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: Y9GR2

Calculation Name: 1RHF-A-Xray547

Preferred Name: Tyrosine-protein kinase receptor TYRO3

Target Type: SINGLE PROTEIN

Ligand Name: 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid | acetate ion

Ligand 3-letter code: EPE | ACT

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1RHF

Chain ID: A

ChEMBL ID: CHEMBL5314

UniProt ID: Q06418

Base Structure: X-ray

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 174
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1492835.603734
FMO2-HF: Nuclear repulsion 1425851.536972
FMO2-HF: Total energy -66984.066762
FMO2-MP2: Total energy -67178.687661


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:7:GLY)


Summations of interaction energy for fragment #1(A:7: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.
-124.744-121.833.21-3.164-2.96-0.033
Interaction energy analysis for fragmet #1(A:7:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.847 / q_NPA : 0.916
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].
3A9PRO00.0110.0263.5935.9497.275-0.008-0.552-0.765-0.003
82A89GLN00.0200.0072.246-24.398-22.8183.219-2.605-2.195-0.030
83A90PRO00.000-0.0074.7733.1393.147-0.001-0.0070.0000.000
4A10VAL00.0420.0236.1362.6182.6180.0000.0000.0000.000
5A11LYS10.9260.9539.34430.04930.0490.0000.0000.0000.000
6A12LEU00.0260.02712.4411.0181.0180.0000.0000.0000.000
7A13THR00.006-0.00215.7240.0880.0880.0000.0000.0000.000
8A14VAL0-0.0100.00118.6170.4470.4470.0000.0000.0000.000
9A15SER0-0.018-0.01321.809-0.080-0.0800.0000.0000.0000.000
10A16GLN0-0.030-0.04625.2590.0520.0520.0000.0000.0000.000
11A17GLY00.0110.01726.7540.3140.3140.0000.0000.0000.000
12A18GLN0-0.069-0.02325.6700.2820.2820.0000.0000.0000.000
13A19PRO0-0.0130.01025.924-0.310-0.3100.0000.0000.0000.000
14A20VAL0-0.023-0.01820.028-0.230-0.2300.0000.0000.0000.000
15A21LYS10.8880.94120.87912.37312.3730.0000.0000.0000.000
16A22LEU0-0.0120.01315.289-0.558-0.5580.0000.0000.0000.000
17A23ASN0-0.044-0.03815.3900.2770.2770.0000.0000.0000.000
18A24CYS0-0.0040.01111.1150.8700.8700.0000.0000.0000.000
19A25SER00.0440.01712.8491.8011.8010.0000.0000.0000.000
20A26VAL00.004-0.01112.947-1.781-1.7810.0000.0000.0000.000
21A27GLU-1-0.900-0.95514.715-16.628-16.6280.0000.0000.0000.000
22A28GLY00.0270.01116.011-0.821-0.8210.0000.0000.0000.000
23A29MET00.0180.01718.5360.0610.0610.0000.0000.0000.000
24A30GLU-1-0.955-0.97620.576-11.458-11.4580.0000.0000.0000.000
25A31GLU-1-0.956-0.97723.948-10.916-10.9160.0000.0000.0000.000
26A32PRO0-0.022-0.00718.916-0.090-0.0900.0000.0000.0000.000
27A33ASP-1-0.872-0.93920.913-13.175-13.1750.0000.0000.0000.000
28A34ILE0-0.062-0.03316.341-0.875-0.8750.0000.0000.0000.000
29A35GLN0-0.011-0.00517.4260.3570.3570.0000.0000.0000.000
30A36TRP0-0.031-0.01813.396-1.767-1.7670.0000.0000.0000.000
31A37VAL0-0.027-0.00113.3710.9350.9350.0000.0000.0000.000
32A38LYS10.8880.94814.22814.87714.8770.0000.0000.0000.000
33A39ASP-1-0.888-0.95312.730-19.965-19.9650.0000.0000.0000.000
34A40GLY0-0.011-0.00113.5280.2860.2860.0000.0000.0000.000
35A41ALA0-0.0240.00114.4100.6870.6870.0000.0000.0000.000
36A42VAL00.0540.02517.234-0.639-0.6390.0000.0000.0000.000
37A43VAL0-0.029-0.01517.6790.6560.6560.0000.0000.0000.000
38A44GLN0-0.007-0.00720.3390.6660.6660.0000.0000.0000.000
39A45ASN0-0.062-0.04124.0460.0080.0080.0000.0000.0000.000
40A46LEU00.0220.01721.2650.1410.1410.0000.0000.0000.000
41A47ASP-1-0.924-0.96024.612-10.982-10.9820.0000.0000.0000.000
42A48GLN0-0.0040.00221.009-0.894-0.8940.0000.0000.0000.000
43A49LEU0-0.045-0.01622.2460.6020.6020.0000.0000.0000.000
44A50TYR00.0440.00418.252-0.983-0.9830.0000.0000.0000.000
45A51ILE0-0.022-0.00722.0530.6920.6920.0000.0000.0000.000
46A52PRO00.0540.04822.214-0.639-0.6390.0000.0000.0000.000
47A53VAL0-0.051-0.03021.0350.4630.4630.0000.0000.0000.000
48A54SER0-0.097-0.06323.4040.3970.3970.0000.0000.0000.000
49A55GLU-1-0.879-0.93824.076-11.225-11.2250.0000.0000.0000.000
50A56GLN0-0.060-0.02421.126-0.314-0.3140.0000.0000.0000.000
51A57HIS0-0.0010.01517.199-0.542-0.5420.0000.0000.0000.000
52A58TRP00.0380.00818.7450.9230.9230.0000.0000.0000.000
53A59ILE0-0.032-0.01017.518-1.082-1.0820.0000.0000.0000.000
54A60GLY00.0440.01217.1250.9040.9040.0000.0000.0000.000
55A61PHE0-0.036-0.04217.504-0.504-0.5040.0000.0000.0000.000
56A62LEU00.0270.02418.0000.4940.4940.0000.0000.0000.000
57A63SER0-0.032-0.02320.351-0.033-0.0330.0000.0000.0000.000
58A64LEU00.0340.02319.7610.2570.2570.0000.0000.0000.000
59A65LYS10.9580.96024.03410.25510.2550.0000.0000.0000.000
60A66SER00.011-0.00626.9390.3720.3720.0000.0000.0000.000
61A67VAL0-0.052-0.00221.9370.0450.0450.0000.0000.0000.000
62A68GLU-1-0.762-0.88824.793-10.702-10.7020.0000.0000.0000.000
63A69ARG10.8700.92223.18411.80511.8050.0000.0000.0000.000
64A70SER0-0.0110.00221.953-0.393-0.3930.0000.0000.0000.000
65A71ASP-1-0.861-0.92921.021-13.381-13.3810.0000.0000.0000.000
66A72ALA0-0.0180.00917.989-0.813-0.8130.0000.0000.0000.000
67A73GLY00.0250.01115.0390.5000.5000.0000.0000.0000.000
68A74ARG10.8370.9158.73326.71526.7150.0000.0000.0000.000
69A75TYR00.015-0.02011.6770.7090.7090.0000.0000.0000.000
70A76TRP0-0.068-0.0409.232-3.163-3.1630.0000.0000.0000.000
71A78GLN00.0060.00811.584-2.968-2.9680.0000.0000.0000.000
72A79VAL00.0570.02713.9380.9240.9240.0000.0000.0000.000
73A80GLU-1-0.960-0.97316.363-14.650-14.6500.0000.0000.0000.000
74A81ASP-1-0.954-0.98419.089-14.554-14.5540.0000.0000.0000.000
75A82GLY00.0150.01816.354-1.044-1.0440.0000.0000.0000.000
76A83GLY0-0.0070.00117.0790.2350.2350.0000.0000.0000.000
77A84GLU-1-0.999-1.00414.869-21.222-21.2220.0000.0000.0000.000
78A85THR0-0.038-0.02514.2280.1510.1510.0000.0000.0000.000
79A86GLU-1-0.958-0.96311.416-25.122-25.1220.0000.0000.0000.000
80A87ILE0-0.004-0.0169.7611.4001.4000.0000.0000.0000.000
81A88SER0-0.050-0.0058.393-2.656-2.6560.0000.0000.0000.000
84A91VAL00.0280.0147.725-1.765-1.7650.0000.0000.0000.000
85A92TRP0-0.045-0.0376.8971.5841.5840.0000.0000.0000.000
86A93LEU00.0160.02411.6650.4930.4930.0000.0000.0000.000
87A94THR0-0.017-0.01615.1670.1520.1520.0000.0000.0000.000
88A95VAL00.0220.00517.4330.3240.3240.0000.0000.0000.000
89A96GLU-1-0.883-0.94421.210-13.378-13.3780.0000.0000.0000.000
90A97GLY00.017-0.00723.5660.3260.3260.0000.0000.0000.000
91A98VAL00.0040.02227.249-0.151-0.1510.0000.0000.0000.000
92A99PRO0-0.052-0.02128.621-0.259-0.2590.0000.0000.0000.000
93A100PHE00.0180.00427.3030.2680.2680.0000.0000.0000.000
94A101PHE00.024-0.01429.047-0.191-0.1910.0000.0000.0000.000
95A102THR0-0.0070.00426.537-0.019-0.0190.0000.0000.0000.000
96A103VAL0-0.052-0.01929.6880.1510.1510.0000.0000.0000.000
97A104GLU-1-0.736-0.87633.176-8.538-8.5380.0000.0000.0000.000
98A105PRO0-0.0260.00736.3330.0810.0810.0000.0000.0000.000
99A106LYS10.9060.94436.7428.4058.4050.0000.0000.0000.000
100A107ASP-1-0.739-0.83542.143-6.984-6.9840.0000.0000.0000.000
101A108LEU0-0.063-0.02845.042-0.030-0.0300.0000.0000.0000.000
102A109ALA00.0340.02748.3100.0830.0830.0000.0000.0000.000
103A110VAL0-0.025-0.01350.898-0.028-0.0280.0000.0000.0000.000
104A111PRO00.0430.01853.5590.0820.0820.0000.0000.0000.000
105A112PRO00.0200.01156.351-0.074-0.0740.0000.0000.0000.000
106A113ASN0-0.098-0.06757.3380.0200.0200.0000.0000.0000.000
107A114ALA00.0220.03354.5200.0110.0110.0000.0000.0000.000
108A115PRO0-0.006-0.00451.286-0.068-0.0680.0000.0000.0000.000
109A116PHE0-0.023-0.01747.041-0.031-0.0310.0000.0000.0000.000
110A117GLN0-0.033-0.02841.261-0.147-0.1470.0000.0000.0000.000
111A118LEU0-0.0280.00642.386-0.016-0.0160.0000.0000.0000.000
112A119SER00.001-0.01637.311-0.024-0.0240.0000.0000.0000.000
113A120CYS0-0.073-0.02035.8460.1470.1470.0000.0000.0000.000
114A121GLU-1-0.880-0.94629.810-10.387-10.3870.0000.0000.0000.000
115A122ALA0-0.0120.00230.0610.0480.0480.0000.0000.0000.000
116A123VAL00.0170.01324.734-0.119-0.1190.0000.0000.0000.000
117A124GLY00.0490.04624.9680.2730.2730.0000.0000.0000.000
118A125PRO0-0.038-0.00519.919-0.107-0.1070.0000.0000.0000.000
119A126PRO00.0510.00922.9100.2340.2340.0000.0000.0000.000
120A127GLU-1-0.805-0.90122.878-11.925-11.9250.0000.0000.0000.000
121A128PRO0-0.056-0.03225.079-0.178-0.1780.0000.0000.0000.000
122A129VAL0-0.0060.00627.3510.3120.3120.0000.0000.0000.000
123A130THR0-0.086-0.03429.6340.1930.1930.0000.0000.0000.000
124A131ILE00.000-0.01832.826-0.005-0.0050.0000.0000.0000.000
125A132VAL0-0.016-0.00735.9960.1490.1490.0000.0000.0000.000
126A133TRP00.001-0.00539.1810.0380.0380.0000.0000.0000.000
127A134TRP0-0.018-0.02942.1520.2800.2800.0000.0000.0000.000
128A135ARG10.9290.96945.3226.1276.1270.0000.0000.0000.000
129A136GLY0-0.004-0.00348.5100.1400.1400.0000.0000.0000.000
130A137THR00.008-0.00348.397-0.116-0.1160.0000.0000.0000.000
131A138THR0-0.0200.00149.8150.0270.0270.0000.0000.0000.000
132A139LYS10.9420.98543.2207.2147.2140.0000.0000.0000.000
133A140ILE0-0.052-0.02945.8980.1370.1370.0000.0000.0000.000
134A141GLY00.0220.01643.1200.0300.0300.0000.0000.0000.000
135A142GLY00.0220.02040.177-0.099-0.0990.0000.0000.0000.000
136A143PRO0-0.023-0.03437.6070.2080.2080.0000.0000.0000.000
137A144ALA0-0.0260.00337.0190.0830.0830.0000.0000.0000.000
138A145PRO00.0230.00731.878-0.096-0.0960.0000.0000.0000.000
139A146SER00.0270.02729.7760.3970.3970.0000.0000.0000.000
140A147PRO00.0170.00830.089-0.264-0.2640.0000.0000.0000.000
141A148SER00.0160.00232.4850.2760.2760.0000.0000.0000.000
142A149VAL0-0.005-0.02036.2110.0300.0300.0000.0000.0000.000
143A150LEU0-0.0120.00939.5970.0860.0860.0000.0000.0000.000
144A151ASN00.0170.01343.2330.0090.0090.0000.0000.0000.000
145A152VAL0-0.031-0.01446.0410.0680.0680.0000.0000.0000.000
146A153THR00.016-0.00349.3340.0060.0060.0000.0000.0000.000
147A154GLY00.0820.04652.8900.0780.0780.0000.0000.0000.000
148A155VAL0-0.049-0.02552.451-0.040-0.0400.0000.0000.0000.000
149A156THR00.0440.01855.3570.0160.0160.0000.0000.0000.000
150A157GLN00.0020.01056.8990.1610.1610.0000.0000.0000.000
151A158SER00.0350.00754.307-0.092-0.0920.0000.0000.0000.000
152A159THR0-0.073-0.03150.8170.0800.0800.0000.0000.0000.000
153A160MET00.0080.01248.164-0.077-0.0770.0000.0000.0000.000
154A161PHE00.019-0.01444.9630.0870.0870.0000.0000.0000.000
155A162SER0-0.0040.01141.713-0.086-0.0860.0000.0000.0000.000
156A164GLU-1-0.862-0.91837.911-7.872-7.8720.0000.0000.0000.000
157A165ALA00.0090.00432.720-0.017-0.0170.0000.0000.0000.000
158A166HIS0-0.068-0.04333.6750.0950.0950.0000.0000.0000.000
159A167ASN00.050-0.00327.0740.1190.1190.0000.0000.0000.000
160A168LEU00.004-0.00326.8210.2280.2280.0000.0000.0000.000
161A169LYS10.8490.93025.33912.27812.2780.0000.0000.0000.000
162A170GLY00.0030.01329.9730.2160.2160.0000.0000.0000.000
163A171LEU0-0.016-0.00633.395-0.102-0.1020.0000.0000.0000.000
164A172ALA00.0490.02333.179-0.031-0.0310.0000.0000.0000.000
165A173SER0-0.0040.00335.1850.0400.0400.0000.0000.0000.000
166A174SER0-0.017-0.00936.484-0.148-0.1480.0000.0000.0000.000
167A175ARG10.7780.85137.4887.7377.7370.0000.0000.0000.000
168A176THR0-0.040-0.02139.8690.0480.0480.0000.0000.0000.000
169A177ALA0-0.0220.00142.7440.0110.0110.0000.0000.0000.000
170A178THR0-0.029-0.03744.4920.1680.1680.0000.0000.0000.000
171A179VAL00.0010.00948.032-0.048-0.0480.0000.0000.0000.000
172A180HIS00.000-0.01750.0890.1090.1090.0000.0000.0000.000
173A181LEU0-0.016-0.01053.466-0.040-0.0400.0000.0000.0000.000
174A182GLN-1-0.939-0.95854.607-5.392-5.3920.0000.0000.0000.000