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: MVKRZ

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 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 228
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2705683.344475
FMO2-HF: Nuclear repulsion 2616344.775224
FMO2-HF: Total energy -89338.569251
FMO2-MP2: Total energy -89598.258578


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.
-5.092-0.820.444-2.15-2.566-0.005
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 : -0.034 / q_NPA : -0.011
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].
3A855THR00.0480.0213.030-4.201-0.8200.205-1.832-1.754-0.002
4A856GLU-1-0.856-0.9215.153-0.234-0.117-0.001-0.004-0.1120.000
5A857ILE00.0320.0097.2870.0470.0470.0000.0000.0000.000
6A858SER0-0.043-0.04010.7470.0580.0580.0000.0000.0000.000
7A859ASP-1-0.924-0.95712.316-0.260-0.2600.0000.0000.0000.000
8A860LYS10.9540.97212.7860.1720.1720.0000.0000.0000.000
9A861ILE0-0.081-0.02615.2280.0300.0300.0000.0000.0000.000
10A862THR00.0520.03217.6040.0060.0060.0000.0000.0000.000
11A863SER00.008-0.01020.2860.0100.0100.0000.0000.0000.000
12A864GLU-1-0.910-0.95623.730-0.055-0.0550.0000.0000.0000.000
13A865LEU00.0050.01419.2710.0080.0080.0000.0000.0000.000
14A866VAL00.016-0.01021.7200.0080.0080.0000.0000.0000.000
15A867SER0-0.057-0.02224.1690.0080.0080.0000.0000.0000.000
16A868LYS10.8730.91425.4790.0460.0460.0000.0000.0000.000
17A869ILE00.0060.00122.4390.0060.0060.0000.0000.0000.000
18A870GLY0-0.035-0.02327.0170.0040.0040.0000.0000.0000.000
19A871ASP-1-0.801-0.88829.856-0.024-0.0240.0000.0000.0000.000
20A872LYS10.9620.96232.3500.0200.0200.0000.0000.0000.000
21A873ASN0-0.043-0.01435.0400.0040.0040.0000.0000.0000.000
22A874TRP00.0580.01333.659-0.001-0.0010.0000.0000.0000.000
23A875LYS10.9310.95532.4450.0090.0090.0000.0000.0000.000
24A876ILE00.0230.02930.0790.0000.0000.0000.0000.0000.000
25A877ARG10.7850.88328.9660.0150.0150.0000.0000.0000.000
26A878LYS10.8240.89727.6770.0040.0040.0000.0000.0000.000
27A879GLU-1-0.849-0.87726.822-0.028-0.0280.0000.0000.0000.000
28A880GLY00.0330.01424.494-0.003-0.0030.0000.0000.0000.000
29A881LEU0-0.013-0.02522.958-0.004-0.0040.0000.0000.0000.000
30A882ASP-1-0.796-0.88622.733-0.006-0.0060.0000.0000.0000.000
31A883GLU-1-0.927-0.95219.812-0.063-0.0630.0000.0000.0000.000
32A884VAL0-0.003-0.00718.037-0.005-0.0050.0000.0000.0000.000
33A885ALA0-0.0030.00117.674-0.004-0.0040.0000.0000.0000.000
34A886GLY00.0040.00318.1310.0100.0100.0000.0000.0000.000
35A887ILE0-0.006-0.00313.5310.0040.0040.0000.0000.0000.000
36A888ILE0-0.020-0.01013.257-0.013-0.0130.0000.0000.0000.000
37A889ASN0-0.073-0.04113.2670.0240.0240.0000.0000.0000.000
38A890ASP-1-0.971-0.97213.1650.0410.0410.0000.0000.0000.000
39A891ALA00.0370.0288.9740.0270.0270.0000.0000.0000.000
40A892LYS10.9190.9879.098-0.200-0.2000.0000.0000.0000.000
41A893PHE0-0.072-0.0656.6090.0400.0400.0000.0000.0000.000
42A894ILE00.012-0.0067.293-0.201-0.2010.0000.0000.0000.000
43A895GLN0-0.002-0.0122.852-0.5460.2280.240-0.314-0.700-0.003
44A896PRO00.009-0.0216.9660.0420.0420.0000.0000.0000.000
45A897ASN0-0.0130.0059.8990.0610.0610.0000.0000.0000.000
46A898ILE00.0210.00711.672-0.035-0.0350.0000.0000.0000.000
47A899GLY00.0780.02814.0510.0160.0160.0000.0000.0000.000
48A900GLU-1-0.907-0.96016.702-0.064-0.0640.0000.0000.0000.000
49A901LEU0-0.0030.00616.7170.0130.0130.0000.0000.0000.000
50A902PRO00.001-0.00817.8810.0130.0130.0000.0000.0000.000
51A903THR00.0110.00420.7820.0100.0100.0000.0000.0000.000
52A904ALA00.0070.00922.8620.0060.0060.0000.0000.0000.000
53A905LEU00.011-0.00919.9880.0060.0060.0000.0000.0000.000
54A906LYS10.9310.96824.1380.0340.0340.0000.0000.0000.000
55A907GLY0-0.0330.00026.3080.0040.0040.0000.0000.0000.000
56A908ARG10.8290.91526.7020.0240.0240.0000.0000.0000.000
57A909LEU00.0130.00425.9690.0030.0030.0000.0000.0000.000
58A910ASN0-0.032-0.01429.6030.0040.0040.0000.0000.0000.000
59A911ASP-1-0.756-0.84231.545-0.014-0.0140.0000.0000.0000.000
60A912SER00.0220.00633.5260.0010.0010.0000.0000.0000.000
61A913ASN0-0.068-0.03034.7100.0010.0010.0000.0000.0000.000
62A914LYS10.9290.92933.9060.0000.0000.0000.0000.0000.000
63A915ILE00.0310.00732.5880.0010.0010.0000.0000.0000.000
64A916LEU00.0010.00929.8130.0010.0010.0000.0000.0000.000
65A917VAL0-0.0020.02828.736-0.001-0.0010.0000.0000.0000.000
66A918GLN0-0.019-0.02428.4650.0000.0000.0000.0000.0000.000
67A919GLN0-0.036-0.02824.7860.0030.0030.0000.0000.0000.000
68A920THR00.003-0.00524.296-0.002-0.0020.0000.0000.0000.000
69A921LEU0-0.010-0.01223.588-0.001-0.0010.0000.0000.0000.000
70A922ASN00.0080.00123.5390.0050.0050.0000.0000.0000.000
71A923ILE00.0180.02219.1280.0050.0050.0000.0000.0000.000
72A924LEU00.003-0.00918.972-0.003-0.0030.0000.0000.0000.000
73A925GLN0-0.022-0.00819.2210.0070.0070.0000.0000.0000.000
74A926GLN0-0.040-0.02316.8290.0040.0040.0000.0000.0000.000
75A927LEU0-0.0020.00014.6260.0040.0040.0000.0000.0000.000
76A928ALA00.0000.01714.116-0.003-0.0030.0000.0000.0000.000
77A929VAL00.0120.00513.7500.0130.0130.0000.0000.0000.000
78A930ALA00.0100.01511.3410.0310.0310.0000.0000.0000.000
79A931MET0-0.0430.0139.661-0.018-0.0180.0000.0000.0000.000
80A932GLY0-0.0100.00510.2380.0290.0290.0000.0000.0000.000
81A933PRO00.0690.01111.451-0.024-0.0240.0000.0000.0000.000
82A934ASN0-0.028-0.0118.581-0.013-0.0130.0000.0000.0000.000
83A935ILE00.0080.00612.481-0.022-0.0220.0000.0000.0000.000
84A936LYS10.9700.97214.641-0.051-0.0510.0000.0000.0000.000
85A937GLN0-0.051-0.02212.9070.0100.0100.0000.0000.0000.000
86A938HIS0-0.015-0.00414.0320.0020.0020.0000.0000.0000.000
87A939VAL00.0070.01218.7640.0000.0000.0000.0000.0000.000
88A940LYS10.8490.92921.564-0.003-0.0030.0000.0000.0000.000
89A941ASN00.0080.00921.5130.0020.0020.0000.0000.0000.000
90A942LEU0-0.035-0.02419.376-0.001-0.0010.0000.0000.0000.000
91A943GLY00.0340.01622.7090.0020.0020.0000.0000.0000.000
92A944ILE00.0640.02023.6810.0030.0030.0000.0000.0000.000
93A945PRO0-0.007-0.00425.8030.0020.0020.0000.0000.0000.000
94A946ILE00.0040.01523.0310.0010.0010.0000.0000.0000.000
95A947ILE00.0080.01227.6780.0020.0020.0000.0000.0000.000
96A948THR0-0.053-0.02430.3980.0010.0010.0000.0000.0000.000
97A949VAL00.0020.00329.8560.0000.0000.0000.0000.0000.000
98A950LEU00.004-0.00131.5530.0010.0010.0000.0000.0000.000
99A951GLY0-0.015-0.00934.0630.0010.0010.0000.0000.0000.000
100A952ASP-1-0.810-0.89335.2520.0020.0020.0000.0000.0000.000
101A953SER00.020-0.00537.3030.0010.0010.0000.0000.0000.000
102A954LYS10.8950.95637.508-0.003-0.0030.0000.0000.0000.000
103A955ASN00.0900.03537.2710.0000.0000.0000.0000.0000.000
104A956ASN00.0370.01634.9880.0000.0000.0000.0000.0000.000
105A957VAL0-0.020-0.00232.5550.0010.0010.0000.0000.0000.000
106A958ARG10.8520.93832.335-0.010-0.0100.0000.0000.0000.000
107A959ALA00.0200.01432.6750.0010.0010.0000.0000.0000.000
108A960ALA00.0150.01228.7790.0030.0030.0000.0000.0000.000
109A961ALA00.0230.03327.9170.0010.0010.0000.0000.0000.000
110A962LEU00.0380.01828.0780.0010.0010.0000.0000.0000.000
111A963ALA0-0.006-0.00726.5960.0030.0030.0000.0000.0000.000
112A964THR00.001-0.01823.0710.0040.0040.0000.0000.0000.000
113A965VAL0-0.0020.00023.4060.0020.0020.0000.0000.0000.000
114A966ASN00.0400.01824.2480.0030.0030.0000.0000.0000.000
115A967ALA00.0380.02920.4590.0050.0050.0000.0000.0000.000
116A968TRP0-0.023-0.03519.4820.0050.0050.0000.0000.0000.000
117A969ALA0-0.011-0.00319.8480.0050.0050.0000.0000.0000.000
118A970GLU-1-0.998-0.98719.5510.0790.0790.0000.0000.0000.000
119A971GLN0-0.041-0.01814.5570.0210.0210.0000.0000.0000.000
120A972THR0-0.046-0.04317.0850.0040.0040.0000.0000.0000.000
121A973GLY0-0.043-0.00219.279-0.002-0.0020.0000.0000.0000.000
122A974MET00.0310.00222.411-0.003-0.0030.0000.0000.0000.000
123A975LYS10.9310.97024.360-0.026-0.0260.0000.0000.0000.000
124A976GLU-1-0.862-0.93922.6000.0050.0050.0000.0000.0000.000
125A977TRP0-0.042-0.02622.559-0.005-0.0050.0000.0000.0000.000
126A978LEU0-0.064-0.04226.922-0.002-0.0020.0000.0000.0000.000
127A979GLU-1-0.929-0.94627.7630.0020.0020.0000.0000.0000.000
128A980GLY00.0600.03829.801-0.001-0.0010.0000.0000.0000.000
129A981GLU-1-0.925-0.98332.140-0.001-0.0010.0000.0000.0000.000
130A982ASP-1-0.863-0.91929.894-0.003-0.0030.0000.0000.0000.000
131A983LEU00.0250.01030.9920.0000.0000.0000.0000.0000.000
132A984SER0-0.048-0.04232.8180.0000.0000.0000.0000.0000.000
133A985GLU-1-0.906-0.95735.200-0.001-0.0010.0000.0000.0000.000
134A986GLU-1-0.858-0.93232.604-0.002-0.0020.0000.0000.0000.000
135A987LEU0-0.038-0.02336.0010.0000.0000.0000.0000.0000.000
136A988LYS10.9590.97938.3000.0010.0010.0000.0000.0000.000
137A989LYS10.8400.92935.5110.0020.0020.0000.0000.0000.000
138A990GLU-1-0.946-0.96541.1810.0030.0030.0000.0000.0000.000
139A991ASN0-0.041-0.01739.8960.0010.0010.0000.0000.0000.000
140A992PRO00.0380.00641.5420.0010.0010.0000.0000.0000.000
141A993PHE0-0.011-0.01539.3710.0010.0010.0000.0000.0000.000
142A994LEU00.0400.02034.9220.0010.0010.0000.0000.0000.000
143A995ARG10.8770.92637.372-0.004-0.0040.0000.0000.0000.000
144A996GLN0-0.021-0.00939.3320.0020.0020.0000.0000.0000.000
145A997GLU-1-0.894-0.95334.8270.0180.0180.0000.0000.0000.000
146A998LEU0-0.0050.00732.6750.0020.0020.0000.0000.0000.000
147A999LEU0-0.021-0.02735.3140.0010.0010.0000.0000.0000.000
148A1000GLY0-0.017-0.00536.8170.0010.0010.0000.0000.0000.000
149A1001TRP0-0.003-0.01226.5880.0000.0000.0000.0000.0000.000
150A1002LEU0-0.014-0.01932.6170.0020.0020.0000.0000.0000.000
151A1003ALA0-0.016-0.00734.4500.0010.0010.0000.0000.0000.000
152A1004GLU-1-0.941-0.95830.5480.0350.0350.0000.0000.0000.000
153A1005LYS10.9530.96825.966-0.039-0.0390.0000.0000.0000.000
154A1006LEU0-0.001-0.00130.9550.0020.0020.0000.0000.0000.000
155A1007PRO00.0000.00933.3640.0000.0000.0000.0000.0000.000
156A1008THR0-0.079-0.02928.7180.0030.0030.0000.0000.0000.000
157A1009LEU0-0.045-0.01128.1840.0030.0030.0000.0000.0000.000
158A1010ARG10.9970.98620.493-0.069-0.0690.0000.0000.0000.000
159A1011SER0-0.069-0.03726.5390.0000.0000.0000.0000.0000.000
160A1012THR00.0340.00828.686-0.001-0.0010.0000.0000.0000.000
161A1013PRO00.0010.02231.455-0.001-0.0010.0000.0000.0000.000
162A1014THR0-0.020-0.02231.7210.0000.0000.0000.0000.0000.000
163A1015ASP-1-0.791-0.88233.0210.0050.0050.0000.0000.0000.000
164A1016LEU00.0220.02035.111-0.001-0.0010.0000.0000.0000.000
165A1017ILE0-0.035-0.03736.465-0.001-0.0010.0000.0000.0000.000
166A1018LEU00.0260.01335.758-0.001-0.0010.0000.0000.0000.000
167A1019CYS00.000-0.00235.917-0.001-0.0010.0000.0000.0000.000
168A1020VAL0-0.0260.00639.0800.0000.0000.0000.0000.0000.000
169A1021PRO0-0.042-0.02342.2330.0000.0000.0000.0000.0000.000
170A1022HIS00.0770.02939.9390.0000.0000.0000.0000.0000.000
171A1023LEU00.0180.02741.4230.0000.0000.0000.0000.0000.000
172A1024TYR0-0.018-0.05543.2340.0000.0000.0000.0000.0000.000
173A1025SER0-0.0130.00345.4660.0000.0000.0000.0000.0000.000
174A1026CYS0-0.047-0.01543.0680.0000.0000.0000.0000.0000.000
175A1027LEU0-0.002-0.00945.7500.0000.0000.0000.0000.0000.000
176A1028GLU-1-0.871-0.91148.2580.0060.0060.0000.0000.0000.000
177A1029ASP-1-0.821-0.88746.2370.0060.0060.0000.0000.0000.000
178A1030ARG10.9720.97549.036-0.004-0.0040.0000.0000.0000.000
179A1031ASN0-0.020-0.02146.2410.0010.0010.0000.0000.0000.000
180A1032GLY00.027-0.00148.0860.0000.0000.0000.0000.0000.000
181A1033ASP-1-0.855-0.92244.0520.0120.0120.0000.0000.0000.000
182A1034VAL0-0.088-0.04043.0570.0010.0010.0000.0000.0000.000
183A1035ARG10.8910.96444.636-0.008-0.0080.0000.0000.0000.000
184A1036LYS10.9260.97844.903-0.014-0.0140.0000.0000.0000.000
185A1037LYS10.9980.98839.032-0.017-0.0170.0000.0000.0000.000
186A1038ALA00.0110.01941.8290.0010.0010.0000.0000.0000.000
187A1039GLN0-0.046-0.04343.6640.0010.0010.0000.0000.0000.000
188A1040ASP-1-0.907-0.95341.3960.0170.0170.0000.0000.0000.000
189A1041ALA0-0.001-0.00439.5030.0010.0010.0000.0000.0000.000
190A1042LEU0-0.0060.00240.7880.0000.0000.0000.0000.0000.000
191A1043PRO00.0490.01342.6750.0000.0000.0000.0000.0000.000
192A1044PHE00.0170.00937.4680.0010.0010.0000.0000.0000.000
193A1045PHE00.002-0.00438.3830.0000.0000.0000.0000.0000.000
194A1046MET0-0.028-0.01040.0870.0000.0000.0000.0000.0000.000
195A1047MET0-0.0140.01236.6980.0000.0000.0000.0000.0000.000
196A1048HIS0-0.060-0.03533.9310.0000.0000.0000.0000.0000.000
197A1049LEU0-0.068-0.03738.747-0.001-0.0010.0000.0000.0000.000
198A1050GLY00.0320.01641.539-0.001-0.0010.0000.0000.0000.000
199A1051TYR0-0.047-0.11444.5540.0000.0000.0000.0000.0000.000
200A1052GLU-1-0.875-0.94247.9120.0080.0080.0000.0000.0000.000
201A1053LYS10.9270.98242.727-0.008-0.0080.0000.0000.0000.000
202A1054MET00.0120.00943.7700.0000.0000.0000.0000.0000.000
203A1055ALA00.1000.06746.842-0.001-0.0010.0000.0000.0000.000
204A1056LYS10.9651.00548.878-0.005-0.0050.0000.0000.0000.000
205A1057ALA0-0.074-0.03846.369-0.001-0.0010.0000.0000.0000.000
206A1058THR0-0.002-0.02548.406-0.001-0.0010.0000.0000.0000.000
207A1059GLY0-0.021-0.01151.2700.0000.0000.0000.0000.0000.000
208A1060LYS10.9020.95045.532-0.005-0.0050.0000.0000.0000.000
209A1061LEU0-0.0030.03049.6530.0000.0000.0000.0000.0000.000
210A1062LYS10.9830.98953.239-0.004-0.0040.0000.0000.0000.000
211A1063PRO00.006-0.01556.5700.0000.0000.0000.0000.0000.000
212A1064THR00.0750.02957.8950.0000.0000.0000.0000.0000.000
213A1065SER0-0.062-0.04753.4130.0000.0000.0000.0000.0000.000
214A1066LYS10.8970.94154.124-0.004-0.0040.0000.0000.0000.000
215A1067ASP-1-0.948-0.96255.1790.0070.0070.0000.0000.0000.000
216A1068GLN00.0150.01454.4420.0010.0010.0000.0000.0000.000
217A1069VAL00.009-0.00749.6960.0010.0010.0000.0000.0000.000
218A1070LEU00.0300.01151.7580.0010.0010.0000.0000.0000.000
219A1071ALA00.0420.03853.6960.0010.0010.0000.0000.0000.000
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