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

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FMODB ID: 5J6QZ

Calculation Name: 3R6D-A-Xray372

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: 2023-09-23

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 OptHSide
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 221
LigandCharge MLZ=1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2705823.327174
FMO2-HF: Nuclear repulsion 2619704.866888
FMO2-HF: Total energy -86118.460286
FMO2-MP2: Total energy -86372.462608


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.
-1.4820.410.008-0.658-1.2420
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 : 0 / q_Mulliken : -0.012 / q_NPA : -0.025
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].
3A0ALA00.0520.0373.822-0.6220.529-0.006-0.471-0.6740.001
4A1MET0-0.057-0.0215.7180.5390.5390.0000.0000.0000.000
5A2TYR0-0.041-0.0358.7310.3030.3030.0000.0000.0000.000
6A3MLZ10.9050.9658.733-0.429-0.4290.0000.0000.0000.000
7A4TYR0-0.010-0.01310.4670.1410.1410.0000.0000.0000.000
8A5ILE00.0400.02912.994-0.070-0.0700.0000.0000.0000.000
9A6THR0-0.020-0.02315.2900.0550.0550.0000.0000.0000.000
10A7ILE0-0.0010.00615.375-0.041-0.0410.0000.0000.0000.000
11A8LEU00.009-0.00519.5390.0270.0270.0000.0000.0000.000
12A9GLY00.017-0.00222.543-0.014-0.0140.0000.0000.0000.000
13A10ALA00.0200.00721.486-0.006-0.0060.0000.0000.0000.000
14A11ALA00.0040.00222.0580.0070.0070.0000.0000.0000.000
15A12GLY00.0050.02224.0100.0010.0010.0000.0000.0000.000
16A13GLN00.0470.00922.342-0.003-0.0030.0000.0000.0000.000
17A14ILE00.0670.02818.3960.0120.0120.0000.0000.0000.000
18A15ALA00.0230.02618.087-0.009-0.0090.0000.0000.0000.000
19A16GLN00.000-0.00717.8250.0280.0280.0000.0000.0000.000
20A17MLZ10.8490.93816.9350.1080.1080.0000.0000.0000.000
21A18LEU00.0370.02312.4000.0140.0140.0000.0000.0000.000
22A19THR00.000-0.01212.9350.0220.0220.0000.0000.0000.000
23A20ALA00.0350.02013.4940.0760.0760.0000.0000.0000.000
24A21THR0-0.053-0.02410.2070.0640.0640.0000.0000.0000.000
25A22LEU00.0280.0078.6280.1090.1090.0000.0000.0000.000
26A23LEU0-0.0140.0119.1430.2790.2790.0000.0000.0000.000
27A24THR0-0.065-0.0329.8200.2280.2280.0000.0000.0000.000
28A25TYR0-0.045-0.0315.8210.2080.2080.0000.0000.0000.000
29A26THR0-0.034-0.0134.3730.4710.676-0.001-0.020-0.1840.000
30A27ASP-1-0.869-0.9505.4041.3151.3150.0000.0000.0000.000
31A28MET0-0.0120.0007.215-0.432-0.4320.0000.0000.0000.000
32A29HIS0-0.085-0.0399.4940.0240.0240.0000.0000.0000.000
33A30ILE00.0290.01012.543-0.102-0.1020.0000.0000.0000.000
34A31THR00.0100.01115.5190.0300.0300.0000.0000.0000.000
35A32LEU0-0.0010.00118.287-0.039-0.0390.0000.0000.0000.000
36A33TYR00.008-0.01521.5070.0080.0080.0000.0000.0000.000
37A34GLY00.010-0.01024.881-0.012-0.0120.0000.0000.0000.000
38A35ARG10.9720.98427.7590.0110.0110.0000.0000.0000.000
39A36GLN00.021-0.01430.0140.0020.0020.0000.0000.0000.000
40A37LEU00.0370.02624.0900.0000.0000.0000.0000.0000.000
41A38LYS10.9940.99626.357-0.103-0.1030.0000.0000.0000.000
42A39THR00.0030.00727.7880.0040.0040.0000.0000.0000.000
43A40ARG10.8430.92027.991-0.008-0.0080.0000.0000.0000.000
44A41ILE0-0.0220.00421.695-0.014-0.0140.0000.0000.0000.000
45A42PRO00.0190.02921.7250.0030.0030.0000.0000.0000.000
46A43PRO00.0640.02122.8060.0090.0090.0000.0000.0000.000
47A44GLU-1-0.862-0.92819.1650.1590.1590.0000.0000.0000.000
48A45ILE0-0.060-0.03117.6120.0380.0380.0000.0000.0000.000
49A46ILE0-0.078-0.04819.3980.0170.0170.0000.0000.0000.000
50A47ASP-1-0.928-0.96721.9260.1780.1780.0000.0000.0000.000
51A48HIS0-0.0120.00613.204-0.034-0.0340.0000.0000.0000.000
52A49GLU-1-0.898-0.95815.1750.5610.5610.0000.0000.0000.000
53A50ARG10.7980.9129.313-1.182-1.1820.0000.0000.0000.000
54A51VAL0-0.022-0.00315.270-0.049-0.0490.0000.0000.0000.000
55A52THR0-0.0040.01517.920-0.012-0.0120.0000.0000.0000.000
56A53VAL0-0.028-0.01920.890-0.022-0.0220.0000.0000.0000.000
57A54ILE0-0.017-0.00623.9010.0000.0000.0000.0000.0000.000
58A55GLU-1-0.849-0.92026.3380.0140.0140.0000.0000.0000.000
59A56GLY00.0380.00629.699-0.002-0.0020.0000.0000.0000.000
60A57SER0-0.061-0.02930.432-0.003-0.0030.0000.0000.0000.000
61A58PHE00.0370.01126.8300.0010.0010.0000.0000.0000.000
62A59GLN0-0.0010.00131.8100.0010.0010.0000.0000.0000.000
63A60ASN0-0.032-0.00333.2140.0060.0060.0000.0000.0000.000
64A61PRO00.0690.03232.5640.0020.0020.0000.0000.0000.000
65A62GLY00.0310.01931.870-0.001-0.0010.0000.0000.0000.000
66A63MLZ10.8350.90530.523-0.017-0.0170.0000.0000.0000.000
67A64LEU00.0260.02326.8230.0040.0040.0000.0000.0000.000
68A65GLU-1-0.841-0.93126.900-0.025-0.0250.0000.0000.0000.000
69A66GLN0-0.038-0.01226.6430.0060.0060.0000.0000.0000.000
70A67ALA00.0020.00124.1470.0060.0060.0000.0000.0000.000
71A68VAL00.0050.01322.2500.0020.0020.0000.0000.0000.000
72A69THR0-0.035-0.02722.398-0.014-0.0140.0000.0000.0000.000
73A70ASN0-0.039-0.02719.9290.0030.0030.0000.0000.0000.000
74A71ALA0-0.0160.01417.8360.0080.0080.0000.0000.0000.000
75A72GLU-1-0.830-0.90913.183-0.119-0.1190.0000.0000.0000.000
76A73VAL0-0.018-0.00913.453-0.042-0.0420.0000.0000.0000.000
77A74VAL0-0.022-0.01116.8330.0480.0480.0000.0000.0000.000
78A75PHE00.0390.02116.717-0.024-0.0240.0000.0000.0000.000
79A76VAL0-0.021-0.03018.7780.0390.0390.0000.0000.0000.000
80A77GLY00.012-0.00321.832-0.014-0.0140.0000.0000.0000.000
81A78ALA0-0.0050.00222.656-0.003-0.0030.0000.0000.0000.000
82A79MET0-0.027-0.00225.538-0.001-0.0010.0000.0000.0000.000
83A80GLU-1-0.870-0.94628.204-0.069-0.0690.0000.0000.0000.000
84A81SER0-0.020-0.03431.6280.0050.0050.0000.0000.0000.000
85A82GLY00.0710.03332.794-0.004-0.0040.0000.0000.0000.000
86A83SER00.0200.01034.313-0.001-0.0010.0000.0000.0000.000
87A84ASP-1-0.824-0.89331.451-0.046-0.0460.0000.0000.0000.000
88A85MET00.0420.03326.124-0.001-0.0010.0000.0000.0000.000
89A86ALA00.0030.00030.409-0.003-0.0030.0000.0000.0000.000
90A87SER0-0.080-0.05132.4790.0030.0030.0000.0000.0000.000
91A88ILE00.0120.00425.9760.0040.0040.0000.0000.0000.000
92A89VAL00.0120.01428.144-0.002-0.0020.0000.0000.0000.000
93A90LYS10.9290.96829.2290.0460.0460.0000.0000.0000.000
94A91ALA00.001-0.00828.5940.0030.0030.0000.0000.0000.000
95A92LEU00.0480.01622.9310.0060.0060.0000.0000.0000.000
96A93SER0-0.036-0.01426.668-0.002-0.0020.0000.0000.0000.000
97A94ARG10.8040.89229.2700.0340.0340.0000.0000.0000.000
98A95MLZ10.8680.95325.6050.0230.0230.0000.0000.0000.000
99A96ASN0-0.036-0.00825.3650.0040.0040.0000.0000.0000.000
100A97ILE00.0190.02720.875-0.010-0.0100.0000.0000.0000.000
101A98ARG10.8560.89721.5350.1460.1460.0000.0000.0000.000
102A99ARG10.8080.89316.1910.4420.4420.0000.0000.0000.000
103A100VAL0-0.006-0.00219.4820.0230.0230.0000.0000.0000.000
104A101ILE00.0400.02614.953-0.014-0.0140.0000.0000.0000.000
105A102GLY00.0010.00019.1460.0300.0300.0000.0000.0000.000
106A103VAL0-0.035-0.01120.680-0.021-0.0210.0000.0000.0000.000
107A104SER0-0.027-0.03723.1610.0190.0190.0000.0000.0000.000
108A105MET0-0.0330.00326.098-0.005-0.0050.0000.0000.0000.000
109A106ALA0-0.020-0.01527.718-0.003-0.0030.0000.0000.0000.000
110A107GLY00.0460.01629.3490.0110.0110.0000.0000.0000.000
111A108LEU0-0.075-0.03931.7020.0100.0100.0000.0000.0000.000
112A109SER0-0.090-0.06531.0510.0070.0070.0000.0000.0000.000
113A110GLY00.0070.01433.762-0.003-0.0030.0000.0000.0000.000
114A111GLU-1-0.746-0.86730.160-0.155-0.1550.0000.0000.0000.000
115A112PHE0-0.0080.01430.543-0.005-0.0050.0000.0000.0000.000
116A113PRO00.0330.02734.0820.0070.0070.0000.0000.0000.000
117A114VAL00.0490.00737.0790.0020.0020.0000.0000.0000.000
118A115ALA0-0.0060.00639.7080.0030.0030.0000.0000.0000.000
119A116LEU00.0410.02832.2530.0030.0030.0000.0000.0000.000
120A117GLU-1-0.957-0.96536.608-0.096-0.0960.0000.0000.0000.000
121A118LYS10.8260.88937.6030.0680.0680.0000.0000.0000.000
122A119TRP00.0530.02034.6670.0030.0030.0000.0000.0000.000
123A120THR00.0180.00033.9900.0010.0010.0000.0000.0000.000
124A121PHE0-0.043-0.03336.1830.0030.0030.0000.0000.0000.000
125A122ASP-1-0.853-0.89339.184-0.061-0.0610.0000.0000.0000.000
126A123ASN0-0.116-0.06237.3880.0080.0080.0000.0000.0000.000
127A124LEU00.0080.00733.757-0.001-0.0010.0000.0000.0000.000
128A125PRO0-0.0010.01637.2600.0020.0020.0000.0000.0000.000
129A126ILE00.0780.02038.889-0.004-0.0040.0000.0000.0000.000
130A127SER0-0.002-0.00739.800-0.004-0.0040.0000.0000.0000.000
131A128TYR0-0.032-0.02830.1100.0020.0020.0000.0000.0000.000
132A129VAL00.0360.02135.114-0.006-0.0060.0000.0000.0000.000
133A130GLN0-0.059-0.04235.831-0.003-0.0030.0000.0000.0000.000
134A131GLY00.0310.02535.831-0.002-0.0020.0000.0000.0000.000
135A132GLU-1-0.733-0.84329.602-0.127-0.1270.0000.0000.0000.000
136A133ARG10.9100.96232.1480.0850.0850.0000.0000.0000.000
137A134GLN0-0.025-0.01734.116-0.003-0.0030.0000.0000.0000.000
138A135ALA0-0.0110.00630.293-0.001-0.0010.0000.0000.0000.000
139A136ARG10.9340.96629.2410.1200.1200.0000.0000.0000.000
140A137ASN0-0.092-0.05730.535-0.012-0.0120.0000.0000.0000.000
141A138VAL00.0540.03731.440-0.001-0.0010.0000.0000.0000.000
142A139LEU0-0.012-0.00624.488-0.001-0.0010.0000.0000.0000.000
143A140ARG10.9260.97028.7000.1330.1330.0000.0000.0000.000
144A141GLU-1-0.886-0.93529.961-0.099-0.0990.0000.0000.0000.000
145A142SER0-0.042-0.00928.2970.0040.0040.0000.0000.0000.000
146A143ASN00.0280.01728.976-0.014-0.0140.0000.0000.0000.000
147A144LEU00.0150.01424.418-0.005-0.0050.0000.0000.0000.000
148A145ASN0-0.024-0.01619.1520.0040.0040.0000.0000.0000.000
149A146TYR0-0.0020.00120.986-0.013-0.0130.0000.0000.0000.000
150A147THR00.0160.00618.546-0.026-0.0260.0000.0000.0000.000
151A148ILE0-0.048-0.02420.9670.0120.0120.0000.0000.0000.000
152A149LEU00.0200.01317.386-0.016-0.0160.0000.0000.0000.000
153A150ARG10.7840.86622.0330.2340.2340.0000.0000.0000.000
154A151LEU00.0270.00721.104-0.013-0.0130.0000.0000.0000.000
155A152THR00.0150.00524.9730.0220.0220.0000.0000.0000.000
156A153TRP0-0.066-0.03326.8320.0030.0030.0000.0000.0000.000
157A154LEU00.002-0.00123.295-0.003-0.0030.0000.0000.0000.000
158A155TYR0-0.125-0.09625.1980.0220.0220.0000.0000.0000.000
159A156ASN0-0.026-0.01723.446-0.025-0.0250.0000.0000.0000.000
160A157ASP-1-0.824-0.93822.548-0.102-0.1020.0000.0000.0000.000
161A158PRO0-0.017-0.00119.623-0.022-0.0220.0000.0000.0000.000
162A159GLU-1-0.900-0.94118.765-0.125-0.1250.0000.0000.0000.000
163A160MLZ10.8220.92520.5870.1310.1310.0000.0000.0000.000
164A161THR0-0.050-0.04315.467-0.035-0.0350.0000.0000.0000.000
165A162ASP-1-0.873-0.92816.230-0.408-0.4080.0000.0000.0000.000
166A163TYR0-0.097-0.09012.6530.0880.0880.0000.0000.0000.000
167A164GLU-1-0.823-0.86318.484-0.278-0.2780.0000.0000.0000.000
168A165LEU0-0.022-0.02216.3890.0190.0190.0000.0000.0000.000
169A166ILE0-0.015-0.00320.7690.0130.0130.0000.0000.0000.000
170A167PRO00.0470.02024.0700.0040.0040.0000.0000.0000.000
171A168GLU-1-0.852-0.94225.356-0.190-0.1900.0000.0000.0000.000
172A169GLY0-0.033-0.01428.2550.0010.0010.0000.0000.0000.000
173A170ALA0-0.043-0.00628.1680.0100.0100.0000.0000.0000.000
174A171GLN00.000-0.00430.2930.0030.0030.0000.0000.0000.000
175A172PHE0-0.0190.00525.778-0.015-0.0150.0000.0000.0000.000
176A173ASN00.008-0.02129.8390.0150.0150.0000.0000.0000.000
177A174ASH0-0.089-0.07425.4870.0150.0150.0000.0000.0000.000
178A175ALA00.0490.02928.904-0.001-0.0010.0000.0000.0000.000
179A176GLN0-0.048-0.05427.3610.0230.0230.0000.0000.0000.000
180A177VAL00.0320.01621.407-0.014-0.0140.0000.0000.0000.000
181A178SER0-0.0090.00020.4750.0110.0110.0000.0000.0000.000
182A179ARG10.9010.91620.6530.0800.0800.0000.0000.0000.000
183A180GLU-1-0.775-0.90217.223-0.139-0.1390.0000.0000.0000.000
184A181ALA00.0210.02515.924-0.050-0.0500.0000.0000.0000.000
185A182VAL00.0100.00216.326-0.054-0.0540.0000.0000.0000.000
186A183VAL0-0.032-0.02213.022-0.040-0.0400.0000.0000.0000.000
187A184LYS10.9370.97811.3160.4880.4880.0000.0000.0000.000
188A185ALA00.0590.04411.676-0.146-0.1460.0000.0000.0000.000
189A186ILE0-0.045-0.02612.906-0.063-0.0630.0000.0000.0000.000
190A187PHE0-0.007-0.0054.398-0.0440.027-0.001-0.002-0.0680.000
191A188ASP-1-0.793-0.8708.517-1.631-1.6310.0000.0000.0000.000
192A189ILE0-0.053-0.0279.899-0.119-0.1190.0000.0000.0000.000
193A190LEU0-0.072-0.0359.2240.0340.0340.0000.0000.0000.000
194A191HIS0-0.028-0.0233.725-0.770-0.3050.016-0.165-0.316-0.001
195A192ALA0-0.0200.0097.485-0.246-0.2460.0000.0000.0000.000
196A193ALA00.008-0.00710.0960.1670.1670.0000.0000.0000.000
197A194ASP-1-0.864-0.90311.616-0.357-0.3570.0000.0000.0000.000
198A195GLU-1-0.734-0.84714.436-0.533-0.5330.0000.0000.0000.000
199A196THR0-0.038-0.05416.0480.0740.0740.0000.0000.0000.000
200A197PRO0-0.017-0.00117.2250.0460.0460.0000.0000.0000.000
201A198PHE0-0.022-0.00914.1620.0280.0280.0000.0000.0000.000
202A199HIS00.0090.03319.1710.0500.0500.0000.0000.0000.000
203A200ARG10.8100.89121.3180.2030.2030.0000.0000.0000.000
204A201THR0-0.013-0.00121.7880.0150.0150.0000.0000.0000.000
205A202SER0-0.020-0.02423.375-0.006-0.0060.0000.0000.0000.000
206A203ILE00.0010.01220.2410.0110.0110.0000.0000.0000.000
207A204GLY0-0.0070.00022.7780.0060.0060.0000.0000.0000.000
208A205VAL00.0200.00319.074-0.030-0.0300.0000.0000.0000.000
209A206GLY00.022-0.00121.9970.0310.0310.0000.0000.0000.000
210A207GLU-1-0.712-0.81122.253-0.195-0.1950.0000.0000.0000.000
211A208PRO00.0720.05521.5310.0270.0270.0000.0000.0000.000
212A209GLY00.0190.01424.6210.0100.0100.0000.0000.0000.000
213A210THR0-0.068-0.04327.2040.0170.0170.0000.0000.0000.000
214A211HIS0-0.021-0.00428.6350.0040.0040.0000.0000.0000.000
215A212TYR0-0.039-0.02630.7940.0100.0100.0000.0000.0000.000
216A213ASP-1-0.852-0.93834.892-0.092-0.0920.0000.0000.0000.000
217A214MLZ10.8340.92035.6280.0810.0810.0000.0000.0000.000
218A215PRO0-0.0090.01431.241-0.003-0.0030.0000.0000.0000.000
219A216SER00.0200.01731.7020.0060.0060.0000.0000.0000.000
220A217PHE0-0.024-0.01832.9440.0010.0010.0000.0000.0000.000
221A218HIS10.9310.98328.6220.1040.1040.0000.0000.0000.000