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

tag_button

FMODB ID: R4RL8

Calculation Name: 1VQO-N-Xray549

Preferred Name:

Target Type:

Ligand Name: puromycin-5'-monophosphate | 6-hydro-1-methyladenosine-5'-monophosphate | pseudouridine-5'-monophosphate | o2'-methylguanosine-5'-monophosphate | 3-methyluridine-5'-monophoshate | o2'-methyluridine 5'-monophosphate | cadmium ion | magnesium ion | strontium ion | chloride ion | potassium ion

Ligand 3-letter code: PPU | 1MA | PSU | OMG | UR3 | OMU | CD | MG | SR | CL | K

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1VQO

Chain ID: N

ChEMBL ID:

UniProt ID: P60617

Base Structure: X-ray

Registration Date: 2025-10-11

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 OptH
Protonation MOE:Protonate 3D
Complement ac.sh, 23 2024 Oct
Water No
Procedure Manual calculation
Remarks
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 -1851427.516426
FMO2-HF: Nuclear repulsion 1780249.146779
FMO2-HF: Total energy -71178.369646
FMO2-MP2: Total energy -71389.218586


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(N:1:ALA)


Summations of interaction energy for fragment #1(N:1:ALA)
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.
31.58237.0498.221-5.669-8.018-0.066
Interaction energy analysis for fragmet #1(N:1:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.804 / q_NPA : 0.898
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].
3N3GLY00.0790.0503.3639.79211.877-0.005-0.937-1.144-0.003
4N4PRO00.0270.0043.769-12.153-11.8510.001-0.172-0.131-0.001
6N6TYR00.0220.0112.126-14.068-11.7578.160-4.340-6.130-0.061
7N7LYS10.9560.9714.04127.13427.320-0.001-0.040-0.1440.000
8N8VAL00.0320.0162.971-1.086-0.5030.066-0.180-0.469-0.001
5N5ARG10.9821.0006.11825.31225.3120.0000.0000.0000.000
9N9PRO00.0110.0115.5985.6445.6440.0000.0000.0000.000
10N10MET00.0760.0399.036-1.502-1.5020.0000.0000.0000.000
11N11ARG10.9230.93811.30619.03719.0370.0000.0000.0000.000
12N12ARG10.9920.99712.32415.50515.5050.0000.0000.0000.000
13N13ARG10.9450.97312.69720.67720.6770.0000.0000.0000.000
14N14ARG10.8650.9317.35732.28632.2860.0000.0000.0000.000
15N15GLU-1-0.786-0.89210.955-18.261-18.2610.0000.0000.0000.000
16N16ALA0-0.0110.00814.0980.9960.9960.0000.0000.0000.000
17N17ARG10.9830.99315.97915.79915.7990.0000.0000.0000.000
18N18THR0-0.046-0.03317.8600.7510.7510.0000.0000.0000.000
19N19ASP-1-0.810-0.88218.158-15.147-15.1470.0000.0000.0000.000
20N20TYR00.032-0.01916.3130.0640.0640.0000.0000.0000.000
21N21HIS0-0.0020.01319.1980.8670.8670.0000.0000.0000.000
22N22GLN0-0.044-0.02022.9780.7120.7120.0000.0000.0000.000
23N23ARG10.8740.92122.15613.45313.4530.0000.0000.0000.000
24N24LEU0-0.016-0.00923.8000.3820.3820.0000.0000.0000.000
25N25ARG10.9210.94825.08712.24812.2480.0000.0000.0000.000
26N26LEU00.0460.03727.5050.2420.2420.0000.0000.0000.000
27N27LEU00.0150.01125.7060.2350.2350.0000.0000.0000.000
28N28LYS10.8870.94128.13411.22011.2200.0000.0000.0000.000
29N29SER0-0.016-0.00731.4740.2990.2990.0000.0000.0000.000
30N30GLY0-0.022-0.00833.2820.2670.2670.0000.0000.0000.000
31N31LYS10.8410.92234.7198.0018.0010.0000.0000.0000.000
32N32PRO00.0190.01833.689-0.385-0.3850.0000.0000.0000.000
33N33ARG10.7690.87626.25311.47211.4720.0000.0000.0000.000
34N34LEU00.1120.06232.574-0.043-0.0430.0000.0000.0000.000
35N35VAL0-0.085-0.04428.145-0.254-0.2540.0000.0000.0000.000
36N36ALA00.0630.05430.7800.1490.1490.0000.0000.0000.000
37N37ARG10.7210.83225.13310.94010.9400.0000.0000.0000.000
38N38LYS10.9810.99629.24610.52810.5280.0000.0000.0000.000
39N39SER0-0.067-0.03528.758-0.451-0.4510.0000.0000.0000.000
40N40ASN0-0.011-0.01928.7530.1650.1650.0000.0000.0000.000
41N41LYS11.0081.01031.8358.8968.8960.0000.0000.0000.000
42N42HIS0-0.0080.02432.9730.0750.0750.0000.0000.0000.000
43N43VAL00.0150.00033.165-0.359-0.3590.0000.0000.0000.000
44N44ARG10.9230.97328.72210.22210.2220.0000.0000.0000.000
45N45ALA00.0210.03132.843-0.245-0.2450.0000.0000.0000.000
46N46GLN0-0.046-0.03329.164-0.122-0.1220.0000.0000.0000.000
47N47LEU00.0660.04933.389-0.218-0.2180.0000.0000.0000.000
48N48VAL0-0.063-0.03528.725-0.109-0.1090.0000.0000.0000.000
49N49THR00.0710.03632.157-0.017-0.0170.0000.0000.0000.000
50N50LEU0-0.049-0.03326.077-0.518-0.5180.0000.0000.0000.000
51N51GLY00.1050.06328.2540.3580.3580.0000.0000.0000.000
52N52PRO0-0.066-0.04827.308-0.449-0.4490.0000.0000.0000.000
53N53ASN0-0.027-0.01824.751-0.645-0.6450.0000.0000.0000.000
54N54GLY0-0.057-0.03023.788-0.659-0.6590.0000.0000.0000.000
55N55ASP-1-0.852-0.91224.715-12.100-12.1000.0000.0000.0000.000
56N56ASP-1-0.849-0.92127.030-10.424-10.4240.0000.0000.0000.000
57N57THR0-0.086-0.05530.3950.0410.0410.0000.0000.0000.000
58N58LEU00.0150.00832.5710.0250.0250.0000.0000.0000.000
59N59ALA00.1020.07836.1310.2010.2010.0000.0000.0000.000
60N60SER0-0.113-0.07334.616-0.366-0.3660.0000.0000.0000.000
61N61ALA00.1240.09136.3520.2020.2020.0000.0000.0000.000
62N62HIS0-0.108-0.07132.626-0.265-0.2650.0000.0000.0000.000
63N63SER00.0700.04036.3900.0920.0920.0000.0000.0000.000
64N64SER0-0.072-0.04536.8600.1360.1360.0000.0000.0000.000
65N65ASP-1-0.709-0.85638.390-8.051-8.0510.0000.0000.0000.000
66N66LEU00.0090.01041.0680.1060.1060.0000.0000.0000.000
67N67ALA0-0.017-0.01542.9280.1530.1530.0000.0000.0000.000
68N68GLU-1-1.006-0.99643.571-7.081-7.0810.0000.0000.0000.000
69N69TYR0-0.021-0.03144.2200.0450.0450.0000.0000.0000.000
70N70GLY0-0.0010.01548.3820.1310.1310.0000.0000.0000.000
71N71TRP0-0.062-0.04543.3660.0060.0060.0000.0000.0000.000
72N72GLU-1-0.949-0.97446.472-6.306-6.3060.0000.0000.0000.000
73N73ALA00.0300.04146.104-0.073-0.0730.0000.0000.0000.000
74N74PRO0-0.037-0.01441.335-0.233-0.2330.0000.0000.0000.000
75N75THR00.027-0.00137.6500.0040.0040.0000.0000.0000.000
76N76GLY0-0.045-0.01136.675-0.201-0.2010.0000.0000.0000.000
77N77ASN00.0260.01437.509-0.222-0.2220.0000.0000.0000.000
78N78MET0-0.015-0.01739.799-0.267-0.2670.0000.0000.0000.000
79N79PRO00.0990.06541.363-0.116-0.1160.0000.0000.0000.000
80N80SER00.0430.01538.874-0.023-0.0230.0000.0000.0000.000
81N81ALA0-0.094-0.05237.762-0.125-0.1250.0000.0000.0000.000
82N82TYR0-0.008-0.04239.023-0.154-0.1540.0000.0000.0000.000
83N83LEU00.0490.03541.928-0.054-0.0540.0000.0000.0000.000
84N84THR0-0.037-0.03136.793-0.070-0.0700.0000.0000.0000.000
85N85GLY0-0.059-0.04738.736-0.110-0.1100.0000.0000.0000.000
86N86LEU00.0140.02739.636-0.068-0.0680.0000.0000.0000.000
87N87LEU00.0450.03941.650-0.008-0.0080.0000.0000.0000.000
88N88ALA0-0.074-0.04837.833-0.045-0.0450.0000.0000.0000.000
89N89GLY0-0.005-0.01439.860-0.050-0.0500.0000.0000.0000.000
90N90LEU00.0560.02841.8630.0090.0090.0000.0000.0000.000
91N91ARG10.8180.88239.8517.6217.6210.0000.0000.0000.000
92N92ALA0-0.093-0.06039.961-0.087-0.0870.0000.0000.0000.000
93N93GLN00.0230.01841.537-0.104-0.1040.0000.0000.0000.000
94N94GLU-1-0.911-0.94044.901-6.569-6.5690.0000.0000.0000.000
95N95ALA0-0.107-0.04940.7260.0110.0110.0000.0000.0000.000
96N96GLY0-0.023-0.00942.307-0.110-0.1100.0000.0000.0000.000
97N97VAL0-0.135-0.07438.705-0.132-0.1320.0000.0000.0000.000
98N98GLU-1-0.843-0.91241.777-6.805-6.8050.0000.0000.0000.000
99N99GLU-1-0.820-0.89640.242-7.758-7.7580.0000.0000.0000.000
100N100ALA0-0.045-0.03136.510-0.231-0.2310.0000.0000.0000.000
101N101VAL0-0.019-0.02033.8120.0970.0970.0000.0000.0000.000
102N102LEU00.0130.02633.224-0.291-0.2910.0000.0000.0000.000
103N103ASP-1-0.820-0.91827.369-11.944-11.9440.0000.0000.0000.000
104N104ILE00.0980.06028.803-0.126-0.1260.0000.0000.0000.000
105N105GLY0-0.049-0.02125.304-0.225-0.2250.0000.0000.0000.000
106N106LEU0-0.089-0.05219.777-0.104-0.1040.0000.0000.0000.000
107N107ASN0-0.009-0.00524.4060.1120.1120.0000.0000.0000.000
108N108SER00.0300.00927.914-0.075-0.0750.0000.0000.0000.000
109N109PRO00.001-0.00129.7470.1620.1620.0000.0000.0000.000
110N110THR0-0.0080.00032.8850.1170.1170.0000.0000.0000.000
111N111PRO00.0500.03035.161-0.024-0.0240.0000.0000.0000.000
112N112GLY00.0420.03138.850-0.001-0.0010.0000.0000.0000.000
113N113SER0-0.065-0.04535.235-0.029-0.0290.0000.0000.0000.000
114N114LYS10.9310.93734.5208.7588.7580.0000.0000.0000.000
115N115VAL0-0.068-0.03631.453-0.009-0.0090.0000.0000.0000.000
116N116PHE0-0.030-0.01534.829-0.102-0.1020.0000.0000.0000.000
117N117ALA00.0840.05338.0250.1310.1310.0000.0000.0000.000
118N118ILE0-0.029-0.01334.4670.0310.0310.0000.0000.0000.000
119N119GLN0-0.034-0.03037.524-0.065-0.0650.0000.0000.0000.000
120N120GLU-1-0.855-0.93239.145-6.954-6.9540.0000.0000.0000.000
121N121GLY00.0580.02742.0570.1370.1370.0000.0000.0000.000
122N122ALA0-0.028-0.02639.6970.0720.0720.0000.0000.0000.000
123N123ILE0-0.049-0.03141.8110.0460.0460.0000.0000.0000.000
124N124ASP-1-0.774-0.85644.213-6.512-6.5120.0000.0000.0000.000
125N125ALA0-0.042-0.00244.4690.1270.1270.0000.0000.0000.000
126N126GLY0-0.018-0.00546.4840.0750.0750.0000.0000.0000.000
127N127LEU0-0.0330.00339.951-0.080-0.0800.0000.0000.0000.000
128N128ASP-1-0.881-0.94643.809-6.998-6.9980.0000.0000.0000.000
129N129ILE0-0.030-0.03138.230-0.313-0.3130.0000.0000.0000.000
130N130PRO0-0.090-0.04138.7170.1390.1390.0000.0000.0000.000
131N131HIS10.8170.90038.8717.0347.0340.0000.0000.0000.000
132N132ASN0-0.036-0.03440.7570.2430.2430.0000.0000.0000.000
133N133ASP-1-0.770-0.87942.386-6.978-6.9780.0000.0000.0000.000
134N134ASP-1-0.922-0.94743.683-7.207-7.2070.0000.0000.0000.000
135N135VAL0-0.049-0.02838.047-0.106-0.1060.0000.0000.0000.000
136N136LEU0-0.005-0.00440.425-0.266-0.2660.0000.0000.0000.000
137N137ALA0-0.031-0.01342.4980.0410.0410.0000.0000.0000.000
138N138ASP-1-0.848-0.92543.987-6.468-6.4680.0000.0000.0000.000
139N139TRP00.0770.02446.907-0.088-0.0880.0000.0000.0000.000
140N140GLN00.0500.04349.249-0.034-0.0340.0000.0000.0000.000
141N141ARG10.9210.98340.8177.2587.2580.0000.0000.0000.000
142N142THR0-0.096-0.05743.880-0.162-0.1620.0000.0000.0000.000
143N143ARG10.8110.87645.5295.8995.8990.0000.0000.0000.000
144N144GLY0-0.039-0.02145.9170.0080.0080.0000.0000.0000.000
145N145ALA00.0420.02546.8120.0170.0170.0000.0000.0000.000
146N146HIS0-0.013-0.01743.0000.0780.0780.0000.0000.0000.000
147N147ILE0-0.127-0.04543.764-0.126-0.1260.0000.0000.0000.000
148N148ALA00.1290.07247.2150.0240.0240.0000.0000.0000.000
149N149GLU-1-0.968-0.99250.199-6.089-6.0890.0000.0000.0000.000
150N150TYR0-0.117-0.05644.295-0.012-0.0120.0000.0000.0000.000
151N151ASP-1-0.774-0.89949.162-6.115-6.1150.0000.0000.0000.000
152N152GLU-1-0.915-0.96050.920-5.484-5.4840.0000.0000.0000.000
153N153GLN0-0.199-0.09749.8620.0400.0400.0000.0000.0000.000
154N154LEU0-0.0080.01152.141-0.026-0.0260.0000.0000.0000.000
155N155GLU-1-1.018-0.99452.394-5.914-5.9140.0000.0000.0000.000
156N156GLU-1-1.017-1.02649.952-6.233-6.2330.0000.0000.0000.000
157N157PRO0-0.016-0.01150.544-0.061-0.0610.0000.0000.0000.000
158N158LEU0-0.0130.01244.718-0.176-0.1760.0000.0000.0000.000
159N159TYR0-0.120-0.08144.266-0.394-0.3940.0000.0000.0000.000
160N160SER0-0.054-0.02944.8720.1310.1310.0000.0000.0000.000
161N161GLY0-0.056-0.03546.1930.1100.1100.0000.0000.0000.000
162N162ASP-1-0.936-0.97548.009-5.937-5.9370.0000.0000.0000.000
163N163PHE0-0.0020.00348.757-0.026-0.0260.0000.0000.0000.000
164N164ASP-1-0.798-0.92750.648-6.092-6.0920.0000.0000.0000.000
165N165ALA0-0.030-0.01451.693-0.065-0.0650.0000.0000.0000.000
166N166ALA00.0170.01551.964-0.090-0.0900.0000.0000.0000.000
167N167ASP-1-0.853-0.93548.553-6.548-6.5480.0000.0000.0000.000
168N168LEU00.0070.01351.1710.1480.1480.0000.0000.0000.000
169N169PRO0-0.047-0.02550.263-0.101-0.1010.0000.0000.0000.000
170N170GLU-1-0.824-0.91251.334-5.847-5.8470.0000.0000.0000.000
171N171HIS0-0.0020.00149.327-0.109-0.1090.0000.0000.0000.000
172N172PHE0-0.046-0.02145.454-0.136-0.1360.0000.0000.0000.000
173N173ASP-1-0.831-0.91449.662-6.003-6.0030.0000.0000.0000.000
174N174GLU-1-0.877-0.92352.773-5.797-5.7970.0000.0000.0000.000
175N175LEU00.0020.02046.348-0.023-0.0230.0000.0000.0000.000
176N176ARG10.8550.90749.1796.3006.3000.0000.0000.0000.000
177N177GLU-1-0.962-0.97950.103-5.693-5.6930.0000.0000.0000.000
178N178THR0-0.056-0.04951.1240.0400.0400.0000.0000.0000.000
179N179LEU0-0.066-0.03745.583-0.075-0.0750.0000.0000.0000.000
180N180LEU0-0.050-0.04049.545-0.061-0.0610.0000.0000.0000.000
181N181ASP-1-0.884-0.92951.812-5.629-5.6290.0000.0000.0000.000
182N182GLY0-0.047-0.01752.846-0.110-0.1100.0000.0000.0000.000
183N183ASP-1-0.992-1.00053.784-5.599-5.5990.0000.0000.0000.000
184N184ILE0-0.081-0.02647.664-0.062-0.0620.0000.0000.0000.000
185N185GLU-1-0.957-0.97949.428-6.231-6.2310.0000.0000.0000.000
186N186LEU-1-0.870-0.90544.443-7.380-7.3800.0000.0000.0000.000