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: JQQL9

Calculation Name: 4D1E-A-Xray372

Preferred Name:

Target Type:

Ligand Name: n-methyl-lysine

ligand 3-letter code: MLZ

PDB ID: 4D1E

Chain ID: A

ChEMBL ID:

UniProt ID: P35609

Base Structure: X-ray

Registration Date: 2023-09-21

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 859
LigandResidueName
LigandFragmentNumber 0
LigandCharge MLZ=1
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -14279057.311247
FMO2-HF: Nuclear repulsion 13927109.054719
FMO2-HF: Total energy -351948.256528
FMO2-MP2: Total energy -352966.098535


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:34:PRO)


Summations of interaction energy for fragment #1(A:34: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.
-12.163-6.1612.143-3.352-4.791-0.016
Interaction energy analysis for fragmet #1(A:34:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.010 / q_NPA : -0.031
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].
3A36TRP00.012-0.0053.854-2.336-0.322-0.010-0.806-1.1980.002
4A37GLU-1-0.816-0.8892.306-5.685-2.6582.125-2.321-2.831-0.018
5A38LYS10.8520.9253.2160.3731.1110.030-0.203-0.5640.000
6A39GLN00.0560.0184.7340.1250.205-0.001-0.007-0.0710.000
7A40GLN0-0.037-0.0127.254-0.199-0.1990.0000.0000.0000.000
8A41ARG10.7670.8503.9730.6820.825-0.001-0.015-0.1270.000
9A42MLZ10.9000.9778.9830.3590.3590.0000.0000.0000.000
10A43THR0-0.007-0.00411.0580.0250.0250.0000.0000.0000.000
11A44PHE00.029-0.00212.1720.0100.0100.0000.0000.0000.000
12A45THR00.014-0.00112.140-0.009-0.0090.0000.0000.0000.000
13A46ALA00.0190.00914.738-0.002-0.0020.0000.0000.0000.000
14A47TRP00.0850.02316.6230.0050.0050.0000.0000.0000.000
15A48CYS0-0.071-0.01816.7880.0050.0050.0000.0000.0000.000
16A49ASN00.0490.01918.7290.0110.0110.0000.0000.0000.000
17A50SER0-0.043-0.02420.934-0.005-0.0050.0000.0000.0000.000
18A51HIS00.0510.02021.944-0.012-0.0120.0000.0000.0000.000
19A52LEU0-0.001-0.00621.098-0.003-0.0030.0000.0000.0000.000
20A53ARG10.8410.88924.6740.0030.0030.0000.0000.0000.000
21A54LYS10.8000.89426.445-0.046-0.0460.0000.0000.0000.000
22A55ALA0-0.027-0.01227.6720.0020.0020.0000.0000.0000.000
23A56GLY0-0.0180.00429.395-0.002-0.0020.0000.0000.0000.000
24A57THR0-0.040-0.02324.598-0.009-0.0090.0000.0000.0000.000
25A58GLN00.0450.01721.6500.0130.0130.0000.0000.0000.000
26A59ILE0-0.101-0.04216.1060.0050.0050.0000.0000.0000.000
27A60GLU-1-0.884-0.93517.550-0.143-0.1430.0000.0000.0000.000
28A61ASN0-0.020-0.02612.534-0.049-0.0490.0000.0000.0000.000
29A62ILE00.0150.00910.7150.0410.0410.0000.0000.0000.000
30A63GLU-1-0.863-0.9188.796-0.391-0.3910.0000.0000.0000.000
31A64GLU-1-0.922-0.96912.882-0.162-0.1620.0000.0000.0000.000
32A65ASP-1-0.768-0.87616.535-0.055-0.0550.0000.0000.0000.000
33A66PHE0-0.012-0.02916.3340.0090.0090.0000.0000.0000.000
34A67ARG10.8250.94415.5750.0470.0470.0000.0000.0000.000
35A68ASN0-0.058-0.01919.6280.0090.0090.0000.0000.0000.000
36A69GLY00.1100.04122.383-0.001-0.0010.0000.0000.0000.000
37A70LEU0-0.016-0.03123.1620.0090.0090.0000.0000.0000.000
38A71MLZ10.8520.90921.7750.0440.0440.0000.0000.0000.000
39A72LEU00.0350.02719.7330.0020.0020.0000.0000.0000.000
40A73MET0-0.061-0.01222.5340.0040.0040.0000.0000.0000.000
41A74LEU00.0320.01525.9530.0020.0020.0000.0000.0000.000
42A75LEU00.0100.01020.522-0.001-0.0010.0000.0000.0000.000
43A76LEU00.0110.00423.2750.0050.0050.0000.0000.0000.000
44A77GLU-1-0.850-0.90626.1450.0490.0490.0000.0000.0000.000
45A78VAL0-0.054-0.02327.059-0.002-0.0020.0000.0000.0000.000
46A79ILE0-0.047-0.01923.598-0.001-0.0010.0000.0000.0000.000
47A80SER0-0.066-0.03027.5350.0070.0070.0000.0000.0000.000
48A81GLY0-0.0150.00430.279-0.002-0.0020.0000.0000.0000.000
49A82GLU-1-0.815-0.89133.1670.0720.0720.0000.0000.0000.000
50A83ARG10.9170.95933.000-0.039-0.0390.0000.0000.0000.000
51A84LEU00.0110.02028.3990.0000.0000.0000.0000.0000.000
52A85PRO0-0.051-0.03732.045-0.007-0.0070.0000.0000.0000.000
53A86LYS10.9910.97532.793-0.030-0.0300.0000.0000.0000.000
54A87PRO00.0170.01629.6360.0000.0000.0000.0000.0000.000
55A88ASP-1-0.836-0.90931.5620.0190.0190.0000.0000.0000.000
56A89ARG10.8300.89930.421-0.014-0.0140.0000.0000.0000.000
57A90GLY00.0700.03930.151-0.003-0.0030.0000.0000.0000.000
58A91LYS10.9620.96828.1410.0380.0380.0000.0000.0000.000
59A92MET00.0220.03227.062-0.003-0.0030.0000.0000.0000.000
60A93ARG10.8710.87720.826-0.059-0.0590.0000.0000.0000.000
61A94PHE00.0670.02126.0350.0070.0070.0000.0000.0000.000
62A95HIS00.0350.02628.5970.0040.0040.0000.0000.0000.000
63A96MLZ10.9220.98122.9850.0100.0100.0000.0000.0000.000
64A97ILE00.0370.02423.6510.0090.0090.0000.0000.0000.000
65A98ALA00.0200.01825.5800.0100.0100.0000.0000.0000.000
66A99ASN0-0.042-0.03326.6280.0030.0030.0000.0000.0000.000
67A100VAL00.0540.01921.0280.0040.0040.0000.0000.0000.000
68A101ASN0-0.006-0.01524.3070.0210.0210.0000.0000.0000.000
69A102MLZ10.8860.95026.470-0.052-0.0520.0000.0000.0000.000
70A103ALA0-0.021-0.00324.229-0.001-0.0010.0000.0000.0000.000
71A104LEU00.000-0.00721.1440.0100.0100.0000.0000.0000.000
72A105ASP-1-0.867-0.93724.8050.1260.1260.0000.0000.0000.000
73A106TYR0-0.063-0.03427.5910.0010.0010.0000.0000.0000.000
74A107ILE00.016-0.00222.2340.0020.0020.0000.0000.0000.000
75A108ALA0-0.024-0.00826.3700.0040.0040.0000.0000.0000.000
76A109SER0-0.058-0.04427.369-0.002-0.0020.0000.0000.0000.000
77A110LYS10.8060.90028.844-0.095-0.0950.0000.0000.0000.000
78A111GLY00.0010.01329.038-0.001-0.0010.0000.0000.0000.000
79A112VAL0-0.008-0.00922.6940.0140.0140.0000.0000.0000.000
80A113LYS10.9060.95525.086-0.225-0.2250.0000.0000.0000.000
81A114LEU00.0410.02920.9220.0260.0260.0000.0000.0000.000
82A115VAL0-0.022-0.03519.926-0.026-0.0260.0000.0000.0000.000
83A116SER0-0.016-0.01317.9580.0160.0160.0000.0000.0000.000
84A117ILE00.0150.02515.3640.0350.0350.0000.0000.0000.000
85A118GLY00.0610.02917.985-0.021-0.0210.0000.0000.0000.000
86A119ALA00.0120.00619.1680.0080.0080.0000.0000.0000.000
87A120GLU-1-0.868-0.94520.3840.1610.1610.0000.0000.0000.000
88A121GLU-1-0.827-0.91914.7790.2260.2260.0000.0000.0000.000
89A122ILE0-0.023-0.01215.6900.0030.0030.0000.0000.0000.000
90A123VAL0-0.024-0.01617.090-0.029-0.0290.0000.0000.0000.000
91A124ASP-1-0.830-0.86516.6230.0350.0350.0000.0000.0000.000
92A125GLY0-0.018-0.01314.503-0.035-0.0350.0000.0000.0000.000
93A126ASN0-0.032-0.02610.5080.0760.0760.0000.0000.0000.000
94A127VAL00.0760.0406.3580.1030.1030.0000.0000.0000.000
95A128LYS10.9540.9755.207-1.384-1.3840.0000.0000.0000.000
96A129MET00.0110.0108.9390.0460.0460.0000.0000.0000.000
97A130THR0-0.007-0.00512.172-0.038-0.0380.0000.0000.0000.000
98A131LEU00.002-0.0078.429-0.051-0.0510.0000.0000.0000.000
99A132GLY0-0.0020.00511.6490.0030.0030.0000.0000.0000.000
100A133MET00.0070.00713.311-0.053-0.0530.0000.0000.0000.000
101A134ILE00.0130.01814.463-0.036-0.0360.0000.0000.0000.000
102A135TRP00.0320.00613.994-0.001-0.0010.0000.0000.0000.000
103A136THR0-0.071-0.04815.925-0.042-0.0420.0000.0000.0000.000
104A137ILE00.0130.01519.120-0.031-0.0310.0000.0000.0000.000
105A138ILE00.0120.00416.014-0.021-0.0210.0000.0000.0000.000
106A139LEU0-0.011-0.00819.679-0.019-0.0190.0000.0000.0000.000
107A140ARG10.8580.92121.310-0.175-0.1750.0000.0000.0000.000
108A141PHE0-0.028-0.04123.699-0.015-0.0150.0000.0000.0000.000
109A142ALA0-0.0020.01822.538-0.016-0.0160.0000.0000.0000.000
110A143ILE0-0.037-0.01319.3500.0020.0020.0000.0000.0000.000
111A144GLN0-0.003-0.01923.901-0.001-0.0010.0000.0000.0000.000
112A145ASP-1-0.901-0.94826.3410.1170.1170.0000.0000.0000.000
113A146ILE0-0.0320.01527.386-0.011-0.0110.0000.0000.0000.000
114A147SER00.015-0.01530.3800.0100.0100.0000.0000.0000.000
115A148VAL0-0.063-0.02632.090-0.009-0.0090.0000.0000.0000.000
116A149GLU-1-0.800-0.88034.5010.0890.0890.0000.0000.0000.000
117A150GLU-1-0.907-0.93736.5820.0960.0960.0000.0000.0000.000
118A151THR0-0.044-0.00731.0490.0100.0100.0000.0000.0000.000
119A152SER00.038-0.00430.032-0.010-0.0100.0000.0000.0000.000
120A153ALA00.0020.01425.9200.0130.0130.0000.0000.0000.000
121A154LYS10.8940.94519.361-0.391-0.3910.0000.0000.0000.000
122A155GLU-1-0.834-0.93524.4360.2050.2050.0000.0000.0000.000
123A156GLY00.0310.02027.172-0.013-0.0130.0000.0000.0000.000
124A157LEU0-0.005-0.00222.655-0.012-0.0120.0000.0000.0000.000
125A158LEU0-0.039-0.00823.624-0.010-0.0100.0000.0000.0000.000
126A159LEU00.0020.00626.448-0.011-0.0110.0000.0000.0000.000
127A160TRP0-0.002-0.02427.784-0.011-0.0110.0000.0000.0000.000
128A161CYS0-0.040-0.02225.706-0.010-0.0100.0000.0000.0000.000
129A162GLN0-0.0030.01228.077-0.015-0.0150.0000.0000.0000.000
130A163ARG10.7920.86729.928-0.095-0.0950.0000.0000.0000.000
131A164MLZ10.8010.91030.838-0.077-0.0770.0000.0000.0000.000
132A165THR0-0.023-0.04127.987-0.007-0.0070.0000.0000.0000.000
133A166ALA00.0310.03431.300-0.005-0.0050.0000.0000.0000.000
134A167PRO0-0.045-0.02933.715-0.004-0.0040.0000.0000.0000.000
135A168TYR0-0.024-0.02531.613-0.003-0.0030.0000.0000.0000.000
136A169ARG10.9110.94032.196-0.040-0.0400.0000.0000.0000.000
137A170ASN0-0.0050.00529.4770.0050.0050.0000.0000.0000.000
138A171VAL0-0.0060.01526.8250.0030.0030.0000.0000.0000.000
139A172ASN00.0030.00527.1100.0090.0090.0000.0000.0000.000
140A173ILE0-0.053-0.02124.5790.0090.0090.0000.0000.0000.000
141A174GLN0-0.022-0.01124.1410.0060.0060.0000.0000.0000.000
142A175ASN0-0.004-0.00819.081-0.010-0.0100.0000.0000.0000.000
143A176PHE00.0390.00218.466-0.011-0.0110.0000.0000.0000.000
144A177HIS00.021-0.01215.0130.0160.0160.0000.0000.0000.000
145A178THR00.0400.00816.249-0.029-0.0290.0000.0000.0000.000
146A179SER00.0070.01818.076-0.025-0.0250.0000.0000.0000.000
147A180TRP00.0430.01518.794-0.027-0.0270.0000.0000.0000.000
148A181MLZ10.8000.91214.245-0.053-0.0530.0000.0000.0000.000
149A182ASP-1-0.807-0.91418.2500.0140.0140.0000.0000.0000.000
150A183GLY00.0380.01620.847-0.021-0.0210.0000.0000.0000.000
151A184LEU0-0.0150.00722.0200.0000.0000.0000.0000.0000.000
152A185GLY00.0350.00424.5750.0000.0000.0000.0000.0000.000
153A186LEU0-0.026-0.01920.0450.0050.0050.0000.0000.0000.000
154A187CYS0-0.0070.00124.056-0.005-0.0050.0000.0000.0000.000
155A188ALA0-0.0230.00626.878-0.003-0.0030.0000.0000.0000.000
156A189LEU00.002-0.00625.607-0.002-0.0020.0000.0000.0000.000
157A190ILE00.0250.03625.664-0.001-0.0010.0000.0000.0000.000
158A191HIS00.0380.03729.7680.0020.0020.0000.0000.0000.000
159A192ARG10.8620.93632.356-0.043-0.0430.0000.0000.0000.000
160A193HIS0-0.043-0.03031.1020.0040.0040.0000.0000.0000.000
161A194ARG10.8460.89332.945-0.011-0.0110.0000.0000.0000.000
162A195PRO00.0340.01234.191-0.004-0.0040.0000.0000.0000.000
163A196ASP-1-0.849-0.89236.3100.0020.0020.0000.0000.0000.000
164A197LEU0-0.0260.00130.829-0.004-0.0040.0000.0000.0000.000
165A198ILE0-0.036-0.01928.871-0.006-0.0060.0000.0000.0000.000
166A199ASP-1-0.780-0.86232.989-0.010-0.0100.0000.0000.0000.000
167A200TYR00.000-0.02628.831-0.004-0.0040.0000.0000.0000.000
168A201SER0-0.034-0.03832.5870.0010.0010.0000.0000.0000.000
169A202LYS10.8110.90132.3180.0250.0250.0000.0000.0000.000
170A203LEU0-0.0110.01927.820-0.007-0.0070.0000.0000.0000.000
171A204ASN00.003-0.00428.4340.0160.0160.0000.0000.0000.000
172A205LYS10.9350.96024.147-0.012-0.0120.0000.0000.0000.000
173A206ASP-1-0.885-0.94124.351-0.041-0.0410.0000.0000.0000.000
174A207ASP-1-0.814-0.89723.015-0.120-0.1200.0000.0000.0000.000
175A208PRO0-0.0150.00419.6570.0040.0040.0000.0000.0000.000
176A209ILE0-0.016-0.01216.7670.0050.0050.0000.0000.0000.000
177A210GLY00.0360.01819.548-0.002-0.0020.0000.0000.0000.000
178A211ASN0-0.053-0.04122.8260.0040.0040.0000.0000.0000.000
179A212ILE0-0.020-0.01516.9680.0110.0110.0000.0000.0000.000
180A213ASN0-0.013-0.02019.9430.0050.0050.0000.0000.0000.000
181A214LEU00.0350.02921.0020.0030.0030.0000.0000.0000.000
182A215ALA00.024-0.00222.4670.0070.0070.0000.0000.0000.000
183A216MET0-0.100-0.04016.5310.0050.0050.0000.0000.0000.000
184A217GLU-1-0.869-0.92221.756-0.065-0.0650.0000.0000.0000.000
185A218ILE00.0010.01224.6970.0040.0040.0000.0000.0000.000
186A219ALA00.0350.01924.6100.0050.0050.0000.0000.0000.000
187A220GLU-1-0.880-0.94823.216-0.057-0.0570.0000.0000.0000.000
188A221LYS10.8050.89426.1630.0470.0470.0000.0000.0000.000
189A222HIS0-0.045-0.04229.287-0.003-0.0030.0000.0000.0000.000
190A223LEU0-0.047-0.02128.0410.0040.0040.0000.0000.0000.000
191A224ASP-1-0.821-0.86327.870-0.002-0.0020.0000.0000.0000.000
192A225ILE00.0140.01523.7940.0090.0090.0000.0000.0000.000
193A226PRO00.0470.02019.917-0.006-0.0060.0000.0000.0000.000
194A227LYS10.8700.94719.1430.1080.1080.0000.0000.0000.000
195A228MET0-0.055-0.02116.208-0.029-0.0290.0000.0000.0000.000
196A229LEU00.023-0.01013.8940.0600.0600.0000.0000.0000.000
197A230ASP-1-0.867-0.9388.924-0.747-0.7470.0000.0000.0000.000
198A231ALA00.017-0.00211.9750.0060.0060.0000.0000.0000.000
199A232GLU-1-0.830-0.8889.178-0.996-0.9960.0000.0000.0000.000
200A233ASP-1-0.758-0.8796.496-1.273-1.2730.0000.0000.0000.000
201A234ILE0-0.053-0.00910.0190.1630.1630.0000.0000.0000.000
202A235VAL00.0410.01913.1780.0500.0500.0000.0000.0000.000
203A236ASN0-0.018-0.01611.1740.0610.0610.0000.0000.0000.000
204A237THR0-0.039-0.0288.3290.0240.0240.0000.0000.0000.000
205A238PRO0-0.013-0.00910.0070.0370.0370.0000.0000.0000.000
206A239MLZ10.9160.95711.546-0.775-0.7750.0000.0000.0000.000
207A240PRO00.0000.00810.9510.1890.1890.0000.0000.0000.000
208A241ASP-1-0.793-0.9029.0351.3591.3590.0000.0000.0000.000
209A242GLU-1-0.843-0.92511.0940.3550.3550.0000.0000.0000.000
210A243ARG10.8970.96110.748-1.109-1.1090.0000.0000.0000.000
211A244ALA0-0.0280.00011.122-0.112-0.1120.0000.0000.0000.000
212A245ILE00.0250.01813.242-0.082-0.0820.0000.0000.0000.000
213A246MET0-0.0260.01016.254-0.046-0.0460.0000.0000.0000.000
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