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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: V5LK1

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 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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1963212.666807
FMO2-HF: Nuclear repulsion 1892158.420302
FMO2-HF: Total energy -71054.246505
FMO2-MP2: Total energy -71264.594744


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.
-11.427-5.1243.548-3.512-6.339-0.012
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 : 0.026 / q_NPA : 0.003
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].
3K9THR0-0.050-0.0172.782-3.937-0.5630.086-1.700-1.7610.001
4K10GLY0-0.0100.0014.628-0.823-0.762-0.001-0.004-0.0560.000
5K11VAL0-0.033-0.0267.9320.0780.0780.0000.0000.0000.000
6K12VAL00.0150.0184.978-0.165-0.074-0.001-0.021-0.0680.000
7K13PRO0-0.004-0.0017.9500.1250.1250.0000.0000.0000.000
8K14ILE00.0280.0049.408-0.078-0.0780.0000.0000.0000.000
9K15LEU0-0.034-0.00411.9250.0440.0440.0000.0000.0000.000
10K16ILE0-0.008-0.01413.976-0.027-0.0270.0000.0000.0000.000
11K17GLU-1-0.932-0.95216.617-0.187-0.1870.0000.0000.0000.000
12K18LEU00.010-0.00219.460-0.005-0.0050.0000.0000.0000.000
13K19ASP-1-0.830-0.89322.142-0.101-0.1010.0000.0000.0000.000
14K20GLY0-0.006-0.02225.3420.0000.0000.0000.0000.0000.000
15K21ASP-1-0.826-0.89727.996-0.069-0.0690.0000.0000.0000.000
16K22VAL00.0300.00830.8380.0010.0010.0000.0000.0000.000
17K23ASN0-0.021-0.03333.2670.0010.0010.0000.0000.0000.000
18K24GLY0-0.0080.00935.5480.0020.0020.0000.0000.0000.000
19K25HIS0-0.068-0.03935.550-0.003-0.0030.0000.0000.0000.000
20K26LYS10.7830.86631.5810.0680.0680.0000.0000.0000.000
21K27PHE0-0.038-0.01231.5350.0020.0020.0000.0000.0000.000
22K28PHE0-0.0320.00626.6760.0010.0010.0000.0000.0000.000
23K29VAL0-0.046-0.04323.0330.0010.0010.0000.0000.0000.000
24K37ALA00.0350.0287.887-0.016-0.0160.0000.0000.0000.000
25K38THR00.0070.0008.1000.0670.0670.0000.0000.0000.000
26K39ILE0-0.058-0.02910.354-0.064-0.0640.0000.0000.0000.000
27K40GLY00.0570.02612.579-0.086-0.0860.0000.0000.0000.000
28K41LYS10.8460.93413.149-0.298-0.2980.0000.0000.0000.000
29K42LEU00.0410.01512.177-0.007-0.0070.0000.0000.0000.000
30K43SER0-0.051-0.03115.0930.0120.0120.0000.0000.0000.000
31K44LEU0-0.0160.00814.929-0.026-0.0260.0000.0000.0000.000
32K45LYS10.9300.95018.8340.0320.0320.0000.0000.0000.000
33K46PHE00.0550.03718.713-0.009-0.0090.0000.0000.0000.000
34K47ILE00.015-0.00323.0580.0090.0090.0000.0000.0000.000
35K48ALA00.0530.03525.839-0.007-0.0070.0000.0000.0000.000
36K49THR0-0.014-0.00625.7650.0060.0060.0000.0000.0000.000
37K50THR00.0110.00828.6800.0020.0020.0000.0000.0000.000
38K51GLY0-0.031-0.01131.6560.0040.0040.0000.0000.0000.000
39K52LYS10.9050.93533.3780.0330.0330.0000.0000.0000.000
40K53LEU00.0490.03928.125-0.002-0.0020.0000.0000.0000.000
41K54PRO0-0.038-0.00832.4730.0040.0040.0000.0000.0000.000
42K55VAL00.0140.00330.4850.0020.0020.0000.0000.0000.000
43K56PRO00.0200.02831.665-0.002-0.0020.0000.0000.0000.000
44K57TRP00.0690.02624.916-0.002-0.0020.0000.0000.0000.000
45K58PRO00.0310.01626.745-0.004-0.0040.0000.0000.0000.000
46K59THR0-0.072-0.03526.634-0.001-0.0010.0000.0000.0000.000
47K60LEU00.0490.03124.616-0.003-0.0030.0000.0000.0000.000
48K61VAL00.0130.03221.873-0.009-0.0090.0000.0000.0000.000
49K62THR0-0.014-0.03320.640-0.005-0.0050.0000.0000.0000.000
50K63THR0-0.095-0.05619.903-0.008-0.0080.0000.0000.0000.000
51K64LEU00.0390.02519.049-0.017-0.0170.0000.0000.0000.000
52K65ALA0-0.0160.00716.465-0.013-0.0130.0000.0000.0000.000
53K68VAL00.0310.00911.029-0.024-0.0240.0000.0000.0000.000
54K69GLN00.0490.02311.7680.0090.0090.0000.0000.0000.000
55K70CYS0-0.0220.0046.7370.0670.0670.0000.0000.0000.000
56K71PHE0-0.024-0.0177.6750.2600.2600.0000.0000.0000.000
57K72SER0-0.063-0.0429.6510.0800.0800.0000.0000.0000.000
58K82ASP-1-0.814-0.8999.4160.8590.8590.0000.0000.0000.000
59K83PHE00.0640.0138.6390.0550.0550.0000.0000.0000.000
60K84PHE00.0130.0118.179-0.155-0.1550.0000.0000.0000.000
61K85LYS10.7700.8674.369-1.525-1.377-0.001-0.010-0.1360.000
62K86SER-1-0.800-0.8893.541-1.288-0.7530.012-0.211-0.336-0.001
63K87ALA0-0.026-0.0095.211-0.409-0.4090.0000.0000.0000.000
64K88MET0-0.074-0.0042.458-0.508-0.1381.351-0.402-1.3190.001
65K89PRO0-0.033-0.0482.411-3.294-1.6302.094-1.149-2.609-0.013
66K90GLU-1-0.878-0.9473.919-0.436-0.3760.008-0.015-0.0540.000
67K91GLY00.0230.0146.8820.1720.1720.0000.0000.0000.000
68K92TYR0-0.021-0.0328.3700.0720.0720.0000.0000.0000.000
69K93VAL00.0450.03711.5460.0110.0110.0000.0000.0000.000
70K94GLN0-0.014-0.01115.2130.0300.0300.0000.0000.0000.000
71K95GLU-1-0.871-0.92016.942-0.119-0.1190.0000.0000.0000.000
72K96ARG10.8170.87119.1130.0580.0580.0000.0000.0000.000
73K97THR0-0.049-0.01223.581-0.005-0.0050.0000.0000.0000.000
74K98ILE0-0.010-0.00524.4870.0050.0050.0000.0000.0000.000
75K99TYR00.0150.01728.564-0.004-0.0040.0000.0000.0000.000
76K100PHE0-0.005-0.00429.3200.0060.0060.0000.0000.0000.000
77K101LYS10.8810.92834.145-0.003-0.0030.0000.0000.0000.000
78K102CYS0-0.035-0.02037.0060.0010.0010.0000.0000.0000.000
79K103ASP-1-0.747-0.87536.919-0.017-0.0170.0000.0000.0000.000
80K104GLY00.0460.03436.1930.0000.0000.0000.0000.0000.000
81K105THR0-0.074-0.04831.4460.0030.0030.0000.0000.0000.000
82K106TYR00.006-0.01227.295-0.005-0.0050.0000.0000.0000.000
83K107LYS10.8450.92627.3810.0470.0470.0000.0000.0000.000
84K108THR0-0.019-0.00922.3110.0000.0000.0000.0000.0000.000
85K109ARG10.8760.92420.8320.1120.1120.0000.0000.0000.000
86K110ALA00.0110.01516.7320.0070.0070.0000.0000.0000.000
87K111GLU-1-0.793-0.85211.294-0.274-0.2740.0000.0000.0000.000
88K119LEU0-0.037-0.0276.006-0.001-0.0010.0000.0000.0000.000
89K120VAL00.001-0.0088.0810.1240.1240.0000.0000.0000.000
90K121ASN0-0.0100.00111.153-0.048-0.0480.0000.0000.0000.000
91K122ARG10.8560.90713.8090.2750.2750.0000.0000.0000.000
92K123ILE0-0.009-0.01017.016-0.001-0.0010.0000.0000.0000.000
93K124GLU-1-0.821-0.88219.912-0.104-0.1040.0000.0000.0000.000
94K125LEU0-0.016-0.02523.3860.0060.0060.0000.0000.0000.000
95K126LYS10.8390.90225.9670.0940.0940.0000.0000.0000.000
96K127GLY0-0.008-0.00929.2570.0020.0020.0000.0000.0000.000
97K128ILE0-0.003-0.00631.8190.0000.0000.0000.0000.0000.000
98K129ASP-1-0.840-0.93535.260-0.032-0.0320.0000.0000.0000.000
99K130PHE0-0.0170.01132.2630.0020.0020.0000.0000.0000.000
100K131LYS10.8320.91538.1830.0120.0120.0000.0000.0000.000
101K132GLU-1-0.790-0.90840.904-0.025-0.0250.0000.0000.0000.000
102K133ASP-1-0.964-0.98142.617-0.010-0.0100.0000.0000.0000.000
103K134GLY0-0.0060.01441.1150.0020.0020.0000.0000.0000.000
104K135ASN0-0.024-0.03237.5710.0000.0000.0000.0000.0000.000
105K136ILE0-0.031-0.01333.6600.0010.0010.0000.0000.0000.000
106K137LEU0-0.022-0.02336.007-0.002-0.0020.0000.0000.0000.000
107K138GLY00.0400.03138.178-0.001-0.0010.0000.0000.0000.000
108K139HIS0-0.074-0.04733.6560.0030.0030.0000.0000.0000.000
109K140LYS10.8560.93637.2220.0030.0030.0000.0000.0000.000
110K141LEU0-0.064-0.03933.0080.0030.0030.0000.0000.0000.000
111K142GLU-1-0.825-0.89034.4460.0170.0170.0000.0000.0000.000
112K143TYR0-0.050-0.02628.210-0.003-0.0030.0000.0000.0000.000
113K144ASN0-0.039-0.04630.3230.0050.0050.0000.0000.0000.000
114K145PHE00.000-0.01823.762-0.006-0.0060.0000.0000.0000.000
115K146ASN0-0.065-0.02527.7400.0090.0090.0000.0000.0000.000
116K147SER0-0.039-0.01524.2550.0020.0020.0000.0000.0000.000
117K148HIS00.0200.00524.086-0.013-0.0130.0000.0000.0000.000
118K149LYS10.8990.96122.529-0.099-0.0990.0000.0000.0000.000
119K150VAL0-0.013-0.01019.322-0.015-0.0150.0000.0000.0000.000
120K151TYR0-0.013-0.00720.3550.0170.0170.0000.0000.0000.000
121K152ILE0-0.004-0.00416.252-0.019-0.0190.0000.0000.0000.000
122K153THR0-0.002-0.02619.9650.0110.0110.0000.0000.0000.000
123K154ALA00.0470.02718.886-0.015-0.0150.0000.0000.0000.000
124K155ASP-1-0.867-0.93819.004-0.064-0.0640.0000.0000.0000.000
125K156LYS10.9830.98119.3600.0130.0130.0000.0000.0000.000
126K157GLN0-0.068-0.02020.602-0.007-0.0070.0000.0000.0000.000
127K158ASN0-0.089-0.05619.681-0.017-0.0170.0000.0000.0000.000
128K159ASN0-0.010-0.00714.5080.0110.0110.0000.0000.0000.000
129K160GLY00.0790.03815.003-0.034-0.0340.0000.0000.0000.000
130K161ILE0-0.056-0.01014.3530.0320.0320.0000.0000.0000.000
131K162LYS10.8880.93917.2360.0270.0270.0000.0000.0000.000
132K163ALA00.0100.00619.3690.0190.0190.0000.0000.0000.000
133K164ASN0-0.012-0.00721.388-0.019-0.0190.0000.0000.0000.000
134K165PHE0-0.013-0.01221.5850.0130.0130.0000.0000.0000.000
135K166THR0-0.007-0.01626.189-0.007-0.0070.0000.0000.0000.000
136K167ILE0-0.060-0.01224.3780.0070.0070.0000.0000.0000.000
137K168ARG10.9470.95828.508-0.040-0.0400.0000.0000.0000.000
138K169HIS00.0270.02227.7650.0060.0060.0000.0000.0000.000
139K170ASN00.013-0.00432.2290.0000.0000.0000.0000.0000.000
140K171VAL00.0000.00535.172-0.003-0.0030.0000.0000.0000.000
141K172GLU-1-0.860-0.92138.1980.0010.0010.0000.0000.0000.000
142K173ASP-1-0.878-0.92740.5580.0030.0030.0000.0000.0000.000
143K174GLY0-0.0150.00041.7620.0010.0010.0000.0000.0000.000
144K175SER0-0.040-0.01340.9180.0010.0010.0000.0000.0000.000
145K176VAL00.010-0.01934.8650.0010.0010.0000.0000.0000.000
146K177GLN0-0.0130.00834.259-0.002-0.0020.0000.0000.0000.000
147K178LEU0-0.027-0.02533.1970.0010.0010.0000.0000.0000.000
148K179ALA00.0420.02129.723-0.005-0.0050.0000.0000.0000.000
149K180ASP-1-0.824-0.86829.2830.0090.0090.0000.0000.0000.000
150K181HIS0-0.004-0.00323.817-0.011-0.0110.0000.0000.0000.000
151K182TYR00.0100.00525.2150.0090.0090.0000.0000.0000.000
152K183GLN0-0.007-0.01716.9870.0020.0020.0000.0000.0000.000
153K184GLN00.0170.01019.6990.0200.0200.0000.0000.0000.000
154K185ASN00.0070.00313.9360.0220.0220.0000.0000.0000.000
155K186THR00.0190.01915.2900.0180.0180.0000.0000.0000.000
156K187PRO00.0270.02811.370-0.024-0.0240.0000.0000.0000.000
157K188ILE0-0.052-0.02711.2170.0500.0500.0000.0000.0000.000
158K189GLY0-0.0090.00710.8560.0270.0270.0000.0000.0000.000
159K190ASP-1-0.966-0.98610.892-0.230-0.2300.0000.0000.0000.000
160K191GLY0-0.0130.0078.7690.0290.0290.0000.0000.0000.000
161K192PRO0-0.092-0.0599.7090.0380.0380.0000.0000.0000.000
162K193VAL0-0.008-0.0087.624-0.056-0.0560.0000.0000.0000.000
163K194ASP-1-0.861-0.93610.1630.0580.0580.0000.0000.0000.000
164K195LEU0-0.084-0.04312.5440.0050.0050.0000.0000.0000.000
165K196PRO0-0.051-0.00515.0570.0210.0210.0000.0000.0000.000
166K197ASP-1-0.894-0.95317.2690.0860.0860.0000.0000.0000.000
167K198ASP-1-0.875-0.91820.0720.0680.0680.0000.0000.0000.000
168K199HIS0-0.095-0.05218.1770.0360.0360.0000.0000.0000.000
169K200TYR00.009-0.01720.498-0.017-0.0170.0000.0000.0000.000
170K201LEU0-0.0380.00215.997-0.013-0.0130.0000.0000.0000.000
171K202SER0-0.025-0.02718.985-0.027-0.0270.0000.0000.0000.000
172K203THR00.0060.00819.2690.0230.0230.0000.0000.0000.000
173K204GLN00.005-0.00320.291-0.018-0.0180.0000.0000.0000.000
174K205THR00.0220.00820.5100.0070.0070.0000.0000.0000.000
175K206ILE00.0190.00722.8550.0030.0030.0000.0000.0000.000
176K207LEU00.0100.03024.568-0.007-0.0070.0000.0000.0000.000
177K222GLU-1-0.890-0.96318.2050.0110.0110.0000.0000.0000.000
178K223TYR00.0050.00917.2380.0270.0270.0000.0000.0000.000
179K224VAL0-0.020-0.01515.102-0.021-0.0210.0000.0000.0000.000
180K225THR00.0210.02514.6670.0490.0490.0000.0000.0000.000
181K226ALA00.0440.01814.316-0.053-0.0530.0000.0000.0000.000
182K227ALA00.0150.00716.2300.0170.0170.0000.0000.0000.000
183K228GLY00.0540.04019.629-0.025-0.0250.0000.0000.0000.000