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: 1NZMZ

Calculation Name: 4KF7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4KF7

Chain ID: A

ChEMBL ID:

UniProt ID: G2QD05

Base Structure: X-ray

Registration Date: 2023-09-24

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 1096
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -34057379.744862
FMO2-HF: Nuclear repulsion 33631708.963052
FMO2-HF: Total energy -425670.78181
FMO2-MP2: Total energy -426911.850211


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-1.5570.732-0.006-0.96-1.322-0.001
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.040 / q_NPA : -0.041
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].
3A3THR0-0.006-0.0053.460-0.8101.381-0.005-0.949-1.237-0.001
4A4LEU00.0040.0204.6281.0841.182-0.001-0.011-0.0850.000
5A5THR0-0.015-0.0337.042-0.013-0.0130.0000.0000.0000.000
6A6ASP-1-0.700-0.8668.1830.0700.0700.0000.0000.0000.000
7A7ARG10.8760.9517.279-1.047-1.0470.0000.0000.0000.000
8A8SER0-0.025-0.00612.744-0.034-0.0340.0000.0000.0000.000
9A9TYR00.0880.06414.522-0.041-0.0410.0000.0000.0000.000
10A10PHE0-0.023-0.00715.498-0.032-0.0320.0000.0000.0000.000
11A11PRO00.0090.01615.9190.0430.0430.0000.0000.0000.000
12A12PRO00.021-0.00215.627-0.008-0.0080.0000.0000.0000.000
13A13LEU00.1010.04917.878-0.017-0.0170.0000.0000.0000.000
14A14GLY00.0070.00421.068-0.014-0.0140.0000.0000.0000.000
15A15GLU-1-0.897-0.95419.0090.1670.1670.0000.0000.0000.000
16A16CYS0-0.0270.01021.123-0.012-0.0120.0000.0000.0000.000
17A17LEU0-0.008-0.00824.071-0.011-0.0110.0000.0000.0000.000
18A18SER0-0.0100.00026.004-0.007-0.0070.0000.0000.0000.000
19A19GLY00.0560.03226.857-0.008-0.0080.0000.0000.0000.000
20A20ASN0-0.079-0.02324.492-0.011-0.0110.0000.0000.0000.000
21A21LYS10.8300.90818.604-0.159-0.1590.0000.0000.0000.000
22A22ILE00.0170.00523.7070.0000.0000.0000.0000.0000.000
23A23ILE0-0.008-0.00821.5700.0010.0010.0000.0000.0000.000
24A24LEU0-0.0050.00222.053-0.008-0.0080.0000.0000.0000.000
25A25SER0-0.0140.00023.106-0.002-0.0020.0000.0000.0000.000
26A26TRP00.0780.00620.549-0.006-0.0060.0000.0000.0000.000
27A27ARG10.8310.90126.052-0.011-0.0110.0000.0000.0000.000
28A28LEU0-0.031-0.01327.499-0.004-0.0040.0000.0000.0000.000
29A29VAL00.0190.03023.576-0.004-0.0040.0000.0000.0000.000
30A30ALA00.0280.01426.874-0.006-0.0060.0000.0000.0000.000
31A31THR0-0.083-0.06129.738-0.001-0.0010.0000.0000.0000.000
32A32ALA0-0.061-0.05128.213-0.001-0.0010.0000.0000.0000.000
33A33LEU0-0.025-0.02026.150-0.004-0.0040.0000.0000.0000.000
34A34GLU-1-0.928-0.94130.584-0.015-0.0150.0000.0000.0000.000
35A35ASP-1-0.848-0.95034.290-0.031-0.0310.0000.0000.0000.000
36A36LEU0-0.038-0.00736.805-0.001-0.0010.0000.0000.0000.000
37A37ALA0-0.075-0.02632.5850.0000.0000.0000.0000.0000.000
38A38CYS00.0230.03932.699-0.003-0.0030.0000.0000.0000.000
39A39ASP-1-0.858-0.94931.586-0.015-0.0150.0000.0000.0000.000
40A40ARG10.8380.90030.4090.0110.0110.0000.0000.0000.000
41A41LEU00.0370.03626.7610.0040.0040.0000.0000.0000.000
42A42ARG10.9210.96526.5390.0300.0300.0000.0000.0000.000
43A43SER0-0.036-0.00926.2470.0020.0020.0000.0000.0000.000
44A44ALA00.0530.00922.413-0.003-0.0030.0000.0000.0000.000
45A45ALA00.0110.01321.5570.0020.0020.0000.0000.0000.000
46A46VAL00.0680.02821.4080.0050.0050.0000.0000.0000.000
47A47SER00.0010.00521.778-0.011-0.0110.0000.0000.0000.000
48A48ALA0-0.027-0.02817.446-0.013-0.0130.0000.0000.0000.000
49A49PHE0-0.015-0.00517.0020.0040.0040.0000.0000.0000.000
50A50LEU00.0390.01018.061-0.007-0.0070.0000.0000.0000.000
51A51ARG10.8920.95916.1700.0670.0670.0000.0000.0000.000
52A52ASP-1-0.846-0.92612.5190.0820.0820.0000.0000.0000.000
53A53GLY00.0540.02311.172-0.033-0.0330.0000.0000.0000.000
54A54TYR0-0.041-0.02611.071-0.054-0.0540.0000.0000.0000.000
55A55VAL00.0250.00512.581-0.018-0.0180.0000.0000.0000.000
56A56HIS0-0.008-0.01614.616-0.038-0.0380.0000.0000.0000.000
57A57GLN0-0.067-0.03410.6660.0380.0380.0000.0000.0000.000
58A58LEU0-0.026-0.00115.6010.0050.0050.0000.0000.0000.000
59A59LEU0-0.0070.00418.4270.0040.0040.0000.0000.0000.000
60A60ARG10.8670.95414.3080.2850.2850.0000.0000.0000.000
61A61GLU-1-0.884-0.93218.660-0.095-0.0950.0000.0000.0000.000
62A62PRO00.0570.02620.0660.0100.0100.0000.0000.0000.000
63A63THR0-0.048-0.03322.4620.0120.0120.0000.0000.0000.000
64A64LYS10.9200.95514.2270.1300.1300.0000.0000.0000.000
65A65THR0-0.0190.00219.5090.0130.0130.0000.0000.0000.000
66A66PHE0-0.030-0.02520.7500.0140.0140.0000.0000.0000.000
67A67ALA00.0260.03320.0600.0000.0000.0000.0000.0000.000
68A68PRO00.0830.04422.1720.0100.0100.0000.0000.0000.000
69A69PRO00.0020.01022.0930.0010.0010.0000.0000.0000.000
70A70THR00.0180.01419.061-0.003-0.0030.0000.0000.0000.000
71A71ASN0-0.018-0.03720.4370.0110.0110.0000.0000.0000.000
72A72GLU-1-0.932-0.95913.2130.0170.0170.0000.0000.0000.000
73A73THR00.0430.01515.7910.0130.0130.0000.0000.0000.000
74A74LYS10.9370.98117.696-0.063-0.0630.0000.0000.0000.000
75A75LEU0-0.013-0.00314.8310.0070.0070.0000.0000.0000.000
76A76ASP-1-0.872-0.94314.0170.2140.2140.0000.0000.0000.000
77A77PHE00.0000.00715.7670.0140.0140.0000.0000.0000.000
78A78GLU-1-0.927-0.96219.2220.1010.1010.0000.0000.0000.000
79A79THR0-0.023-0.01313.8650.0090.0090.0000.0000.0000.000
80A80LYS10.7640.88414.670-0.227-0.2270.0000.0000.0000.000
81A81THR0-0.096-0.06817.438-0.009-0.0090.0000.0000.0000.000
82A82GLY00.0320.03219.569-0.013-0.0130.0000.0000.0000.000
83A83ALA0-0.062-0.02717.9650.0030.0030.0000.0000.0000.000
84A84ILE0-0.0100.00119.865-0.005-0.0050.0000.0000.0000.000
85A92ASP-1-0.933-0.97033.2410.0560.0560.0000.0000.0000.000
86A93PRO0-0.041-0.02832.9240.0040.0040.0000.0000.0000.000
87A94TYR00.0410.01628.840-0.001-0.0010.0000.0000.0000.000
88A95ASN0-0.014-0.01232.6100.0010.0010.0000.0000.0000.000
89A96LEU00.0570.02125.229-0.001-0.0010.0000.0000.0000.000
90A97ASP-1-0.869-0.94528.7620.0750.0750.0000.0000.0000.000
91A98THR0-0.0090.01231.029-0.004-0.0040.0000.0000.0000.000
92A99ILE00.0130.00626.731-0.002-0.0020.0000.0000.0000.000
93A100LYS10.8650.92422.918-0.104-0.1040.0000.0000.0000.000
94A101ASP-1-0.928-0.96227.9260.0480.0480.0000.0000.0000.000
95A102ASP-1-0.811-0.88830.5380.0400.0400.0000.0000.0000.000
96A103ALA0-0.0270.00125.274-0.004-0.0040.0000.0000.0000.000
97A104ARG10.9700.97025.685-0.076-0.0760.0000.0000.0000.000
98A105TRP0-0.034-0.01528.215-0.003-0.0030.0000.0000.0000.000
99A106LEU00.0010.00827.591-0.003-0.0030.0000.0000.0000.000
100A107SER0-0.067-0.03025.498-0.003-0.0030.0000.0000.0000.000
101A108ARG10.9590.98427.544-0.041-0.0410.0000.0000.0000.000
102A109ASN00.011-0.00730.426-0.005-0.0050.0000.0000.0000.000
103A110VAL0-0.025-0.01029.030-0.003-0.0030.0000.0000.0000.000
104A111ASN0-0.044-0.01528.250-0.005-0.0050.0000.0000.0000.000
105A112ILE00.0160.02624.500-0.003-0.0030.0000.0000.0000.000
106A113ASN0-0.015-0.03819.4190.0180.0180.0000.0000.0000.000
107A114GLU-1-0.812-0.92521.5040.0590.0590.0000.0000.0000.000
108A115VAL0-0.0050.00516.4770.0040.0040.0000.0000.0000.000
109A116ALA00.0240.01019.7010.0040.0040.0000.0000.0000.000
110A117ALA00.004-0.00321.569-0.002-0.0020.0000.0000.0000.000
111A118LEU0-0.019-0.02020.4250.0000.0000.0000.0000.0000.000
112A119ARG10.8490.92119.551-0.059-0.0590.0000.0000.0000.000
113A120VAL00.0040.00522.733-0.003-0.0030.0000.0000.0000.000
114A121VAL0-0.002-0.00126.306-0.002-0.0020.0000.0000.0000.000
115A122ILE0-0.013-0.00622.758-0.001-0.0010.0000.0000.0000.000
116A123ILE00.0010.01024.442-0.002-0.0020.0000.0000.0000.000
117A124GLU-1-0.825-0.90627.6810.0340.0340.0000.0000.0000.000
118A125TYR0-0.029-0.00728.849-0.003-0.0030.0000.0000.0000.000
119A126GLN0-0.041-0.03925.602-0.004-0.0040.0000.0000.0000.000
120A127SER0-0.047-0.02830.486-0.004-0.0040.0000.0000.0000.000
121A128ARG10.9530.97433.215-0.045-0.0450.0000.0000.0000.000
122A129ALA0-0.0140.00236.054-0.003-0.0030.0000.0000.0000.000
123A130HIS00.0410.00835.080-0.004-0.0040.0000.0000.0000.000
124A131SER00.0070.00536.243-0.002-0.0020.0000.0000.0000.000
125A132HIS10.8480.93438.911-0.026-0.0260.0000.0000.0000.000
126A133LEU0-0.041-0.01341.630-0.001-0.0010.0000.0000.0000.000
127A134THR0-0.019-0.00939.902-0.001-0.0010.0000.0000.0000.000
128A135GLY00.0030.02342.910-0.001-0.0010.0000.0000.0000.000
129A136PRO00.0280.01744.854-0.001-0.0010.0000.0000.0000.000
130A137LEU0-0.040-0.02648.6160.0010.0010.0000.0000.0000.000
131A138SER0-0.016-0.00251.1090.0000.0000.0000.0000.0000.000
132A139THR00.033-0.01453.269-0.001-0.0010.0000.0000.0000.000
133A140GLN00.0080.00456.757-0.001-0.0010.0000.0000.0000.000
134A141ASP-1-0.859-0.94152.4190.0110.0110.0000.0000.0000.000
135A142VAL00.004-0.00155.415-0.001-0.0010.0000.0000.0000.000
136A143ALA00.0090.01257.436-0.001-0.0010.0000.0000.0000.000
137A144ASN0-0.015-0.00156.963-0.001-0.0010.0000.0000.0000.000
138A145VAL00.0090.00055.618-0.001-0.0010.0000.0000.0000.000
139A146GLN00.006-0.01458.8730.0000.0000.0000.0000.0000.000
140A147GLU-1-0.875-0.93062.0510.0050.0050.0000.0000.0000.000
141A148ALA0-0.081-0.04660.4930.0000.0000.0000.0000.0000.000
142A149ALA0-0.070-0.02361.848-0.001-0.0010.0000.0000.0000.000
143A150GLY00.0330.02463.4380.0000.0000.0000.0000.0000.000
144A151VAL0-0.061-0.02166.5590.0000.0000.0000.0000.0000.000
145A152GLY0-0.029-0.01869.0790.0000.0000.0000.0000.0000.000
146A153ASP-1-0.840-0.91070.9220.0000.0000.0000.0000.0000.000
147A154ALA0-0.031-0.04166.4660.0000.0000.0000.0000.0000.000
148A155GLN00.018-0.00965.0130.0000.0000.0000.0000.0000.000
149A156ALA00.0370.03464.2280.0000.0000.0000.0000.0000.000
150A157SER00.0180.00762.0630.0000.0000.0000.0000.0000.000
151A158ALA00.0360.01560.4830.0000.0000.0000.0000.0000.000
152A159ILE0-0.020-0.02159.8640.0010.0010.0000.0000.0000.000
153A160VAL0-0.003-0.01258.8420.0000.0000.0000.0000.0000.000
154A161ALA0-0.0120.00556.1300.0000.0000.0000.0000.0000.000
155A162LEU0-0.0170.00055.2200.0000.0000.0000.0000.0000.000
156A163LEU0-0.058-0.04455.7340.0010.0010.0000.0000.0000.000
157A164ASN0-0.0010.00252.9350.0010.0010.0000.0000.0000.000
158A165VAL0-0.0070.02750.8700.0000.0000.0000.0000.0000.000
159A166THR0-0.091-0.04849.8060.0010.0010.0000.0000.0000.000
160A167THR00.012-0.01451.7170.0010.0010.0000.0000.0000.000
161A168VAL0-0.040-0.00553.9310.0000.0000.0000.0000.0000.000
162A169ALA00.0890.03051.2930.0010.0010.0000.0000.0000.000
163A170ASP-1-0.833-0.84253.3740.0140.0140.0000.0000.0000.000
164A171ALA00.005-0.02251.0590.0010.0010.0000.0000.0000.000
165A172ASP-1-0.950-0.96750.0320.0210.0210.0000.0000.0000.000
166A173SER0-0.028-0.06850.0520.0010.0010.0000.0000.0000.000
167A174ALA00.0360.02548.1460.0010.0010.0000.0000.0000.000
168A175TRP0-0.072-0.04042.8250.0010.0010.0000.0000.0000.000
169A176ALA00.0210.00244.9170.0020.0020.0000.0000.0000.000
170A177ASP-1-0.880-0.93245.6310.0190.0190.0000.0000.0000.000
171A178PHE0-0.135-0.07238.5400.0010.0010.0000.0000.0000.000
172A179GLU-1-0.895-0.96340.0290.0350.0350.0000.0000.0000.000
173A180SER0-0.0290.00540.9200.0020.0020.0000.0000.0000.000
174A181GLU-1-0.937-0.98337.8570.0350.0350.0000.0000.0000.000
175A182THR00.0150.00238.7260.0000.0000.0000.0000.0000.000
176A183THR00.012-0.00940.048-0.001-0.0010.0000.0000.0000.000
177A184ARG10.8810.93334.460-0.040-0.0400.0000.0000.0000.000
178A185ARG10.9030.95333.977-0.037-0.0370.0000.0000.0000.000
179A186ARG10.9771.00235.711-0.017-0.0170.0000.0000.0000.000
180A187ARG10.8560.92335.780-0.030-0.0300.0000.0000.0000.000
181A188LEU0-0.0060.02230.2130.0000.0000.0000.0000.0000.000
182A189LEU00.0050.00932.0260.0000.0000.0000.0000.0000.000
183A190ALA00.0470.02833.726-0.002-0.0020.0000.0000.0000.000
184A191THR0-0.048-0.03529.555-0.002-0.0020.0000.0000.0000.000
185A192TYR00.0180.01327.285-0.002-0.0020.0000.0000.0000.000
186A193LEU00.0070.01229.945-0.003-0.0030.0000.0000.0000.000
187A194SER00.0240.01331.500-0.004-0.0040.0000.0000.0000.000
188A195GLU-1-0.820-0.89525.8920.0160.0160.0000.0000.0000.000
189A196ARG10.8450.92227.7890.0050.0050.0000.0000.0000.000
190A197ARG10.8510.93329.041-0.004-0.0040.0000.0000.0000.000
191A198SER0-0.042-0.06028.653-0.004-0.0040.0000.0000.0000.000
192A199PHE0-0.0230.00122.131-0.003-0.0030.0000.0000.0000.000
193A200LEU00.0470.03026.610-0.007-0.0070.0000.0000.0000.000
194A201ALA00.0090.01428.628-0.005-0.0050.0000.0000.0000.000
195A202ALA0-0.053-0.02626.049-0.003-0.0030.0000.0000.0000.000
196A203VAL00.0050.00224.108-0.006-0.0060.0000.0000.0000.000
197A204ASP-1-0.772-0.87426.592-0.051-0.0510.0000.0000.0000.000
198A205ALA00.012-0.00830.034-0.003-0.0030.0000.0000.0000.000
199A206LEU0-0.047-0.01822.601-0.002-0.0020.0000.0000.0000.000
200A207LEU00.0230.00325.399-0.007-0.0070.0000.0000.0000.000
201A208ALA00.0320.03628.228-0.003-0.0030.0000.0000.0000.000
202A209PHE0-0.018-0.00925.5620.0000.0000.0000.0000.0000.000
203A210LEU0-0.065-0.05323.718-0.003-0.0030.0000.0000.0000.000
204A211LEU0-0.020-0.01127.759-0.006-0.0060.0000.0000.0000.000
205A212HIS0-0.0070.01630.4960.0030.0030.0000.0000.0000.000
206A213SER0-0.030-0.01831.6280.0030.0030.0000.0000.0000.000
207A214ARG10.9280.95532.9010.0690.0690.0000.0000.0000.000
208A215ALA00.0980.06234.3360.0030.0030.0000.0000.0000.000
209A216PRO00.0070.00536.120-0.001-0.0010.0000.0000.0000.000
210A217GLY0-0.0170.00935.1000.0030.0030.0000.0000.0000.000
211A218THR00.003-0.03535.1330.0000.0000.0000.0000.0000.000
212A219GLY0-0.025-0.01534.034-0.001-0.0010.0000.0000.0000.000
213A220VAL0-0.0270.01532.828-0.002-0.0020.0000.0000.0000.000
214A221GLU-1-0.916-0.95530.346-0.064-0.0640.0000.0000.0000.000
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