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: YZ8N2

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 OptHSide
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 -1959502.138676
FMO2-HF: Nuclear repulsion 1888449.838047
FMO2-HF: Total energy -71052.30063
FMO2-MP2: Total energy -71262.769377


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.
-8.672-3.2232.728-2.712-5.465-0.001
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 : 0.041 / q_NPA : 0.009
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].
3K9THR0-0.030-0.0013.000-3.460-0.080-0.014-1.609-1.7580.003
4K10GLY0-0.021-0.0124.913-0.539-0.513-0.001-0.004-0.0200.000
5K11VAL0-0.024-0.0248.2990.1040.1040.0000.0000.0000.000
6K12VAL00.0280.0244.781-0.178-0.091-0.001-0.018-0.0680.000
7K13PRO0-0.018-0.0037.8730.0970.0970.0000.0000.0000.000
8K14ILE00.0230.0039.372-0.042-0.0420.0000.0000.0000.000
9K15LEU0-0.029-0.00711.7120.0160.0160.0000.0000.0000.000
10K16ILE0-0.035-0.02814.010-0.013-0.0130.0000.0000.0000.000
11K17GLU-1-0.936-0.95716.603-0.124-0.1240.0000.0000.0000.000
12K18LEU0-0.008-0.02119.289-0.003-0.0030.0000.0000.0000.000
13K19ASP-1-0.843-0.90421.890-0.059-0.0590.0000.0000.0000.000
14K20GLY0-0.012-0.02924.9620.0000.0000.0000.0000.0000.000
15K21ASP-1-0.848-0.90927.452-0.038-0.0380.0000.0000.0000.000
16K22VAL00.0320.01530.8930.0010.0010.0000.0000.0000.000
17K23ASN0-0.003-0.00833.2920.0000.0000.0000.0000.0000.000
18K24GLY0-0.0020.00735.6390.0010.0010.0000.0000.0000.000
19K25HIS0-0.0310.00035.513-0.003-0.0030.0000.0000.0000.000
20K26LYS10.8000.88331.4640.0390.0390.0000.0000.0000.000
21K27PHE0-0.020-0.02430.8830.0020.0020.0000.0000.0000.000
22K28PHE0-0.0450.00026.1810.0020.0020.0000.0000.0000.000
23K29VAL0-0.0110.00921.9990.0030.0030.0000.0000.0000.000
24K37ALA00.0630.0327.657-0.029-0.0290.0000.0000.0000.000
25K38THR0-0.0020.0048.3640.0420.0420.0000.0000.0000.000
26K39ILE0-0.041-0.02510.315-0.065-0.0650.0000.0000.0000.000
27K40GLY00.0410.03012.264-0.078-0.0780.0000.0000.0000.000
28K41LYS10.8330.93813.199-0.346-0.3460.0000.0000.0000.000
29K42LEU00.0290.01412.1040.0180.0180.0000.0000.0000.000
30K43SER0-0.042-0.01815.193-0.014-0.0140.0000.0000.0000.000
31K44LEU00.0250.01915.067-0.019-0.0190.0000.0000.0000.000
32K45LYS10.9400.96718.635-0.019-0.0190.0000.0000.0000.000
33K46PHE00.0520.02918.704-0.011-0.0110.0000.0000.0000.000
34K47ILE0-0.012-0.02323.0910.0050.0050.0000.0000.0000.000
35K48ALA00.0610.04425.562-0.005-0.0050.0000.0000.0000.000
36K49THR0-0.015-0.01226.1340.0030.0030.0000.0000.0000.000
37K50THR00.0190.00628.9210.0000.0000.0000.0000.0000.000
38K51GLY0-0.026-0.01331.8030.0020.0020.0000.0000.0000.000
39K52LYS10.9230.95432.4150.0080.0080.0000.0000.0000.000
40K53LEU00.0610.03328.198-0.002-0.0020.0000.0000.0000.000
41K54PRO0-0.044-0.00232.3480.0030.0030.0000.0000.0000.000
42K55VAL00.0190.00330.9960.0010.0010.0000.0000.0000.000
43K56PRO00.0090.01932.1070.0000.0000.0000.0000.0000.000
44K57TRP00.0850.02924.8190.0000.0000.0000.0000.0000.000
45K58PRO00.0440.01927.0190.0010.0010.0000.0000.0000.000
46K59THR0-0.084-0.03426.8100.0030.0030.0000.0000.0000.000
47K60LEU00.0440.02124.901-0.002-0.0020.0000.0000.0000.000
48K61VAL00.0030.01422.128-0.001-0.0010.0000.0000.0000.000
49K62THR0-0.020-0.02820.9890.0030.0030.0000.0000.0000.000
50K63THR0-0.026-0.00419.9120.0030.0030.0000.0000.0000.000
51K64LEU00.0040.03319.104-0.009-0.0090.0000.0000.0000.000
52K65ALA00.0090.00316.1310.0030.0030.0000.0000.0000.000
53K68VAL0-0.011-0.02811.057-0.023-0.0230.0000.0000.0000.000
54K69GLN00.0730.04011.4520.0380.0380.0000.0000.0000.000
55K70CYS0-0.0250.0236.5730.0250.0250.0000.0000.0000.000
56K71PHE0-0.031-0.0237.2330.3650.3650.0000.0000.0000.000
57K72SER0-0.056-0.0349.3060.0390.0390.0000.0000.0000.000
58K82ASP-1-0.882-0.9449.0891.2611.2610.0000.0000.0000.000
59K83PHE00.1110.0468.9390.1190.1190.0000.0000.0000.000
60K84PHE0-0.003-0.0078.206-0.100-0.1000.0000.0000.0000.000
61K85LYS10.8100.8864.951-2.004-2.0040.0000.0000.0000.000
62K86SER-1-0.825-0.8683.995-0.314-0.0770.000-0.060-0.1780.000
63K87ALA0-0.051-0.0146.173-0.317-0.3170.0000.0000.0000.000
64K88MET0-0.081-0.0032.338-0.498-0.1771.313-0.387-1.2470.000
65K89PRO0-0.042-0.0502.236-2.443-1.1001.413-0.633-2.122-0.004
66K90GLU-1-0.905-0.9613.781-0.420-0.3650.018-0.001-0.0720.000
67K91GLY00.001-0.0086.8520.1670.1670.0000.0000.0000.000
68K92TYR0-0.034-0.0428.3500.0720.0720.0000.0000.0000.000
69K93VAL00.0170.02511.4410.0050.0050.0000.0000.0000.000
70K94GLN0-0.021-0.01915.1400.0460.0460.0000.0000.0000.000
71K95GLU-1-0.872-0.92216.826-0.068-0.0680.0000.0000.0000.000
72K96ARG10.8170.86818.686-0.024-0.0240.0000.0000.0000.000
73K97THR0-0.044-0.01023.286-0.008-0.0080.0000.0000.0000.000
74K98ILE0-0.036-0.02724.4170.0060.0060.0000.0000.0000.000
75K99TYR00.0240.01728.367-0.005-0.0050.0000.0000.0000.000
76K100PHE00.0000.00529.6260.0060.0060.0000.0000.0000.000
77K101LYS10.9710.98633.899-0.026-0.0260.0000.0000.0000.000
78K102CYS0-0.071-0.03736.8720.0000.0000.0000.0000.0000.000
79K103ASP-1-0.773-0.89136.6060.0070.0070.0000.0000.0000.000
80K104GLY00.0870.05635.585-0.001-0.0010.0000.0000.0000.000
81K105THR0-0.063-0.04231.0780.0030.0030.0000.0000.0000.000
82K106TYR0-0.010-0.01927.267-0.005-0.0050.0000.0000.0000.000
83K107LYS10.9270.97326.9310.0180.0180.0000.0000.0000.000
84K108THR00.016-0.00821.2190.0020.0020.0000.0000.0000.000
85K109ARG10.8730.93420.6400.0650.0650.0000.0000.0000.000
86K110ALA00.0200.01416.2210.0040.0040.0000.0000.0000.000
87K111GLU-1-0.781-0.84811.080-0.201-0.2010.0000.0000.0000.000
88K119LEU0-0.042-0.0246.138-0.003-0.0030.0000.0000.0000.000
89K120VAL00.006-0.0088.0200.0920.0920.0000.0000.0000.000
90K121ASN00.0030.00111.265-0.030-0.0300.0000.0000.0000.000
91K122ARG10.8750.92713.9100.1970.1970.0000.0000.0000.000
92K123ILE0-0.039-0.03416.8560.0030.0030.0000.0000.0000.000
93K124GLU-1-0.812-0.88319.715-0.071-0.0710.0000.0000.0000.000
94K125LEU0-0.029-0.02423.1750.0070.0070.0000.0000.0000.000
95K126LYS10.8490.91925.9360.0540.0540.0000.0000.0000.000
96K127GLY0-0.013-0.01829.3630.0030.0030.0000.0000.0000.000
97K128ILE0-0.046-0.03532.105-0.002-0.0020.0000.0000.0000.000
98K129ASP-1-0.901-0.96035.415-0.006-0.0060.0000.0000.0000.000
99K130PHE0-0.0160.00832.2750.0020.0020.0000.0000.0000.000
100K131LYS10.8230.90238.221-0.010-0.0100.0000.0000.0000.000
101K132GLU-1-0.851-0.96540.892-0.002-0.0020.0000.0000.0000.000
102K133ASP-1-0.958-0.96442.4200.0070.0070.0000.0000.0000.000
103K134GLY00.0080.02240.9860.0020.0020.0000.0000.0000.000
104K135ASN0-0.010-0.02637.8790.0000.0000.0000.0000.0000.000
105K136ILE0-0.016-0.01133.7300.0010.0010.0000.0000.0000.000
106K137LEU0-0.017-0.02236.2440.0000.0000.0000.0000.0000.000
107K138GLY00.0300.03438.189-0.001-0.0010.0000.0000.0000.000
108K139HIS0-0.125-0.06733.6720.0030.0030.0000.0000.0000.000
109K140LYS10.8940.94737.733-0.017-0.0170.0000.0000.0000.000
110K141LEU0-0.054-0.02032.7510.0030.0030.0000.0000.0000.000
111K142GLU-1-0.842-0.91134.5680.0410.0410.0000.0000.0000.000
112K143TYR0-0.034-0.02328.6080.0010.0010.0000.0000.0000.000
113K144ASN0-0.043-0.03629.9450.0060.0060.0000.0000.0000.000
114K145PHE00.008-0.01623.594-0.004-0.0040.0000.0000.0000.000
115K146ASN0-0.049-0.01827.9110.0060.0060.0000.0000.0000.000
116K147SER0-0.042-0.01224.2510.0050.0050.0000.0000.0000.000
117K148HIS00.0230.00324.071-0.018-0.0180.0000.0000.0000.000
118K149LYS10.9090.96222.799-0.124-0.1240.0000.0000.0000.000
119K150VAL0-0.009-0.00419.065-0.015-0.0150.0000.0000.0000.000
120K151TYR0-0.012-0.01820.7760.0230.0230.0000.0000.0000.000
121K152ILE0-0.006-0.00616.162-0.016-0.0160.0000.0000.0000.000
122K153THR0-0.010-0.02120.1930.0030.0030.0000.0000.0000.000
123K154ALA00.0480.02418.831-0.008-0.0080.0000.0000.0000.000
124K155ASP-1-0.886-0.92718.976-0.024-0.0240.0000.0000.0000.000
125K156LYS10.9770.96319.631-0.015-0.0150.0000.0000.0000.000
126K157GLN0-0.042-0.01620.480-0.015-0.0150.0000.0000.0000.000
127K158ASN0-0.069-0.03819.647-0.018-0.0180.0000.0000.0000.000
128K159ASN0-0.011-0.00514.3930.0090.0090.0000.0000.0000.000
129K160GLY00.0840.03214.920-0.028-0.0280.0000.0000.0000.000
130K161ILE0-0.082-0.03514.5710.0300.0300.0000.0000.0000.000
131K162LYS10.9230.96717.257-0.021-0.0210.0000.0000.0000.000
132K163ALA0-0.001-0.00819.0460.0200.0200.0000.0000.0000.000
133K164ASN0-0.011-0.01021.105-0.020-0.0200.0000.0000.0000.000
134K165PHE00.001-0.00521.2230.0150.0150.0000.0000.0000.000
135K166THR0-0.007-0.00825.873-0.007-0.0070.0000.0000.0000.000
136K167ILE0-0.061-0.01424.3490.0070.0070.0000.0000.0000.000
137K168ARG10.9350.95528.496-0.067-0.0670.0000.0000.0000.000
138K169HIS00.0220.02127.8710.0060.0060.0000.0000.0000.000
139K170ASN00.0200.00632.163-0.001-0.0010.0000.0000.0000.000
140K171VAL0-0.017-0.00834.888-0.002-0.0020.0000.0000.0000.000
141K172GLU-1-0.850-0.91837.6930.0210.0210.0000.0000.0000.000
142K173ASP-1-0.892-0.93340.1560.0190.0190.0000.0000.0000.000
143K174GLY0-0.024-0.00441.3180.0000.0000.0000.0000.0000.000
144K175SER0-0.059-0.01541.1600.0020.0020.0000.0000.0000.000
145K176VAL00.027-0.01535.0500.0020.0020.0000.0000.0000.000
146K177GLN0-0.036-0.00334.258-0.003-0.0030.0000.0000.0000.000
147K178LEU0-0.020-0.02733.0530.0030.0030.0000.0000.0000.000
148K179ALA00.0530.02429.304-0.005-0.0050.0000.0000.0000.000
149K180ASP-1-0.894-0.91929.0720.0430.0430.0000.0000.0000.000
150K181HIS00.000-0.00723.442-0.007-0.0070.0000.0000.0000.000
151K182TYR0-0.0010.00724.9420.0070.0070.0000.0000.0000.000
152K183GLN0-0.015-0.02416.551-0.005-0.0050.0000.0000.0000.000
153K184GLN00.0200.01319.5240.0150.0150.0000.0000.0000.000
154K185ASN0-0.008-0.00813.5830.0150.0150.0000.0000.0000.000
155K186THR00.0280.02715.5750.0110.0110.0000.0000.0000.000
156K187PRO00.0610.04311.731-0.006-0.0060.0000.0000.0000.000
157K188ILE0-0.040-0.01211.1850.0350.0350.0000.0000.0000.000
158K189GLY0-0.0040.00811.1940.0260.0260.0000.0000.0000.000
159K190ASP-1-0.963-0.97911.894-0.241-0.2410.0000.0000.0000.000
160K191GLY00.0450.0258.831-0.052-0.0520.0000.0000.0000.000
161K192PRO0-0.140-0.0869.7330.0230.0230.0000.0000.0000.000
162K193VAL00.0430.0358.455-0.057-0.0570.0000.0000.0000.000
163K194ASP-1-0.744-0.89810.3460.1040.1040.0000.0000.0000.000
164K195LEU0-0.212-0.11112.289-0.013-0.0130.0000.0000.0000.000
165K196PRO0-0.091-0.03015.5300.0180.0180.0000.0000.0000.000
166K197ASP-1-0.879-0.93017.5210.1000.1000.0000.0000.0000.000
167K198ASP-1-0.880-0.93120.3260.1050.1050.0000.0000.0000.000
168K199HIS0-0.064-0.03719.1910.0190.0190.0000.0000.0000.000
169K200TYR0-0.085-0.10520.272-0.021-0.0210.0000.0000.0000.000
170K201LEU00.1690.18016.4920.0230.0230.0000.0000.0000.000
171K202SER0-0.138-0.09219.267-0.040-0.0400.0000.0000.0000.000
172K203THR0-0.0070.00519.3240.0280.0280.0000.0000.0000.000
173K204GLN00.0160.00420.409-0.032-0.0320.0000.0000.0000.000
174K205THR00.0230.00020.3890.0130.0130.0000.0000.0000.000
175K206ILE00.0030.01122.780-0.005-0.0050.0000.0000.0000.000
176K207LEU00.0200.03224.615-0.003-0.0030.0000.0000.0000.000
177K222GLU-1-0.938-0.99518.6400.0920.0920.0000.0000.0000.000
178K223TYR0-0.010-0.00817.2600.0290.0290.0000.0000.0000.000
179K224VAL0-0.034-0.01715.337-0.028-0.0280.0000.0000.0000.000
180K225THR00.0370.01514.8090.0600.0600.0000.0000.0000.000
181K226ALA00.0530.02815.218-0.057-0.0570.0000.0000.0000.000
182K227ALA0-0.007-0.01817.0450.0190.0190.0000.0000.0000.000
183K228GLY00.0490.03020.079-0.022-0.0220.0000.0000.0000.000