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: YV872

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 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 221
LigandCharge MLZ=1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2712133.16183
FMO2-HF: Nuclear repulsion 2626014.394765
FMO2-HF: Total energy -86118.767065
FMO2-MP2: Total energy -86372.658065


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.
-2.771-0.7020.017-0.793-1.292-0.001
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 : 0.005 / q_NPA : -0.016
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].
3A0ALA00.0510.0353.899-0.2770.863-0.002-0.499-0.6400.000
4A1MET0-0.076-0.0245.6620.6740.6740.0000.0000.0000.000
5A2TYR0-0.030-0.0278.7320.3880.3880.0000.0000.0000.000
6A3MLZ10.8550.9478.746-0.531-0.5310.0000.0000.0000.000
7A4TYR0-0.009-0.01310.5520.1310.1310.0000.0000.0000.000
8A5ILE00.0250.01312.451-0.056-0.0560.0000.0000.0000.000
9A6THR0-0.008-0.02215.1330.0560.0560.0000.0000.0000.000
10A7ILE0-0.017-0.00114.949-0.042-0.0420.0000.0000.0000.000
11A8LEU00.008-0.00419.2590.0410.0410.0000.0000.0000.000
12A9GLY00.0180.00422.687-0.017-0.0170.0000.0000.0000.000
13A10ALA00.0100.00220.983-0.007-0.0070.0000.0000.0000.000
14A11ALA00.0100.00521.6370.0020.0020.0000.0000.0000.000
15A12GLY00.0130.02323.7120.0060.0060.0000.0000.0000.000
16A13GLN00.0380.00421.797-0.019-0.0190.0000.0000.0000.000
17A14ILE00.0560.02818.3940.0050.0050.0000.0000.0000.000
18A15ALA00.0400.03017.670-0.032-0.0320.0000.0000.0000.000
19A16GLN0-0.012-0.00417.3850.0170.0170.0000.0000.0000.000
20A17MLZ10.8510.93216.5500.2070.2070.0000.0000.0000.000
21A18LEU00.0190.02312.148-0.011-0.0110.0000.0000.0000.000
22A19THR0-0.007-0.02012.498-0.016-0.0160.0000.0000.0000.000
23A20ALA00.0230.01212.9740.0590.0590.0000.0000.0000.000
24A21THR0-0.022-0.00610.1270.0670.0670.0000.0000.0000.000
25A22LEU00.0190.0088.1460.0210.0210.0000.0000.0000.000
26A23LEU0-0.0120.0108.2800.2440.2440.0000.0000.0000.000
27A24THR0-0.063-0.0349.8570.2930.2930.0000.0000.0000.000
28A25TYR0-0.041-0.0245.2780.2400.2400.0000.0000.0000.000
29A26THR0-0.030-0.0193.834-0.1190.2990.003-0.102-0.3180.000
30A27ASP-1-0.814-0.9265.2151.0731.084-0.001-0.001-0.0080.000
31A28MET0-0.0120.0067.333-0.368-0.3680.0000.0000.0000.000
32A29HIS0-0.076-0.0399.6000.1220.1220.0000.0000.0000.000
33A30ILE00.0200.00611.894-0.105-0.1050.0000.0000.0000.000
34A31THR00.0030.00715.5160.0480.0480.0000.0000.0000.000
35A32LEU00.0180.00917.732-0.043-0.0430.0000.0000.0000.000
36A33TYR00.000-0.02620.9590.0190.0190.0000.0000.0000.000
37A34GLY00.008-0.00924.337-0.016-0.0160.0000.0000.0000.000
38A35ARG10.9820.98427.4450.0550.0550.0000.0000.0000.000
39A36GLN00.013-0.01329.705-0.002-0.0020.0000.0000.0000.000
40A37LEU00.0340.02723.4960.0010.0010.0000.0000.0000.000
41A38LYS10.9970.99725.850-0.074-0.0740.0000.0000.0000.000
42A39THR00.0020.00827.2400.0050.0050.0000.0000.0000.000
43A40ARG10.8300.91427.5240.0410.0410.0000.0000.0000.000
44A41ILE0-0.0030.00921.118-0.019-0.0190.0000.0000.0000.000
45A42PRO00.0180.03021.1310.0070.0070.0000.0000.0000.000
46A43PRO00.0590.02722.1080.0030.0030.0000.0000.0000.000
47A44GLU-1-0.870-0.93918.7530.1100.1100.0000.0000.0000.000
48A45ILE0-0.062-0.02816.9000.0260.0260.0000.0000.0000.000
49A46ILE0-0.079-0.05518.8070.0110.0110.0000.0000.0000.000
50A47ASP-1-0.923-0.96321.7380.1380.1380.0000.0000.0000.000
51A48HIS0-0.0050.00413.529-0.020-0.0200.0000.0000.0000.000
52A49GLU-1-0.913-0.96114.9460.5890.5890.0000.0000.0000.000
53A50ARG10.8020.9119.323-0.945-0.9450.0000.0000.0000.000
54A51VAL0-0.017-0.00315.190-0.073-0.0730.0000.0000.0000.000
55A52THR0-0.019-0.00117.7740.0070.0070.0000.0000.0000.000
56A53VAL0-0.030-0.01820.864-0.027-0.0270.0000.0000.0000.000
57A54ILE0-0.0110.00223.6610.0050.0050.0000.0000.0000.000
58A55GLU-1-0.838-0.91226.307-0.026-0.0260.0000.0000.0000.000
59A56GLY00.026-0.00129.4680.0000.0000.0000.0000.0000.000
60A57SER0-0.058-0.02830.411-0.004-0.0040.0000.0000.0000.000
61A58PHE00.0620.02726.5710.0010.0010.0000.0000.0000.000
62A59GLN0-0.009-0.00831.4750.0010.0010.0000.0000.0000.000
63A60ASN0-0.050-0.01732.7650.0090.0090.0000.0000.0000.000
64A61PRO00.0750.03532.3130.0000.0000.0000.0000.0000.000
65A62GLY00.0540.02631.525-0.004-0.0040.0000.0000.0000.000
66A63MLZ10.8310.90430.3290.0200.0200.0000.0000.0000.000
67A64LEU00.0040.01726.5340.0010.0010.0000.0000.0000.000
68A65GLU-1-0.804-0.89526.706-0.072-0.0720.0000.0000.0000.000
69A66GLN0-0.028-0.00126.9320.0010.0010.0000.0000.0000.000
70A67ALA00.0020.00324.0630.0030.0030.0000.0000.0000.000
71A68VAL0-0.0010.01822.258-0.008-0.0080.0000.0000.0000.000
72A69THR0-0.025-0.03022.745-0.013-0.0130.0000.0000.0000.000
73A70ASN0-0.055-0.03320.0170.0000.0000.0000.0000.0000.000
74A71ALA0-0.0040.02518.1260.0010.0010.0000.0000.0000.000
75A72GLU-1-0.816-0.90613.227-0.290-0.2900.0000.0000.0000.000
76A73VAL0-0.023-0.00813.193-0.038-0.0380.0000.0000.0000.000
77A74VAL0-0.021-0.01116.5580.0520.0520.0000.0000.0000.000
78A75PHE00.0360.01416.551-0.029-0.0290.0000.0000.0000.000
79A76VAL0-0.007-0.01918.6060.0480.0480.0000.0000.0000.000
80A77GLY00.0190.00221.533-0.014-0.0140.0000.0000.0000.000
81A78ALA0-0.014-0.00322.3680.0020.0020.0000.0000.0000.000
82A79MET0-0.0150.00625.655-0.003-0.0030.0000.0000.0000.000
83A80GLU-1-0.898-0.95328.212-0.115-0.1150.0000.0000.0000.000
84A81SER0-0.025-0.03531.5830.0090.0090.0000.0000.0000.000
85A82GLY00.0720.03432.460-0.007-0.0070.0000.0000.0000.000
86A83SER00.008-0.00434.126-0.002-0.0020.0000.0000.0000.000
87A84ASP-1-0.821-0.87231.250-0.091-0.0910.0000.0000.0000.000
88A85MET00.0430.03525.899-0.005-0.0050.0000.0000.0000.000
89A86ALA00.0240.01129.983-0.006-0.0060.0000.0000.0000.000
90A87SER0-0.091-0.05932.2840.0050.0050.0000.0000.0000.000
91A88ILE00.0150.00625.6460.0040.0040.0000.0000.0000.000
92A89VAL00.0100.01027.827-0.003-0.0030.0000.0000.0000.000
93A90LYS10.9230.96328.9360.0860.0860.0000.0000.0000.000
94A91ALA00.003-0.00628.2590.0050.0050.0000.0000.0000.000
95A92LEU00.0500.01722.6470.0060.0060.0000.0000.0000.000
96A93SER0-0.017-0.00726.406-0.001-0.0010.0000.0000.0000.000
97A94ARG10.7900.89229.1160.0730.0730.0000.0000.0000.000
98A95MLZ10.8240.90225.7600.0810.0810.0000.0000.0000.000
99A96ASN0-0.016-0.00225.5540.0010.0010.0000.0000.0000.000
100A97ILE00.0310.03720.966-0.015-0.0150.0000.0000.0000.000
101A98ARG10.8310.89721.3240.2120.2120.0000.0000.0000.000
102A99ARG10.7990.88016.3260.5670.5670.0000.0000.0000.000
103A100VAL0-0.026-0.01319.4420.0230.0230.0000.0000.0000.000
104A101ILE00.0390.02414.984-0.013-0.0130.0000.0000.0000.000
105A102GLY0-0.010-0.01019.1740.0280.0280.0000.0000.0000.000
106A103VAL0-0.0220.00120.913-0.020-0.0200.0000.0000.0000.000
107A104SER0-0.031-0.05023.3190.0250.0250.0000.0000.0000.000
108A105MET0-0.0060.01226.461-0.011-0.0110.0000.0000.0000.000
109A106ALA00.000-0.00127.740-0.003-0.0030.0000.0000.0000.000
110A107GLY00.0400.00529.4410.0130.0130.0000.0000.0000.000
111A108LEU0-0.090-0.04831.2650.0140.0140.0000.0000.0000.000
112A109SER0-0.079-0.05931.4690.0090.0090.0000.0000.0000.000
113A110GLY00.0270.03834.141-0.001-0.0010.0000.0000.0000.000
114A111GLU-1-0.750-0.86930.021-0.198-0.1980.0000.0000.0000.000
115A112PHE0-0.0040.01130.447-0.006-0.0060.0000.0000.0000.000
116A113PRO00.0400.03433.6670.0080.0080.0000.0000.0000.000
117A114VAL00.040-0.00236.6740.0010.0010.0000.0000.0000.000
118A115ALA00.0050.01639.2690.0030.0030.0000.0000.0000.000
119A116LEU00.0400.03831.7920.0040.0040.0000.0000.0000.000
120A117GLU-1-0.971-0.97436.121-0.128-0.1280.0000.0000.0000.000
121A118LYS10.8200.88937.2850.0890.0890.0000.0000.0000.000
122A119TRP00.0660.02434.7900.0020.0020.0000.0000.0000.000
123A120THR00.000-0.00733.5680.0000.0000.0000.0000.0000.000
124A121PHE0-0.019-0.02536.1780.0010.0010.0000.0000.0000.000
125A122ASP-1-0.851-0.90139.133-0.085-0.0850.0000.0000.0000.000
126A123ASN0-0.103-0.05137.3930.0090.0090.0000.0000.0000.000
127A124LEU00.0140.00433.701-0.003-0.0030.0000.0000.0000.000
128A125PRO0-0.0080.01437.1730.0030.0030.0000.0000.0000.000
129A126ILE00.0620.00938.825-0.005-0.0050.0000.0000.0000.000
130A127SER00.0120.00239.723-0.005-0.0050.0000.0000.0000.000
131A128TYR0-0.027-0.02730.0540.0010.0010.0000.0000.0000.000
132A129VAL00.0420.01435.146-0.008-0.0080.0000.0000.0000.000
133A130GLN0-0.071-0.04036.132-0.004-0.0040.0000.0000.0000.000
134A131GLY00.0240.01735.767-0.003-0.0030.0000.0000.0000.000
135A132GLU-1-0.740-0.82429.777-0.187-0.1870.0000.0000.0000.000
136A133ARG10.9120.97032.2070.1210.1210.0000.0000.0000.000
137A134GLN0-0.021-0.01634.342-0.003-0.0030.0000.0000.0000.000
138A135ALA0-0.0110.00530.351-0.003-0.0030.0000.0000.0000.000
139A136ARG10.9120.94629.2750.1620.1620.0000.0000.0000.000
140A137ASN0-0.084-0.04130.448-0.015-0.0150.0000.0000.0000.000
141A138VAL00.0600.03131.512-0.004-0.0040.0000.0000.0000.000
142A139LEU0-0.008-0.01424.453-0.001-0.0010.0000.0000.0000.000
143A140ARG10.9230.97728.3380.1810.1810.0000.0000.0000.000
144A141GLU-1-0.878-0.93529.846-0.140-0.1400.0000.0000.0000.000
145A142SER0-0.056-0.02628.1340.0040.0040.0000.0000.0000.000
146A143ASN00.0260.01528.647-0.019-0.0190.0000.0000.0000.000
147A144LEU00.0090.01424.172-0.004-0.0040.0000.0000.0000.000
148A145ASN00.0000.00019.1720.0110.0110.0000.0000.0000.000
149A146TYR0-0.027-0.01720.989-0.018-0.0180.0000.0000.0000.000
150A147THR00.0170.00118.741-0.035-0.0350.0000.0000.0000.000
151A148ILE0-0.059-0.02421.1390.0050.0050.0000.0000.0000.000
152A149LEU00.0180.00317.472-0.014-0.0140.0000.0000.0000.000
153A150ARG10.7910.87522.1230.2900.2900.0000.0000.0000.000
154A151LEU00.020-0.00321.391-0.016-0.0160.0000.0000.0000.000
155A152THR0-0.0010.00025.1650.0290.0290.0000.0000.0000.000
156A153TRP0-0.065-0.04426.653-0.004-0.0040.0000.0000.0000.000
157A154LEU00.0170.01523.499-0.005-0.0050.0000.0000.0000.000
158A155TYR0-0.108-0.08924.9340.0260.0260.0000.0000.0000.000
159A156ASN0-0.024-0.02823.245-0.034-0.0340.0000.0000.0000.000
160A157ASP-1-0.841-0.94722.187-0.147-0.1470.0000.0000.0000.000
161A158PRO0-0.0130.00119.179-0.029-0.0290.0000.0000.0000.000
162A159GLU-1-0.865-0.92518.248-0.164-0.1640.0000.0000.0000.000
163A160MLZ10.8290.91919.3160.1600.1600.0000.0000.0000.000
164A161THR0-0.024-0.00414.905-0.051-0.0510.0000.0000.0000.000
165A162ASP-1-0.843-0.91915.254-0.507-0.5070.0000.0000.0000.000
166A163TYR0-0.105-0.10312.4220.0900.0900.0000.0000.0000.000
167A164GLU-1-0.813-0.85318.341-0.311-0.3110.0000.0000.0000.000
168A165LEU0-0.019-0.02316.3550.0000.0000.0000.0000.0000.000
169A166ILE0-0.0140.00320.8430.0180.0180.0000.0000.0000.000
170A167PRO00.0460.02023.968-0.001-0.0010.0000.0000.0000.000
171A168GLU-1-0.857-0.94525.290-0.240-0.2400.0000.0000.0000.000
172A169GLY0-0.028-0.01328.4160.0020.0020.0000.0000.0000.000
173A170ALA0-0.032-0.00427.9920.0120.0120.0000.0000.0000.000
174A171GLN00.0100.00730.144-0.001-0.0010.0000.0000.0000.000
175A172PHE0-0.024-0.01225.295-0.018-0.0180.0000.0000.0000.000
176A173ASN0-0.018-0.03329.5580.0150.0150.0000.0000.0000.000
177A174ASH0-0.082-0.06925.2940.0160.0160.0000.0000.0000.000
178A175ALA00.0550.03028.605-0.005-0.0050.0000.0000.0000.000
179A176GLN0-0.026-0.03926.9780.0260.0260.0000.0000.0000.000
180A177VAL00.0130.00621.209-0.016-0.0160.0000.0000.0000.000
181A178SER0-0.010-0.00120.1800.0150.0150.0000.0000.0000.000
182A179ARG10.8770.91020.5960.1400.1400.0000.0000.0000.000
183A180GLU-1-0.761-0.89217.237-0.239-0.2390.0000.0000.0000.000
184A181ALA00.0210.02415.954-0.072-0.0720.0000.0000.0000.000
185A182VAL0-0.009-0.00616.299-0.062-0.0620.0000.0000.0000.000
186A183VAL0-0.028-0.02013.160-0.046-0.0460.0000.0000.0000.000
187A184LYS10.8590.94111.1880.6300.6300.0000.0000.0000.000
188A185ALA00.0740.04911.720-0.162-0.1620.0000.0000.0000.000
189A186ILE0-0.052-0.03113.120-0.057-0.0570.0000.0000.0000.000
190A187PHE0-0.002-0.0034.8410.0230.0230.0000.0000.0000.000
191A188ASP-1-0.806-0.8778.472-1.954-1.9540.0000.0000.0000.000
192A189ILE0-0.028-0.0129.539-0.124-0.1240.0000.0000.0000.000
193A190LEU0-0.058-0.0249.0950.0640.0640.0000.0000.0000.000
194A191HIS0-0.031-0.0293.844-1.684-1.1840.017-0.191-0.326-0.001
195A192ALA0-0.025-0.0017.699-0.034-0.0340.0000.0000.0000.000
196A193ALA0-0.005-0.01410.1860.1680.1680.0000.0000.0000.000
197A194ASP-1-0.848-0.89311.674-0.416-0.4160.0000.0000.0000.000
198A195GLU-1-0.728-0.84114.573-0.708-0.7080.0000.0000.0000.000
199A196THR0-0.046-0.05616.2070.0780.0780.0000.0000.0000.000
200A197PRO0-0.023-0.00717.5500.0450.0450.0000.0000.0000.000
201A198PHE00.0080.00414.3020.0260.0260.0000.0000.0000.000
202A199HIS0-0.0110.01919.3010.0620.0620.0000.0000.0000.000
203A200ARG10.8250.90221.4290.2670.2670.0000.0000.0000.000
204A201THR0-0.0080.01221.7910.0270.0270.0000.0000.0000.000
205A202SER0-0.020-0.02623.551-0.014-0.0140.0000.0000.0000.000
206A203ILE00.0050.01819.9880.0230.0230.0000.0000.0000.000
207A204GLY0-0.005-0.00222.5440.0010.0010.0000.0000.0000.000
208A205VAL00.0110.00018.813-0.032-0.0320.0000.0000.0000.000
209A206GLY00.021-0.00121.6510.0350.0350.0000.0000.0000.000
210A207GLU-1-0.714-0.81221.897-0.241-0.2410.0000.0000.0000.000
211A208PRO00.0580.04321.1000.0310.0310.0000.0000.0000.000
212A209GLY00.0230.02024.2140.0140.0140.0000.0000.0000.000
213A210THR0-0.088-0.05526.7520.0200.0200.0000.0000.0000.000
214A211HIS0-0.026-0.01428.3030.0060.0060.0000.0000.0000.000
215A212TYR0-0.0100.00430.7010.0100.0100.0000.0000.0000.000
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