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

tag_button

FMODB ID: GY581

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 OptAll
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 -2560385.448942
FMO2-HF: Nuclear repulsion 2473796.109785
FMO2-HF: Total energy -86589.339157
FMO2-MP2: Total energy -86845.483098


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.
-1.3463.5376.451-3.3-8.034-0.014
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 : 0.015 / q_NPA : 0.010
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].
3B3HIS00.0590.0092.639-4.409-2.2643.732-1.872-4.006-0.002
4B4GLY00.0390.0175.1090.1460.189-0.001-0.002-0.0400.000
5B5ILE0-0.019-0.0148.753-0.067-0.0670.0000.0000.0000.000
6B6LEU00.0100.01810.6760.0210.0210.0000.0000.0000.000
7B7VAL00.0060.00012.731-0.030-0.0300.0000.0000.0000.000
8B8ALA00.0240.01315.6060.0130.0130.0000.0000.0000.000
9B9TYR00.027-0.04217.3020.0030.0030.0000.0000.0000.000
10B10LYS10.7280.87119.9830.0520.0520.0000.0000.0000.000
11B11PRO00.0560.02121.9260.0070.0070.0000.0000.0000.000
12B12LYS10.7950.84025.0580.0140.0140.0000.0000.0000.000
13B13GLY00.0230.00928.1010.0010.0010.0000.0000.0000.000
14B14PRO00.0280.02822.566-0.005-0.0050.0000.0000.0000.000
15B15THR0-0.037-0.07422.4120.0110.0110.0000.0000.0000.000
16B16SER00.045-0.00920.530-0.002-0.0020.0000.0000.0000.000
17B17HIS0-0.038-0.02016.482-0.024-0.0240.0000.0000.0000.000
18B18ASP-1-0.768-0.83317.329-0.184-0.1840.0000.0000.0000.000
19B19VAL00.0430.02916.135-0.023-0.0230.0000.0000.0000.000
20B20VAL0-0.017-0.00112.738-0.026-0.0260.0000.0000.0000.000
21B21ASP-1-0.794-0.90012.922-0.472-0.4720.0000.0000.0000.000
22B22GLU-1-0.748-0.85113.854-0.284-0.2840.0000.0000.0000.000
23B23VAL00.0320.0159.636-0.033-0.0330.0000.0000.0000.000
24B24ARG10.7320.8618.9700.3850.3850.0000.0000.0000.000
25B25LYS10.8320.9109.5980.0920.0920.0000.0000.0000.000
26B26LYS10.7980.90510.8080.0610.0610.0000.0000.0000.000
27B27LEU00.0200.0075.6670.0230.0230.0000.0000.0000.000
28B28LYS10.9270.9856.030-0.091-0.0910.0000.0000.0000.000
29B29THR00.0180.0033.457-1.594-1.1580.015-0.085-0.3660.000
30B30ARG10.8820.9175.7091.0021.0020.0000.0000.0000.000
31B31LYS10.9310.9794.9730.4240.4240.0000.0000.0000.000
32B32VAL00.0500.0256.9290.0020.0020.0000.0000.0000.000
33B33GLY00.0100.0109.5770.0360.0360.0000.0000.0000.000
34B34HIS00.0120.00813.2750.0230.0230.0000.0000.0000.000
35B35GLY00.0160.01016.3620.0120.0120.0000.0000.0000.000
36B36GLY0-0.010-0.02118.2260.0140.0140.0000.0000.0000.000
37B37THR0-0.0160.01021.757-0.001-0.0010.0000.0000.0000.000
38B38LEU0-0.0050.00123.2450.0110.0110.0000.0000.0000.000
39B39ASP-1-0.799-0.86325.067-0.056-0.0560.0000.0000.0000.000
40B40PRO00.004-0.01026.5980.0020.0020.0000.0000.0000.000
41B41PHE00.0550.02627.6540.0010.0010.0000.0000.0000.000
42B42ALA0-0.0310.00128.8670.0060.0060.0000.0000.0000.000
43B43CYM-1-0.758-0.75026.317-0.027-0.0270.0000.0000.0000.000
44B44GLY00.0470.01925.1640.0050.0050.0000.0000.0000.000
45B45VAL00.0160.01520.773-0.010-0.0100.0000.0000.0000.000
46B46LEU0-0.065-0.03118.203-0.003-0.0030.0000.0000.0000.000
47B47ILE00.0130.01815.695-0.004-0.0040.0000.0000.0000.000
48B48ILE00.0260.01611.402-0.024-0.0240.0000.0000.0000.000
49B49GLY00.0220.02111.0760.0420.0420.0000.0000.0000.000
50B50VAL00.021-0.0035.154-0.094-0.0940.0000.0000.0000.000
51B51ASN00.0540.0032.411-1.831-0.3492.685-1.099-3.067-0.011
52B52GLN0-0.040-0.0375.550-0.581-0.5810.0000.0000.0000.000
53B53GLY00.0530.0437.244-0.146-0.1460.0000.0000.0000.000
54B54THR0-0.053-0.0349.037-0.070-0.0700.0000.0000.0000.000
55B55ARG10.8650.92510.685-0.393-0.3930.0000.0000.0000.000
56B56ILE00.0260.02112.416-0.020-0.0200.0000.0000.0000.000
57B57LEU00.0080.01213.824-0.018-0.0180.0000.0000.0000.000
58B58GLU-1-0.881-0.92015.9900.0550.0550.0000.0000.0000.000
59B59PHE00.0920.03717.494-0.009-0.0090.0000.0000.0000.000
60B60TYR00.0710.02515.326-0.003-0.0030.0000.0000.0000.000
61B61LYS10.7910.89019.7100.0170.0170.0000.0000.0000.000
62B62ASP-1-0.845-0.93523.5650.0260.0260.0000.0000.0000.000
63B63LEU0-0.0320.00421.457-0.002-0.0020.0000.0000.0000.000
64B64LYS10.9020.95625.804-0.030-0.0300.0000.0000.0000.000
65B65LYS10.7380.87224.149-0.002-0.0020.0000.0000.0000.000
66B66VAL00.0370.02728.2500.0000.0000.0000.0000.0000.000
67B67TYR00.0320.01628.700-0.003-0.0030.0000.0000.0000.000
68B108GLY00.0610.03541.0480.0000.0000.0000.0000.0000.000
69B109GLU-1-0.833-0.94240.6220.0080.0080.0000.0000.0000.000
70B110TYR0-0.006-0.00238.8030.0000.0000.0000.0000.0000.000
71B111ASP-1-0.791-0.89040.754-0.001-0.0010.0000.0000.0000.000
72B112GLN0-0.0080.00337.4170.0000.0000.0000.0000.0000.000
73B113VAL00.0260.01139.000-0.001-0.0010.0000.0000.0000.000
74B114PRO0-0.062-0.03134.909-0.001-0.0010.0000.0000.0000.000
75B115PRO00.0480.03934.846-0.001-0.0010.0000.0000.0000.000
76B116ALA00.0730.04935.663-0.003-0.0030.0000.0000.0000.000
77B117TYR0-0.024-0.01433.455-0.004-0.0040.0000.0000.0000.000
78B118SER00.041-0.01031.2020.0010.0010.0000.0000.0000.000
79B119ALA0-0.039-0.02426.453-0.003-0.0030.0000.0000.0000.000
80B120LYS10.9290.96428.2750.0280.0280.0000.0000.0000.000
81B121LYS10.9300.96927.0660.0560.0560.0000.0000.0000.000
82B122TYR00.0230.00832.2240.0030.0030.0000.0000.0000.000
83B123LYS10.9610.97635.6200.0370.0370.0000.0000.0000.000
84B124GLY00.0490.04032.4970.0010.0010.0000.0000.0000.000
85B125GLU-1-0.811-0.91730.913-0.053-0.0530.0000.0000.0000.000
86B126ARG10.8590.92323.8310.0810.0810.0000.0000.0000.000
87B127LEU00.0560.03730.951-0.002-0.0020.0000.0000.0000.000
88B128TYR00.0360.01525.8820.0010.0010.0000.0000.0000.000
89B129LYS10.8470.92530.6000.0670.0670.0000.0000.0000.000
90B130LEU00.0200.00932.8530.0010.0010.0000.0000.0000.000
91B131ALA00.0530.03236.0180.0010.0010.0000.0000.0000.000
92B132ARG10.8780.93531.1290.0700.0700.0000.0000.0000.000
93B133GLU-1-0.851-0.89235.485-0.059-0.0590.0000.0000.0000.000
94B134GLY00.0770.03738.5430.0020.0020.0000.0000.0000.000
95B135LYS10.8530.92639.2580.0500.0500.0000.0000.0000.000
96B136ILE00.007-0.01639.492-0.002-0.0020.0000.0000.0000.000
97B137ILE00.0120.02338.8310.0020.0020.0000.0000.0000.000
98B138ASN0-0.060-0.04438.780-0.001-0.0010.0000.0000.0000.000
99B139LEU0-0.019-0.01535.3170.0000.0000.0000.0000.0000.000
100B140PRO00.0690.02739.3390.0010.0010.0000.0000.0000.000
101B141PRO0-0.0010.01038.875-0.001-0.0010.0000.0000.0000.000
102B142LYS10.8510.92932.4430.0030.0030.0000.0000.0000.000
103B143ARG10.8970.92137.640-0.002-0.0020.0000.0000.0000.000
104B144VAL0-0.093-0.02534.9990.0010.0010.0000.0000.0000.000
105B145LYS10.8880.94935.658-0.010-0.0100.0000.0000.0000.000
106B146ILE0-0.009-0.00836.065-0.001-0.0010.0000.0000.0000.000
107B147PHE0-0.013-0.02733.0520.0010.0010.0000.0000.0000.000
108B148LYS10.9210.95435.381-0.021-0.0210.0000.0000.0000.000
109B149ILE00.0610.04137.970-0.002-0.0020.0000.0000.0000.000
110B162ARG10.9020.94831.880-0.010-0.0100.0000.0000.0000.000
111B163VAL0-0.016-0.01634.3750.0000.0000.0000.0000.0000.000
112B164GLU-1-0.795-0.87732.1910.0230.0230.0000.0000.0000.000
113B165VAL0-0.020-0.01331.357-0.001-0.0010.0000.0000.0000.000
114B166SER00.0090.00831.2610.0020.0020.0000.0000.0000.000
115B167PRO00.0490.03627.689-0.005-0.0050.0000.0000.0000.000
116B168GLY0-0.043-0.03629.1130.0000.0000.0000.0000.0000.000
117B169THR00.012-0.00330.565-0.003-0.0030.0000.0000.0000.000
118B170TYR0-0.020-0.00529.765-0.001-0.0010.0000.0000.0000.000
119B171ILE00.0620.03232.1910.0010.0010.0000.0000.0000.000
120B172ARG10.7810.87631.1220.0400.0400.0000.0000.0000.000
121B192VAL00.004-0.01428.548-0.001-0.0010.0000.0000.0000.000
122B193ARG10.7410.86422.6210.0360.0360.0000.0000.0000.000
123B194GLU-1-0.793-0.90326.1630.0130.0130.0000.0000.0000.000
124B195SER00.0030.00324.9980.0040.0040.0000.0000.0000.000
125B196VAL0-0.050-0.03421.971-0.008-0.0080.0000.0000.0000.000
126B197GLY00.0090.00822.6580.0050.0050.0000.0000.0000.000
127B198PRO0-0.009-0.00222.337-0.004-0.0040.0000.0000.0000.000
128B199HIS10.7360.85119.153-0.070-0.0700.0000.0000.0000.000
129B200THR00.030-0.02722.153-0.012-0.0120.0000.0000.0000.000
130B201ILE00.039-0.00222.670-0.003-0.0030.0000.0000.0000.000
131B202GLU-1-0.895-0.92323.0200.0520.0520.0000.0000.0000.000
132B203GLU-1-0.800-0.84719.8200.0790.0790.0000.0000.0000.000
133B204SER0-0.091-0.05418.3900.0070.0070.0000.0000.0000.000
134B205LEU00.0830.03913.7040.0140.0140.0000.0000.0000.000
135B206ASN00.000-0.01917.635-0.043-0.0430.0000.0000.0000.000
136B207VAL00.004-0.00914.0230.0000.0000.0000.0000.0000.000
137B208PHE0-0.036-0.03615.705-0.021-0.0210.0000.0000.0000.000
138B209GLU-1-0.869-0.91218.387-0.012-0.0120.0000.0000.0000.000
139B210ALA00.0010.02514.7410.0070.0070.0000.0000.0000.000
140B211ALA00.0370.01613.848-0.055-0.0550.0000.0000.0000.000
141B212PRO0-0.041-0.0418.9500.0050.0050.0000.0000.0000.000
142B213GLU-1-0.839-0.9308.8140.4840.4840.0000.0000.0000.000
143B214GLU-1-0.824-0.9079.9590.2410.2410.0000.0000.0000.000
144B215ILE0-0.034-0.0349.106-0.039-0.0390.0000.0000.0000.000
145B216GLU-1-0.890-0.9423.5725.6266.1970.021-0.232-0.360-0.001
146B217ASN0-0.065-0.0287.832-0.032-0.0320.0000.0000.0000.000
147B218ARG10.8790.95211.163-0.202-0.2020.0000.0000.0000.000
148B219ILE0-0.091-0.0356.872-0.122-0.1220.0000.0000.0000.000
149B220ILE00.0310.01610.6070.0670.0670.0000.0000.0000.000
150B221PRO00.0410.0109.359-0.060-0.0600.0000.0000.0000.000
151B222LEU00.0540.0149.3060.0060.0060.0000.0000.0000.000
152B223GLU-1-0.828-0.91011.0540.2640.2640.0000.0000.0000.000
153B224LYS10.9090.95113.654-0.187-0.1870.0000.0000.0000.000
154B225CYS0-0.111-0.03712.496-0.025-0.0250.0000.0000.0000.000
155B226LEU0-0.042-0.02115.2870.0070.0070.0000.0000.0000.000
156B227GLU-1-0.739-0.86618.6580.0870.0870.0000.0000.0000.000
157B228TRP0-0.040-0.01219.7760.0000.0000.0000.0000.0000.000
158B229LEU00.006-0.00520.7100.0050.0050.0000.0000.0000.000
159B230PRO00.0490.04523.4400.0080.0080.0000.0000.0000.000
160B231ARG10.7450.83222.126-0.106-0.1060.0000.0000.0000.000
161B232VAL00.0130.02023.2900.0030.0030.0000.0000.0000.000
162B233VAL00.0020.01323.0340.0120.0120.0000.0000.0000.000
163B234VAL0-0.030-0.01422.812-0.010-0.0100.0000.0000.0000.000
164B235HIS00.0640.01524.5700.0120.0120.0000.0000.0000.000
165B236GLN0-0.034-0.02919.9020.0150.0150.0000.0000.0000.000
166B237GLU-1-0.909-0.94423.2560.1050.1050.0000.0000.0000.000
167B238SER0-0.003-0.01224.6300.0010.0010.0000.0000.0000.000
168B239THR0-0.025-0.03718.3980.0100.0100.0000.0000.0000.000
169B240LYS10.9040.94819.527-0.146-0.1460.0000.0000.0000.000
170B241MET00.0120.02121.118-0.003-0.0030.0000.0000.0000.000
171B242ILE00.0660.02419.6310.0050.0050.0000.0000.0000.000
172B243LEU0-0.085-0.03615.2910.0180.0180.0000.0000.0000.000
173B244ASN0-0.063-0.04117.2790.0270.0270.0000.0000.0000.000
174B245GLY00.0080.01919.867-0.016-0.0160.0000.0000.0000.000
175B246SER00.0100.00522.3980.0030.0030.0000.0000.0000.000
176B247GLN0-0.044-0.02824.148-0.002-0.0020.0000.0000.0000.000
177B248ILE00.0190.00222.4790.0040.0040.0000.0000.0000.000
178B249HIS00.045-0.00526.610-0.006-0.0060.0000.0000.0000.000
179B250LEU00.0180.00030.1630.0040.0040.0000.0000.0000.000
180B251GLU-1-0.917-0.95732.5660.0670.0670.0000.0000.0000.000
181B252MET0-0.0390.01925.5160.0010.0010.0000.0000.0000.000
182B253LEU0-0.052-0.01227.2580.0070.0070.0000.0000.0000.000
183B254LYS10.9070.94628.034-0.105-0.1050.0000.0000.0000.000
184B255GLU-1-0.836-0.88326.9200.0980.0980.0000.0000.0000.000
185B256TRP00.032-0.00628.2260.0040.0040.0000.0000.0000.000
186B257ASP-1-0.840-0.90526.7210.0920.0920.0000.0000.0000.000
187B258GLY0-0.011-0.01329.353-0.003-0.0030.0000.0000.0000.000
188B259PHE0-0.0260.00527.785-0.003-0.0030.0000.0000.0000.000
189B260LYS10.9750.99330.916-0.045-0.0450.0000.0000.0000.000
190B261LYS10.8560.91531.556-0.051-0.0510.0000.0000.0000.000
191B262GLY0-0.0270.00231.0160.0020.0020.0000.0000.0000.000
192B263GLU-1-0.888-0.95827.3090.0610.0610.0000.0000.0000.000
193B264VAL0-0.009-0.00121.4710.0030.0030.0000.0000.0000.000
194B265VAL00.0160.00323.546-0.003-0.0030.0000.0000.0000.000
195B266ARG10.7990.89018.522-0.104-0.1040.0000.0000.0000.000
196B267VAL00.0110.01019.708-0.007-0.0070.0000.0000.0000.000
197B268PHE00.029-0.00716.8780.0240.0240.0000.0000.0000.000
198B269ASN00.0160.00418.443-0.007-0.0070.0000.0000.0000.000
199B270GLU-1-0.769-0.89221.1020.1140.1140.0000.0000.0000.000
200B271GLU-1-0.904-0.92518.3460.1630.1630.0000.0000.0000.000
201B272GLY0-0.0070.01019.0640.0050.0050.0000.0000.0000.000
202B273ARG10.8690.93612.746-0.382-0.3820.0000.0000.0000.000
203B274LEU0-0.055-0.03113.853-0.017-0.0170.0000.0000.0000.000
204B275LEU0-0.041-0.01414.0900.0520.0520.0000.0000.0000.000
205B276ALA0-0.009-0.02615.8350.0370.0370.0000.0000.0000.000
206B277LEU0-0.046-0.00316.910-0.014-0.0140.0000.0000.0000.000
207B278ALA00.0170.00619.3670.0010.0010.0000.0000.0000.000
208B279GLU-1-0.829-0.91623.0540.0640.0640.0000.0000.0000.000
209B280ALA00.0110.02126.3670.0000.0000.0000.0000.0000.000
210B281GLU-1-0.840-0.92729.5830.0460.0460.0000.0000.0000.000
211B282ARG10.9110.95432.066-0.053-0.0530.0000.0000.0000.000
212B283ASN0-0.007-0.00433.1480.0010.0010.0000.0000.0000.000
213B303ARG10.8940.95521.256-0.081-0.0810.0000.0000.0000.000
214B304LYS10.7220.82815.433-0.127-0.1270.0000.0000.0000.000
215B305VAL00.0750.05014.859-0.004-0.0040.0000.0000.0000.000
216B306PHE0-0.0140.00311.1450.0460.0460.0000.0000.0000.000
217B307GLN00.0100.00010.495-0.062-0.0620.0000.0000.0000.000
218B308THR00.0040.0275.7270.5540.760-0.001-0.010-0.1950.000