FMODB

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

Last updated: 2024-04-25

All entries: 37426

Number of unique PDB entries: 7782

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FMODB ID: 16N5Z

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 OptHSide
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 -2558103.74521
FMO2-HF: Nuclear repulsion 2471516.23477
FMO2-HF: Total energy -86587.510439
FMO2-MP2: Total energy -86843.817072


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.
-5.326-0.896.225-2.848-7.812-0.004
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 : -0.010 / q_NPA : -0.007
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].
3B3HIS00.0680.0092.899-4.138-2.1284.468-1.879-4.5990.003
4B4GLY00.005-0.0054.5540.1010.152-0.001-0.010-0.0390.000
5B5ILE0-0.0170.0028.2230.0520.0520.0000.0000.0000.000
6B6LEU00.0020.02211.061-0.024-0.0240.0000.0000.0000.000
7B7VAL0-0.027-0.00312.909-0.004-0.0040.0000.0000.0000.000
8B8ALA00.0320.01515.915-0.004-0.0040.0000.0000.0000.000
9B9TYR00.048-0.03817.8150.0100.0100.0000.0000.0000.000
10B10LYS10.7520.89520.3320.0250.0250.0000.0000.0000.000
11B11PRO00.0560.03522.4640.0070.0070.0000.0000.0000.000
12B12LYS10.8010.83725.4980.0160.0160.0000.0000.0000.000
13B13GLY00.0180.01328.078-0.002-0.0020.0000.0000.0000.000
14B14PRO00.0170.01822.6940.0000.0000.0000.0000.0000.000
15B15THR0-0.043-0.07522.6060.0120.0120.0000.0000.0000.000
16B16SER00.043-0.00420.519-0.007-0.0070.0000.0000.0000.000
17B17HIS0-0.058-0.04316.726-0.001-0.0010.0000.0000.0000.000
18B18ASP-1-0.769-0.83517.870-0.105-0.1050.0000.0000.0000.000
19B19VAL00.0340.02815.855-0.021-0.0210.0000.0000.0000.000
20B20VAL00.013-0.00813.071-0.027-0.0270.0000.0000.0000.000
21B21ASP-1-0.833-0.91413.177-0.280-0.2800.0000.0000.0000.000
22B22GLU-1-0.800-0.90913.869-0.247-0.2470.0000.0000.0000.000
23B23VAL0-0.006-0.0089.539-0.032-0.0320.0000.0000.0000.000
24B24ARG10.7100.8648.9400.1130.1130.0000.0000.0000.000
25B25LYS10.9230.9789.5690.1090.1090.0000.0000.0000.000
26B26LYS10.8330.91810.7650.0840.0840.0000.0000.0000.000
27B27LEU00.0450.0205.716-0.029-0.0290.0000.0000.0000.000
28B28LYS10.9400.9986.0780.1440.1440.0000.0000.0000.000
29B29THR0-0.016-0.0173.038-1.148-0.6960.030-0.075-0.4060.000
30B30ARG10.9360.9625.8490.6970.6970.0000.0000.0000.000
31B31LYS10.9160.9725.383-1.011-1.0110.0000.0000.0000.000
32B32VAL00.0570.0337.3700.0330.0330.0000.0000.0000.000
33B33GLY00.0150.01810.1010.0030.0030.0000.0000.0000.000
34B34HIS00.0230.02113.6020.0150.0150.0000.0000.0000.000
35B35GLY00.010-0.00116.2290.0180.0180.0000.0000.0000.000
36B36GLY0-0.023-0.03117.7540.0020.0020.0000.0000.0000.000
37B37THR0-0.053-0.02021.284-0.007-0.0070.0000.0000.0000.000
38B38LEU0-0.0040.00123.0440.0060.0060.0000.0000.0000.000
39B39ASP-1-0.832-0.89124.661-0.015-0.0150.0000.0000.0000.000
40B40PRO00.0390.00526.5490.0000.0000.0000.0000.0000.000
41B41PHE00.0130.00227.590-0.001-0.0010.0000.0000.0000.000
42B42ALA0-0.035-0.01328.5390.0020.0020.0000.0000.0000.000
43B43CYM-1-0.743-0.74626.239-0.018-0.0180.0000.0000.0000.000
44B44GLY00.016-0.01225.0850.0060.0060.0000.0000.0000.000
45B45VAL00.0270.04120.572-0.006-0.0060.0000.0000.0000.000
46B46LEU0-0.095-0.04918.0840.0070.0070.0000.0000.0000.000
47B47ILE00.0070.00815.436-0.007-0.0070.0000.0000.0000.000
48B48ILE00.025-0.00711.190-0.002-0.0020.0000.0000.0000.000
49B49GLY00.0410.03110.706-0.009-0.0090.0000.0000.0000.000
50B50VAL00.0220.0034.9580.0240.0240.0000.0000.0000.000
51B51ASN00.068-0.0022.745-0.3561.4101.729-0.865-2.631-0.007
52B52GLN0-0.017-0.0174.963-0.876-0.8760.0000.0000.0000.000
53B53GLY00.0190.0136.880-0.246-0.2460.0000.0000.0000.000
54B54THR0-0.047-0.0218.842-0.147-0.1470.0000.0000.0000.000
55B55ARG10.8620.92710.153-0.746-0.7460.0000.0000.0000.000
56B56ILE00.0180.01211.921-0.055-0.0550.0000.0000.0000.000
57B57LEU00.0020.02113.779-0.047-0.0470.0000.0000.0000.000
58B58GLU-1-0.923-0.98515.5870.1670.1670.0000.0000.0000.000
59B59PHE00.0560.03716.979-0.012-0.0120.0000.0000.0000.000
60B60TYR00.0750.03814.982-0.020-0.0200.0000.0000.0000.000
61B61LYS10.8620.92420.356-0.105-0.1050.0000.0000.0000.000
62B62ASP-1-0.890-0.94423.1290.0740.0740.0000.0000.0000.000
63B63LEU0-0.0060.01020.969-0.008-0.0080.0000.0000.0000.000
64B64LYS10.9070.96825.285-0.039-0.0390.0000.0000.0000.000
65B65LYS10.7580.88123.992-0.042-0.0420.0000.0000.0000.000
66B66VAL00.0650.04028.1960.0000.0000.0000.0000.0000.000
67B67TYR0-0.0020.02428.384-0.003-0.0030.0000.0000.0000.000
68B108GLY00.0670.02641.051-0.001-0.0010.0000.0000.0000.000
69B109GLU-1-0.864-0.96240.0260.0270.0270.0000.0000.0000.000
70B110TYR0-0.0090.00338.7970.0010.0010.0000.0000.0000.000
71B111ASP-1-0.790-0.90040.1450.0220.0220.0000.0000.0000.000
72B112GLN00.0010.00837.290-0.002-0.0020.0000.0000.0000.000
73B113VAL00.0320.01339.1830.0020.0020.0000.0000.0000.000
74B114PRO0-0.078-0.04034.823-0.001-0.0010.0000.0000.0000.000
75B115PRO00.0420.02534.630-0.001-0.0010.0000.0000.0000.000
76B116ALA00.0720.04836.0090.0000.0000.0000.0000.0000.000
77B117TYR00.0060.00033.4030.0000.0000.0000.0000.0000.000
78B118SER00.012-0.01531.3680.0010.0010.0000.0000.0000.000
79B119ALA0-0.036-0.02426.690-0.001-0.0010.0000.0000.0000.000
80B120LYS10.9260.95828.746-0.018-0.0180.0000.0000.0000.000
81B121LYS10.9500.97426.920-0.022-0.0220.0000.0000.0000.000
82B122TYR00.0240.01432.5770.0010.0010.0000.0000.0000.000
83B123LYS10.9770.98935.656-0.006-0.0060.0000.0000.0000.000
84B124GLY00.0380.03732.232-0.001-0.0010.0000.0000.0000.000
85B125GLU-1-0.811-0.92331.1350.0010.0010.0000.0000.0000.000
86B126ARG10.8280.91523.963-0.002-0.0020.0000.0000.0000.000
87B127LEU00.0890.03331.033-0.003-0.0030.0000.0000.0000.000
88B128TYR00.0110.00126.0980.0000.0000.0000.0000.0000.000
89B129LYS10.8420.91531.0150.0140.0140.0000.0000.0000.000
90B130LEU00.0160.01632.847-0.002-0.0020.0000.0000.0000.000
91B131ALA00.0310.00935.995-0.001-0.0010.0000.0000.0000.000
92B132ARG10.9130.95531.6030.0250.0250.0000.0000.0000.000
93B133GLU-1-0.869-0.91635.540-0.015-0.0150.0000.0000.0000.000
94B134GLY00.0280.02238.2700.0000.0000.0000.0000.0000.000
95B135LYS10.8910.94639.2740.0120.0120.0000.0000.0000.000
96B136ILE00.0170.01039.8770.0010.0010.0000.0000.0000.000
97B137ILE00.0080.01239.0050.0010.0010.0000.0000.0000.000
98B138ASN0-0.040-0.02139.051-0.001-0.0010.0000.0000.0000.000
99B139LEU0-0.022-0.02135.8440.0010.0010.0000.0000.0000.000
100B140PRO00.0420.01239.636-0.001-0.0010.0000.0000.0000.000
101B141PRO00.0100.01839.1090.0010.0010.0000.0000.0000.000
102B142LYS10.9210.96932.083-0.033-0.0330.0000.0000.0000.000
103B143ARG10.8740.92537.229-0.024-0.0240.0000.0000.0000.000
104B144VAL0-0.130-0.05334.5530.0030.0030.0000.0000.0000.000
105B145LYS10.9150.96834.843-0.032-0.0320.0000.0000.0000.000
106B146ILE0-0.022-0.01436.2440.0000.0000.0000.0000.0000.000
107B147PHE0-0.021-0.01632.5430.0010.0010.0000.0000.0000.000
108B148LYS10.9370.96235.015-0.024-0.0240.0000.0000.0000.000
109B149ILE00.0520.04037.715-0.001-0.0010.0000.0000.0000.000
110B162ARG10.9220.95231.789-0.007-0.0070.0000.0000.0000.000
111B163VAL0-0.023-0.02034.5240.0010.0010.0000.0000.0000.000
112B164GLU-1-0.816-0.88231.9310.0290.0290.0000.0000.0000.000
113B165VAL0-0.016-0.02530.915-0.001-0.0010.0000.0000.0000.000
114B166SER00.0330.03030.8410.0030.0030.0000.0000.0000.000
115B167PRO00.0500.00727.326-0.004-0.0040.0000.0000.0000.000
116B168GLY0-0.096-0.05528.372-0.001-0.0010.0000.0000.0000.000
117B169THR00.0310.02230.072-0.002-0.0020.0000.0000.0000.000
118B170TYR0-0.015-0.00629.9950.0010.0010.0000.0000.0000.000
119B171ILE00.0780.04232.1370.0000.0000.0000.0000.0000.000
120B172ARG10.8450.92531.0250.0050.0050.0000.0000.0000.000
121B192VAL0-0.008-0.01328.5990.0010.0010.0000.0000.0000.000
122B193ARG10.8040.89922.768-0.004-0.0040.0000.0000.0000.000
123B194GLU-1-0.765-0.90325.9270.0070.0070.0000.0000.0000.000
124B195SER00.0630.02924.7700.0010.0010.0000.0000.0000.000
125B196VAL0-0.097-0.03921.7370.0010.0010.0000.0000.0000.000
126B197GLY00.0060.00222.3980.0060.0060.0000.0000.0000.000
127B198PRO0-0.005-0.00221.746-0.004-0.0040.0000.0000.0000.000
128B199HIS10.7360.85018.889-0.048-0.0480.0000.0000.0000.000
129B200THR00.023-0.02021.851-0.005-0.0050.0000.0000.0000.000
130B201ILE00.0500.00823.695-0.003-0.0030.0000.0000.0000.000
131B202GLU-1-0.923-0.94223.7990.0070.0070.0000.0000.0000.000
132B203GLU-1-0.799-0.84220.0250.0330.0330.0000.0000.0000.000
133B204SER0-0.120-0.07519.013-0.002-0.0020.0000.0000.0000.000
134B205LEU00.1210.04813.9800.0040.0040.0000.0000.0000.000
135B206ASN0-0.013-0.01618.079-0.020-0.0200.0000.0000.0000.000
136B207VAL00.0580.00814.159-0.002-0.0020.0000.0000.0000.000
137B208PHE0-0.090-0.05316.349-0.016-0.0160.0000.0000.0000.000
138B209GLU-1-0.883-0.92618.383-0.036-0.0360.0000.0000.0000.000
139B210ALA00.0320.05914.8710.0060.0060.0000.0000.0000.000
140B211ALA00.0150.00914.053-0.041-0.0410.0000.0000.0000.000
141B212PRO0-0.031-0.0419.1330.0010.0010.0000.0000.0000.000
142B213GLU-1-0.850-0.9308.8810.1680.1680.0000.0000.0000.000
143B214GLU-1-0.872-0.94110.4580.0570.0570.0000.0000.0000.000
144B215ILE0-0.047-0.0379.484-0.023-0.0230.0000.0000.0000.000
145B216GLU-1-0.926-0.9754.3482.5312.688-0.001-0.019-0.1370.000
146B217ASN0-0.047-0.0208.244-0.060-0.0600.0000.0000.0000.000
147B218ARG10.9150.98011.359-0.062-0.0620.0000.0000.0000.000
148B219ILE0-0.054-0.0126.784-0.082-0.0820.0000.0000.0000.000
149B220ILE0-0.015-0.01810.7410.0360.0360.0000.0000.0000.000
150B221PRO00.0660.0139.187-0.028-0.0280.0000.0000.0000.000
151B222LEU00.022-0.0038.8740.0550.0550.0000.0000.0000.000
152B223GLU-1-0.868-0.94010.6490.1650.1650.0000.0000.0000.000
153B224LYS10.9310.96913.364-0.080-0.0800.0000.0000.0000.000
154B225CYS0-0.083-0.02812.475-0.009-0.0090.0000.0000.0000.000
155B226LEU0-0.052-0.03515.4110.0140.0140.0000.0000.0000.000
156B227GLU-1-0.778-0.88918.6600.0650.0650.0000.0000.0000.000
157B228TRP0-0.032-0.01619.388-0.001-0.0010.0000.0000.0000.000
158B229LEU00.007-0.00320.2870.0070.0070.0000.0000.0000.000
159B230PRO00.0890.05623.0280.0040.0040.0000.0000.0000.000
160B231ARG10.7790.86021.760-0.081-0.0810.0000.0000.0000.000
161B232VAL00.0150.03323.146-0.002-0.0020.0000.0000.0000.000
162B233VAL00.003-0.00222.8740.0130.0130.0000.0000.0000.000
163B234VAL0-0.029-0.00922.762-0.008-0.0080.0000.0000.0000.000
164B235HIS00.1120.04725.0150.0010.0010.0000.0000.0000.000
165B236GLN0-0.070-0.04519.8280.0250.0250.0000.0000.0000.000
166B237GLU-1-0.893-0.93123.1240.0910.0910.0000.0000.0000.000
167B238SER0-0.004-0.01524.4440.0060.0060.0000.0000.0000.000
168B239THR0-0.012-0.04018.2030.0170.0170.0000.0000.0000.000
169B240LYS10.8740.94219.112-0.166-0.1660.0000.0000.0000.000
170B241MET0-0.0090.00321.038-0.001-0.0010.0000.0000.0000.000
171B242ILE00.0560.01620.0340.0130.0130.0000.0000.0000.000
172B243LEU0-0.053-0.00515.2200.0290.0290.0000.0000.0000.000
173B244ASN0-0.068-0.04117.4800.0190.0190.0000.0000.0000.000
174B245GLY0-0.0030.01319.514-0.013-0.0130.0000.0000.0000.000
175B246SER00.0100.01521.926-0.006-0.0060.0000.0000.0000.000
176B247GLN0-0.037-0.03423.9920.0010.0010.0000.0000.0000.000
177B248ILE00.013-0.00722.3930.0020.0020.0000.0000.0000.000
178B249HIS00.024-0.01926.341-0.006-0.0060.0000.0000.0000.000
179B250LEU00.013-0.01129.6720.0020.0020.0000.0000.0000.000
180B251GLU-1-0.961-0.96032.3350.0720.0720.0000.0000.0000.000
181B252MET0-0.0160.02725.2650.0030.0030.0000.0000.0000.000
182B253LEU0-0.030-0.01526.6580.0010.0010.0000.0000.0000.000
183B254LYS10.9190.96727.774-0.083-0.0830.0000.0000.0000.000
184B255GLU-1-0.868-0.90226.2160.0770.0770.0000.0000.0000.000
185B256TRP0-0.002-0.02028.3440.0050.0050.0000.0000.0000.000
186B257ASP-1-0.866-0.93526.2990.0840.0840.0000.0000.0000.000
187B258GLY0-0.021-0.01429.507-0.002-0.0020.0000.0000.0000.000
188B259PHE0-0.0190.00627.1740.0010.0010.0000.0000.0000.000
189B260LYS11.0190.99730.682-0.061-0.0610.0000.0000.0000.000
190B261LYS10.8440.90931.356-0.078-0.0780.0000.0000.0000.000
191B262GLY00.0150.04330.0580.0050.0050.0000.0000.0000.000
192B263GLU-1-0.966-0.99627.0670.0790.0790.0000.0000.0000.000
193B264VAL0-0.017-0.02021.2760.0060.0060.0000.0000.0000.000
194B265VAL00.0190.00623.153-0.007-0.0070.0000.0000.0000.000
195B266ARG10.7880.88318.297-0.090-0.0900.0000.0000.0000.000
196B267VAL00.0230.01919.796-0.011-0.0110.0000.0000.0000.000
197B268PHE00.0070.00016.5550.0270.0270.0000.0000.0000.000
198B269ASN00.0570.02817.831-0.005-0.0050.0000.0000.0000.000
199B270GLU-1-0.751-0.89120.7670.0820.0820.0000.0000.0000.000
200B271GLU-1-0.939-0.94517.6560.0950.0950.0000.0000.0000.000
201B272GLY00.0280.01318.381-0.008-0.0080.0000.0000.0000.000
202B273ARG10.8990.96512.550-0.344-0.3440.0000.0000.0000.000
203B274LEU0-0.065-0.03213.4420.0080.0080.0000.0000.0000.000
204B275LEU0-0.031-0.01113.9050.0590.0590.0000.0000.0000.000
205B276ALA0-0.014-0.02915.5780.0630.0630.0000.0000.0000.000
206B277LEU0-0.0420.00116.484-0.023-0.0230.0000.0000.0000.000
207B278ALA0-0.005-0.00718.8980.0080.0080.0000.0000.0000.000
208B279GLU-1-0.832-0.91722.5890.1170.1170.0000.0000.0000.000
209B280ALA00.0030.00925.8710.0000.0000.0000.0000.0000.000
210B281GLU-1-0.815-0.90529.1330.0800.0800.0000.0000.0000.000
211B282ARG10.9140.94631.720-0.071-0.0710.0000.0000.0000.000
212B283ASN00.0170.03033.4980.0000.0000.0000.0000.0000.000
213B303ARG10.9290.96521.022-0.160-0.1600.0000.0000.0000.000
214B304LYS10.7200.85815.005-0.280-0.2800.0000.0000.0000.000
215B305VAL00.0760.03314.581-0.014-0.0140.0000.0000.0000.000
216B306PHE0-0.024-0.00910.7670.0990.0990.0000.0000.0000.000
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218B308THR0-0.0180.0105.8940.6740.6740.0000.0000.0000.000