000.000
80A80THR00.002-0.01229.6150.3850.3850.0000.0000.0000.000
81A81PRO00.0280.01532.1990.3180.3180.0000.0000.0000.000
82A82LEU00.0170.00632.8080.3140.3140.0000.0000.0000.000
83A83ILE00.0240.01330.5100.2180.2180.0000.0000.0000.000
84A84VAL00.007-0.00135.0830.2620.2620.0000.0000.0000.000
85A85TYR0-0.0110.00038.0450.2880.2880.0000.0000.0000.000
86A86PHE00.0100.00037.4930.2350.2350.0000.0000.0000.000
87A87LEU0-0.012-0.01036.7530.2290.2290.0000.0000.0000.000
88A88GLY00.0510.01640.5530.2130.2130.0000.0000.0000.000
89A89LEU0-0.022-0.00541.7580.2490.2490.0000.0000.0000.000
90A90LEU0-0.046-0.00840.9230.1840.1840.0000.0000.0000.000
91A91ALA00.008-0.00544.6630.1690.1690.0000.0000.0000.000
92A92GLY0-0.063-0.01546.6080.1690.1690.0000.0000.0000.000
93A93LEU0-0.0180.00744.9320.0950.0950.0000.0000.0000.000
94A94ASP-1-0.779-0.87848.706-6.321-6.3210.0000.0000.0000.000
95A95SER0-0.005-0.03648.132-0.163-0.1630.0000.0000.0000.000
96A96ARG10.8970.96647.9456.3216.3210.0000.0000.0000.000
97A97GLU-1-0.850-0.93648.019-6.581-6.5810.0000.0000.0000.000
98A98PHE0-0.001-0.00642.988-0.219-0.2190.0000.0000.0000.000
99A99GLY00.0180.01243.469-0.196-0.1960.0000.0000.0000.000
100A100ILE0-0.047-0.00143.879-0.136-0.1360.0000.0000.0000.000
101A101VAL00.0430.01141.197-0.181-0.1810.0000.0000.0000.000
102A102ILE00.0030.00538.641-0.277-0.2770.0000.0000.0000.000
103A103THR0-0.023-0.00938.695-0.243-0.2430.0000.0000.0000.000
104A104LEU0-0.020-0.01339.090-0.174-0.1740.0000.0000.0000.000
105A105ASN00.031-0.00533.554-0.248-0.2480.0000.0000.0000.000
106A106THR0-0.028-0.02934.495-0.369-0.3690.0000.0000.0000.000
107A107VAL0-0.013-0.00334.591-0.232-0.2320.0000.0000.0000.000
108A108VAL0-0.035-0.01031.578-0.205-0.2050.0000.0000.0000.000
109A109MET0-0.015-0.00129.094-0.467-0.4670.0000.0000.0000.000
110A110LEU0-0.015-0.01029.727-0.387-0.3870.0000.0000.0000.000
111A111ALA0-0.0120.01130.940-0.181-0.1810.0000.0000.0000.000
112A112GLY00.0110.00628.183-0.211-0.2110.0000.0000.0000.000
113A113PHE0-0.008-0.01324.509-0.516-0.5160.0000.0000.0000.000
114A114ALA00.0140.00626.329-0.332-0.3320.0000.0000.0000.000
115A115GLY00.0450.00527.776-0.139-0.1390.0000.0000.0000.000
116A116ALA0-0.047-0.02122.640-0.262-0.2620.0000.0000.0000.000
117A117MET0-0.044-0.02021.151-0.767-0.7670.0000.0000.0000.000
118A118VAL00.0040.02224.7240.1000.1000.0000.0000.0000.000
119A119PRO0-0.002-0.01024.532-0.135-0.1350.0000.0000.0000.000
120A120GLY00.0300.02326.3660.4060.4060.0000.0000.0000.000
121A121ILE00.015-0.01028.634-0.269-0.2690.0000.0000.0000.000
122A122GLU-1-0.886-0.93531.125-9.354-9.3540.0000.0000.0000.000
123A123ARG10.8300.90324.48912.19812.1980.0000.0000.0000.000
124A124TYR00.010-0.00426.848-0.184-0.1840.0000.0000.0000.000
125A125ALA00.0000.01231.7020.1910.1910.0000.0000.0000.000
126A126LEU0-0.008-0.00130.9240.1360.1360.0000.0000.0000.000
127A127PHE00.0170.00328.7290.1190.1190.0000.0000.0000.000
128A128GLY00.0140.00631.7930.1000.1000.0000.0000.0000.000
129A129MET0-0.009-0.00235.2410.2670.2670.0000.0000.0000.000
130A130GLY00.0380.00933.3490.1370.1370.0000.0000.0000.000
131A131ALA0-0.003-0.00433.8580.0700.0700.0000.0000.0000.000
132A132VAL00.003-0.00235.1670.1580.1580.0000.0000.0000.000
133A133ALA00.0010.00636.8710.1810.1810.0000.0000.0000.000
134A134PHE00.005-0.00134.1150.0870.0870.0000.0000.0000.000
135A135LEU00.0000.00036.6350.1140.1140.0000.0000.0000.000
136A136GLY00.0170.01539.4330.1830.1830.0000.0000.0000.000
137A137LEU0-0.010-0.01436.1800.1570.1570.0000.0000.0000.000
138A138VAL00.002-0.00337.2810.0850.0850.0000.0000.0000.000
139A139TYR0-0.0010.00540.0240.1470.1470.0000.0000.0000.000
140A140TYR00.0240.00243.0910.1360.1360.0000.0000.0000.000
141A141LEU00.0340.01338.0400.0900.0900.0000.0000.0000.000
142A142VAL0-0.032-0.01841.5950.0630.0630.0000.0000.0000.000
143A143GLY00.0400.03044.1730.1310.1310.0000.0000.0000.000
144A144PRO00.0500.02847.366-0.026-0.0260.0000.0000.0000.000
145A145MET0-0.0200.00741.6950.0260.0260.0000.0000.0000.000
146A146THR00.0070.00845.384-0.060-0.0600.0000.0000.0000.000
147A147GLU-1-0.945-0.95947.303-6.133-6.1330.0000.0000.0000.000
148A148SER00.016-0.00449.1260.1360.1360.0000.0000.0000.000
149A149ALA00.0220.00446.6500.0590.0590.0000.0000.0000.000
150A150SER0-0.121-0.07248.7460.0040.0040.0000.0000.0000.000
151A151GLN0-0.0160.01351.7380.1900.1900.0000.0000.0000.000
152A152ARG10.8230.92947.7346.6556.6550.0000.0000.0000.000
153A153SER00.014-0.01250.2590.0650.0650.0000.0000.0000.000
154A154SER00.0300.00550.207-0.093-0.0930.0000.0000.0000.000
155A155GLY0-0.005-0.01247.304-0.137-0.1370.0000.0000.0000.000
156A156ILE0-0.0060.00245.766-0.220-0.2200.0000.0000.0000.000
157A157LYS10.8970.94945.4506.3576.3570.0000.0000.0000.000
158A158SER00.001-0.00345.022-0.217-0.2170.0000.0000.0000.000
159A159LEU0-0.020-0.01539.190-0.188-0.1880.0000.0000.0000.000
160A160TYR0-0.010-0.01840.799-0.254-0.2540.0000.0000.0000.000
161A161VAL0-0.006-0.00841.166-0.176-0.1760.0000.0000.0000.000
162A162ARG10.8970.96337.7637.6247.6240.0000.0000.0000.000
163A163LEU00.0240.01335.473-0.238-0.2380.0000.0000.0000.000
164A164ARG10.8730.94036.4197.2667.2660.0000.0000.0000.000
165A165ASN0-0.005-0.00237.611-0.058-0.0580.0000.0000.0000.000
166A166LEU0-0.0170.00331.091-0.171-0.1710.0000.0000.0000.000
167A167THR00.002-0.01632.679-0.356-0.3560.0000.0000.0000.000
168A168VAL0-0.013-0.01333.313-0.218-0.2180.0000.0000.0000.000
169A169ILE0-0.021-0.01032.301-0.110-0.1100.0000.0000.0000.000
170A170LEU00.0090.00128.242-0.259-0.2590.0000.0000.0000.000
171A171TRP0-0.012-0.01429.025-0.318-0.3180.0000.0000.0000.000
172A172ALA00.0100.00930.263-0.129-0.1290.0000.0000.0000.000
173A173ILE0-0.022-0.01125.611-0.082-0.0820.0000.0000.0000.000
174A174TYR00.003-0.02124.600-0.241-0.2410.0000.0000.0000.000
175A175PRO0-0.0050.00425.465-0.421-0.4210.0000.0000.0000.000
176A176PHE00.0260.00926.870-0.066-0.0660.0000.0000.0000.000
177A177ILE00.0110.01120.525-0.307-0.3070.0000.0000.0000.000
178A178TRP0-0.075-0.03422.095-0.522-0.5220.0000.0000.0000.000
179A179LEU00.001-0.00523.631-0.190-0.1900.0000.0000.0000.000
180A180LEU00.0160.00922.637-0.056-0.0560.0000.0000.0000.000
181A181GLY00.0320.02819.186-0.537-0.5370.0000.0000.0000.000
182A182PRO0-0.011-0.01016.1560.4980.4980.0000.0000.0000.000
183A183PRO00.0060.01718.8520.2700.2700.0000.0000.0000.000
184A184GLY00.0390.04022.3700.4570.4570.0000.0000.0000.000
185A185VAL0-0.026-0.02323.346-0.085-0.0850.0000.0000.0000.000
186A186ALA0-0.055-0.01318.040-0.188-0.1880.0000.0000.0000.000
187A187LEU00.0180.01518.481-0.511-0.5110.0000.0000.0000.000
188A188LEU0-0.049-0.01917.484-0.606-0.6060.0000.0000.0000.000
189A189THR00.0590.01512.148-0.133-0.1330.0000.0000.0000.000
190A190PRO00.0870.02011.3260.1610.1610.0000.0000.0000.000
191A191THR0-0.020-0.0138.770-0.324-0.3240.0000.0000.0000.000
192A192VAL00.0050.01411.2890.3720.3720.0000.0000.0000.000
193A193ASP-1-0.792-0.87614.673-16.574-16.5740.0000.0000.0000.000
194A194VAL0-0.002-0.00113.0050.8630.8630.0000.0000.0000.000
195A195ALA0-0.015-0.00113.6890.6250.6250.0000.0000.0000.000
196A196LEU0-0.010-0.00715.4550.9590.9590.0000.0000.0000.000
197A197ILE0-0.0010.00018.6300.8380.8380.0000.0000.0000.000
198A198VAL00.0100.01215.5910.6790.6790.0000.0000.0000.000
199A199TYR0-0.022-0.00918.8370.7720.7720.0000.0000.0000.000
200A200LEU00.0410.01220.9320.6860.6860.0000.0000.0000.000
201A201ASP-1-0.714-0.80621.956-13.174-13.1740.0000.0000.0000.000
202A202LEU0-0.015-0.00519.8250.5670.5670.0000.0000.0000.000
203A203VAL0-0.009-0.00623.9250.5990.5990.0000.0000.0000.000
204A204THR0-0.050-0.04926.7490.5420.5420.0000.0000.0000.000
205A205LYS10.8200.92725.35612.65112.6510.0000.0000.0000.000
206A206VAL0-0.001-0.00225.3140.3890.3890.0000.0000.0000.000
207A207GLY00.004-0.00127.9680.3370.3370.0000.0000.0000.000
208A208PHE00.011-0.00229.7000.4200.4200.0000.0000.0000.000
209A209GLY00.0440.01631.6080.3380.3380.0000.0000.0000.000
210A210PHE0-0.002-0.01828.6040.2770.2770.0000.0000.0000.000
211A211ILE0-0.016-0.00333.4100.3010.3010.0000.0000.0000.000
212A212ALA0-0.013-0.01035.8490.2970.2970.0000.0000.0000.000
213A213LEU0-0.050-0.03134.4120.2210.2210.0000.0000.0000.000
214A214ASP-1-0.974-0.97137.373-7.959-7.9590.0000.0000.0000.000
215A215ALA00.001-0.00439.1180.2280.2280.0000.0000.0000.000
216A216ALA00.0060.00341.1930.2300.2300.0000.0000.0000.000
217A217ALA0-0.016-0.00642.9780.1690.1690.0000.0000.0000.000
218A218THR00.007-0.00545.0150.1840.1840.0000.0000.0000.000
219A219LEU0-0.043-0.02843.7190.1380.1380.0000.0000.0000.000
220A220ARG10.8830.95943.6657.2097.2090.0000.0000.0000.000
221A221ALA00.0590.04249.3330.1390.1390.0000.0000.0000.000
222A222GLU-1-0.844-0.90049.872-6.317-6.3170.0000.0000.0000.000
223A223HIS0-0.081-0.04050.8980.2080.2080.0000.0000.0000.000
224A224GLY0-0.055-0.01854.4910.1070.1070.0000.0000.0000.000
225A225GLU-2-1.868-1.93750.886-12.531-12.5310.0000.0000.0000.000