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: 5YG3Z

Calculation Name: 4L7V-A-Xray547

Preferred Name:

Target Type:

Ligand Name: s-adenosyl-l-homocysteine | acetate ion | calcium ion

Ligand 3-letter code: SAH | ACT | CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4L7V

Chain ID: A

ChEMBL ID:

UniProt ID: A5F9C1

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 186
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2006886.462251
FMO2-HF: Nuclear repulsion 1936421.703979
FMO2-HF: Total energy -70464.758272
FMO2-MP2: Total energy -70675.428612


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:ASN)


Summations of interaction energy for fragment #1(A:3:ASN)
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.
-83.218-80.69419.426-12.514-9.434-0.143
Interaction energy analysis for fragmet #1(A:3:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.786 / q_NPA : 0.865
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].
3A5LYS10.9600.9813.38434.41736.3460.006-0.677-1.2580.002
4A6ALA00.0620.0463.4006.0846.6580.012-0.161-0.425-0.001
5A7ASP-1-0.740-0.8691.783-145.156-145.83919.401-11.421-7.296-0.142
6A8ARG10.9700.9844.68134.43734.586-0.001-0.023-0.1240.000
26A28HIS0-0.073-0.0433.0575.5706.1250.008-0.232-0.331-0.002
7A9LEU0-0.027-0.0027.5474.5534.5530.0000.0000.0000.000
8A10ILE00.0290.0087.3493.1273.1270.0000.0000.0000.000
9A11GLN0-0.016-0.0078.7620.4810.4810.0000.0000.0000.000
10A12PHE0-0.023-0.00510.7042.7562.7560.0000.0000.0000.000
11A13LEU00.0060.00011.8491.9861.9860.0000.0000.0000.000
12A14THR0-0.034-0.02312.7061.1951.1950.0000.0000.0000.000
13A15GLU-1-0.899-0.94114.688-19.216-19.2160.0000.0000.0000.000
14A16GLN0-0.120-0.05516.7322.0272.0270.0000.0000.0000.000
15A17GLY00.0080.00918.4680.8430.8430.0000.0000.0000.000
16A18ILE0-0.054-0.01416.0390.3640.3640.0000.0000.0000.000
17A19THR00.020-0.01515.839-1.177-1.1770.0000.0000.0000.000
18A20SER00.0170.02416.859-0.421-0.4210.0000.0000.0000.000
19A21PRO00.028-0.00214.219-0.952-0.9520.0000.0000.0000.000
20A22GLN0-0.026-0.00613.653-1.512-1.5120.0000.0000.0000.000
21A23VAL00.0170.01014.859-0.815-0.8150.0000.0000.0000.000
22A24LEU0-0.0100.00210.998-1.349-1.3490.0000.0000.0000.000
23A25ALA00.0130.0019.910-2.905-2.9050.0000.0000.0000.000
24A26ALA00.0010.00210.493-1.637-1.6370.0000.0000.0000.000
25A27ILE0-0.019-0.01410.319-0.210-0.2100.0000.0000.0000.000
27A29ALA0-0.030-0.0076.769-3.800-3.8000.0000.0000.0000.000
28A30LEU0-0.051-0.0179.0132.5442.5440.0000.0000.0000.000
29A31PRO00.0030.0057.625-0.877-0.8770.0000.0000.0000.000
30A32ARG10.9370.9608.79526.11926.1190.0000.0000.0000.000
31A33GLU-1-0.863-0.9388.867-24.737-24.7370.0000.0000.0000.000
32A34PHE0-0.0210.00611.8781.0301.0300.0000.0000.0000.000
33A35PHE0-0.075-0.05812.8561.3001.3000.0000.0000.0000.000
34A36VAL0-0.028-0.02615.4860.6070.6070.0000.0000.0000.000
35A37ALA0-0.064-0.01117.8740.3540.3540.0000.0000.0000.000
36A38PRO-1-0.901-0.92918.917-12.615-12.6150.0000.0000.0000.000
37A59SER00.0520.02418.5060.2770.2770.0000.0000.0000.000
38A60GLN00.0440.00417.655-1.783-1.7830.0000.0000.0000.000
39A61PRO0-0.0070.00113.8070.2990.2990.0000.0000.0000.000
40A62TYR0-0.023-0.03816.224-0.656-0.6560.0000.0000.0000.000
41A63ILE00.0100.01818.1210.3050.3050.0000.0000.0000.000
42A64VAL00.0330.01616.7020.3310.3310.0000.0000.0000.000
43A65ALA00.0080.01815.8080.2570.2570.0000.0000.0000.000
44A66LYS10.9520.99217.60213.68313.6830.0000.0000.0000.000
45A67MET0-0.011-0.00321.0480.4710.4710.0000.0000.0000.000
46A68THR0-0.010-0.03018.2510.4080.4080.0000.0000.0000.000
47A69GLU-1-0.910-0.96919.803-15.438-15.4380.0000.0000.0000.000
48A70LEU0-0.031-0.00921.4550.5520.5520.0000.0000.0000.000
49A71LEU0-0.002-0.00323.6230.5620.5620.0000.0000.0000.000
50A72ALA0-0.042-0.01224.5970.3460.3460.0000.0000.0000.000
51A73LEU00.0030.00921.1230.4250.4250.0000.0000.0000.000
52A74THR00.0170.00723.398-0.365-0.3650.0000.0000.0000.000
53A75PRO00.0750.03123.1620.0830.0830.0000.0000.0000.000
54A76GLU-1-0.863-0.93324.656-11.638-11.6380.0000.0000.0000.000
55A77THR0-0.054-0.01326.3650.4610.4610.0000.0000.0000.000
56A78LYS10.8490.91227.3699.1799.1790.0000.0000.0000.000
57A79VAL00.0130.00224.9390.2720.2720.0000.0000.0000.000
58A80LEU0-0.044-0.01328.2750.1540.1540.0000.0000.0000.000
59A81GLU-1-0.749-0.83723.143-13.387-13.3870.0000.0000.0000.000
60A82ILE0-0.049-0.01527.7020.3370.3370.0000.0000.0000.000
61A83GLY00.0530.03527.890-0.075-0.0750.0000.0000.0000.000
62A84THR0-0.029-0.03223.677-0.284-0.2840.0000.0000.0000.000
63A85GLY00.0450.02023.114-0.633-0.6330.0000.0000.0000.000
64A86SER0-0.008-0.01118.7930.1300.1300.0000.0000.0000.000
65A87GLY00.0540.01319.978-0.318-0.3180.0000.0000.0000.000
66A88TYR0-0.025-0.00711.8450.0110.0110.0000.0000.0000.000
67A89GLN00.021-0.00217.032-0.638-0.6380.0000.0000.0000.000
68A90THR00.025-0.02019.363-0.236-0.2360.0000.0000.0000.000
69A91ALA00.0040.00115.8830.0630.0630.0000.0000.0000.000
70A92VAL0-0.012-0.01114.605-0.543-0.5430.0000.0000.0000.000
71A93LEU0-0.026-0.00716.883-0.038-0.0380.0000.0000.0000.000
72A94ALA00.0070.00119.5850.1440.1440.0000.0000.0000.000
73A95LYS10.9000.95913.24521.15121.1510.0000.0000.0000.000
74A96LEU0-0.038-0.01516.603-0.419-0.4190.0000.0000.0000.000
75A97VAL0-0.0240.00519.6700.5470.5470.0000.0000.0000.000
76A98ASN00.004-0.01123.163-0.456-0.4560.0000.0000.0000.000
77A99HIS0-0.053-0.04725.345-0.053-0.0530.0000.0000.0000.000
78A100VAL00.0020.02522.9150.2030.2030.0000.0000.0000.000
79A101PHE0-0.046-0.02526.2070.2880.2880.0000.0000.0000.000
80A102THR0-0.004-0.02425.2270.0760.0760.0000.0000.0000.000
81A103VAL0-0.015-0.01028.0250.2940.2940.0000.0000.0000.000
82A104GLU-1-0.794-0.88127.892-10.756-10.7560.0000.0000.0000.000
83A105ARG10.9230.94630.2268.8338.8330.0000.0000.0000.000
84A106ILE0-0.0090.00729.7710.2670.2670.0000.0000.0000.000
85A107LYS10.8960.93430.1858.8018.8010.0000.0000.0000.000
86A108THR00.007-0.00528.672-0.201-0.2010.0000.0000.0000.000
87A109LEU00.0830.04624.646-0.333-0.3330.0000.0000.0000.000
88A110GLN00.0520.03525.518-0.087-0.0870.0000.0000.0000.000
89A111TRP0-0.057-0.04326.996-0.159-0.1590.0000.0000.0000.000
90A112ASP-1-0.789-0.89022.916-12.090-12.0900.0000.0000.0000.000
91A113ALA00.0260.01721.508-0.592-0.5920.0000.0000.0000.000
92A114LYS10.8920.94821.94410.26710.2670.0000.0000.0000.000
93A115ARG10.8270.91721.01612.72612.7260.0000.0000.0000.000
94A116ARG10.8620.92317.42214.10014.1000.0000.0000.0000.000
95A117LEU00.0370.01117.878-0.752-0.7520.0000.0000.0000.000
96A118LYS10.8880.94919.15411.68811.6880.0000.0000.0000.000
97A119GLN0-0.006-0.01017.358-0.138-0.1380.0000.0000.0000.000
98A120LEU0-0.0310.00212.633-0.969-0.9690.0000.0000.0000.000
99A121ASP-1-0.864-0.91015.874-16.677-16.6770.0000.0000.0000.000
100A122ILE0-0.052-0.01815.5430.0580.0580.0000.0000.0000.000
101A123TYR0-0.062-0.06919.6130.9050.9050.0000.0000.0000.000
102A124ASN0-0.064-0.01621.4600.3620.3620.0000.0000.0000.000
103A125VAL00.0370.01322.0920.0130.0130.0000.0000.0000.000
104A126SER0-0.084-0.01525.2890.3150.3150.0000.0000.0000.000
105A127THR00.005-0.01326.033-0.050-0.0500.0000.0000.0000.000
106A128LYS10.8960.95628.7648.8878.8870.0000.0000.0000.000
107A129HIS0-0.047-0.02231.352-0.142-0.1420.0000.0000.0000.000
108A130GLY0-0.011-0.03033.4870.2770.2770.0000.0000.0000.000
109A131ASP-1-0.745-0.87134.506-8.377-8.3770.0000.0000.0000.000
110A132GLY00.023-0.00633.8730.0060.0060.0000.0000.0000.000
111A133TRP0-0.040-0.04134.620-0.003-0.0030.0000.0000.0000.000
112A134GLN0-0.030-0.02237.8220.2000.2000.0000.0000.0000.000
113A135GLY00.0280.03634.8840.0350.0350.0000.0000.0000.000
114A136TRP0-0.109-0.08530.8310.0280.0280.0000.0000.0000.000
115A137PRO00.0740.03136.387-0.073-0.0730.0000.0000.0000.000
116A138ALA0-0.0240.00138.9750.0470.0470.0000.0000.0000.000
117A139ARG10.8500.93833.9759.0929.0920.0000.0000.0000.000
118A140GLY00.0610.03336.8850.0050.0050.0000.0000.0000.000
119A141PRO00.0360.01136.295-0.252-0.2520.0000.0000.0000.000
120A142PHE0-0.019-0.00931.735-0.156-0.1560.0000.0000.0000.000
121A143ASP-1-0.833-0.89330.366-9.870-9.8700.0000.0000.0000.000
122A144ALA00.0130.00827.521-0.120-0.1200.0000.0000.0000.000
123A145ILE0-0.021-0.00629.5870.0140.0140.0000.0000.0000.000
124A146LEU00.0090.00723.639-0.035-0.0350.0000.0000.0000.000
125A147VAL0-0.022-0.01328.0070.1900.1900.0000.0000.0000.000
126A148THR0-0.023-0.02524.078-0.040-0.0400.0000.0000.0000.000
127A149ALA0-0.007-0.00326.885-0.140-0.1400.0000.0000.0000.000
128A150ALA00.0100.01329.9160.0970.0970.0000.0000.0000.000
129A151ALA00.0090.00232.6810.2130.2130.0000.0000.0000.000
130A152ALA00.0580.03736.259-0.037-0.0370.0000.0000.0000.000
131A153LYS10.9060.94039.3307.4597.4590.0000.0000.0000.000
132A154VAL00.0290.02336.662-0.116-0.1160.0000.0000.0000.000
133A155PRO00.0080.00636.1900.2250.2250.0000.0000.0000.000
134A156GLN00.0090.00139.028-0.155-0.1550.0000.0000.0000.000
135A157SER00.0470.01939.7810.0040.0040.0000.0000.0000.000
136A158LEU0-0.025-0.00833.961-0.096-0.0960.0000.0000.0000.000
137A159LEU0-0.011-0.00337.083-0.195-0.1950.0000.0000.0000.000
138A160ASP-1-0.850-0.91639.188-7.407-7.4070.0000.0000.0000.000
139A161GLN0-0.060-0.04736.667-0.170-0.1700.0000.0000.0000.000
140A162LEU0-0.0140.01433.552-0.249-0.2490.0000.0000.0000.000
141A163ALA0-0.007-0.00935.1300.3100.3100.0000.0000.0000.000
142A164GLU-1-0.802-0.90837.043-7.979-7.9790.0000.0000.0000.000
143A165GLY00.0070.00535.436-0.137-0.1370.0000.0000.0000.000
144A166GLY0-0.0180.00733.145-0.387-0.3870.0000.0000.0000.000
145A167ARG10.8220.88728.12210.97610.9760.0000.0000.0000.000
146A168MET0-0.025-0.00630.420-0.173-0.1730.0000.0000.0000.000
147A169VAL0-0.016-0.00726.153-0.021-0.0210.0000.0000.0000.000
148A170ILE00.0400.00829.386-0.070-0.0700.0000.0000.0000.000
149A171PRO0-0.0070.01428.6050.1060.1060.0000.0000.0000.000
150A172VAL0-0.028-0.01931.4200.2200.2200.0000.0000.0000.000
151A173GLY00.0370.01635.215-0.085-0.0850.0000.0000.0000.000
152A174GLU-1-0.952-0.98236.943-7.631-7.6310.0000.0000.0000.000
153A175ASP-1-0.870-0.91936.127-8.171-8.1710.0000.0000.0000.000
154A176GLU-1-0.944-0.98435.971-8.793-8.7930.0000.0000.0000.000
155A177GLN00.012-0.01631.665-0.311-0.3110.0000.0000.0000.000
156A178TYR0-0.024-0.01132.042-0.139-0.1390.0000.0000.0000.000
157A179LEU0-0.016-0.00525.6200.0670.0670.0000.0000.0000.000
158A180TYR00.008-0.00830.1810.1920.1920.0000.0000.0000.000
159A181LYS10.8830.94828.00510.80310.8030.0000.0000.0000.000
160A182ILE0-0.014-0.01131.5040.3250.3250.0000.0000.0000.000
161A183VAL00.0050.00632.640-0.334-0.3340.0000.0000.0000.000
162A184ARG10.8630.94135.1298.2978.2970.0000.0000.0000.000
163A185GLN00.003-0.00635.351-0.309-0.3090.0000.0000.0000.000
164A186GLY00.0290.02239.3050.1440.1440.0000.0000.0000.000
165A187GLY0-0.043-0.02442.2400.2010.2010.0000.0000.0000.000
166A188GLN0-0.034-0.01242.687-0.011-0.0110.0000.0000.0000.000
167A189PHE00.0160.00238.936-0.228-0.2280.0000.0000.0000.000
168A190ILE0-0.0090.00037.9560.1660.1660.0000.0000.0000.000
169A191SER0-0.031-0.02536.435-0.326-0.3260.0000.0000.0000.000
170A192GLU-1-0.884-0.93731.185-10.202-10.2020.0000.0000.0000.000
171A193ARG10.9000.96133.5368.6358.6350.0000.0000.0000.000
172A194VAL0-0.021-0.00427.2970.0060.0060.0000.0000.0000.000
173A195GLU-1-0.806-0.90425.274-12.778-12.7780.0000.0000.0000.000
174A196ALA00.0040.01129.7720.1200.1200.0000.0000.0000.000
175A197VAL0-0.034-0.01926.981-0.476-0.4760.0000.0000.0000.000
176A198ARG10.8480.91527.8469.7069.7060.0000.0000.0000.000
177A199PHE0-0.016-0.00624.745-0.506-0.5060.0000.0000.0000.000
178A200VAL00.0250.00928.2490.3600.3600.0000.0000.0000.000
179A201PRO00.0340.02030.677-0.104-0.1040.0000.0000.0000.000
180A202LEU00.007-0.00432.277-0.112-0.1120.0000.0000.0000.000
181A203VAL0-0.049-0.01934.1820.2660.2660.0000.0000.0000.000
182A204ALA00.0130.01336.637-0.103-0.1030.0000.0000.0000.000
183A205GLY0-0.011-0.00139.3030.0970.0970.0000.0000.0000.000
184A206ASP-1-0.882-0.93640.063-7.276-7.2760.0000.0000.0000.000
185A207LEU0-0.086-0.03636.109-0.230-0.2300.0000.0000.0000.000
186A208ALA-1-0.822-0.89334.152-8.764-8.7640.0000.0000.0000.000