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

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FMODB ID: 9LZZ2

Calculation Name: 1OY2-A-Other547

Preferred Name: SHC-transforming protein 1

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1OY2

Chain ID: A

ChEMBL ID: CHEMBL5626

UniProt ID: P29353

Base Structure: SolutionNMR

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
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 191
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1899145.296711
FMO2-HF: Nuclear repulsion 1823895.630197
FMO2-HF: Total energy -75249.666514
FMO2-MP2: Total energy -75462.440715


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:17:GLY)


Summations of interaction energy for fragment #1(A:17: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.
7.0277.8040.002-0.474-0.304-0.002
Interaction energy analysis for fragmet #1(A:17:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.836 / q_NPA : 0.911
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].
3A19LEU00.0310.0063.807-8.591-7.8140.002-0.474-0.304-0.002
4A20GLY00.0000.0186.4924.7804.7800.0000.0000.0000.000
5A21GLY0-0.013-0.0177.803-4.767-4.7670.0000.0000.0000.000
6A22GLU-1-0.958-0.98310.202-17.346-17.3460.0000.0000.0000.000
7A23GLU-1-0.940-0.95011.000-25.149-25.1490.0000.0000.0000.000
8A24TRP0-0.044-0.02913.2150.1630.1630.0000.0000.0000.000
9A25THR00.0190.01016.8730.3060.3060.0000.0000.0000.000
10A26ARG10.9270.96320.51914.06614.0660.0000.0000.0000.000
11A27HIS00.0280.01818.7670.6700.6700.0000.0000.0000.000
12A28GLY0-0.0030.00423.6790.4100.4100.0000.0000.0000.000
13A29SER00.0280.01226.509-0.211-0.2110.0000.0000.0000.000
14A30PHE00.007-0.00627.924-0.020-0.0200.0000.0000.0000.000
15A31VAL0-0.028-0.00630.8580.2100.2100.0000.0000.0000.000
16A32ASN00.0290.00133.2740.0070.0070.0000.0000.0000.000
17A33LYS10.9370.96935.5608.6878.6870.0000.0000.0000.000
18A34PRO00.0230.03135.533-0.243-0.2430.0000.0000.0000.000
19A35THR0-0.003-0.01632.5620.0730.0730.0000.0000.0000.000
20A36ARG10.9260.97136.0588.2648.2640.0000.0000.0000.000
21A37GLY00.0460.01833.143-0.061-0.0610.0000.0000.0000.000
22A38TRP0-0.058-0.04232.1990.1680.1680.0000.0000.0000.000
23A39LEU00.0090.03334.082-0.186-0.1860.0000.0000.0000.000
24A40HIS00.006-0.01735.6360.2370.2370.0000.0000.0000.000
25A41PRO0-0.0060.01132.7710.0180.0180.0000.0000.0000.000
26A42ASN00.042-0.00329.5060.1990.1990.0000.0000.0000.000
27A43ASP-1-0.887-0.94327.859-11.956-11.9560.0000.0000.0000.000
28A44LYS10.9420.97628.0329.2569.2560.0000.0000.0000.000
29A45VAL0-0.022-0.02127.9220.0130.0130.0000.0000.0000.000
30A46MET0-0.029-0.00724.252-0.354-0.3540.0000.0000.0000.000
31A47GLY00.0470.03723.252-0.621-0.6210.0000.0000.0000.000
32A48PRO0-0.105-0.04024.370-0.283-0.2830.0000.0000.0000.000
33A49GLY00.0480.03326.954-0.161-0.1610.0000.0000.0000.000
34A50VAL0-0.093-0.05127.9750.3490.3490.0000.0000.0000.000
35A51SER00.0170.00629.948-0.125-0.1250.0000.0000.0000.000
36A52TYR00.0260.00031.8950.2640.2640.0000.0000.0000.000
37A53LEU0-0.021-0.00934.794-0.159-0.1590.0000.0000.0000.000
38A54VAL0-0.019-0.00834.9700.2380.2380.0000.0000.0000.000
39A55ARG10.9350.97436.8617.4777.4770.0000.0000.0000.000
40A56TYR0-0.006-0.00632.8560.0280.0280.0000.0000.0000.000
41A57MET0-0.035-0.00336.4590.1950.1950.0000.0000.0000.000
42A58GLY00.0140.00837.312-0.166-0.1660.0000.0000.0000.000
43A59CYS00.0020.00535.086-0.023-0.0230.0000.0000.0000.000
44A60VAL0-0.029-0.01637.8110.2410.2410.0000.0000.0000.000
45A61GLU-1-0.903-0.94437.911-8.517-8.5170.0000.0000.0000.000
46A62VAL0-0.029-0.02440.0440.3090.3090.0000.0000.0000.000
47A63LEU00.0530.01941.020-0.144-0.1440.0000.0000.0000.000
48A64GLN00.0080.02642.5080.1870.1870.0000.0000.0000.000
49A65SER0-0.022-0.02142.618-0.146-0.1460.0000.0000.0000.000
50A66MET00.0210.01343.7960.0090.0090.0000.0000.0000.000
51A67ARG10.9460.98046.7796.2216.2210.0000.0000.0000.000
52A68ALA00.0400.02147.7410.0160.0160.0000.0000.0000.000
53A69LEU0-0.036-0.00649.8340.1290.1290.0000.0000.0000.000
54A70ASP-1-0.886-0.94851.815-5.804-5.8040.0000.0000.0000.000
55A71PHE0-0.026-0.00849.088-0.077-0.0770.0000.0000.0000.000
56A72ASN0-0.050-0.00747.517-0.164-0.1640.0000.0000.0000.000
57A73THR00.076-0.02146.1040.1520.1520.0000.0000.0000.000
58A74ARG10.9020.96239.8527.6817.6810.0000.0000.0000.000
59A75THR00.0660.04345.899-0.048-0.0480.0000.0000.0000.000
60A76GLN00.0180.00948.393-0.075-0.0750.0000.0000.0000.000
61A77VAL00.0330.00643.9110.0430.0430.0000.0000.0000.000
62A78THR00.0270.00543.489-0.097-0.0970.0000.0000.0000.000
63A79ARG11.0211.01845.3915.9315.9310.0000.0000.0000.000
64A80GLU-1-0.886-0.92848.571-6.305-6.3050.0000.0000.0000.000
65A81ALA00.014-0.00243.241-0.026-0.0260.0000.0000.0000.000
66A82ILE00.0240.01443.757-0.080-0.0800.0000.0000.0000.000
67A83SER0-0.023-0.02945.4840.0550.0550.0000.0000.0000.000
68A84LEU0-0.032-0.01345.7810.0430.0430.0000.0000.0000.000
69A85VAL00.002-0.00741.142-0.011-0.0110.0000.0000.0000.000
70A86CYS0-0.0300.00544.2770.0520.0520.0000.0000.0000.000
71A87GLU-1-0.826-0.90847.014-6.010-6.0100.0000.0000.0000.000
72A88ALA0-0.058-0.01744.4950.0620.0620.0000.0000.0000.000
73A89VAL0-0.035-0.01643.027-0.015-0.0150.0000.0000.0000.000
74A90PRO00.0080.00345.8420.0290.0290.0000.0000.0000.000
75A91GLY0-0.044-0.02447.9710.1050.1050.0000.0000.0000.000
76A92ALA00.0460.03145.3110.0160.0160.0000.0000.0000.000
77A93LYS10.8620.94147.3196.3356.3350.0000.0000.0000.000
78A94GLY00.0650.01949.2230.0060.0060.0000.0000.0000.000
79A95ALA00.0150.00450.1740.1140.1140.0000.0000.0000.000
80A96THR0-0.051-0.03050.7150.1980.1980.0000.0000.0000.000
81A97ARG10.9930.97452.4465.4265.4260.0000.0000.0000.000
82A98ARG10.8950.95153.1085.8415.8410.0000.0000.0000.000
83A99ARG11.0070.99452.6125.8865.8860.0000.0000.0000.000
84A100LYS10.8570.94054.0565.5215.5210.0000.0000.0000.000
85A101PRO00.0880.05953.861-0.025-0.0250.0000.0000.0000.000
86A102CYS0-0.054-0.03154.4260.1610.1610.0000.0000.0000.000
87A103SER00.0280.01255.299-0.064-0.0640.0000.0000.0000.000
88A104ARG10.8910.94855.2775.5475.5470.0000.0000.0000.000
89A105PRO00.0520.03649.756-0.019-0.0190.0000.0000.0000.000
90A106LEU0-0.015-0.01653.1130.0950.0950.0000.0000.0000.000
91A107SER00.004-0.01652.127-0.087-0.0870.0000.0000.0000.000
92A108SER0-0.035-0.01051.0560.0110.0110.0000.0000.0000.000
93A109ILE0-0.034-0.02747.503-0.150-0.1500.0000.0000.0000.000
94A110LEU00.0030.00944.8970.0230.0230.0000.0000.0000.000
95A111GLY00.0150.02344.5980.0670.0670.0000.0000.0000.000
96A112ARG10.9070.94742.2267.4507.4500.0000.0000.0000.000
97A113SER00.0320.02941.944-0.173-0.1730.0000.0000.0000.000
98A114ASN0-0.067-0.04237.2290.0770.0770.0000.0000.0000.000
99A115LEU00.0860.04339.912-0.117-0.1170.0000.0000.0000.000
100A116LYS10.9050.95432.6039.3599.3590.0000.0000.0000.000
101A117PHE00.0330.00531.174-0.240-0.2400.0000.0000.0000.000
102A118ALA00.0060.00536.259-0.081-0.0810.0000.0000.0000.000
103A119GLY00.0280.00239.2710.1030.1030.0000.0000.0000.000
104A120MET0-0.0030.01133.2820.1290.1290.0000.0000.0000.000
105A121PRO00.006-0.00737.169-0.163-0.1630.0000.0000.0000.000
106A122ILE0-0.080-0.03031.784-0.143-0.1430.0000.0000.0000.000
107A123THR00.0390.01331.6200.2360.2360.0000.0000.0000.000
108A124LEU00.0050.00430.269-0.412-0.4120.0000.0000.0000.000
109A125THR00.017-0.00227.1140.2890.2890.0000.0000.0000.000
110A126VAL0-0.041-0.01227.862-0.296-0.2960.0000.0000.0000.000
111A127SER00.0590.02224.2480.0870.0870.0000.0000.0000.000
112A128THR0-0.009-0.01523.5890.3340.3340.0000.0000.0000.000
113A129SER0-0.054-0.03122.935-0.417-0.4170.0000.0000.0000.000
114A130SER00.0270.01920.997-0.444-0.4440.0000.0000.0000.000
115A131LEU0-0.006-0.00823.6010.5110.5110.0000.0000.0000.000
116A132ASN00.0070.02420.920-0.159-0.1590.0000.0000.0000.000
117A133LEU00.0260.00725.2600.4480.4480.0000.0000.0000.000
118A134MET0-0.0020.00626.803-0.467-0.4670.0000.0000.0000.000
119A135ALA00.000-0.00329.1160.4250.4250.0000.0000.0000.000
120A136ALA00.0290.01931.7820.0160.0160.0000.0000.0000.000
121A137ASP-1-0.914-0.94934.499-8.173-8.1730.0000.0000.0000.000
122A138CYS0-0.009-0.01633.0360.0160.0160.0000.0000.0000.000
123A139LYS10.8460.92632.6788.7738.7730.0000.0000.0000.000
124A140GLN00.0150.01127.885-0.262-0.2620.0000.0000.0000.000
125A141ILE00.003-0.00423.6140.1810.1810.0000.0000.0000.000
126A142ILE0-0.020-0.00525.873-0.046-0.0460.0000.0000.0000.000
127A143ALA00.0350.02121.388-0.085-0.0850.0000.0000.0000.000
128A144ASN0-0.039-0.04123.1050.4800.4800.0000.0000.0000.000
129A145HIS00.0320.01118.946-0.178-0.1780.0000.0000.0000.000
130A146HIS00.0110.03121.640-0.636-0.6360.0000.0000.0000.000
131A147MET0-0.038-0.03124.105-0.088-0.0880.0000.0000.0000.000
132A148GLN00.000-0.00121.155-0.246-0.2460.0000.0000.0000.000
133A149SER00.0390.01524.366-0.045-0.0450.0000.0000.0000.000
134A150ILE00.0220.03427.2860.3720.3720.0000.0000.0000.000
135A151SER0-0.065-0.04429.877-0.220-0.2200.0000.0000.0000.000
136A152PHE0-0.014-0.01332.5070.1090.1090.0000.0000.0000.000
137A153ALA00.0820.06036.324-0.014-0.0140.0000.0000.0000.000
138A154SER0-0.037-0.04338.3210.0480.0480.0000.0000.0000.000
139A155GLY0-0.0330.00441.6700.1390.1390.0000.0000.0000.000
140A156GLY00.015-0.00143.0730.0630.0630.0000.0000.0000.000
141A157ASP-1-0.952-0.95546.639-6.466-6.4660.0000.0000.0000.000
142A158PRO00.0090.01448.3410.1460.1460.0000.0000.0000.000
143A159ASP-1-0.885-0.95943.825-7.252-7.2520.0000.0000.0000.000
144A160THR0-0.084-0.08146.9880.0550.0550.0000.0000.0000.000
145A161ALA0-0.050-0.01349.1480.0080.0080.0000.0000.0000.000
146A162GLU-1-0.896-0.94845.402-7.135-7.1350.0000.0000.0000.000
147A163TYR0-0.029-0.03943.593-0.062-0.0620.0000.0000.0000.000
148A164VAL00.0390.03339.2070.0160.0160.0000.0000.0000.000
149A165ALA0-0.015-0.01139.661-0.060-0.0600.0000.0000.0000.000
150A166TYR00.018-0.00231.573-0.025-0.0250.0000.0000.0000.000
151A167VAL0-0.025-0.01433.2990.0400.0400.0000.0000.0000.000
152A168ALA00.0010.00631.959-0.286-0.2860.0000.0000.0000.000
153A169LYS10.8550.92130.14210.03810.0380.0000.0000.0000.000
154A170ASP-1-0.853-0.92528.929-10.609-10.6090.0000.0000.0000.000
155A171PRO00.031-0.00330.7800.2020.2020.0000.0000.0000.000
156A172VAL00.0250.00628.6670.1770.1770.0000.0000.0000.000
157A173ASN0-0.084-0.04531.7070.3290.3290.0000.0000.0000.000
158A174GLN0-0.013-0.01434.9450.2580.2580.0000.0000.0000.000
159A175ARG10.9200.99434.8998.5098.5090.0000.0000.0000.000
160A176ALA00.0950.05134.9080.2520.2520.0000.0000.0000.000
161A177CYS0-0.045-0.02036.154-0.133-0.1330.0000.0000.0000.000
162A178HIS00.0640.04130.4530.1320.1320.0000.0000.0000.000
163A179ILE0-0.014-0.00936.1560.1520.1520.0000.0000.0000.000
164A180LEU0-0.014-0.01135.271-0.245-0.2450.0000.0000.0000.000
165A181GLU-1-0.844-0.90738.968-7.021-7.0210.0000.0000.0000.000
166A182CYS0-0.089-0.03639.612-0.209-0.2090.0000.0000.0000.000
167A183PRO00.0720.05641.6340.0390.0390.0000.0000.0000.000
168A184GLU-1-0.936-0.97642.793-7.105-7.1050.0000.0000.0000.000
169A185GLY00.0160.00539.745-0.193-0.1930.0000.0000.0000.000
170A186LEU0-0.005-0.01633.8880.0130.0130.0000.0000.0000.000
171A187ALA00.0370.00337.820-0.072-0.0720.0000.0000.0000.000
172A188GLN00.0240.01140.8750.0990.0990.0000.0000.0000.000
173A189ASP-1-0.767-0.90036.185-8.810-8.8100.0000.0000.0000.000
174A190VAL0-0.061-0.03535.388-0.029-0.0290.0000.0000.0000.000
175A191ILE0-0.0100.01737.909-0.014-0.0140.0000.0000.0000.000
176A192SER0-0.066-0.03139.3200.0360.0360.0000.0000.0000.000
177A193THR0-0.009-0.00840.4600.2420.2420.0000.0000.0000.000
178A194ILE0-0.0290.00139.5330.0560.0560.0000.0000.0000.000
179A195GLY0-0.040-0.01438.050-0.222-0.2220.0000.0000.0000.000
180A196GLN0-0.013-0.03034.636-0.067-0.0670.0000.0000.0000.000
181A197ALA0-0.0030.01229.337-0.054-0.0540.0000.0000.0000.000
182A198PHE0-0.016-0.00931.1560.0740.0740.0000.0000.0000.000
183A199GLU-1-0.881-0.94926.088-11.547-11.5470.0000.0000.0000.000
184A200LEU0-0.023-0.00325.530-0.444-0.4440.0000.0000.0000.000
185A201ARG10.9680.97228.5999.6309.6300.0000.0000.0000.000
186A202PHE0-0.029-0.01629.9760.0970.0970.0000.0000.0000.000
187A203LYS10.8370.92226.90011.29111.2910.0000.0000.0000.000
188A204GLN0-0.012-0.01723.211-0.080-0.0800.0000.0000.0000.000
189A205TYR00.0400.00816.299-0.090-0.0900.0000.0000.0000.000
190A206LEU00.0200.03621.094-0.352-0.3520.0000.0000.0000.000
191A207ARG00.0900.06720.4682.8742.8740.0000.0000.0000.000