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: 728YK

Calculation Name: 4QMI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4QMI

Chain ID: A

ChEMBL ID:

UniProt ID: Q14008

Base Structure: X-ray

Registration Date: 2023-09-20

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 228
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2708568.650337
FMO2-HF: Nuclear repulsion 2619229.095187
FMO2-HF: Total energy -89339.55515
FMO2-MP2: Total energy -89599.279434


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(A:853:PRO)


Summations of interaction energy for fragment #1(A:853:PRO)
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.
-4.072-0.850.618-1.587-2.252-0.002
Interaction energy analysis for fragmet #1(A:853:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.044 / q_NPA : -0.023
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].
3A855THR00.0530.0243.140-3.449-0.8930.113-1.297-1.371-0.001
4A856GLU-1-0.811-0.8815.385-0.210-0.102-0.001-0.005-0.1030.000
5A857ILE00.0350.0107.2390.0510.0510.0000.0000.0000.000
6A858SER0-0.052-0.05210.7930.0810.0810.0000.0000.0000.000
7A859ASP-1-0.910-0.95412.143-0.366-0.3660.0000.0000.0000.000
8A860LYS10.9450.97113.0300.2500.2500.0000.0000.0000.000
9A861ILE0-0.082-0.02615.2700.0410.0410.0000.0000.0000.000
10A862THR00.0430.02817.6030.0110.0110.0000.0000.0000.000
11A863SER00.0520.00620.2620.0120.0120.0000.0000.0000.000
12A864GLU-1-0.919-0.95623.717-0.087-0.0870.0000.0000.0000.000
13A865LEU00.0190.02019.2580.0110.0110.0000.0000.0000.000
14A866VAL00.018-0.00821.6490.0110.0110.0000.0000.0000.000
15A867SER0-0.022-0.01024.1720.0100.0100.0000.0000.0000.000
16A868LYS10.7790.90124.5220.0860.0860.0000.0000.0000.000
17A869ILE00.0140.00422.5380.0090.0090.0000.0000.0000.000
18A870GLY0-0.025-0.01727.0990.0060.0060.0000.0000.0000.000
19A871ASP-1-0.807-0.88629.888-0.039-0.0390.0000.0000.0000.000
20A872LYS10.9760.97232.4120.0330.0330.0000.0000.0000.000
21A873ASN0-0.044-0.02235.1380.0060.0060.0000.0000.0000.000
22A874TRP00.0580.01233.797-0.002-0.0020.0000.0000.0000.000
23A875LYS10.9290.95832.6280.0190.0190.0000.0000.0000.000
24A876ILE00.0310.03230.2480.0000.0000.0000.0000.0000.000
25A877ARG10.7830.87829.1200.0290.0290.0000.0000.0000.000
26A878LYS10.7880.87027.8410.0190.0190.0000.0000.0000.000
27A879GLU-1-0.882-0.92526.825-0.056-0.0560.0000.0000.0000.000
28A880GLY00.0480.01924.663-0.005-0.0050.0000.0000.0000.000
29A881LEU0-0.022-0.02723.139-0.008-0.0080.0000.0000.0000.000
30A882ASP-1-0.806-0.89222.964-0.028-0.0280.0000.0000.0000.000
31A883GLU-1-0.875-0.92920.147-0.105-0.1050.0000.0000.0000.000
32A884VAL00.006-0.00218.272-0.011-0.0110.0000.0000.0000.000
33A885ALA0-0.0020.00317.917-0.009-0.0090.0000.0000.0000.000
34A886GLY00.0040.00518.1360.0090.0090.0000.0000.0000.000
35A887ILE0-0.001-0.00213.850-0.002-0.0020.0000.0000.0000.000
36A888ILE0-0.011-0.00713.404-0.030-0.0300.0000.0000.0000.000
37A889ASN0-0.073-0.04113.2050.0220.0220.0000.0000.0000.000
38A890ASP-1-0.976-0.97312.805-0.048-0.0480.0000.0000.0000.000
39A891ALA00.0250.0209.1080.0150.0150.0000.0000.0000.000
40A892LYS10.9250.9898.757-0.225-0.2250.0000.0000.0000.000
41A893PHE0-0.069-0.0626.5980.0870.0870.0000.0000.0000.000
42A894ILE00.017-0.0047.313-0.301-0.3010.0000.0000.0000.000
43A895GLN0-0.032-0.0262.529-0.1340.4240.506-0.285-0.778-0.001
44A896PRO00.012-0.0237.0440.0520.0520.0000.0000.0000.000
45A897ASN0-0.036-0.0179.9690.0840.0840.0000.0000.0000.000
46A898ILE00.0210.00911.792-0.047-0.0470.0000.0000.0000.000
47A899GLY00.0780.03014.1690.0210.0210.0000.0000.0000.000
48A900GLU-1-0.864-0.93116.781-0.086-0.0860.0000.0000.0000.000
49A901LEU0-0.0030.00816.8500.0170.0170.0000.0000.0000.000
50A902PRO0-0.001-0.00718.0570.0170.0170.0000.0000.0000.000
51A903THR0-0.013-0.02220.8740.0150.0150.0000.0000.0000.000
52A904ALA00.0050.00522.9260.0080.0080.0000.0000.0000.000
53A905LEU00.002-0.00920.0590.0090.0090.0000.0000.0000.000
54A906LYS10.9080.95324.2490.0520.0520.0000.0000.0000.000
55A907GLY0-0.0270.00126.3970.0060.0060.0000.0000.0000.000
56A908ARG10.8090.90026.7230.0430.0430.0000.0000.0000.000
57A909LEU00.006-0.00126.1990.0050.0050.0000.0000.0000.000
58A910ASN0-0.039-0.02029.6950.0060.0060.0000.0000.0000.000
59A911ASP-1-0.748-0.82331.671-0.028-0.0280.0000.0000.0000.000
60A912SER00.0160.00433.6430.0020.0020.0000.0000.0000.000
61A913ASN0-0.066-0.02734.7380.0020.0020.0000.0000.0000.000
62A914LYS10.9670.95034.0300.0080.0080.0000.0000.0000.000
63A915ILE00.0220.00632.8100.0010.0010.0000.0000.0000.000
64A916LEU00.0100.01329.9550.0010.0010.0000.0000.0000.000
65A917VAL0-0.0040.03228.857-0.003-0.0030.0000.0000.0000.000
66A918GLN00.012-0.00828.5660.0000.0000.0000.0000.0000.000
67A919GLN0-0.033-0.01825.0590.0040.0040.0000.0000.0000.000
68A920THR00.005-0.01424.601-0.004-0.0040.0000.0000.0000.000
69A921LEU0-0.015-0.01123.686-0.002-0.0020.0000.0000.0000.000
70A922ASN0-0.005-0.00623.6170.0060.0060.0000.0000.0000.000
71A923ILE00.0230.02319.3380.0040.0040.0000.0000.0000.000
72A924LEU00.010-0.00319.068-0.006-0.0060.0000.0000.0000.000
73A925GLN0-0.019-0.00819.2800.0090.0090.0000.0000.0000.000
74A926GLN0-0.037-0.02316.7790.0060.0060.0000.0000.0000.000
75A927LEU0-0.0020.00014.6520.0010.0010.0000.0000.0000.000
76A928ALA00.0010.01614.167-0.005-0.0050.0000.0000.0000.000
77A929VAL00.0180.00813.8020.0180.0180.0000.0000.0000.000
78A930ALA00.0170.01611.3280.0390.0390.0000.0000.0000.000
79A931MET0-0.0510.0179.661-0.028-0.0280.0000.0000.0000.000
80A932GLY00.0020.01310.2200.0400.0400.0000.0000.0000.000
81A933PRO00.0760.01111.536-0.030-0.0300.0000.0000.0000.000
82A934ASN0-0.050-0.0238.606-0.004-0.0040.0000.0000.0000.000
83A935ILE00.0400.02012.428-0.027-0.0270.0000.0000.0000.000
84A936LYS10.9500.97113.745-0.066-0.0660.0000.0000.0000.000
85A937GLN0-0.046-0.02512.6910.0110.0110.0000.0000.0000.000
86A938HIS0-0.010-0.00414.1350.0050.0050.0000.0000.0000.000
87A939VAL00.0010.00918.7770.0000.0000.0000.0000.0000.000
88A940LYS10.8280.91321.5580.0030.0030.0000.0000.0000.000
89A941ASN00.0110.01721.2260.0040.0040.0000.0000.0000.000
90A942LEU0-0.029-0.02519.375-0.001-0.0010.0000.0000.0000.000
91A943GLY00.0350.01922.7260.0030.0030.0000.0000.0000.000
92A944ILE00.0610.01823.7020.0040.0040.0000.0000.0000.000
93A945PRO00.000-0.00225.8530.0020.0020.0000.0000.0000.000
94A946ILE00.0060.01723.0470.0010.0010.0000.0000.0000.000
95A947ILE00.0020.00827.7210.0030.0030.0000.0000.0000.000
96A948THR0-0.042-0.02130.4220.0010.0010.0000.0000.0000.000
97A949VAL0-0.001-0.00229.8060.0010.0010.0000.0000.0000.000
98A950LEU0-0.005-0.00331.3800.0020.0020.0000.0000.0000.000
99A951GLY0-0.009-0.00734.1000.0010.0010.0000.0000.0000.000
100A952ASP-1-0.821-0.89535.339-0.005-0.0050.0000.0000.0000.000
101A953SER00.022-0.00437.3660.0010.0010.0000.0000.0000.000
102A954LYS10.8780.94637.5550.0020.0020.0000.0000.0000.000
103A955ASN00.0830.02737.3380.0000.0000.0000.0000.0000.000
104A956ASN00.0210.00735.0210.0010.0010.0000.0000.0000.000
105A957VAL0-0.019-0.00532.6330.0010.0010.0000.0000.0000.000
106A958ARG10.8450.93432.398-0.008-0.0080.0000.0000.0000.000
107A959ALA0-0.0060.00032.6770.0010.0010.0000.0000.0000.000
108A960ALA00.0150.01128.8600.0030.0030.0000.0000.0000.000
109A961ALA00.0210.02727.9160.0010.0010.0000.0000.0000.000
110A962LEU00.0450.01728.1100.0010.0010.0000.0000.0000.000
111A963ALA00.0040.00026.6310.0030.0030.0000.0000.0000.000
112A964THR0-0.004-0.01223.0910.0040.0040.0000.0000.0000.000
113A965VAL00.000-0.00123.4150.0010.0010.0000.0000.0000.000
114A966ASN00.0330.01424.2620.0060.0060.0000.0000.0000.000
115A967ALA00.0490.03820.5090.0070.0070.0000.0000.0000.000
116A968TRP0-0.024-0.03619.4460.0060.0060.0000.0000.0000.000
117A969ALA0-0.0060.00419.8680.0070.0070.0000.0000.0000.000
118A970GLU-1-0.978-0.97919.5230.0880.0880.0000.0000.0000.000
119A971GLN0-0.068-0.03014.6550.0310.0310.0000.0000.0000.000
120A972THR0-0.046-0.03717.1120.0040.0040.0000.0000.0000.000
121A973GLY0-0.0340.00219.311-0.002-0.0020.0000.0000.0000.000
122A974MET00.033-0.00122.439-0.005-0.0050.0000.0000.0000.000
123A975LYS10.9500.97724.235-0.024-0.0240.0000.0000.0000.000
124A976GLU-1-0.851-0.93922.1330.0000.0000.0000.0000.0000.000
125A977TRP0-0.048-0.03122.440-0.007-0.0070.0000.0000.0000.000
126A978LEU0-0.042-0.03026.880-0.002-0.0020.0000.0000.0000.000
127A979GLU-1-0.940-0.93827.691-0.002-0.0020.0000.0000.0000.000
128A980GLY00.0590.03729.736-0.002-0.0020.0000.0000.0000.000
129A981GLU-1-0.920-0.98132.086-0.005-0.0050.0000.0000.0000.000
130A982ASP-1-0.863-0.91329.311-0.009-0.0090.0000.0000.0000.000
131A983LEU00.0190.00430.3050.0000.0000.0000.0000.0000.000
132A984SER0-0.036-0.03532.7980.0000.0000.0000.0000.0000.000
133A985GLU-1-0.750-0.86935.346-0.006-0.0060.0000.0000.0000.000
134A986GLU-1-0.806-0.88932.635-0.008-0.0080.0000.0000.0000.000
135A987LEU0-0.043-0.02636.0070.0000.0000.0000.0000.0000.000
136A988LYS10.8010.88738.2920.0060.0060.0000.0000.0000.000
137A989LYS10.7870.89035.2920.0080.0080.0000.0000.0000.000
138A990GLU-1-0.858-0.91441.1970.0020.0020.0000.0000.0000.000
139A991ASN0-0.055-0.02639.9020.0010.0010.0000.0000.0000.000
140A992PRO00.0430.01141.5630.0010.0010.0000.0000.0000.000
141A993PHE00.001-0.01539.5940.0010.0010.0000.0000.0000.000
142A994LEU00.0400.02234.9800.0010.0010.0000.0000.0000.000
143A995ARG10.7930.88037.381-0.001-0.0010.0000.0000.0000.000
144A996GLN0-0.0010.00839.3260.0030.0030.0000.0000.0000.000
145A997GLU-1-0.836-0.91534.8570.0170.0170.0000.0000.0000.000
146A998LEU0-0.0070.00332.9280.0030.0030.0000.0000.0000.000
147A999LEU0-0.011-0.02135.3340.0020.0020.0000.0000.0000.000
148A1000GLY0-0.025-0.00836.8260.0020.0020.0000.0000.0000.000
149A1001TRP0-0.022-0.01526.4920.0000.0000.0000.0000.0000.000
150A1002LEU00.007-0.01032.6320.0030.0030.0000.0000.0000.000
151A1003ALA0-0.015-0.00634.4710.0020.0020.0000.0000.0000.000
152A1004GLU-1-0.874-0.91429.8430.0420.0420.0000.0000.0000.000
153A1005LYS10.8530.90326.841-0.043-0.0430.0000.0000.0000.000
154A1006LEU00.0010.01030.9740.0020.0020.0000.0000.0000.000
155A1007PRO0-0.0070.00233.4750.0000.0000.0000.0000.0000.000
156A1008THR0-0.065-0.03528.6410.0040.0040.0000.0000.0000.000
157A1009LEU0-0.049-0.01228.2030.0040.0040.0000.0000.0000.000
158A1010ARG10.9910.98220.528-0.087-0.0870.0000.0000.0000.000
159A1011SER0-0.040-0.01926.5610.0000.0000.0000.0000.0000.000
160A1012THR00.0320.01928.727-0.001-0.0010.0000.0000.0000.000
161A1013PRO0-0.0020.00931.345-0.001-0.0010.0000.0000.0000.000
162A1014THR0-0.038-0.05231.8000.0000.0000.0000.0000.0000.000
163A1015ASP-1-0.798-0.87432.5910.0050.0050.0000.0000.0000.000
164A1016LEU00.0320.02535.056-0.001-0.0010.0000.0000.0000.000
165A1017ILE0-0.031-0.03436.393-0.001-0.0010.0000.0000.0000.000
166A1018LEU00.0020.00435.666-0.001-0.0010.0000.0000.0000.000
167A1019CYS00.0040.00636.171-0.001-0.0010.0000.0000.0000.000
168A1020VAL0-0.0280.00139.0340.0000.0000.0000.0000.0000.000
169A1021PRO0-0.040-0.01942.1700.0000.0000.0000.0000.0000.000
170A1022HIS00.0770.03639.6370.0000.0000.0000.0000.0000.000
171A1023LEU00.0210.02741.4180.0000.0000.0000.0000.0000.000
172A1024TYR0-0.013-0.05643.1980.0010.0010.0000.0000.0000.000
173A1025SER0-0.004-0.00145.4990.0000.0000.0000.0000.0000.000
174A1026CYS0-0.038-0.01043.0990.0000.0000.0000.0000.0000.000
175A1027LEU0-0.006-0.00945.7330.0010.0010.0000.0000.0000.000
176A1028GLU-1-0.837-0.88348.2290.0050.0050.0000.0000.0000.000
177A1029ASP-1-0.794-0.86946.0730.0040.0040.0000.0000.0000.000
178A1030ARG10.9820.99149.032-0.002-0.0020.0000.0000.0000.000
179A1031ASN0-0.051-0.04545.7850.0010.0010.0000.0000.0000.000
180A1032GLY00.0280.00548.0990.0000.0000.0000.0000.0000.000
181A1033ASP-1-0.831-0.91044.2190.0120.0120.0000.0000.0000.000
182A1034VAL0-0.064-0.02942.8790.0010.0010.0000.0000.0000.000
183A1035ARG10.8480.93244.652-0.007-0.0070.0000.0000.0000.000
184A1036LYS10.8390.91544.851-0.018-0.0180.0000.0000.0000.000
185A1037LYS10.9340.95238.030-0.016-0.0160.0000.0000.0000.000
186A1038ALA00.0060.01441.8440.0010.0010.0000.0000.0000.000
187A1039GLN0-0.036-0.03643.6830.0010.0010.0000.0000.0000.000
188A1040ASP-1-0.843-0.90541.5510.0200.0200.0000.0000.0000.000
189A1041ALA00.0090.00439.5770.0010.0010.0000.0000.0000.000
190A1042LEU0-0.0080.00040.8060.0010.0010.0000.0000.0000.000
191A1043PRO00.0510.01542.7630.0000.0000.0000.0000.0000.000
192A1044PHE00.0090.00837.4840.0010.0010.0000.0000.0000.000
193A1045PHE00.013-0.00438.2930.0000.0000.0000.0000.0000.000
194A1046MET0-0.025-0.01040.1170.0000.0000.0000.0000.0000.000
195A1047MET0-0.0390.00336.3130.0000.0000.0000.0000.0000.000
196A1048HIS0-0.039-0.02233.783-0.001-0.0010.0000.0000.0000.000
197A1049LEU0-0.068-0.03638.782-0.001-0.0010.0000.0000.0000.000
198A1050GLY00.0340.01641.544-0.001-0.0010.0000.0000.0000.000
199A1051TYR0-0.009-0.06244.590-0.001-0.0010.0000.0000.0000.000
200A1052GLU-1-0.854-0.93447.9470.0090.0090.0000.0000.0000.000
201A1053LYS10.9160.97342.301-0.009-0.0090.0000.0000.0000.000
202A1054MET00.0170.01543.616-0.001-0.0010.0000.0000.0000.000
203A1055ALA00.0870.06346.762-0.001-0.0010.0000.0000.0000.000
204A1056LYS10.9620.99048.831-0.005-0.0050.0000.0000.0000.000
205A1057ALA0-0.053-0.02646.306-0.001-0.0010.0000.0000.0000.000
206A1058THR00.006-0.00248.337-0.001-0.0010.0000.0000.0000.000
207A1059GLY0-0.003-0.00651.2090.0000.0000.0000.0000.0000.000
208A1060LYS10.9330.96745.405-0.004-0.0040.0000.0000.0000.000
209A1061LEU0-0.0020.02549.5410.0000.0000.0000.0000.0000.000
210A1062LYS10.9380.95353.197-0.003-0.0030.0000.0000.0000.000
211A1063PRO00.0400.00056.5300.0010.0010.0000.0000.0000.000
212A1064THR00.0660.02558.0870.0000.0000.0000.0000.0000.000
213A1065SER0-0.023-0.03353.3460.0000.0000.0000.0000.0000.000
214A1066LYS10.7820.88954.073-0.003-0.0030.0000.0000.0000.000
215A1067ASP-1-0.915-0.94855.1280.0070.0070.0000.0000.0000.000
216A1068GLN0-0.029-0.01053.9830.0010.0010.0000.0000.0000.000
217A1069VAL00.007-0.00549.6080.0010.0010.0000.0000.0000.000
218A1070LEU00.0350.01651.7870.0010.0010.0000.0000.0000.000
219A1071ALA00.0330.03353.7250.0010.0010.0000.0000.0000.000
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