FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 72YJK

Calculation Name: 4YB9-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4YB9

Chain ID: D

ChEMBL ID:

UniProt ID: P58353

Base Structure: X-ray

Registration Date: 2023-06-22

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 437
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -7761894.726233
FMO2-HF: Nuclear repulsion 7594518.134103
FMO2-HF: Total energy -167376.59213
FMO2-MP2: Total energy -167864.59303


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(D:19:LEU)


Summations of interaction energy for fragment #1(D:19: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.
-7.739-3.2841.173-2.156-3.4720.008
Interaction energy analysis for fragmet #1(D:19:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.029 / q_NPA : 0.008
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].
3D21THR00.0150.0003.691-1.1581.018-0.002-1.015-1.1590.005
4D22LEU00.0000.0032.429-3.679-1.9991.174-0.935-1.9190.002
5D23ILE0-0.019-0.0113.930-1.693-1.0940.001-0.206-0.3940.001
6D24ALA0-0.010-0.0045.622-0.127-0.1270.0000.0000.0000.000
7D25ALA0-0.0120.0157.568-0.123-0.1230.0000.0000.0000.000
8D26PHE0-0.020-0.0137.385-0.157-0.1570.0000.0000.0000.000
9D27GLY00.0380.01010.975-0.118-0.1180.0000.0000.0000.000
10D28SER00.011-0.00812.279-0.036-0.0360.0000.0000.0000.000
11D29SER0-0.006-0.00315.021-0.043-0.0430.0000.0000.0000.000
12D30PHE00.0160.01914.305-0.027-0.0270.0000.0000.0000.000
13D31GLN00.0550.03416.314-0.033-0.0330.0000.0000.0000.000
14D32TYR0-0.015-0.01018.927-0.018-0.0180.0000.0000.0000.000
15D33GLY00.028-0.00119.635-0.013-0.0130.0000.0000.0000.000
16D34TYR0-0.099-0.08819.957-0.012-0.0120.0000.0000.0000.000
17D35ASN00.0280.00421.744-0.015-0.0150.0000.0000.0000.000
18D36VAL0-0.0320.00124.242-0.007-0.0070.0000.0000.0000.000
19D37ALA00.0340.01024.814-0.006-0.0060.0000.0000.0000.000
20D38ALA0-0.0190.00225.286-0.004-0.0040.0000.0000.0000.000
21D39ILE0-0.048-0.02227.0120.0000.0000.0000.0000.0000.000
22D40ASN00.0080.01429.665-0.004-0.0040.0000.0000.0000.000
23D41SER00.0160.02429.087-0.001-0.0010.0000.0000.0000.000
24D42PRO00.0190.01730.038-0.002-0.0020.0000.0000.0000.000
25D43SER0-0.030-0.02633.031-0.001-0.0010.0000.0000.0000.000
26D44GLU-1-0.924-0.95835.6160.0200.0200.0000.0000.0000.000
27D45PHE00.0850.04134.9170.0000.0000.0000.0000.0000.000
28D46MET0-0.085-0.01733.9090.0030.0030.0000.0000.0000.000
29D47LYS10.9140.94537.683-0.028-0.0280.0000.0000.0000.000
30D48ASP-1-0.801-0.89640.8390.0280.0280.0000.0000.0000.000
31D49PHE0-0.011-0.00139.5130.0000.0000.0000.0000.0000.000
32D50TYR0-0.0710.00137.5360.0020.0020.0000.0000.0000.000
33D51ALA00.0200.00842.8960.0000.0000.0000.0000.0000.000
34D52TYR00.0710.01641.982-0.001-0.0010.0000.0000.0000.000
35D53THR0-0.040-0.07243.2550.0010.0010.0000.0000.0000.000
36D54TYR0-0.085-0.03946.0200.0010.0010.0000.0000.0000.000
37D55TYR0-0.011-0.00148.3380.0000.0000.0000.0000.0000.000
38D56ASP-1-0.838-0.91348.3810.0330.0330.0000.0000.0000.000
39D57ARG10.7230.86445.250-0.041-0.0410.0000.0000.0000.000
40D58VAL0-0.017-0.00451.180-0.001-0.0010.0000.0000.0000.000
41D59GLY00.0030.02253.233-0.001-0.0010.0000.0000.0000.000
42D60GLU-1-0.953-0.98254.7340.0220.0220.0000.0000.0000.000
43D61TYR00.012-0.00351.6990.0010.0010.0000.0000.0000.000
44D62MET0-0.047-0.00345.6870.0000.0000.0000.0000.0000.000
45D63ASN00.014-0.00350.861-0.001-0.0010.0000.0000.0000.000
46D64GLU-1-0.810-0.91749.6060.0220.0220.0000.0000.0000.000
47D65PHE00.0000.00748.2090.0010.0010.0000.0000.0000.000
48D66TYR00.014-0.00747.2440.0020.0020.0000.0000.0000.000
49D67LEU00.0700.03743.3250.0030.0030.0000.0000.0000.000
50D68THR0-0.024-0.00843.3670.0020.0020.0000.0000.0000.000
51D69LEU0-0.068-0.03142.7930.0010.0010.0000.0000.0000.000
52D70LEU0-0.009-0.00441.6570.0020.0020.0000.0000.0000.000
53D71TRP00.015-0.00734.6830.0040.0040.0000.0000.0000.000
54D72SER00.0490.00537.8880.0020.0020.0000.0000.0000.000
55D73VAL0-0.0260.01237.9560.0020.0020.0000.0000.0000.000
56D74THR00.0000.00234.4540.0050.0050.0000.0000.0000.000
57D75VAL00.0200.01732.6280.0060.0060.0000.0000.0000.000
58D76SER0-0.041-0.03732.8180.0040.0040.0000.0000.0000.000
59D77MET00.0380.00434.4490.0010.0010.0000.0000.0000.000
60D78PHE0-0.0290.01424.6800.0050.0050.0000.0000.0000.000
61D79PRO0-0.031-0.00629.8260.0060.0060.0000.0000.0000.000
62D80PHE00.0220.00530.8600.0000.0000.0000.0000.0000.000
63D81GLY00.0370.00331.1960.0010.0010.0000.0000.0000.000
64D82GLY00.0080.01528.1950.0070.0070.0000.0000.0000.000
65D83PHE00.022-0.00228.9660.0030.0030.0000.0000.0000.000
66D84LEU0-0.0130.00031.7570.0010.0010.0000.0000.0000.000
67D85GLY00.030-0.00228.5090.0030.0030.0000.0000.0000.000
68D86SER0-0.098-0.03227.4070.0060.0060.0000.0000.0000.000
69D87LEU0-0.033-0.01828.431-0.001-0.0010.0000.0000.0000.000
70D88MET0-0.032-0.01229.2610.0020.0020.0000.0000.0000.000
71D89VAL00.0340.01324.3660.0080.0080.0000.0000.0000.000
72D90GLY0-0.0020.00026.9830.0060.0060.0000.0000.0000.000
73D91PRO00.008-0.00329.3680.0030.0030.0000.0000.0000.000
74D92LEU00.0720.05426.2980.0030.0030.0000.0000.0000.000
75D93VAL00.0180.02023.3970.0110.0110.0000.0000.0000.000
76D94ASN0-0.077-0.04125.5060.0040.0040.0000.0000.0000.000
77D95ASN0-0.061-0.04528.067-0.010-0.0100.0000.0000.0000.000
78D96LEU00.0390.05525.0710.0030.0030.0000.0000.0000.000
79D97GLY00.0370.03723.1100.0170.0170.0000.0000.0000.000
80D98ARG10.7920.88218.966-0.163-0.1630.0000.0000.0000.000
81D99LYS10.9550.97414.938-0.505-0.5050.0000.0000.0000.000
82D100GLY00.0190.01918.1920.0140.0140.0000.0000.0000.000
83D101THR00.002-0.01521.409-0.011-0.0110.0000.0000.0000.000
84D102LEU0-0.038-0.02015.529-0.007-0.0070.0000.0000.0000.000
85D103LEU00.0110.01016.6640.0220.0220.0000.0000.0000.000
86D104PHE0-0.0200.00119.851-0.014-0.0140.0000.0000.0000.000
87D105ASN00.041-0.00920.3630.0070.0070.0000.0000.0000.000
88D106ASN00.0490.03316.791-0.028-0.0280.0000.0000.0000.000
89D107ILE0-0.018-0.00920.881-0.010-0.0100.0000.0000.0000.000
90D108PHE0-0.061-0.02023.383-0.019-0.0190.0000.0000.0000.000
91D109SER0-0.005-0.02021.932-0.024-0.0240.0000.0000.0000.000
92D110ILE0-0.028-0.01321.268-0.008-0.0080.0000.0000.0000.000
93D111VAL00.0090.00825.020-0.012-0.0120.0000.0000.0000.000
94D112PRO00.0150.00926.695-0.010-0.0100.0000.0000.0000.000
95D113ALA00.0040.00824.736-0.009-0.0090.0000.0000.0000.000
96D114LEU00.0190.00326.763-0.008-0.0080.0000.0000.0000.000
97D115LEU0-0.035-0.01328.974-0.009-0.0090.0000.0000.0000.000
98D116MET0-0.017-0.01327.183-0.011-0.0110.0000.0000.0000.000
99D117GLY0-0.0040.00929.688-0.006-0.0060.0000.0000.0000.000
100D118PHE00.010-0.00230.078-0.004-0.0040.0000.0000.0000.000
101D119SER0-0.032-0.03133.579-0.006-0.0060.0000.0000.0000.000
102D120GLU-1-0.960-0.97034.5800.0660.0660.0000.0000.0000.000
103D121LEU0-0.035-0.00936.711-0.004-0.0040.0000.0000.0000.000
104D122ALA0-0.031-0.00239.189-0.004-0.0040.0000.0000.0000.000
105D123LYS10.9270.93839.893-0.050-0.0500.0000.0000.0000.000
106D124SER00.0770.05938.2060.0040.0040.0000.0000.0000.000
107D125PHE0-0.012-0.03338.4790.0030.0030.0000.0000.0000.000
108D126GLU-1-0.926-0.95637.8370.0720.0720.0000.0000.0000.000
109D127MET0-0.012-0.01435.2140.0020.0020.0000.0000.0000.000
110D128ILE00.0450.05133.7040.0050.0050.0000.0000.0000.000
111D129ILE00.0010.00633.9300.0040.0040.0000.0000.0000.000
112D130VAL0-0.005-0.00935.2400.0020.0020.0000.0000.0000.000
113D131ALA00.0310.02031.1800.0060.0060.0000.0000.0000.000
114D132ARG10.8580.92728.301-0.066-0.0660.0000.0000.0000.000
115D133VAL0-0.0020.00830.4230.0040.0040.0000.0000.0000.000
116D134LEU00.006-0.00830.1800.0050.0050.0000.0000.0000.000
117D135VAL00.0240.01425.1040.0110.0110.0000.0000.0000.000
118D136GLY00.0190.00625.8080.0070.0070.0000.0000.0000.000
119D137ILE0-0.076-0.02427.0140.0030.0030.0000.0000.0000.000
120D138CYS0-0.024-0.00323.0010.0090.0090.0000.0000.0000.000
121D139ALA00.0700.02822.2670.0140.0140.0000.0000.0000.000
122D140GLY0-0.0160.00222.9160.0010.0010.0000.0000.0000.000
123D141LEU0-0.0120.02423.656-0.001-0.0010.0000.0000.0000.000
124D142SER0-0.037-0.03018.9010.0080.0080.0000.0000.0000.000
125D143SER00.011-0.01919.5460.0080.0080.0000.0000.0000.000
126D144ASN0-0.049-0.01221.104-0.008-0.0080.0000.0000.0000.000
127D145VAL00.0450.00118.8930.0000.0000.0000.0000.0000.000
128D146VAL00.0360.02714.3340.0230.0230.0000.0000.0000.000
129D147PRO00.0280.01515.7150.0220.0220.0000.0000.0000.000
130D148MET0-0.046-0.00917.288-0.010-0.0100.0000.0000.0000.000
131D149TYR0-0.061-0.07212.3000.0150.0150.0000.0000.0000.000
132D150LEU00.008-0.00910.1950.0240.0240.0000.0000.0000.000
133D151GLY00.0060.01914.204-0.028-0.0280.0000.0000.0000.000
134D152GLU-1-0.818-0.90317.1820.1450.1450.0000.0000.0000.000
135D153LEU0-0.055-0.02112.245-0.011-0.0110.0000.0000.0000.000
136D154ALA0-0.0300.01413.406-0.017-0.0170.0000.0000.0000.000
137D155PRO00.0070.00313.283-0.004-0.0040.0000.0000.0000.000
138D156LYS10.9660.97916.241-0.013-0.0130.0000.0000.0000.000
139D157ASN0-0.025-0.02118.7670.0040.0040.0000.0000.0000.000
140D158TRP00.0070.0158.7370.0030.0030.0000.0000.0000.000
141D159ARG11.0030.99015.192-0.047-0.0470.0000.0000.0000.000
142D160GLY00.0260.00015.5300.0090.0090.0000.0000.0000.000
143D161ALA00.0200.02713.002-0.005-0.0050.0000.0000.0000.000
144D162LEU0-0.020-0.01713.617-0.018-0.0180.0000.0000.0000.000
145D163GLY00.0030.00214.7550.0190.0190.0000.0000.0000.000
146D164VAL00.0470.02317.0030.0150.0150.0000.0000.0000.000
147D165VAL00.0050.01810.8710.0000.0000.0000.0000.0000.000
148D166PRO00.001-0.00113.5530.0030.0030.0000.0000.0000.000
149D167GLN00.0590.02114.6750.0220.0220.0000.0000.0000.000
150D168LEU00.0480.02312.177-0.001-0.0010.0000.0000.0000.000
151D169PHE00.0070.0168.6150.0060.0060.0000.0000.0000.000
152D170ILE0-0.047-0.00714.6750.0190.0190.0000.0000.0000.000
153D171THR0-0.052-0.05717.265-0.004-0.0040.0000.0000.0000.000
154D172ILE00.0220.01012.918-0.004-0.0040.0000.0000.0000.000
155D173GLY00.0190.00716.9580.0060.0060.0000.0000.0000.000
156D174ILE0-0.023-0.00418.6340.0030.0030.0000.0000.0000.000
157D175LEU0-0.0030.00818.286-0.001-0.0010.0000.0000.0000.000
158D176VAL0-0.003-0.01316.6340.0000.0000.0000.0000.0000.000
159D177ALA00.0460.00519.9380.0030.0030.0000.0000.0000.000
160D178GLN00.0120.01323.168-0.007-0.0070.0000.0000.0000.000
161D179ILE0-0.034-0.01219.756-0.003-0.0030.0000.0000.0000.000
162D180PHE0-0.033-0.02619.1050.0020.0020.0000.0000.0000.000
163D181GLY00.0170.01324.2780.0040.0040.0000.0000.0000.000
164D182LEU0-0.011-0.00526.928-0.004-0.0040.0000.0000.0000.000
165D183ARG10.9320.95728.658-0.005-0.0050.0000.0000.0000.000
166D184SER0-0.051-0.01630.0810.0030.0030.0000.0000.0000.000
167D185LEU0-0.031-0.01624.4630.0020.0020.0000.0000.0000.000
168D186LEU0-0.021-0.00925.3260.0050.0050.0000.0000.0000.000
169D187ALA0-0.061-0.01129.0370.0040.0040.0000.0000.0000.000
170D188ASN00.0700.03031.485-0.001-0.0010.0000.0000.0000.000
171D189GLU-1-0.893-0.95434.9590.0330.0330.0000.0000.0000.000
172D190GLU-1-0.906-0.95534.9140.0400.0400.0000.0000.0000.000
173D191GLY0-0.027-0.01231.9850.0050.0050.0000.0000.0000.000
174D192TRP00.016-0.00130.5050.0100.0100.0000.0000.0000.000
175D193PRO00.0410.02030.3440.0070.0070.0000.0000.0000.000
176D194ILE00.0000.01026.5050.0120.0120.0000.0000.0000.000
177D195LEU00.0130.02325.1660.0120.0120.0000.0000.0000.000
178D196LEU00.0060.03425.6440.0090.0090.0000.0000.0000.000
179D197GLY00.0130.00626.0730.0100.0100.0000.0000.0000.000
180D198LEU0-0.022-0.00521.0990.0220.0220.0000.0000.0000.000
181D199THR0-0.027-0.02820.9970.0280.0280.0000.0000.0000.000
182D200GLY00.0250.00520.7390.0190.0190.0000.0000.0000.000
183D201ILE0-0.0070.00517.2500.0340.0340.0000.0000.0000.000
184D202PRO00.003-0.00915.3130.0550.0550.0000.0000.0000.000
185D203ALA00.0190.01315.3950.0700.0700.0000.0000.0000.000
186D204VAL00.009-0.00717.3860.0390.0390.0000.0000.0000.000
187D205LEU0-0.0310.00210.8570.0470.0470.0000.0000.0000.000
188D206GLN00.0060.00012.5380.0860.0860.0000.0000.0000.000
189D207LEU0-0.037-0.03313.6280.0620.0620.0000.0000.0000.000
190D208LEU0-0.0260.00813.112-0.018-0.0180.0000.0000.0000.000
191D209PHE00.013-0.0218.4980.1350.1350.0000.0000.0000.000
192D210LEU0-0.0030.01910.4630.1070.1070.0000.0000.0000.000
193D211PRO00.0180.01212.133-0.045-0.0450.0000.0000.0000.000
194D212PHE0-0.0010.0148.097-0.102-0.1020.0000.0000.0000.000
195D213PHE0-0.039-0.0245.858-0.020-0.0200.0000.0000.0000.000
196D214PRO0-0.007-0.01210.586-0.142-0.1420.0000.0000.0000.000
197D215GLU-1-0.907-0.94113.7090.3280.3280.0000.0000.0000.000
198D216SER0-0.046-0.04716.613-0.005-0.0050.0000.0000.0000.000
199D217PRO00.0630.01817.551-0.017-0.0170.0000.0000.0000.000
200D218ARG10.8930.94720.612-0.114-0.1140.0000.0000.0000.000
201D219TYR0-0.100-0.09122.449-0.011-0.0110.0000.0000.0000.000
202D220LEU00.015-0.01320.820-0.013-0.0130.0000.0000.0000.000
203D221LEU00.0430.04524.621-0.008-0.0080.0000.0000.0000.000
204D222ILE0-0.063-0.01226.732-0.011-0.0110.0000.0000.0000.000
205D223GLN0-0.104-0.06427.572-0.014-0.0140.0000.0000.0000.000
206D224LYS10.9230.95926.112-0.156-0.1560.0000.0000.0000.000
207D225LYS10.8820.97828.767-0.092-0.0920.0000.0000.0000.000
208D226ASP-1-0.872-0.93926.7770.1190.1190.0000.0000.0000.000
209D227GLU-1-0.919-0.96826.2240.0790.0790.0000.0000.0000.000
210D228ALA0-0.020-0.01825.4280.0030.0030.0000.0000.0000.000
211D229ALA00.005-0.00322.8040.0090.0090.0000.0000.0000.000
212D230ALA00.0100.01721.1720.0220.0220.0000.0000.0000.000
213D231LYS10.9740.97820.695-0.064-0.0640.0000.0000.0000.000
214D232SER0-0.047-0.01319.7300.0050.0050.0000.0000.0000.000
215D233ALA0-0.003-0.01116.2800.0150.0150.0000.0000.0000.000
216D234LEU00.0050.01115.6060.0210.0210.0000.0000.0000.000
217D235ARG10.9440.96616.506-0.072-0.0720.0000.0000.0000.000
218D236ARG10.9050.96210.902-0.527-0.5270.0000.0000.0000.000
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