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: G79R1

Calculation Name: 1VQO-C-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: C

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 246
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2555062.576118
FMO2-HF: Nuclear repulsion 2463376.661028
FMO2-HF: Total energy -91685.915089
FMO2-MP2: Total energy -91957.956668


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(C:1:MET)


Summations of interaction energy for fragment #1(C:1:MET)
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.
-472.203-464.89618.193-13.263-12.236-0.143
Interaction energy analysis for fragmet #1(C:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.739 / q_NPA : 0.864
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].
3C3ALA00.0150.0023.451-1.1611.5240.058-1.256-1.487-0.005
17C17ASP-1-0.939-0.9754.202-53.192-52.944-0.001-0.057-0.1890.000
18C18LEU0-0.0140.0002.2373.8525.9942.074-1.427-2.7890.001
19C19PRO00.0160.0072.062-32.865-30.4753.580-3.328-2.643-0.050
20C20ASP-1-0.850-0.9424.814-48.525-48.413-0.001-0.003-0.1080.000
23C23GLU-1-0.852-0.9161.757-116.311-116.72312.485-7.190-4.884-0.089
119C119ALA00.0140.0094.7390.0580.115-0.001-0.002-0.0530.000
120C120ASP-1-0.921-0.9395.199-25.316-25.231-0.0010.000-0.0830.000
4C4THR0-0.017-0.0255.9021.0721.0720.0000.0000.0000.000
5C5ILE0-0.0260.0109.4180.2730.2730.0000.0000.0000.000
6C6TYR0-0.0020.00311.6790.5090.5090.0000.0000.0000.000
7C7ASP-1-0.718-0.85315.587-14.235-14.2350.0000.0000.0000.000
8C8LEU0-0.017-0.01819.213-0.004-0.0040.0000.0000.0000.000
9C9ASP-1-0.999-1.00022.063-11.528-11.5280.0000.0000.0000.000
10C10GLY0-0.033-0.02319.1550.2360.2360.0000.0000.0000.000
11C11ASN0-0.105-0.05018.377-0.205-0.2050.0000.0000.0000.000
12C12THR0-0.042-0.02413.639-0.325-0.3250.0000.0000.0000.000
13C13ASP-1-0.976-0.98814.821-15.653-15.6530.0000.0000.0000.000
14C14GLY0-0.0010.00113.230-0.461-0.4610.0000.0000.0000.000
15C15GLU-1-0.924-0.9777.702-33.526-33.5260.0000.0000.0000.000
16C16VAL00.0060.0158.0791.3381.3380.0000.0000.0000.000
21C21VAL0-0.060-0.0165.7822.8822.8820.0000.0000.0000.000
22C22PHE00.0340.0095.1485.4465.4460.0000.0000.0000.000
24C24THR0-0.117-0.0646.4705.4355.4350.0000.0000.0000.000
25C25PRO0-0.042-0.0219.7720.7340.7340.0000.0000.0000.000
26C26VAL00.0920.05910.2271.3641.3640.0000.0000.0000.000
27C27ARG10.8320.90912.84216.93816.9380.0000.0000.0000.000
28C28SER00.0900.03116.5830.4290.4290.0000.0000.0000.000
29C29ASP-1-0.872-0.92118.819-13.670-13.6700.0000.0000.0000.000
30C30LEU0-0.023-0.01919.3220.6060.6060.0000.0000.0000.000
31C31ILE00.0570.04315.2600.6480.6480.0000.0000.0000.000
32C32GLY00.0460.01719.8940.5210.5210.0000.0000.0000.000
33C33LYS10.7180.83623.11812.28112.2810.0000.0000.0000.000
34C34ALA00.0440.01122.0250.5180.5180.0000.0000.0000.000
35C35VAL00.0180.02822.0710.4810.4810.0000.0000.0000.000
36C36ARG10.9220.96124.80511.68711.6870.0000.0000.0000.000
37C37ALA00.0110.00327.4670.4660.4660.0000.0000.0000.000
38C38ALA00.0460.03026.5160.4250.4250.0000.0000.0000.000
39C39GLN0-0.070-0.04327.2850.6730.6730.0000.0000.0000.000
40C40ALA0-0.053-0.01030.3460.4110.4110.0000.0000.0000.000
41C41ASN00.0620.01630.7320.6240.6240.0000.0000.0000.000
42C42ARG10.8260.90328.28910.85510.8550.0000.0000.0000.000
43C43LYS10.7570.87233.3419.4829.4820.0000.0000.0000.000
44C44GLN00.0180.01437.5930.1810.1810.0000.0000.0000.000
45C45ASP-1-0.828-0.91141.183-7.492-7.4920.0000.0000.0000.000
46C46TYR0-0.065-0.04842.5050.0710.0710.0000.0000.0000.000
47C47GLY00.0370.01246.692-0.054-0.0540.0000.0000.0000.000
48C48SER0-0.075-0.03149.8300.0360.0360.0000.0000.0000.000
49C49ASP-1-0.769-0.86553.215-5.491-5.4910.0000.0000.0000.000
50C50GLU-1-0.880-0.93955.137-5.808-5.8080.0000.0000.0000.000
51C51TYR0-0.001-0.00757.3500.1300.1300.0000.0000.0000.000
52C52ALA0-0.033-0.01658.2740.1150.1150.0000.0000.0000.000
53C53GLY0-0.019-0.01560.231-0.013-0.0130.0000.0000.0000.000
54C54LEU0-0.004-0.01961.4520.1050.1050.0000.0000.0000.000
55C55ARG10.8260.91160.4285.3335.3330.0000.0000.0000.000
56C56THR0-0.017-0.02266.7750.0650.0650.0000.0000.0000.000
57C57PRO00.0660.04169.970-0.041-0.0410.0000.0000.0000.000
58C58ALA0-0.038-0.00170.9640.0430.0430.0000.0000.0000.000
59C59GLU-1-0.825-0.90672.470-4.273-4.2730.0000.0000.0000.000
60C60SER0-0.063-0.03873.4700.0260.0260.0000.0000.0000.000
61C61PHE00.000-0.01675.2610.0300.0300.0000.0000.0000.000
62C62GLY00.0220.03477.3670.0470.0470.0000.0000.0000.000
63C63SER00.004-0.02878.6620.0030.0030.0000.0000.0000.000
64C64GLY00.0190.01980.9630.0240.0240.0000.0000.0000.000
65C65ARG10.9350.96780.0063.9663.9660.0000.0000.0000.000
66C66GLY00.0240.01781.813-0.017-0.0170.0000.0000.0000.000
67C67GLN0-0.0040.00176.660-0.048-0.0480.0000.0000.0000.000
68C68ALA00.0670.03572.7980.0000.0000.0000.0000.0000.000
69C69HIS00.0260.03973.6090.0450.0450.0000.0000.0000.000
70C70VAL0-0.022-0.01669.466-0.061-0.0610.0000.0000.0000.000
71C71PRO0-0.002-0.00969.6760.0600.0600.0000.0000.0000.000
72C72LYS10.8540.91271.5264.1914.1910.0000.0000.0000.000
73C73LEU00.0610.03273.5170.0140.0140.0000.0000.0000.000
74C74ASP-1-0.856-0.92074.942-4.239-4.2390.0000.0000.0000.000
75C75GLY0-0.011-0.00176.9820.0000.0000.0000.0000.0000.000
76C76ARG10.8930.93870.5614.4034.4030.0000.0000.0000.000
77C77ALA00.0170.01269.734-0.012-0.0120.0000.0000.0000.000
78C78ARG10.9180.93967.7664.5964.5960.0000.0000.0000.000
79C79ARG10.9010.96065.4474.6834.6830.0000.0000.0000.000
80C80VAL0-0.013-0.00764.074-0.091-0.0910.0000.0000.0000.000
81C81PRO00.0280.00259.6360.0190.0190.0000.0000.0000.000
82C82GLN00.0540.03761.309-0.102-0.1020.0000.0000.0000.000
83C83ALA0-0.034-0.00463.5360.0670.0670.0000.0000.0000.000
84C84VAL00.0550.01963.646-0.075-0.0750.0000.0000.0000.000
85C85LYS10.8690.91963.1435.0385.0380.0000.0000.0000.000
86C86GLY00.0020.02263.7060.0430.0430.0000.0000.0000.000
87C87ARG10.9060.95257.7065.3755.3750.0000.0000.0000.000
88C88SER00.0250.01054.0520.0130.0130.0000.0000.0000.000
89C89ALA0-0.006-0.01356.3020.0180.0180.0000.0000.0000.000
90C90HIS00.0250.00552.081-0.005-0.0050.0000.0000.0000.000
91C91PRO0-0.0220.00951.712-0.080-0.0800.0000.0000.0000.000
92C92PRO0-0.009-0.01146.908-0.042-0.0420.0000.0000.0000.000
93C93LYS10.9420.97847.6936.3286.3280.0000.0000.0000.000
94C94THR00.0490.02347.074-0.191-0.1910.0000.0000.0000.000
95C95GLU-1-0.826-0.92946.834-6.487-6.4870.0000.0000.0000.000
96C96LYS10.8250.93341.1797.5517.5510.0000.0000.0000.000
97C97ASP-1-0.741-0.85139.621-8.272-8.2720.0000.0000.0000.000
98C98ARG10.7290.85238.6037.4687.4680.0000.0000.0000.000
99C99SER0-0.032-0.01535.595-0.236-0.2360.0000.0000.0000.000
100C100LEU0-0.078-0.05631.5160.0930.0930.0000.0000.0000.000
101C101ASP-1-0.852-0.91531.829-9.798-9.7980.0000.0000.0000.000
102C102LEU0-0.066-0.04324.488-0.127-0.1270.0000.0000.0000.000
103C103ASN00.0040.00926.6950.1310.1310.0000.0000.0000.000
104C104ASP-1-0.784-0.88024.457-12.613-12.6130.0000.0000.0000.000
105C105LYS10.9730.98021.75012.40512.4050.0000.0000.0000.000
106C106GLU-1-0.843-0.89820.866-12.940-12.9400.0000.0000.0000.000
107C107ARG10.8820.91121.42612.58012.5800.0000.0000.0000.000
108C108GLN00.0240.00918.563-0.553-0.5530.0000.0000.0000.000
109C109LEU0-0.0070.00815.691-0.841-0.8410.0000.0000.0000.000
110C110ALA0-0.016-0.01616.418-0.903-0.9030.0000.0000.0000.000
111C111VAL00.0060.00615.724-0.299-0.2990.0000.0000.0000.000
112C112ARG10.8680.90212.74919.58719.5870.0000.0000.0000.000
113C113SER0-0.025-0.02512.009-1.381-1.3810.0000.0000.0000.000
114C114ALA0-0.038-0.02812.421-0.392-0.3920.0000.0000.0000.000
115C115LEU00.0350.02410.6010.3780.3780.0000.0000.0000.000
116C116ALA00.0200.0197.959-1.089-1.0890.0000.0000.0000.000
117C117ALA0-0.052-0.0358.024-0.583-0.5830.0000.0000.0000.000
118C118THR0-0.058-0.03510.3531.6561.6560.0000.0000.0000.000
121C121ALA00.0800.0206.9832.0042.0040.0000.0000.0000.000
122C122ASP-1-0.913-0.9469.015-18.343-18.3430.0000.0000.0000.000
123C123LEU0-0.036-0.03210.4391.5341.5340.0000.0000.0000.000
124C124VAL0-0.029-0.00511.0391.3741.3740.0000.0000.0000.000
125C125ALA00.0250.01713.0841.1061.1060.0000.0000.0000.000
126C126ASP-1-0.945-0.97114.752-14.270-14.2700.0000.0000.0000.000
127C127ARG10.6490.81415.96715.63915.6390.0000.0000.0000.000
128C128GLY0-0.062-0.03717.8420.6410.6410.0000.0000.0000.000
129C129HIS0-0.110-0.06116.3910.3730.3730.0000.0000.0000.000
130C130GLU-1-0.931-0.97417.739-12.523-12.5230.0000.0000.0000.000
131C131PHE0-0.068-0.05212.0920.1810.1810.0000.0000.0000.000
132C132ASP-1-0.943-0.95616.625-13.205-13.2050.0000.0000.0000.000
133C133ARG10.8500.9139.95322.66422.6640.0000.0000.0000.000
134C134ASP-1-0.928-0.96610.227-18.528-18.5280.0000.0000.0000.000
135C135GLU-1-0.870-0.9077.063-26.567-26.5670.0000.0000.0000.000
136C136VAL0-0.0290.0047.0062.0802.0800.0000.0000.0000.000
137C137PRO0-0.001-0.0076.598-2.795-2.7950.0000.0000.0000.000
138C138VAL00.001-0.0029.404-0.740-0.7400.0000.0000.0000.000
139C139VAL00.0210.0098.686-0.213-0.2130.0000.0000.0000.000
140C140VAL0-0.030-0.01111.9020.6960.6960.0000.0000.0000.000
141C141SER00.0530.00615.439-0.233-0.2330.0000.0000.0000.000
142C142ASP-1-0.719-0.83917.428-17.855-17.8550.0000.0000.0000.000
143C143ASP-1-0.904-0.93019.587-13.516-13.5160.0000.0000.0000.000
144C144PHE0-0.038-0.03219.7410.7360.7360.0000.0000.0000.000
145C145GLU-1-0.787-0.91821.022-14.283-14.2830.0000.0000.0000.000
146C146ASP-1-0.939-0.95023.734-11.389-11.3890.0000.0000.0000.000
147C147LEU0-0.055-0.00723.2590.6040.6040.0000.0000.0000.000
148C148VAL0-0.038-0.02426.9650.2420.2420.0000.0000.0000.000
149C149LYS10.8250.89530.1939.2719.2710.0000.0000.0000.000
150C150THR00.027-0.00128.364-0.061-0.0610.0000.0000.0000.000
151C151GLN0-0.057-0.03928.233-0.194-0.1940.0000.0000.0000.000
152C152GLU-1-0.817-0.89427.180-10.589-10.5890.0000.0000.0000.000
153C153VAL00.0350.02022.968-0.297-0.2970.0000.0000.0000.000
154C154VAL0-0.071-0.03823.944-0.345-0.3450.0000.0000.0000.000
155C155SER00.0220.00124.980-0.110-0.1100.0000.0000.0000.000
156C156LEU00.0200.02319.482-0.088-0.0880.0000.0000.0000.000
157C157LEU0-0.020-0.02319.415-0.517-0.5170.0000.0000.0000.000
158C158GLU-1-0.999-1.01721.001-10.985-10.9850.0000.0000.0000.000
159C159ALA0-0.028-0.00921.754-0.053-0.0530.0000.0000.0000.000
160C160LEU00.0020.01515.812-0.463-0.4630.0000.0000.0000.000
161C161ASP-1-0.934-0.94616.882-15.076-15.0760.0000.0000.0000.000
162C162VAL00.0270.00416.544-0.134-0.1340.0000.0000.0000.000
163C163HIS10.8230.90318.90811.55011.5500.0000.0000.0000.000
164C164ALA00.0590.03421.3650.3650.3650.0000.0000.0000.000
165C165ASP-1-0.663-0.80919.571-13.377-13.3770.0000.0000.0000.000
166C166ILE0-0.047-0.02821.7220.3240.3240.0000.0000.0000.000
167C167ASP-1-0.841-0.91224.676-10.355-10.3550.0000.0000.0000.000
168C168ARG10.7910.90921.17613.28313.2830.0000.0000.0000.000
169C169ALA0-0.025-0.01125.1450.2550.2550.0000.0000.0000.000
170C170ASP-1-0.912-0.96027.004-9.098-9.0980.0000.0000.0000.000
171C171GLU-1-0.901-0.93530.176-8.946-8.9460.0000.0000.0000.000
172C172THR0-0.094-0.06031.306-0.135-0.1350.0000.0000.0000.000
173C173LYS10.9620.98133.4398.8798.8790.0000.0000.0000.000
174C174ILE0-0.009-0.01835.0810.0090.0090.0000.0000.0000.000
175C175LYS10.8060.90135.2028.3738.3730.0000.0000.0000.000
176C176ALA00.0470.03038.6180.1980.1980.0000.0000.0000.000
177C177GLY00.0410.01840.623-0.113-0.1130.0000.0000.0000.000
178C178GLN0-0.011-0.03243.346-0.077-0.0770.0000.0000.0000.000
179C179GLY00.0020.00340.7630.0060.0060.0000.0000.0000.000
180C180SER00.0280.01441.773-0.043-0.0430.0000.0000.0000.000
181C181ALA00.002-0.00343.2710.0110.0110.0000.0000.0000.000
182C182ARG10.9090.95443.2336.9506.9500.0000.0000.0000.000
183C183GLY00.0900.05642.531-0.120-0.1200.0000.0000.0000.000
184C184ARG10.9300.97238.0487.6007.6000.0000.0000.0000.000
185C185LYS10.9740.99138.6927.0317.0310.0000.0000.0000.000
186C186TYR00.0850.03236.0210.1580.1580.0000.0000.0000.000
187C187ARG10.9010.95427.24310.20810.2080.0000.0000.0000.000
188C188ARG10.8610.94028.73910.03610.0360.0000.0000.0000.000
189C189PRO0-0.031-0.01125.283-0.029-0.0290.0000.0000.0000.000
190C190ALA0-0.0100.01022.9600.1840.1840.0000.0000.0000.000
191C191SER0-0.015-0.03221.430-0.310-0.3100.0000.0000.0000.000
192C192ILE00.0680.05017.841-0.316-0.3160.0000.0000.0000.000
193C193LEU0-0.083-0.02816.8470.8570.8570.0000.0000.0000.000
194C194PHE00.026-0.00617.510-0.673-0.6730.0000.0000.0000.000
195C195VAL0-0.030-0.01815.5690.7340.7340.0000.0000.0000.000
196C196THR00.004-0.03416.903-0.944-0.9440.0000.0000.0000.000
197C197SER0-0.076-0.05618.100-0.363-0.3630.0000.0000.0000.000
198C198ASP-1-0.916-0.95119.735-13.089-13.0890.0000.0000.0000.000
199C199GLU-1-1.018-1.02123.499-10.483-10.4830.0000.0000.0000.000
200C200PRO0-0.0290.01523.577-0.314-0.3140.0000.0000.0000.000
201C201SER00.0850.04223.0400.7220.7220.0000.0000.0000.000
202C202THR0-0.003-0.02824.9160.2870.2870.0000.0000.0000.000
203C203ALA0-0.0050.01626.6780.3230.3230.0000.0000.0000.000
204C204ALA00.0830.04623.4650.2790.2790.0000.0000.0000.000
205C205ARG10.9520.97825.51410.40910.4090.0000.0000.0000.000
206C206ASN0-0.109-0.05127.1610.3980.3980.0000.0000.0000.000
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