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

tag_button

FMODB ID: Z697N

Calculation Name: 1XL3-A-Xray372

Preferred Name:

Target Type:

Ligand Name: n-dimethyl-lysine

ligand 3-letter code: MLY

PDB ID: 1XL3

Chain ID: A

ChEMBL ID:

UniProt ID: P69968

Base Structure: X-ray

Registration Date: 2023-06-26

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 206
LigandCharge MLY=1
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2237822.107947
FMO2-HF: Nuclear repulsion 2156821.926847
FMO2-HF: Total energy -81000.1811
FMO2-MP2: Total energy -81239.182363


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:78:ALA)


Summations of interaction energy for fragment #1(A:78:ALA)
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.
-10.182-4.3721.28-3.004-4.0870.005
Interaction energy analysis for fragmet #1(A:78:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.007 / q_NPA : -0.003
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].
3A80VAL00.0270.0123.082-4.383-1.2400.442-1.676-1.9090.012
4A81SER00.015-0.0012.289-6.297-3.9520.836-1.272-1.909-0.007
5A82ASP-1-0.895-0.9313.864-1.111-0.7890.002-0.056-0.2690.000
6A83VAL00.004-0.0026.4070.1630.1630.0000.0000.0000.000
7A84GLU-1-0.845-0.9286.6770.0990.0990.0000.0000.0000.000
8A85GLU-1-0.990-0.9837.950-0.778-0.7780.0000.0000.0000.000
9A86GLN0-0.007-0.0109.7790.1180.1180.0000.0000.0000.000
10A87VAL00.0130.00011.5900.0160.0160.0000.0000.0000.000
11A88ASN00.000-0.00711.2300.0380.0380.0000.0000.0000.000
12A89GLN0-0.0210.00114.102-0.034-0.0340.0000.0000.0000.000
13A90TYR0-0.0010.00016.103-0.003-0.0030.0000.0000.0000.000
14A91LEU00.008-0.01217.0050.0040.0040.0000.0000.0000.000
15A92SER0-0.042-0.01118.4230.0070.0070.0000.0000.0000.000
16A93MLY10.8590.93819.8630.0590.0590.0000.0000.0000.000
17A94VAL0-0.0170.00422.235-0.001-0.0010.0000.0000.0000.000
18A95PRO0-0.027-0.01422.5940.0100.0100.0000.0000.0000.000
19A96GLU-1-0.855-0.94322.7320.0370.0370.0000.0000.0000.000
20A97LEU0-0.085-0.03918.5250.0190.0190.0000.0000.0000.000
21A98GLU-1-0.950-0.95122.8660.0080.0080.0000.0000.0000.000
22A99GLN00.022-0.00125.5280.0060.0060.0000.0000.0000.000
23A100LYS10.8730.91925.245-0.083-0.0830.0000.0000.0000.000
24A101GLN00.0280.01721.6370.0070.0070.0000.0000.0000.000
25A102ASN00.0180.01222.557-0.019-0.0190.0000.0000.0000.000
26A103VAL00.0110.00518.1380.0060.0060.0000.0000.0000.000
27A104SER00.0430.01320.7700.0100.0100.0000.0000.0000.000
28A105GLU-1-0.891-0.94923.6630.1050.1050.0000.0000.0000.000
29A106LEU00.017-0.00119.7640.0010.0010.0000.0000.0000.000
30A107LEU00.0170.02719.8640.0070.0070.0000.0000.0000.000
31A108SER0-0.0060.00422.5510.0020.0020.0000.0000.0000.000
32A109LEU0-0.0180.00425.330-0.005-0.0050.0000.0000.0000.000
33A110LEU00.0080.01019.6640.0040.0040.0000.0000.0000.000
34A111SER0-0.057-0.04023.711-0.004-0.0040.0000.0000.0000.000
35A112ASN0-0.086-0.03824.880-0.013-0.0130.0000.0000.0000.000
36A113SER0-0.048-0.02626.7550.0110.0110.0000.0000.0000.000
37A114PRO00.0850.03723.9770.0110.0110.0000.0000.0000.000
38A115ASN0-0.066-0.03823.7030.0170.0170.0000.0000.0000.000
39A116ILE00.0030.02121.198-0.004-0.0040.0000.0000.0000.000
40A117SER00.011-0.00421.3510.0170.0170.0000.0000.0000.000
41A118LEU00.039-0.00214.698-0.005-0.0050.0000.0000.0000.000
42A119SER0-0.018-0.02118.6150.0150.0150.0000.0000.0000.000
43A120GLN00.1130.06820.924-0.001-0.0010.0000.0000.0000.000
44A121LEU0-0.0080.01215.994-0.011-0.0110.0000.0000.0000.000
45A122MLY10.9750.97015.729-0.447-0.4470.0000.0000.0000.000
46A123ALA00.0670.04419.168-0.012-0.0120.0000.0000.0000.000
47A124TYR0-0.034-0.01821.737-0.024-0.0240.0000.0000.0000.000
48A125LEU0-0.031-0.03716.691-0.017-0.0170.0000.0000.0000.000
49A126GLU-1-0.927-0.95120.8520.2240.2240.0000.0000.0000.000
50A127GLY0-0.040-0.00522.487-0.020-0.0200.0000.0000.0000.000
51A128MLY10.8360.91522.501-0.148-0.1480.0000.0000.0000.000
52A129SER0-0.010-0.01020.899-0.013-0.0130.0000.0000.0000.000
53A130GLU-1-0.823-0.91021.9820.1460.1460.0000.0000.0000.000
54A131GLU-1-0.747-0.80519.4180.1890.1890.0000.0000.0000.000
55A132PRO00.0340.01016.8960.0210.0210.0000.0000.0000.000
56A133SER0-0.017-0.04315.0860.0500.0500.0000.0000.0000.000
57A134GLU-1-0.846-0.93815.4240.1570.1570.0000.0000.0000.000
58A135GLN0-0.064-0.03416.7710.0470.0470.0000.0000.0000.000
59A136PHE00.031-0.0057.507-0.014-0.0140.0000.0000.0000.000
60A137MLY10.9450.97412.375-0.044-0.0440.0000.0000.0000.000
61A138MET0-0.042-0.01614.182-0.022-0.0220.0000.0000.0000.000
62A139LEU0-0.0020.00611.996-0.031-0.0310.0000.0000.0000.000
63A140CYS0-0.0020.0119.6660.0570.0570.0000.0000.0000.000
64A141GLY00.0070.01211.338-0.079-0.0790.0000.0000.0000.000
65A142LEU0-0.050-0.04614.856-0.043-0.0430.0000.0000.0000.000
66A143ARG10.8110.9186.748-0.489-0.4890.0000.0000.0000.000
67A144ASP-1-0.863-0.93411.5330.0190.0190.0000.0000.0000.000
68A145ALA0-0.046-0.01913.785-0.036-0.0360.0000.0000.0000.000
69A146LEU0-0.014-0.01113.700-0.012-0.0120.0000.0000.0000.000
70A147MLY10.9030.95212.1580.0800.0800.0000.0000.0000.000
71A148GLY0-0.041-0.02016.002-0.017-0.0170.0000.0000.0000.000
72A149ARG10.9310.97419.256-0.092-0.0920.0000.0000.0000.000
73A150PRO00.0190.00817.3380.0190.0190.0000.0000.0000.000
74A151GLU-1-0.939-0.97119.7450.0630.0630.0000.0000.0000.000
75A152LEU0-0.025-0.02021.1740.0050.0050.0000.0000.0000.000
76A153ALA0-0.0120.03419.8550.0120.0120.0000.0000.0000.000
77A154HIS00.012-0.03714.2560.0340.0340.0000.0000.0000.000
78A155LEU00.0460.01316.497-0.006-0.0060.0000.0000.0000.000
79A156SER00.0380.02213.1500.0130.0130.0000.0000.0000.000
80A157HIS0-0.0220.00112.3570.0900.0900.0000.0000.0000.000
81A158LEU0-0.023-0.00212.2700.1010.1010.0000.0000.0000.000
82A159VAL00.0180.00911.3120.0770.0770.0000.0000.0000.000
83A160GLU-1-0.857-0.9367.5801.0201.0200.0000.0000.0000.000
84A161GLN0-0.034-0.0198.4570.3020.3020.0000.0000.0000.000
85A162ALA0-0.056-0.02910.8710.0570.0570.0000.0000.0000.000
86A163LEU00.0320.0167.4420.0090.0090.0000.0000.0000.000
87A164VAL00.0120.0085.0510.3400.3400.0000.0000.0000.000
88A165SER0-0.060-0.0157.563-0.278-0.2780.0000.0000.0000.000
89A166MET00.0060.00410.872-0.084-0.0840.0000.0000.0000.000
90A167ALA0-0.021-0.0116.932-0.148-0.1480.0000.0000.0000.000
91A168GLU-1-0.995-1.0027.1470.8200.8200.0000.0000.0000.000
92A169GLU-1-0.942-0.9719.4420.3090.3090.0000.0000.0000.000
93A170GLN0-0.036-0.02512.442-0.047-0.0470.0000.0000.0000.000
94A171GLY00.0510.03111.482-0.043-0.0430.0000.0000.0000.000
95A172GLU-1-0.896-0.95812.1390.0360.0360.0000.0000.0000.000
96A173THR00.0440.00315.268-0.028-0.0280.0000.0000.0000.000
97A174ILE0-0.0420.00812.130-0.041-0.0410.0000.0000.0000.000
98A175VAL00.0280.00712.501-0.031-0.0310.0000.0000.0000.000
99A176LEU0-0.022-0.01215.077-0.034-0.0340.0000.0000.0000.000
100A177GLY00.0290.02118.259-0.017-0.0170.0000.0000.0000.000
101A178ALA0-0.0150.00515.922-0.014-0.0140.0000.0000.0000.000
102A179ARG10.7800.87217.940-0.021-0.0210.0000.0000.0000.000
103A180ILE0-0.0210.00819.736-0.012-0.0120.0000.0000.0000.000
104A181THR00.0090.00320.9720.0030.0030.0000.0000.0000.000
105A182PRO00.0060.00021.909-0.001-0.0010.0000.0000.0000.000
106A183GLU-1-0.868-0.93524.9190.0020.0020.0000.0000.0000.000
107A184ALA00.0120.00326.1870.0000.0000.0000.0000.0000.000
108A185TYR0-0.0060.00626.652-0.002-0.0020.0000.0000.0000.000
109A186ARG10.8960.96928.503-0.013-0.0130.0000.0000.0000.000
110A187GLU-1-0.803-0.88331.1340.0250.0250.0000.0000.0000.000
111A188SER0-0.063-0.06230.9030.0020.0020.0000.0000.0000.000
112A189GLN0-0.034-0.01632.058-0.002-0.0020.0000.0000.0000.000
113A190SER0-0.033-0.02534.6820.0000.0000.0000.0000.0000.000
114A191GLY0-0.0240.00836.785-0.001-0.0010.0000.0000.0000.000
115A192VAL0-0.055-0.02837.8150.0030.0030.0000.0000.0000.000
116A193ASN0-0.010-0.00534.4730.0040.0040.0000.0000.0000.000
117A194PRO00.0230.00632.4560.0000.0000.0000.0000.0000.000
118A195LEU00.0710.02625.7300.0000.0000.0000.0000.0000.000
119A196GLN00.0350.02123.364-0.005-0.0050.0000.0000.0000.000
120A197PRO00.0670.02727.2760.0040.0040.0000.0000.0000.000
121A198LEU0-0.0090.02228.826-0.002-0.0020.0000.0000.0000.000
122A199ARG10.7980.87922.042-0.116-0.1160.0000.0000.0000.000
123A200ASP-1-0.866-0.94025.0000.1260.1260.0000.0000.0000.000
124A201THR0-0.052-0.03526.224-0.001-0.0010.0000.0000.0000.000
125A202TYR0-0.085-0.09622.176-0.002-0.0020.0000.0000.0000.000
126A203ARG10.8050.88119.549-0.158-0.1580.0000.0000.0000.000
127A204ASP-1-0.790-0.89324.0060.1010.1010.0000.0000.0000.000
128A205ALA0-0.068-0.03726.443-0.005-0.0050.0000.0000.0000.000
129A206VAL0-0.033-0.01422.149-0.008-0.0080.0000.0000.0000.000
130A207MET0-0.036-0.01318.6460.0020.0020.0000.0000.0000.000
131A208GLY0-0.053-0.02123.3720.0050.0050.0000.0000.0000.000
132A209TYR0-0.087-0.09326.300-0.001-0.0010.0000.0000.0000.000
133A210GLN0-0.006-0.02029.461-0.004-0.0040.0000.0000.0000.000
134A211GLY0-0.0140.00932.490-0.002-0.0020.0000.0000.0000.000
135A212ILE00.0430.01235.4240.0030.0030.0000.0000.0000.000
136A213TYR0-0.003-0.00437.7240.0000.0000.0000.0000.0000.000
137A214ALA00.0390.04234.2350.0010.0010.0000.0000.0000.000
138A215ILE00.0570.03132.1830.0020.0020.0000.0000.0000.000
139A216TRP00.0130.00435.0280.0010.0010.0000.0000.0000.000
140A217SER0-0.035-0.04237.6010.0000.0000.0000.0000.0000.000
141A218ASP-1-0.890-0.95732.4210.0690.0690.0000.0000.0000.000
142A219LEU0-0.047-0.02234.4960.0020.0020.0000.0000.0000.000
143A220GLN0-0.009-0.00936.2960.0010.0010.0000.0000.0000.000
144A221MLY10.8960.95630.606-0.081-0.0810.0000.0000.0000.000
145A222ARG10.7850.88928.817-0.081-0.0810.0000.0000.0000.000
146A223PHE0-0.0160.00232.0400.0020.0020.0000.0000.0000.000
147A224PRO0-0.0070.00837.545-0.004-0.0040.0000.0000.0000.000
148A225ASN0-0.061-0.03740.443-0.005-0.0050.0000.0000.0000.000
149A226GLY00.0490.02538.8170.0000.0000.0000.0000.0000.000
150A227ASP-1-0.912-0.96938.9790.0200.0200.0000.0000.0000.000
151A228ILE00.0590.00938.3430.0000.0000.0000.0000.0000.000
152A229ASP-1-0.915-0.95538.4200.0180.0180.0000.0000.0000.000
153A230SER0-0.078-0.03737.052-0.003-0.0030.0000.0000.0000.000
154A231VAL00.0400.02533.159-0.001-0.0010.0000.0000.0000.000
155A232ILE0-0.005-0.00934.064-0.001-0.0010.0000.0000.0000.000
156A233LEU0-0.027-0.00635.219-0.003-0.0030.0000.0000.0000.000
157A234PHE0-0.009-0.01227.631-0.005-0.0050.0000.0000.0000.000
158A235LEU00.0260.01029.508-0.002-0.0020.0000.0000.0000.000
159A236GLN0-0.022-0.01030.881-0.006-0.0060.0000.0000.0000.000
160A237MLY10.9140.96431.879-0.005-0.0050.0000.0000.0000.000
161A238ALA00.0110.01526.889-0.005-0.0050.0000.0000.0000.000
162A239LEU00.0460.01527.272-0.005-0.0050.0000.0000.0000.000
163A240SER0-0.039-0.02828.712-0.007-0.0070.0000.0000.0000.000
164A241ALA0-0.024-0.00626.868-0.006-0.0060.0000.0000.0000.000
165A242ASP-1-0.738-0.82224.240-0.012-0.0120.0000.0000.0000.000
166A243LEU0-0.039-0.02525.204-0.011-0.0110.0000.0000.0000.000
167A244GLN0-0.064-0.03627.902-0.005-0.0050.0000.0000.0000.000
168A245SER0-0.045-0.01922.396-0.006-0.0060.0000.0000.0000.000
169A246GLN0-0.0310.01321.519-0.008-0.0080.0000.0000.0000.000
170A247GLN00.008-0.02923.731-0.006-0.0060.0000.0000.0000.000
171A248SER00.0600.04323.386-0.004-0.0040.0000.0000.0000.000
172A249GLY0-0.009-0.02425.7140.0020.0020.0000.0000.0000.000
173A250SER00.0300.02026.0730.0050.0050.0000.0000.0000.000
174A251GLY00.0430.03124.3080.0060.0060.0000.0000.0000.000
175A252ARG10.9340.97825.2560.0400.0400.0000.0000.0000.000
176A253GLU-1-0.947-0.97827.902-0.003-0.0030.0000.0000.0000.000
177A254MLY10.9600.96324.603-0.024-0.0240.0000.0000.0000.000
178A255LEU00.0530.02725.0780.0040.0040.0000.0000.0000.000
179A256GLY00.0150.01029.0900.0020.0020.0000.0000.0000.000
180A257ILE0-0.018-0.00632.3120.0010.0010.0000.0000.0000.000
181A258VAL00.0220.03029.7030.0020.0020.0000.0000.0000.000
182A259ILE0-0.002-0.00230.9830.0010.0010.0000.0000.0000.000
183A260SER0-0.007-0.00834.337-0.001-0.0010.0000.0000.0000.000
184A261ASP-1-0.851-0.86535.7540.0210.0210.0000.0000.0000.000
185A262LEU0-0.012-0.01533.0500.0010.0010.0000.0000.0000.000
186A263GLN0-0.030-0.01837.4090.0000.0000.0000.0000.0000.000
187A264MLY10.9970.99240.137-0.014-0.0140.0000.0000.0000.000
188A265LEU0-0.043-0.00738.0930.0000.0000.0000.0000.0000.000
189A266MLY10.9610.98641.313-0.010-0.0100.0000.0000.0000.000
190A267GLU-1-0.950-0.98342.9680.0050.0050.0000.0000.0000.000
191A268PHE0-0.039-0.02344.3560.0000.0000.0000.0000.0000.000
192A269GLY00.0260.01745.6810.0010.0010.0000.0000.0000.000
193A270SER0-0.074-0.02546.9640.0000.0000.0000.0000.0000.000
194A271VAL00.0050.00349.892-0.001-0.0010.0000.0000.0000.000
195A272SER0-0.026-0.01148.7650.0010.0010.0000.0000.0000.000
196A273ASP-1-0.859-0.93550.7040.0160.0160.0000.0000.0000.000
197A274GLN0-0.007-0.01354.2170.0000.0000.0000.0000.0000.000
198A275VAL0-0.025-0.00650.5820.0000.0000.0000.0000.0000.000
199A276MLY10.9771.00352.913-0.018-0.0180.0000.0000.0000.000
200A277GLY0-0.010-0.01554.3160.0000.0000.0000.0000.0000.000
201A278PHE0-0.001-0.00456.2060.0000.0000.0000.0000.0000.000
202A279TRP00.009-0.00752.3400.0000.0000.0000.0000.0000.000
203A280GLN0-0.0160.00655.8260.0010.0010.0000.0000.0000.000
204A281PHE0-0.071-0.01658.1450.0000.0000.0000.0000.0000.000
205A282PHE0-0.025-0.02158.5690.0000.0000.0000.0000.0000.000
206A283SER0-0.071-0.02656.0540.0010.0010.0000.0000.0000.000