FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: VKQV1

Calculation Name: 1ZE2-B-Xray372

Preferred Name:

Target Type:

Ligand Name: (5s,6r)-5-fluoro-6-hydroxy-pseudouridine-5'-monophosphate

ligand 3-letter code: FHU

PDB ID: 1ZE2

Chain ID: B

ChEMBL ID:

UniProt ID: Q9WZW0

Base Structure: X-ray

Registration Date: 2023-09-27

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 218
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2558700.942631
FMO2-HF: Nuclear repulsion 2472115.767213
FMO2-HF: Total energy -86585.175418
FMO2-MP2: Total energy -86841.642676


3D Structure
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(B:1:MET)


Summations of interaction energy for fragment #1(B: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.
-5.774-1.4694.161-2.397-6.0670.001
Interaction energy analysis for fragmet #1(B:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / q_NPA : -0.001
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].
3B3HIS00.0870.0142.890-4.298-2.0413.016-1.710-3.5620.006
4B4GLY00.001-0.0114.6950.0770.123-0.001-0.007-0.0380.000
5B5ILE0-0.028-0.0028.2970.0560.0560.0000.0000.0000.000
6B6LEU0-0.0010.02011.117-0.020-0.0200.0000.0000.0000.000
7B7VAL0-0.0230.00212.820-0.006-0.0060.0000.0000.0000.000
8B8ALA00.0400.01815.931-0.003-0.0030.0000.0000.0000.000
9B9TYR00.0590.01217.8190.0050.0050.0000.0000.0000.000
10B10LYS10.7360.87420.335-0.008-0.0080.0000.0000.0000.000
11B11PRO00.0460.02622.3730.0040.0040.0000.0000.0000.000
12B12LYS10.8900.92925.501-0.006-0.0060.0000.0000.0000.000
13B13GLY00.0160.01328.160-0.003-0.0030.0000.0000.0000.000
14B14PRO00.0250.03122.7670.0000.0000.0000.0000.0000.000
15B15THR00.008-0.00623.2450.0120.0120.0000.0000.0000.000
16B16SER00.025-0.01120.583-0.005-0.0050.0000.0000.0000.000
17B17HIS0-0.070-0.05517.1110.0040.0040.0000.0000.0000.000
18B18ASP-1-0.743-0.86818.149-0.067-0.0670.0000.0000.0000.000
19B19VAL00.0220.01416.157-0.019-0.0190.0000.0000.0000.000
20B20VAL0-0.031-0.01313.250-0.020-0.0200.0000.0000.0000.000
21B21ASP-1-0.898-0.97213.264-0.183-0.1830.0000.0000.0000.000
22B22GLU-1-0.838-0.92914.065-0.200-0.2000.0000.0000.0000.000
23B23VAL0-0.017-0.0099.546-0.029-0.0290.0000.0000.0000.000
24B24ARG10.7340.8879.1090.0250.0250.0000.0000.0000.000
25B25LYS10.9460.9869.7680.0960.0960.0000.0000.0000.000
26B26LYS10.8330.92010.6820.0260.0260.0000.0000.0000.000
27B27LEU00.0480.0205.027-0.044-0.0440.0000.0000.0000.000
28B28LYS10.9430.9976.0060.1770.1770.0000.0000.0000.000
29B29THR0-0.006-0.0053.706-1.110-0.8010.001-0.042-0.2670.000
30B30ARG10.9630.9816.1280.5950.5950.0000.0000.0000.000
31B31LYS10.9270.9795.773-1.564-1.5640.0000.0000.0000.000
32B32VAL00.0620.0407.7510.0730.0730.0000.0000.0000.000
33B33GLY00.0080.01410.375-0.017-0.0170.0000.0000.0000.000
34B34HIS00.0400.01713.5070.0130.0130.0000.0000.0000.000
35B35GLY00.007-0.00716.1530.0130.0130.0000.0000.0000.000
36B36GLY0-0.041-0.03617.645-0.004-0.0040.0000.0000.0000.000
37B37THR0-0.053-0.01821.150-0.005-0.0050.0000.0000.0000.000
38B38LEU0-0.022-0.00923.0040.0030.0030.0000.0000.0000.000
39B39ASP-1-0.846-0.92324.8220.0120.0120.0000.0000.0000.000
40B40PRO00.008-0.00626.6840.0000.0000.0000.0000.0000.000
41B41PHE00.0200.00927.7130.0000.0000.0000.0000.0000.000
42B42ALA0-0.047-0.01828.6570.0010.0010.0000.0000.0000.000
43B43CYM-1-0.785-0.85926.4030.0110.0110.0000.0000.0000.000
44B44GLY0-0.013-0.02825.1640.0040.0040.0000.0000.0000.000
45B45VAL00.0260.03720.313-0.003-0.0030.0000.0000.0000.000
46B46LEU0-0.091-0.04618.0570.0040.0040.0000.0000.0000.000
47B47ILE00.0050.00515.393-0.001-0.0010.0000.0000.0000.000
48B48ILE00.0350.00011.1440.0010.0010.0000.0000.0000.000
49B49GLY00.0100.01610.628-0.006-0.0060.0000.0000.0000.000
50B50VAL00.0540.0155.1820.0730.0730.0000.0000.0000.000
51B51ASN00.043-0.0122.9140.0981.6671.146-0.630-2.084-0.005
52B52GLN0-0.044-0.0375.033-0.704-0.7040.0000.0000.0000.000
53B53GLY00.0360.0196.913-0.246-0.2460.0000.0000.0000.000
54B54THR0-0.065-0.0228.808-0.132-0.1320.0000.0000.0000.000
55B55ARG10.8740.94010.125-0.883-0.8830.0000.0000.0000.000
56B56ILE00.0050.00712.054-0.058-0.0580.0000.0000.0000.000
57B57LEU0-0.0190.01613.821-0.047-0.0470.0000.0000.0000.000
58B58GLU-1-0.964-1.01515.5580.1860.1860.0000.0000.0000.000
59B59PHE00.0450.03017.604-0.015-0.0150.0000.0000.0000.000
60B60TYR00.0460.02514.710-0.019-0.0190.0000.0000.0000.000
61B61LYS10.8570.92020.382-0.147-0.1470.0000.0000.0000.000
62B62ASP-1-0.890-0.94223.0950.1050.1050.0000.0000.0000.000
63B63LEU0-0.0230.00921.239-0.009-0.0090.0000.0000.0000.000
64B64LYS10.9810.99525.296-0.069-0.0690.0000.0000.0000.000
65B65LYS10.7750.89924.238-0.075-0.0750.0000.0000.0000.000
66B66VAL00.0690.04528.137-0.002-0.0020.0000.0000.0000.000
67B67TYR0-0.011-0.00328.0280.0010.0010.0000.0000.0000.000
68B108GLY00.0420.00341.430-0.001-0.0010.0000.0000.0000.000
69B109GLU-1-0.927-0.99740.1690.0410.0410.0000.0000.0000.000
70B110TYR00.0200.03139.0570.0000.0000.0000.0000.0000.000
71B111ASP-1-0.780-0.90340.0710.0370.0370.0000.0000.0000.000
72B112GLN0-0.038-0.03436.618-0.003-0.0030.0000.0000.0000.000
73B113VAL00.0280.01239.0650.0020.0020.0000.0000.0000.000
74B114PRO0-0.090-0.04634.770-0.001-0.0010.0000.0000.0000.000
75B115PRO00.0420.02534.704-0.002-0.0020.0000.0000.0000.000
76B116ALA00.0810.05736.1250.0010.0010.0000.0000.0000.000
77B117TYR00.0190.00933.7050.0010.0010.0000.0000.0000.000
78B118SER00.009-0.02831.5160.0020.0020.0000.0000.0000.000
79B119ALA0-0.033-0.02126.992-0.001-0.0010.0000.0000.0000.000
80B120LYS10.9310.96029.072-0.042-0.0420.0000.0000.0000.000
81B121LYS10.9580.97727.288-0.049-0.0490.0000.0000.0000.000
82B122TYR00.0480.03033.1120.0010.0010.0000.0000.0000.000
83B123LYS11.0020.99036.114-0.020-0.0200.0000.0000.0000.000
84B124GLY00.0400.03732.718-0.002-0.0020.0000.0000.0000.000
85B125GLU-1-0.888-0.94331.6100.0130.0130.0000.0000.0000.000
86B126ARG10.8550.91224.810-0.035-0.0350.0000.0000.0000.000
87B127LEU00.0720.03431.538-0.003-0.0030.0000.0000.0000.000
88B128TYR0-0.009-0.01026.7130.0000.0000.0000.0000.0000.000
89B129LYS10.8680.94231.214-0.003-0.0030.0000.0000.0000.000
90B130LEU00.0300.02533.313-0.002-0.0020.0000.0000.0000.000
91B131ALA00.000-0.00636.471-0.002-0.0020.0000.0000.0000.000
92B132ARG10.8840.94032.2750.0030.0030.0000.0000.0000.000
93B133GLU-1-0.901-0.94835.539-0.002-0.0020.0000.0000.0000.000
94B134GLY00.0170.01638.706-0.001-0.0010.0000.0000.0000.000
95B135LYS10.9340.97240.865-0.002-0.0020.0000.0000.0000.000
96B136ILE00.0290.01340.3750.0020.0020.0000.0000.0000.000
97B137ILE0-0.0020.00739.1160.0010.0010.0000.0000.0000.000
98B138ASN0-0.025-0.01139.4200.0000.0000.0000.0000.0000.000
99B139LEU0-0.030-0.02936.0800.0010.0010.0000.0000.0000.000
100B140PRO00.0300.01239.235-0.001-0.0010.0000.0000.0000.000
101B141PRO00.0290.02538.9970.0020.0020.0000.0000.0000.000
102B142LYS10.9300.96932.220-0.055-0.0550.0000.0000.0000.000
103B143ARG10.8960.95437.108-0.038-0.0380.0000.0000.0000.000
104B144VAL0-0.145-0.04834.3930.0040.0040.0000.0000.0000.000
105B145LYS10.9981.01633.958-0.055-0.0550.0000.0000.0000.000
106B146ILE0-0.032-0.02136.1880.0010.0010.0000.0000.0000.000
107B147PHE0-0.044-0.02332.3560.0010.0010.0000.0000.0000.000
108B148LYS10.9920.99135.657-0.040-0.0400.0000.0000.0000.000
109B149ILE00.0450.03937.6570.0000.0000.0000.0000.0000.000
110B162ARG10.9430.95631.515-0.029-0.0290.0000.0000.0000.000
111B163VAL00.0140.02334.3360.0000.0000.0000.0000.0000.000
112B164GLU-1-0.905-0.93231.9350.0520.0520.0000.0000.0000.000
113B165VAL0-0.015-0.02130.730-0.002-0.0020.0000.0000.0000.000
114B166SER00.0070.01230.7970.0040.0040.0000.0000.0000.000
115B167PRO00.0530.00927.421-0.004-0.0040.0000.0000.0000.000
116B168GLY0-0.084-0.05228.277-0.002-0.0020.0000.0000.0000.000
117B169THR00.0400.02429.975-0.004-0.0040.0000.0000.0000.000
118B170TYR0-0.030-0.01230.4970.0020.0020.0000.0000.0000.000
119B171ILE00.0960.05831.730-0.001-0.0010.0000.0000.0000.000
120B172ARG10.9050.97831.501-0.019-0.0190.0000.0000.0000.000
121B192VAL0-0.004-0.00628.5050.0010.0010.0000.0000.0000.000
122B193ARG10.8230.92223.877-0.044-0.0440.0000.0000.0000.000
123B194GLU-1-0.829-0.94625.7980.0340.0340.0000.0000.0000.000
124B195SER00.0740.03224.7330.0010.0010.0000.0000.0000.000
125B196VAL0-0.079-0.03621.500-0.002-0.0020.0000.0000.0000.000
126B197GLY0-0.009-0.01422.3800.0090.0090.0000.0000.0000.000
127B198PRO00.0160.02121.676-0.005-0.0050.0000.0000.0000.000
128B199HIS10.8210.90717.568-0.102-0.1020.0000.0000.0000.000
129B200THR00.033-0.00321.844-0.006-0.0060.0000.0000.0000.000
130B201ILE00.0430.00023.623-0.001-0.0010.0000.0000.0000.000
131B202GLU-1-0.941-0.96523.8100.0390.0390.0000.0000.0000.000
132B203GLU-1-0.839-0.87520.0660.0800.0800.0000.0000.0000.000
133B204SER0-0.131-0.07219.0510.0040.0040.0000.0000.0000.000
134B205LEU00.1160.04913.9040.0050.0050.0000.0000.0000.000
135B206ASN00.0350.02218.092-0.016-0.0160.0000.0000.0000.000
136B207VAL00.0480.00413.931-0.002-0.0020.0000.0000.0000.000
137B208PHE0-0.082-0.04616.358-0.014-0.0140.0000.0000.0000.000
138B209GLU-1-0.926-0.95818.472-0.013-0.0130.0000.0000.0000.000
139B210ALA00.0390.06614.8320.0050.0050.0000.0000.0000.000
140B211ALA00.0220.00414.077-0.042-0.0420.0000.0000.0000.000
141B212PRO0-0.040-0.0449.2110.0120.0120.0000.0000.0000.000
142B213GLU-1-0.839-0.9248.9080.2000.2000.0000.0000.0000.000
143B214GLU-1-0.905-0.94810.4920.1120.1120.0000.0000.0000.000
144B215ILE0-0.054-0.0399.656-0.015-0.0150.0000.0000.0000.000
145B216GLU-1-0.972-0.9964.5922.5942.718-0.001-0.008-0.1160.000
146B217ASN0-0.026-0.0078.271-0.047-0.0470.0000.0000.0000.000
147B218ARG10.9700.98711.390-0.133-0.1330.0000.0000.0000.000
148B219ILE0-0.048-0.0036.876-0.077-0.0770.0000.0000.0000.000
149B220ILE0-0.026-0.02410.7550.0300.0300.0000.0000.0000.000
150B221PRO00.0590.0139.369-0.018-0.0180.0000.0000.0000.000
151B222LEU00.015-0.0139.1770.0430.0430.0000.0000.0000.000
152B223GLU-1-0.859-0.93610.8850.1980.1980.0000.0000.0000.000
153B224LYS10.9360.97513.587-0.131-0.1310.0000.0000.0000.000
154B225CYS0-0.079-0.02712.550-0.009-0.0090.0000.0000.0000.000
155B226LEU0-0.060-0.03915.5650.0090.0090.0000.0000.0000.000
156B227GLU-1-0.859-0.92418.8040.0950.0950.0000.0000.0000.000
157B228TRP00.002-0.00619.831-0.003-0.0030.0000.0000.0000.000
158B229LEU0-0.015-0.01020.3660.0090.0090.0000.0000.0000.000
159B230PRO00.1270.07023.2410.0060.0060.0000.0000.0000.000
160B231ARG10.8660.93321.197-0.104-0.1040.0000.0000.0000.000
161B232VAL00.0280.05223.420-0.003-0.0030.0000.0000.0000.000
162B233VAL00.006-0.00322.8120.0140.0140.0000.0000.0000.000
163B234VAL0-0.022-0.00722.853-0.009-0.0090.0000.0000.0000.000
164B235HIS00.1260.05224.9100.0020.0020.0000.0000.0000.000
165B236GLN0-0.034-0.02520.1810.0240.0240.0000.0000.0000.000
166B237GLU-1-0.908-0.94322.9950.0870.0870.0000.0000.0000.000
167B238SER0-0.004-0.00824.2910.0030.0030.0000.0000.0000.000
168B239THR0-0.018-0.03917.9560.0160.0160.0000.0000.0000.000
169B240LYS10.9190.96118.974-0.133-0.1330.0000.0000.0000.000
170B241MET0-0.0130.00120.923-0.002-0.0020.0000.0000.0000.000
171B242ILE00.0570.01719.8640.0120.0120.0000.0000.0000.000
172B243LEU0-0.073-0.02314.7820.0290.0290.0000.0000.0000.000
173B244ASN0-0.060-0.03617.6070.0200.0200.0000.0000.0000.000
174B245GLY00.0070.02719.643-0.012-0.0120.0000.0000.0000.000
175B246SER0-0.0060.00422.064-0.006-0.0060.0000.0000.0000.000
176B247GLN0-0.028-0.02824.4400.0060.0060.0000.0000.0000.000
177B248ILE00.015-0.00422.8900.0020.0020.0000.0000.0000.000
178B249HIS00.028-0.01626.644-0.005-0.0050.0000.0000.0000.000
179B250LEU00.016-0.01129.9910.0030.0030.0000.0000.0000.000
180B251GLU-1-0.964-0.96132.5770.0730.0730.0000.0000.0000.000
181B252MET0-0.0280.01925.6340.0030.0030.0000.0000.0000.000
182B253LEU0-0.034-0.02126.9710.0020.0020.0000.0000.0000.000
183B254LYS10.9020.96127.557-0.091-0.0910.0000.0000.0000.000
184B255GLU-1-0.920-0.96226.2120.0940.0940.0000.0000.0000.000
185B256TRP0-0.025-0.02228.6600.0050.0050.0000.0000.0000.000
186B257ASP-1-0.944-0.98727.1060.1030.1030.0000.0000.0000.000
187B258GLY00.004-0.00129.779-0.001-0.0010.0000.0000.0000.000
188B259PHE0-0.0310.00327.1310.0020.0020.0000.0000.0000.000
189B260LYS11.0080.99530.923-0.075-0.0750.0000.0000.0000.000
190B261LYS10.8930.92831.538-0.088-0.0880.0000.0000.0000.000
191B262GLY00.0360.05430.2280.0050.0050.0000.0000.0000.000
192B263GLU-1-0.983-0.99927.3050.0980.0980.0000.0000.0000.000
193B264VAL0-0.022-0.02021.3530.0060.0060.0000.0000.0000.000
194B265VAL00.0210.01023.386-0.007-0.0070.0000.0000.0000.000
195B266ARG10.8310.89618.398-0.124-0.1240.0000.0000.0000.000
196B267VAL00.0270.02320.089-0.013-0.0130.0000.0000.0000.000
197B268PHE0-0.019-0.00917.7040.0290.0290.0000.0000.0000.000
198B269ASN00.0230.02316.592-0.016-0.0160.0000.0000.0000.000
199B270GLU-1-0.740-0.91220.6100.0880.0880.0000.0000.0000.000
200B271GLU-1-0.931-0.94117.5380.0950.0950.0000.0000.0000.000
201B272GLY0-0.012-0.01618.400-0.005-0.0050.0000.0000.0000.000
202B273ARG10.9380.98312.524-0.323-0.3230.0000.0000.0000.000
203B274LEU0-0.079-0.03713.5970.0050.0050.0000.0000.0000.000
204B275LEU0-0.010-0.00314.2400.0570.0570.0000.0000.0000.000
205B276ALA0-0.006-0.02915.8880.0630.0630.0000.0000.0000.000
206B277LEU0-0.0580.00016.137-0.021-0.0210.0000.0000.0000.000
207B278ALA00.009-0.00119.1340.0070.0070.0000.0000.0000.000
208B279GLU-1-0.919-0.97222.8260.1320.1320.0000.0000.0000.000
209B280ALA0-0.0070.01126.084-0.002-0.0020.0000.0000.0000.000
210B281GLU-1-0.831-0.91329.3630.0950.0950.0000.0000.0000.000
211B282ARG10.8630.91931.951-0.080-0.0800.0000.0000.0000.000
212B283ASN00.0380.03533.7350.0020.0020.0000.0000.0000.000
213B303ARG10.9980.98920.894-0.180-0.1800.0000.0000.0000.000
214B304LYS10.8470.94414.790-0.358-0.3580.0000.0000.0000.000
215B305VAL00.0690.03014.738-0.014-0.0140.0000.0000.0000.000
216B306PHE0-0.047-0.03411.0440.1090.1090.0000.0000.0000.000
217B307GLN00.0050.00110.489-0.173-0.1730.0000.0000.0000.000
218B308THR0-0.0150.0105.8280.5760.5760.0000.0000.0000.000