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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: 4JZKN

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 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 221
LigandCharge MLZ=1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2705931.190383
FMO2-HF: Nuclear repulsion 2619813.268028
FMO2-HF: Total energy -86117.922355
FMO2-MP2: Total energy -86371.943155


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.
-2.1530.0199999999999990.009-0.679-1.503-0.001
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 : 0.010 / q_NPA : -0.017
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].
3A0ALA00.0500.0353.573-1.2900.040-0.002-0.502-0.8270.000
4A1MET0-0.058-0.0235.6900.5290.5290.0000.0000.0000.000
5A2TYR0-0.052-0.0558.8210.2210.2210.0000.0000.0000.000
6A3MLZ10.9480.9818.900-0.601-0.6010.0000.0000.0000.000
7A4TYR0-0.023-0.00910.6290.1230.1230.0000.0000.0000.000
8A5ILE00.0440.03213.075-0.090-0.0900.0000.0000.0000.000
9A6THR0-0.020-0.02615.4150.0470.0470.0000.0000.0000.000
10A7ILE0-0.0020.00815.366-0.046-0.0460.0000.0000.0000.000
11A8LEU00.006-0.00519.5190.0180.0180.0000.0000.0000.000
12A9GLY00.017-0.00222.528-0.017-0.0170.0000.0000.0000.000
13A10ALA00.0260.00821.478-0.012-0.0120.0000.0000.0000.000
14A11ALA00.0010.00222.0460.0030.0030.0000.0000.0000.000
15A12GLY00.0070.02123.986-0.005-0.0050.0000.0000.0000.000
16A13GLN00.0430.00522.337-0.004-0.0040.0000.0000.0000.000
17A14ILE00.0700.03318.2290.0070.0070.0000.0000.0000.000
18A15ALA00.0260.02718.084-0.010-0.0100.0000.0000.0000.000
19A16GLN0-0.015-0.00917.8170.0280.0280.0000.0000.0000.000
20A17MLZ10.9190.96716.8710.1420.1420.0000.0000.0000.000
21A18LEU00.0380.02412.360-0.006-0.0060.0000.0000.0000.000
22A19THR00.008-0.01312.9280.0360.0360.0000.0000.0000.000
23A20ALA00.0320.01713.4820.0840.0840.0000.0000.0000.000
24A21THR0-0.068-0.02810.5010.0370.0370.0000.0000.0000.000
25A22LEU00.0390.0098.8130.0420.0420.0000.0000.0000.000
26A23LEU0-0.0060.0208.8830.3720.3720.0000.0000.0000.000
27A24THR0-0.044-0.0109.0060.2490.2490.0000.0000.0000.000
28A25TYR0-0.051-0.0295.7010.1110.1110.0000.0000.0000.000
29A26THR0-0.037-0.0184.3530.2560.5660.000-0.043-0.2670.000
30A27ASP-1-0.891-0.9525.4251.4711.532-0.0010.000-0.0590.000
31A28MET0-0.045-0.0227.255-0.606-0.6060.0000.0000.0000.000
32A29HIS0-0.056-0.0209.865-0.096-0.0960.0000.0000.0000.000
33A30ILE00.0170.00112.409-0.109-0.1090.0000.0000.0000.000
34A31THR00.0070.01015.716-0.004-0.0040.0000.0000.0000.000
35A32LEU0-0.006-0.00318.367-0.042-0.0420.0000.0000.0000.000
36A33TYR00.013-0.01221.4840.0050.0050.0000.0000.0000.000
37A34GLY00.005-0.01124.858-0.016-0.0160.0000.0000.0000.000
38A35ARG10.9790.98727.739-0.003-0.0030.0000.0000.0000.000
39A36GLN00.011-0.01529.998-0.002-0.0020.0000.0000.0000.000
40A37LEU00.0460.02824.060-0.004-0.0040.0000.0000.0000.000
41A38LYS10.9860.99226.175-0.126-0.1260.0000.0000.0000.000
42A39THR00.0010.00727.4050.0010.0010.0000.0000.0000.000
43A40ARG10.8500.92227.834-0.021-0.0210.0000.0000.0000.000
44A41ILE0-0.0220.00021.642-0.015-0.0150.0000.0000.0000.000
45A42PRO00.0160.02921.5050.0060.0060.0000.0000.0000.000
46A43PRO00.0780.02222.3600.0140.0140.0000.0000.0000.000
47A44GLU-1-0.856-0.92218.7460.1200.1200.0000.0000.0000.000
48A45ILE0-0.064-0.03317.4670.0370.0370.0000.0000.0000.000
49A46ILE0-0.077-0.04918.9230.0310.0310.0000.0000.0000.000
50A47ASP-1-0.930-0.96521.4320.1840.1840.0000.0000.0000.000
51A48HIS0-0.0260.00412.829-0.015-0.0150.0000.0000.0000.000
52A49GLU-1-0.891-0.95714.7720.6340.6340.0000.0000.0000.000
53A50ARG10.7970.8979.164-1.316-1.3160.0000.0000.0000.000
54A51VAL0-0.024-0.00215.132-0.027-0.0270.0000.0000.0000.000
55A52THR0-0.0080.01217.782-0.020-0.0200.0000.0000.0000.000
56A53VAL0-0.024-0.01420.938-0.022-0.0220.0000.0000.0000.000
57A54ILE0-0.019-0.00223.912-0.002-0.0020.0000.0000.0000.000
58A55GLU-1-0.861-0.91326.5230.0400.0400.0000.0000.0000.000
59A56GLY00.0450.00829.8280.0000.0000.0000.0000.0000.000
60A57SER0-0.047-0.01430.410-0.005-0.0050.0000.0000.0000.000
61A58PHE00.0460.01626.7660.0050.0050.0000.0000.0000.000
62A59GLN0-0.014-0.00531.7890.0010.0010.0000.0000.0000.000
63A60ASN0-0.039-0.01633.1430.0040.0040.0000.0000.0000.000
64A61PRO00.0620.02932.6590.0040.0040.0000.0000.0000.000
65A62GLY00.0440.02332.1040.0020.0020.0000.0000.0000.000
66A63MLZ10.8170.89030.748-0.043-0.0430.0000.0000.0000.000
67A64LEU00.0200.01926.7410.0080.0080.0000.0000.0000.000
68A65GLU-1-0.888-0.96727.1100.0270.0270.0000.0000.0000.000
69A66GLN0-0.037-0.01526.7400.0160.0160.0000.0000.0000.000
70A67ALA00.006-0.00324.2810.0130.0130.0000.0000.0000.000
71A68VAL00.0060.01622.5170.0120.0120.0000.0000.0000.000
72A69THR0-0.042-0.02922.607-0.009-0.0090.0000.0000.0000.000
73A70ASN0-0.037-0.02720.0060.0050.0050.0000.0000.0000.000
74A71ALA0-0.0120.01618.0530.0280.0280.0000.0000.0000.000
75A72GLU-1-0.839-0.92413.2060.1760.1760.0000.0000.0000.000
76A73VAL0-0.018-0.01013.419-0.055-0.0550.0000.0000.0000.000
77A74VAL0-0.019-0.01016.8070.0500.0500.0000.0000.0000.000
78A75PHE00.0400.01916.716-0.032-0.0320.0000.0000.0000.000
79A76VAL0-0.022-0.03018.7610.0350.0350.0000.0000.0000.000
80A77GLY00.009-0.00521.823-0.019-0.0190.0000.0000.0000.000
81A78ALA0-0.0040.00322.646-0.009-0.0090.0000.0000.0000.000
82A79MET0-0.046-0.01225.5220.0040.0040.0000.0000.0000.000
83A80GLU-1-0.841-0.93128.194-0.061-0.0610.0000.0000.0000.000
84A81SER00.0130.01931.6200.0030.0030.0000.0000.0000.000
85A82GLY00.0650.02532.781-0.002-0.0020.0000.0000.0000.000
86A83SER0-0.003-0.00634.2980.0000.0000.0000.0000.0000.000
87A84ASP-1-0.814-0.91931.280-0.021-0.0210.0000.0000.0000.000
88A85MET00.0020.01426.0750.0010.0010.0000.0000.0000.000
89A86ALA00.0020.00030.3880.0000.0000.0000.0000.0000.000
90A87SER0-0.057-0.03732.5520.0050.0050.0000.0000.0000.000
91A88ILE00.0050.00625.9080.0070.0070.0000.0000.0000.000
92A89VAL00.0070.01128.1210.0030.0030.0000.0000.0000.000
93A90LYS10.9260.96529.2070.0150.0150.0000.0000.0000.000
94A91ALA00.009-0.00628.5280.0050.0050.0000.0000.0000.000
95A92LEU00.0340.01223.0580.0090.0090.0000.0000.0000.000
96A93SER0-0.060-0.02326.6800.0030.0030.0000.0000.0000.000
97A94ARG10.8810.94229.330-0.004-0.0040.0000.0000.0000.000
98A95MLZ10.8850.96125.768-0.045-0.0450.0000.0000.0000.000
99A96ASN0-0.037-0.01025.4650.0090.0090.0000.0000.0000.000
100A97ILE00.0190.03121.045-0.004-0.0040.0000.0000.0000.000
101A98ARG10.8730.91321.5100.0720.0720.0000.0000.0000.000
102A99ARG10.8500.93415.7420.3350.3350.0000.0000.0000.000
103A100VAL0-0.0080.00019.4590.0270.0270.0000.0000.0000.000
104A101ILE00.0400.02514.917-0.021-0.0210.0000.0000.0000.000
105A102GLY0-0.003-0.00419.1340.0310.0310.0000.0000.0000.000
106A103VAL0-0.032-0.01020.696-0.025-0.0250.0000.0000.0000.000
107A104SER0-0.014-0.00623.1570.0200.0200.0000.0000.0000.000
108A105MET0-0.0050.01126.099-0.008-0.0080.0000.0000.0000.000
109A106ALA0-0.027-0.01527.780-0.002-0.0020.0000.0000.0000.000
110A107GLY00.0360.02029.3550.0100.0100.0000.0000.0000.000
111A108LEU0-0.072-0.04231.8180.0100.0100.0000.0000.0000.000
112A109SER0-0.091-0.05631.2660.0070.0070.0000.0000.0000.000
113A110GLY00.0010.00833.766-0.003-0.0030.0000.0000.0000.000
114A111GLU-1-0.742-0.87430.113-0.153-0.1530.0000.0000.0000.000
115A112PHE0-0.0120.00230.316-0.007-0.0070.0000.0000.0000.000
116A113PRO00.0370.03134.0910.0080.0080.0000.0000.0000.000
117A114VAL00.0540.01137.1730.0020.0020.0000.0000.0000.000
118A115ALA0-0.0080.00039.8840.0030.0030.0000.0000.0000.000
119A116LEU00.0460.02932.2200.0040.0040.0000.0000.0000.000
120A117GLU-1-0.961-0.96936.620-0.098-0.0980.0000.0000.0000.000
121A118LYS10.8950.94137.6140.0740.0740.0000.0000.0000.000
122A119TRP00.0450.01434.5170.0030.0030.0000.0000.0000.000
123A120THR00.009-0.00834.1010.0010.0010.0000.0000.0000.000
124A121PHE0-0.035-0.03136.2910.0030.0030.0000.0000.0000.000
125A122ASP-1-0.880-0.92239.191-0.065-0.0650.0000.0000.0000.000
126A123ASN0-0.129-0.06537.3250.0070.0070.0000.0000.0000.000
127A124LEU0-0.0020.00133.771-0.001-0.0010.0000.0000.0000.000
128A125PRO00.0090.01837.2840.0020.0020.0000.0000.0000.000
129A126ILE00.0720.02538.888-0.003-0.0030.0000.0000.0000.000
130A127SER0-0.017-0.01939.797-0.003-0.0030.0000.0000.0000.000
131A128TYR00.0370.02730.251-0.001-0.0010.0000.0000.0000.000
132A129VAL00.0400.02535.110-0.004-0.0040.0000.0000.0000.000
133A130GLN0-0.075-0.04935.828-0.001-0.0010.0000.0000.0000.000
134A131GLY00.0330.02635.8230.0000.0000.0000.0000.0000.000
135A132GLU-1-0.803-0.91829.625-0.107-0.1070.0000.0000.0000.000
136A133ARG10.9090.96132.1420.0780.0780.0000.0000.0000.000
137A134GLN0-0.048-0.03234.109-0.001-0.0010.0000.0000.0000.000
138A135ALA00.0060.01430.2570.0010.0010.0000.0000.0000.000
139A136ARG10.9130.95129.3900.1090.1090.0000.0000.0000.000
140A137ASN0-0.045-0.02330.527-0.012-0.0120.0000.0000.0000.000
141A138VAL00.0570.03931.3300.0000.0000.0000.0000.0000.000
142A139LEU0-0.005-0.00924.4810.0020.0020.0000.0000.0000.000
143A140ARG10.9160.95528.7230.1160.1160.0000.0000.0000.000
144A141GLU-1-0.935-0.95729.950-0.073-0.0730.0000.0000.0000.000
145A142SER0-0.040-0.00128.2340.0070.0070.0000.0000.0000.000
146A143ASN00.0280.00529.122-0.010-0.0100.0000.0000.0000.000
147A144LEU00.0050.01024.361-0.003-0.0030.0000.0000.0000.000
148A145ASN00.0170.00719.263-0.007-0.0070.0000.0000.0000.000
149A146TYR00.0030.00220.969-0.006-0.0060.0000.0000.0000.000
150A147THR00.0250.01318.539-0.025-0.0250.0000.0000.0000.000
151A148ILE0-0.052-0.02720.9590.0140.0140.0000.0000.0000.000
152A149LEU00.0190.01517.471-0.019-0.0190.0000.0000.0000.000
153A150ARG10.7900.87822.0340.2300.2300.0000.0000.0000.000
154A151LEU00.0240.00621.143-0.017-0.0170.0000.0000.0000.000
155A152THR00.0200.01524.9800.0240.0240.0000.0000.0000.000
156A153TRP0-0.065-0.02926.8410.0020.0020.0000.0000.0000.000
157A154LEU00.003-0.00323.190-0.007-0.0070.0000.0000.0000.000
158A155TYR0-0.150-0.11725.2070.0240.0240.0000.0000.0000.000
159A156ASN0-0.036-0.02623.456-0.025-0.0250.0000.0000.0000.000
160A157ASP-1-0.849-0.94222.550-0.162-0.1620.0000.0000.0000.000
161A158PRO00.0120.00619.532-0.024-0.0240.0000.0000.0000.000
162A159GLU-1-0.919-0.94918.672-0.253-0.2530.0000.0000.0000.000
163A160MLZ10.7990.90620.4810.1860.1860.0000.0000.0000.000
164A161THR0-0.041-0.04315.172-0.033-0.0330.0000.0000.0000.000
165A162ASP-1-0.873-0.92916.311-0.483-0.4830.0000.0000.0000.000
166A163TYR0-0.108-0.09212.7780.1030.1030.0000.0000.0000.000
167A164GLU-1-0.818-0.85518.581-0.310-0.3100.0000.0000.0000.000
168A165LEU0-0.023-0.02616.4450.0240.0240.0000.0000.0000.000
169A166ILE0-0.019-0.00520.8450.0130.0130.0000.0000.0000.000
170A167PRO00.0510.02024.0340.0090.0090.0000.0000.0000.000
171A168GLU-1-0.852-0.94125.407-0.178-0.1780.0000.0000.0000.000
172A169GLY0-0.026-0.01128.3050.0010.0010.0000.0000.0000.000
173A170ALA0-0.043-0.00828.2880.0090.0090.0000.0000.0000.000
174A171GLN0-0.002-0.00530.3520.0040.0040.0000.0000.0000.000
175A172PHE0-0.0210.00325.780-0.016-0.0160.0000.0000.0000.000
176A173ASN00.023-0.01529.9410.0180.0180.0000.0000.0000.000
177A174ASH0-0.099-0.07825.5500.0150.0150.0000.0000.0000.000
178A175ALA00.0440.02129.0120.0010.0010.0000.0000.0000.000
179A176GLN0-0.023-0.02727.1670.0270.0270.0000.0000.0000.000
180A177VAL00.0300.01521.439-0.016-0.0160.0000.0000.0000.000
181A178SER00.0030.01120.4640.0160.0160.0000.0000.0000.000
182A179ARG10.9070.92320.6030.1070.1070.0000.0000.0000.000
183A180GLU-1-0.823-0.92117.239-0.209-0.2090.0000.0000.0000.000
184A181ALA00.0210.02115.939-0.062-0.0620.0000.0000.0000.000
185A182VAL0-0.002-0.00416.342-0.052-0.0520.0000.0000.0000.000
186A183VAL0-0.034-0.02412.995-0.026-0.0260.0000.0000.0000.000
187A184LYS10.9480.98410.6700.6940.6940.0000.0000.0000.000
188A185ALA00.0690.05011.690-0.140-0.1400.0000.0000.0000.000
189A186ILE0-0.050-0.02812.853-0.045-0.0450.0000.0000.0000.000
190A187PHE0-0.016-0.0094.3180.0450.114-0.001-0.003-0.0650.000
191A188ASP-1-0.786-0.8688.518-1.694-1.6940.0000.0000.0000.000
192A189ILE0-0.063-0.0329.909-0.089-0.0890.0000.0000.0000.000
193A190LEU0-0.073-0.0359.1920.0540.0540.0000.0000.0000.000
194A191HIS0-0.027-0.0253.584-0.1430.2600.013-0.131-0.285-0.001
195A192ALA0-0.0170.0117.479-0.294-0.2940.0000.0000.0000.000
196A193ALA00.010-0.00510.0410.1870.1870.0000.0000.0000.000
197A194ASP-1-0.877-0.91911.560-0.303-0.3030.0000.0000.0000.000
198A195GLU-1-0.782-0.88114.437-0.442-0.4420.0000.0000.0000.000
199A196THR0-0.041-0.04516.0360.0680.0680.0000.0000.0000.000
200A197PRO0-0.0110.00017.2080.0440.0440.0000.0000.0000.000
201A198PHE0-0.026-0.01214.5540.0210.0210.0000.0000.0000.000
202A199HIS0-0.0050.02419.1670.0510.0510.0000.0000.0000.000
203A200ARG10.8160.89621.3090.1560.1560.0000.0000.0000.000
204A201THR0-0.0020.01421.7570.0110.0110.0000.0000.0000.000
205A202SER0-0.023-0.02323.371-0.003-0.0030.0000.0000.0000.000
206A203ILE00.0050.01220.2040.0080.0080.0000.0000.0000.000
207A204GLY0-0.012-0.00422.7830.0070.0070.0000.0000.0000.000
208A205VAL00.0230.00519.136-0.031-0.0310.0000.0000.0000.000
209A206GLY00.018-0.00522.0090.0330.0330.0000.0000.0000.000
210A207GLU-1-0.723-0.81822.363-0.247-0.2470.0000.0000.0000.000
211A208PRO00.0640.05221.6080.0330.0330.0000.0000.0000.000
212A209GLY00.0200.01124.7260.0080.0080.0000.0000.0000.000
213A210THR0-0.074-0.04427.3280.0180.0180.0000.0000.0000.000
214A211HIS0-0.018-0.00228.9000.0080.0080.0000.0000.0000.000
215A212TYR0-0.022-0.01331.3610.0070.0070.0000.0000.0000.000
216A213ASP-1-0.855-0.93935.008-0.105-0.1050.0000.0000.0000.000
217A214MLZ10.8310.91535.6300.1010.1010.0000.0000.0000.000
218A215PRO0-0.0020.01931.200-0.004-0.0040.0000.0000.0000.000
219A216SER00.0110.00931.6040.0100.0100.0000.0000.0000.000
220A217PHE0-0.024-0.01732.9630.0020.0020.0000.0000.0000.000
221A218HIS10.9490.98929.4730.1310.1310.0000.0000.0000.000