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: Z6MQN

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 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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1840671.853558
FMO2-HF: Nuclear repulsion 1769487.297634
FMO2-HF: Total energy -71184.555925
FMO2-MP2: Total energy -71388.847473


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.
-2.1520.850.963-2.08-1.883-0.007
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 : 0.028 / q_NPA : 0.019
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].
3A2LYS10.8610.9043.8742.6784.478-0.012-1.054-0.7330.004
4A3THR00.0340.0027.184-0.062-0.0620.0000.0000.0000.000
5A4THR00.0330.0089.0420.0080.0080.0000.0000.0000.000
6A5GLU-1-0.773-0.8557.551-2.616-2.6160.0000.0000.0000.000
7A6TYR00.0520.0132.604-2.192-0.9900.975-1.026-1.150-0.011
8A7VAL0-0.025-0.0068.3250.2260.2260.0000.0000.0000.000
9A8ALA00.0040.00211.7100.1070.1070.0000.0000.0000.000
10A9GLU-1-0.850-0.9178.633-0.772-0.7720.0000.0000.0000.000
11A10ILE0-0.024-0.01211.1620.1640.1640.0000.0000.0000.000
12A11LEU00.004-0.00213.4070.0930.0930.0000.0000.0000.000
13A12ASN0-0.037-0.02212.2270.1330.1330.0000.0000.0000.000
14A13GLU-1-0.766-0.85412.011-0.139-0.1390.0000.0000.0000.000
15A14LEU0-0.024-0.02015.7150.0580.0580.0000.0000.0000.000
16A15HIS0-0.0190.00418.6100.0270.0270.0000.0000.0000.000
17A16ASN00.0140.00818.3730.0560.0560.0000.0000.0000.000
18A17SER0-0.012-0.01219.6900.0360.0360.0000.0000.0000.000
19A18ALA00.038-0.00121.3920.0220.0220.0000.0000.0000.000
20A19ALA0-0.0180.00223.6780.0150.0150.0000.0000.0000.000
21A20TYR0-0.092-0.05221.3070.0160.0160.0000.0000.0000.000
22A21ILE0-0.022-0.00525.9600.0170.0170.0000.0000.0000.000
23A22SER0-0.066-0.04229.184-0.007-0.0070.0000.0000.0000.000
24A23ASN00.016-0.01433.005-0.003-0.0030.0000.0000.0000.000
25A24GLU-1-0.910-0.93934.873-0.047-0.0470.0000.0000.0000.000
26A25GLU-1-0.866-0.93735.246-0.036-0.0360.0000.0000.0000.000
27A26ALA0-0.026-0.01433.8050.0030.0030.0000.0000.0000.000
28A27ASP-1-0.789-0.90135.820-0.063-0.0630.0000.0000.0000.000
29A28GLN00.0500.03738.8810.0050.0050.0000.0000.0000.000
30A29LEU0-0.010-0.01035.4570.0030.0030.0000.0000.0000.000
31A30ALA0-0.002-0.00438.5390.0020.0020.0000.0000.0000.000
32A31ASP-1-0.792-0.90740.013-0.044-0.0440.0000.0000.0000.000
33A32HIS0-0.019-0.00641.8460.0030.0030.0000.0000.0000.000
34A33ILE0-0.033-0.01937.8830.0020.0020.0000.0000.0000.000
35A34LEU0-0.071-0.03242.4490.0010.0010.0000.0000.0000.000
36A35SER0-0.089-0.05145.2420.0020.0020.0000.0000.0000.000
37A36SER0-0.021-0.01145.2450.0020.0020.0000.0000.0000.000
38A37HIS0-0.0130.00147.035-0.003-0.0030.0000.0000.0000.000
39A38GLN0-0.097-0.05546.088-0.001-0.0010.0000.0000.0000.000
40A39ILE00.0210.01139.8700.0000.0000.0000.0000.0000.000
41A40PHE0-0.025-0.00740.3130.0010.0010.0000.0000.0000.000
42A41THR0-0.017-0.02034.6410.0010.0010.0000.0000.0000.000
43A42ALA00.013-0.00135.0110.0050.0050.0000.0000.0000.000
44A43GLY00.0560.01830.994-0.005-0.0050.0000.0000.0000.000
45A44ALA0-0.017-0.01229.6710.0030.0030.0000.0000.0000.000
46A45GLY00.0240.00726.315-0.001-0.0010.0000.0000.0000.000
47A46ARG10.8780.90717.410-0.050-0.0500.0000.0000.0000.000
48A47SER00.011-0.00124.880-0.016-0.0160.0000.0000.0000.000
49A48GLY0-0.0170.00226.668-0.009-0.0090.0000.0000.0000.000
50A49LEU0-0.014-0.01125.205-0.004-0.0040.0000.0000.0000.000
51A50MET0-0.0270.00322.358-0.009-0.0090.0000.0000.0000.000
52A51ALA00.0550.04127.865-0.007-0.0070.0000.0000.0000.000
53A52LYS10.8560.93431.309-0.012-0.0120.0000.0000.0000.000
54A53SER0-0.044-0.03229.220-0.006-0.0060.0000.0000.0000.000
55A54PHE00.0410.01731.257-0.004-0.0040.0000.0000.0000.000
56A55ALA00.0380.01433.062-0.002-0.0020.0000.0000.0000.000
57A56MET0-0.020-0.00732.858-0.003-0.0030.0000.0000.0000.000
58A57ARG10.8550.90829.9110.0770.0770.0000.0000.0000.000
59A58LEU00.0210.00635.695-0.001-0.0010.0000.0000.0000.000
60A59MET0-0.0010.01838.5320.0000.0000.0000.0000.0000.000
61A60HIS0-0.024-0.02134.982-0.004-0.0040.0000.0000.0000.000
62A61MET0-0.010-0.00638.467-0.001-0.0010.0000.0000.0000.000
63A62GLY0-0.035-0.00741.1660.0000.0000.0000.0000.0000.000
64A63PHE00.008-0.00441.0930.0020.0020.0000.0000.0000.000
65A64ASN0-0.0060.00043.3570.0010.0010.0000.0000.0000.000
66A65ALA0-0.016-0.00439.5770.0020.0020.0000.0000.0000.000
67A66HIS0-0.003-0.00540.7290.0020.0020.0000.0000.0000.000
68A67ILE0-0.003-0.00335.606-0.001-0.0010.0000.0000.0000.000
69A68VAL0-0.014-0.00937.6570.0030.0030.0000.0000.0000.000
70A69GLY0-0.046-0.02537.1730.0020.0020.0000.0000.0000.000
71A70GLU-1-0.832-0.90136.0860.0120.0120.0000.0000.0000.000
72A71ILE0-0.043-0.03439.8090.0000.0000.0000.0000.0000.000
73A72LEU0-0.007-0.00542.5510.0000.0000.0000.0000.0000.000
74A73THR0-0.027-0.01341.066-0.001-0.0010.0000.0000.0000.000
75A74PRO00.0210.02843.6830.0020.0020.0000.0000.0000.000
76A75PRO0-0.034-0.02646.3160.0010.0010.0000.0000.0000.000
77A76LEU0-0.020-0.00244.601-0.002-0.0020.0000.0000.0000.000
78A77ALA0-0.031-0.02847.9990.0020.0020.0000.0000.0000.000
79A78GLU-1-0.904-0.95949.657-0.004-0.0040.0000.0000.0000.000
80A79GLY0-0.008-0.00249.808-0.001-0.0010.0000.0000.0000.000
81A80ASP-1-0.763-0.85646.143-0.012-0.0120.0000.0000.0000.000
82A81LEU0-0.0070.00340.5930.0010.0010.0000.0000.0000.000
83A82VAL0-0.032-0.02438.8960.0010.0010.0000.0000.0000.000
84A83ILE00.0090.01534.6700.0000.0000.0000.0000.0000.000
85A84ILE0-0.020-0.01833.9800.0030.0030.0000.0000.0000.000
86A85GLY00.0570.03930.321-0.002-0.0020.0000.0000.0000.000
87A86SER0-0.059-0.05129.1810.0110.0110.0000.0000.0000.000
88A87GLY00.0540.03726.108-0.002-0.0020.0000.0000.0000.000
89A88SER00.018-0.00927.125-0.005-0.0050.0000.0000.0000.000
90A89GLY00.0680.03528.796-0.001-0.0010.0000.0000.0000.000
91A90GLU-1-0.770-0.87131.6850.0470.0470.0000.0000.0000.000
92A91THR00.0040.00831.1970.0080.0080.0000.0000.0000.000
93A92LYS10.8950.92933.345-0.065-0.0650.0000.0000.0000.000
94A93SER00.0400.02535.055-0.003-0.0030.0000.0000.0000.000
95A94LEU0-0.0010.01832.267-0.004-0.0040.0000.0000.0000.000
96A95ILE00.0100.00836.376-0.004-0.0040.0000.0000.0000.000
97A96HIS00.0050.00538.843-0.002-0.0020.0000.0000.0000.000
98A97THR0-0.014-0.01938.873-0.003-0.0030.0000.0000.0000.000
99A98ALA00.0230.01539.639-0.003-0.0030.0000.0000.0000.000
100A99ALA00.0560.03741.521-0.002-0.0020.0000.0000.0000.000
101A100LYS10.7990.90744.330-0.014-0.0140.0000.0000.0000.000
102A101ALA00.0750.04043.666-0.001-0.0010.0000.0000.0000.000
103A102LYS10.8400.89744.5080.0000.0000.0000.0000.0000.000
104A103SER0-0.075-0.04747.171-0.001-0.0010.0000.0000.0000.000
105A104LEU0-0.082-0.05548.0450.0020.0020.0000.0000.0000.000
106A105HIS00.0080.01350.552-0.001-0.0010.0000.0000.0000.000
107A106GLY00.0560.05246.961-0.002-0.0020.0000.0000.0000.000
108A107ILE0-0.030-0.00843.2700.0020.0020.0000.0000.0000.000
109A108VAL0-0.030-0.02339.6380.0010.0010.0000.0000.0000.000
110A109ALA00.0460.02437.863-0.001-0.0010.0000.0000.0000.000
111A110ALA0-0.032-0.01234.7110.0010.0010.0000.0000.0000.000
112A111LEU00.0150.01630.298-0.005-0.0050.0000.0000.0000.000
113A112THR0-0.019-0.03429.3230.0080.0080.0000.0000.0000.000
114A113ILE0-0.0360.00524.022-0.007-0.0070.0000.0000.0000.000
115A114ASN00.000-0.00228.169-0.006-0.0060.0000.0000.0000.000
116A115PRO00.0450.02831.3130.0020.0020.0000.0000.0000.000
117A116GLU-1-0.860-0.92134.6340.0160.0160.0000.0000.0000.000
118A117SER0-0.074-0.03333.3000.0040.0040.0000.0000.0000.000
119A118SER0-0.007-0.04535.416-0.004-0.0040.0000.0000.0000.000
120A119ILE0-0.060-0.01533.721-0.002-0.0020.0000.0000.0000.000
121A120GLY00.0150.01336.001-0.004-0.0040.0000.0000.0000.000
122A121LYS10.8460.90136.951-0.022-0.0220.0000.0000.0000.000
123A122GLN0-0.101-0.05540.031-0.001-0.0010.0000.0000.0000.000
124A123ALA0-0.029-0.00938.685-0.001-0.0010.0000.0000.0000.000
125A124ASP-1-0.801-0.86940.716-0.005-0.0050.0000.0000.0000.000
126A125LEU0-0.0170.00638.147-0.002-0.0020.0000.0000.0000.000
127A126ILE0-0.012-0.01434.1010.0030.0030.0000.0000.0000.000
128A127ILE00.0520.03330.825-0.003-0.0030.0000.0000.0000.000
129A128ARG10.8080.88627.3140.0460.0460.0000.0000.0000.000
130A129MET00.0090.01625.815-0.013-0.0130.0000.0000.0000.000
131A130PRO0-0.068-0.01823.0400.0110.0110.0000.0000.0000.000
132A131GLY00.032-0.00321.9580.0030.0030.0000.0000.0000.000
133A132SER0-0.050-0.04622.9900.0220.0220.0000.0000.0000.000
134A133PRO00.026-0.01224.257-0.004-0.0040.0000.0000.0000.000
135A134LYS10.9510.99025.0800.0280.0280.0000.0000.0000.000
136A135ASP-1-0.796-0.88122.936-0.026-0.0260.0000.0000.0000.000
137A136GLN00.0120.00219.070-0.001-0.0010.0000.0000.0000.000
138A137SER0-0.057-0.00919.2100.0280.0280.0000.0000.0000.000
139A138ASN0-0.056-0.03320.4110.0110.0110.0000.0000.0000.000
140A139GLY00.0220.01117.608-0.004-0.0040.0000.0000.0000.000
141A140SER0-0.022-0.00417.956-0.036-0.0360.0000.0000.0000.000
142A141TYR00.0480.02318.080-0.027-0.0270.0000.0000.0000.000
143A142LYS10.9160.95613.2750.2640.2640.0000.0000.0000.000
144A143THR0-0.037-0.05513.188-0.023-0.0230.0000.0000.0000.000
145A144ILE0-0.0080.0016.7750.0830.0830.0000.0000.0000.000
146A145GLN0-0.048-0.03010.1340.1650.1650.0000.0000.0000.000
147A146PRO0-0.007-0.00911.9210.0470.0470.0000.0000.0000.000
148A147MET00.015-0.00114.729-0.076-0.0760.0000.0000.0000.000
149A148GLY00.0600.04318.026-0.021-0.0210.0000.0000.0000.000
150A149SER0-0.046-0.03615.933-0.028-0.0280.0000.0000.0000.000
151A150LEU00.0580.05816.292-0.020-0.0200.0000.0000.0000.000
152A151PHE00.0450.04018.361-0.017-0.0170.0000.0000.0000.000
153A152GLU-1-0.791-0.87621.2170.0320.0320.0000.0000.0000.000
154A153GLN00.022-0.00515.658-0.024-0.0240.0000.0000.0000.000
155A154THR00.009-0.01221.254-0.018-0.0180.0000.0000.0000.000
156A155LEU0-0.060-0.02123.3960.0000.0000.0000.0000.0000.000
157A156LEU0-0.004-0.00223.082-0.001-0.0010.0000.0000.0000.000
158A157LEU00.003-0.00421.492-0.003-0.0030.0000.0000.0000.000
159A158PHE00.0290.01225.7260.0000.0000.0000.0000.0000.000
160A159TYR00.005-0.00828.6840.0060.0060.0000.0000.0000.000
161A160ASP-1-0.739-0.86528.644-0.086-0.0860.0000.0000.0000.000
162A161ALA0-0.030-0.00229.549-0.002-0.0020.0000.0000.0000.000
163A162VAL0-0.003-0.00531.3330.0030.0030.0000.0000.0000.000
164A163ILE0-0.014-0.00433.4250.0040.0040.0000.0000.0000.000
165A164LEU00.0260.00231.2980.0020.0020.0000.0000.0000.000
166A165LYS10.7760.89735.3110.0730.0730.0000.0000.0000.000
167A166LEU0-0.020-0.01337.5280.0040.0040.0000.0000.0000.000
168A167MET0-0.058-0.01736.9530.0020.0020.0000.0000.0000.000
169A168GLU-1-0.827-0.89439.353-0.070-0.0700.0000.0000.0000.000
170A169LYS10.7800.88341.0990.0550.0550.0000.0000.0000.000
171A170LYS10.8440.93243.2140.0470.0470.0000.0000.0000.000
172A171GLY0-0.0290.00144.3200.0020.0020.0000.0000.0000.000
173A172LEU0-0.049-0.02441.5220.0000.0000.0000.0000.0000.000
174A173ASP-1-0.749-0.87239.721-0.088-0.0880.0000.0000.0000.000
175A174SER0-0.063-0.04235.4490.0010.0010.0000.0000.0000.000
176A175GLU-1-1.007-0.99237.683-0.089-0.0890.0000.0000.0000.000
177A176THR0-0.072-0.06639.7350.0050.0050.0000.0000.0000.000
178A177MET0-0.052-0.01038.1640.0050.0050.0000.0000.0000.000
179A178PHE0-0.016-0.00341.514-0.001-0.0010.0000.0000.0000.000
180A179THR00.0080.00238.5190.0010.0010.0000.0000.0000.000
181A180HIS0-0.0130.00141.7930.0020.0020.0000.0000.0000.000
182A181HIS0-0.072-0.04038.8290.0030.0030.0000.0000.0000.000
183A182ALA00.0120.00439.1460.0020.0020.0000.0000.0000.000
184A183ASN00.020-0.00840.684-0.002-0.0020.0000.0000.0000.000
185A184LEU0-0.037-0.01642.7070.0010.0010.0000.0000.0000.000
186A185GLU-1-0.985-0.97538.876-0.017-0.0170.0000.0000.0000.000