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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: P8JRY

Calculation Name: 3R6D-A-Xray13

Preferred Name:

Target Type:

Ligand Name: n-methyl-lysine

ligand 3-letter code: MLZ

PDB ID: 3R6D

Chain ID: A

ChEMBL ID:

UniProt ID: D1BQI7

Base Structure: X-ray

Registration Date: 2018-03-01

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water No
Procedure Auto-FMO protocol ver. 1.20181228
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 221
LigandCharge MLZ=1
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -2705595.505809
FMO2-HF: Nuclear repulsion 2619478.191113
FMO2-HF: Total energy -86117.314697
FMO2-MP2: Total energy -86371.360775


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:-2:SER)


Summations of interaction energy for fragment #1(A:-2:SER)
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.
-107.191-104.9660.009-0.752-1.483-0.004
Interaction energy analysis for fragmet #1(A:-2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.859 / q_NPA : 0.904
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].
3A0ALA00.0800.0543.5672.0523.4550.003-0.542-0.864-0.003
4A1MET0-0.070-0.0245.7311.9371.9370.0000.0000.0000.000
5A2TYR0-0.038-0.0468.8143.7893.7890.0000.0000.0000.000
6A3MLZ10.9390.9768.88619.14919.1490.0000.0000.0000.000
7A4TYR0-0.019-0.00810.6160.0470.0470.0000.0000.0000.000
8A5ILE00.0330.02813.1020.4220.4220.0000.0000.0000.000
9A6THR0-0.014-0.02315.4480.2900.2900.0000.0000.0000.000
10A7ILE00.0040.01015.3870.0900.0900.0000.0000.0000.000
11A8LEU00.009-0.00719.5440.7850.7850.0000.0000.0000.000
12A9GLY00.0180.00222.550-0.188-0.1880.0000.0000.0000.000
13A10ALA00.0150.00321.495-0.124-0.1240.0000.0000.0000.000
14A11ALA00.0040.00022.059-0.207-0.2070.0000.0000.0000.000
15A12GLY00.0110.02523.9980.2680.2680.0000.0000.0000.000
16A13GLN00.0530.01122.345-0.776-0.7760.0000.0000.0000.000
17A14ILE00.0790.03718.236-0.417-0.4170.0000.0000.0000.000
18A15ALA00.0240.02218.092-0.875-0.8750.0000.0000.0000.000
19A16GLN0-0.021-0.01217.828-0.964-0.9640.0000.0000.0000.000
20A17MLZ10.9310.97416.86414.01314.0130.0000.0000.0000.000
21A18LEU00.0350.02512.371-1.111-1.1110.0000.0000.0000.000
22A19THR0-0.002-0.01812.937-1.501-1.5010.0000.0000.0000.000
23A20ALA00.0400.02113.490-1.004-1.0040.0000.0000.0000.000
24A21THR0-0.061-0.02410.496-1.916-1.9160.0000.0000.0000.000
25A22LEU00.0320.0048.823-2.779-2.7790.0000.0000.0000.000
26A23LEU0-0.0140.0178.883-1.860-1.8600.0000.0000.0000.000
27A24THR0-0.034-0.0039.257-0.431-0.4310.0000.0000.0000.000
28A25TYR0-0.045-0.0245.715-0.445-0.4450.0000.0000.0000.000
29A26THR0-0.060-0.0374.353-6.774-6.477-0.001-0.043-0.2540.000
30A27ASP-1-0.907-0.9585.367-25.682-25.6820.0000.0000.0000.000
31A28MET0-0.047-0.0226.7972.2502.2500.0000.0000.0000.000
32A29HIS0-0.050-0.0169.6792.1312.1310.0000.0000.0000.000
33A30ILE00.010-0.00212.3950.2850.2850.0000.0000.0000.000
34A31THR00.0080.01015.5831.0671.0670.0000.0000.0000.000
35A32LEU00.000-0.00118.385-0.028-0.0280.0000.0000.0000.000
36A33TYR00.007-0.01521.5060.5930.5930.0000.0000.0000.000
37A34GLY00.011-0.00724.882-0.094-0.0940.0000.0000.0000.000
38A35ARG10.9710.98527.7609.5389.5380.0000.0000.0000.000
39A36GLN00.009-0.01630.014-0.203-0.2030.0000.0000.0000.000
40A37LEU00.0520.02924.0780.0500.0500.0000.0000.0000.000
41A38LYS10.9790.99026.11310.60010.6000.0000.0000.0000.000
42A39THR00.0000.00827.257-0.007-0.0070.0000.0000.0000.000
43A40ARG10.8550.92527.84410.53610.5360.0000.0000.0000.000
44A41ILE0-0.0140.00321.642-0.119-0.1190.0000.0000.0000.000
45A42PRO00.0120.02821.5600.3700.3700.0000.0000.0000.000
46A43PRO00.0780.02122.266-0.441-0.4410.0000.0000.0000.000
47A44GLU-1-0.857-0.92418.750-14.121-14.1210.0000.0000.0000.000
48A45ILE0-0.055-0.02917.462-0.971-0.9710.0000.0000.0000.000
49A46ILE0-0.077-0.04918.700-0.161-0.1610.0000.0000.0000.000
50A47ASP-1-0.933-0.96521.088-12.179-12.1790.0000.0000.0000.000
51A48HIS0-0.0280.00312.4180.3660.3660.0000.0000.0000.000
52A49GLU-1-0.891-0.95714.059-17.517-17.5170.0000.0000.0000.000
53A50ARG10.7930.8938.91326.03926.0390.0000.0000.0000.000
54A51VAL0-0.021-0.00214.691-0.457-0.4570.0000.0000.0000.000
55A52THR0-0.0080.01217.4910.8900.8900.0000.0000.0000.000
56A53VAL0-0.026-0.01420.639-0.093-0.0930.0000.0000.0000.000
57A54ILE0-0.022-0.00423.7080.3760.3760.0000.0000.0000.000
58A55GLU-1-0.854-0.90626.350-9.339-9.3390.0000.0000.0000.000
59A56GLY00.0390.01129.7060.1050.1050.0000.0000.0000.000
60A57SER0-0.037-0.01430.434-0.176-0.1760.0000.0000.0000.000
61A58PHE00.0480.01726.791-0.099-0.0990.0000.0000.0000.000
62A59GLN0-0.015-0.00531.8170.0920.0920.0000.0000.0000.000
63A60ASN0-0.037-0.01433.1730.1500.1500.0000.0000.0000.000
64A61PRO00.0600.02932.689-0.297-0.2970.0000.0000.0000.000
65A62GLY00.0430.02132.135-0.238-0.2380.0000.0000.0000.000
66A63MLZ10.8080.88330.7678.8258.8250.0000.0000.0000.000
67A64LEU00.0210.01926.771-0.369-0.3690.0000.0000.0000.000
68A65GLU-1-0.875-0.96127.143-10.008-10.0080.0000.0000.0000.000
69A66GLN0-0.041-0.01626.728-0.566-0.5660.0000.0000.0000.000
70A67ALA00.003-0.00524.311-0.385-0.3850.0000.0000.0000.000
71A68VAL00.0010.01322.503-0.640-0.6400.0000.0000.0000.000
72A69THR0-0.038-0.02922.593-0.104-0.1040.0000.0000.0000.000
73A70ASN0-0.034-0.02519.997-0.090-0.0900.0000.0000.0000.000
74A71ALA0-0.0170.01418.038-0.770-0.7700.0000.0000.0000.000
75A72GLU-1-0.835-0.92313.195-20.536-20.5360.0000.0000.0000.000
76A73VAL0-0.019-0.01213.4540.1350.1350.0000.0000.0000.000
77A74VAL0-0.018-0.00916.8440.1490.1490.0000.0000.0000.000
78A75PHE00.0390.01916.7420.0200.0200.0000.0000.0000.000
79A76VAL0-0.019-0.02918.7880.5930.5930.0000.0000.0000.000
80A77GLY00.004-0.00721.841-0.021-0.0210.0000.0000.0000.000
81A78ALA00.0020.00422.6650.1270.1270.0000.0000.0000.000
82A79MET0-0.051-0.01525.540-0.088-0.0880.0000.0000.0000.000
83A80GLU-1-0.838-0.93028.215-9.911-9.9110.0000.0000.0000.000
84A81SER00.0080.01831.6400.4120.4120.0000.0000.0000.000
85A82GLY00.0710.02532.806-0.221-0.2210.0000.0000.0000.000
86A83SER0-0.001-0.00534.326-0.150-0.1500.0000.0000.0000.000
87A84ASP-1-0.817-0.91831.306-9.371-9.3710.0000.0000.0000.000
88A85MET0-0.0050.01026.168-0.323-0.3230.0000.0000.0000.000
89A86ALA00.007-0.00130.421-0.185-0.1850.0000.0000.0000.000
90A87SER0-0.056-0.03832.5820.0470.0470.0000.0000.0000.000
91A88ILE00.0010.00325.937-0.100-0.1000.0000.0000.0000.000
92A89VAL00.0170.01828.154-0.224-0.2240.0000.0000.0000.000
93A90LYS10.9260.96429.2418.5558.5550.0000.0000.0000.000
94A91ALA0-0.001-0.01128.5640.0490.0490.0000.0000.0000.000
95A92LEU00.0310.01123.092-0.078-0.0780.0000.0000.0000.000
96A93SER0-0.047-0.01926.717-0.138-0.1380.0000.0000.0000.000
97A94ARG10.8770.94129.3689.1249.1240.0000.0000.0000.000
98A95MLZ10.8820.96125.74910.74010.7400.0000.0000.0000.000
99A96ASN0-0.034-0.00825.452-0.121-0.1210.0000.0000.0000.000
100A97ILE00.0110.02721.030-0.413-0.4130.0000.0000.0000.000
101A98ARG10.8770.91321.53612.62312.6230.0000.0000.0000.000
102A99ARG10.8580.93815.77218.45418.4540.0000.0000.0000.000
103A100VAL0-0.0100.00019.495-0.049-0.0490.0000.0000.0000.000
104A101ILE00.0440.02614.9460.1250.1250.0000.0000.0000.000
105A102GLY00.006-0.00219.1610.1230.1230.0000.0000.0000.000
106A103VAL0-0.021-0.00420.713-0.188-0.1880.0000.0000.0000.000
107A104SER0-0.023-0.01323.1740.5460.5460.0000.0000.0000.000
108A105MET00.0060.01826.112-0.188-0.1880.0000.0000.0000.000
109A106ALA0-0.027-0.01527.7870.0590.0590.0000.0000.0000.000
110A107GLY00.0350.01929.3650.2390.2390.0000.0000.0000.000
111A108LEU0-0.069-0.04331.8370.4010.4010.0000.0000.0000.000
112A109SER0-0.095-0.05831.2940.1560.1560.0000.0000.0000.000
113A110GLY00.0030.01033.7810.0080.0080.0000.0000.0000.000
114A111GLU-1-0.753-0.87830.059-10.191-10.1910.0000.0000.0000.000
115A112PHE0-0.0060.00430.253-0.156-0.1560.0000.0000.0000.000
116A113PRO00.0370.03133.8920.2820.2820.0000.0000.0000.000
117A114VAL00.0480.00936.9750.0140.0140.0000.0000.0000.000
118A115ALA0-0.013-0.00139.6360.0500.0500.0000.0000.0000.000
119A116LEU00.0560.03432.0860.0470.0470.0000.0000.0000.000
120A117GLU-1-0.963-0.97036.623-8.297-8.2970.0000.0000.0000.000
121A118LYS10.8900.93637.6197.2367.2360.0000.0000.0000.000
122A119TRP00.0470.01534.5190.0080.0080.0000.0000.0000.000
123A120THR00.018-0.00434.108-0.123-0.1230.0000.0000.0000.000
124A121PHE0-0.042-0.03636.303-0.046-0.0460.0000.0000.0000.000
125A122ASP-1-0.885-0.92439.198-7.263-7.2630.0000.0000.0000.000
126A123ASN0-0.125-0.06137.3290.1440.1440.0000.0000.0000.000
127A124LEU00.0030.00433.778-0.241-0.2410.0000.0000.0000.000
128A125PRO00.0000.01437.2940.2150.2150.0000.0000.0000.000
129A126ILE00.0760.02538.901-0.180-0.1800.0000.0000.0000.000
130A127SER0-0.017-0.02039.813-0.154-0.1540.0000.0000.0000.000
131A128TYR00.0320.02730.265-0.040-0.0400.0000.0000.0000.000
132A129VAL00.0440.02735.126-0.221-0.2210.0000.0000.0000.000
133A130GLN0-0.087-0.05435.845-0.076-0.0760.0000.0000.0000.000
134A131GLY00.0360.02635.844-0.019-0.0190.0000.0000.0000.000
135A132GLU-1-0.785-0.91329.642-10.802-10.8020.0000.0000.0000.000
136A133ARG10.9080.96332.1638.2408.2400.0000.0000.0000.000
137A134GLN0-0.062-0.03834.131-0.104-0.1040.0000.0000.0000.000
138A135ALA00.0010.01030.281-0.049-0.0490.0000.0000.0000.000
139A136ARG10.9120.95229.4129.3889.3880.0000.0000.0000.000
140A137ASN0-0.036-0.02030.551-0.341-0.3410.0000.0000.0000.000
141A138VAL00.0620.04331.360-0.034-0.0340.0000.0000.0000.000
142A139LEU0-0.019-0.01024.508-0.094-0.0940.0000.0000.0000.000
143A140ARG10.9210.95628.7539.7339.7330.0000.0000.0000.000
144A141GLU-1-0.939-0.96029.979-8.824-8.8240.0000.0000.0000.000
145A142SER0-0.040-0.00128.2670.0010.0010.0000.0000.0000.000
146A143ASN00.0280.00429.159-0.374-0.3740.0000.0000.0000.000
147A144LEU00.0050.01024.396-0.234-0.2340.0000.0000.0000.000
148A145ASN00.0110.00619.2970.6100.6100.0000.0000.0000.000
149A146TYR0-0.001-0.00121.003-0.588-0.5880.0000.0000.0000.000
150A147THR00.0230.01318.561-0.422-0.4220.0000.0000.0000.000
151A148ILE0-0.055-0.02920.985-0.052-0.0520.0000.0000.0000.000
152A149LEU00.0190.01417.488-0.165-0.1650.0000.0000.0000.000
153A150ARG10.7790.87222.05012.12512.1250.0000.0000.0000.000
154A151LEU00.0210.00521.153-0.255-0.2550.0000.0000.0000.000
155A152THR00.0180.01124.9880.6200.6200.0000.0000.0000.000
156A153TRP0-0.067-0.02726.845-0.269-0.2690.0000.0000.0000.000
157A154LEU0-0.009-0.01223.192-0.280-0.2800.0000.0000.0000.000
158A155TYR0-0.074-0.07125.2130.4430.4430.0000.0000.0000.000
159A156ASN0-0.071-0.04323.448-0.920-0.9200.0000.0000.0000.000
160A157ASP-1-0.804-0.91722.540-12.382-12.3820.0000.0000.0000.000
161A158PRO0-0.012-0.00619.680-0.513-0.5130.0000.0000.0000.000
162A159GLU-1-0.929-0.95618.975-15.751-15.7510.0000.0000.0000.000
163A160MLZ10.8100.91320.57912.17012.1700.0000.0000.0000.000
164A161THR0-0.047-0.04915.109-0.882-0.8820.0000.0000.0000.000
165A162ASP-1-0.889-0.93716.039-17.151-17.1510.0000.0000.0000.000
166A163TYR0-0.102-0.08812.5811.4461.4460.0000.0000.0000.000
167A164GLU-1-0.824-0.85718.369-13.243-13.2430.0000.0000.0000.000
168A165LEU0-0.023-0.02716.3260.2380.2380.0000.0000.0000.000
169A166ILE0-0.024-0.00520.7030.3620.3620.0000.0000.0000.000
170A167PRO00.0520.01923.9560.0410.0410.0000.0000.0000.000
171A168GLU-1-0.869-0.94725.338-11.168-11.1680.0000.0000.0000.000
172A169GLY0-0.025-0.01328.2390.0780.0780.0000.0000.0000.000
173A170ALA0-0.042-0.00728.1900.3140.3140.0000.0000.0000.000
174A171GLN0-0.004-0.00530.2600.0460.0460.0000.0000.0000.000
175A172PHE0-0.0180.00125.763-0.413-0.4130.0000.0000.0000.000
176A173ASN00.022-0.01629.7530.4230.4230.0000.0000.0000.000
177A174ASH0-0.102-0.07725.3350.3940.3940.0000.0000.0000.000
178A175ALA00.0420.01728.769-0.082-0.0820.0000.0000.0000.000
179A176GLN00.004-0.00726.9480.5700.5700.0000.0000.0000.000
180A177VAL00.000-0.00121.434-0.272-0.2720.0000.0000.0000.000
181A178SER00.0440.03120.4390.1840.1840.0000.0000.0000.000
182A179ARG10.8950.91920.60211.87911.8790.0000.0000.0000.000
183A180GLU-1-0.838-0.92817.231-15.611-15.6110.0000.0000.0000.000
184A181ALA00.0270.02415.932-1.422-1.4220.0000.0000.0000.000
185A182VAL0-0.007-0.00616.339-0.860-0.8600.0000.0000.0000.000
186A183VAL0-0.041-0.02712.992-0.693-0.6930.0000.0000.0000.000
187A184LYS10.9470.98310.81022.69522.6950.0000.0000.0000.000
188A185ALA00.0740.05411.691-1.777-1.7770.0000.0000.0000.000
189A186ILE0-0.047-0.02612.871-0.564-0.5640.0000.0000.0000.000
190A187PHE0-0.028-0.0144.316-0.933-0.857-0.001-0.004-0.0700.000
191A188ASP-1-0.789-0.8718.535-33.185-33.1850.0000.0000.0000.000
192A189ILE0-0.053-0.0269.918-0.701-0.7010.0000.0000.0000.000
193A190LEU0-0.061-0.0279.2170.3980.3980.0000.0000.0000.000
194A191HIS0-0.051-0.0403.618-9.127-8.6780.008-0.163-0.295-0.001
195A192ALA0-0.0140.0137.506-2.002-2.0020.0000.0000.0000.000
196A193ALA00.000-0.01310.2331.4861.4860.0000.0000.0000.000
197A194ASP-1-0.878-0.91911.782-16.194-16.1940.0000.0000.0000.000
198A195GLU-1-0.787-0.88414.466-19.777-19.7770.0000.0000.0000.000
199A196THR0-0.041-0.04316.0871.2181.2180.0000.0000.0000.000
200A197PRO0-0.0060.00217.2930.8630.8630.0000.0000.0000.000
201A198PHE0-0.022-0.01014.5630.4300.4300.0000.0000.0000.000
202A199HIS0-0.0030.02519.1920.7630.7630.0000.0000.0000.000
203A200ARG10.8090.89321.33912.10912.1090.0000.0000.0000.000
204A201THR00.0020.01321.7790.4120.4120.0000.0000.0000.000
205A202SER0-0.023-0.02023.394-0.385-0.3850.0000.0000.0000.000
206A203ILE00.0050.01220.1010.3920.3920.0000.0000.0000.000
207A204GLY0-0.001-0.00322.797-0.073-0.0730.0000.0000.0000.000
208A205VAL00.0080.00219.140-0.584-0.5840.0000.0000.0000.000
209A206GLY00.0340.00221.9570.5500.5500.0000.0000.0000.000
210A207GLU-1-0.724-0.81522.116-13.103-13.1030.0000.0000.0000.000
211A208PRO00.0540.04221.3800.7740.7740.0000.0000.0000.000
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