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: 3M69L

Calculation Name: 5A24-A-Xray547

Preferred Name:

Target Type:

Ligand Name: n-[n-[1-hydroxycarboxyethyl-carbonyl]leucylamino-butyl]-guanidine | phosphate ion

Ligand 3-letter code: E64 | PO4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5A24

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0E3

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 219
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2436728.296984
FMO2-HF: Nuclear repulsion 2353653.682057
FMO2-HF: Total energy -83074.614926
FMO2-MP2: Total energy -83310.700931


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:2:VAL)


Summations of interaction energy for fragment #1(A:2:VAL)
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.
-160.907-154.8654.394-3.326-7.108-0.029
Interaction energy analysis for fragmet #1(A:2:VAL)
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 : 0.919
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].
3A4ALA00.0470.0162.665-3.399-1.0850.599-1.236-1.676-0.012
4A5ALA0-0.0050.0045.1532.8632.981-0.001-0.003-0.1140.000
122A125GLN0-0.0230.0054.5520.4530.563-0.001-0.006-0.1030.000
123A126ALA0-0.023-0.0204.933-5.138-5.022-0.001-0.002-0.1120.000
125A128GLN0-0.019-0.0092.576-2.070-1.2050.448-0.341-0.972-0.003
126A129GLN0-0.073-0.0572.419-7.237-6.4812.131-0.773-2.114-0.005
127A130ALA00.0410.0373.914-0.341-0.2700.0040.013-0.0880.000
129A132ALA0-0.068-0.0322.696-0.1400.4010.204-0.231-0.514-0.002
130A133THR0-0.118-0.0634.8181.0761.093-0.001-0.007-0.0090.000
169A172TYR0-0.039-0.0322.364-1.293-0.1591.012-0.740-1.406-0.007
5A6VAL0-0.022-0.0055.363-2.324-2.3240.0000.0000.0000.000
6A7ASP-1-0.744-0.8558.108-17.584-17.5840.0000.0000.0000.000
7A8TRP00.025-0.0048.6001.7091.7090.0000.0000.0000.000
8A9ARG10.8090.89513.09017.83017.8300.0000.0000.0000.000
9A10THR0-0.025-0.01814.5620.8080.8080.0000.0000.0000.000
10A11ALA0-0.059-0.01713.3580.2770.2770.0000.0000.0000.000
11A12GLY00.0040.01015.5160.3310.3310.0000.0000.0000.000
12A13ALA00.0030.00514.8780.6810.6810.0000.0000.0000.000
13A14VAL0-0.013-0.02215.745-0.192-0.1920.0000.0000.0000.000
14A15THR0-0.021-0.02718.5160.3270.3270.0000.0000.0000.000
15A16PRO00.015-0.00821.789-0.338-0.3380.0000.0000.0000.000
16A17VAL0-0.0320.00722.495-0.156-0.1560.0000.0000.0000.000
17A18LYS10.7950.90624.70411.69811.6980.0000.0000.0000.000
18A19ASN0-0.021-0.04326.917-0.215-0.2150.0000.0000.0000.000
19A20GLN00.0920.04827.398-0.140-0.1400.0000.0000.0000.000
20A21GLN0-0.0110.00230.2940.4150.4150.0000.0000.0000.000
21A22GLN0-0.021-0.00432.979-0.285-0.2850.0000.0000.0000.000
22A23CYS0-0.033-0.01432.133-0.058-0.0580.0000.0000.0000.000
23A24GLY00.0390.03630.958-0.301-0.3010.0000.0000.0000.000
24A25CYS0-0.009-0.01129.483-0.152-0.1520.0000.0000.0000.000
25A26CYS0-0.0460.00224.801-0.183-0.1830.0000.0000.0000.000
26A27TRP00.0170.01623.783-0.606-0.6060.0000.0000.0000.000
27A28ALA00.0120.01723.725-0.405-0.4050.0000.0000.0000.000
28A29PHE00.018-0.00524.096-0.306-0.3060.0000.0000.0000.000
29A30SER0-0.065-0.03519.108-0.486-0.4860.0000.0000.0000.000
30A31ALA00.0230.02819.301-0.725-0.7250.0000.0000.0000.000
31A32VAL00.0300.01020.475-0.521-0.5210.0000.0000.0000.000
32A33ALA0-0.0020.00819.117-0.284-0.2840.0000.0000.0000.000
33A34ALA00.001-0.00116.186-0.673-0.6730.0000.0000.0000.000
34A35ILE00.003-0.00117.339-0.560-0.5600.0000.0000.0000.000
35A36GLU-1-0.756-0.83620.117-12.567-12.5670.0000.0000.0000.000
36A37GLY00.0370.01816.440-0.023-0.0230.0000.0000.0000.000
37A38ALA0-0.030-0.01116.014-0.561-0.5610.0000.0000.0000.000
38A39THR00.005-0.01716.9520.1230.1230.0000.0000.0000.000
39A40GLN0-0.0480.00117.532-0.601-0.6010.0000.0000.0000.000
40A41ILE0-0.026-0.01612.494-0.013-0.0130.0000.0000.0000.000
41A42LYS10.7670.88916.50314.12314.1230.0000.0000.0000.000
42A43THR0-0.042-0.04818.9620.5650.5650.0000.0000.0000.000
43A44GLY0-0.0110.00520.2380.5720.5720.0000.0000.0000.000
44A45THR0-0.041-0.02321.3240.2990.2990.0000.0000.0000.000
45A46LEU0-0.0150.00220.158-0.184-0.1840.0000.0000.0000.000
46A47THR0-0.043-0.04323.0710.7090.7090.0000.0000.0000.000
47A48SER0-0.041-0.01124.634-0.478-0.4780.0000.0000.0000.000
48A49LEU0-0.043-0.02223.7240.3740.3740.0000.0000.0000.000
49A50SER00.013-0.00927.228-0.078-0.0780.0000.0000.0000.000
50A51GLU-1-0.737-0.88425.578-11.249-11.2490.0000.0000.0000.000
51A52GLU-1-0.751-0.85728.832-8.550-8.5500.0000.0000.0000.000
52A53GLN00.0800.04731.0850.0240.0240.0000.0000.0000.000
53A54ILE0-0.060-0.03226.3280.0730.0730.0000.0000.0000.000
54A55VAL0-0.052-0.03330.5510.0970.0970.0000.0000.0000.000
55A56ASP-1-0.727-0.83032.655-8.029-8.0290.0000.0000.0000.000
56A57CYS0-0.083-0.04033.6990.1600.1600.0000.0000.0000.000
57A58ASP0-0.094-0.06429.1130.0820.0820.0000.0000.0000.000
58A59THR0-0.012-0.01232.716-0.041-0.0410.0000.0000.0000.000
59A60ASN0-0.060-0.03535.5370.2870.2870.0000.0000.0000.000
60A61GLY00.0410.03932.216-0.006-0.0060.0000.0000.0000.000
61A62ASN0-0.013-0.02929.5710.4930.4930.0000.0000.0000.000
62A63ASP-1-0.782-0.84428.390-10.444-10.4440.0000.0000.0000.000
63A64LYS10.8250.90531.3898.9608.9600.0000.0000.0000.000
64A65GLY00.1020.06132.9340.1990.1990.0000.0000.0000.000
65A67ASN0-0.051-0.02733.918-0.033-0.0330.0000.0000.0000.000
66A68GLY00.0420.02730.0930.0110.0110.0000.0000.0000.000
67A69GLY00.019-0.00328.7040.2550.2550.0000.0000.0000.000
68A70THR0-0.047-0.02723.901-0.336-0.3360.0000.0000.0000.000
69A71PRO00.0660.02120.1410.2750.2750.0000.0000.0000.000
70A72ASP0-0.031-0.04020.264-0.120-0.1200.0000.0000.0000.000
71A73GLY0-0.0040.01622.6930.1660.1660.0000.0000.0000.000
72A74ALA00.0330.01124.1370.2640.2640.0000.0000.0000.000
73A75PHE0-0.023-0.01718.0580.1960.1960.0000.0000.0000.000
74A76GLN0-0.022-0.01823.645-0.066-0.0660.0000.0000.0000.000
75A77TYR00.0110.01126.4040.3030.3030.0000.0000.0000.000
76A78VAL00.0240.00525.3900.2560.2560.0000.0000.0000.000
77A79VAL0-0.026-0.00624.1270.1510.1510.0000.0000.0000.000
78A80ASN0-0.037-0.02427.0580.0560.0560.0000.0000.0000.000
79A81ASN0-0.073-0.03630.4630.5800.5800.0000.0000.0000.000
80A82GLN0-0.074-0.03229.3500.1490.1490.0000.0000.0000.000
81A83GLY00.012-0.00528.484-0.060-0.0600.0000.0000.0000.000
82A84ILE0-0.060-0.01725.6810.0940.0940.0000.0000.0000.000
83A85ASP-1-0.762-0.89929.124-9.206-9.2060.0000.0000.0000.000
84A86THR0-0.036-0.04729.763-0.325-0.3250.0000.0000.0000.000
85A87GLU-1-0.844-0.93728.854-9.894-9.8940.0000.0000.0000.000
86A88SER0-0.037-0.03031.3160.2300.2300.0000.0000.0000.000
87A89ASP-1-0.915-0.92634.243-8.399-8.3990.0000.0000.0000.000
88A90TYR0-0.076-0.06733.6250.2440.2440.0000.0000.0000.000
89A91PRO00.0090.02933.372-0.278-0.2780.0000.0000.0000.000
90A92TYR0-0.045-0.04231.5400.1270.1270.0000.0000.0000.000
91A93THR0-0.102-0.06333.6700.2490.2490.0000.0000.0000.000
92A94ALA00.0230.00434.7390.1710.1710.0000.0000.0000.000
93A95GLY00.0050.01234.879-0.004-0.0040.0000.0000.0000.000
94A96GLY0-0.035-0.03435.7200.0480.0480.0000.0000.0000.000
95A97GLY0-0.0170.00037.2890.1610.1610.0000.0000.0000.000
96A98SER0-0.107-0.07838.3110.2160.2160.0000.0000.0000.000
97A99PRO00.0130.00936.260-0.019-0.0190.0000.0000.0000.000
98A100GLY00.0100.02338.1720.2450.2450.0000.0000.0000.000
99A101THR0-0.061-0.03239.932-0.024-0.0240.0000.0000.0000.000
100A103SER00.008-0.01037.9710.2280.2280.0000.0000.0000.000
101A104ALA00.0530.02934.9140.0440.0440.0000.0000.0000.000
102A105SER0-0.059-0.02436.556-0.059-0.0590.0000.0000.0000.000
103A106SER0-0.067-0.03939.2020.2270.2270.0000.0000.0000.000
104A107TYR0-0.039-0.01136.0760.1800.1800.0000.0000.0000.000
105A108GLN0-0.018-0.00333.5560.2390.2390.0000.0000.0000.000
106A109PRO0-0.005-0.00130.989-0.179-0.1790.0000.0000.0000.000
107A110ALA0-0.035-0.01329.1690.0180.0180.0000.0000.0000.000
108A111ALA0-0.018-0.00124.445-0.328-0.3280.0000.0000.0000.000
109A112SER0-0.018-0.01125.1610.3880.3880.0000.0000.0000.000
110A113ILE0-0.018-0.00121.127-0.498-0.4980.0000.0000.0000.000
111A114THR0-0.015-0.01521.5310.3950.3950.0000.0000.0000.000
112A115GLY00.004-0.00121.1780.4030.4030.0000.0000.0000.000
113A116TYR0-0.022-0.00118.176-0.214-0.2140.0000.0000.0000.000
114A117GLN0-0.0220.00113.296-0.425-0.4250.0000.0000.0000.000
115A118ASP-1-0.803-0.86515.427-15.363-15.3630.0000.0000.0000.000
116A119VAL0-0.038-0.02410.182-1.020-1.0200.0000.0000.0000.000
117A120PRO0-0.065-0.04210.8240.9990.9990.0000.0000.0000.000
118A121ALA00.0530.03312.883-0.781-0.7810.0000.0000.0000.000
119A122ASN0-0.059-0.03815.0810.0550.0550.0000.0000.0000.000
120A123ASN00.0440.0179.281-1.949-1.9490.0000.0000.0000.000
121A124GLU-1-0.708-0.8578.922-22.800-22.8000.0000.0000.0000.000
124A127LEU00.0410.0307.198-1.210-1.2100.0000.0000.0000.000
128A131ALA00.0700.0376.3470.5280.5280.0000.0000.0000.000
131A134GLN00.016-0.0068.0311.8191.8190.0000.0000.0000.000
132A135PRO0-0.025-0.0129.965-1.086-1.0860.0000.0000.0000.000
133A136ILE0-0.061-0.0189.6950.3310.3310.0000.0000.0000.000
134A137SER00.007-0.00712.9920.3920.3920.0000.0000.0000.000
135A138VAL0-0.030-0.02513.493-0.655-0.6550.0000.0000.0000.000
136A139ALA00.0200.01716.7820.7050.7050.0000.0000.0000.000
137A140ILE0-0.026-0.02618.162-0.692-0.6920.0000.0000.0000.000
138A141ASP-1-0.773-0.85120.566-10.444-10.4440.0000.0000.0000.000
139A142ALA0-0.004-0.01923.376-0.264-0.2640.0000.0000.0000.000
140A143SER0-0.033-0.03124.9430.4190.4190.0000.0000.0000.000
141A144ASP-1-0.828-0.88326.692-9.817-9.8170.0000.0000.0000.000
142A145PRO00.022-0.00828.261-0.152-0.1520.0000.0000.0000.000
143A146SER0-0.054-0.01726.610-0.138-0.1380.0000.0000.0000.000
144A147PHE00.0240.01320.637-0.297-0.2970.0000.0000.0000.000
145A148GLN0-0.024-0.03425.6030.1300.1300.0000.0000.0000.000
146A149SER0-0.097-0.06328.7540.1110.1110.0000.0000.0000.000
147A150TYR0-0.011-0.00120.729-0.036-0.0360.0000.0000.0000.000
148A151SER0-0.019-0.00825.9070.1810.1810.0000.0000.0000.000
149A152SER0-0.006-0.01823.231-0.217-0.2170.0000.0000.0000.000
150A153GLY00.0410.02821.1740.1410.1410.0000.0000.0000.000
151A154ILE0-0.024-0.00115.760-0.279-0.2790.0000.0000.0000.000
152A155TYR00.013-0.00818.8010.3120.3120.0000.0000.0000.000
153A156SER00.010-0.01518.405-0.694-0.6940.0000.0000.0000.000
154A157GLY00.0180.03020.137-0.075-0.0750.0000.0000.0000.000
155A158PRO0-0.060-0.03623.0210.0970.0970.0000.0000.0000.000
156A159CYS0-0.041-0.01317.060-0.349-0.3490.0000.0000.0000.000
157A160ASN0-0.026-0.00323.909-0.121-0.1210.0000.0000.0000.000
158A161THR00.012-0.01220.901-0.368-0.3680.0000.0000.0000.000
159A162ASN0-0.084-0.04323.3340.0820.0820.0000.0000.0000.000
160A163LEU0-0.041-0.02320.5030.0830.0830.0000.0000.0000.000
161A164ASP-1-0.852-0.92124.191-10.551-10.5510.0000.0000.0000.000
162A165HIS0-0.008-0.01323.7020.4170.4170.0000.0000.0000.000
163A166ALA0-0.010-0.00421.242-0.501-0.5010.0000.0000.0000.000
164A167VAL00.0040.00617.6860.3040.3040.0000.0000.0000.000
165A168THR00.0360.02415.368-0.193-0.1930.0000.0000.0000.000
166A169VAL0-0.0180.0099.9730.0560.0560.0000.0000.0000.000
167A170VAL00.010-0.00812.551-0.336-0.3360.0000.0000.0000.000
168A171GLY00.0380.0039.241-0.313-0.3130.0000.0000.0000.000
170A173GLY00.0250.0208.373-1.477-1.4770.0000.0000.0000.000
171A174THR0-0.017-0.0229.887-0.690-0.6900.0000.0000.0000.000
172A175ASP-1-0.789-0.86011.956-14.699-14.6990.0000.0000.0000.000
173A176PRO0-0.052-0.02515.781-0.076-0.0760.0000.0000.0000.000
174A177ASN0-0.046-0.01917.1230.4790.4790.0000.0000.0000.000
175A178SER0-0.063-0.06418.5120.2250.2250.0000.0000.0000.000
176A179GLY00.0030.01015.5070.0520.0520.0000.0000.0000.000
177A180ASN0-0.030-0.01114.030-1.576-1.5760.0000.0000.0000.000
178A181SER00.0420.0139.347-0.753-0.7530.0000.0000.0000.000
179A182TYR0-0.023-0.02010.9300.9190.9190.0000.0000.0000.000
180A183TRP00.022-0.0036.867-2.454-2.4540.0000.0000.0000.000
181A184ILE0-0.037-0.01411.5011.6901.6900.0000.0000.0000.000
182A185VAL00.009-0.00513.397-0.686-0.6860.0000.0000.0000.000
183A186LYS10.8900.94615.97114.13414.1340.0000.0000.0000.000
184A187ASN00.0310.02418.768-0.120-0.1200.0000.0000.0000.000
185A188SER00.004-0.00721.967-0.139-0.1390.0000.0000.0000.000
186A189TRP0-0.001-0.00225.0320.3570.3570.0000.0000.0000.000
187A190GLY00.0110.00527.2120.3610.3610.0000.0000.0000.000
188A191THR0-0.002-0.01826.460-0.162-0.1620.0000.0000.0000.000
189A192SER0-0.036-0.01927.862-0.059-0.0590.0000.0000.0000.000
190A193TRP00.0050.02222.027-0.030-0.0300.0000.0000.0000.000
191A194GLY0-0.006-0.00623.993-0.342-0.3420.0000.0000.0000.000
192A195GLN0-0.052-0.04019.3330.2920.2920.0000.0000.0000.000
193A196GLU-1-0.933-0.96422.598-11.245-11.2450.0000.0000.0000.000
194A197GLY00.0200.00824.200-0.136-0.1360.0000.0000.0000.000
195A198TYR0-0.052-0.03617.824-0.697-0.6970.0000.0000.0000.000
196A199ILE00.0060.00618.2960.4610.4610.0000.0000.0000.000
197A200TRP0-0.046-0.00415.753-1.060-1.0600.0000.0000.0000.000
198A201MET00.0180.01715.1290.7000.7000.0000.0000.0000.000
199A202GLN0-0.002-0.01013.768-0.660-0.6600.0000.0000.0000.000
200A203MET0-0.046-0.0186.4120.2520.2520.0000.0000.0000.000
201A204GLY0-0.018-0.01811.7540.5410.5410.0000.0000.0000.000
202A205LEU0-0.055-0.01612.9461.1391.1390.0000.0000.0000.000
203A206ASN0-0.030-0.02415.9800.0560.0560.0000.0000.0000.000
204A207ALA00.0180.03715.305-0.195-0.1950.0000.0000.0000.000
205A208PRO0-0.050-0.03615.3910.7830.7830.0000.0000.0000.000
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