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: K8MG3

Calculation Name: 5AJH-A-Xray547

Preferred Name:

Target Type:

Ligand Name: (4s)-2-methyl-2,4-pentanediol

Ligand 3-letter code: MPD

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5AJH

Chain ID: A

ChEMBL ID:

UniProt ID: X0BTD8

Base Structure: X-ray

Registration Date: 2025-10-04

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 199
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2034504.435268
FMO2-HF: Nuclear repulsion 1962934.935345
FMO2-HF: Total energy -71569.499922
FMO2-MP2: Total energy -71778.842322


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:18:SER)


Summations of interaction energy for fragment #1(A:18:SER)
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.
53.51760.1281.635-3.995-4.251-0.041
Interaction energy analysis for fragmet #1(A:18:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.831 / q_NPA : 0.906
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].
3A20THR00.0030.0052.69412.28614.5010.105-0.992-1.328-0.002
4A21ARG10.6870.7922.26413.45717.2211.522-2.814-2.473-0.039
5A22ASN00.0380.0194.7615.9926.024-0.001-0.011-0.0200.000
32A49LEU0-0.0120.0134.5232.8012.961-0.001-0.043-0.1150.000
37A54PRO0-0.035-0.0313.709-1.067-0.6270.010-0.135-0.3150.000
6A23ASP-1-0.721-0.8127.166-37.354-37.3540.0000.0000.0000.000
7A24LEU00.0170.0389.7531.6281.6280.0000.0000.0000.000
8A25ALA00.0000.00411.8551.3401.3400.0000.0000.0000.000
9A26ASN0-0.058-0.04710.0012.5222.5220.0000.0000.0000.000
10A27GLY00.0250.03913.2880.4610.4610.0000.0000.0000.000
11A28ASN0-0.028-0.03714.8661.6061.6060.0000.0000.0000.000
12A29SER00.0920.02618.658-0.392-0.3920.0000.0000.0000.000
13A30GLY00.0020.01521.5440.3240.3240.0000.0000.0000.000
14A31SER0-0.098-0.06117.646-0.077-0.0770.0000.0000.0000.000
15A32CYS0-0.033-0.00317.402-1.142-1.1420.0000.0000.0000.000
16A33PRO0-0.0350.00915.2960.3720.3720.0000.0000.0000.000
17A34GLY00.0380.01717.7130.7840.7840.0000.0000.0000.000
18A35VAL0-0.023-0.00816.0390.4310.4310.0000.0000.0000.000
19A36ILE00.0280.00514.311-1.492-1.4920.0000.0000.0000.000
20A37PHE0-0.016-0.01310.0710.5470.5470.0000.0000.0000.000
21A38ILE0-0.011-0.00112.107-2.005-2.0050.0000.0000.0000.000
22A39TYR00.0050.00610.4451.4831.4830.0000.0000.0000.000
23A40ALA00.0150.01011.992-1.336-1.3360.0000.0000.0000.000
24A41ARG10.7890.90510.70624.89524.8950.0000.0000.0000.000
25A42GLY00.0670.03712.8541.6501.6500.0000.0000.0000.000
26A43SER00.026-0.00115.222-0.540-0.5400.0000.0000.0000.000
27A44THR0-0.075-0.03616.1890.0230.0230.0000.0000.0000.000
28A45GLU-1-0.738-0.83311.191-26.354-26.3540.0000.0000.0000.000
29A46SER00.0200.0048.7500.4730.4730.0000.0000.0000.000
30A47GLY0-0.015-0.0076.838-2.792-2.7920.0000.0000.0000.000
31A48ASN0-0.007-0.0286.646-1.443-1.4430.0000.0000.0000.000
33A50GLY0-0.0080.0067.8763.0973.0970.0000.0000.0000.000
34A51THR0-0.069-0.0656.628-3.803-3.8030.0000.0000.0000.000
35A52LEU0-0.006-0.0108.4390.0380.0380.0000.0000.0000.000
36A53GLY00.0910.0458.6440.5530.5530.0000.0000.0000.000
38A55ARG10.8550.9475.77225.16625.1660.0000.0000.0000.000
39A56VAL00.0770.0448.5820.9440.9440.0000.0000.0000.000
40A57ALA00.0310.0136.3450.9480.9480.0000.0000.0000.000
41A58SER0-0.085-0.0487.3981.8371.8370.0000.0000.0000.000
42A59LYS10.9410.9688.61922.28122.2810.0000.0000.0000.000
43A60LEU00.0560.03911.2221.2531.2530.0000.0000.0000.000
44A61GLU-1-0.770-0.8627.223-37.978-37.9780.0000.0000.0000.000
45A62ALA0-0.065-0.02711.4071.0991.0990.0000.0000.0000.000
46A63LYS10.8230.92013.79315.91215.9120.0000.0000.0000.000
47A64TYR0-0.020-0.04814.9730.7220.7220.0000.0000.0000.000
48A65GLY00.0600.03514.0560.5590.5590.0000.0000.0000.000
49A66LYS10.8050.8556.16438.17838.1780.0000.0000.0000.000
50A67ASN00.0040.01011.915-1.918-1.9180.0000.0000.0000.000
51A68GLY00.0480.04015.0850.9310.9310.0000.0000.0000.000
52A69VAL0-0.057-0.03611.4620.6650.6650.0000.0000.0000.000
53A70TRP00.0130.02511.277-1.928-1.9280.0000.0000.0000.000
54A71ILE0-0.041-0.0336.6290.4230.4230.0000.0000.0000.000
55A72GLN0-0.003-0.0108.286-2.821-2.8210.0000.0000.0000.000
56A73GLY00.0330.0108.3291.2851.2850.0000.0000.0000.000
57A74VAL0-0.016-0.0079.4250.8340.8340.0000.0000.0000.000
58A75GLY00.005-0.01411.626-0.943-0.9430.0000.0000.0000.000
59A76GLY00.0480.02612.2711.4841.4840.0000.0000.0000.000
60A77ALA0-0.034-0.02615.3220.1820.1820.0000.0000.0000.000
61A78TYR0-0.037-0.02714.3201.4001.4000.0000.0000.0000.000
62A79ARG10.9220.94815.32816.53916.5390.0000.0000.0000.000
63A80ALA0-0.0050.01715.900-0.370-0.3700.0000.0000.0000.000
64A81THR00.0430.01617.930-0.184-0.1840.0000.0000.0000.000
65A82LEU00.0600.02520.9640.3290.3290.0000.0000.0000.000
66A83GLY00.0380.02622.8900.2920.2920.0000.0000.0000.000
67A84ASP-1-0.850-0.92323.192-12.791-12.7910.0000.0000.0000.000
68A85ASN0-0.066-0.04721.868-0.004-0.0040.0000.0000.0000.000
69A86ALA0-0.012-0.00625.4050.2790.2790.0000.0000.0000.000
70A87LEU00.0030.02626.3250.4910.4910.0000.0000.0000.000
71A88PRO00.017-0.00429.307-0.191-0.1910.0000.0000.0000.000
72A89ARG10.8240.86127.24411.32411.3240.0000.0000.0000.000
73A90GLY0-0.0130.00725.721-0.317-0.3170.0000.0000.0000.000
74A91THR00.018-0.01021.368-0.676-0.6760.0000.0000.0000.000
75A92SER00.0160.00623.2900.5010.5010.0000.0000.0000.000
76A93SER00.030-0.00823.525-0.512-0.5120.0000.0000.0000.000
77A94ALA0-0.023-0.00223.056-0.127-0.1270.0000.0000.0000.000
78A95ALA00.0170.01019.144-0.531-0.5310.0000.0000.0000.000
79A96ILE00.0450.01619.649-0.602-0.6020.0000.0000.0000.000
80A97ARG10.9540.97821.54413.17313.1730.0000.0000.0000.000
81A98GLU-1-0.829-0.89515.500-19.096-19.0960.0000.0000.0000.000
82A99MET0-0.032-0.00515.830-0.495-0.4950.0000.0000.0000.000
83A100LEU00.0280.02018.060-0.151-0.1510.0000.0000.0000.000
84A101GLY0-0.0010.02319.5570.3900.3900.0000.0000.0000.000
85A102HIS0-0.038-0.03113.614-0.286-0.2860.0000.0000.0000.000
86A103PHE00.035-0.00816.979-0.106-0.1060.0000.0000.0000.000
87A104SER0-0.020-0.01319.6930.6930.6930.0000.0000.0000.000
88A105ASP-1-0.818-0.90416.795-17.243-17.2430.0000.0000.0000.000
89A106ALA00.001-0.01017.3790.0670.0670.0000.0000.0000.000
90A107ASN0-0.0030.00818.9140.4230.4230.0000.0000.0000.000
91A108GLN0-0.037-0.01022.3300.1270.1270.0000.0000.0000.000
92A109LYS10.7710.87516.07218.58818.5880.0000.0000.0000.000
93A111PRO00.0140.02121.717-0.180-0.1800.0000.0000.0000.000
94A112ASP-1-0.853-0.94124.819-11.373-11.3730.0000.0000.0000.000
95A113ALA0-0.052-0.00619.552-0.104-0.1040.0000.0000.0000.000
96A114VAL0-0.0090.00020.7420.1930.1930.0000.0000.0000.000
97A115LEU00.0190.00518.700-1.215-1.2150.0000.0000.0000.000
98A116ILE0-0.013-0.00815.2180.5220.5220.0000.0000.0000.000
99A117ALA00.0210.01216.385-1.082-1.0820.0000.0000.0000.000
100A118GLY00.029-0.00715.8800.4130.4130.0000.0000.0000.000
101A119GLY00.0100.00614.786-0.941-0.9410.0000.0000.0000.000
102A120TYR0-0.081-0.05013.7860.8400.8400.0000.0000.0000.000
103A121SER0-0.014-0.00616.474-0.289-0.2890.0000.0000.0000.000
104A122GLN00.0310.00618.9730.1260.1260.0000.0000.0000.000
105A123GLY00.0440.01716.5370.3920.3920.0000.0000.0000.000
106A124ALA0-0.044-0.01317.5810.0230.0230.0000.0000.0000.000
107A125ALA00.0090.00319.7930.5370.5370.0000.0000.0000.000
108A126LEU0-0.016-0.00116.9900.3930.3930.0000.0000.0000.000
109A127ALA00.0190.01217.9930.3120.3120.0000.0000.0000.000
110A128ALA0-0.011-0.00519.8240.4300.4300.0000.0000.0000.000
111A129ALA0-0.009-0.01223.5640.4240.4240.0000.0000.0000.000
112A130SER00.009-0.03120.7770.3970.3970.0000.0000.0000.000
113A131VAL0-0.0020.00821.3070.1650.1650.0000.0000.0000.000
114A132THR0-0.085-0.05823.8700.3900.3900.0000.0000.0000.000
115A133ASP-1-0.804-0.87625.863-11.022-11.0220.0000.0000.0000.000
116A134VAL0-0.059-0.01223.2590.1980.1980.0000.0000.0000.000
117A135ASP-1-0.810-0.91325.966-10.265-10.2650.0000.0000.0000.000
118A136ALA00.0050.00527.757-0.312-0.3120.0000.0000.0000.000
119A137GLY00.0870.05329.465-0.092-0.0920.0000.0000.0000.000
120A138ILE0-0.049-0.03123.277-0.356-0.3560.0000.0000.0000.000
121A139ARG10.8340.89524.79910.51410.5140.0000.0000.0000.000
122A140GLU-1-0.935-0.96526.143-10.196-10.1960.0000.0000.0000.000
123A141LYS10.8900.96024.14012.39012.3900.0000.0000.0000.000
124A142ILE0-0.0430.00320.575-0.699-0.6990.0000.0000.0000.000
125A143ALA00.0340.04221.9760.5710.5710.0000.0000.0000.000
126A144GLY00.010-0.00921.5230.5280.5280.0000.0000.0000.000
127A145ALA0-0.0060.00319.442-0.811-0.8110.0000.0000.0000.000
128A146VAL0-0.044-0.01316.1050.6010.6010.0000.0000.0000.000
129A147LEU0-0.023-0.00317.955-0.794-0.7940.0000.0000.0000.000
130A148PHE00.002-0.00514.2730.5340.5340.0000.0000.0000.000
131A149GLY00.0470.01718.786-0.319-0.3190.0000.0000.0000.000
132A150TYR00.006-0.03421.082-0.196-0.1960.0000.0000.0000.000
133A151THR00.0400.00422.6100.6360.6360.0000.0000.0000.000
134A152LYS10.8590.94825.16211.53711.5370.0000.0000.0000.000
135A153ASN0-0.006-0.00426.5530.1770.1770.0000.0000.0000.000
136A154LEU00.0240.02328.3420.2380.2380.0000.0000.0000.000
137A155GLN00.0410.01330.7980.1130.1130.0000.0000.0000.000
138A156ASN0-0.009-0.02327.8900.6310.6310.0000.0000.0000.000
139A157ARG10.8530.92931.4628.9758.9750.0000.0000.0000.000
140A158GLY00.0070.01128.9620.1380.1380.0000.0000.0000.000
141A159LYS10.9150.96727.9009.1719.1710.0000.0000.0000.000
142A160ILE00.0130.03222.690-0.233-0.2330.0000.0000.0000.000
143A161PRO0-0.016-0.01227.1450.3140.3140.0000.0000.0000.000
144A162SER00.0110.00729.106-0.199-0.1990.0000.0000.0000.000
145A163TYR0-0.008-0.01423.835-0.142-0.1420.0000.0000.0000.000
146A164PRO00.0430.02828.0170.1970.1970.0000.0000.0000.000
147A165GLU-1-0.833-0.91628.205-10.508-10.5080.0000.0000.0000.000
148A166ASP-1-0.886-0.94428.385-10.712-10.7120.0000.0000.0000.000
149A167ARG10.8630.92825.12211.19211.1920.0000.0000.0000.000
150A168THR0-0.017-0.01623.882-0.821-0.8210.0000.0000.0000.000
151A169LYS10.8840.95321.90312.83612.8360.0000.0000.0000.000
152A170VAL00.0270.01421.709-0.768-0.7680.0000.0000.0000.000
153A171PHE0-0.041-0.02419.5350.4260.4260.0000.0000.0000.000
154A172CYS0-0.071-0.03021.637-0.476-0.4760.0000.0000.0000.000
155A173ASN0-0.021-0.00920.3170.5350.5350.0000.0000.0000.000
156A174THR00.020-0.00324.4200.1390.1390.0000.0000.0000.000
157A175GLY00.0570.02627.241-0.075-0.0750.0000.0000.0000.000
158A176ASP-1-0.767-0.86122.826-13.272-13.2720.0000.0000.0000.000
159A177LEU00.0530.01225.9460.2140.2140.0000.0000.0000.000
160A178VAL00.0060.02123.2570.2250.2250.0000.0000.0000.000
161A180THR0-0.022-0.01127.0920.3370.3370.0000.0000.0000.000
162A181GLY00.0090.00829.6640.3550.3550.0000.0000.0000.000
163A182SER0-0.0170.00330.1500.2850.2850.0000.0000.0000.000
164A183LEU0-0.021-0.01727.969-0.429-0.4290.0000.0000.0000.000
165A184ILE00.005-0.00327.8830.0310.0310.0000.0000.0000.000
166A185VAL00.0020.00821.431-0.136-0.1360.0000.0000.0000.000
167A186ALA00.0390.02524.6390.2350.2350.0000.0000.0000.000
168A187ALA00.0530.01022.443-0.462-0.4620.0000.0000.0000.000
169A188PRO00.0310.01721.508-0.625-0.6250.0000.0000.0000.000
170A189HIS0-0.032-0.00219.973-0.986-0.9860.0000.0000.0000.000
171A190LEU00.0010.00617.593-0.858-0.8580.0000.0000.0000.000
172A191ALA00.0010.02416.837-0.736-0.7360.0000.0000.0000.000
173A192TYR0-0.008-0.02116.0000.4950.4950.0000.0000.0000.000
174A193GLN00.006-0.01412.3670.1270.1270.0000.0000.0000.000
175A194SER00.025-0.00213.641-1.009-1.0090.0000.0000.0000.000
176A195ALA00.0080.02316.2690.2610.2610.0000.0000.0000.000
177A196ALA00.0060.00011.865-0.104-0.1040.0000.0000.0000.000
178A197SER0-0.024-0.02010.839-1.251-1.2510.0000.0000.0000.000
179A198GLY00.0380.01313.0240.2160.2160.0000.0000.0000.000
180A199ALA00.0250.01616.5980.0150.0150.0000.0000.0000.000
181A200ALA0-0.015-0.00415.7590.4610.4610.0000.0000.0000.000
182A201PRO00.001-0.00213.5860.2280.2280.0000.0000.0000.000
183A202GLU-1-0.888-0.94015.720-15.048-15.0480.0000.0000.0000.000
184A203PHE0-0.040-0.01119.1600.5790.5790.0000.0000.0000.000
185A204LEU0-0.025-0.02214.9480.3230.3230.0000.0000.0000.000
186A205ILE00.0270.01915.8360.1910.1910.0000.0000.0000.000
187A206GLN0-0.0100.00019.3670.5330.5330.0000.0000.0000.000
188A207LYS10.8460.92021.88912.26712.2670.0000.0000.0000.000
189A208ALA00.0210.00519.5170.3950.3950.0000.0000.0000.000
190A209ASP-1-0.777-0.85421.503-13.867-13.8670.0000.0000.0000.000
191A210ALA0-0.030-0.00623.5400.4490.4490.0000.0000.0000.000
192A211ALA0-0.002-0.00624.0910.3910.3910.0000.0000.0000.000
193A212GLY00.0210.00824.5830.2190.2190.0000.0000.0000.000
194A213ALA0-0.029-0.01925.4000.2940.2940.0000.0000.0000.000
195A214ALA0-0.036-0.02528.6050.3500.3500.0000.0000.0000.000
196A215ALA0-0.013-0.00727.5290.2820.2820.0000.0000.0000.000
197A216ALA0-0.020-0.01328.7680.1840.1840.0000.0000.0000.000
198A217ALA0-0.081-0.03330.5330.2540.2540.0000.0000.0000.000
199A218LEU-1-0.971-0.96133.257-8.879-8.8790.0000.0000.0000.000