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: YY562

Calculation Name: 3MTV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3MTV

Chain ID: A

ChEMBL ID:

UniProt ID: B2ZAB4

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 202
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2241473.188908
FMO2-HF: Nuclear repulsion 2161697.459505
FMO2-HF: Total energy -79775.729403
FMO2-MP2: Total energy -80012.481729


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:ALA)


Summations of interaction energy for fragment #1(A:1:ALA)
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.
-2.319-0.7423.98-3.341-2.215-0.003
Interaction energy analysis for fragmet #1(A:1:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.043 / q_NPA : -0.025
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].
3A3VAL0-0.080-0.0443.8920.7422.216-0.005-0.854-0.6160.001
4A4TYR00.0300.0206.1860.1460.1460.0000.0000.0000.000
5A5ASP-1-0.833-0.9069.982-0.171-0.1710.0000.0000.0000.000
6A6ILE0-0.024-0.03212.230-0.017-0.0170.0000.0000.0000.000
7A7GLY0-0.008-0.00114.9980.0490.0490.0000.0000.0000.000
8A8ARG10.8740.92017.1830.1620.1620.0000.0000.0000.000
9A9GLY00.0160.01618.4820.0220.0220.0000.0000.0000.000
10A10ALA0-0.0120.00514.1180.0250.0250.0000.0000.0000.000
11A11VAL0-0.012-0.0029.871-0.058-0.0580.0000.0000.0000.000
12A12MET0-0.003-0.0178.7320.1670.1670.0000.0000.0000.000
13A13TYR0-0.043-0.0124.014-0.312-0.215-0.001-0.015-0.0810.000
14A14VAL00.021-0.0154.4800.6250.761-0.001-0.015-0.1190.000
15A15ALA00.0340.0251.971-2.096-2.3473.978-2.442-1.284-0.004
16A16GLY00.0270.0323.7300.4200.5410.009-0.015-0.1150.000
17A17GLY00.0070.0027.253-0.430-0.4300.0000.0000.0000.000
18A18LYS10.8700.9277.691-1.098-1.0980.0000.0000.0000.000
19A19VAL00.0640.0326.8520.0270.0270.0000.0000.0000.000
20A20SER0-0.007-0.0017.6330.0510.0510.0000.0000.0000.000
21A21TRP00.0290.0069.337-0.177-0.1770.0000.0000.0000.000
22A22ALA00.0370.02110.6010.0860.0860.0000.0000.0000.000
23A23PRO00.026-0.00112.291-0.065-0.0650.0000.0000.0000.000
24A24ARG10.8590.96613.5150.2420.2420.0000.0000.0000.000
25A25GLY00.0760.02414.1460.0030.0030.0000.0000.0000.000
26A26GLY00.0830.03316.899-0.005-0.0050.0000.0000.0000.000
27A27ASN0-0.086-0.04318.259-0.032-0.0320.0000.0000.0000.000
28A28GLU-1-0.871-0.95116.971-0.137-0.1370.0000.0000.0000.000
29A29VAL0-0.053-0.02313.118-0.044-0.0440.0000.0000.0000.000
30A30LYS10.8520.92714.6500.2580.2580.0000.0000.0000.000
31A31PHE00.0540.0388.633-0.010-0.0100.0000.0000.0000.000
32A32GLU-1-0.886-0.95011.698-0.997-0.9970.0000.0000.0000.000
33A33PRO0-0.036-0.01712.605-0.016-0.0160.0000.0000.0000.000
34A34VAL00.0300.02912.442-0.077-0.0770.0000.0000.0000.000
35A35PRO00.0800.03911.6640.1350.1350.0000.0000.0000.000
36A36LYS10.8320.91214.8900.3730.3730.0000.0000.0000.000
37A37GLU-1-0.898-0.95314.758-0.424-0.4240.0000.0000.0000.000
38A38LEU00.0440.00610.2890.0280.0280.0000.0000.0000.000
39A39LYS10.9300.97414.5850.3570.3570.0000.0000.0000.000
40A40LEU0-0.0190.00517.0190.0400.0400.0000.0000.0000.000
41A41VAL00.084-0.00712.4550.0410.0410.0000.0000.0000.000
42A42ALA00.0360.05714.2870.0370.0370.0000.0000.0000.000
43A43ASN0-0.008-0.02115.2190.0230.0230.0000.0000.0000.000
44A44ARG10.9590.99517.4200.0700.0700.0000.0000.0000.000
45A45LEU00.0930.04311.8020.0240.0240.0000.0000.0000.000
46A46HIS0-0.0270.00215.7870.0190.0190.0000.0000.0000.000
47A47THR00.0090.02016.9530.0160.0160.0000.0000.0000.000
48A48SER0-0.047-0.04419.4320.0170.0170.0000.0000.0000.000
49A49PHE00.0170.02016.3880.0190.0190.0000.0000.0000.000
50A50PRO00.0250.01517.715-0.029-0.0290.0000.0000.0000.000
51A51PRO00.0130.00114.3050.0320.0320.0000.0000.0000.000
52A52HIS0-0.0120.00811.5380.0520.0520.0000.0000.0000.000
53A53HIS0-0.055-0.02812.5930.0870.0870.0000.0000.0000.000
54A54VAL00.0250.0228.735-0.031-0.0310.0000.0000.0000.000
55A55VAL00.0080.00411.320-0.045-0.0450.0000.0000.0000.000
56A56ASP-1-0.798-0.86811.6330.3580.3580.0000.0000.0000.000
57A57MET0-0.075-0.04013.046-0.049-0.0490.0000.0000.0000.000
58A58SER0-0.027-0.04415.124-0.047-0.0470.0000.0000.0000.000
59A59LYS10.8500.92316.812-0.323-0.3230.0000.0000.0000.000
60A60PHE00.0260.02616.9630.0030.0030.0000.0000.0000.000
61A61THR00.002-0.00420.457-0.020-0.0200.0000.0000.0000.000
62A62PHE00.014-0.00917.991-0.009-0.0090.0000.0000.0000.000
63A63ILE00.0560.02723.548-0.005-0.0050.0000.0000.0000.000
64A64THR0-0.050-0.01426.217-0.008-0.0080.0000.0000.0000.000
65A65PRO00.036-0.00824.7940.0070.0070.0000.0000.0000.000
66A66GLY00.0230.02527.119-0.003-0.0030.0000.0000.0000.000
67A67SER0-0.055-0.02929.2770.0040.0040.0000.0000.0000.000
68A68GLY00.0620.03127.9670.0040.0040.0000.0000.0000.000
69A69VAL0-0.005-0.00226.890-0.003-0.0030.0000.0000.0000.000
70A70SER00.021-0.00623.1810.0100.0100.0000.0000.0000.000
71A71MET0-0.039-0.02721.5420.0070.0070.0000.0000.0000.000
72A72ARG10.8090.92619.897-0.035-0.0350.0000.0000.0000.000
73A73VAL00.0330.02023.312-0.012-0.0120.0000.0000.0000.000
74A74GLU-1-0.898-0.95423.1370.0560.0560.0000.0000.0000.000
75A75TYR0-0.070-0.02822.710-0.012-0.0120.0000.0000.0000.000
76A76GLN00.008-0.00626.7770.0050.0050.0000.0000.0000.000
77A77TYR00.0110.01628.9670.0060.0060.0000.0000.0000.000
78A78GLY0-0.027-0.02725.311-0.004-0.0040.0000.0000.0000.000
79A79CYS0-0.083-0.05422.298-0.016-0.0160.0000.0000.0000.000
80A80LEU0-0.0030.01221.2970.0010.0010.0000.0000.0000.000
81A81PRO00.0850.08025.109-0.008-0.0080.0000.0000.0000.000
82A82ALA00.0270.01427.5210.0130.0130.0000.0000.0000.000
83A83ASP-1-0.896-0.92529.6510.0700.0700.0000.0000.0000.000
84A84THR0-0.108-0.11525.1910.0110.0110.0000.0000.0000.000
85A85VAL00.0190.00824.2780.0200.0200.0000.0000.0000.000
86A86PRO0-0.033-0.01225.544-0.009-0.0090.0000.0000.0000.000
87A87GLU-1-0.867-0.93328.7730.0750.0750.0000.0000.0000.000
88A88GLY0-0.041-0.01231.287-0.005-0.0050.0000.0000.0000.000
89A89ASN0-0.001-0.01332.1540.0060.0060.0000.0000.0000.000
90A90CYS0-0.0500.01430.8070.0020.0020.0000.0000.0000.000
91A91TRP00.012-0.01634.0160.0010.0010.0000.0000.0000.000
92A92TRP00.0290.00535.732-0.001-0.0010.0000.0000.0000.000
93A93ARG11.0221.04234.145-0.115-0.1150.0000.0000.0000.000
94A94LEU0-0.019-0.03035.817-0.001-0.0010.0000.0000.0000.000
95A95LEU0-0.087-0.04539.486-0.002-0.0020.0000.0000.0000.000
96A96ASP-1-0.854-0.93442.1180.0820.0820.0000.0000.0000.000
97A97SER0-0.093-0.02544.168-0.005-0.0050.0000.0000.0000.000
98A98LEU0-0.034-0.02645.782-0.003-0.0030.0000.0000.0000.000
99A99PRO00.0580.05048.5540.0000.0000.0000.0000.0000.000
100A100PRO00.1180.05749.4040.0020.0020.0000.0000.0000.000
101A101GLU-1-0.886-0.96149.4580.0510.0510.0000.0000.0000.000
102A102VAL0-0.012-0.01548.2070.0000.0000.0000.0000.0000.000
103A103GLN00.0030.02045.0880.0030.0030.0000.0000.0000.000
104A104TYR00.027-0.00945.5340.0000.0000.0000.0000.0000.000
105A105LYS10.8720.93546.623-0.047-0.0470.0000.0000.0000.000
106A106GLU-1-0.797-0.89543.4290.0710.0710.0000.0000.0000.000
107A107ILE0-0.028-0.00141.4570.0020.0020.0000.0000.0000.000
108A108ARG10.9670.97542.395-0.047-0.0470.0000.0000.0000.000
109A109HIS0-0.034-0.00843.809-0.002-0.0020.0000.0000.0000.000
110A110ALA0-0.027-0.03338.8860.0000.0000.0000.0000.0000.000
111A111ASN00.024-0.01739.7790.0030.0030.0000.0000.0000.000
112A112GLN0-0.0810.00741.191-0.005-0.0050.0000.0000.0000.000
113A113PHE0-0.072-0.01738.9170.0000.0000.0000.0000.0000.000
114A114GLY00.0310.01536.432-0.002-0.0020.0000.0000.0000.000
115A115TYR00.027-0.02434.165-0.002-0.0020.0000.0000.0000.000
116A116GLN00.0080.05135.2830.0050.0050.0000.0000.0000.000
117A117THR0-0.048-0.02531.548-0.003-0.0030.0000.0000.0000.000
118A118LYS10.9640.98826.521-0.073-0.0730.0000.0000.0000.000
119A119HIS0-0.036-0.02625.9930.0090.0090.0000.0000.0000.000
120A120GLY00.0430.03329.1130.0100.0100.0000.0000.0000.000
121A121VAL0-0.049-0.03332.118-0.007-0.0070.0000.0000.0000.000
122A122PRO00.007-0.00131.4020.0090.0090.0000.0000.0000.000
123A123GLY00.0790.04231.3580.0090.0090.0000.0000.0000.000
124A124LYS10.9390.96631.815-0.126-0.1260.0000.0000.0000.000
125A125TYR0-0.0260.00035.494-0.006-0.0060.0000.0000.0000.000
126A126LEU00.0370.01233.802-0.004-0.0040.0000.0000.0000.000
127A127GLN0-0.021-0.01936.5070.0020.0020.0000.0000.0000.000
128A128ARG10.9751.00338.105-0.092-0.0920.0000.0000.0000.000
129A129ARG10.8820.95440.372-0.076-0.0760.0000.0000.0000.000
130A130LEU00.1000.01739.2410.0030.0030.0000.0000.0000.000
131A131GLN0-0.0130.01842.185-0.001-0.0010.0000.0000.0000.000
132A132VAL0-0.074-0.03443.917-0.003-0.0030.0000.0000.0000.000
133A133ASN0-0.089-0.06845.198-0.006-0.0060.0000.0000.0000.000
134A134GLY00.0170.03847.292-0.002-0.0020.0000.0000.0000.000
135A135LEU0-0.0090.00043.3540.0020.0020.0000.0000.0000.000
136A136ARG10.7640.85342.010-0.092-0.0920.0000.0000.0000.000
137A137ALA0-0.0110.02037.2740.0000.0000.0000.0000.0000.000
138A138VAL00.016-0.00638.2110.0040.0040.0000.0000.0000.000
139A139THR0-0.069-0.04033.3980.0030.0030.0000.0000.0000.000
140A140ASP-1-0.578-0.81035.3470.1280.1280.0000.0000.0000.000
141A141THR00.0850.00534.0730.0080.0080.0000.0000.0000.000
142A142HIS0-0.132-0.10534.6000.0090.0090.0000.0000.0000.000
143A143GLY0-0.171-0.08236.625-0.007-0.0070.0000.0000.0000.000
144A144PRO0-0.004-0.01435.9420.0070.0070.0000.0000.0000.000
145A145ILE00.0290.00933.5820.0020.0020.0000.0000.0000.000
146A146VAL00.0050.03328.5070.0060.0060.0000.0000.0000.000
147A147ILE0-0.060-0.02827.506-0.005-0.0050.0000.0000.0000.000
148A148GLN0-0.027-0.04424.5430.0050.0050.0000.0000.0000.000
149A149TYR0-0.0120.00517.974-0.004-0.0040.0000.0000.0000.000
150A150PHE00.0640.01617.9900.0190.0190.0000.0000.0000.000
151A151SER0-0.039-0.00514.5680.0300.0300.0000.0000.0000.000
152A152VAL0-0.012-0.01713.5880.1000.1000.0000.0000.0000.000
153A153LYS10.9820.99814.243-0.791-0.7910.0000.0000.0000.000
154A154GLU-1-0.954-0.98016.4910.4900.4900.0000.0000.0000.000
155A155SER0-0.015-0.00118.582-0.052-0.0520.0000.0000.0000.000
156A156TRP0-0.067-0.04818.828-0.007-0.0070.0000.0000.0000.000
157A157ILE0-0.0060.00220.804-0.027-0.0270.0000.0000.0000.000
158A158ARG10.9120.91923.001-0.213-0.2130.0000.0000.0000.000
159A159HIS00.010-0.01225.855-0.028-0.0280.0000.0000.0000.000
160A160LEU0-0.029-0.00228.1210.0110.0110.0000.0000.0000.000
161A161LYS10.8770.95128.139-0.198-0.1980.0000.0000.0000.000
162A162LEU00.0310.00432.2520.0080.0080.0000.0000.0000.000
163A163VAL0-0.068-0.05032.4600.0060.0060.0000.0000.0000.000
164A164GLU-1-0.899-0.95532.3310.1220.1220.0000.0000.0000.000
165A165GLU-1-0.871-0.90032.5260.1190.1190.0000.0000.0000.000
166A166PRO00.0450.01929.2610.0130.0130.0000.0000.0000.000
167A167SER0-0.051-0.03524.673-0.012-0.0120.0000.0000.0000.000
168A168LEU00.0640.04524.875-0.006-0.0060.0000.0000.0000.000
169A169PRO00.0160.00221.2720.0300.0300.0000.0000.0000.000
170A170GLY0-0.002-0.00218.279-0.003-0.0030.0000.0000.0000.000
171A171PHE0-0.035-0.02919.1480.0210.0210.0000.0000.0000.000
172A172GLU-1-0.949-0.97018.3230.4580.4580.0000.0000.0000.000
173A173ASP-1-0.883-0.93121.9570.2380.2380.0000.0000.0000.000
174A174LEU0-0.072-0.03423.6340.0200.0200.0000.0000.0000.000
175A175LEU0-0.014-0.01925.0340.0000.0000.0000.0000.0000.000
176A176ARG10.8801.04728.728-0.171-0.1710.0000.0000.0000.000
177A177ILE0-0.0260.00932.241-0.002-0.0020.0000.0000.0000.000
178A178ARG10.8810.92635.280-0.114-0.1140.0000.0000.0000.000
179A179VAL0-0.042-0.02838.8610.0020.0020.0000.0000.0000.000
180A180GLU-1-0.806-0.88141.0650.0950.0950.0000.0000.0000.000
181A181PRO00.0700.02344.5820.0000.0000.0000.0000.0000.000
182A182ASN0-0.041-0.01745.6360.0030.0030.0000.0000.0000.000
183A183THR00.018-0.01647.089-0.002-0.0020.0000.0000.0000.000
184A184SER0-0.0020.01149.607-0.004-0.0040.0000.0000.0000.000
185A185PRO00.005-0.00148.8920.0040.0040.0000.0000.0000.000
186A186LEU00.002-0.00142.0020.0000.0000.0000.0000.0000.000
187A187ALA00.0460.02845.779-0.002-0.0020.0000.0000.0000.000
188A188GLY00.0590.04545.0460.0040.0040.0000.0000.0000.000
189A189LYS10.8840.91743.274-0.102-0.1020.0000.0000.0000.000
190A190ASP-1-0.880-0.93739.6690.1190.1190.0000.0000.0000.000
191A191GLU-1-0.866-0.90338.5190.1260.1260.0000.0000.0000.000
192A192LYS10.8640.90836.135-0.140-0.1400.0000.0000.0000.000
193A193ILE00.0630.03937.5780.0040.0040.0000.0000.0000.000
194A194PHE00.0290.00530.2390.0070.0070.0000.0000.0000.000
195A195ARG10.9460.98531.881-0.163-0.1630.0000.0000.0000.000
196A196PHE00.0740.02631.7690.0120.0120.0000.0000.0000.000
197A197GLY00.0190.02728.9640.0070.0070.0000.0000.0000.000
198A198SER0-0.029-0.03229.425-0.016-0.0160.0000.0000.0000.000
199A199HIS0-0.035-0.04026.5570.0090.0090.0000.0000.0000.000
200A200LYS10.9170.99022.769-0.248-0.2480.0000.0000.0000.000
201A201TRP0-0.0040.00426.990-0.021-0.0210.0000.0000.0000.000
202A202TYR00.0450.02027.7520.0150.0150.0000.0000.0000.000