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: R4M58

Calculation Name: 7LS2-A-Other547

Preferred Name:

Target Type:

Ligand Name: 2-methyl, 7-(3-methyl-pentane), guanosine-5'-monophosphate | (2~{r})-2-azanyl-4-[5-[(2~{s},3~{r},4~{s},5~{r})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic acid | guanosine-5'-diphosphate | n7-methyl-guanosine-5'-monophosphate | 7-propyl, guanosine-5'-monophosphate | 7-ethyl, guanosine-5'-monophosphate | 6-propyl, guanosine-5'-monophosphate | n(4)-acetylcytidine-5'-monophosphate | 6-ethyl, guanosine-5'-monophosphate | 2n-methylguanosine-5'-monophosphate | 6-methyl, guanosine-5'-monophosphate | 4-isopropyl, uridine-5'-monophosphate | 2'-methyl, 3-propyl, cytidine-5'-monophosphate | 6-hydro-1-methyladenosine-5'-monophosphate | n6-methyladenosine-5'-monophosphate | {3-[4-(2-amino-2-carboxy-ethyl)-1h-imidazol-2-yl]-1-carbamoyl-propyl}-trimethyl-ammonium | pseudouridine-5'-monophosphate | 5-methylcytidine-5'-monophosphate | 4-methyl, cytidine-5'-monophosphate | o2'-methylguanosine-5'-monophosphate | 3-methyluridine-5'-monophoshate | 3-methyl, cytidine-5'-monophosphate | o2'-methylycytidine-5'-monophosphate | o2'-methyluridine 5'-monophosphate | 2'-o-methyladenosine 5'-(dihydrogen phosphate) | n-methyl-lysine | magnesium ion | zinc ion

Ligand 3-letter code: MHG | B8N | GDP | G7M | P7G | E7G | B9B | 4AC | E6G | 2MG | B8W | I4U | B9H | 1MA | 6MZ | DDE | PSU | 5MC | B8T | OMG | UR3 | B8Q | OMC | OMU | A2M | MLZ | MG | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 7LS2

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: ElectronMicroscopy

Registration Date: 2025-10-06

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 206
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2239213.360943
FMO2-HF: Nuclear repulsion 2156634.359206
FMO2-HF: Total energy -82579.001737
FMO2-MP2: Total energy -82819.348741


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:5:VAL)


Summations of interaction energy for fragment #1(A:5: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.
139.955141.4867.74-4.394-4.876-0.044
Interaction energy analysis for fragmet #1(A:5:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.904 / q_NPA : 0.936
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].
3A7ARG10.9440.9593.70439.98741.3600.005-0.463-0.9160.000
4A8ASP-1-0.870-0.9351.682-69.718-70.5597.729-3.530-3.357-0.043
5A9THR00.0100.0023.57911.90412.9030.006-0.401-0.603-0.001
6A10LEU0-0.069-0.0365.6717.0197.0190.0000.0000.0000.000
7A11TYR00.0150.0195.9301.7061.7060.0000.0000.0000.000
8A12GLU-1-0.823-0.9178.316-24.862-24.8620.0000.0000.0000.000
9A13ALA0-0.064-0.02110.2512.7162.7160.0000.0000.0000.000
10A14VAL0-0.013-0.01312.2762.1182.1180.0000.0000.0000.000
11A15ARG10.9921.00113.37819.21219.2120.0000.0000.0000.000
12A16GLU-1-0.886-0.96114.008-17.497-17.4970.0000.0000.0000.000
13A17VAL0-0.055-0.03116.2741.1861.1860.0000.0000.0000.000
14A18LEU0-0.047-0.00218.3420.9880.9880.0000.0000.0000.000
15A19HIS0-0.063-0.04418.5770.9830.9830.0000.0000.0000.000
16A20GLY00.0380.04518.4480.4820.4820.0000.0000.0000.000
17A21ASN0-0.038-0.02919.3270.8030.8030.0000.0000.0000.000
18A22GLN00.0910.06122.3040.7940.7940.0000.0000.0000.000
19A23ARG10.9200.93824.79412.62412.6240.0000.0000.0000.000
20A24LYS10.9030.94527.2169.8299.8290.0000.0000.0000.000
21A25ARG11.0111.02728.16010.63810.6380.0000.0000.0000.000
22A26ARG10.9090.95726.56211.52411.5240.0000.0000.0000.000
23A27LYS10.9610.98930.5838.5368.5360.0000.0000.0000.000
24A28PHE0-0.024-0.02029.5110.2120.2120.0000.0000.0000.000
25A29LEU0-0.010-0.01127.1140.0060.0060.0000.0000.0000.000
26A30GLU-1-0.855-0.94224.297-12.531-12.5310.0000.0000.0000.000
27A31THR0-0.032-0.02823.452-0.223-0.2230.0000.0000.0000.000
28A32VAL00.0720.07118.2550.3580.3580.0000.0000.0000.000
29A33GLU-1-1.008-0.99921.242-12.583-12.5830.0000.0000.0000.000
30A34LEU0-0.0050.00514.484-0.363-0.3630.0000.0000.0000.000
31A35GLN0-0.008-0.01317.3020.7480.7480.0000.0000.0000.000
32A36ILE00.0250.01615.412-1.004-1.0040.0000.0000.0000.000
33A37SER00.0140.00016.2251.1431.1430.0000.0000.0000.000
34A38LEU00.0120.01317.408-0.499-0.4990.0000.0000.0000.000
35A39LYS10.9290.97916.91814.74114.7410.0000.0000.0000.000
36A40ASN00.0460.00319.768-0.047-0.0470.0000.0000.0000.000
37A41TYR00.0310.03723.0640.1530.1530.0000.0000.0000.000
38A42ASP-1-0.778-0.87324.836-10.288-10.2880.0000.0000.0000.000
39A43PRO0-0.009-0.01828.6700.0310.0310.0000.0000.0000.000
40A44GLN0-0.001-0.01030.1590.1940.1940.0000.0000.0000.000
41A45LYS10.9490.98531.3209.1249.1240.0000.0000.0000.000
42A46ASP-1-0.816-0.90332.185-8.758-8.7580.0000.0000.0000.000
43A47LYS10.8340.89727.76210.07910.0790.0000.0000.0000.000
44A48ARG10.8910.94628.1119.1599.1590.0000.0000.0000.000
45A49PHE00.0800.04323.9730.1470.1470.0000.0000.0000.000
46A50SER0-0.026-0.04426.5790.3830.3830.0000.0000.0000.000
47A51GLY00.0380.03426.1350.1190.1190.0000.0000.0000.000
48A52THR0-0.060-0.03526.394-0.051-0.0510.0000.0000.0000.000
49A53VAL0-0.0080.01121.2120.0660.0660.0000.0000.0000.000
50A54ARG10.9400.97024.29911.27011.2700.0000.0000.0000.000
51A55LEU0-0.020-0.00620.433-0.658-0.6580.0000.0000.0000.000
52A56LYS11.0391.02020.16814.94614.9460.0000.0000.0000.000
53A57SER0-0.057-0.03820.4650.3040.3040.0000.0000.0000.000
54A58THR00.0250.00123.5970.0400.0400.0000.0000.0000.000
55A59PRO00.0330.01721.5490.1240.1240.0000.0000.0000.000
56A60ARG10.9470.95923.43711.31911.3190.0000.0000.0000.000
57A61PRO00.0090.01026.9260.2690.2690.0000.0000.0000.000
58A62LYS10.9390.98729.9759.5199.5190.0000.0000.0000.000
59A63PHE0-0.034-0.02629.286-0.137-0.1370.0000.0000.0000.000
60A64SER0-0.0040.01534.1820.1090.1090.0000.0000.0000.000
61A65VAL00.0520.02435.314-0.168-0.1680.0000.0000.0000.000
62A66CYS0-0.031-0.00938.1540.2710.2710.0000.0000.0000.000
63A67VAL00.0070.00140.277-0.161-0.1610.0000.0000.0000.000
64A68LEU0-0.026-0.00742.6390.2000.2000.0000.0000.0000.000
65A69GLY0-0.005-0.01544.486-0.153-0.1530.0000.0000.0000.000
66A70ASP-1-0.802-0.87946.596-6.566-6.5660.0000.0000.0000.000
67A71GLN00.0550.02749.242-0.008-0.0080.0000.0000.0000.000
68A72GLN0-0.017-0.02648.9640.0220.0220.0000.0000.0000.000
69A73HIS10.8810.94045.1386.8826.8820.0000.0000.0000.000
70A74CYS0-0.103-0.04747.551-0.089-0.0890.0000.0000.0000.000
71A75ASP-1-0.828-0.92449.736-6.367-6.3670.0000.0000.0000.000
72A76GLU-1-0.834-0.91444.704-7.193-7.1930.0000.0000.0000.000
73A77ARG10.8210.89644.5386.6996.6990.0000.0000.0000.000
74A78LYS10.8790.95145.2586.5346.5340.0000.0000.0000.000
75A79ALA00.0680.04145.378-0.051-0.0510.0000.0000.0000.000
76A80VAL0-0.053-0.02339.436-0.142-0.1420.0000.0000.0000.000
77A81ASP-1-0.894-0.93441.411-7.430-7.4300.0000.0000.0000.000
78A82ILE0-0.081-0.03439.355-0.098-0.0980.0000.0000.0000.000
79A83PRO0-0.049-0.04442.7780.2120.2120.0000.0000.0000.000
80A84HIS0-0.012-0.01345.205-0.227-0.2270.0000.0000.0000.000
81A85MET0-0.047-0.00746.7770.1260.1260.0000.0000.0000.000
82A86ASP-1-0.739-0.87848.519-6.113-6.1130.0000.0000.0000.000
83A87ILE0-0.001-0.01351.638-0.028-0.0280.0000.0000.0000.000
84A88GLU-1-0.790-0.90253.752-5.815-5.8150.0000.0000.0000.000
85A89ALA00.0360.02851.8650.0350.0350.0000.0000.0000.000
86A90LEU0-0.006-0.01248.511-0.024-0.0240.0000.0000.0000.000
87A91LYS10.8830.93352.4075.8635.8630.0000.0000.0000.000
88A92LYS10.9050.95555.4705.7115.7110.0000.0000.0000.000
89A93LEU00.0590.02350.7610.0180.0180.0000.0000.0000.000
90A94ASN0-0.021-0.00953.000-0.122-0.1220.0000.0000.0000.000
91A95LYS10.9330.96453.9555.4045.4040.0000.0000.0000.000
92A96ASN00.0700.04453.583-0.004-0.0040.0000.0000.0000.000
93A97LYS10.9270.97851.2245.9875.9870.0000.0000.0000.000
94A98LYS10.9180.93449.2926.1246.1240.0000.0000.0000.000
95A99LEU00.0450.01648.355-0.176-0.1760.0000.0000.0000.000
96A100VAL00.0840.04447.349-0.132-0.1320.0000.0000.0000.000
97A101LYS10.9080.97844.6106.4996.4990.0000.0000.0000.000
98A102LYS10.9160.95543.5346.6016.6010.0000.0000.0000.000
99A103LEU00.0340.02243.887-0.143-0.1430.0000.0000.0000.000
100A104ALA00.0750.03041.560-0.146-0.1460.0000.0000.0000.000
101A105LYS10.8660.92439.3767.4987.4980.0000.0000.0000.000
102A106LYS10.9230.96538.8927.4167.4160.0000.0000.0000.000
103A107TYR00.022-0.00639.298-0.053-0.0530.0000.0000.0000.000
104A108ASP-1-0.880-0.92334.652-9.322-9.3220.0000.0000.0000.000
105A109ALA00.0130.01934.0190.0400.0400.0000.0000.0000.000
106A110PHE0-0.013-0.01436.1720.2200.2200.0000.0000.0000.000
107A111LEU00.0430.02337.828-0.212-0.2120.0000.0000.0000.000
108A112ALA00.0170.00040.0100.2060.2060.0000.0000.0000.000
109A113SER00.017-0.02742.314-0.161-0.1610.0000.0000.0000.000
110A114GLU-1-0.835-0.93244.799-6.603-6.6030.0000.0000.0000.000
111A115SER00.0330.03446.1360.1070.1070.0000.0000.0000.000
112A116LEU00.0170.00347.5650.0920.0920.0000.0000.0000.000
113A117ILE0-0.025-0.00842.5370.0300.0300.0000.0000.0000.000
114A118LYS10.8940.94646.8926.4756.4750.0000.0000.0000.000
115A119GLN0-0.037-0.00850.2510.0580.0580.0000.0000.0000.000
116A120ILE00.0440.01246.3400.0790.0790.0000.0000.0000.000
117A121PRO0-0.005-0.01948.1330.0460.0460.0000.0000.0000.000
118A122ARG10.9530.99349.7975.7605.7600.0000.0000.0000.000
119A123ILE00.0300.00452.3860.0890.0890.0000.0000.0000.000
120A124LEU0-0.046-0.01048.988-0.058-0.0580.0000.0000.0000.000
121A125GLY00.0480.01946.675-0.127-0.1270.0000.0000.0000.000
122A126PRO00.0260.00846.410-0.153-0.1530.0000.0000.0000.000
123A127GLY0-0.0330.00247.544-0.046-0.0460.0000.0000.0000.000
124A128LEU0-0.051-0.04845.028-0.029-0.0290.0000.0000.0000.000
125A129ASN00.0470.02741.571-0.290-0.2900.0000.0000.0000.000
126A130LYS10.9410.97441.0936.9886.9880.0000.0000.0000.000
127A131ALA0-0.026-0.01239.673-0.121-0.1210.0000.0000.0000.000
128A132GLY0-0.012-0.00436.895-0.244-0.2440.0000.0000.0000.000
129A133LYS10.7970.90634.7108.8058.8050.0000.0000.0000.000
130A134PHE00.0050.00537.0390.2200.2200.0000.0000.0000.000
131A135PRO0-0.021-0.00837.113-0.220-0.2200.0000.0000.0000.000
132A136SER00.0050.01934.6480.0620.0620.0000.0000.0000.000
133A137LEU00.0070.00637.1800.2160.2160.0000.0000.0000.000
134A138LEU00.0210.00938.290-0.235-0.2350.0000.0000.0000.000
135A139THR0-0.037-0.04038.529-0.185-0.1850.0000.0000.0000.000
136A140HIS00.0940.02841.461-0.102-0.1020.0000.0000.0000.000
137A141ASN0-0.021-0.00738.215-0.052-0.0520.0000.0000.0000.000
138A142GLU-1-0.830-0.89841.096-7.027-7.0270.0000.0000.0000.000
139A143ASN00.0550.03737.616-0.151-0.1510.0000.0000.0000.000
140A144MET0-0.021-0.02038.771-0.102-0.1020.0000.0000.0000.000
141A145VAL00.0340.03235.109-0.051-0.0510.0000.0000.0000.000
142A146ALA00.0800.03933.015-0.241-0.2410.0000.0000.0000.000
143A147LYS10.8530.93132.4388.4178.4170.0000.0000.0000.000
144A148VAL0-0.020-0.01433.889-0.090-0.0900.0000.0000.0000.000
145A149ASP-1-0.855-0.91430.228-10.054-10.0540.0000.0000.0000.000
146A150GLU-1-0.881-0.94126.274-12.256-12.2560.0000.0000.0000.000
147A151VAL0-0.033-0.01128.786-0.184-0.1840.0000.0000.0000.000
148A152LYS10.8300.89429.8579.9219.9210.0000.0000.0000.000
149A153SER0-0.005-0.00624.802-0.270-0.2700.0000.0000.0000.000
150A154THR0-0.0270.00425.293-0.477-0.4770.0000.0000.0000.000
151A155ILE0-0.0010.00621.2840.2940.2940.0000.0000.0000.000
152A156LYS10.9190.95125.35810.53010.5300.0000.0000.0000.000
153A157PHE00.0430.03319.9190.3980.3980.0000.0000.0000.000
154A158GLN0-0.044-0.03725.2500.3110.3110.0000.0000.0000.000
155A159MET0-0.0210.03326.7290.0640.0640.0000.0000.0000.000
156A160LYS10.9310.95327.65010.27110.2710.0000.0000.0000.000
157A161LYS10.9890.98428.6238.5878.5870.0000.0000.0000.000
158A162VAL00.0380.02727.1400.1880.1880.0000.0000.0000.000
159A163LEU0-0.0090.00423.250-0.193-0.1930.0000.0000.0000.000
160A164CYS0-0.015-0.02221.857-0.420-0.4200.0000.0000.0000.000
161A165LEU0-0.023-0.00420.7880.6670.6670.0000.0000.0000.000
162A166ALA00.0310.02620.871-0.619-0.6190.0000.0000.0000.000
163A167VAL0-0.019-0.01819.3390.4170.4170.0000.0000.0000.000
164A168ALA00.0460.02521.180-0.518-0.5180.0000.0000.0000.000
165A169VAL0-0.061-0.03018.3180.3440.3440.0000.0000.0000.000
166A170GLY00.1060.03819.175-0.838-0.8380.0000.0000.0000.000
167A171HIS0-0.093-0.07320.1560.9570.9570.0000.0000.0000.000
168A172VAL00.0250.02320.412-0.451-0.4510.0000.0000.0000.000
169A173LYS10.9250.97221.21411.16211.1620.0000.0000.0000.000
170A174MET0-0.052-0.00219.8410.6040.6040.0000.0000.0000.000
171A175THR00.020-0.01618.040-0.169-0.1690.0000.0000.0000.000
172A176ASP-1-0.856-0.92113.550-20.976-20.9760.0000.0000.0000.000
173A177ASP-1-0.881-0.95611.299-25.962-25.9620.0000.0000.0000.000
174A178GLU-1-0.780-0.86213.086-16.710-16.7100.0000.0000.0000.000
175A179LEU0-0.026-0.00415.5940.2880.2880.0000.0000.0000.000
176A180VAL0-0.017-0.0169.960-0.119-0.1190.0000.0000.0000.000
177A181TYR00.0020.01611.374-1.490-1.4900.0000.0000.0000.000
178A182ASN0-0.017-0.02412.8070.5920.5920.0000.0000.0000.000
179A183ILE0-0.033-0.00711.4380.8700.8700.0000.0000.0000.000
180A184HIS00.0270.0289.941-0.909-0.9090.0000.0000.0000.000
181A185LEU0-0.0200.00012.8350.6630.6630.0000.0000.0000.000
182A186ALA00.000-0.00415.8960.9590.9590.0000.0000.0000.000
183A187VAL0-0.016-0.01812.9910.8970.8970.0000.0000.0000.000
184A188ASN00.013-0.01412.2320.0930.0930.0000.0000.0000.000
185A189PHE00.0080.01015.4620.7530.7530.0000.0000.0000.000
186A190LEU0-0.020-0.01618.3350.8090.8090.0000.0000.0000.000
187A191VAL0-0.053-0.03113.6810.6180.6180.0000.0000.0000.000
188A192SER00.0110.00217.0080.1560.1560.0000.0000.0000.000
189A193LEU0-0.0200.01219.5290.6700.6700.0000.0000.0000.000
190A194LEU0-0.025-0.00918.7490.7260.7260.0000.0000.0000.000
191A195LYS10.8620.92421.90411.05211.0520.0000.0000.0000.000
192A196LYS10.8780.91819.82912.74512.7450.0000.0000.0000.000
193A197ASN00.0910.06217.349-0.128-0.1280.0000.0000.0000.000
194A198TRP00.0170.0127.380-0.122-0.1220.0000.0000.0000.000
195A199GLN00.0370.01613.9470.1690.1690.0000.0000.0000.000
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