Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: QY7QY

Calculation Name: 4UID-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4UID

Chain ID: A

ChEMBL ID:

UniProt ID: O68840

Base Structure: X-ray

Registration Date: 2023-06-21

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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1711637.508439
FMO2-HF: Nuclear repulsion 1639752.425558
FMO2-HF: Total energy -71885.082881
FMO2-MP2: Total energy -72099.822073


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(A:447:ALA)


Summations of interaction energy for fragment #1(A:447:ALA)
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.
-3.6522.734.988-4.759-6.609-0.019
Interaction energy analysis for fragmet #1(A:447:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.027 / q_NPA : 0.015
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].
3A449VAL00.0140.0063.574-0.7881.5590.007-1.334-1.0190.004
4A450SER00.0290.0236.1670.2530.2530.0000.0000.0000.000
5A451GLU-1-0.873-0.9308.710-0.132-0.1320.0000.0000.0000.000
6A452LEU00.000-0.00710.288-0.044-0.0440.0000.0000.0000.000
7A453LYS10.8330.92512.9520.3080.3080.0000.0000.0000.000
8A454LEU00.0450.03116.5720.0140.0140.0000.0000.0000.000
9A455THR0-0.059-0.05018.3380.0090.0090.0000.0000.0000.000
10A456LYS10.8730.92421.0660.0690.0690.0000.0000.0000.000
11A457ASP-1-0.846-0.92223.900-0.057-0.0570.0000.0000.0000.000
12A458ASN0-0.033-0.02320.7210.0000.0000.0000.0000.0000.000
13A459LYS10.8570.94021.8210.0590.0590.0000.0000.0000.000
14A460GLU-1-0.786-0.88919.702-0.248-0.2480.0000.0000.0000.000
15A461VAL0-0.040-0.01622.2290.0070.0070.0000.0000.0000.000
16A462VAL0-0.011-0.00223.989-0.018-0.0180.0000.0000.0000.000
17A463THR0-0.054-0.02226.6710.0040.0040.0000.0000.0000.000
18A464LEU00.0540.03425.5230.0050.0050.0000.0000.0000.000
19A465TYR0-0.019-0.00229.017-0.005-0.0050.0000.0000.0000.000
20A466ALA00.0450.01231.2190.0000.0000.0000.0000.0000.000
21A467ASN0-0.023-0.01232.796-0.001-0.0010.0000.0000.0000.000
22A468GLY00.0360.02029.8920.0050.0050.0000.0000.0000.000
23A469ASN0-0.090-0.04229.868-0.001-0.0010.0000.0000.0000.000
24A470ALA00.0410.01127.272-0.007-0.0070.0000.0000.0000.000
25A471PHE0-0.012-0.01128.9020.0080.0080.0000.0000.0000.000
26A472ASP-1-0.743-0.87127.620-0.103-0.1030.0000.0000.0000.000
27A473LYS10.8320.89822.9170.1690.1690.0000.0000.0000.000
28A474ASP-1-0.920-0.93729.237-0.097-0.0970.0000.0000.0000.000
29A475GLY0-0.012-0.00832.4320.0040.0040.0000.0000.0000.000
30A476ASN0-0.084-0.04732.6770.0110.0110.0000.0000.0000.000
31A477GLN0-0.012-0.00631.920-0.006-0.0060.0000.0000.0000.000
32A478ILE00.0000.00626.2610.0050.0050.0000.0000.0000.000
33A479SER00.0160.00329.9470.0000.0000.0000.0000.0000.000
34A480SER00.0100.01229.1640.0050.0050.0000.0000.0000.000
35A481GLY00.0280.02326.266-0.007-0.0070.0000.0000.0000.000
36A482THR00.0320.01223.089-0.003-0.0030.0000.0000.0000.000
37A483LEU0-0.024-0.00823.609-0.006-0.0060.0000.0000.0000.000
38A484THR00.003-0.01517.9810.0160.0160.0000.0000.0000.000
39A485LEU00.0220.02515.637-0.020-0.0200.0000.0000.0000.000
40A486THR0-0.060-0.01814.0570.0400.0400.0000.0000.0000.000
41A487ALA00.0520.0189.543-0.046-0.0460.0000.0000.0000.000
42A488LYS10.8010.9018.6860.3870.3870.0000.0000.0000.000
43A489PHE00.0460.0093.243-0.389-0.0700.018-0.065-0.2720.000
44A490LYS10.8060.9243.8161.2191.4420.000-0.053-0.1700.000
45A491ASP-1-0.710-0.8532.531-2.745-1.0112.848-2.278-2.303-0.025
46A492GLN0-0.046-0.0323.393-1.059-0.7290.061-0.021-0.370-0.001
47A493TYR0-0.069-0.0354.522-0.200-0.167-0.001-0.015-0.0170.000
48A494GLY00.0150.0196.322-0.086-0.0860.0000.0000.0000.000
49A495ASN0-0.097-0.0627.366-0.163-0.1630.0000.0000.0000.000
50A496GLU-1-0.780-0.8906.858-0.525-0.5250.0000.0000.0000.000
51A497LEU0-0.019-0.0162.945-0.2550.1070.159-0.117-0.4040.000
52A498THR0-0.012-0.0047.218-0.076-0.0760.0000.0000.0000.000
53A499GLY0-0.010-0.00710.5040.0960.0960.0000.0000.0000.000
54A500LYS10.7740.8857.244-0.650-0.6500.0000.0000.0000.000
55A501VAL00.0190.00410.855-0.080-0.0800.0000.0000.0000.000
56A502ALA00.0170.01512.2070.0300.0300.0000.0000.0000.000
57A503GLY00.0160.00713.0960.0000.0000.0000.0000.0000.000
58A504THR0-0.118-0.06212.9940.0040.0040.0000.0000.0000.000
59A505ASP-1-0.770-0.8538.1410.7920.7920.0000.0000.0000.000
60A506TYR0-0.009-0.0047.4130.0650.0650.0000.0000.0000.000
61A507THR0-0.041-0.0159.2860.0030.0030.0000.0000.0000.000
62A508PHE0-0.015-0.01011.529-0.092-0.0920.0000.0000.0000.000
63A509GLU-1-0.795-0.88213.641-0.124-0.1240.0000.0000.0000.000
64A510SER0-0.018-0.02416.692-0.041-0.0410.0000.0000.0000.000
65A511LEU0-0.013-0.01517.5380.0130.0130.0000.0000.0000.000
66A512ASN00.0190.00821.137-0.007-0.0070.0000.0000.0000.000
67A513PRO00.0380.02023.5100.0030.0030.0000.0000.0000.000
68A514GLU-1-0.915-0.95725.274-0.071-0.0710.0000.0000.0000.000
69A515VAL0-0.058-0.01927.0240.0030.0030.0000.0000.0000.000
70A516LEU00.015-0.01422.4280.0020.0020.0000.0000.0000.000
71A517VAL00.0270.04023.779-0.008-0.0080.0000.0000.0000.000
72A518VAL0-0.017-0.01817.711-0.007-0.0070.0000.0000.0000.000
73A519ALA00.0070.02020.3260.0050.0050.0000.0000.0000.000
74A520PRO00.022-0.00816.530-0.014-0.0140.0000.0000.0000.000
75A521ASP-1-0.788-0.88815.152-0.015-0.0150.0000.0000.0000.000
76A522GLY00.014-0.00115.979-0.009-0.0090.0000.0000.0000.000
77A523SER0-0.045-0.03217.207-0.021-0.0210.0000.0000.0000.000
78A524VAL0-0.052-0.02620.554-0.006-0.0060.0000.0000.0000.000
79A525THR0-0.013-0.01022.9830.0100.0100.0000.0000.0000.000
80A526PRO0-0.031-0.01126.584-0.004-0.0040.0000.0000.0000.000
81A527ILE0-0.0130.00928.2720.0090.0090.0000.0000.0000.000
82A528VAL0-0.011-0.00630.9270.0050.0050.0000.0000.0000.000
83A529PRO0-0.033-0.02031.146-0.006-0.0060.0000.0000.0000.000
84A530GLY00.0380.01730.5770.0030.0030.0000.0000.0000.000
85A531THR0-0.064-0.03725.226-0.008-0.0080.0000.0000.0000.000
86A532ALA00.0150.02823.1780.0070.0070.0000.0000.0000.000
87A533LEU0-0.013-0.00319.368-0.019-0.0190.0000.0000.0000.000
88A534VAL00.0170.00916.4440.0230.0230.0000.0000.0000.000
89A535LYS10.9400.97011.9580.3480.3480.0000.0000.0000.000
90A536VAL00.0050.0128.7300.0580.0580.0000.0000.0000.000
91A537LYS10.8280.8818.195-0.058-0.0580.0000.0000.0000.000
92A538TYR00.020-0.0053.9960.0700.3600.000-0.027-0.2630.000
93A539GLY00.0160.0164.4980.0220.081-0.001-0.007-0.0510.000
94A540GLU-1-0.904-0.9726.145-0.083-0.0830.0000.0000.0000.000
95A541VAL0-0.0520.0052.116-1.069-0.4651.898-0.839-1.6630.003
96A542THR0-0.037-0.0265.1940.5070.588-0.001-0.003-0.0770.000
97A543LYS10.8740.9338.1140.9310.9310.0000.0000.0000.000
98A544THR0-0.001-0.01610.5500.1060.1060.0000.0000.0000.000
99A545ILE0-0.0080.00714.337-0.038-0.0380.0000.0000.0000.000
100A546PRO00.0250.00517.3860.0260.0260.0000.0000.0000.000
101A547VAL00.0000.00420.315-0.005-0.0050.0000.0000.0000.000
102A548THR0-0.019-0.01323.0010.0070.0070.0000.0000.0000.000
103A549VAL0-0.0300.00326.8290.0020.0020.0000.0000.0000.000
104A550LYS10.9410.96029.3800.1110.1110.0000.0000.0000.000
105A551ALA00.0450.01432.7960.0040.0040.0000.0000.0000.000
106A552ASN00.0530.02135.790-0.005-0.0050.0000.0000.0000.000
107A553PRO00.0240.02436.7470.0010.0010.0000.0000.0000.000
108A554VAL0-0.017-0.01139.9020.0040.0040.0000.0000.0000.000
109A555LEU0-0.050-0.01043.543-0.002-0.0020.0000.0000.0000.000
110A556GLU-1-0.818-0.89645.512-0.051-0.0510.0000.0000.0000.000
111A557THR0-0.024-0.01747.4210.0010.0010.0000.0000.0000.000
112A558ILE00.0010.01049.6170.0000.0000.0000.0000.0000.000
113A559ALA0-0.019-0.00850.9560.0000.0000.0000.0000.0000.000
114A560VAL00.001-0.01552.8040.0010.0010.0000.0000.0000.000
115A561ASP-1-0.836-0.88556.078-0.034-0.0340.0000.0000.0000.000
116A562SER00.008-0.00857.1620.0010.0010.0000.0000.0000.000
117A563THR00.0220.01060.297-0.001-0.0010.0000.0000.0000.000
118A564GLY0-0.023-0.01162.5460.0000.0000.0000.0000.0000.000
119A565VAL0-0.032-0.00465.1960.0000.0000.0000.0000.0000.000
120A566SER00.0050.00067.5550.0010.0010.0000.0000.0000.000
121A567VAL0-0.026-0.00170.3100.0000.0000.0000.0000.0000.000
122A568ALA00.0290.01772.1560.0000.0000.0000.0000.0000.000
123A569LYS10.8740.90374.9190.0150.0150.0000.0000.0000.000
124A570GLY0-0.011-0.00176.7280.0000.0000.0000.0000.0000.000
125A571GLN0-0.050-0.00972.9350.0000.0000.0000.0000.0000.000
126A572LYS10.9710.97765.1770.0200.0200.0000.0000.0000.000
127A573ALA0-0.0020.00666.8490.0000.0000.0000.0000.0000.000
128A574THR0-0.040-0.03360.9300.0010.0010.0000.0000.0000.000
129A575PHE0-0.0040.01459.0140.0000.0000.0000.0000.0000.000
130A576LYS10.8660.90254.4290.0320.0320.0000.0000.0000.000
131A577VAL00.0050.00253.6010.0000.0000.0000.0000.0000.000
132A578THR0-0.034-0.02948.4670.0000.0000.0000.0000.0000.000
133A579LEU00.0100.02048.385-0.001-0.0010.0000.0000.0000.000
134A580LYS10.9230.95945.3450.0490.0490.0000.0000.0000.000
135A581ASP-1-0.726-0.86039.750-0.067-0.0670.0000.0000.0000.000
136A582GLN00.030-0.00739.5600.0020.0020.0000.0000.0000.000
137A583TYR0-0.124-0.07736.701-0.005-0.0050.0000.0000.0000.000
138A584GLY00.0020.01840.252-0.002-0.0020.0000.0000.0000.000
139A585ASN0-0.075-0.04037.6920.0010.0010.0000.0000.0000.000
140A586LYS10.8600.90741.4530.0500.0500.0000.0000.0000.000
141A587PHE00.0080.00342.239-0.001-0.0010.0000.0000.0000.000
142A588THR0-0.018-0.02143.8440.0010.0010.0000.0000.0000.000
143A589GLY00.0380.01945.7200.0000.0000.0000.0000.0000.000
144A590ASN00.0050.01948.6270.0000.0000.0000.0000.0000.000
145A591VAL0-0.0310.00452.318-0.001-0.0010.0000.0000.0000.000
146A592ASN0-0.014-0.00255.2140.0020.0020.0000.0000.0000.000
147A593VAL0-0.0020.00058.931-0.001-0.0010.0000.0000.0000.000
148A594THR00.0000.00061.8700.0010.0010.0000.0000.0000.000
149A595SER00.002-0.03465.488-0.001-0.0010.0000.0000.0000.000
150A596ASP-1-0.897-0.94468.621-0.023-0.0230.0000.0000.0000.000
151A597LYS10.8710.92471.0320.0190.0190.0000.0000.0000.000
152A598THR00.0170.01771.4910.0000.0000.0000.0000.0000.000
153A599GLU-1-0.847-0.91973.633-0.017-0.0170.0000.0000.0000.000
154A600THR0-0.067-0.01675.4490.0000.0000.0000.0000.0000.000
155A601ALA00.0500.00971.3470.0000.0000.0000.0000.0000.000
156A602THR00.0260.04370.1400.0000.0000.0000.0000.0000.000
157A603VAL0-0.013-0.01063.8260.0000.0000.0000.0000.0000.000
158A604SER0-0.031-0.00163.9120.0010.0010.0000.0000.0000.000
159A605VAL00.024-0.00357.384-0.001-0.0010.0000.0000.0000.000
160A606SER00.0170.01055.3590.0010.0010.0000.0000.0000.000
161A607ASN00.0360.00652.827-0.001-0.0010.0000.0000.0000.000
162A608SER00.0260.01555.4130.0000.0000.0000.0000.0000.000
163A609GLY00.0370.03456.1490.0000.0000.0000.0000.0000.000
164A610ILE0-0.056-0.02852.062-0.001-0.0010.0000.0000.0000.000
165A611GLY00.0330.01248.8660.0000.0000.0000.0000.0000.000
166A612GLN0-0.044-0.02148.0350.0000.0000.0000.0000.0000.000
167A613SER00.0160.00145.6280.0000.0000.0000.0000.0000.000
168A614GLU-1-0.861-0.90647.190-0.044-0.0440.0000.0000.0000.000
169A615TYR00.0070.00050.6300.0020.0020.0000.0000.0000.000
170A616THR0-0.010-0.01654.230-0.001-0.0010.0000.0000.0000.000
171A617VAL00.0000.00757.5020.0010.0010.0000.0000.0000.000
172A618THR0-0.032-0.02660.4690.0000.0000.0000.0000.0000.000
173A619VAL00.0120.00664.0010.0000.0000.0000.0000.0000.000
174A620ASN0-0.005-0.01967.1960.0000.0000.0000.0000.0000.000
175A621GLY00.0550.03170.7810.0000.0000.0000.0000.0000.000
176A622VAL0-0.063-0.02773.9790.0010.0010.0000.0000.0000.000
177A623ALA0-0.005-0.01676.7790.0010.0010.0000.0000.0000.000
178A624GLU-1-0.812-0.88878.078-0.016-0.0160.0000.0000.0000.000
179A625GLY00.0040.01178.3850.0000.0000.0000.0000.0000.000
180A626SER0-0.019-0.01374.1600.0000.0000.0000.0000.0000.000
181A627THR00.0190.00670.8670.0010.0010.0000.0000.0000.000
182A628THR0-0.027-0.00966.680-0.001-0.0010.0000.0000.0000.000
183A629ILE00.0020.01863.4940.0010.0010.0000.0000.0000.000
184A630THR0-0.050-0.01462.783-0.001-0.0010.0000.0000.0000.000
185A631ILE00.0200.00256.9980.0010.0010.0000.0000.0000.000
186A632LYS10.8750.91357.6360.0250.0250.0000.0000.0000.000
187A633SER0-0.006-0.03352.2250.0000.0000.0000.0000.0000.000
188A634GLY00.0420.02351.576-0.001-0.0010.0000.0000.0000.000
189A635THR0-0.032-0.01751.9310.0010.0010.0000.0000.0000.000
190A636LYS10.8020.90249.1790.0470.0470.0000.0000.0000.000
191A637GLU-1-0.786-0.88954.960-0.027-0.0270.0000.0000.0000.000
192A638VAL0-0.0090.01156.172-0.001-0.0010.0000.0000.0000.000
193A639LYS10.9000.93259.0450.0290.0290.0000.0000.0000.000
194A640VAL00.0110.01361.607-0.001-0.0010.0000.0000.0000.000
195A641PRO00.0200.02864.2500.0010.0010.0000.0000.0000.000
196A642VAL00.001-0.01667.6870.0000.0000.0000.0000.0000.000
197A643ASN0-0.015-0.01170.0900.0010.0010.0000.0000.0000.000
198A644VAL0-0.017-0.00273.0070.0000.0000.0000.0000.0000.000
199A645VAL0-0.003-0.00175.5520.0000.0000.0000.0000.0000.000
200A646ALA00.0340.01877.9720.0000.0000.0000.0000.0000.000