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: 2JZ1R

Calculation Name: 1M3S-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1M3S

Chain ID: A

ChEMBL ID:

UniProt ID: P42404

Base Structure: X-ray

Registration Date: 2023-09-20

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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1834444.169701
FMO2-HF: Nuclear repulsion 1763261.567594
FMO2-HF: Total energy -71182.602107
FMO2-MP2: Total energy -71386.86992


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:0:GLY)


Summations of interaction energy for fragment #1(A:0:GLY)
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.
0.1851.908-0.014-0.931-0.78-0.001
Interaction energy analysis for fragmet #1(A:0:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / q_NPA : -0.006
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].
3A2LYS10.9210.9563.9011.8283.294-0.018-0.839-0.610-0.001
4A3THR00.0360.0127.4210.2180.2180.0000.0000.0000.000
5A4THR00.010-0.0069.3960.0480.0480.0000.0000.0000.000
6A5GLU-1-0.841-0.9187.822-1.774-1.7740.0000.0000.0000.000
7A6TYR00.0660.0283.864-0.554-0.2970.004-0.092-0.1700.000
8A7VAL0-0.034-0.0099.3640.0810.0810.0000.0000.0000.000
9A8ALA00.0030.01111.8050.0320.0320.0000.0000.0000.000
10A9GLU-1-0.913-0.9649.3210.2340.2340.0000.0000.0000.000
11A10ILE0-0.019-0.00511.4660.0300.0300.0000.0000.0000.000
12A11LEU00.0040.00714.223-0.012-0.0120.0000.0000.0000.000
13A12ASN00.013-0.00213.008-0.013-0.0130.0000.0000.0000.000
14A13GLU-1-0.760-0.84613.0190.4930.4930.0000.0000.0000.000
15A14LEU0-0.023-0.02616.366-0.014-0.0140.0000.0000.0000.000
16A15HIS0-0.0350.00319.016-0.006-0.0060.0000.0000.0000.000
17A16ASN00.000-0.01818.569-0.011-0.0110.0000.0000.0000.000
18A17SER0-0.012-0.00620.134-0.007-0.0070.0000.0000.0000.000
19A18ALA00.028-0.00121.855-0.005-0.0050.0000.0000.0000.000
20A19ALA0-0.0130.00724.099-0.006-0.0060.0000.0000.0000.000
21A20TYR0-0.076-0.03722.345-0.004-0.0040.0000.0000.0000.000
22A21ILE0-0.056-0.02526.9920.0040.0040.0000.0000.0000.000
23A22SER0-0.053-0.01929.674-0.008-0.0080.0000.0000.0000.000
24A23ASN00.0450.00133.3640.0040.0040.0000.0000.0000.000
25A24GLU-1-0.902-0.93335.6130.0250.0250.0000.0000.0000.000
26A25GLU-1-0.937-0.98536.1440.0450.0450.0000.0000.0000.000
27A26ALA0-0.002-0.02034.5810.0010.0010.0000.0000.0000.000
28A27ASP-1-0.890-0.94836.5460.0240.0240.0000.0000.0000.000
29A28GLN00.0010.00839.536-0.002-0.0020.0000.0000.0000.000
30A29LEU0-0.026-0.01336.0630.0010.0010.0000.0000.0000.000
31A30ALA0-0.013-0.01039.3700.0000.0000.0000.0000.0000.000
32A31ASP-1-0.907-0.95440.8440.0230.0230.0000.0000.0000.000
33A32HIS00.020-0.00142.798-0.001-0.0010.0000.0000.0000.000
34A33ILE0-0.037-0.02238.7600.0000.0000.0000.0000.0000.000
35A34LEU0-0.074-0.04543.398-0.002-0.0020.0000.0000.0000.000
36A35SER0-0.074-0.02346.096-0.001-0.0010.0000.0000.0000.000
37A36SER0-0.0010.01246.0070.0000.0000.0000.0000.0000.000
38A37HIS0-0.034-0.00547.801-0.001-0.0010.0000.0000.0000.000
39A38GLN0-0.080-0.06046.4630.0000.0000.0000.0000.0000.000
40A39ILE00.0040.00940.5420.0010.0010.0000.0000.0000.000
41A40PHE0-0.038-0.01741.2420.0010.0010.0000.0000.0000.000
42A41THR00.003-0.00335.5440.0020.0020.0000.0000.0000.000
43A42ALA00.010-0.01335.8610.0000.0000.0000.0000.0000.000
44A43GLY00.0510.02431.8910.0030.0030.0000.0000.0000.000
45A44ALA0-0.005-0.00230.778-0.004-0.0040.0000.0000.0000.000
46A45GLY00.0220.00327.5230.0080.0080.0000.0000.0000.000
47A46ARG10.9420.93919.055-0.254-0.2540.0000.0000.0000.000
48A47SER00.0480.02825.752-0.008-0.0080.0000.0000.0000.000
49A48GLY0-0.0160.00527.782-0.010-0.0100.0000.0000.0000.000
50A49LEU0-0.016-0.01025.632-0.007-0.0070.0000.0000.0000.000
51A50MET00.0020.01323.754-0.011-0.0110.0000.0000.0000.000
52A51ALA00.0200.00828.740-0.009-0.0090.0000.0000.0000.000
53A52LYS10.8650.93231.969-0.091-0.0910.0000.0000.0000.000
54A53SER0-0.028-0.00829.178-0.008-0.0080.0000.0000.0000.000
55A54PHE00.0600.02531.671-0.006-0.0060.0000.0000.0000.000
56A55ALA00.005-0.01233.715-0.006-0.0060.0000.0000.0000.000
57A56MET0-0.0090.00133.376-0.005-0.0050.0000.0000.0000.000
58A57ARG10.9470.97632.143-0.039-0.0390.0000.0000.0000.000
59A58LEU00.011-0.00336.507-0.005-0.0050.0000.0000.0000.000
60A59MET00.0220.02639.359-0.004-0.0040.0000.0000.0000.000
61A60HIS0-0.029-0.00736.009-0.003-0.0030.0000.0000.0000.000
62A61MET00.0070.02239.512-0.002-0.0020.0000.0000.0000.000
63A62GLY0-0.017-0.01042.194-0.002-0.0020.0000.0000.0000.000
64A63PHE0-0.044-0.02841.791-0.001-0.0010.0000.0000.0000.000
65A64ASN0-0.0030.01444.4160.0020.0020.0000.0000.0000.000
66A65ALA00.002-0.00240.4080.0010.0010.0000.0000.0000.000
67A66HIS00.0150.00541.6170.0020.0020.0000.0000.0000.000
68A67ILE00.0020.00836.2360.0030.0030.0000.0000.0000.000
69A68VAL0-0.009-0.00438.624-0.002-0.0020.0000.0000.0000.000
70A69GLY0-0.032-0.02338.1630.0040.0040.0000.0000.0000.000
71A70GLU-1-0.849-0.90436.8490.0740.0740.0000.0000.0000.000
72A71ILE0-0.006-0.00840.472-0.002-0.0020.0000.0000.0000.000
73A72LEU0-0.041-0.03243.404-0.002-0.0020.0000.0000.0000.000
74A73THR0-0.054-0.02341.838-0.001-0.0010.0000.0000.0000.000
75A74PRO00.0080.02544.6950.0000.0000.0000.0000.0000.000
76A75PRO0-0.037-0.03447.1660.0020.0020.0000.0000.0000.000
77A76LEU0-0.0090.00245.8440.0000.0000.0000.0000.0000.000
78A77ALA0-0.058-0.04148.792-0.001-0.0010.0000.0000.0000.000
79A78GLU-1-0.942-0.98450.6600.0310.0310.0000.0000.0000.000
80A79GLY0-0.006-0.00550.600-0.001-0.0010.0000.0000.0000.000
81A80ASP-1-0.771-0.85846.9040.0360.0360.0000.0000.0000.000
82A81LEU0-0.0030.00441.3460.0020.0020.0000.0000.0000.000
83A82VAL0-0.029-0.02239.9550.0010.0010.0000.0000.0000.000
84A83ILE00.0180.01235.5550.0010.0010.0000.0000.0000.000
85A84ILE0-0.043-0.03734.7290.0040.0040.0000.0000.0000.000
86A85GLY00.0640.04931.4090.0000.0000.0000.0000.0000.000
87A86SER0-0.070-0.05730.2180.0100.0100.0000.0000.0000.000
88A87GLY00.0770.06526.948-0.004-0.0040.0000.0000.0000.000
89A88SER0-0.008-0.00927.907-0.007-0.0070.0000.0000.0000.000
90A89GLY00.0920.03329.640-0.006-0.0060.0000.0000.0000.000
91A90GLU-1-0.799-0.88032.4650.0890.0890.0000.0000.0000.000
92A91THR0-0.070-0.02731.6860.0010.0010.0000.0000.0000.000
93A92LYS11.0481.01334.223-0.101-0.1010.0000.0000.0000.000
94A93SER00.0200.00636.023-0.004-0.0040.0000.0000.0000.000
95A94LEU00.0300.01933.131-0.004-0.0040.0000.0000.0000.000
96A95ILE00.0060.01337.292-0.005-0.0050.0000.0000.0000.000
97A96HIS0-0.012-0.00839.655-0.003-0.0030.0000.0000.0000.000
98A97THR00.003-0.00439.893-0.004-0.0040.0000.0000.0000.000
99A98ALA00.0240.02340.272-0.003-0.0030.0000.0000.0000.000
100A99ALA00.0570.02842.253-0.004-0.0040.0000.0000.0000.000
101A100LYS10.8990.94845.188-0.050-0.0500.0000.0000.0000.000
102A101ALA00.0510.02744.520-0.003-0.0030.0000.0000.0000.000
103A102LYS10.8430.92245.177-0.048-0.0480.0000.0000.0000.000
104A103SER0-0.122-0.06047.877-0.003-0.0030.0000.0000.0000.000
105A104LEU0-0.062-0.04649.015-0.002-0.0020.0000.0000.0000.000
106A105HIS00.0260.02851.053-0.001-0.0010.0000.0000.0000.000
107A106GLY00.0580.04947.604-0.001-0.0010.0000.0000.0000.000
108A107ILE0-0.0290.00144.1060.0010.0010.0000.0000.0000.000
109A108VAL0-0.041-0.03540.2850.0020.0020.0000.0000.0000.000
110A109ALA00.0560.03838.428-0.001-0.0010.0000.0000.0000.000
111A110ALA0-0.032-0.02235.6760.0040.0040.0000.0000.0000.000
112A111LEU00.0050.01531.193-0.001-0.0010.0000.0000.0000.000
113A112THR0-0.026-0.05530.3010.0080.0080.0000.0000.0000.000
114A113ILE0-0.0170.01325.007-0.005-0.0050.0000.0000.0000.000
115A114ASN0-0.013-0.01029.066-0.010-0.0100.0000.0000.0000.000
116A115PRO00.0310.01931.983-0.001-0.0010.0000.0000.0000.000
117A116GLU-1-0.962-0.97835.3760.0640.0640.0000.0000.0000.000
118A117SER0-0.040-0.01533.850-0.001-0.0010.0000.0000.0000.000
119A118SER0-0.040-0.07935.965-0.008-0.0080.0000.0000.0000.000
120A119ILE0-0.089-0.03834.584-0.004-0.0040.0000.0000.0000.000
121A120GLY00.0190.01436.642-0.004-0.0040.0000.0000.0000.000
122A121LYS10.9310.96037.618-0.068-0.0680.0000.0000.0000.000
123A122GLN0-0.073-0.03440.821-0.006-0.0060.0000.0000.0000.000
124A123ALA0-0.055-0.01939.308-0.002-0.0020.0000.0000.0000.000
125A124ASP-1-0.790-0.88041.3530.0440.0440.0000.0000.0000.000
126A125LEU0-0.0170.01138.852-0.002-0.0020.0000.0000.0000.000
127A126ILE0-0.012-0.01235.3330.0050.0050.0000.0000.0000.000
128A127ILE00.0540.02731.939-0.002-0.0020.0000.0000.0000.000
129A128ARG10.9190.95828.864-0.072-0.0720.0000.0000.0000.000
130A129MET0-0.052-0.01826.816-0.002-0.0020.0000.0000.0000.000
131A130PRO0-0.003-0.00423.7850.0000.0000.0000.0000.0000.000
132A131GLY00.030-0.01322.8900.0130.0130.0000.0000.0000.000
133A132SER0-0.0170.00223.7920.0080.0080.0000.0000.0000.000
134A133PRO00.037-0.00624.8510.0060.0060.0000.0000.0000.000
135A134LYS10.9621.00825.516-0.072-0.0720.0000.0000.0000.000
136A135ASP-1-0.810-0.89923.6310.1140.1140.0000.0000.0000.000
137A136GLN0-0.057-0.04320.0290.0080.0080.0000.0000.0000.000
138A137SER0-0.051-0.02120.4240.0310.0310.0000.0000.0000.000
139A138ASN0-0.070-0.04021.270-0.014-0.0140.0000.0000.0000.000
140A139GLY0-0.019-0.01317.7000.0180.0180.0000.0000.0000.000
141A140SER0-0.020-0.00517.957-0.001-0.0010.0000.0000.0000.000
142A141TYR00.0760.05419.4110.0070.0070.0000.0000.0000.000
143A142LYS10.9160.95213.116-0.185-0.1850.0000.0000.0000.000
144A143THR0-0.027-0.04914.318-0.010-0.0100.0000.0000.0000.000
145A144ILE0-0.013-0.0018.0370.0610.0610.0000.0000.0000.000
146A145GLN0-0.063-0.02810.9690.1620.1620.0000.0000.0000.000
147A146PRO0-0.001-0.00612.828-0.048-0.0480.0000.0000.0000.000
148A147MET0-0.005-0.02115.594-0.062-0.0620.0000.0000.0000.000
149A148GLY00.0510.03219.094-0.008-0.0080.0000.0000.0000.000
150A149SER0-0.0250.00116.886-0.031-0.0310.0000.0000.0000.000
151A150LEU00.0490.03517.378-0.035-0.0350.0000.0000.0000.000
152A151PHE00.0190.01519.203-0.035-0.0350.0000.0000.0000.000
153A152GLU-1-0.839-0.92121.7260.2100.2100.0000.0000.0000.000
154A153GLN00.011-0.00916.419-0.029-0.0290.0000.0000.0000.000
155A154THR0-0.002-0.01722.095-0.024-0.0240.0000.0000.0000.000
156A155LEU0-0.039-0.01824.106-0.016-0.0160.0000.0000.0000.000
157A156LEU0-0.0120.00624.302-0.009-0.0090.0000.0000.0000.000
158A157LEU00.0080.00222.562-0.012-0.0120.0000.0000.0000.000
159A158PHE00.0250.01626.834-0.010-0.0100.0000.0000.0000.000
160A159TYR0-0.032-0.03529.432-0.004-0.0040.0000.0000.0000.000
161A160ASP-1-0.855-0.93228.9010.0470.0470.0000.0000.0000.000
162A161ALA0-0.036-0.00730.548-0.007-0.0070.0000.0000.0000.000
163A162VAL0-0.008-0.00432.307-0.005-0.0050.0000.0000.0000.000
164A163ILE00.0110.00034.296-0.004-0.0040.0000.0000.0000.000
165A164LEU00.004-0.00232.140-0.004-0.0040.0000.0000.0000.000
166A165LYS10.8700.94036.138-0.020-0.0200.0000.0000.0000.000
167A166LEU0-0.026-0.01738.344-0.002-0.0020.0000.0000.0000.000
168A167MET0-0.031-0.01637.840-0.001-0.0010.0000.0000.0000.000
169A168GLU-1-0.865-0.91340.0330.0090.0090.0000.0000.0000.000
170A169LYS10.9130.96041.792-0.018-0.0180.0000.0000.0000.000
171A170LYS10.8840.94643.998-0.021-0.0210.0000.0000.0000.000
172A171GLY0-0.0200.00745.083-0.001-0.0010.0000.0000.0000.000
173A172LEU0-0.056-0.03542.479-0.001-0.0010.0000.0000.0000.000
174A173ASP-1-0.797-0.92540.435-0.004-0.0040.0000.0000.0000.000
175A174SER0-0.043-0.03436.5630.0020.0020.0000.0000.0000.000
176A175GLU-1-1.006-0.97638.684-0.011-0.0110.0000.0000.0000.000
177A176THR0-0.062-0.03840.3470.0010.0010.0000.0000.0000.000
178A177MET0-0.058-0.00239.4550.0020.0020.0000.0000.0000.000
179A178PHE0-0.009-0.00642.4510.0000.0000.0000.0000.0000.000
180A179THR0-0.001-0.01239.2470.0020.0020.0000.0000.0000.000
181A180HIS0-0.025-0.00842.416-0.001-0.0010.0000.0000.0000.000
182A181HIS0-0.065-0.03239.6250.0030.0030.0000.0000.0000.000
183A182ALA00.0090.00340.174-0.001-0.0010.0000.0000.0000.000
184A183ASN00.018-0.01241.6590.0010.0010.0000.0000.0000.000
185A184LEU00.0160.00843.579-0.001-0.0010.0000.0000.0000.000
186A185GLU-1-1.013-0.98339.0810.0370.0370.0000.0000.0000.000