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: ZYJ2N

Calculation Name: 4EQ6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4EQ6

Chain ID: A

ChEMBL ID:

UniProt ID: P40465

Base Structure: X-ray

Registration Date: 2023-06-20

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 192
LigandCharge DGL=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2300067.565395
FMO2-HF: Nuclear repulsion 2221207.926688
FMO2-HF: Total energy -78859.638707
FMO2-MP2: Total energy -79091.046638


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.
-11.238-1.5484.344-4.481-9.55-0.015
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 : -0.001 / q_NPA : 0.000
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].
3A3TYR00.027-0.0173.810-0.4562.6360.115-1.458-1.748-0.001
4A4GLU-1-0.928-0.9825.774-0.005-0.0050.0000.0000.0000.000
5A5ASP-1-0.919-0.9432.585-1.613-0.8771.555-0.677-1.615-0.006
6A6LEU0-0.127-0.0542.507-4.446-2.1132.268-1.469-3.131-0.007
7A7GLU-1-0.902-0.9454.544-2.000-1.9860.0080.096-0.1180.000
8A8LEU0-0.059-0.0217.1000.1850.1850.0000.0000.0000.000
9A9ILE0-0.040-0.02810.1260.0520.0520.0000.0000.0000.000
10A10THR0-0.0050.0124.184-0.147-0.016-0.001-0.007-0.1240.000
11A11ILE0-0.007-0.0047.4940.0510.0510.0000.0000.0000.000
12A12TRP00.003-0.0025.4690.2850.2850.0000.0000.0000.000
13A13PRO0-0.004-0.0088.186-0.106-0.1060.0000.0000.0000.000
14A14SER0-0.038-0.02511.0090.1060.1060.0000.0000.0000.000
15A15PRO00.0210.0548.4620.0780.0780.0000.0000.0000.000
16A16THR00.016-0.01110.382-0.135-0.1350.0000.0000.0000.000
17A17LYS11.0290.99510.878-0.169-0.1690.0000.0000.0000.000
18A18ASN0-0.029-0.02011.741-0.069-0.0690.0000.0000.0000.000
19A19LYS11.0071.0016.635-2.333-2.3330.0000.0000.0000.000
20A20LEU00.0640.0626.550-0.045-0.0450.0000.0000.0000.000
21A21CYS0-0.045-0.0248.139-0.227-0.2270.0000.0000.0000.000
22A22GLN0-0.026-0.0156.5030.1270.1270.0000.0000.0000.000
23A23PHE00.0550.0352.612-0.9140.3370.268-0.369-1.1500.001
24A24ILE00.0250.0115.070-0.374-0.377-0.001-0.0020.0060.000
25A25LYS10.8890.9518.3930.1790.1790.0000.0000.0000.000
26A26GLN0-0.025-0.0283.553-0.0360.3220.004-0.098-0.2630.000
27A27ASN00.0210.0053.9490.3830.706-0.001-0.159-0.1620.000
28A28LEU0-0.060-0.0367.8910.1990.1990.0000.0000.0000.000
29A29SER0-0.078-0.02710.7680.1170.1170.0000.0000.0000.000
30A30LYS10.9761.01710.1410.6150.6150.0000.0000.0000.000
31A31DGL-1-0.875-0.93612.518-0.191-0.1910.0000.0000.0000.000
32A32HIS0-0.040-0.02915.650-0.015-0.0150.0000.0000.0000.000
33A33VAL00.0330.03712.8580.0070.0070.0000.0000.0000.000
34A34VAL0-0.045-0.02116.225-0.004-0.0040.0000.0000.0000.000
35A35THR00.0240.0149.9110.0400.0400.0000.0000.0000.000
36A36GLN0-0.037-0.02513.1000.0330.0330.0000.0000.0000.000
37A37LEU0-0.0150.0069.966-0.020-0.0200.0000.0000.0000.000
38A38PHE0-0.010-0.01012.8290.0380.0380.0000.0000.0000.000
39A39PHE00.0130.00012.7660.0110.0110.0000.0000.0000.000
40A40ILE0-0.017-0.01015.1660.0000.0000.0000.0000.0000.000
41A41ASP-1-0.661-0.78616.6290.1220.1220.0000.0000.0000.000
42A42ALA0-0.0080.00918.716-0.013-0.0130.0000.0000.0000.000
43A43THR0-0.111-0.10820.508-0.002-0.0020.0000.0000.0000.000
44A44SER0-0.055-0.01221.403-0.003-0.0030.0000.0000.0000.000
45A45SER0-0.037-0.04818.7640.0000.0000.0000.0000.0000.000
46A46PHE0-0.0050.01413.7030.0290.0290.0000.0000.0000.000
47A47PRO0-0.0160.00513.8130.0010.0010.0000.0000.0000.000
48A48LEU00.0580.00916.633-0.005-0.0050.0000.0000.0000.000
49A49SER00.0180.01018.869-0.004-0.0040.0000.0000.0000.000
50A50GLN0-0.007-0.02615.805-0.003-0.0030.0000.0000.0000.000
51A51PHE00.0630.01812.0010.0060.0060.0000.0000.0000.000
52A52GLN00.0220.01215.739-0.015-0.0150.0000.0000.0000.000
53A53LYS10.9010.96817.293-0.130-0.1300.0000.0000.0000.000
54A54LEU0-0.072-0.05512.3280.0060.0060.0000.0000.0000.000
55A55VAL0-0.0240.00312.865-0.030-0.0300.0000.0000.0000.000
56A56PRO00.0490.03915.949-0.003-0.0030.0000.0000.0000.000
57A57PRO00.0120.00719.777-0.016-0.0160.0000.0000.0000.000
58A58THR0-0.019-0.01121.363-0.004-0.0040.0000.0000.0000.000
59A59LEU0-0.0270.00619.5190.0040.0040.0000.0000.0000.000
60A60PRO00.0710.02821.415-0.010-0.0100.0000.0000.0000.000
61A61GLU-1-0.901-0.95717.782-0.113-0.1130.0000.0000.0000.000
62A62ASN0-0.007-0.02416.352-0.064-0.0640.0000.0000.0000.000
63A63VAL00.0010.01218.151-0.006-0.0060.0000.0000.0000.000
64A64ARG10.9110.92915.4250.3030.3030.0000.0000.0000.000
65A65ILE0-0.0030.00112.795-0.004-0.0040.0000.0000.0000.000
66A66TYR0-0.059-0.05416.0920.0110.0110.0000.0000.0000.000
67A67GLU-1-0.912-0.94418.470-0.109-0.1090.0000.0000.0000.000
68A68ASN0-0.054-0.00715.9670.0190.0190.0000.0000.0000.000
69A69ILE00.0140.02213.913-0.019-0.0190.0000.0000.0000.000
70A70ARG10.8270.89116.4440.1340.1340.0000.0000.0000.000
71A71ILE00.0180.01017.3540.0050.0050.0000.0000.0000.000
72A72ASN0-0.022-0.02919.3950.0030.0030.0000.0000.0000.000
73A73THR0-0.0050.01520.4050.0110.0110.0000.0000.0000.000
74A74CYS0-0.0130.00221.334-0.009-0.0090.0000.0000.0000.000
75A75LEU00.0370.00323.0830.0100.0100.0000.0000.0000.000
76A76ASP-1-0.853-0.91425.6400.0200.0200.0000.0000.0000.000
77A77LEU00.016-0.00822.620-0.002-0.0020.0000.0000.0000.000
78A78GLU-1-0.866-0.92924.9320.0040.0040.0000.0000.0000.000
79A79GLU-1-0.856-0.92525.1450.0050.0050.0000.0000.0000.000
80A80LEU00.0410.01018.386-0.006-0.0060.0000.0000.0000.000
81A81SER0-0.0280.00021.808-0.010-0.0100.0000.0000.0000.000
82A82ALA00.019-0.00124.107-0.008-0.0080.0000.0000.0000.000
83A83ILE0-0.046-0.02619.507-0.009-0.0090.0000.0000.0000.000
84A84THR00.0100.00319.631-0.010-0.0100.0000.0000.0000.000
85A85VAL0-0.050-0.02420.945-0.010-0.0100.0000.0000.0000.000
86A86LYS10.9680.99222.1580.0390.0390.0000.0000.0000.000
87A87LEU00.0220.00616.433-0.007-0.0070.0000.0000.0000.000
88A88LEU00.0080.00520.156-0.009-0.0090.0000.0000.0000.000
89A89GLN0-0.033-0.02421.768-0.005-0.0050.0000.0000.0000.000
90A90ILE0-0.005-0.00119.979-0.002-0.0020.0000.0000.0000.000
91A91LEU00.0100.00416.531-0.004-0.0040.0000.0000.0000.000
92A92SER0-0.008-0.00620.746-0.005-0.0050.0000.0000.0000.000
93A93MET0-0.031-0.01624.1150.0010.0010.0000.0000.0000.000
94A94ASN0-0.028-0.00221.232-0.002-0.0020.0000.0000.0000.000
95A95LYS10.8780.91319.4620.1260.1260.0000.0000.0000.000
96A96ILE0-0.025-0.01524.0430.0020.0020.0000.0000.0000.000
97A97ASN0-0.073-0.04726.9900.0060.0060.0000.0000.0000.000
98A98ALA0-0.0080.02224.5240.0010.0010.0000.0000.0000.000
99A99GLN0-0.060-0.01525.6240.0010.0010.0000.0000.0000.000
100A108GLU-1-0.907-0.95019.864-0.163-0.1630.0000.0000.0000.000
101A109PRO00.0500.04116.4880.0020.0020.0000.0000.0000.000
102A110LEU0-0.048-0.02016.470-0.023-0.0230.0000.0000.0000.000
103A111LYS10.8540.93411.1230.3110.3110.0000.0000.0000.000
104A112ILE00.002-0.00412.596-0.024-0.0240.0000.0000.0000.000
105A113ILE00.0300.0136.9790.0080.0080.0000.0000.0000.000
106A114LEU0-0.029-0.00910.0690.0100.0100.0000.0000.0000.000
107A115TYR0-0.051-0.0517.9000.0600.0600.0000.0000.0000.000
108A116ILE0-0.002-0.00711.539-0.012-0.0120.0000.0000.0000.000
109A117ASN00.0260.01413.7190.0560.0560.0000.0000.0000.000
110A118GLY00.0770.03715.428-0.024-0.0240.0000.0000.0000.000
111A119LEU00.0570.01616.702-0.017-0.0170.0000.0000.0000.000
112A120GLU-1-0.834-0.93818.9890.1240.1240.0000.0000.0000.000
113A121VAL0-0.053-0.02021.112-0.010-0.0100.0000.0000.0000.000
114A122MET0-0.0200.00919.162-0.012-0.0120.0000.0000.0000.000
115A123PHE00.0220.00222.769-0.007-0.0070.0000.0000.0000.000
116A124ARG10.9160.95824.568-0.081-0.0810.0000.0000.0000.000
117A125ASN0-0.006-0.01127.002-0.003-0.0030.0000.0000.0000.000
118A126SER00.0400.01227.108-0.004-0.0040.0000.0000.0000.000
119A127GLN0-0.062-0.02828.701-0.007-0.0070.0000.0000.0000.000
120A128PHE0-0.047-0.01430.5840.0010.0010.0000.0000.0000.000
121A129LYS10.8390.91430.850-0.021-0.0210.0000.0000.0000.000
122A130SER0-0.039-0.00931.973-0.004-0.0040.0000.0000.0000.000
123A131SER00.0440.02033.6550.0020.0020.0000.0000.0000.000
124A132PRO00.0750.02730.6930.0000.0000.0000.0000.0000.000
125A133GLN00.0120.01829.8990.0000.0000.0000.0000.0000.000
126A134ARG10.9620.99330.4640.0020.0020.0000.0000.0000.000
127A135SER00.0440.01527.275-0.003-0.0030.0000.0000.0000.000
128A136HIS0-0.053-0.04925.7030.0030.0030.0000.0000.0000.000
129A137GLU-1-0.882-0.93625.603-0.010-0.0100.0000.0000.0000.000
130A138LEU00.0080.01425.766-0.005-0.0050.0000.0000.0000.000
131A139LEU0-0.016-0.00819.637-0.003-0.0030.0000.0000.0000.000
132A140ARG10.8760.94121.4780.0170.0170.0000.0000.0000.000
133A141ASP-1-0.839-0.92422.192-0.030-0.0300.0000.0000.0000.000
134A142THR0-0.064-0.03419.540-0.008-0.0080.0000.0000.0000.000
135A143LEU0-0.001-0.00116.127-0.006-0.0060.0000.0000.0000.000
136A144LEU00.016-0.00217.887-0.011-0.0110.0000.0000.0000.000
137A145LYS10.9310.98319.8600.0350.0350.0000.0000.0000.000
138A146LEU00.016-0.01315.516-0.010-0.0100.0000.0000.0000.000
139A147ARG10.7810.87912.4870.1250.1250.0000.0000.0000.000
140A148VAL00.0080.00116.265-0.017-0.0170.0000.0000.0000.000
141A149MET0-0.085-0.03417.390-0.004-0.0040.0000.0000.0000.000
142A150GLY00.001-0.00413.775-0.009-0.0090.0000.0000.0000.000
143A151ASN0-0.046-0.03513.990-0.041-0.0410.0000.0000.0000.000
144A152ASP-1-0.871-0.89615.671-0.135-0.1350.0000.0000.0000.000
145A153GLU-1-0.906-0.94717.069-0.167-0.1670.0000.0000.0000.000
146A154ASN0-0.095-0.05718.685-0.012-0.0120.0000.0000.0000.000
147A155GLU-1-0.831-0.91316.058-0.262-0.2620.0000.0000.0000.000
148A156ASN0-0.079-0.05517.632-0.008-0.0080.0000.0000.0000.000
149A157ALA0-0.0020.00317.309-0.002-0.0020.0000.0000.0000.000
150A158SER0-0.0040.01113.347-0.003-0.0030.0000.0000.0000.000
151A159ILE0-0.020-0.01512.550-0.004-0.0040.0000.0000.0000.000
152A160ARG10.9390.9887.9300.1710.1710.0000.0000.0000.000
153A161THR00.0140.0049.899-0.026-0.0260.0000.0000.0000.000
154A162LEU0-0.021-0.0044.9180.0390.0390.0000.0000.0000.000
155A163LEU0-0.024-0.0168.903-0.047-0.0470.0000.0000.0000.000
156A164GLU-1-0.842-0.91010.5400.3880.3880.0000.0000.0000.000
157A165PHE0-0.009-0.02111.994-0.069-0.0690.0000.0000.0000.000
158A166PRO00.0260.03213.9630.0700.0700.0000.0000.0000.000
159A167LYS11.0030.99515.017-0.468-0.4680.0000.0000.0000.000
160A168GLU-1-0.898-0.96116.2650.2310.2310.0000.0000.0000.000
161A169GLN0-0.085-0.04417.900-0.030-0.0300.0000.0000.0000.000
162A170LEU00.0300.01513.294-0.023-0.0230.0000.0000.0000.000
163A171LEU00.0220.00617.3770.0080.0080.0000.0000.0000.000
164A172ASP-1-0.803-0.89619.5890.0890.0890.0000.0000.0000.000
165A173TYR0-0.060-0.02011.388-0.044-0.0440.0000.0000.0000.000
166A174TYR0-0.059-0.05212.953-0.009-0.0090.0000.0000.0000.000
167A175LEU0-0.0040.01117.809-0.004-0.0040.0000.0000.0000.000
168A176LYS10.9280.98114.482-0.110-0.1100.0000.0000.0000.000
169A177LYS10.8070.89313.642-0.349-0.3490.0000.0000.0000.000
170A178ASN00.0320.05019.3160.0150.0150.0000.0000.0000.000
171A192ARG10.8780.92222.637-0.110-0.1100.0000.0000.0000.000
172A193ILE00.0100.02329.382-0.003-0.0030.0000.0000.0000.000
173A194LYS10.7510.86123.175-0.072-0.0720.0000.0000.0000.000
174A195ASN0-0.009-0.00629.152-0.006-0.0060.0000.0000.0000.000
175A196GLY00.0300.01527.885-0.001-0.0010.0000.0000.0000.000
176A197ASP-1-0.838-0.89422.2240.0560.0560.0000.0000.0000.000
177A198SER0-0.018-0.01119.999-0.008-0.0080.0000.0000.0000.000
178A199LEU00.0420.01218.171-0.003-0.0030.0000.0000.0000.000
179A200ALA00.0390.02215.840-0.009-0.0090.0000.0000.0000.000
180A201GLU-1-0.755-0.88016.3110.1060.1060.0000.0000.0000.000
181A202TYR0-0.010-0.00418.347-0.018-0.0180.0000.0000.0000.000
182A203ILE00.0270.00114.248-0.016-0.0160.0000.0000.0000.000
183A204TRP0-0.006-0.00712.231-0.008-0.0080.0000.0000.0000.000
184A205LYS10.7910.88614.633-0.060-0.0600.0000.0000.0000.000
185A206TYR0-0.044-0.02117.376-0.012-0.0120.0000.0000.0000.000
186A207TYR0-0.014-0.01516.269-0.010-0.0100.0000.0000.0000.000
187A208ALA0-0.0080.00310.957-0.007-0.0070.0000.0000.0000.000
188A209ASP-1-0.742-0.8468.737-0.199-0.1990.0000.0000.0000.000
189A210SER00.0080.0055.3410.0230.0230.0000.0000.0000.000
190A211LEU0-0.032-0.0147.6770.1170.1170.0000.0000.0000.000
191A212PHE00.0040.0053.614-0.9110.5440.129-0.338-1.245-0.002
192A213GLU-1-0.863-0.9605.8531.0681.0680.0000.0000.0000.000