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: 19N3Z

Calculation Name: 1XTQ-A-Xray547

Preferred Name: GTP-binding protein Rheb

Target Type: SINGLE PROTEIN

Ligand Name: guanosine-5'-diphosphate | magnesium ion

Ligand 3-letter code: GDP | MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1XTQ

Chain ID: A

ChEMBL ID: CHEMBL3108656

UniProt ID: Q15382

Base Structure: X-ray

Registration Date: 2025-10-05

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 169
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1804279.019017
FMO2-HF: Nuclear repulsion 1738183.196456
FMO2-HF: Total energy -66095.822561
FMO2-MP2: Total energy -66291.485468


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:3:GLN)


Summations of interaction energy for fragment #1(A:3:GLN)
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.
-80.167-77.957-0.004-0.915-1.2920
Interaction energy analysis for fragmet #1(A:3:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.851 / q_NPA : 0.913
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].
3A5LYS10.8870.9293.85229.56931.154-0.002-0.792-0.7920.000
50A52GLN0-0.081-0.0354.195-4.092-3.734-0.001-0.103-0.2540.000
51A53GLU-1-0.870-0.9334.168-43.665-43.398-0.001-0.020-0.2460.000
4A6SER00.0110.0156.5353.2723.2720.0000.0000.0000.000
5A7ARG10.7950.8789.21727.80427.8040.0000.0000.0000.000
6A8LYS10.9020.97212.86216.41416.4140.0000.0000.0000.000
7A9ILE00.002-0.00116.1610.3200.3200.0000.0000.0000.000
8A10ALA00.0160.02119.1520.2600.2600.0000.0000.0000.000
9A11ILE0-0.018-0.00222.4100.1050.1050.0000.0000.0000.000
10A12LEU00.0160.02325.5880.3780.3780.0000.0000.0000.000
11A13GLY00.0550.00928.930-0.040-0.0400.0000.0000.0000.000
12A14TYR00.0460.03032.3500.1090.1090.0000.0000.0000.000
13A15ARG10.9970.99434.8277.7007.7000.0000.0000.0000.000
14A16SER00.009-0.01136.6230.0520.0520.0000.0000.0000.000
15A17VAL0-0.0150.00032.3760.1390.1390.0000.0000.0000.000
16A18GLY00.0280.02332.375-0.087-0.0870.0000.0000.0000.000
17A19LYS10.8220.93828.53910.11610.1160.0000.0000.0000.000
18A20SER00.0650.02027.526-0.284-0.2840.0000.0000.0000.000
19A21SER0-0.014-0.00427.570-0.268-0.2680.0000.0000.0000.000
20A22LEU00.002-0.00525.668-0.187-0.1870.0000.0000.0000.000
21A23THR0-0.010-0.01022.404-0.660-0.6600.0000.0000.0000.000
22A24ILE00.0040.01522.888-0.652-0.6520.0000.0000.0000.000
23A25GLN0-0.0010.00824.184-0.652-0.6520.0000.0000.0000.000
24A26PHE0-0.007-0.01415.947-0.501-0.5010.0000.0000.0000.000
25A27VAL0-0.055-0.03819.331-0.836-0.8360.0000.0000.0000.000
26A28GLU-1-0.915-0.96419.867-13.491-13.4910.0000.0000.0000.000
27A29GLY0-0.055-0.00922.6670.1390.1390.0000.0000.0000.000
28A30GLN00.0160.00623.3860.5330.5330.0000.0000.0000.000
29A31PHE0-0.010-0.02027.079-0.041-0.0410.0000.0000.0000.000
30A32VAL0-0.018-0.00329.9530.2400.2400.0000.0000.0000.000
31A33ASP-1-0.964-0.97531.587-8.473-8.4730.0000.0000.0000.000
32A34SER0-0.021-0.01235.1920.0840.0840.0000.0000.0000.000
33A35TYR00.0520.00328.383-0.362-0.3620.0000.0000.0000.000
34A36ASP-1-0.837-0.92631.881-9.839-9.8390.0000.0000.0000.000
35A37PRO0-0.071-0.04633.683-0.180-0.1800.0000.0000.0000.000
36A38THR0-0.079-0.04734.6280.1110.1110.0000.0000.0000.000
37A39ILE0-0.0160.01829.805-0.013-0.0130.0000.0000.0000.000
38A40GLU-1-0.804-0.90126.850-11.679-11.6790.0000.0000.0000.000
39A41ASN00.009-0.00124.644-0.248-0.2480.0000.0000.0000.000
40A42THR0-0.046-0.03018.972-0.356-0.3560.0000.0000.0000.000
41A43PHE00.0160.01620.485-0.325-0.3250.0000.0000.0000.000
42A44THR00.0010.00315.510-0.546-0.5460.0000.0000.0000.000
43A45LYS10.8170.90915.01218.53418.5340.0000.0000.0000.000
44A46LEU00.0050.0288.470-1.467-1.4670.0000.0000.0000.000
45A47ILE00.009-0.00810.7682.3442.3440.0000.0000.0000.000
46A48THR0-0.0070.0027.577-2.873-2.8730.0000.0000.0000.000
47A49VAL00.004-0.0059.3053.2723.2720.0000.0000.0000.000
48A50ASN0-0.002-0.0119.657-1.139-1.1390.0000.0000.0000.000
49A51GLY00.0200.0207.273-0.029-0.0290.0000.0000.0000.000
52A54TYR0-0.029-0.0525.912-6.143-6.1430.0000.0000.0000.000
53A55HIS0-0.054-0.0346.0841.6781.6780.0000.0000.0000.000
54A56LEU00.011-0.0019.9330.5770.5770.0000.0000.0000.000
55A57GLN00.0130.00613.5850.1360.1360.0000.0000.0000.000
56A58LEU00.006-0.00316.1690.3550.3550.0000.0000.0000.000
57A59VAL00.0150.00319.4870.5250.5250.0000.0000.0000.000
58A60ASP-1-0.786-0.88022.432-11.574-11.5740.0000.0000.0000.000
59A61THR0-0.017-0.02125.4830.4590.4590.0000.0000.0000.000
60A62ALA00.0510.02828.1440.1730.1730.0000.0000.0000.000
61A63GLY0-0.069-0.03531.4600.2820.2820.0000.0000.0000.000
62A64GLN0-0.012-0.00630.5280.1490.1490.0000.0000.0000.000
63A65ASP-1-0.847-0.93535.168-8.206-8.2060.0000.0000.0000.000
64A66GLU-1-0.779-0.89538.034-7.954-7.9540.0000.0000.0000.000
65A67TYR0-0.020-0.01540.6420.0680.0680.0000.0000.0000.000
66A68SER0-0.019-0.02136.054-0.065-0.0650.0000.0000.0000.000
67A69ILE00.0010.00435.933-0.026-0.0260.0000.0000.0000.000
68A70PHE00.000-0.01030.819-0.047-0.0470.0000.0000.0000.000
69A71PRO00.0670.04229.6890.0530.0530.0000.0000.0000.000
70A72GLN00.0420.01127.856-0.118-0.1180.0000.0000.0000.000
71A73THR0-0.020-0.00724.931-0.353-0.3530.0000.0000.0000.000
72A74TYR0-0.048-0.02724.302-0.339-0.3390.0000.0000.0000.000
73A75SER00.0060.00825.040-0.126-0.1260.0000.0000.0000.000
74A76ILE0-0.0290.00120.974-0.306-0.3060.0000.0000.0000.000
75A77ASP-1-0.879-0.95517.204-16.822-16.8220.0000.0000.0000.000
76A78ILE0-0.072-0.02217.616-1.131-1.1310.0000.0000.0000.000
77A79ASN00.017-0.00114.783-1.007-1.0070.0000.0000.0000.000
78A80GLY00.0390.01717.758-0.087-0.0870.0000.0000.0000.000
79A81TYR0-0.035-0.03920.217-0.143-0.1430.0000.0000.0000.000
80A82ILE00.0130.00721.6840.2050.2050.0000.0000.0000.000
81A83LEU0-0.022-0.00925.2550.2870.2870.0000.0000.0000.000
82A84VAL0-0.002-0.00228.9690.1780.1780.0000.0000.0000.000
83A85TYR00.0280.00830.6530.1710.1710.0000.0000.0000.000
84A86SER0-0.025-0.01533.650-0.092-0.0920.0000.0000.0000.000
85A87VAL00.0330.01235.5090.2070.2070.0000.0000.0000.000
86A88THR00.0170.00838.0640.2350.2350.0000.0000.0000.000
87A89SER0-0.033-0.02140.0190.1900.1900.0000.0000.0000.000
88A90ILE00.1310.07440.436-0.212-0.2120.0000.0000.0000.000
89A91LYS10.8120.91242.0227.6467.6460.0000.0000.0000.000
90A92SER0-0.028-0.03637.216-0.201-0.2010.0000.0000.0000.000
91A93PHE00.0380.01936.586-0.268-0.2680.0000.0000.0000.000
92A94GLU-1-0.796-0.89138.593-7.902-7.9020.0000.0000.0000.000
93A95VAL0-0.039-0.01436.549-0.085-0.0850.0000.0000.0000.000
94A96ILE0-0.0130.00331.693-0.165-0.1650.0000.0000.0000.000
95A97LYS10.8420.91534.4317.7647.7640.0000.0000.0000.000
96A98VAL00.0000.00436.347-0.102-0.1020.0000.0000.0000.000
97A99ILE0-0.041-0.01331.677-0.095-0.0950.0000.0000.0000.000
98A100HIS10.9460.97630.31410.04510.0450.0000.0000.0000.000
99A101GLY0-0.031-0.00432.811-0.136-0.1360.0000.0000.0000.000
100A102LYS10.8970.94834.4208.4708.4700.0000.0000.0000.000
101A103LEU0-0.013-0.00526.994-0.083-0.0830.0000.0000.0000.000
102A104LEU0-0.023-0.01429.312-0.282-0.2820.0000.0000.0000.000
103A105ASP-1-0.927-0.95831.512-8.979-8.9790.0000.0000.0000.000
104A106MET0-0.077-0.04230.2560.1100.1100.0000.0000.0000.000
105A107VAL0-0.035-0.00626.197-0.274-0.2740.0000.0000.0000.000
106A108GLY00.0150.02028.518-0.136-0.1360.0000.0000.0000.000
107A109LYS10.8880.91729.7479.6229.6220.0000.0000.0000.000
108A110VAL00.0040.00523.383-0.070-0.0700.0000.0000.0000.000
109A111GLN0-0.030-0.00924.130-0.695-0.6950.0000.0000.0000.000
110A112ILE00.0360.02922.924-0.442-0.4420.0000.0000.0000.000
111A113PRO00.0520.03919.1960.5200.5200.0000.0000.0000.000
112A114ILE00.007-0.00422.3560.0660.0660.0000.0000.0000.000
113A115MET0-0.0240.00723.461-0.156-0.1560.0000.0000.0000.000
114A116LEU0-0.0200.00825.5870.0880.0880.0000.0000.0000.000
115A117VAL0-0.007-0.02126.512-0.125-0.1250.0000.0000.0000.000
116A118GLY00.0620.03429.6440.2540.2540.0000.0000.0000.000
117A119ASN0-0.003-0.01130.988-0.124-0.1240.0000.0000.0000.000
118A120LYS10.8780.94132.6149.0359.0350.0000.0000.0000.000
119A121LYS10.8800.93231.26110.10110.1010.0000.0000.0000.000
120A122ASP-1-0.798-0.86835.129-8.934-8.9340.0000.0000.0000.000
121A123LEU0-0.031-0.00336.7500.2060.2060.0000.0000.0000.000
122A124HIS00.008-0.00837.7620.1900.1900.0000.0000.0000.000
123A125MET0-0.040-0.02641.4460.0800.0800.0000.0000.0000.000
124A126GLU-1-0.918-0.95742.204-7.497-7.4970.0000.0000.0000.000
125A127ARG10.7150.81736.3928.4348.4340.0000.0000.0000.000
126A128VAL0-0.027-0.02142.2110.1810.1810.0000.0000.0000.000
127A129ILE0-0.0460.00238.6250.0450.0450.0000.0000.0000.000
128A130SER0-0.018-0.04339.991-0.134-0.1340.0000.0000.0000.000
129A131TYR00.0230.01231.513-0.179-0.1790.0000.0000.0000.000
130A132GLU-1-0.852-0.91936.122-8.425-8.4250.0000.0000.0000.000
131A133GLU-1-0.856-0.91438.192-7.830-7.8300.0000.0000.0000.000
132A134GLY00.0150.00435.137-0.096-0.0960.0000.0000.0000.000
133A135LYS10.8580.93232.5739.4209.4200.0000.0000.0000.000
134A136ALA00.0620.02834.315-0.181-0.1810.0000.0000.0000.000
135A137LEU0-0.045-0.00234.6920.0300.0300.0000.0000.0000.000
136A138ALA00.0110.00330.472-0.121-0.1210.0000.0000.0000.000
137A139GLU-1-0.876-0.94631.721-9.538-9.5380.0000.0000.0000.000
138A140SER0-0.059-0.04333.7390.0740.0740.0000.0000.0000.000
139A141TRP0-0.068-0.05630.423-0.070-0.0700.0000.0000.0000.000
140A142ASN0-0.053-0.01328.167-0.245-0.2450.0000.0000.0000.000
141A143ALA00.0060.02027.007-0.429-0.4290.0000.0000.0000.000
142A144ALA0-0.015-0.00824.3070.1660.1660.0000.0000.0000.000
143A145PHE0-0.004-0.01726.4240.2000.2000.0000.0000.0000.000
144A146LEU0-0.013-0.00724.441-0.195-0.1950.0000.0000.0000.000
145A147GLU-1-0.783-0.84628.528-8.915-8.9150.0000.0000.0000.000
146A148SER0-0.004-0.02627.993-0.272-0.2720.0000.0000.0000.000
147A149SER0-0.033-0.04729.5990.3690.3690.0000.0000.0000.000
148A150ALA00.0080.01228.807-0.299-0.2990.0000.0000.0000.000
149A151LYS10.9140.96429.4838.6418.6410.0000.0000.0000.000
150A152GLU-1-0.845-0.90629.261-10.003-10.0030.0000.0000.0000.000
151A153ASN00.0040.00222.611-0.506-0.5060.0000.0000.0000.000
152A154GLN0-0.017-0.01021.294-0.450-0.4500.0000.0000.0000.000
153A155THR00.013-0.00523.518-0.284-0.2840.0000.0000.0000.000
154A156ALA00.0360.01523.874-0.109-0.1090.0000.0000.0000.000
155A157VAL0-0.013-0.00818.320-0.724-0.7240.0000.0000.0000.000
156A158ASP-1-0.880-0.93919.520-14.771-14.7710.0000.0000.0000.000
157A159VAL00.0040.00121.263-0.297-0.2970.0000.0000.0000.000
158A160PHE00.013-0.00718.280-0.348-0.3480.0000.0000.0000.000
159A161ARG10.9230.96715.22217.00417.0040.0000.0000.0000.000
160A162ARG10.8720.93817.24713.21813.2180.0000.0000.0000.000
161A163ILE00.013-0.00218.741-0.018-0.0180.0000.0000.0000.000
162A164ILE00.0080.01612.880-0.346-0.3460.0000.0000.0000.000
163A165LEU0-0.043-0.02915.073-0.351-0.3510.0000.0000.0000.000
164A166GLU-1-0.826-0.89617.195-13.646-13.6460.0000.0000.0000.000
165A167ALA00.002-0.02016.1810.3550.3550.0000.0000.0000.000
166A168GLU-1-0.747-0.83511.016-28.348-28.3480.0000.0000.0000.000
167A169LYS10.8100.91415.27214.31314.3130.0000.0000.0000.000
168A170LEU0-0.082-0.04818.6900.8750.8750.0000.0000.0000.000
169A171GLU-2-1.856-1.89912.021-43.495-43.4950.0000.0000.0000.000