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: VZ7N1

Calculation Name: 1VQO-E-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: E

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 172
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1595750.725848
FMO2-HF: Nuclear repulsion 1527711.177417
FMO2-HF: Total energy -68039.548431
FMO2-MP2: Total energy -68237.9541


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(E:1:PRO)


Summations of interaction energy for fragment #1(E:1:PRO)
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.
-527.335-524.25223.874-11.875-15.08-0.131
Interaction energy analysis for fragmet #1(E:1:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.720 / q_NPA : 0.833
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].
3E3VAL0-0.041-0.0133.8840.6052.431-0.015-0.843-0.968-0.003
50E50GLU-1-0.894-0.9504.530-46.829-46.520-0.001-0.073-0.2340.000
51E51SER00.037-0.0102.8816.3867.9770.093-0.598-1.086-0.003
52E52ASP-1-0.909-0.9411.756-89.704-90.80211.726-6.585-4.043-0.078
53E53GLU-1-0.950-0.9753.371-39.037-37.4740.054-0.774-0.843-0.006
54E54ASP-1-0.904-0.9762.332-65.525-65.9857.713-2.612-4.641-0.026
55E55ASN0-0.073-0.0183.10010.90110.0560.1270.925-0.2080.000
58E58THR00.0860.0404.5333.8193.880-0.001-0.005-0.0540.000
59E59MET00.0080.0072.727-6.918-7.4714.114-1.113-2.447-0.013
62E62ILE00.0330.0243.1160.0880.7770.064-0.197-0.556-0.002
4E4GLU-1-0.853-0.9166.703-27.698-27.6980.0000.0000.0000.000
5E5LEU0-0.035-0.01610.4460.6970.6970.0000.0000.0000.000
6E6GLU-1-0.919-0.95813.506-16.660-16.6600.0000.0000.0000.000
7E7ILE0-0.037-0.00216.964-0.049-0.0490.0000.0000.0000.000
8E8PRO0-0.036-0.02319.5230.4660.4660.0000.0000.0000.000
9E9GLU-1-0.973-0.99422.801-10.944-10.9440.0000.0000.0000.000
10E10ASP-1-0.933-0.96526.010-10.545-10.5450.0000.0000.0000.000
11E11VAL0-0.042-0.02221.9770.0950.0950.0000.0000.0000.000
12E12ASP-1-0.907-0.94523.733-12.501-12.5010.0000.0000.0000.000
13E13ALA0-0.035-0.03319.646-0.085-0.0850.0000.0000.0000.000
14E14GLU-1-0.968-0.97521.489-12.850-12.8500.0000.0000.0000.000
15E15GLN0-0.022-0.03614.732-0.097-0.0970.0000.0000.0000.000
16E16ASP-1-0.925-0.94320.019-13.608-13.6080.0000.0000.0000.000
17E17HIS0-0.080-0.05618.347-0.597-0.5970.0000.0000.0000.000
18E18LEU0-0.028-0.02015.267-0.984-0.9840.0000.0000.0000.000
19E19ASP-1-0.914-0.95917.453-15.390-15.3900.0000.0000.0000.000
20E20ILE00.0240.00314.970-0.149-0.1490.0000.0000.0000.000
21E21THR0-0.005-0.01119.5650.2970.2970.0000.0000.0000.000
22E22VAL0-0.017-0.01319.757-0.468-0.4680.0000.0000.0000.000
23E23GLU-1-0.929-0.98022.838-10.825-10.8250.0000.0000.0000.000
24E24GLY00.0820.03725.779-0.403-0.4030.0000.0000.0000.000
25E25ASP-1-0.934-0.95928.074-9.359-9.3590.0000.0000.0000.000
26E26ASN0-0.145-0.05629.1120.6420.6420.0000.0000.0000.000
27E27GLY0-0.021-0.00630.5820.0380.0380.0000.0000.0000.000
28E28SER00.002-0.01426.907-0.272-0.2720.0000.0000.0000.000
29E29VAL0-0.0200.00022.9250.1470.1470.0000.0000.0000.000
30E30THR00.0070.00722.867-0.263-0.2630.0000.0000.0000.000
31E31ARG10.8410.92118.72415.61715.6170.0000.0000.0000.000
32E32ARG10.8960.97918.69814.92414.9240.0000.0000.0000.000
33E33LEU0-0.048-0.01413.496-0.080-0.0800.0000.0000.0000.000
34E34TRP0-0.007-0.01114.3020.1360.1360.0000.0000.0000.000
35E35TYR0-0.005-0.0209.2901.1381.1380.0000.0000.0000.000
36E36PRO0-0.058-0.03711.086-0.266-0.2660.0000.0000.0000.000
37E37ASP-1-0.896-0.9458.024-30.404-30.4040.0000.0000.0000.000
38E38ILE0-0.062-0.0025.996-6.739-6.7390.0000.0000.0000.000
39E39ASP-1-0.926-0.9387.283-27.514-27.5140.0000.0000.0000.000
40E40VAL0-0.030-0.0388.589-3.032-3.0320.0000.0000.0000.000
41E41SER0-0.0140.00611.3291.9581.9580.0000.0000.0000.000
42E42VAL00.0390.01913.627-0.702-0.7020.0000.0000.0000.000
43E43ASP-1-0.986-0.98014.247-20.133-20.1330.0000.0000.0000.000
44E44GLY0-0.029-0.01716.2560.0420.0420.0000.0000.0000.000
45E45ASP-1-0.907-0.94719.442-15.556-15.5560.0000.0000.0000.000
46E46THR0-0.027-0.01914.515-0.783-0.7830.0000.0000.0000.000
47E47VAL00.0240.01012.9930.0920.0920.0000.0000.0000.000
48E48VAL0-0.018-0.0048.675-1.531-1.5310.0000.0000.0000.000
49E49ILE00.0020.0066.7560.7940.7940.0000.0000.0000.000
56E56ALA00.030-0.0046.399-1.234-1.2340.0000.0000.0000.000
57E57LYS10.8870.9628.42221.71621.7160.0000.0000.0000.000
60E60SER0-0.046-0.0315.8302.3712.3710.0000.0000.0000.000
61E61THR0-0.0140.0028.8412.4452.4450.0000.0000.0000.000
63E63GLY00.0190.0117.0221.9401.9400.0000.0000.0000.000
64E64THR0-0.064-0.0449.0392.5652.5650.0000.0000.0000.000
65E65PHE00.007-0.0189.8081.8271.8270.0000.0000.0000.000
66E66GLN0-0.051-0.0249.155-1.063-1.0630.0000.0000.0000.000
67E67SER00.0270.01311.2611.3111.3110.0000.0000.0000.000
68E68HIS0-0.022-0.01414.3551.5831.5830.0000.0000.0000.000
69E69ILE00.0140.01012.6610.9690.9690.0000.0000.0000.000
70E70GLU-1-0.842-0.91413.865-19.275-19.2750.0000.0000.0000.000
71E71ASN00.005-0.01917.0371.2021.2020.0000.0000.0000.000
72E72MET0-0.0180.00417.5960.9020.9020.0000.0000.0000.000
73E73PHE00.0400.01416.6820.6220.6220.0000.0000.0000.000
74E74HIS10.8300.91821.19712.59512.5950.0000.0000.0000.000
75E75GLY00.0100.01323.1210.5440.5440.0000.0000.0000.000
76E76VAL00.0160.00123.8550.5210.5210.0000.0000.0000.000
77E77THR0-0.023-0.01324.8800.3160.3160.0000.0000.0000.000
78E78GLU-1-0.928-0.95626.767-10.835-10.8350.0000.0000.0000.000
79E79GLY00.0090.02327.5270.4030.4030.0000.0000.0000.000
80E80TRP0-0.134-0.05422.132-0.218-0.2180.0000.0000.0000.000
81E81GLU-1-0.843-0.94928.632-8.555-8.5550.0000.0000.0000.000
82E82TYR0-0.043-0.02326.514-0.138-0.1380.0000.0000.0000.000
83E83GLY0-0.029-0.00832.9080.2260.2260.0000.0000.0000.000
84E84MET0-0.077-0.04236.197-0.203-0.2030.0000.0000.0000.000
85E85GLU-1-0.813-0.86838.683-7.209-7.2090.0000.0000.0000.000
86E86VAL0-0.037-0.01042.290-0.083-0.0830.0000.0000.0000.000
87E87PHE0-0.008-0.00744.8560.1470.1470.0000.0000.0000.000
88E88TYR00.002-0.00746.9860.0310.0310.0000.0000.0000.000
89E89SER0-0.061-0.06250.0650.1170.1170.0000.0000.0000.000
90E90HIS0-0.129-0.06752.9900.1810.1810.0000.0000.0000.000
91E91PHE0-0.042-0.02753.7490.1460.1460.0000.0000.0000.000
92E92PRO00.0070.00453.098-0.092-0.0920.0000.0000.0000.000
93E93MET0-0.0100.03246.5990.0110.0110.0000.0000.0000.000
94E94GLN0-0.065-0.02550.4230.0680.0680.0000.0000.0000.000
95E95VAL00.0550.01744.227-0.077-0.0770.0000.0000.0000.000
96E96ASN0-0.022-0.01246.6250.0870.0870.0000.0000.0000.000
97E97VAL00.0740.04142.165-0.101-0.1010.0000.0000.0000.000
98E98GLU-1-0.953-0.97944.752-6.309-6.3090.0000.0000.0000.000
99E99GLY0-0.037-0.02044.632-0.015-0.0150.0000.0000.0000.000
100E100ASP-1-0.882-0.93639.323-7.877-7.8770.0000.0000.0000.000
101E101GLU-1-0.861-0.92839.661-7.416-7.4160.0000.0000.0000.000
102E102VAL00.0270.02839.4510.1690.1690.0000.0000.0000.000
103E103VAL0-0.053-0.03342.492-0.028-0.0280.0000.0000.0000.000
104E104ILE00.0340.01142.9360.0490.0490.0000.0000.0000.000
105E105GLU-1-0.909-0.96247.196-5.976-5.9760.0000.0000.0000.000
106E106ASN0-0.065-0.04550.9420.0570.0570.0000.0000.0000.000
107E107PHE00.0890.04546.1720.0590.0590.0000.0000.0000.000
108E108LEU0-0.030-0.01949.4220.0670.0670.0000.0000.0000.000
109E109GLY0-0.0130.00552.0430.0970.0970.0000.0000.0000.000
110E110GLU-1-0.907-0.92649.507-6.369-6.3690.0000.0000.0000.000
111E111LYS10.9100.92953.7145.3095.3090.0000.0000.0000.000
112E112ALA0-0.045-0.01351.6110.0530.0530.0000.0000.0000.000
113E113PRO00.0180.00849.836-0.056-0.0560.0000.0000.0000.000
114E114ARG10.7410.84944.4426.8546.8540.0000.0000.0000.000
115E115ARG10.8020.88143.8926.8846.8840.0000.0000.0000.000
116E116THR0-0.026-0.01037.410-0.056-0.0560.0000.0000.0000.000
117E117THR0-0.016-0.00837.8140.1080.1080.0000.0000.0000.000
118E118ILE00.0070.01435.536-0.184-0.1840.0000.0000.0000.000
119E119HIS0-0.082-0.03331.056-0.275-0.2750.0000.0000.0000.000
120E120GLY00.0160.00931.258-0.157-0.1570.0000.0000.0000.000
121E121ASP-1-0.936-0.96131.940-9.356-9.3560.0000.0000.0000.000
122E122THR0-0.061-0.03731.940-0.213-0.2130.0000.0000.0000.000
123E123ASP-1-0.907-0.94033.736-8.382-8.3820.0000.0000.0000.000
124E124VAL0-0.046-0.05336.189-0.120-0.1200.0000.0000.0000.000
125E125GLU-1-0.959-0.96538.875-7.350-7.3500.0000.0000.0000.000
126E126ILE0-0.048-0.03441.367-0.095-0.0950.0000.0000.0000.000
127E127ASP-1-0.969-0.97444.147-6.444-6.4440.0000.0000.0000.000
128E128GLY0-0.031-0.02346.562-0.007-0.0070.0000.0000.0000.000
129E129GLU-1-0.912-0.97547.126-6.362-6.3620.0000.0000.0000.000
130E130GLU-1-0.957-0.96842.113-7.430-7.4300.0000.0000.0000.000
131E131LEU0-0.021-0.02539.7710.0840.0840.0000.0000.0000.000
132E132THR0-0.046-0.01236.788-0.211-0.2110.0000.0000.0000.000
133E133VAL0-0.001-0.00233.2860.1320.1320.0000.0000.0000.000
134E134SER00.0170.00232.282-0.244-0.2440.0000.0000.0000.000
135E135GLY00.1170.05131.3440.1540.1540.0000.0000.0000.000
136E136PRO00.0280.02427.451-0.249-0.2490.0000.0000.0000.000
137E137ASP-1-0.843-0.94224.321-13.097-13.0970.0000.0000.0000.000
138E138ILE0-0.008-0.00421.6100.3560.3560.0000.0000.0000.000
139E139GLU-1-0.925-0.96022.047-13.970-13.9700.0000.0000.0000.000
140E140ALA0-0.012-0.00425.1720.4070.4070.0000.0000.0000.000
141E141VAL00.0310.04828.4010.4070.4070.0000.0000.0000.000
142E142GLY00.0180.00427.6110.3160.3160.0000.0000.0000.000
143E143GLN0-0.120-0.06728.1550.0660.0660.0000.0000.0000.000
144E144THR00.0200.01130.2200.4210.4210.0000.0000.0000.000
145E145ALA00.0250.01432.0090.3380.3380.0000.0000.0000.000
146E146ALA00.002-0.00831.0760.2720.2720.0000.0000.0000.000
147E147ASP-1-0.861-0.95233.164-9.144-9.1440.0000.0000.0000.000
148E148ILE0-0.010-0.00135.4650.3320.3320.0000.0000.0000.000
149E149GLU-1-0.854-0.90635.585-8.458-8.4580.0000.0000.0000.000
150E150GLN0-0.069-0.04434.5170.3610.3610.0000.0000.0000.000
151E151LEU0-0.0250.00937.8400.2000.2000.0000.0000.0000.000
152E152THR0-0.032-0.01240.8510.2620.2620.0000.0000.0000.000
153E153ARG10.9090.96837.6368.2188.2180.0000.0000.0000.000
154E154ILE0-0.003-0.00441.8920.1850.1850.0000.0000.0000.000
155E155ASN0-0.027-0.02541.992-0.288-0.2880.0000.0000.0000.000
156E156ASP-1-0.858-0.91944.756-6.541-6.5410.0000.0000.0000.000
157E157LYS10.8350.91748.1516.4146.4140.0000.0000.0000.000
158E158ASP-1-0.816-0.87947.765-6.646-6.6460.0000.0000.0000.000
159E159VAL00.1120.05242.8120.1120.1120.0000.0000.0000.000
160E160ARG10.7920.86746.0896.5116.5110.0000.0000.0000.000
161E161VAL0-0.074-0.02747.6720.1030.1030.0000.0000.0000.000
162E162PHE0-0.032-0.04048.9400.1080.1080.0000.0000.0000.000
163E163GLN00.0380.01045.467-0.029-0.0290.0000.0000.0000.000
164E164ASP-1-0.825-0.84945.809-6.365-6.3650.0000.0000.0000.000
165E165GLY0-0.008-0.01543.561-0.053-0.0530.0000.0000.0000.000
166E166VAL00.0170.00940.3570.1430.1430.0000.0000.0000.000
167E167TYR0-0.073-0.04338.710-0.186-0.1860.0000.0000.0000.000
168E168ILE00.008-0.00632.453-0.009-0.0090.0000.0000.0000.000
169E169THR0-0.075-0.05535.630-0.147-0.1470.0000.0000.0000.000
170E170ARG10.8610.92334.0018.4598.4590.0000.0000.0000.000
171E171LYS10.9120.95628.7339.9929.9920.0000.0000.0000.000
172E172PRO-1-0.890-0.92226.401-11.425-11.4250.0000.0000.0000.000