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: R5NK8

Calculation Name: 4U7U-K-Xray319

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 219
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2550354.856461
FMO2-HF: Nuclear repulsion 2463653.063654
FMO2-HF: Total energy -86701.792807
FMO2-MP2: Total energy -86952.817846


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.
-7.345-2.1281.155-2.215-4.1570
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 : -0.018 / q_NPA : -0.017
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].
3K3SER 00.0090.0083.4561.7503.2180.009-0.614-0.8630.002
4K4TYR 0-0.014-0.0165.451-0.213-0.2130.0000.0000.0000.000
5K5LEU 00.0060.0069.2430.0430.0430.0000.0000.0000.000
6K6ILE 0-0.035-0.01811.5650.0420.0420.0000.0000.0000.000
7K7LEU 00.0220.01515.020-0.023-0.0230.0000.0000.0000.000
8K8ARG 10.9140.95918.758-0.083-0.0830.0000.0000.0000.000
9K9LEU 0-0.055-0.01921.794-0.021-0.0210.0000.0000.0000.000
10K10ALA 00.0770.02924.5570.0110.0110.0000.0000.0000.000
11K11GLY 00.0210.00427.801-0.011-0.0110.0000.0000.0000.000
12K12PRO 00.0080.01831.4740.0050.0050.0000.0000.0000.000
13K13MET 00.0260.00434.0980.0030.0030.0000.0000.0000.000
14K14GLN 0-0.002-0.00927.359-0.010-0.0100.0000.0000.0000.000
15K15ALA 00.0050.00730.7730.0040.0040.0000.0000.0000.000
16K16TRP 00.0150.02425.996-0.017-0.0170.0000.0000.0000.000
17K17GLY 0-0.008-0.00328.6620.0050.0050.0000.0000.0000.000
18K18GLN 00.0420.01128.7590.0080.0080.0000.0000.0000.000
19K19PRO 0-0.010-0.01829.953-0.003-0.0030.0000.0000.0000.000
20K20THR 0-0.0110.00632.7830.0040.0040.0000.0000.0000.000
21K21PHE 0-0.017-0.00535.562-0.005-0.0050.0000.0000.0000.000
22K22GLU -1-0.848-0.90439.069-0.016-0.0160.0000.0000.0000.000
23K23GLY 00.007-0.01140.386-0.002-0.0020.0000.0000.0000.000
24K24THR 0-0.003-0.02139.2010.0010.0010.0000.0000.0000.000
25K25ARG 10.8110.91136.1530.0240.0240.0000.0000.0000.000
26K26PRO 00.0790.02333.6310.0010.0010.0000.0000.0000.000
27K27THR 0-0.0120.00030.687-0.007-0.0070.0000.0000.0000.000
28K28GLY 00.0260.03528.2820.0040.0040.0000.0000.0000.000
29K29ARG 10.9400.93927.006-0.053-0.0530.0000.0000.0000.000
30K30PHE 00.0170.00820.5780.0130.0130.0000.0000.0000.000
31K31PRO 0-0.037-0.00621.733-0.010-0.0100.0000.0000.0000.000
32K32THR 00.0570.04122.1210.0000.0000.0000.0000.0000.000
33K33ARG 10.8240.88815.5240.2390.2390.0000.0000.0000.000
34K34SER 0-0.001-0.00820.912-0.012-0.0120.0000.0000.0000.000
35K35GLY 0-0.0070.01023.984-0.006-0.0060.0000.0000.0000.000
36K36LEU 00.008-0.00218.434-0.004-0.0040.0000.0000.0000.000
37K37LEU 00.0120.00718.965-0.009-0.0090.0000.0000.0000.000
38K38GLY 0-0.0070.00321.837-0.009-0.0090.0000.0000.0000.000
39K39LEU 0-0.033-0.00822.8620.0010.0010.0000.0000.0000.000
40K40LEU 00.0350.01118.161-0.002-0.0020.0000.0000.0000.000
41K41GLY 00.022-0.00122.616-0.007-0.0070.0000.0000.0000.000
42K42ALA 0-0.042-0.00124.9720.0050.0050.0000.0000.0000.000
43K43CYS 0-0.049-0.03024.1640.0080.0080.0000.0000.0000.000
44K44LEU 00.0670.03221.6150.0010.0010.0000.0000.0000.000
45K45GLY 0-0.039-0.01225.8760.0120.0120.0000.0000.0000.000
46K46ILE 0-0.022-0.00624.6670.0000.0000.0000.0000.0000.000
47K47GLN 0-0.022-0.00629.2570.0130.0130.0000.0000.0000.000
48K48ARG 10.9470.94531.1810.0740.0740.0000.0000.0000.000
49K49ASP -1-0.902-0.94732.203-0.108-0.1080.0000.0000.0000.000
50K50ASP -1-0.807-0.86129.559-0.171-0.1710.0000.0000.0000.000
51K51THR 00.013-0.02828.808-0.008-0.0080.0000.0000.0000.000
52K52SER 00.0140.00826.894-0.008-0.0080.0000.0000.0000.000
53K53SER 0-0.007-0.01125.072-0.027-0.0270.0000.0000.0000.000
54K54LEU 0-0.069-0.03323.955-0.015-0.0150.0000.0000.0000.000
55K55GLN 0-0.021-0.00623.058-0.006-0.0060.0000.0000.0000.000
56K56ALA 00.0510.03720.845-0.023-0.0230.0000.0000.0000.000
57K57LEU 0-0.0140.05219.018-0.043-0.0430.0000.0000.0000.000
58K58SER 0-0.039-0.03618.411-0.026-0.0260.0000.0000.0000.000
59K59GLU -1-0.901-0.96617.148-0.299-0.2990.0000.0000.0000.000
60K60SER 0-0.037-0.06815.011-0.069-0.0690.0000.0000.0000.000
61K61VAL 0-0.0280.01413.434-0.106-0.1060.0000.0000.0000.000
62K62GLN 0-0.017-0.00110.617-0.021-0.0210.0000.0000.0000.000
63K63PHE 00.0080.00112.3720.0060.0060.0000.0000.0000.000
64K64ALA 00.0180.00111.9160.0110.0110.0000.0000.0000.000
65K65VAL 0-0.023-0.00713.8990.0180.0180.0000.0000.0000.000
66K66ARG 10.8380.92317.192-0.267-0.2670.0000.0000.0000.000
67K67CYS 0-0.060-0.02718.845-0.032-0.0320.0000.0000.0000.000
68K68ASP -1-0.745-0.83221.9020.1880.1880.0000.0000.0000.000
69K69GLU -1-0.926-0.96924.3670.1020.1020.0000.0000.0000.000
70K70LEU 0-0.0140.00727.8280.0070.0070.0000.0000.0000.000
71K71ILE 0-0.014-0.01629.9320.0010.0010.0000.0000.0000.000
72K72LEU 00.007-0.00832.232-0.002-0.0020.0000.0000.0000.000
73K73ASP -1-0.947-0.94735.2560.0600.0600.0000.0000.0000.000
74K74ASP -1-0.953-0.99334.7340.0830.0830.0000.0000.0000.000
75K75ARG 10.9240.96035.801-0.074-0.0740.0000.0000.0000.000
76K76ARG 10.9340.96629.586-0.136-0.1360.0000.0000.0000.000
77K77VAL 00.0080.00933.151-0.006-0.0060.0000.0000.0000.000
78K78SER 00.0040.00032.1520.0010.0010.0000.0000.0000.000
79K79VAL 00.0170.01828.948-0.006-0.0060.0000.0000.0000.000
80K80THR 0-0.017-0.00432.247-0.003-0.0030.0000.0000.0000.000
81K81GLY 0-0.009-0.00534.522-0.003-0.0030.0000.0000.0000.000
82K82LEU 00.0190.01236.2520.0000.0000.0000.0000.0000.000
83K83ARG 10.9540.96838.383-0.010-0.0100.0000.0000.0000.000
84K84ASP -1-0.883-0.93940.943-0.003-0.0030.0000.0000.0000.000
85K85TYR 0-0.069-0.05342.699-0.002-0.0020.0000.0000.0000.000
86K86HIS 00.0110.01241.629-0.002-0.0020.0000.0000.0000.000
87K87THR 00.009-0.00245.355-0.002-0.0020.0000.0000.0000.000
88K88VAL 0-0.022-0.02345.718-0.002-0.0020.0000.0000.0000.000
89K89LEU 00.0490.03048.8160.0010.0010.0000.0000.0000.000
90K90GLY 00.0470.03952.036-0.001-0.0010.0000.0000.0000.000
91K91ALA 0-0.081-0.03348.478-0.002-0.0020.0000.0000.0000.000
92K92ARG 10.9460.96542.7690.0390.0390.0000.0000.0000.000
93K93GLU -1-0.893-0.94449.627-0.022-0.0220.0000.0000.0000.000
94K94ASP -1-0.879-0.92850.107-0.029-0.0290.0000.0000.0000.000
95K95TYR 0-0.112-0.06943.438-0.002-0.0020.0000.0000.0000.000
96K96ARG 10.9640.97047.8670.0390.0390.0000.0000.0000.000
97K97GLY 00.0090.01450.8010.0020.0020.0000.0000.0000.000
98K98LEU 00.002-0.01852.653-0.001-0.0010.0000.0000.0000.000
99K99LYS 10.9491.00554.9000.0260.0260.0000.0000.0000.000
100K100SER 0-0.003-0.01553.474-0.001-0.0010.0000.0000.0000.000
101K101HIS 00.0200.01151.4810.0000.0000.0000.0000.0000.000
102K102GLU -1-0.893-0.94554.507-0.014-0.0140.0000.0000.0000.000
103K103THR 0-0.009-0.02852.9440.0000.0000.0000.0000.0000.000
104K104ILE 0-0.0460.00246.7940.0000.0000.0000.0000.0000.000
105K105GLN 00.0300.02147.9720.0010.0010.0000.0000.0000.000
106K106THR 0-0.081-0.02742.520-0.002-0.0020.0000.0000.0000.000
107K107TRP 00.0450.02642.4290.0010.0010.0000.0000.0000.000
108K108ARG 10.8650.92738.2160.0190.0190.0000.0000.0000.000
109K109GLU -1-0.857-0.93035.8320.0110.0110.0000.0000.0000.000
110K110TYR 0-0.036-0.02234.325-0.008-0.0080.0000.0000.0000.000
111K111LEU 0-0.051-0.02228.9630.0040.0040.0000.0000.0000.000
112K112CYS 0-0.003-0.00732.966-0.006-0.0060.0000.0000.0000.000
113K113ASP -1-0.832-0.91732.9610.0520.0520.0000.0000.0000.000
114K114ALA 0-0.042-0.00528.2260.0090.0090.0000.0000.0000.000
115K115SER 0-0.004-0.01926.319-0.013-0.0130.0000.0000.0000.000
116K116PHE 00.0220.00621.6830.0090.0090.0000.0000.0000.000
117K117THR 0-0.039-0.05617.598-0.015-0.0150.0000.0000.0000.000
118K118VAL 0-0.045-0.02616.2090.0210.0210.0000.0000.0000.000
119K119ALA 00.0270.01311.7450.0090.0090.0000.0000.0000.000
120K120LEU 0-0.022-0.01012.545-0.025-0.0250.0000.0000.0000.000
121K121TRP 0-0.006-0.0237.7730.0950.0950.0000.0000.0000.000
122K122LEU 0-0.0020.0059.4850.0740.0740.0000.0000.0000.000
123K123THR 0-0.017-0.0318.767-0.242-0.2420.0000.0000.0000.000
124K124PRO 0-0.014-0.0298.128-0.004-0.0040.0000.0000.0000.000
125K125HIS 0-0.0160.00210.3240.0010.0010.0000.0000.0000.000
126K126ALA 0-0.0290.00912.9890.0830.0830.0000.0000.0000.000
127K127THR 0-0.015-0.00114.6460.0220.0220.0000.0000.0000.000
128K128MET 0-0.019-0.00316.6140.0350.0350.0000.0000.0000.000
129K129VAL 00.0290.00314.514-0.107-0.1070.0000.0000.0000.000
130K130ILE 00.0700.02410.0160.0840.0840.0000.0000.0000.000
131K131SER 00.0300.01114.1410.0710.0710.0000.0000.0000.000
132K132GLU -1-0.895-0.95516.265-0.323-0.3230.0000.0000.0000.000
133K133LEU 0-0.006-0.00215.2940.0530.0530.0000.0000.0000.000
134K134GLU -1-0.944-0.96915.567-0.225-0.2250.0000.0000.0000.000
135K135LYS 10.9390.96717.9980.2510.2510.0000.0000.0000.000
136K136ALA 0-0.007-0.00621.0380.0270.0270.0000.0000.0000.000
137K137VAL 0-0.013-0.02019.6750.0250.0250.0000.0000.0000.000
138K138LEU 0-0.046-0.01419.8040.0240.0240.0000.0000.0000.000
139K139LYS 10.8560.93323.4440.1360.1360.0000.0000.0000.000
140K140PRO 00.0060.03126.262-0.010-0.0100.0000.0000.0000.000
141K141ARG 10.9130.94327.5120.1420.1420.0000.0000.0000.000
142K142TYR 0-0.034-0.00829.9920.0100.0100.0000.0000.0000.000
143K143THR 0-0.044-0.03430.4870.0000.0000.0000.0000.0000.000
144K144PRO 00.0340.03227.739-0.001-0.0010.0000.0000.0000.000
145K145TYR 0-0.041-0.03929.0260.0050.0050.0000.0000.0000.000
146K146LEU 00.0130.02426.706-0.006-0.0060.0000.0000.0000.000
147K147GLY 00.0700.04528.6900.0070.0070.0000.0000.0000.000
148K148ARG 10.8000.88330.0080.0070.0070.0000.0000.0000.000
149K149ARG 10.9440.97333.4870.0590.0590.0000.0000.0000.000
150K150SER 00.0170.00335.300-0.001-0.0010.0000.0000.0000.000
151K151CYS 0-0.064-0.01332.7350.0060.0060.0000.0000.0000.000
152K152PRO 00.0380.01332.354-0.004-0.0040.0000.0000.0000.000
153K153LEU 0-0.0010.00426.5560.0030.0030.0000.0000.0000.000
154K154THR 0-0.059-0.03630.0800.0000.0000.0000.0000.0000.000
155K155HIS 0-0.008-0.02222.5570.0140.0140.0000.0000.0000.000
156K156PRO 0-0.0060.00324.005-0.009-0.0090.0000.0000.0000.000
157K157LEU 00.0450.04022.1570.0110.0110.0000.0000.0000.000
158K158PHE 00.0360.00316.0740.0090.0090.0000.0000.0000.000
159K159LEU 0-0.039-0.00417.5850.0130.0130.0000.0000.0000.000
160K160GLY 00.031-0.00415.3240.0080.0080.0000.0000.0000.000
161K161THR 0-0.0140.00311.145-0.029-0.0290.0000.0000.0000.000
162K162CYS 0-0.038-0.0018.6310.1640.1640.0000.0000.0000.000
163K163GLN 00.024-0.0113.370-1.585-1.3360.012-0.079-0.1810.000
164K164ALA 0-0.029-0.0033.719-0.5370.2090.047-0.280-0.5140.002
165K165SER 00.0320.0082.902-2.452-0.0971.057-1.401-2.010-0.002
166K166ASP -1-0.860-0.9243.544-1.542-1.1430.0300.159-0.589-0.002
167K167PRO 00.0110.0116.3140.1610.1610.0000.0000.0000.000
168K168GLN 00.0610.0238.7050.0680.0680.0000.0000.0000.000
169K169LYS 10.9280.9647.458-1.499-1.4990.0000.0000.0000.000
170K170ALA 00.0360.0168.438-0.019-0.0190.0000.0000.0000.000
171K171LEU 00.021-0.0039.822-0.199-0.1990.0000.0000.0000.000
172K172LEU 0-0.069-0.04212.520-0.074-0.0740.0000.0000.0000.000
173K173ASN 0-0.080-0.0159.999-0.076-0.0760.0000.0000.0000.000
174K174TYR 00.0190.00512.301-0.128-0.1280.0000.0000.0000.000
175K175GLU -1-0.906-0.92616.9430.2520.2520.0000.0000.0000.000
176K176PRO 0-0.026-0.02020.418-0.026-0.0260.0000.0000.0000.000
177K177VAL 00.015-0.00717.9750.0130.0130.0000.0000.0000.000
178K178GLY 00.011-0.00120.014-0.021-0.0210.0000.0000.0000.000
179K179GLY 0-0.0110.00821.135-0.017-0.0170.0000.0000.0000.000
180K180ASP -1-0.869-0.93619.7060.2260.2260.0000.0000.0000.000
181K181ILE 0-0.018-0.03214.029-0.005-0.0050.0000.0000.0000.000
182K182TYR 0-0.0130.00616.8330.0020.0020.0000.0000.0000.000
183K183SER 00.002-0.03510.707-0.052-0.0520.0000.0000.0000.000
184K184GLU -1-0.810-0.91412.235-0.216-0.2160.0000.0000.0000.000
185K185GLU -1-0.931-0.9595.245-0.692-0.6920.0000.0000.0000.000
186K186SER 0-0.032-0.0029.7430.1510.1510.0000.0000.0000.000
187K187VAL 00.0700.0338.7470.0020.0020.0000.0000.0000.000
188K188THR 0-0.003-0.0118.689-0.064-0.0640.0000.0000.0000.000
189K189GLY 0-0.0170.00711.337-0.062-0.0620.0000.0000.0000.000
190K190HIS 0-0.025-0.01413.666-0.096-0.0960.0000.0000.0000.000
191K191HIS 00.0480.01815.337-0.041-0.0410.0000.0000.0000.000
192K192LEU 0-0.050-0.01017.943-0.033-0.0330.0000.0000.0000.000
193K193LYS 10.9610.98016.668-0.001-0.0010.0000.0000.0000.000
194K194PHE 0-0.032-0.00919.9830.0030.0030.0000.0000.0000.000
195K195THR 00.0230.01621.635-0.011-0.0110.0000.0000.0000.000
196K196ALA 00.0070.01022.6730.0050.0050.0000.0000.0000.000
197K197ARG 10.9060.93924.5780.0360.0360.0000.0000.0000.000
198K198ASP -1-0.826-0.91821.851-0.044-0.0440.0000.0000.0000.000
199K199GLU -1-0.805-0.90219.541-0.183-0.1830.0000.0000.0000.000
200K200PRO 0-0.0230.00522.5800.0140.0140.0000.0000.0000.000
201K201MET 00.0040.00424.927-0.012-0.0120.0000.0000.0000.000
202K202ILE 00.0430.02723.9360.0100.0100.0000.0000.0000.000
203K203THR 0-0.012-0.00227.8550.0060.0060.0000.0000.0000.000
204K204LEU 0-0.025-0.01530.2710.0080.0080.0000.0000.0000.000
205K205PRO 00.0470.01431.5310.0010.0010.0000.0000.0000.000
206K206ARG 10.8660.93131.1420.0750.0750.0000.0000.0000.000
207K207GLN 00.0520.04231.0810.0100.0100.0000.0000.0000.000
208K208PHE 0-0.013-0.01226.758-0.006-0.0060.0000.0000.0000.000
209K209ALA 00.019-0.00325.3730.0090.0090.0000.0000.0000.000
210K210SER 0-0.055-0.04324.737-0.003-0.0030.0000.0000.0000.000
211K211ARG 10.9050.96316.7700.0720.0720.0000.0000.0000.000
212K212GLU -1-0.907-0.97019.3530.0160.0160.0000.0000.0000.000
213K213TRP 0-0.068-0.00616.116-0.022-0.0220.0000.0000.0000.000
214K214TYR 00.0310.00713.6570.0200.0200.0000.0000.0000.000
215K215VAL 0-0.020-0.01915.8610.0110.0110.0000.0000.0000.000
216K216ILE 0-0.027-0.00913.1120.0190.0190.0000.0000.0000.000
217K217LYS 10.9410.96316.815-0.195-0.1950.0000.0000.0000.000
218K218GLY 00.0400.03119.2050.0390.0390.0000.0000.0000.000
219K219NME 0-0.049-0.01520.9430.0140.0140.0000.0000.0000.000