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: 526RZ

Calculation Name: 4W6R-K-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4W6R

Chain ID: K

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-09-19

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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1962525.603699
FMO2-HF: Nuclear repulsion 1891475.286432
FMO2-HF: Total energy -71050.317266
FMO2-MP2: Total energy -71260.98224


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:7:LEU)


Summations of interaction energy for fragment #1(K:7:LEU)
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.
-9.874-4.983.661-2.83-5.7250
Interaction energy analysis for fragmet #1(K:7:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.047 / q_NPA : 0.013
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].
3K9THR0-0.037-0.0083.122-3.736-0.367-0.008-1.620-1.7410.004
4K10GLY0-0.021-0.0105.021-0.617-0.592-0.001-0.004-0.0200.000
5K11VAL0-0.021-0.0228.2990.1070.1070.0000.0000.0000.000
6K12VAL00.0270.0244.809-0.095-0.0950.0000.0000.0000.000
7K13PRO0-0.026-0.0057.7540.0870.0870.0000.0000.0000.000
8K14ILE00.0240.0099.310-0.052-0.0520.0000.0000.0000.000
9K15LEU0-0.038-0.01511.6560.0210.0210.0000.0000.0000.000
10K16ILE0-0.041-0.02813.978-0.021-0.0210.0000.0000.0000.000
11K17GLU-1-0.951-0.96216.571-0.139-0.1390.0000.0000.0000.000
12K18LEU0-0.011-0.01219.078-0.006-0.0060.0000.0000.0000.000
13K19ASP-1-0.841-0.91221.678-0.072-0.0720.0000.0000.0000.000
14K20GLY0-0.016-0.03224.775-0.001-0.0010.0000.0000.0000.000
15K21ASP-1-0.917-0.97027.262-0.051-0.0510.0000.0000.0000.000
16K22VAL00.0330.02130.6850.0000.0000.0000.0000.0000.000
17K23ASN0-0.007-0.00733.1110.0010.0010.0000.0000.0000.000
18K24GLY0-0.012-0.00235.4610.0010.0010.0000.0000.0000.000
19K25HIS0-0.0200.00035.312-0.002-0.0020.0000.0000.0000.000
20K26LYS10.8870.95431.7420.0490.0490.0000.0000.0000.000
21K27PHE0-0.012-0.02430.6670.0030.0030.0000.0000.0000.000
22K28PHE0-0.0340.01025.9960.0020.0020.0000.0000.0000.000
23K29VAL0-0.0140.00321.8200.0050.0050.0000.0000.0000.000
24K37ALA00.0670.0417.709-0.036-0.0360.0000.0000.0000.000
25K38THR0-0.022-0.0078.3990.0060.0060.0000.0000.0000.000
26K39ILE0-0.033-0.01810.448-0.081-0.0810.0000.0000.0000.000
27K40GLY00.0450.02912.264-0.089-0.0890.0000.0000.0000.000
28K41LYS10.8610.95213.194-0.421-0.4210.0000.0000.0000.000
29K42LEU00.0340.01012.1170.0250.0250.0000.0000.0000.000
30K43SER0-0.034-0.01215.167-0.016-0.0160.0000.0000.0000.000
31K44LEU00.0260.01114.943-0.018-0.0180.0000.0000.0000.000
32K45LYS10.9530.97618.574-0.027-0.0270.0000.0000.0000.000
33K46PHE00.0490.02818.365-0.012-0.0120.0000.0000.0000.000
34K47ILE0-0.010-0.01923.0420.0060.0060.0000.0000.0000.000
35K48ALA00.0640.04325.520-0.007-0.0070.0000.0000.0000.000
36K49THR0-0.023-0.01526.0700.0040.0040.0000.0000.0000.000
37K50THR00.0090.00628.8820.0010.0010.0000.0000.0000.000
38K51GLY0-0.027-0.01531.7650.0020.0020.0000.0000.0000.000
39K52LYS10.9260.95532.3740.0130.0130.0000.0000.0000.000
40K53LEU00.0530.03028.137-0.003-0.0030.0000.0000.0000.000
41K54PRO0-0.0350.00232.1810.0030.0030.0000.0000.0000.000
42K55VAL00.0240.00731.0630.0020.0020.0000.0000.0000.000
43K56PRO0-0.0080.01332.1480.0000.0000.0000.0000.0000.000
44K57TRP00.0980.04425.023-0.001-0.0010.0000.0000.0000.000
45K58PRO00.0400.01327.000-0.001-0.0010.0000.0000.0000.000
46K59THR0-0.080-0.05226.7970.0010.0010.0000.0000.0000.000
47K60LEU00.0390.01524.704-0.004-0.0040.0000.0000.0000.000
48K61VAL0-0.0010.02222.092-0.003-0.0030.0000.0000.0000.000
49K62THR0-0.032-0.02820.9760.0020.0020.0000.0000.0000.000
50K63THR0-0.021-0.01819.9060.0000.0000.0000.0000.0000.000
51K64LEU0-0.0020.03318.936-0.013-0.0130.0000.0000.0000.000
52K65ALA00.000-0.00316.1970.0040.0040.0000.0000.0000.000
53K68VAL0-0.021-0.02511.099-0.029-0.0290.0000.0000.0000.000
54K69GLN00.0920.05211.4430.0470.0470.0000.0000.0000.000
55K70CYS0-0.0200.0206.5860.0520.0520.0000.0000.0000.000
56K71PHE0-0.042-0.0247.2370.3610.3610.0000.0000.0000.000
57K72SER0-0.048-0.0339.2990.0880.0880.0000.0000.0000.000
58K82ASP-1-0.933-0.9879.2371.2341.2340.0000.0000.0000.000
59K83PHE00.0970.0318.9920.0900.0900.0000.0000.0000.000
60K84PHE0-0.010-0.0288.230-0.126-0.1260.0000.0000.0000.000
61K85LYS10.8110.9064.956-2.110-2.1100.0000.0000.0000.000
62K86SER-1-0.857-0.8294.045-0.713-0.4840.000-0.055-0.1740.000
63K87ALA0-0.029-0.0026.261-0.323-0.3230.0000.0000.0000.000
64K88MET0-0.117-0.0142.264-0.407-0.3201.865-0.513-1.439-0.001
65K89PRO0-0.052-0.0552.140-2.445-1.3151.781-0.645-2.265-0.003
66K90GLU-1-0.922-0.9663.779-0.521-0.4670.0240.007-0.0860.000
67K91GLY0-0.002-0.0086.8060.2050.2050.0000.0000.0000.000
68K92TYR0-0.024-0.0418.3070.0830.0830.0000.0000.0000.000
69K93VAL0-0.0010.02311.3600.0100.0100.0000.0000.0000.000
70K94GLN0-0.028-0.02115.0430.0390.0390.0000.0000.0000.000
71K95GLU-1-0.957-0.98416.714-0.099-0.0990.0000.0000.0000.000
72K96ARG10.8410.89718.8330.0040.0040.0000.0000.0000.000
73K97THR0-0.061-0.01723.174-0.007-0.0070.0000.0000.0000.000
74K98ILE0-0.028-0.01924.4220.0060.0060.0000.0000.0000.000
75K99TYR00.0290.01928.244-0.005-0.0050.0000.0000.0000.000
76K100PHE00.0050.01429.6240.0070.0070.0000.0000.0000.000
77K101LYS10.9700.98533.770-0.018-0.0180.0000.0000.0000.000
78K102CYS0-0.082-0.04136.7530.0010.0010.0000.0000.0000.000
79K103ASP-1-0.803-0.90436.3060.0010.0010.0000.0000.0000.000
80K104GLY00.0650.02735.419-0.001-0.0010.0000.0000.0000.000
81K105THR0-0.083-0.04830.6750.0030.0030.0000.0000.0000.000
82K106TYR00.020-0.00327.130-0.005-0.0050.0000.0000.0000.000
83K107LYS10.9250.96726.8000.0340.0340.0000.0000.0000.000
84K108THR00.0250.00421.4100.0030.0030.0000.0000.0000.000
85K109ARG10.9560.97720.5260.0910.0910.0000.0000.0000.000
86K110ALA00.0330.02515.8440.0070.0070.0000.0000.0000.000
87K111GLU-1-0.903-0.93410.945-0.276-0.2760.0000.0000.0000.000
88K119LEU0-0.032-0.0186.427-0.016-0.0160.0000.0000.0000.000
89K120VAL00.007-0.0097.9910.1160.1160.0000.0000.0000.000
90K121ASN00.0260.01411.061-0.046-0.0460.0000.0000.0000.000
91K122ARG10.9690.99713.7020.2340.2340.0000.0000.0000.000
92K123ILE0-0.021-0.02216.6630.0000.0000.0000.0000.0000.000
93K124GLU-1-0.911-0.94219.535-0.106-0.1060.0000.0000.0000.000
94K125LEU0-0.019-0.02323.0090.0060.0060.0000.0000.0000.000
95K126LYS10.9420.97625.7700.0680.0680.0000.0000.0000.000
96K127GLY00.007-0.00729.2070.0030.0030.0000.0000.0000.000
97K128ILE0-0.039-0.03331.946-0.002-0.0020.0000.0000.0000.000
98K129ASP-1-0.915-0.96335.266-0.016-0.0160.0000.0000.0000.000
99K130PHE0-0.0300.00532.0590.0020.0020.0000.0000.0000.000
100K131LYS10.8860.94538.066-0.002-0.0020.0000.0000.0000.000
101K132GLU-1-0.886-0.97040.717-0.008-0.0080.0000.0000.0000.000
102K133ASP-1-0.966-0.96942.3020.0040.0040.0000.0000.0000.000
103K134GLY00.0170.02740.9720.0020.0020.0000.0000.0000.000
104K135ASN0-0.002-0.02437.8560.0010.0010.0000.0000.0000.000
105K136ILE0-0.0010.00033.6600.0020.0020.0000.0000.0000.000
106K137LEU0-0.002-0.01936.1940.0000.0000.0000.0000.0000.000
107K138GLY00.0290.03238.067-0.001-0.0010.0000.0000.0000.000
108K139HIS0-0.122-0.06133.4960.0040.0040.0000.0000.0000.000
109K140LYS10.9821.01037.714-0.013-0.0130.0000.0000.0000.000
110K141LEU0-0.042-0.01932.8360.0030.0030.0000.0000.0000.000
111K142GLU-1-0.871-0.94134.7590.0400.0400.0000.0000.0000.000
112K143TYR0-0.033-0.01728.5390.0000.0000.0000.0000.0000.000
113K144ASN0-0.012-0.01029.8900.0070.0070.0000.0000.0000.000
114K145PHE00.009-0.01723.486-0.005-0.0050.0000.0000.0000.000
115K146ASN00.0010.01627.9010.0040.0040.0000.0000.0000.000
116K147SER0-0.054-0.03124.1190.0060.0060.0000.0000.0000.000
117K148HIS00.017-0.00524.074-0.019-0.0190.0000.0000.0000.000
118K149LYS10.9410.97822.799-0.114-0.1140.0000.0000.0000.000
119K150VAL0-0.0130.00119.150-0.017-0.0170.0000.0000.0000.000
120K151TYR0-0.034-0.02920.7990.0230.0230.0000.0000.0000.000
121K152ILE00.0270.00616.094-0.017-0.0170.0000.0000.0000.000
122K153THR0-0.0070.00220.1790.0040.0040.0000.0000.0000.000
123K154ALA00.0620.02818.877-0.012-0.0120.0000.0000.0000.000
124K155ASP-1-0.897-0.91819.005-0.054-0.0540.0000.0000.0000.000
125K156LYS10.9700.95419.6660.0110.0110.0000.0000.0000.000
126K157GLN0-0.040-0.01820.542-0.020-0.0200.0000.0000.0000.000
127K158ASN0-0.042-0.03219.700-0.015-0.0150.0000.0000.0000.000
128K159ASN0-0.026-0.02514.1390.0070.0070.0000.0000.0000.000
129K160GLY00.0850.03114.939-0.038-0.0380.0000.0000.0000.000
130K161ILE0-0.074-0.03314.6020.0370.0370.0000.0000.0000.000
131K162LYS10.9670.99317.250-0.002-0.0020.0000.0000.0000.000
132K163ALA0-0.008-0.01118.9710.0200.0200.0000.0000.0000.000
133K164ASN00.000-0.00721.057-0.019-0.0190.0000.0000.0000.000
134K165PHE0-0.020-0.00921.5800.0160.0160.0000.0000.0000.000
135K166THR00.0110.00825.819-0.008-0.0080.0000.0000.0000.000
136K167ILE0-0.042-0.00424.4940.0080.0080.0000.0000.0000.000
137K168ARG10.9050.93928.500-0.063-0.0630.0000.0000.0000.000
138K169HIS00.0200.02127.6870.0080.0080.0000.0000.0000.000
139K170ASN00.0220.00432.158-0.002-0.0020.0000.0000.0000.000
140K171VAL0-0.027-0.01034.881-0.002-0.0020.0000.0000.0000.000
141K172GLU-1-0.886-0.94937.6830.0210.0210.0000.0000.0000.000
142K173ASP-1-0.942-0.96340.1430.0180.0180.0000.0000.0000.000
143K174GLY0-0.048-0.01541.3150.0000.0000.0000.0000.0000.000
144K175SER0-0.069-0.02341.1560.0020.0020.0000.0000.0000.000
145K176VAL00.028-0.01435.0460.0020.0020.0000.0000.0000.000
146K177GLN0-0.058-0.03534.185-0.004-0.0040.0000.0000.0000.000
147K178LEU0-0.033-0.02833.0620.0030.0030.0000.0000.0000.000
148K179ALA00.0560.03229.217-0.006-0.0060.0000.0000.0000.000
149K180ASP-1-0.917-0.93429.0140.0310.0310.0000.0000.0000.000
150K181HIS0-0.014-0.02523.461-0.009-0.0090.0000.0000.0000.000
151K182TYR0-0.026-0.00324.8670.0060.0060.0000.0000.0000.000
152K183GLN0-0.033-0.03816.5750.0020.0020.0000.0000.0000.000
153K184GLN00.005-0.00319.4360.0140.0140.0000.0000.0000.000
154K185ASN00.007-0.00413.2700.0200.0200.0000.0000.0000.000
155K186THR00.0520.03815.5390.0230.0230.0000.0000.0000.000
156K187PRO00.0250.02811.885-0.009-0.0090.0000.0000.0000.000
157K188ILE0-0.028-0.01111.2480.0500.0500.0000.0000.0000.000
158K189GLY0-0.009-0.00111.1300.0360.0360.0000.0000.0000.000
159K190ASP-1-0.935-0.97011.864-0.330-0.3300.0000.0000.0000.000
160K191GLY00.0560.0358.816-0.064-0.0640.0000.0000.0000.000
161K192PRO0-0.132-0.0869.4460.0870.0870.0000.0000.0000.000
162K193VAL00.1740.0998.870-0.100-0.1000.0000.0000.0000.000
163K194ASP-1-0.847-0.90310.105-0.056-0.0560.0000.0000.0000.000
164K195LEU0-0.079-0.11812.385-0.009-0.0090.0000.0000.0000.000
165K196PRO0-0.138-0.05015.0570.0190.0190.0000.0000.0000.000
166K197ASP-1-0.882-0.92717.5910.0810.0810.0000.0000.0000.000
167K198ASP-1-0.896-0.96620.3760.0870.0870.0000.0000.0000.000
168K199HIS0-0.059-0.02819.5390.0130.0130.0000.0000.0000.000
169K200TYR0-0.120-0.11320.328-0.017-0.0170.0000.0000.0000.000
170K201LEU00.1470.18816.0440.0300.0300.0000.0000.0000.000
171K202SER0-0.099-0.09019.306-0.045-0.0450.0000.0000.0000.000
172K203THR0-0.0010.00019.2550.0300.0300.0000.0000.0000.000
173K204GLN00.0140.01020.399-0.036-0.0360.0000.0000.0000.000
174K205THR00.009-0.00520.7610.0130.0130.0000.0000.0000.000
175K206ILE00.0270.01522.767-0.004-0.0040.0000.0000.0000.000
176K207LEU00.0170.02824.591-0.003-0.0030.0000.0000.0000.000
177K222GLU-1-0.950-0.99618.5650.0960.0960.0000.0000.0000.000
178K223TYR0-0.042-0.02517.2470.0380.0380.0000.0000.0000.000
179K224VAL0-0.036-0.01215.447-0.033-0.0330.0000.0000.0000.000
180K225THR00.0170.00714.8130.0660.0660.0000.0000.0000.000
181K226ALA00.0820.02715.484-0.056-0.0560.0000.0000.0000.000
182K227ALA0-0.008-0.01517.0680.0220.0220.0000.0000.0000.000
183K228GLY00.0280.02520.107-0.024-0.0240.0000.0000.0000.000