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: 2JZ4R

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 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 228
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2718224.747953
FMO2-HF: Nuclear repulsion 2628885.002695
FMO2-HF: Total energy -89339.745258
FMO2-MP2: Total energy -89599.436363


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.
-3.919-0.9260.317-1.479-1.831-0.004
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 : -0.031 / q_NPA : -0.019
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].
3A855THR00.0370.0253.019-3.433-0.9630.173-1.308-1.335-0.004
4A856GLU-1-0.811-0.8885.506-0.226-0.2260.0000.0000.0000.000
5A857ILE00.0230.0087.1820.0440.0440.0000.0000.0000.000
6A858SER0-0.064-0.05510.8550.1100.1100.0000.0000.0000.000
7A859ASP-1-0.877-0.93512.087-0.467-0.4670.0000.0000.0000.000
8A860LYS10.8680.92113.7030.3030.3030.0000.0000.0000.000
9A861ILE0-0.091-0.02815.2450.0480.0480.0000.0000.0000.000
10A862THR00.0320.00617.7360.0140.0140.0000.0000.0000.000
11A863SER00.034-0.00220.4190.0150.0150.0000.0000.0000.000
12A864GLU-1-0.838-0.90223.252-0.136-0.1360.0000.0000.0000.000
13A865LEU0-0.0090.02019.4030.0160.0160.0000.0000.0000.000
14A866VAL00.019-0.00821.5040.0130.0130.0000.0000.0000.000
15A867SER0-0.015-0.00624.0270.0130.0130.0000.0000.0000.000
16A868LYS10.7630.87824.1270.1300.1300.0000.0000.0000.000
17A869ILE00.0030.00122.2340.0110.0110.0000.0000.0000.000
18A870GLY0-0.001-0.00526.7830.0080.0080.0000.0000.0000.000
19A871ASP-1-0.831-0.89629.618-0.058-0.0580.0000.0000.0000.000
20A872LYS10.9780.97632.3060.0490.0490.0000.0000.0000.000
21A873ASN0-0.027-0.01435.1060.0070.0070.0000.0000.0000.000
22A874TRP00.0600.01533.524-0.004-0.0040.0000.0000.0000.000
23A875LYS10.9260.96032.5180.0350.0350.0000.0000.0000.000
24A876ILE00.0190.03330.209-0.001-0.0010.0000.0000.0000.000
25A877ARG10.7830.86828.9460.0460.0460.0000.0000.0000.000
26A878LYS10.7930.87527.7480.0420.0420.0000.0000.0000.000
27A879GLU-1-0.880-0.93226.528-0.092-0.0920.0000.0000.0000.000
28A880GLY00.0450.01524.563-0.009-0.0090.0000.0000.0000.000
29A881LEU0-0.022-0.02323.058-0.011-0.0110.0000.0000.0000.000
30A882ASP-1-0.803-0.88122.904-0.058-0.0580.0000.0000.0000.000
31A883GLU-1-0.784-0.87919.964-0.168-0.1680.0000.0000.0000.000
32A884VAL00.0060.00318.233-0.019-0.0190.0000.0000.0000.000
33A885ALA00.001-0.00217.950-0.014-0.0140.0000.0000.0000.000
34A886GLY00.0010.00818.5270.0090.0090.0000.0000.0000.000
35A887ILE0-0.006-0.00813.870-0.006-0.0060.0000.0000.0000.000
36A888ILE0-0.020-0.01413.486-0.047-0.0470.0000.0000.0000.000
37A889ASN0-0.069-0.03413.4550.0280.0280.0000.0000.0000.000
38A890ASP-1-0.974-0.97713.092-0.190-0.1900.0000.0000.0000.000
39A891ALA00.0410.0219.5520.0000.0000.0000.0000.0000.000
40A892LYS10.9420.9978.664-0.285-0.2850.0000.0000.0000.000
41A893PHE0-0.086-0.0686.9860.1850.1850.0000.0000.0000.000
42A894ILE00.0090.0017.286-0.383-0.3830.0000.0000.0000.000
43A895GLN0-0.011-0.0182.7490.1800.7030.144-0.171-0.4960.000
44A896PRO0-0.016-0.0407.1520.1010.1010.0000.0000.0000.000
45A897ASN0-0.048-0.0219.8480.1230.1230.0000.0000.0000.000
46A898ILE00.0330.01211.277-0.058-0.0580.0000.0000.0000.000
47A899GLY00.0740.03114.0340.0280.0280.0000.0000.0000.000
48A900GLU-1-0.848-0.91816.813-0.116-0.1160.0000.0000.0000.000
49A901LEU00.0030.01616.5730.0210.0210.0000.0000.0000.000
50A902PRO00.000-0.01117.9630.0200.0200.0000.0000.0000.000
51A903THR0-0.018-0.02620.8390.0180.0180.0000.0000.0000.000
52A904ALA00.0020.00322.5810.0110.0110.0000.0000.0000.000
53A905LEU00.003-0.00819.9530.0120.0120.0000.0000.0000.000
54A906LYS10.8700.92524.1420.0770.0770.0000.0000.0000.000
55A907GLY0-0.0200.00626.4880.0080.0080.0000.0000.0000.000
56A908ARG10.7760.87926.3370.0670.0670.0000.0000.0000.000
57A909LEU00.0240.00526.0690.0060.0060.0000.0000.0000.000
58A910ASN0-0.029-0.02329.3930.0080.0080.0000.0000.0000.000
59A911ASP-1-0.737-0.82031.567-0.046-0.0460.0000.0000.0000.000
60A912SER00.0210.00233.5680.0030.0030.0000.0000.0000.000
61A913ASN0-0.049-0.01634.4080.0030.0030.0000.0000.0000.000
62A914LYS10.9220.94333.6660.0190.0190.0000.0000.0000.000
63A915ILE00.0210.00932.7810.0010.0010.0000.0000.0000.000
64A916LEU00.0280.01629.5500.0000.0000.0000.0000.0000.000
65A917VAL0-0.0210.03128.518-0.004-0.0040.0000.0000.0000.000
66A918GLN00.0360.01328.382-0.001-0.0010.0000.0000.0000.000
67A919GLN0-0.042-0.02324.8790.0070.0070.0000.0000.0000.000
68A920THR00.004-0.01724.416-0.007-0.0070.0000.0000.0000.000
69A921LEU0-0.017-0.01123.566-0.004-0.0040.0000.0000.0000.000
70A922ASN00.009-0.00323.5200.0070.0070.0000.0000.0000.000
71A923ILE00.0200.01819.2910.0040.0040.0000.0000.0000.000
72A924LEU00.0080.00118.999-0.011-0.0110.0000.0000.0000.000
73A925GLN0-0.028-0.00419.3720.0100.0100.0000.0000.0000.000
74A926GLN0-0.045-0.02916.8700.0110.0110.0000.0000.0000.000
75A927LEU00.003-0.00114.638-0.003-0.0030.0000.0000.0000.000
76A928ALA00.0010.01414.299-0.012-0.0120.0000.0000.0000.000
77A929VAL00.0170.00813.7320.0220.0220.0000.0000.0000.000
78A930ALA00.0290.01811.2740.0520.0520.0000.0000.0000.000
79A931MET0-0.0330.0349.596-0.039-0.0390.0000.0000.0000.000
80A932GLY00.0020.01410.1710.0440.0440.0000.0000.0000.000
81A933PRO00.0510.00011.510-0.044-0.0440.0000.0000.0000.000
82A934ASN0-0.024-0.0109.2080.0220.0220.0000.0000.0000.000
83A935ILE00.0520.02612.927-0.031-0.0310.0000.0000.0000.000
84A936LYS10.9050.95013.398-0.047-0.0470.0000.0000.0000.000
85A937GLN0-0.030-0.02212.7710.0160.0160.0000.0000.0000.000
86A938HIS00.0000.00414.3000.0090.0090.0000.0000.0000.000
87A939VAL0-0.0040.00919.0360.0020.0020.0000.0000.0000.000
88A940LYS10.8230.90921.9220.0090.0090.0000.0000.0000.000
89A941ASN00.0080.01520.8030.0060.0060.0000.0000.0000.000
90A942LEU0-0.023-0.01219.5660.0000.0000.0000.0000.0000.000
91A943GLY00.0390.01822.7490.0040.0040.0000.0000.0000.000
92A944ILE00.0470.01623.7740.0060.0060.0000.0000.0000.000
93A945PRO00.003-0.00425.9930.0040.0040.0000.0000.0000.000
94A946ILE0-0.0030.02023.1240.0020.0020.0000.0000.0000.000
95A947ILE00.0070.00527.8080.0040.0040.0000.0000.0000.000
96A948THR0-0.052-0.03230.6420.0020.0020.0000.0000.0000.000
97A949VAL0-0.0090.00129.8470.0010.0010.0000.0000.0000.000
98A950LEU00.003-0.00731.1750.0030.0030.0000.0000.0000.000
99A951GLY00.004-0.00134.1720.0020.0020.0000.0000.0000.000
100A952ASP-1-0.822-0.89435.625-0.014-0.0140.0000.0000.0000.000
101A953SER00.0260.00637.6250.0020.0020.0000.0000.0000.000
102A954LYS10.8780.94437.4460.0100.0100.0000.0000.0000.000
103A955ASN00.0850.03137.048-0.001-0.0010.0000.0000.0000.000
104A956ASN00.002-0.00634.9750.0020.0020.0000.0000.0000.000
105A957VAL0-0.021-0.00532.5590.0010.0010.0000.0000.0000.000
106A958ARG10.8200.90532.114-0.004-0.0040.0000.0000.0000.000
107A959ALA00.0030.00832.1320.0020.0020.0000.0000.0000.000
108A960ALA00.0280.01528.6870.0040.0040.0000.0000.0000.000
109A961ALA00.0120.02627.6190.0000.0000.0000.0000.0000.000
110A962LEU00.0430.01127.7790.0010.0010.0000.0000.0000.000
111A963ALA00.0060.00626.3470.0050.0050.0000.0000.0000.000
112A964THR0-0.027-0.02822.9040.0040.0040.0000.0000.0000.000
113A965VAL00.0160.00123.0360.0010.0010.0000.0000.0000.000
114A966ASN00.0070.01924.0770.0080.0080.0000.0000.0000.000
115A967ALA00.0760.04220.2790.0070.0070.0000.0000.0000.000
116A968TRP0-0.044-0.03919.2220.0040.0040.0000.0000.0000.000
117A969ALA00.0060.00819.6230.0090.0090.0000.0000.0000.000
118A970GLU-1-0.973-0.99219.7090.0950.0950.0000.0000.0000.000
119A971GLN0-0.053-0.02014.4550.0430.0430.0000.0000.0000.000
120A972THR0-0.049-0.04816.8120.0050.0050.0000.0000.0000.000
121A973GLY0-0.0220.00818.9510.0000.0000.0000.0000.0000.000
122A974MET00.0390.00922.039-0.009-0.0090.0000.0000.0000.000
123A975LYS10.9560.98724.460-0.024-0.0240.0000.0000.0000.000
124A976GLU-1-0.862-0.93922.328-0.007-0.0070.0000.0000.0000.000
125A977TRP0-0.027-0.01922.492-0.010-0.0100.0000.0000.0000.000
126A978LEU0-0.062-0.03627.254-0.001-0.0010.0000.0000.0000.000
127A979GLU-1-0.936-0.95628.137-0.002-0.0020.0000.0000.0000.000
128A980GLY00.0810.04230.239-0.003-0.0030.0000.0000.0000.000
129A981GLU-1-0.937-0.98532.442-0.010-0.0100.0000.0000.0000.000
130A982ASP-1-0.850-0.89929.185-0.016-0.0160.0000.0000.0000.000
131A983LEU00.012-0.00230.2720.0000.0000.0000.0000.0000.000
132A984SER0-0.045-0.05033.1290.0010.0010.0000.0000.0000.000
133A985GLU-1-0.744-0.86735.664-0.010-0.0100.0000.0000.0000.000
134A986GLU-1-0.813-0.88632.683-0.017-0.0170.0000.0000.0000.000
135A987LEU0-0.025-0.01736.0890.0000.0000.0000.0000.0000.000
136A988LYS10.7990.87738.4160.0110.0110.0000.0000.0000.000
137A989LYS10.7780.89035.3220.0160.0160.0000.0000.0000.000
138A990GLU-1-0.828-0.89241.511-0.001-0.0010.0000.0000.0000.000
139A991ASN0-0.070-0.04440.0390.0010.0010.0000.0000.0000.000
140A992PRO00.0470.01841.6970.0010.0010.0000.0000.0000.000
141A993PHE00.011-0.00739.6140.0020.0020.0000.0000.0000.000
142A994LEU00.0370.02235.1760.0020.0020.0000.0000.0000.000
143A995ARG10.7730.86237.3120.0030.0030.0000.0000.0000.000
144A996GLN0-0.0030.00139.1040.0030.0030.0000.0000.0000.000
145A997GLU-1-0.804-0.88734.9570.0150.0150.0000.0000.0000.000
146A998LEU0-0.0070.00632.7770.0030.0030.0000.0000.0000.000
147A999LEU0-0.007-0.01634.9620.0020.0020.0000.0000.0000.000
148A1000GLY0-0.0100.00536.5280.0020.0020.0000.0000.0000.000
149A1001TRP0-0.005-0.01326.1370.0010.0010.0000.0000.0000.000
150A1002LEU00.001-0.00732.3660.0030.0030.0000.0000.0000.000
151A1003ALA0-0.012-0.01534.3110.0030.0030.0000.0000.0000.000
152A1004GLU-1-0.873-0.91529.6610.0480.0480.0000.0000.0000.000
153A1005LYS10.8370.89926.608-0.048-0.0480.0000.0000.0000.000
154A1006LEU00.0110.01830.8750.0030.0030.0000.0000.0000.000
155A1007PRO0-0.009-0.00133.3250.0010.0010.0000.0000.0000.000
156A1008THR0-0.069-0.04528.3510.0050.0050.0000.0000.0000.000
157A1009LEU0-0.043-0.01127.9980.0060.0060.0000.0000.0000.000
158A1010ARG10.9750.98020.350-0.114-0.1140.0000.0000.0000.000
159A1011SER0-0.032-0.02926.5140.0010.0010.0000.0000.0000.000
160A1012THR00.0230.02428.646-0.001-0.0010.0000.0000.0000.000
161A1013PRO00.0000.01431.232-0.002-0.0020.0000.0000.0000.000
162A1014THR0-0.022-0.04331.899-0.001-0.0010.0000.0000.0000.000
163A1015ASP-1-0.788-0.86932.8550.0030.0030.0000.0000.0000.000
164A1016LEU00.0170.01734.878-0.002-0.0020.0000.0000.0000.000
165A1017ILE0-0.023-0.02736.338-0.001-0.0010.0000.0000.0000.000
166A1018LEU0-0.011-0.00436.121-0.001-0.0010.0000.0000.0000.000
167A1019CYS00.0010.00736.321-0.002-0.0020.0000.0000.0000.000
168A1020VAL0-0.0230.01239.0990.0000.0000.0000.0000.0000.000
169A1021PRO0-0.031-0.02342.3680.0000.0000.0000.0000.0000.000
170A1022HIS00.0740.05339.5520.0000.0000.0000.0000.0000.000
171A1023LEU00.0270.02941.0450.0000.0000.0000.0000.0000.000
172A1024TYR0-0.017-0.05643.0410.0010.0010.0000.0000.0000.000
173A1025SER0-0.018-0.00945.5280.0000.0000.0000.0000.0000.000
174A1026CYS0-0.050-0.02342.8730.0000.0000.0000.0000.0000.000
175A1027LEU0-0.006-0.00845.4710.0010.0010.0000.0000.0000.000
176A1028GLU-1-0.810-0.85548.1600.0040.0040.0000.0000.0000.000
177A1029ASP-1-0.789-0.86845.8720.0010.0010.0000.0000.0000.000
178A1030ARG10.9860.99548.7790.0000.0000.0000.0000.0000.000
179A1031ASN0-0.038-0.03645.3020.0010.0010.0000.0000.0000.000
180A1032GLY00.0210.00347.8520.0000.0000.0000.0000.0000.000
181A1033ASP-1-0.829-0.90444.0750.0110.0110.0000.0000.0000.000
182A1034VAL0-0.062-0.01742.7320.0010.0010.0000.0000.0000.000
183A1035ARG10.8620.93844.233-0.006-0.0060.0000.0000.0000.000
184A1036LYS10.8470.91144.596-0.020-0.0200.0000.0000.0000.000
185A1037LYS10.8750.91437.865-0.015-0.0150.0000.0000.0000.000
186A1038ALA00.0020.00841.3600.0010.0010.0000.0000.0000.000
187A1039GLN0-0.029-0.03543.2410.0010.0010.0000.0000.0000.000
188A1040ASP-1-0.839-0.89841.3900.0230.0230.0000.0000.0000.000
189A1041ALA00.0070.00339.3260.0020.0020.0000.0000.0000.000
190A1042LEU0-0.0210.00140.4950.0010.0010.0000.0000.0000.000
191A1043PRO00.0380.00142.6020.0000.0000.0000.0000.0000.000
192A1044PHE00.0200.01037.3510.0010.0010.0000.0000.0000.000
193A1045PHE00.027-0.00238.0920.0010.0010.0000.0000.0000.000
194A1046MET0-0.019-0.00539.8350.0000.0000.0000.0000.0000.000
195A1047MET0-0.047-0.00935.9340.0000.0000.0000.0000.0000.000
196A1048HIS0-0.023-0.01333.2610.0000.0000.0000.0000.0000.000
197A1049LEU0-0.083-0.04038.157-0.002-0.0020.0000.0000.0000.000
198A1050GLY00.0300.01741.166-0.001-0.0010.0000.0000.0000.000
199A1051TYR00.002-0.04144.331-0.001-0.0010.0000.0000.0000.000
200A1052GLU-1-0.853-0.93847.5630.0120.0120.0000.0000.0000.000
201A1053LYS10.9040.97041.994-0.012-0.0120.0000.0000.0000.000
202A1054MET00.0190.02243.393-0.001-0.0010.0000.0000.0000.000
203A1055ALA00.0790.05246.607-0.001-0.0010.0000.0000.0000.000
204A1056LYS10.9550.98948.981-0.007-0.0070.0000.0000.0000.000
205A1057ALA0-0.025-0.01046.241-0.001-0.0010.0000.0000.0000.000
206A1058THR0-0.007-0.01348.290-0.001-0.0010.0000.0000.0000.000
207A1059GLY0-0.007-0.00251.132-0.001-0.0010.0000.0000.0000.000
208A1060LYS10.9390.96945.431-0.003-0.0030.0000.0000.0000.000
209A1061LEU0-0.0060.02549.535-0.001-0.0010.0000.0000.0000.000
210A1062LYS10.9070.93553.241-0.002-0.0020.0000.0000.0000.000
211A1063PRO00.0410.00556.5640.0010.0010.0000.0000.0000.000
212A1064THR00.0570.02057.7470.0000.0000.0000.0000.0000.000
213A1065SER0-0.019-0.03653.1530.0000.0000.0000.0000.0000.000
214A1066LYS10.7820.88654.068-0.003-0.0030.0000.0000.0000.000
215A1067ASP-1-0.894-0.93755.1180.0080.0080.0000.0000.0000.000
216A1068GLN00.004-0.01153.9820.0010.0010.0000.0000.0000.000
217A1069VAL0-0.007-0.00849.3890.0010.0010.0000.0000.0000.000
218A1070LEU00.0120.01051.4560.0010.0010.0000.0000.0000.000
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