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: K3LJ3

Calculation Name: 4U7U-K-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4U7U

Chain ID: K

ChEMBL ID:

UniProt ID: Q46898

Base Structure: X-ray

Registration Date: 2023-06-19

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
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2547913.590926
FMO2-HF: Nuclear repulsion 2461230.858184
FMO2-HF: Total energy -86682.732742
FMO2-MP2: Total energy -86933.67067


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.
-7.411-2.1491.133-2.222-4.1730
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 : -0.019 / q_NPA : -0.018
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].
3K3SER00.0110.0093.4561.6473.1550.001-0.625-0.8850.002
4K4TYR0-0.013-0.0165.451-0.206-0.2060.0000.0000.0000.000
5K5LEU00.0060.0069.2410.0420.0420.0000.0000.0000.000
6K6ILE0-0.035-0.01811.5630.0420.0420.0000.0000.0000.000
7K7LEU00.0180.01415.017-0.023-0.0230.0000.0000.0000.000
8K8ARG10.9130.95818.756-0.084-0.0840.0000.0000.0000.000
9K9LEU0-0.051-0.01721.792-0.021-0.0210.0000.0000.0000.000
10K10ALA00.0760.02824.5570.0110.0110.0000.0000.0000.000
11K11GLY00.0190.00327.801-0.011-0.0110.0000.0000.0000.000
12K12PRO00.0140.02031.4740.0050.0050.0000.0000.0000.000
13K13MET00.0230.00334.0980.0030.0030.0000.0000.0000.000
14K14GLN0-0.002-0.00927.359-0.010-0.0100.0000.0000.0000.000
15K15ALA00.0060.00630.7730.0040.0040.0000.0000.0000.000
16K16TRP00.0170.02525.996-0.016-0.0160.0000.0000.0000.000
17K17GLY0-0.010-0.00428.6620.0050.0050.0000.0000.0000.000
18K18GLN00.0350.00928.7590.0080.0080.0000.0000.0000.000
19K19PRO0-0.004-0.01629.953-0.003-0.0030.0000.0000.0000.000
20K20THR0-0.0130.00532.7830.0040.0040.0000.0000.0000.000
21K21PHE0-0.017-0.00435.562-0.005-0.0050.0000.0000.0000.000
22K22GLU-1-0.848-0.90439.069-0.014-0.0140.0000.0000.0000.000
23K23GLY00.008-0.01040.386-0.002-0.0020.0000.0000.0000.000
24K24THR0-0.002-0.02239.1980.0010.0010.0000.0000.0000.000
25K25ARG10.8120.91236.1540.0230.0230.0000.0000.0000.000
26K26PRO00.0780.02333.6310.0010.0010.0000.0000.0000.000
27K27THR0-0.014-0.00130.687-0.007-0.0070.0000.0000.0000.000
28K28GLY00.0260.03628.2820.0040.0040.0000.0000.0000.000
29K29ARG10.9430.94027.006-0.056-0.0560.0000.0000.0000.000
30K30PHE00.0130.00720.5780.0130.0130.0000.0000.0000.000
31K31PRO0-0.032-0.00521.733-0.009-0.0090.0000.0000.0000.000
32K32THR00.0620.04222.1210.0000.0000.0000.0000.0000.000
33K33ARG10.8150.88615.5280.2310.2310.0000.0000.0000.000
34K34SER00.000-0.00820.912-0.012-0.0120.0000.0000.0000.000
35K35GLY0-0.0030.01023.984-0.007-0.0070.0000.0000.0000.000
36K36LEU00.010-0.00118.434-0.004-0.0040.0000.0000.0000.000
37K37LEU00.0080.00518.964-0.009-0.0090.0000.0000.0000.000
38K38GLY0-0.0080.00221.837-0.009-0.0090.0000.0000.0000.000
39K39LEU0-0.035-0.00922.8620.0000.0000.0000.0000.0000.000
40K40LEU00.0370.01218.162-0.001-0.0010.0000.0000.0000.000
41K41GLY00.022-0.00122.616-0.007-0.0070.0000.0000.0000.000
42K42ALA0-0.044-0.00224.9720.0040.0040.0000.0000.0000.000
43K43CYS0-0.046-0.02824.1640.0080.0080.0000.0000.0000.000
44K44LEU00.0670.03221.6150.0010.0010.0000.0000.0000.000
45K45GLY0-0.042-0.01425.8760.0120.0120.0000.0000.0000.000
46K46ILE0-0.020-0.00524.6670.0000.0000.0000.0000.0000.000
47K47GLN0-0.024-0.00629.2570.0130.0130.0000.0000.0000.000
48K48ARG10.9480.94531.1810.0730.0730.0000.0000.0000.000
49K49ASP-1-0.904-0.94832.203-0.107-0.1070.0000.0000.0000.000
50K50ASP-1-0.808-0.86229.559-0.169-0.1690.0000.0000.0000.000
51K51THR00.016-0.02728.808-0.008-0.0080.0000.0000.0000.000
52K52SER00.0130.00726.894-0.007-0.0070.0000.0000.0000.000
53K53SER0-0.007-0.01025.072-0.027-0.0270.0000.0000.0000.000
54K54LEU0-0.072-0.03423.955-0.014-0.0140.0000.0000.0000.000
55K55GLN0-0.020-0.00623.058-0.005-0.0050.0000.0000.0000.000
56K56ALA00.0510.03720.845-0.022-0.0220.0000.0000.0000.000
57K57LEU0-0.0120.05119.018-0.042-0.0420.0000.0000.0000.000
58K58SER0-0.042-0.03718.411-0.025-0.0250.0000.0000.0000.000
59K59GLU-1-0.901-0.96717.148-0.293-0.2930.0000.0000.0000.000
60K60SER0-0.037-0.06815.011-0.066-0.0660.0000.0000.0000.000
61K61VAL0-0.0240.01513.434-0.105-0.1050.0000.0000.0000.000
62K62GLN0-0.018-0.00210.617-0.020-0.0200.0000.0000.0000.000
63K63PHE00.0090.00112.3720.0020.0020.0000.0000.0000.000
64K64ALA00.0120.00011.9160.0100.0100.0000.0000.0000.000
65K65VAL0-0.023-0.00813.8990.0160.0160.0000.0000.0000.000
66K66ARG10.8380.92417.192-0.269-0.2690.0000.0000.0000.000
67K67CYS0-0.060-0.02718.845-0.031-0.0310.0000.0000.0000.000
68K68ASP-1-0.740-0.83121.9020.1900.1900.0000.0000.0000.000
69K69GLU-1-0.930-0.97024.3670.1040.1040.0000.0000.0000.000
70K70LEU0-0.0110.00827.8280.0070.0070.0000.0000.0000.000
71K71ILE0-0.015-0.01629.9320.0010.0010.0000.0000.0000.000
72K72LEU00.007-0.00732.232-0.002-0.0020.0000.0000.0000.000
73K73ASP-1-0.946-0.94735.2540.0610.0610.0000.0000.0000.000
74K74ASP-1-0.953-0.99434.7340.0830.0830.0000.0000.0000.000
75K75ARG10.9240.96035.801-0.075-0.0750.0000.0000.0000.000
76K76ARG10.9330.96529.586-0.137-0.1370.0000.0000.0000.000
77K77VAL00.0080.00933.151-0.005-0.0050.0000.0000.0000.000
78K78SER00.0030.00032.1520.0010.0010.0000.0000.0000.000
79K79VAL00.0210.01928.948-0.005-0.0050.0000.0000.0000.000
80K80THR0-0.020-0.00532.247-0.002-0.0020.0000.0000.0000.000
81K81GLY0-0.007-0.00534.522-0.002-0.0020.0000.0000.0000.000
82K82LEU00.0170.01236.2520.0000.0000.0000.0000.0000.000
83K83ARG10.9540.96738.383-0.011-0.0110.0000.0000.0000.000
84K84ASP-1-0.882-0.93840.943-0.002-0.0020.0000.0000.0000.000
85K85TYR0-0.069-0.05442.699-0.002-0.0020.0000.0000.0000.000
86K86HIS00.0100.01141.629-0.002-0.0020.0000.0000.0000.000
87K87THR00.011-0.00145.355-0.002-0.0020.0000.0000.0000.000
88K88VAL0-0.025-0.02445.718-0.002-0.0020.0000.0000.0000.000
89K89LEU00.0500.03048.8160.0010.0010.0000.0000.0000.000
90K90GLY00.0470.03952.036-0.001-0.0010.0000.0000.0000.000
91K91ALA0-0.080-0.03348.478-0.002-0.0020.0000.0000.0000.000
92K92ARG10.9430.96442.7690.0380.0380.0000.0000.0000.000
93K93GLU-1-0.890-0.94349.627-0.021-0.0210.0000.0000.0000.000
94K94ASP-1-0.879-0.92750.107-0.028-0.0280.0000.0000.0000.000
95K95TYR0-0.112-0.06943.438-0.002-0.0020.0000.0000.0000.000
96K96ARG10.9650.96947.8670.0380.0380.0000.0000.0000.000
97K97GLY00.0100.01550.8010.0020.0020.0000.0000.0000.000
98K98LEU00.000-0.01952.653-0.001-0.0010.0000.0000.0000.000
99K99LYS10.9481.00554.9000.0250.0250.0000.0000.0000.000
100K100SER0-0.004-0.01553.474-0.001-0.0010.0000.0000.0000.000
101K101HIS00.0210.01251.4820.0000.0000.0000.0000.0000.000
102K102GLU-1-0.895-0.94654.507-0.013-0.0130.0000.0000.0000.000
103K103THR0-0.009-0.02952.9440.0000.0000.0000.0000.0000.000
104K104ILE0-0.0460.00346.7940.0000.0000.0000.0000.0000.000
105K105GLN00.0290.02047.9720.0010.0010.0000.0000.0000.000
106K106THR0-0.078-0.02542.519-0.001-0.0010.0000.0000.0000.000
107K107TRP00.0450.02542.4290.0010.0010.0000.0000.0000.000
108K108ARG10.8640.92638.2160.0180.0180.0000.0000.0000.000
109K109GLU-1-0.857-0.92935.8320.0130.0130.0000.0000.0000.000
110K110TYR0-0.039-0.02434.325-0.008-0.0080.0000.0000.0000.000
111K111LEU0-0.047-0.02028.9630.0040.0040.0000.0000.0000.000
112K112CYS0-0.006-0.00932.966-0.006-0.0060.0000.0000.0000.000
113K113ASP-1-0.833-0.91732.9610.0530.0530.0000.0000.0000.000
114K114ALA0-0.041-0.00528.2260.0080.0080.0000.0000.0000.000
115K115SER0-0.006-0.02026.308-0.013-0.0130.0000.0000.0000.000
116K116PHE00.0230.00621.6830.0090.0090.0000.0000.0000.000
117K117THR0-0.037-0.05617.597-0.015-0.0150.0000.0000.0000.000
118K118VAL0-0.046-0.02616.2090.0220.0220.0000.0000.0000.000
119K119ALA00.0220.01111.7450.0080.0080.0000.0000.0000.000
120K120LEU0-0.018-0.00912.545-0.020-0.0200.0000.0000.0000.000
121K121TRP0-0.006-0.0227.7730.0960.0960.0000.0000.0000.000
122K122LEU0-0.0040.0059.4850.0780.0780.0000.0000.0000.000
123K123THR0-0.013-0.0298.767-0.234-0.2340.0000.0000.0000.000
124K124PRO0-0.015-0.0298.128-0.006-0.0060.0000.0000.0000.000
125K125HIS0-0.0160.00110.324-0.005-0.0050.0000.0000.0000.000
126K126ALA0-0.0270.00912.9890.0820.0820.0000.0000.0000.000
127K127THR0-0.017-0.00114.6460.0180.0180.0000.0000.0000.000
128K128MET0-0.020-0.00416.6140.0350.0350.0000.0000.0000.000
129K129VAL00.0280.00414.514-0.105-0.1050.0000.0000.0000.000
130K130ILE00.0700.02510.0160.0830.0830.0000.0000.0000.000
131K131SER00.0300.01114.1390.0690.0690.0000.0000.0000.000
132K132GLU-1-0.897-0.95516.263-0.325-0.3250.0000.0000.0000.000
133K133LEU0-0.0020.00015.2940.0530.0530.0000.0000.0000.000
134K134GLU-1-0.944-0.96915.566-0.229-0.2290.0000.0000.0000.000
135K135LYS10.9380.96717.9960.2550.2550.0000.0000.0000.000
136K136ALA0-0.007-0.00621.0360.0260.0260.0000.0000.0000.000
137K137VAL0-0.013-0.02019.6720.0240.0240.0000.0000.0000.000
138K138LEU0-0.043-0.01319.8030.0230.0230.0000.0000.0000.000
139K139LYS10.8550.93423.4420.1370.1370.0000.0000.0000.000
140K140PRO00.0060.03126.260-0.010-0.0100.0000.0000.0000.000
141K141ARG10.9130.94327.5100.1420.1420.0000.0000.0000.000
142K142TYR0-0.033-0.00729.9920.0090.0090.0000.0000.0000.000
143K143THR0-0.045-0.03530.487-0.001-0.0010.0000.0000.0000.000
144K144PRO00.0380.03327.739-0.001-0.0010.0000.0000.0000.000
145K145TYR0-0.045-0.04029.0260.0040.0040.0000.0000.0000.000
146K146LEU00.0120.02526.706-0.006-0.0060.0000.0000.0000.000
147K147GLY00.0760.04728.6900.0070.0070.0000.0000.0000.000
148K148ARG10.7970.88430.0080.0060.0060.0000.0000.0000.000
149K149ARG10.9420.97133.4870.0580.0580.0000.0000.0000.000
150K150SER00.0180.00235.300-0.001-0.0010.0000.0000.0000.000
151K151CYS0-0.064-0.01332.7350.0060.0060.0000.0000.0000.000
152K152PRO00.0390.01432.354-0.004-0.0040.0000.0000.0000.000
153K153LEU00.0010.00426.5560.0030.0030.0000.0000.0000.000
154K154THR0-0.058-0.03630.0770.0000.0000.0000.0000.0000.000
155K155HIS0-0.010-0.02322.5550.0140.0140.0000.0000.0000.000
156K156PRO0-0.0050.00424.003-0.008-0.0080.0000.0000.0000.000
157K157LEU00.0430.03922.1550.0110.0110.0000.0000.0000.000
158K158PHE00.0400.00516.0720.0100.0100.0000.0000.0000.000
159K159LEU0-0.038-0.00417.5830.0120.0120.0000.0000.0000.000
160K160GLY00.027-0.00515.3230.0080.0080.0000.0000.0000.000
161K161THR0-0.0130.00311.143-0.029-0.0290.0000.0000.0000.000
162K162CYS0-0.042-0.0028.6300.1610.1610.0000.0000.0000.000
163K163GLN00.023-0.0113.369-1.614-1.3710.011-0.080-0.1740.000
164K164ALA0-0.029-0.0023.719-0.6510.1020.047-0.282-0.5180.002
165K165SER00.0320.0082.902-2.494-0.1361.045-1.396-2.007-0.002
166K166ASP-1-0.855-0.9213.544-1.388-0.9880.0290.161-0.589-0.002
167K167PRO00.0110.0126.3140.1700.1700.0000.0000.0000.000
168K168GLN00.0590.0218.7050.0610.0610.0000.0000.0000.000
169K169LYS10.9270.9637.455-1.512-1.5120.0000.0000.0000.000
170K170ALA00.0420.0188.438-0.020-0.0200.0000.0000.0000.000
171K171LEU00.018-0.0039.822-0.191-0.1910.0000.0000.0000.000
172K172LEU0-0.072-0.04412.520-0.076-0.0760.0000.0000.0000.000
173K173ASN0-0.080-0.0159.997-0.074-0.0740.0000.0000.0000.000
174K174TYR00.0240.00712.300-0.124-0.1240.0000.0000.0000.000
175K175GLU-1-0.911-0.92816.9410.2530.2530.0000.0000.0000.000
176K176PRO0-0.026-0.02020.417-0.025-0.0250.0000.0000.0000.000
177K177VAL00.016-0.00717.9760.0130.0130.0000.0000.0000.000
178K178GLY00.008-0.00420.015-0.021-0.0210.0000.0000.0000.000
179K179GLY0-0.0090.01021.138-0.017-0.0170.0000.0000.0000.000
180K180ASP-1-0.872-0.93519.7060.2290.2290.0000.0000.0000.000
181K181ILE0-0.015-0.03114.029-0.005-0.0050.0000.0000.0000.000
182K182TYR0-0.0180.00416.8340.0030.0030.0000.0000.0000.000
183K183SER00.005-0.03410.707-0.051-0.0510.0000.0000.0000.000
184K184GLU-1-0.812-0.91512.235-0.204-0.2040.0000.0000.0000.000
185K185GLU-1-0.926-0.9575.245-0.630-0.6300.0000.0000.0000.000
186K186SER0-0.034-0.0039.7430.1440.1440.0000.0000.0000.000
187K187VAL00.0700.0338.7470.0010.0010.0000.0000.0000.000
188K188THR0-0.003-0.0118.689-0.063-0.0630.0000.0000.0000.000
189K189GLY0-0.0170.00511.337-0.062-0.0620.0000.0000.0000.000
190K190HIS0-0.025-0.01413.667-0.094-0.0940.0000.0000.0000.000
191K191HIS00.0460.01815.337-0.038-0.0380.0000.0000.0000.000
192K192LEU0-0.048-0.00917.943-0.032-0.0320.0000.0000.0000.000
193K193LYS10.9600.97916.668-0.008-0.0080.0000.0000.0000.000
194K194PHE0-0.029-0.00719.9830.0020.0020.0000.0000.0000.000
195K195THR00.0190.01421.635-0.010-0.0100.0000.0000.0000.000
196K196ALA00.0110.01222.6710.0050.0050.0000.0000.0000.000
197K197ARG10.9010.93824.5780.0330.0330.0000.0000.0000.000
198K198ASP-1-0.829-0.91921.851-0.039-0.0390.0000.0000.0000.000
199K199GLU-1-0.797-0.89919.541-0.177-0.1770.0000.0000.0000.000
200K200PRO0-0.0220.00622.5800.0140.0140.0000.0000.0000.000
201K201MET00.0020.00324.927-0.012-0.0120.0000.0000.0000.000
202K202ILE00.0430.02623.9390.0100.0100.0000.0000.0000.000
203K203THR0-0.012-0.00327.8550.0050.0050.0000.0000.0000.000
204K204LEU0-0.025-0.01530.2710.0080.0080.0000.0000.0000.000
205K205PRO00.0460.01431.5310.0010.0010.0000.0000.0000.000
206K206ARG10.8660.93131.1420.0730.0730.0000.0000.0000.000
207K207GLN00.0530.04231.0810.0100.0100.0000.0000.0000.000
208K208PHE0-0.012-0.01126.758-0.006-0.0060.0000.0000.0000.000
209K209ALA00.018-0.00325.3730.0090.0090.0000.0000.0000.000
210K210SER0-0.053-0.04224.737-0.003-0.0030.0000.0000.0000.000
211K211ARG10.9040.96216.7700.0650.0650.0000.0000.0000.000
212K212GLU-1-0.908-0.97019.3540.0210.0210.0000.0000.0000.000
213K213TRP0-0.070-0.00516.116-0.021-0.0210.0000.0000.0000.000
214K214TYR00.0280.00613.6570.0180.0180.0000.0000.0000.000
215K215VAL0-0.017-0.01815.8610.0100.0100.0000.0000.0000.000
216K216ILE0-0.029-0.01013.1120.0180.0180.0000.0000.0000.000
217K217LYS10.9540.97416.815-0.199-0.1990.0000.0000.0000.000
218K218GLY0-0.0100.01119.2050.0440.0440.0000.0000.0000.000