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

tag_button

FMODB ID: 53V4Z

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 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 218
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2552850.160057
FMO2-HF: Nuclear repulsion 2466165.67523
FMO2-HF: Total energy -86684.484826
FMO2-MP2: Total energy -86935.64092


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.
-7.615-3.2854.546-3.129-5.746-0.02
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 : -0.045 / q_NPA : -0.026
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].
3K3SER00.0260.0133.8741.8303.348-0.016-0.748-0.7540.001
4K4TYR0-0.044-0.0453.818-0.624-0.408-0.001-0.027-0.1880.000
5K5LEU00.0110.0169.4220.1410.1410.0000.0000.0000.000
6K6ILE0-0.025-0.02111.3540.0080.0080.0000.0000.0000.000
7K7LEU00.0040.00215.014-0.011-0.0110.0000.0000.0000.000
8K8ARG10.8550.91818.442-0.033-0.0330.0000.0000.0000.000
9K9LEU0-0.030-0.01521.200-0.017-0.0170.0000.0000.0000.000
10K10ALA00.0610.03023.8300.0110.0110.0000.0000.0000.000
11K11GLY00.0600.02327.038-0.009-0.0090.0000.0000.0000.000
12K12PRO0-0.028-0.00330.6980.0050.0050.0000.0000.0000.000
13K13MET00.0030.00233.2370.0040.0040.0000.0000.0000.000
14K14GLN0-0.024-0.02326.161-0.013-0.0130.0000.0000.0000.000
15K15ALA0-0.011-0.01029.9100.0050.0050.0000.0000.0000.000
16K16TRP00.0030.01825.321-0.016-0.0160.0000.0000.0000.000
17K17GLY00.0100.01328.2550.0060.0060.0000.0000.0000.000
18K18GLN00.011-0.00128.3490.0010.0010.0000.0000.0000.000
19K19PRO00.000-0.01829.296-0.003-0.0030.0000.0000.0000.000
20K20THR0-0.008-0.01732.2270.0040.0040.0000.0000.0000.000
21K21PHE0-0.040-0.02434.656-0.005-0.0050.0000.0000.0000.000
22K22GLU-1-0.770-0.83438.774-0.023-0.0230.0000.0000.0000.000
23K23GLY00.0390.01940.626-0.002-0.0020.0000.0000.0000.000
24K24THR0-0.010-0.01839.2650.0010.0010.0000.0000.0000.000
25K25ARG10.7810.88135.4810.0330.0330.0000.0000.0000.000
26K26PRO00.0520.00533.5400.0000.0000.0000.0000.0000.000
27K27THR0-0.050-0.01930.057-0.008-0.0080.0000.0000.0000.000
28K28GLY00.0130.02127.6800.0050.0050.0000.0000.0000.000
29K29ARG10.9660.95526.651-0.026-0.0260.0000.0000.0000.000
30K30PHE00.0120.01320.0390.0110.0110.0000.0000.0000.000
31K31PRO0-0.026-0.01121.133-0.006-0.0060.0000.0000.0000.000
32K32THR00.0470.03421.391-0.006-0.0060.0000.0000.0000.000
33K33ARG10.7270.81815.5870.2820.2820.0000.0000.0000.000
34K34SER0-0.008-0.02820.454-0.012-0.0120.0000.0000.0000.000
35K35GLY0-0.030-0.00323.607-0.004-0.0040.0000.0000.0000.000
36K36LEU0-0.011-0.00517.8190.0000.0000.0000.0000.0000.000
37K37LEU00.0150.01318.426-0.009-0.0090.0000.0000.0000.000
38K38GLY0-0.011-0.00421.562-0.005-0.0050.0000.0000.0000.000
39K39LEU0-0.030-0.01122.5880.0030.0030.0000.0000.0000.000
40K40LEU00.0490.01717.6480.0010.0010.0000.0000.0000.000
41K41GLY00.0100.00122.326-0.007-0.0070.0000.0000.0000.000
42K42ALA0-0.0460.00125.0150.0110.0110.0000.0000.0000.000
43K43CYS0-0.054-0.03423.7280.0100.0100.0000.0000.0000.000
44K44LEU00.0520.02321.2570.0030.0030.0000.0000.0000.000
45K45GLY0-0.044-0.02325.6800.0100.0100.0000.0000.0000.000
46K46ILE0-0.007-0.00524.2590.0010.0010.0000.0000.0000.000
47K47GLN0-0.041-0.02528.9110.0100.0100.0000.0000.0000.000
48K48ARG10.9310.93830.7320.0810.0810.0000.0000.0000.000
49K49ASP-1-0.840-0.90732.024-0.110-0.1100.0000.0000.0000.000
50K50ASP-1-0.786-0.81929.132-0.174-0.1740.0000.0000.0000.000
51K51THR00.000-0.03028.295-0.013-0.0130.0000.0000.0000.000
52K52SER00.020-0.00126.775-0.006-0.0060.0000.0000.0000.000
53K53SER0-0.017-0.04724.638-0.026-0.0260.0000.0000.0000.000
54K54LEU0-0.067-0.03423.514-0.016-0.0160.0000.0000.0000.000
55K55GLN0-0.063-0.04422.7800.0050.0050.0000.0000.0000.000
56K56ALA00.0330.03320.615-0.023-0.0230.0000.0000.0000.000
57K57LEU0-0.0130.00918.805-0.044-0.0440.0000.0000.0000.000
58K58SER0-0.036-0.03217.966-0.038-0.0380.0000.0000.0000.000
59K59GLU-1-0.837-0.91017.082-0.282-0.2820.0000.0000.0000.000
60K60SER0-0.003-0.00314.821-0.071-0.0710.0000.0000.0000.000
61K61VAL0-0.0170.00213.278-0.110-0.1100.0000.0000.0000.000
62K62GLN0-0.047-0.02110.819-0.026-0.0260.0000.0000.0000.000
63K63PHE00.026-0.00112.337-0.025-0.0250.0000.0000.0000.000
64K64ALA0-0.019-0.01611.3850.0090.0090.0000.0000.0000.000
65K65VAL0-0.002-0.00113.3980.0180.0180.0000.0000.0000.000
66K66ARG10.8110.90516.569-0.161-0.1610.0000.0000.0000.000
67K67CYS0-0.032-0.01518.140-0.026-0.0260.0000.0000.0000.000
68K68ASP-1-0.732-0.83521.1390.1080.1080.0000.0000.0000.000
69K69GLU-1-0.845-0.90923.5980.0720.0720.0000.0000.0000.000
70K70LEU00.0240.02527.1030.0060.0060.0000.0000.0000.000
71K71ILE0-0.020-0.02428.9790.0040.0040.0000.0000.0000.000
72K72LEU0-0.0010.00131.709-0.003-0.0030.0000.0000.0000.000
73K73ASP-1-0.892-0.94035.0210.0420.0420.0000.0000.0000.000
74K74ASP-1-0.886-0.93934.5340.0650.0650.0000.0000.0000.000
75K75ARG10.8020.89935.614-0.057-0.0570.0000.0000.0000.000
76K76ARG10.8910.93127.860-0.107-0.1070.0000.0000.0000.000
77K77VAL0-0.001-0.00132.263-0.004-0.0040.0000.0000.0000.000
78K78SER0-0.021-0.02431.0250.0000.0000.0000.0000.0000.000
79K79VAL0-0.038-0.01427.871-0.005-0.0050.0000.0000.0000.000
80K80THR00.0180.02131.253-0.001-0.0010.0000.0000.0000.000
81K81GLY0-0.010-0.01533.469-0.003-0.0030.0000.0000.0000.000
82K82LEU00.0020.01235.6990.0010.0010.0000.0000.0000.000
83K83ARG10.9410.95837.7970.0000.0000.0000.0000.0000.000
84K84ASP-1-0.838-0.91740.247-0.016-0.0160.0000.0000.0000.000
85K85TYR0-0.035-0.03542.123-0.001-0.0010.0000.0000.0000.000
86K86HIS00.0180.00541.645-0.002-0.0020.0000.0000.0000.000
87K87THR00.0150.01344.855-0.002-0.0020.0000.0000.0000.000
88K88VAL0-0.044-0.02145.527-0.002-0.0020.0000.0000.0000.000
89K89LEU00.0470.02348.6630.0010.0010.0000.0000.0000.000
90K90GLY00.0460.03551.519-0.001-0.0010.0000.0000.0000.000
91K91ALA0-0.056-0.01748.619-0.002-0.0020.0000.0000.0000.000
92K92ARG10.9160.95042.7260.0430.0430.0000.0000.0000.000
93K93GLU-1-0.819-0.89049.585-0.024-0.0240.0000.0000.0000.000
94K94ASP-1-0.865-0.91649.973-0.030-0.0300.0000.0000.0000.000
95K95TYR0-0.059-0.05142.515-0.002-0.0020.0000.0000.0000.000
96K96ARG10.9420.96147.4330.0400.0400.0000.0000.0000.000
97K97GLY00.0190.01250.3850.0020.0020.0000.0000.0000.000
98K98LEU00.002-0.00552.379-0.001-0.0010.0000.0000.0000.000
99K99LYS10.8150.91954.9010.0270.0270.0000.0000.0000.000
100K100SER00.016-0.01553.373-0.002-0.0020.0000.0000.0000.000
101K101HIS0-0.0090.00050.5640.0000.0000.0000.0000.0000.000
102K102GLU-1-0.893-0.93954.111-0.019-0.0190.0000.0000.0000.000
103K103THR00.005-0.01652.8920.0000.0000.0000.0000.0000.000
104K104ILE0-0.0260.00046.9610.0000.0000.0000.0000.0000.000
105K105GLN00.0260.01647.8150.0010.0010.0000.0000.0000.000
106K106THR0-0.049-0.02042.275-0.002-0.0020.0000.0000.0000.000
107K107TRP0-0.009-0.00342.2000.0010.0010.0000.0000.0000.000
108K108ARG10.8350.92438.0910.0270.0270.0000.0000.0000.000
109K109GLU-1-0.845-0.92335.337-0.003-0.0030.0000.0000.0000.000
110K110TYR0-0.030-0.01033.793-0.008-0.0080.0000.0000.0000.000
111K111LEU0-0.0100.00928.3300.0040.0040.0000.0000.0000.000
112K112CYS0-0.019-0.02632.396-0.007-0.0070.0000.0000.0000.000
113K113ASP-1-0.829-0.91932.3580.0270.0270.0000.0000.0000.000
114K114ALA0-0.043-0.00527.8870.0060.0060.0000.0000.0000.000
115K115SER00.007-0.01424.059-0.011-0.0110.0000.0000.0000.000
116K116PHE0-0.004-0.00320.9980.0050.0050.0000.0000.0000.000
117K117THR00.001-0.00816.641-0.009-0.0090.0000.0000.0000.000
118K118VAL0-0.047-0.02715.7650.0120.0120.0000.0000.0000.000
119K119ALA00.0250.02610.7000.0020.0020.0000.0000.0000.000
120K120LEU0-0.015-0.01211.904-0.027-0.0270.0000.0000.0000.000
121K121TRP0-0.004-0.0167.6320.0460.0460.0000.0000.0000.000
122K122LEU00.0140.0109.2330.1320.1320.0000.0000.0000.000
123K123THR0-0.015-0.0198.520-0.286-0.2860.0000.0000.0000.000
124K124PRO0-0.039-0.0378.237-0.052-0.0520.0000.0000.0000.000
125K125HIS0-0.014-0.00310.4040.0420.0420.0000.0000.0000.000
126K126ALA0-0.0260.00712.9430.0790.0790.0000.0000.0000.000
127K127THR0-0.041-0.02214.6720.0220.0220.0000.0000.0000.000
128K128MET0-0.0110.00416.5350.0460.0460.0000.0000.0000.000
129K129VAL00.016-0.00514.721-0.105-0.1050.0000.0000.0000.000
130K130ILE00.0400.01210.3060.0800.0800.0000.0000.0000.000
131K131SER00.0350.01414.3330.0700.0700.0000.0000.0000.000
132K132GLU-1-0.880-0.93816.320-0.337-0.3370.0000.0000.0000.000
133K133LEU00.0010.00015.2400.0500.0500.0000.0000.0000.000
134K134GLU-1-0.844-0.92514.881-0.253-0.2530.0000.0000.0000.000
135K135LYS10.9510.97118.2120.2600.2600.0000.0000.0000.000
136K136ALA0-0.008-0.00521.2520.0260.0260.0000.0000.0000.000
137K137VAL0-0.021-0.02019.9470.0240.0240.0000.0000.0000.000
138K138LEU0-0.041-0.01319.8940.0230.0230.0000.0000.0000.000
139K139LYS10.8550.92823.6880.1340.1340.0000.0000.0000.000
140K140PRO00.0010.03426.548-0.008-0.0080.0000.0000.0000.000
141K141ARG10.9160.95327.8170.1520.1520.0000.0000.0000.000
142K142TYR0-0.044-0.00629.8690.0090.0090.0000.0000.0000.000
143K143THR0-0.002-0.01030.131-0.002-0.0020.0000.0000.0000.000
144K144PRO00.0580.04127.0830.0000.0000.0000.0000.0000.000
145K145TYR0-0.055-0.03128.4370.0070.0070.0000.0000.0000.000
146K146LEU0-0.0040.01626.072-0.009-0.0090.0000.0000.0000.000
147K147GLY00.0370.02828.3870.0080.0080.0000.0000.0000.000
148K148ARG10.7940.86629.2550.0260.0260.0000.0000.0000.000
149K149ARG10.9290.94832.9680.0710.0710.0000.0000.0000.000
150K150SER00.0010.00434.664-0.001-0.0010.0000.0000.0000.000
151K151CYS0-0.058-0.00731.8660.0060.0060.0000.0000.0000.000
152K152PRO00.0510.01131.519-0.006-0.0060.0000.0000.0000.000
153K153LEU0-0.0030.00525.9930.0030.0030.0000.0000.0000.000
154K154THR0-0.022-0.02429.699-0.002-0.0020.0000.0000.0000.000
155K155HIS0-0.030-0.02322.9230.0160.0160.0000.0000.0000.000
156K156PRO0-0.004-0.00324.308-0.008-0.0080.0000.0000.0000.000
157K157LEU00.0550.04621.8180.0080.0080.0000.0000.0000.000
158K158PHE00.0150.00716.5550.0040.0040.0000.0000.0000.000
159K159LEU0-0.044-0.01818.2450.0140.0140.0000.0000.0000.000
160K160GLY00.0260.00015.6570.0250.0250.0000.0000.0000.000
161K161THR0-0.029-0.00612.134-0.048-0.0480.0000.0000.0000.000
162K162CYS0-0.067-0.0199.0330.1370.1370.0000.0000.0000.000
163K163GLN00.027-0.0023.419-1.611-1.3780.010-0.120-0.1230.000
164K164ALA0-0.0280.0014.316-0.4110.0570.005-0.138-0.3340.000
165K165SER00.0630.0022.204-2.1890.1593.845-3.001-3.191-0.012
166K166ASP-1-0.857-0.8942.766-1.415-1.8890.7040.906-1.137-0.009
167K167PRO00.0550.0265.4600.3360.3360.0000.0000.0000.000
168K168GLN00.0180.0048.0820.1320.1320.0000.0000.0000.000
169K169LYS10.9220.9637.062-1.289-1.2890.0000.0000.0000.000
170K170ALA00.0350.0207.7380.0770.0770.0000.0000.0000.000
171K171LEU00.015-0.0099.437-0.081-0.0810.0000.0000.0000.000
172K172LEU0-0.050-0.03012.153-0.035-0.0350.0000.0000.0000.000
173K173ASN0-0.085-0.02610.133-0.021-0.0210.0000.0000.0000.000
174K174TYR00.0180.01112.519-0.092-0.0920.0000.0000.0000.000
175K175GLU-1-0.791-0.87317.1240.1920.1920.0000.0000.0000.000
176K176PRO0-0.079-0.03320.568-0.023-0.0230.0000.0000.0000.000
177K177VAL00.002-0.02117.4480.0020.0020.0000.0000.0000.000
178K178GLY0-0.010-0.00819.123-0.018-0.0180.0000.0000.0000.000
179K179GLY00.0050.01220.933-0.009-0.0090.0000.0000.0000.000
180K180ASP-1-0.847-0.93119.0860.1660.1660.0000.0000.0000.000
181K181ILE0-0.030-0.02313.283-0.017-0.0170.0000.0000.0000.000
182K182TYR0-0.0210.00416.1770.0070.0070.0000.0000.0000.000
183K183SER0-0.008-0.03810.342-0.049-0.0490.0000.0000.0000.000
184K184GLU-1-0.756-0.86912.110-0.284-0.2840.0000.0000.0000.000
185K185GLU-1-0.823-0.8565.068-1.726-1.705-0.001-0.001-0.0190.000
186K186SER0-0.0130.0099.4070.1090.1090.0000.0000.0000.000
187K187VAL00.0390.0107.978-0.046-0.0460.0000.0000.0000.000
188K188THR00.019-0.0038.493-0.068-0.0680.0000.0000.0000.000
189K189GLY00.0060.02111.022-0.036-0.0360.0000.0000.0000.000
190K190HIS0-0.046-0.02412.530-0.088-0.0880.0000.0000.0000.000
191K191HIS00.0320.01014.883-0.057-0.0570.0000.0000.0000.000
192K192LEU0-0.0250.00617.203-0.028-0.0280.0000.0000.0000.000
193K193LYS10.8890.92516.142-0.005-0.0050.0000.0000.0000.000
194K194PHE0-0.016-0.00519.1850.0060.0060.0000.0000.0000.000
195K195THR0-0.013-0.02120.891-0.015-0.0150.0000.0000.0000.000
196K196ALA0-0.0020.00822.1410.0040.0040.0000.0000.0000.000
197K197ARG10.8500.89924.0950.0480.0480.0000.0000.0000.000
198K198ASP-1-0.768-0.86321.597-0.084-0.0840.0000.0000.0000.000
199K199GLU-1-0.754-0.86420.179-0.199-0.1990.0000.0000.0000.000
200K200PRO0-0.0100.00522.6380.0170.0170.0000.0000.0000.000
201K201MET0-0.005-0.00425.112-0.011-0.0110.0000.0000.0000.000
202K202ILE00.0030.00723.2190.0100.0100.0000.0000.0000.000
203K203THR00.0140.01027.5040.0050.0050.0000.0000.0000.000
204K204LEU0-0.042-0.01730.0300.0090.0090.0000.0000.0000.000
205K205PRO00.0640.01831.6980.0020.0020.0000.0000.0000.000
206K206ARG10.8840.93230.9580.0820.0820.0000.0000.0000.000
207K207GLN00.0380.04231.5830.0090.0090.0000.0000.0000.000
208K208PHE0-0.007-0.00126.604-0.008-0.0080.0000.0000.0000.000
209K209ALA00.0260.01524.8120.0110.0110.0000.0000.0000.000
210K210SER0-0.020-0.02224.788-0.002-0.0020.0000.0000.0000.000
211K211ARG10.8660.93316.3870.1120.1120.0000.0000.0000.000
212K212GLU-1-0.817-0.89118.4670.0210.0210.0000.0000.0000.000
213K213TRP0-0.0430.00515.668-0.034-0.0340.0000.0000.0000.000
214K214TYR00.0270.00412.9880.0190.0190.0000.0000.0000.000
215K215VAL0-0.019-0.02015.288-0.013-0.0130.0000.0000.0000.000
216K216ILE0-0.0090.00311.9670.0220.0220.0000.0000.0000.000
217K217LYS10.9220.96415.462-0.156-0.1560.0000.0000.0000.000
218K218GLY0-0.041-0.01518.0550.0400.0400.0000.0000.0000.000