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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: VQ751

Calculation Name: 3PSS-A-Xray372

Preferred Name:

Target Type:

Ligand Name: n-dimethyl-lysine

ligand 3-letter code: MLY

PDB ID: 3PSS

Chain ID: A

ChEMBL ID:

UniProt ID: A0KF03

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 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 216
LigandCharge MLY=1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2523542.138767
FMO2-HF: Nuclear repulsion 2434576.296093
FMO2-HF: Total energy -88965.842674
FMO2-MP2: Total energy -89213.167933


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.
-10.164-1.8057.931-5.511-10.779-0.033
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 : -0.005 / q_NPA : 0.010
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].
3A3MLY10.8830.9392.346-0.4862.7120.526-1.266-2.4580.001
4A4ASP-1-0.895-0.9544.215-0.0360.1150.001-0.035-0.1160.000
5A5MLY10.9040.9687.7090.6840.6840.0000.0000.0000.000
6A6CYS0-0.018-0.0059.4280.1820.1820.0000.0000.0000.000
7A7PHE0-0.006-0.0189.216-0.135-0.1350.0000.0000.0000.000
8A8GLU-1-0.895-0.95814.979-0.035-0.0350.0000.0000.0000.000
9A9GLY0-0.014-0.00418.683-0.019-0.0190.0000.0000.0000.000
10A10VAL0-0.020-0.01714.905-0.001-0.0010.0000.0000.0000.000
11A11ARG10.7840.89117.8580.1160.1160.0000.0000.0000.000
12A12PHE0-0.0050.00111.941-0.007-0.0070.0000.0000.0000.000
13A13GLU-1-0.890-0.94414.666-0.156-0.1560.0000.0000.0000.000
14A14GLN00.006-0.02013.130-0.029-0.0290.0000.0000.0000.000
15A15GLN0-0.045-0.03712.139-0.014-0.0140.0000.0000.0000.000
16A16ASP-1-0.891-0.9409.917-0.518-0.5180.0000.0000.0000.000
17A17LEU0-0.055-0.0408.303-0.188-0.1880.0000.0000.0000.000
18A18GLU-1-0.925-0.9458.199-0.057-0.0570.0000.0000.0000.000
19A19GLY0-0.045-0.0154.0850.0700.162-0.001-0.018-0.0740.000
20A20GLU-1-0.897-0.9534.4880.0540.187-0.001-0.015-0.1170.000
21A21GLN0-0.063-0.0322.445-4.381-2.9053.257-1.494-3.239-0.015
22A22PHE00.0240.0062.611-3.394-0.8821.608-1.900-2.221-0.020
23A23GLN00.028-0.0103.103-1.375-0.7992.540-0.770-2.3460.001
24A24GLY00.0500.0254.739-1.079-1.0630.003-0.007-0.0120.000
25A25CYS0-0.078-0.0396.750-0.461-0.4610.0000.0000.0000.000
26A26ARG10.8060.8699.513-0.041-0.0410.0000.0000.0000.000
27A27PHE00.003-0.0099.096-0.097-0.0970.0000.0000.0000.000
28A28ILE00.0460.02715.0280.0320.0320.0000.0000.0000.000
29A29GLY00.0470.02518.834-0.024-0.0240.0000.0000.0000.000
30A30CYS0-0.085-0.02416.530-0.024-0.0240.0000.0000.0000.000
31A31ASN0-0.001-0.01518.3400.0290.0290.0000.0000.0000.000
32A32PHE00.1160.04911.981-0.017-0.0170.0000.0000.0000.000
33A33SER00.000-0.01817.0630.0060.0060.0000.0000.0000.000
34A34TRP0-0.083-0.04020.405-0.012-0.0120.0000.0000.0000.000
35A35LEU0-0.0500.01114.943-0.003-0.0030.0000.0000.0000.000
36A36ASP-1-0.889-0.95315.8060.0310.0310.0000.0000.0000.000
37A37LEU00.009-0.01312.567-0.025-0.0250.0000.0000.0000.000
38A38ALA00.0250.01512.9920.0230.0230.0000.0000.0000.000
39A39GLU-1-0.926-0.95411.3990.1360.1360.0000.0000.0000.000
40A40CYS0-0.099-0.0228.555-0.016-0.0160.0000.0000.0000.000
41A41ARG10.8920.9474.623-0.232-0.150-0.001-0.004-0.0770.000
42A42PHE00.0310.0035.1700.1770.300-0.001-0.002-0.1190.000
43A43VAL0-0.013-0.0204.876-0.237-0.2370.0000.0000.0000.000
44A44ASP-1-0.783-0.8547.1831.1881.1880.0000.0000.0000.000
45A45CYS0-0.0460.0037.7620.0170.0170.0000.0000.0000.000
46A46SER0-0.050-0.03310.473-0.100-0.1000.0000.0000.0000.000
47A47PHE00.023-0.01010.865-0.031-0.0310.0000.0000.0000.000
48A48TYR00.0330.02115.939-0.027-0.0270.0000.0000.0000.000
49A49ASP-1-0.809-0.88818.6880.0360.0360.0000.0000.0000.000
50A50ARG10.7830.89320.254-0.095-0.0950.0000.0000.0000.000
51A51GLU-1-0.955-0.97023.7290.0170.0170.0000.0000.0000.000
52A52SER0-0.044-0.03824.262-0.006-0.0060.0000.0000.0000.000
53A53GLU-1-0.984-0.98425.3710.0170.0170.0000.0000.0000.000
54A54GLN0-0.0170.00422.7700.0040.0040.0000.0000.0000.000
55A55SER00.0050.00320.9820.0070.0070.0000.0000.0000.000
56A56CYS0-0.048-0.01017.769-0.019-0.0190.0000.0000.0000.000
57A57LEU0-0.053-0.02619.7820.0110.0110.0000.0000.0000.000
58A58LEU00.0680.00515.634-0.014-0.0140.0000.0000.0000.000
59A59GLN0-0.040-0.02619.6100.0010.0010.0000.0000.0000.000
60A60GLY00.002-0.03022.509-0.008-0.0080.0000.0000.0000.000
61A61CYS0-0.096-0.00417.880-0.004-0.0040.0000.0000.0000.000
62A62ASP-1-0.809-0.87617.8920.0370.0370.0000.0000.0000.000
63A63LEU00.034-0.00114.760-0.002-0.0020.0000.0000.0000.000
64A64ARG10.8310.89016.050-0.024-0.0240.0000.0000.0000.000
65A65GLU-1-0.922-0.96714.6360.0750.0750.0000.0000.0000.000
66A66ALA0-0.0080.03411.5490.0010.0010.0000.0000.0000.000
67A67SER0-0.072-0.0859.4220.0040.0040.0000.0000.0000.000
68A68PHE00.0200.0089.0690.0450.0450.0000.0000.0000.000
69A69LEU0-0.024-0.0098.651-0.049-0.0490.0000.0000.0000.000
70A70ARG10.8220.87410.082-0.375-0.3750.0000.0000.0000.000
71A71CYS0-0.053-0.01510.8090.0550.0550.0000.0000.0000.000
72A72ASP-1-0.794-0.88913.3120.0840.0840.0000.0000.0000.000
73A73LEU00.0270.00914.723-0.010-0.0100.0000.0000.0000.000
74A74THR0-0.013-0.02118.028-0.019-0.0190.0000.0000.0000.000
75A75MET0-0.036-0.00921.526-0.008-0.0080.0000.0000.0000.000
76A76ALA00.0220.03119.375-0.011-0.0110.0000.0000.0000.000
77A77ASP-1-0.812-0.87521.3340.0150.0150.0000.0000.0000.000
78A78CYS00.0470.03819.399-0.004-0.0040.0000.0000.0000.000
79A79SER0-0.046-0.02421.800-0.002-0.0020.0000.0000.0000.000
80A80ARG10.8610.91724.974-0.002-0.0020.0000.0000.0000.000
81A81SER00.0090.01320.910-0.001-0.0010.0000.0000.0000.000
82A82GLN0-0.059-0.02621.1910.0050.0050.0000.0000.0000.000
83A83CYS00.0170.00219.2170.0040.0040.0000.0000.0000.000
84A84LEU0-0.033-0.00219.8950.0050.0050.0000.0000.0000.000
85A85GLY00.0770.02518.3700.0010.0010.0000.0000.0000.000
86A86LEU0-0.070-0.01114.5340.0050.0050.0000.0000.0000.000
87A87GLU-1-0.843-0.88811.8540.1060.1060.0000.0000.0000.000
88A88LEU0-0.025-0.01613.6140.0140.0140.0000.0000.0000.000
89A89ARG10.8300.89613.352-0.135-0.1350.0000.0000.0000.000
90A90ASP-1-0.888-0.94714.2970.2520.2520.0000.0000.0000.000
91A91CYS0-0.051-0.00214.4830.0310.0310.0000.0000.0000.000
92A92GLN0-0.0020.00616.706-0.039-0.0390.0000.0000.0000.000
93A93ALA00.0390.00818.9930.0050.0050.0000.0000.0000.000
94A94LEU0-0.0080.00520.816-0.013-0.0130.0000.0000.0000.000
95A95GLY00.0340.00424.364-0.002-0.0020.0000.0000.0000.000
96A96ILE0-0.0340.00419.048-0.006-0.0060.0000.0000.0000.000
97A97ASN0-0.025-0.03223.375-0.003-0.0030.0000.0000.0000.000
98A98PHE00.0850.02919.229-0.002-0.0020.0000.0000.0000.000
99A99SER00.0200.02125.001-0.004-0.0040.0000.0000.0000.000
100A100ARG10.8990.91628.208-0.016-0.0160.0000.0000.0000.000
101A101ALA00.0050.02523.654-0.003-0.0030.0000.0000.0000.000
102A102SER0-0.022-0.00424.9200.0020.0020.0000.0000.0000.000
103A103PHE00.0620.02120.4720.0010.0010.0000.0000.0000.000
104A104ALA00.0190.00423.9050.0020.0020.0000.0000.0000.000
105A105ASN0-0.022-0.00426.478-0.005-0.0050.0000.0000.0000.000
106A106GLN00.016-0.01128.130-0.001-0.0010.0000.0000.0000.000
107A107ILE00.0070.01531.013-0.002-0.0020.0000.0000.0000.000
108A108THR0-0.022-0.01933.968-0.002-0.0020.0000.0000.0000.000
109A109VAL00.0520.01935.7640.0010.0010.0000.0000.0000.000
110A110MLY10.8990.94437.625-0.017-0.0170.0000.0000.0000.000
111A111SER0-0.042-0.02235.2150.0010.0010.0000.0000.0000.000
112A112TYR0-0.086-0.05131.150-0.002-0.0020.0000.0000.0000.000
113A113PHE00.0130.01824.1090.0000.0000.0000.0000.0000.000
114A114CYS0-0.024-0.01026.242-0.003-0.0030.0000.0000.0000.000
115A115GLU-1-0.823-0.90819.7970.0630.0630.0000.0000.0000.000
116A116ALA00.0150.01619.8080.0000.0000.0000.0000.0000.000
117A117HIS10.7890.85916.568-0.079-0.0790.0000.0000.0000.000
118A118LEU00.0200.01217.1070.0120.0120.0000.0000.0000.000
119A119THR00.0310.03918.249-0.008-0.0080.0000.0000.0000.000
120A120GLY00.0400.02318.3780.0170.0170.0000.0000.0000.000
121A121ASN0-0.051-0.02317.7210.0260.0260.0000.0000.0000.000
122A122ASN0-0.023-0.00720.438-0.021-0.0210.0000.0000.0000.000
123A123PHE00.0410.01319.9230.0040.0040.0000.0000.0000.000
124A124SER00.014-0.02224.519-0.010-0.0100.0000.0000.0000.000
125A125TYR0-0.057-0.04527.2440.0010.0010.0000.0000.0000.000
126A126ALA00.0080.03625.262-0.003-0.0030.0000.0000.0000.000
127A127ASN0-0.048-0.03326.611-0.004-0.0040.0000.0000.0000.000
128A128PHE00.0650.01222.8690.0000.0000.0000.0000.0000.000
129A129GLU-1-0.898-0.93228.2770.0190.0190.0000.0000.0000.000
130A130GLY0-0.042-0.02530.966-0.001-0.0010.0000.0000.0000.000
131A131CYS0-0.095-0.02027.4140.0000.0000.0000.0000.0000.000
132A132LEU0-0.029-0.01129.0940.0000.0000.0000.0000.0000.000
133A133LEU00.020-0.01023.5840.0010.0010.0000.0000.0000.000
134A134GLU-1-0.739-0.82827.4280.0340.0340.0000.0000.0000.000
135A135GLN0-0.056-0.03227.9420.0000.0000.0000.0000.0000.000
136A136CYS0-0.077-0.00323.8120.0020.0020.0000.0000.0000.000
137A137GLU-1-0.791-0.87319.1890.0860.0860.0000.0000.0000.000
138A138LEU0-0.011-0.01521.8080.0050.0050.0000.0000.0000.000
139A139SER00.016-0.00623.8940.0010.0010.0000.0000.0000.000
140A140GLY0-0.027-0.01723.0480.0080.0080.0000.0000.0000.000
141A141ASN0-0.057-0.03721.7510.0180.0180.0000.0000.0000.000
142A142ARG10.8300.92224.504-0.072-0.0720.0000.0000.0000.000
143A143TRP00.015-0.00824.8930.0030.0030.0000.0000.0000.000
144A144GLN0-0.007-0.00128.741-0.005-0.0050.0000.0000.0000.000
145A145GLY00.011-0.00331.0370.0010.0010.0000.0000.0000.000
146A146ALA0-0.036-0.00228.910-0.002-0.0020.0000.0000.0000.000
147A147ASN0-0.073-0.04030.755-0.002-0.0020.0000.0000.0000.000
148A148LEU00.0690.01529.6450.0020.0020.0000.0000.0000.000
149A149PHE00.0080.01332.458-0.001-0.0010.0000.0000.0000.000
150A150GLY00.007-0.01034.748-0.001-0.0010.0000.0000.0000.000
151A151ALA0-0.0350.01030.991-0.001-0.0010.0000.0000.0000.000
152A152SER0-0.080-0.09331.826-0.001-0.0010.0000.0000.0000.000
153A153LEU00.0430.01628.1450.0020.0020.0000.0000.0000.000
154A154ALA00.0230.00930.8110.0020.0020.0000.0000.0000.000
155A155GLY00.010-0.00931.7780.0010.0010.0000.0000.0000.000
156A156SER0-0.039-0.00527.3970.0010.0010.0000.0000.0000.000
157A157ASP-1-0.791-0.85225.8650.0640.0640.0000.0000.0000.000
158A158LEU00.016-0.00426.5420.0030.0030.0000.0000.0000.000
159A159SER0-0.051-0.01628.0330.0020.0020.0000.0000.0000.000
160A160GLY00.017-0.01327.5210.0050.0050.0000.0000.0000.000
161A161SER0-0.022-0.03527.8840.0060.0060.0000.0000.0000.000
162A162GLU-1-0.879-0.93228.5150.0670.0670.0000.0000.0000.000
163A163PHE00.008-0.01330.1470.0020.0020.0000.0000.0000.000
164A164GLY00.0410.01732.299-0.001-0.0010.0000.0000.0000.000
165A165GLN0-0.085-0.05435.275-0.001-0.0010.0000.0000.0000.000
166A166ILE00.0210.02032.648-0.002-0.0020.0000.0000.0000.000
167A167ASP-1-0.797-0.87636.6840.0230.0230.0000.0000.0000.000
168A168TRP0-0.014-0.03134.9900.0000.0000.0000.0000.0000.000
169A169ALA0-0.041-0.00438.9680.0000.0000.0000.0000.0000.000
170A170SER0-0.083-0.06239.248-0.001-0.0010.0000.0000.0000.000
171A171VAL00.0130.01332.9920.0000.0000.0000.0000.0000.000
172A172ASN0-0.028-0.00335.607-0.001-0.0010.0000.0000.0000.000
173A173LEU00.0600.01033.3850.0020.0020.0000.0000.0000.000
174A174GLN0-0.009-0.02235.6950.0000.0000.0000.0000.0000.000
175A175GLY00.0200.00135.6060.0010.0010.0000.0000.0000.000
176A176CYS0-0.0670.01231.7610.0010.0010.0000.0000.0000.000
177A177ASP-1-0.780-0.85130.4620.0490.0490.0000.0000.0000.000
178A178LEU00.026-0.00431.4510.0020.0020.0000.0000.0000.000
179A179ARG10.8650.90232.031-0.048-0.0480.0000.0000.0000.000
180A180GLN0-0.038-0.00931.3490.0020.0020.0000.0000.0000.000
181A181CYS0-0.0210.04331.7580.0040.0040.0000.0000.0000.000
182A182ASP-1-0.835-0.90933.4620.0450.0450.0000.0000.0000.000
183A183LEU00.0310.00235.5040.0000.0000.0000.0000.0000.000
184A184PRO0-0.021-0.00337.367-0.003-0.0030.0000.0000.0000.000
185A185GLY00.0420.01040.4230.0000.0000.0000.0000.0000.000
186A186LEU0-0.0130.01638.916-0.001-0.0010.0000.0000.0000.000
187A187ASP-1-0.809-0.89642.3190.0210.0210.0000.0000.0000.000
188A188LEU00.0660.02343.8480.0000.0000.0000.0000.0000.000
189A189ARG10.7700.86546.069-0.021-0.0210.0000.0000.0000.000
190A190ARG10.7820.89243.340-0.024-0.0240.0000.0000.0000.000
191A191VAL00.0140.00840.2450.0000.0000.0000.0000.0000.000
192A192ASN0-0.0210.00042.2550.0000.0000.0000.0000.0000.000
193A193LEU00.0430.01138.7970.0010.0010.0000.0000.0000.000
194A194ASP-1-0.872-0.93541.0210.0270.0270.0000.0000.0000.000
195A195GLY0-0.002-0.00839.3530.0010.0010.0000.0000.0000.000
196A196VAL0-0.057-0.00136.4220.0020.0020.0000.0000.0000.000
197A197GLN0-0.112-0.05333.7620.0010.0010.0000.0000.0000.000
198A198ILE00.0110.00335.9930.0010.0010.0000.0000.0000.000
199A199ASN0-0.012-0.02235.6850.0010.0010.0000.0000.0000.000
200A200GLU-1-0.946-0.98938.9140.0310.0310.0000.0000.0000.000
201A201ASP-1-0.905-0.95739.5320.0390.0390.0000.0000.0000.000
202A202GLN0-0.005-0.01435.737-0.001-0.0010.0000.0000.0000.000
203A203GLN0-0.0140.00241.109-0.002-0.0020.0000.0000.0000.000
204A204GLN0-0.066-0.04144.355-0.001-0.0010.0000.0000.0000.000
205A205ALA00.0670.02543.452-0.001-0.0010.0000.0000.0000.000
206A206LEU00.0110.00841.004-0.001-0.0010.0000.0000.0000.000
207A207LEU0-0.008-0.00645.303-0.001-0.0010.0000.0000.0000.000
208A208GLU-1-0.847-0.92748.7190.0240.0240.0000.0000.0000.000
209A209GLN0-0.067-0.01645.4980.0000.0000.0000.0000.0000.000
210A210ILE0-0.061-0.03048.461-0.001-0.0010.0000.0000.0000.000
211A211GLY0-0.050-0.02950.908-0.001-0.0010.0000.0000.0000.000
212A212LEU0-0.059-0.01651.743-0.001-0.0010.0000.0000.0000.000
213A213ILE00.013-0.00553.5560.0000.0000.0000.0000.0000.000
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