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About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: JQQY9

Calculation Name: 4R3O-K-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4R3O

Chain ID: K

ChEMBL ID:

UniProt ID: P25786

Base Structure: X-ray

Registration Date: 2023-09-21

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 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 199
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2328815.972337
FMO2-HF: Nuclear repulsion 2248781.788638
FMO2-HF: Total energy -80034.183699
FMO2-MP2: Total energy -80265.756448


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(K:1:MET)


Summations of interaction energy for fragment #1(K: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.
2.2-9.73732.925-5-15.9890.01
Interaction energy analysis for fragmet #1(K:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.002 / q_NPA : 0.019
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].
3K3TYR0-0.032-0.0352.812-1.7950.5790.888-0.526-2.736-0.007
4K4LEU0-0.027-0.0155.154-0.0270.062-0.001-0.007-0.0810.000
5K5ILE0-0.003-0.0028.1320.0530.0530.0000.0000.0000.000
6K6GLY00.0240.01110.929-0.012-0.0120.0000.0000.0000.000
7K7ILE00.003-0.01014.4570.0180.0180.0000.0000.0000.000
8K8GLN00.0000.00317.5670.0010.0010.0000.0000.0000.000
9K9GLY00.0030.02720.8340.0000.0000.0000.0000.0000.000
10K10PRO0-0.036-0.02824.1460.0080.0080.0000.0000.0000.000
11K11ASP-1-0.877-0.95427.516-0.063-0.0630.0000.0000.0000.000
12K12TYR0-0.071-0.05022.036-0.008-0.0080.0000.0000.0000.000
13K13VAL0-0.020-0.00618.6880.0050.0050.0000.0000.0000.000
14K14LEU0-0.0180.00117.705-0.008-0.0080.0000.0000.0000.000
15K15VAL00.007-0.01014.7480.0130.0130.0000.0000.0000.000
16K16ALA00.0220.00112.962-0.018-0.0180.0000.0000.0000.000
17K17SER00.0250.0109.7660.0930.0930.0000.0000.0000.000
18K18ASP-1-0.775-0.8815.547-3.239-3.2390.0000.0000.0000.000
19K19ARG10.9290.9668.4800.6960.6960.0000.0000.0000.000
20K20VAL0-0.027-0.0074.3850.2470.353-0.001-0.006-0.0990.000
21K21ALA0-0.012-0.0025.533-0.475-0.4750.0000.0000.0000.000
22K22ALA0-0.014-0.0103.5570.0450.1940.002-0.026-0.1260.000
23K23SER00.0270.0135.6190.1280.1280.0000.0000.0000.000
24K24ASN00.0050.0028.0360.0020.0020.0000.0000.0000.000
25K25ILE00.0140.0067.9910.3780.3780.0000.0000.0000.000
26K26VAL0-0.028-0.0059.202-0.107-0.1070.0000.0000.0000.000
27K27GLN0-0.007-0.0147.3240.0690.0690.0000.0000.0000.000
28K28MET0-0.053-0.0338.2550.0550.0550.0000.0000.0000.000
29K29LYS10.8370.9269.1250.3840.3840.0000.0000.0000.000
30K30ASP-1-0.851-0.9228.885-0.651-0.6510.0000.0000.0000.000
31K31ASP-1-0.858-0.93110.846-0.406-0.4060.0000.0000.0000.000
32K32HIS0-0.033-0.0268.1440.1150.1150.0000.0000.0000.000
33K33ASP-1-0.835-0.92711.299-0.424-0.4240.0000.0000.0000.000
34K34LYS10.8730.9525.8291.8971.8970.0000.0000.0000.000
35K35MET0-0.082-0.01811.6690.1300.1300.0000.0000.0000.000
36K36PHE00.0030.01313.4030.0010.0010.0000.0000.0000.000
37K37LYS10.9860.99318.0900.1770.1770.0000.0000.0000.000
38K38MET00.0020.00620.3190.0130.0130.0000.0000.0000.000
39K39SER0-0.065-0.03423.1940.0110.0110.0000.0000.0000.000
40K40GLU-1-0.915-0.95625.532-0.068-0.0680.0000.0000.0000.000
41K41LYS10.8910.95125.7320.0310.0310.0000.0000.0000.000
42K42ILE0-0.012-0.00421.1940.0040.0040.0000.0000.0000.000
43K43LEU00.004-0.00117.765-0.010-0.0100.0000.0000.0000.000
44K44LEU0-0.009-0.00615.4160.0170.0170.0000.0000.0000.000
45K45LEU0-0.003-0.00411.443-0.034-0.0340.0000.0000.0000.000
46K46CYS0-0.037-0.01311.2380.1120.1120.0000.0000.0000.000
47K47VAL00.003-0.0074.982-0.246-0.1180.000-0.017-0.1110.000
48K48GLY0-0.008-0.0066.0160.1340.1340.0000.0000.0000.000
49K49GLU-1-0.896-0.9366.3280.0310.0310.0000.0000.0000.000
50K50ALA0-0.026-0.0218.597-0.049-0.0490.0000.0000.0000.000
51K51GLY0-0.009-0.00610.122-0.036-0.0360.0000.0000.0000.000
52K52ASP-1-0.820-0.93212.0620.1920.1920.0000.0000.0000.000
53K53THR00.0170.0069.042-0.035-0.0350.0000.0000.0000.000
54K54VAL00.0280.01112.392-0.014-0.0140.0000.0000.0000.000
55K55GLN0-0.0010.01015.0520.0000.0000.0000.0000.0000.000
56K56PHE00.0170.01415.365-0.009-0.0090.0000.0000.0000.000
57K57ALA00.0090.00315.177-0.010-0.0100.0000.0000.0000.000
58K58GLU-1-0.916-0.97017.180-0.053-0.0530.0000.0000.0000.000
59K59TYR0-0.0160.00120.188-0.008-0.0080.0000.0000.0000.000
60K60ILE0-0.007-0.01119.154-0.007-0.0070.0000.0000.0000.000
61K61GLN00.0080.00221.042-0.004-0.0040.0000.0000.0000.000
62K62LYS10.8790.93222.7680.0240.0240.0000.0000.0000.000
63K63ASN0-0.026-0.01125.127-0.002-0.0020.0000.0000.0000.000
64K64VAL0-0.0020.01323.880-0.001-0.0010.0000.0000.0000.000
65K65GLN0-0.020-0.02026.654-0.003-0.0030.0000.0000.0000.000
66K66LEU0-0.0090.00828.789-0.002-0.0020.0000.0000.0000.000
67K67TYR0-0.003-0.01230.0890.0000.0000.0000.0000.0000.000
68K68LYS10.9640.98230.9010.0320.0320.0000.0000.0000.000
69K69MET0-0.063-0.03632.650-0.002-0.0020.0000.0000.0000.000
70K70ARG10.8880.95033.971-0.008-0.0080.0000.0000.0000.000
71K71ASN0-0.017-0.00534.4810.0010.0010.0000.0000.0000.000
72K72GLY0-0.0100.02136.5520.0000.0000.0000.0000.0000.000
73K73TYR0-0.0060.00234.555-0.003-0.0030.0000.0000.0000.000
74K74GLU-1-0.815-0.93329.702-0.032-0.0320.0000.0000.0000.000
75K75LEU0-0.014-0.00626.9790.0030.0030.0000.0000.0000.000
76K76SER00.0920.04928.342-0.003-0.0030.0000.0000.0000.000
77K77PRO00.0840.02323.2990.0070.0070.0000.0000.0000.000
78K78THR00.0390.02423.4190.0090.0090.0000.0000.0000.000
79K79ALA00.0100.01225.0030.0100.0100.0000.0000.0000.000
80K80ALA00.0250.01223.2640.0070.0070.0000.0000.0000.000
81K81ALA00.0220.01320.5900.0110.0110.0000.0000.0000.000
82K82ASN0-0.023-0.04021.3430.0230.0230.0000.0000.0000.000
83K83PHE00.0020.02023.7770.0080.0080.0000.0000.0000.000
84K84THR0-0.013-0.00918.8830.0140.0140.0000.0000.0000.000
85K85ARG10.9580.96519.555-0.103-0.1030.0000.0000.0000.000
86K86ARG10.8420.93420.557-0.073-0.0730.0000.0000.0000.000
87K87ASN00.005-0.00721.6110.0020.0020.0000.0000.0000.000
88K88LEU00.0210.01414.728-0.004-0.0040.0000.0000.0000.000
89K89ALA0-0.042-0.02719.2010.0120.0120.0000.0000.0000.000
90K90ASP-1-0.901-0.95521.3120.0860.0860.0000.0000.0000.000
91K91CYS0-0.049-0.01820.087-0.007-0.0070.0000.0000.0000.000
92K92LEU00.0030.03717.6770.0030.0030.0000.0000.0000.000
93K93ARG10.9320.95720.276-0.121-0.1210.0000.0000.0000.000
94K94SER0-0.024-0.01822.142-0.014-0.0140.0000.0000.0000.000
95K95ARG10.9690.96622.393-0.082-0.0820.0000.0000.0000.000
96K96THR0-0.066-0.05220.072-0.001-0.0010.0000.0000.0000.000
97K97PRO00.0080.04817.131-0.006-0.0060.0000.0000.0000.000
98K98TYR00.022-0.00114.954-0.006-0.0060.0000.0000.0000.000
99K99HIS00.0130.01210.0770.0720.0720.0000.0000.0000.000
100K100VAL0-0.029-0.0139.8550.0450.0450.0000.0000.0000.000
101K101ASN00.0130.0076.403-0.298-0.2980.0000.0000.0000.000
102K102LEU0-0.009-0.0219.662-0.034-0.0340.0000.0000.0000.000
103K103LEU0-0.005-0.00110.841-0.005-0.0050.0000.0000.0000.000
104K104LEU0-0.031-0.00413.472-0.020-0.0200.0000.0000.0000.000
105K105ALA00.0250.01817.168-0.001-0.0010.0000.0000.0000.000
106K106GLY0-0.006-0.02318.9650.0010.0010.0000.0000.0000.000
107K107TYR00.0020.01122.739-0.003-0.0030.0000.0000.0000.000
108K108ASP-1-0.901-0.97226.168-0.013-0.0130.0000.0000.0000.000
109K109GLU-1-0.849-0.90929.221-0.039-0.0390.0000.0000.0000.000
110K110HIS0-0.058-0.01832.320-0.001-0.0010.0000.0000.0000.000
111K111GLU-1-0.944-0.97729.296-0.004-0.0040.0000.0000.0000.000
112K112GLY0-0.0030.02628.957-0.001-0.0010.0000.0000.0000.000
113K113PRO0-0.035-0.00724.0010.0020.0020.0000.0000.0000.000
114K114ALA0-0.055-0.03122.6360.0080.0080.0000.0000.0000.000
115K115LEU00.0350.02015.174-0.011-0.0110.0000.0000.0000.000
116K116TYR0-0.047-0.03617.6580.0120.0120.0000.0000.0000.000
117K117TYR00.0180.0139.437-0.010-0.0100.0000.0000.0000.000
118K118MET0-0.028-0.00713.262-0.032-0.0320.0000.0000.0000.000
119K119ASP-1-0.845-0.92011.7780.5400.5400.0000.0000.0000.000
120K120TYR00.0650.03110.434-0.068-0.0680.0000.0000.0000.000
121K121LEU0-0.059-0.02312.625-0.067-0.0670.0000.0000.0000.000
122K122ALA0-0.018-0.00615.467-0.044-0.0440.0000.0000.0000.000
123K123ALA0-0.028-0.00716.575-0.038-0.0380.0000.0000.0000.000
124K124LEU0-0.029-0.01716.6820.0170.0170.0000.0000.0000.000
125K125ALA00.002-0.00317.021-0.014-0.0140.0000.0000.0000.000
126K126LYS10.9670.98917.830-0.003-0.0030.0000.0000.0000.000
127K127ALA0-0.006-0.00716.8500.0030.0030.0000.0000.0000.000
128K128PRO00.0070.02418.986-0.007-0.0070.0000.0000.0000.000
129K129PHE00.005-0.01214.973-0.022-0.0220.0000.0000.0000.000
130K130ALA0-0.0100.00512.5710.0310.0310.0000.0000.0000.000
131K131ALA00.015-0.0028.215-0.072-0.0720.0000.0000.0000.000
132K132HIS00.0070.0125.9500.2560.2560.0000.0000.0000.000
133K133GLY00.0580.0242.258-0.087-1.1943.519-1.327-1.0850.003
134K134TYR0-0.022-0.0351.5264.845-7.33321.236-1.522-7.5360.008
135K135GLY00.0600.0253.477-0.200-0.1540.0270.322-0.3950.002
136K136ALA00.0420.0235.1360.0710.0710.0000.0000.0000.000
137K137PHE0-0.026-0.0065.8930.0090.0090.0000.0000.0000.000
138K138LEU0-0.034-0.0128.6020.0180.0180.0000.0000.0000.000
139K139THR0-0.042-0.0178.8820.0250.0250.0000.0000.0000.000
140K140LEU00.0380.01210.4310.0240.0240.0000.0000.0000.000
141K141SER00.0590.03812.757-0.001-0.0010.0000.0000.0000.000
142K142ILE00.0210.01314.2870.0150.0150.0000.0000.0000.000
143K143LEU0-0.006-0.01313.2800.0120.0120.0000.0000.0000.000
144K144ASP-1-0.862-0.94116.865-0.025-0.0250.0000.0000.0000.000
145K145ARG10.8130.92418.8830.0910.0910.0000.0000.0000.000
146K146TYR0-0.074-0.06219.9020.0110.0110.0000.0000.0000.000
147K147TYR0-0.019-0.02219.7440.0020.0020.0000.0000.0000.000
148K148THR0-0.029-0.01421.7970.0120.0120.0000.0000.0000.000
149K149PRO00.0650.01124.800-0.006-0.0060.0000.0000.0000.000
150K150THR0-0.017-0.00325.9290.0010.0010.0000.0000.0000.000
151K151ILE0-0.0360.01121.984-0.002-0.0020.0000.0000.0000.000
152K152SER00.0770.05725.927-0.002-0.0020.0000.0000.0000.000
153K153ARG11.0091.00324.0600.0890.0890.0000.0000.0000.000
154K154GLU-1-0.866-0.94123.718-0.127-0.1270.0000.0000.0000.000
155K155ARG10.8570.91024.2440.1030.1030.0000.0000.0000.000
156K156ALA0-0.0150.00620.767-0.012-0.0120.0000.0000.0000.000
157K157VAL00.0320.01119.635-0.027-0.0270.0000.0000.0000.000
158K158GLU-1-0.890-0.93219.794-0.177-0.1770.0000.0000.0000.000
159K159LEU0-0.012-0.00917.712-0.019-0.0190.0000.0000.0000.000
160K160LEU00.0410.01613.811-0.026-0.0260.0000.0000.0000.000
161K161ARG10.9640.97315.3420.2130.2130.0000.0000.0000.000
162K162LYS10.9640.99416.6760.1370.1370.0000.0000.0000.000
163K163CYS0-0.044-0.01012.385-0.001-0.0010.0000.0000.0000.000
164K164LEU00.001-0.00611.191-0.074-0.0740.0000.0000.0000.000
165K165GLU-1-0.938-0.96912.673-0.365-0.3650.0000.0000.0000.000
166K166GLU-1-0.916-0.95912.652-0.292-0.2920.0000.0000.0000.000
167K167LEU0-0.086-0.0397.500-0.037-0.0370.0000.0000.0000.000
168K168GLN0-0.060-0.0389.9850.0510.0510.0000.0000.0000.000
169K169LYS10.9040.97712.1390.2820.2820.0000.0000.0000.000
170K170ARG10.9100.94012.4200.2490.2490.0000.0000.0000.000
171K171PHE00.0030.0093.280-0.3650.2500.029-0.119-0.5250.001
172K172ILE00.0360.0147.0730.0150.0150.0000.0000.0000.000
173K173LEU0-0.047-0.0092.0750.266-2.1437.224-1.705-3.1100.003
174K174ASN00.0120.0025.405-0.341-0.3410.0000.0000.0000.000
175K175LEU00.0170.0063.5740.0020.2520.002-0.067-0.1850.000
176K176PRO00.0610.0507.1450.2150.2150.0000.0000.0000.000
177K177THR00.022-0.00910.3720.1190.1190.0000.0000.0000.000
178K178PHE00.006-0.0048.593-0.238-0.2380.0000.0000.0000.000
179K179SER00.0150.01312.5350.1030.1030.0000.0000.0000.000
180K180VAL00.0080.00614.526-0.023-0.0230.0000.0000.0000.000
181K181ARG10.8330.92317.0150.2800.2800.0000.0000.0000.000
182K182ILE0-0.016-0.00819.028-0.001-0.0010.0000.0000.0000.000
183K183ILE0-0.0170.00220.1740.0070.0070.0000.0000.0000.000
184K184ASP-1-0.768-0.88923.654-0.084-0.0840.0000.0000.0000.000
185K185LYS10.8270.88627.0610.0440.0440.0000.0000.0000.000
186K186ASN0-0.084-0.05230.0080.0090.0090.0000.0000.0000.000
187K187GLY00.0240.02727.6780.0010.0010.0000.0000.0000.000
188K188ILE0-0.075-0.04722.110-0.006-0.0060.0000.0000.0000.000
189K189HIS0-0.010-0.00324.163-0.003-0.0030.0000.0000.0000.000
190K190ASP-1-0.903-0.97021.815-0.200-0.2000.0000.0000.0000.000
191K191LEU0-0.053-0.02620.8770.0150.0150.0000.0000.0000.000
192K192ASP-1-0.893-0.94220.637-0.225-0.2250.0000.0000.0000.000
193K193ASN0-0.028-0.02316.148-0.024-0.0240.0000.0000.0000.000
194K194ILE0-0.029-0.00115.2570.0310.0310.0000.0000.0000.000
195K195SER0-0.024-0.02214.590-0.083-0.0830.0000.0000.0000.000
196K196PHE00.0140.00313.3990.0500.0500.0000.0000.0000.000
197K197PRO0-0.005-0.00615.475-0.023-0.0230.0000.0000.0000.000
198K198LYS10.8680.95210.4080.6770.6770.0000.0000.0000.000
199K199GLN0-0.0040.00314.696-0.001-0.0010.0000.0000.0000.000