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: Z6JLN

Calculation Name: 4MYB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4MYB

Chain ID: A

ChEMBL ID:

UniProt ID:

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 227
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2820446.953581
FMO2-HF: Nuclear repulsion 2730700.656973
FMO2-HF: Total energy -89746.296609
FMO2-MP2: Total energy -90009.859607


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.
-23.276-13.0958.806-7.898-11.083-0.021
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 : -0.022 / q_NPA : -0.003
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].
3A4LYS10.8320.8963.0682.5655.2830.129-1.522-1.324-0.001
4A5TYR00.000-0.0085.6660.0750.0750.0000.0000.0000.000
5A6VAL0-0.016-0.0068.7320.3140.3140.0000.0000.0000.000
6A7ILE00.0170.01311.988-0.063-0.0630.0000.0000.0000.000
7A8ILE0-0.002-0.00514.6850.0810.0810.0000.0000.0000.000
8A9PRO0-0.030-0.00118.259-0.020-0.0200.0000.0000.0000.000
9A10ALA00.0330.01720.9170.0180.0180.0000.0000.0000.000
10A11ALA0-0.048-0.03724.5050.0120.0120.0000.0000.0000.000
11A12GLY00.0200.00626.6260.0010.0010.0000.0000.0000.000
12A13ILE00.0430.03926.8390.0040.0040.0000.0000.0000.000
13A14GLY0-0.028-0.03130.7410.0020.0020.0000.0000.0000.000
14A15THR00.026-0.01732.1550.0060.0060.0000.0000.0000.000
15A16ARG10.7920.93132.507-0.001-0.0010.0000.0000.0000.000
16A17MET00.0890.07231.1120.0050.0050.0000.0000.0000.000
17A18GLN0-0.054-0.05831.6910.0050.0050.0000.0000.0000.000
18A19LEU00.0120.00433.534-0.002-0.0020.0000.0000.0000.000
19A20ASP-1-0.888-0.92235.001-0.062-0.0620.0000.0000.0000.000
20A21ILE00.008-0.00134.483-0.008-0.0080.0000.0000.0000.000
21A22PRO0-0.040-0.01230.1920.0070.0070.0000.0000.0000.000
22A23LYS10.9830.97030.9110.0190.0190.0000.0000.0000.000
23A24GLN0-0.006-0.00126.0200.0120.0120.0000.0000.0000.000
24A25TYR00.0670.01727.717-0.007-0.0070.0000.0000.0000.000
25A26TYR0-0.017-0.00130.9720.0020.0020.0000.0000.0000.000
26A27LYS10.9200.95331.7060.1090.1090.0000.0000.0000.000
27A28LEU0-0.0130.00930.6390.0040.0040.0000.0000.0000.000
28A29ASN00.0660.02133.3250.0010.0010.0000.0000.0000.000
29A30ASN0-0.018-0.01232.803-0.008-0.0080.0000.0000.0000.000
30A31GLY00.0150.01234.036-0.008-0.0080.0000.0000.0000.000
31A32LYS10.9300.97627.6980.1300.1300.0000.0000.0000.000
32A33THR0-0.043-0.04728.3460.0170.0170.0000.0000.0000.000
33A34ILE0-0.061-0.00726.898-0.005-0.0050.0000.0000.0000.000
34A35LEU00.0570.04222.9270.0030.0030.0000.0000.0000.000
35A36ASP-1-0.791-0.89323.494-0.177-0.1770.0000.0000.0000.000
36A37ASN0-0.026-0.03023.913-0.017-0.0170.0000.0000.0000.000
37A38THR0-0.096-0.04620.2870.0160.0160.0000.0000.0000.000
38A39LEU00.0140.00818.753-0.002-0.0020.0000.0000.0000.000
39A40VAL00.0180.02319.111-0.031-0.0310.0000.0000.0000.000
40A41LYS10.8300.89818.761-0.014-0.0140.0000.0000.0000.000
41A42PHE0-0.006-0.00813.6790.0290.0290.0000.0000.0000.000
42A43ILE0-0.0030.00815.149-0.118-0.1180.0000.0000.0000.000
43A44ASP-1-0.899-0.95216.926-0.362-0.3620.0000.0000.0000.000
44A45ASN0-0.039-0.03013.9350.0010.0010.0000.0000.0000.000
45A46PRO00.008-0.00711.799-0.077-0.0770.0000.0000.0000.000
46A47LEU0-0.048-0.0028.206-0.272-0.2720.0000.0000.0000.000
47A48PHE0-0.005-0.0098.518-0.101-0.1010.0000.0000.0000.000
48A49ASP-1-0.790-0.8796.564-3.729-3.7290.0000.0000.0000.000
49A50LYS10.8290.90010.0881.0131.0130.0000.0000.0000.000
50A51ILE0-0.040-0.01711.5320.0430.0430.0000.0000.0000.000
51A52PHE00.0570.02211.2530.0380.0380.0000.0000.0000.000
52A53VAL00.0120.00315.8420.0710.0710.0000.0000.0000.000
53A54ALA00.0160.00519.333-0.011-0.0110.0000.0000.0000.000
54A55ILE0-0.018-0.01821.2520.0340.0340.0000.0000.0000.000
55A56ALA00.0080.02125.102-0.008-0.0080.0000.0000.0000.000
56A57ALA00.0380.00427.730-0.004-0.0040.0000.0000.0000.000
57A58SER0-0.051-0.03829.500-0.001-0.0010.0000.0000.0000.000
58A59ASP-1-0.813-0.91030.083-0.080-0.0800.0000.0000.0000.000
59A60ASN0-0.049-0.01825.109-0.008-0.0080.0000.0000.0000.000
60A61PHE00.0150.01228.805-0.014-0.0140.0000.0000.0000.000
61A62TRP0-0.018-0.02924.0820.0170.0170.0000.0000.0000.000
62A63ASN00.0040.00028.280-0.006-0.0060.0000.0000.0000.000
63A64ASN00.004-0.00730.270-0.009-0.0090.0000.0000.0000.000
64A65SER0-0.0500.00726.8160.0170.0170.0000.0000.0000.000
65A66LEU0-0.008-0.02129.3170.0130.0130.0000.0000.0000.000
66A67TYR0-0.047-0.02425.851-0.005-0.0050.0000.0000.0000.000
67A68TYR00.0230.01122.403-0.002-0.0020.0000.0000.0000.000
68A69ASN0-0.028-0.00423.815-0.011-0.0110.0000.0000.0000.000
69A70HIS00.0650.03118.888-0.007-0.0070.0000.0000.0000.000
70A71ASP-1-0.819-0.90718.468-0.526-0.5260.0000.0000.0000.000
71A72LYS10.8210.91913.1950.7000.7000.0000.0000.0000.000
72A73ILE0-0.050-0.01415.482-0.042-0.0420.0000.0000.0000.000
73A74VAL00.0210.02015.797-0.045-0.0450.0000.0000.0000.000
74A75VAL00.0040.01018.1900.0300.0300.0000.0000.0000.000
75A76CYS0-0.044-0.00819.362-0.006-0.0060.0000.0000.0000.000
76A77ASN00.0450.01921.6110.0260.0260.0000.0000.0000.000
77A78GLY00.0650.03622.9480.0010.0010.0000.0000.0000.000
78A79GLY0-0.010-0.02823.8890.0000.0000.0000.0000.0000.000
79A80GLU-1-0.937-0.96526.159-0.033-0.0330.0000.0000.0000.000
80A81THR00.000-0.01625.6880.0130.0130.0000.0000.0000.000
81A82ARG10.8980.92919.888-0.049-0.0490.0000.0000.0000.000
82A83PHE00.0500.04020.510-0.015-0.0150.0000.0000.0000.000
83A84ASN00.0360.02420.902-0.002-0.0020.0000.0000.0000.000
84A85SER0-0.005-0.00321.183-0.024-0.0240.0000.0000.0000.000
85A86VAL0-0.003-0.00215.734-0.036-0.0360.0000.0000.0000.000
86A87TYR0-0.023-0.03016.743-0.039-0.0390.0000.0000.0000.000
87A88ASN0-0.041-0.02917.987-0.022-0.0220.0000.0000.0000.000
88A89ALA0-0.002-0.00716.028-0.039-0.0390.0000.0000.0000.000
89A90LEU0-0.012-0.01611.910-0.078-0.0780.0000.0000.0000.000
90A91ASN0-0.046-0.03013.835-0.087-0.0870.0000.0000.0000.000
91A92VAL0-0.053-0.01316.184-0.019-0.0190.0000.0000.0000.000
92A93ILE0-0.060-0.0119.814-0.043-0.0430.0000.0000.0000.000
93A94ASP-1-0.878-0.93212.984-0.796-0.7960.0000.0000.0000.000
94A95GLU-1-0.969-1.0009.920-1.358-1.3580.0000.0000.0000.000
95A96ARG10.7430.8767.9930.1980.1980.0000.0000.0000.000
96A97LYS10.8360.8852.3823.6624.2170.323-0.354-0.523-0.001
97A98ASN00.021-0.0186.5370.0380.0380.0000.0000.0000.000
98A99ASP-1-0.810-0.8972.548-4.210-1.1311.299-1.956-2.421-0.024
99A100ASP-1-0.723-0.8082.178-5.572-4.4254.036-2.372-2.811-0.016
100A101TRP0-0.018-0.0072.290-5.019-3.9242.599-0.892-2.8010.014
101A102VAL00.0010.0054.865-0.764-0.759-0.001-0.002-0.0020.000
102A103PHE00.0280.0077.8850.2900.2900.0000.0000.0000.000
103A104VAL00.0390.04111.294-0.145-0.1450.0000.0000.0000.000
104A105HIS00.0910.03014.6640.0970.0970.0000.0000.0000.000
105A106ASP-1-0.773-0.87017.4630.0240.0240.0000.0000.0000.000
106A107ALA00.0160.00221.277-0.006-0.0060.0000.0000.0000.000
107A108ALA0-0.006-0.02322.641-0.010-0.0100.0000.0000.0000.000
108A109ARG10.7920.89121.316-0.080-0.0800.0000.0000.0000.000
109A110PRO00.0830.04622.1320.0000.0000.0000.0000.0000.000
110A111CYS0-0.026-0.00924.199-0.004-0.0040.0000.0000.0000.000
111A112VAL0-0.0110.02319.1460.0130.0130.0000.0000.0000.000
112A113SER0-0.0010.01121.402-0.024-0.0240.0000.0000.0000.000
113A114ILE00.0720.02115.5690.0150.0150.0000.0000.0000.000
114A115ASP-1-0.859-0.93416.9120.1930.1930.0000.0000.0000.000
115A116SER0-0.004-0.01417.4170.0470.0470.0000.0000.0000.000
116A117ILE00.0070.01213.0020.0670.0670.0000.0000.0000.000
117A118ILE00.0100.00712.7610.1320.1320.0000.0000.0000.000
118A119ASP-1-0.854-0.91412.8460.7240.7240.0000.0000.0000.000
119A120LEU0-0.0060.00112.7770.1160.1160.0000.0000.0000.000
120A121TYR0-0.0170.0053.844-1.032-0.8360.000-0.092-0.1030.000
121A122GLU-1-0.789-0.8839.3311.9751.9750.0000.0000.0000.000
122A123GLN0-0.022-0.01811.0460.1720.1720.0000.0000.0000.000
123A124THR0-0.039-0.0299.665-0.027-0.0270.0000.0000.0000.000
124A125LYS10.8040.8915.683-2.128-2.1280.0000.0000.0000.000
125A126SER0-0.057-0.0358.1360.1080.1080.0000.0000.0000.000
126A127SER0-0.053-0.02011.280-0.257-0.2570.0000.0000.0000.000
127A128HIS00.0290.00412.0860.2270.2270.0000.0000.0000.000
128A129SER0-0.026-0.02413.8820.0310.0310.0000.0000.0000.000
129A130GLN0-0.0300.0017.5670.8170.8170.0000.0000.0000.000
130A131ALA00.0570.0049.7300.1030.1030.0000.0000.0000.000
131A132GLY00.007-0.00312.203-0.039-0.0390.0000.0000.0000.000
132A133ILE0-0.035-0.01114.402-0.046-0.0460.0000.0000.0000.000
133A134LEU00.0080.01616.9040.0080.0080.0000.0000.0000.000
134A135ALA00.001-0.00818.981-0.031-0.0310.0000.0000.0000.000
135A136VAL0-0.0110.01222.615-0.004-0.0040.0000.0000.0000.000
136A137ARG10.8620.93426.142-0.227-0.2270.0000.0000.0000.000
137A138ALA0-0.071-0.03728.634-0.016-0.0160.0000.0000.0000.000
138A139TYR0-0.004-0.01630.6330.0030.0030.0000.0000.0000.000
139A140GLU-1-0.820-0.89533.7720.1120.1120.0000.0000.0000.000
140A141THR0-0.055-0.03535.5950.0030.0030.0000.0000.0000.000
141A142VAL00.0810.04032.593-0.009-0.0090.0000.0000.0000.000
142A143LYS10.8750.93436.045-0.086-0.0860.0000.0000.0000.000
143A144GLN00.0390.02434.813-0.001-0.0010.0000.0000.0000.000
144A145VAL00.0440.02638.862-0.002-0.0020.0000.0000.0000.000
145A146THR0-0.007-0.01340.823-0.001-0.0010.0000.0000.0000.000
146A147LYS10.9570.97443.465-0.029-0.0290.0000.0000.0000.000
147A148ASN00.0140.00244.4580.0000.0000.0000.0000.0000.000
148A149ILE00.0410.04345.5180.0010.0010.0000.0000.0000.000
149A150VAL0-0.006-0.01242.7040.0020.0020.0000.0000.0000.000
150A151VAL0-0.015-0.00642.415-0.001-0.0010.0000.0000.0000.000
151A152LYS10.9190.95538.918-0.081-0.0810.0000.0000.0000.000
152A153THR00.010-0.00339.751-0.004-0.0040.0000.0000.0000.000
153A154LEU00.0140.02433.3560.0010.0010.0000.0000.0000.000
154A155ALA00.0070.00537.470-0.006-0.0060.0000.0000.0000.000
155A156ARG10.9690.98335.962-0.117-0.1170.0000.0000.0000.000
156A157ASP-1-0.818-0.92433.2240.1770.1770.0000.0000.0000.000
157A158ASN0-0.0080.00529.3020.0160.0160.0000.0000.0000.000
158A159ILE0-0.017-0.00329.1560.0090.0090.0000.0000.0000.000
159A160TRP00.0480.01624.8230.0000.0000.0000.0000.0000.000
160A161LEU0-0.035-0.00827.011-0.007-0.0070.0000.0000.0000.000
161A162ALA00.0690.03421.9560.0080.0080.0000.0000.0000.000
162A163GLN0-0.058-0.02421.575-0.052-0.0520.0000.0000.0000.000
163A164THR0-0.011-0.00717.9500.0130.0130.0000.0000.0000.000
164A165PRO00.000-0.02614.219-0.023-0.0230.0000.0000.0000.000
165A166GLN0-0.072-0.04014.9050.0380.0380.0000.0000.0000.000
166A167LEU00.0030.0137.661-0.062-0.0620.0000.0000.0000.000
167A168SER00.0840.0379.7020.1460.1460.0000.0000.0000.000
168A169ARG10.8350.9152.807-9.395-8.0090.421-0.708-1.0980.007
169A170LEU00.0220.0096.212-0.188-0.1880.0000.0000.0000.000
170A171GLY00.0410.0237.872-0.028-0.0280.0000.0000.0000.000
171A172GLN0-0.055-0.0299.807-0.048-0.0480.0000.0000.0000.000
172A173LEU00.0130.01611.029-0.064-0.0640.0000.0000.0000.000
173A174GLU-1-0.844-0.91411.872-0.300-0.3000.0000.0000.0000.000
174A175LYS10.8500.92312.264-0.110-0.1100.0000.0000.0000.000
175A176ALA00.0300.02415.707-0.013-0.0130.0000.0000.0000.000
176A177PHE00.006-0.00416.623-0.025-0.0250.0000.0000.0000.000
177A178ASP-1-0.810-0.88717.800-0.035-0.0350.0000.0000.0000.000
178A179PHE0-0.0390.00820.011-0.008-0.0080.0000.0000.0000.000
179A180CYS0-0.013-0.01620.896-0.005-0.0050.0000.0000.0000.000
180A181TYR0-0.033-0.02022.561-0.008-0.0080.0000.0000.0000.000
181A182SER0-0.046-0.04923.7810.0010.0010.0000.0000.0000.000
182A183ASN0-0.060-0.02825.2390.0000.0000.0000.0000.0000.000
183A184ASN0-0.048-0.02827.7040.0000.0000.0000.0000.0000.000
184A185LEU00.0190.01024.8750.0020.0020.0000.0000.0000.000
185A186VAL00.0060.00324.2980.0090.0090.0000.0000.0000.000
186A187ALA0-0.013-0.00226.0170.0000.0000.0000.0000.0000.000
187A188LYS10.7820.90524.412-0.180-0.1800.0000.0000.0000.000
188A189VAL0-0.043-0.01521.3560.0110.0110.0000.0000.0000.000
189A190THR0-0.057-0.02823.543-0.013-0.0130.0000.0000.0000.000
190A191ASP-1-0.863-0.89620.3050.1980.1980.0000.0000.0000.000
191A192GLU-1-0.821-0.93312.7930.3720.3720.0000.0000.0000.000
192A193ALA00.0270.00917.3860.0270.0270.0000.0000.0000.000
193A194SER0-0.008-0.03018.691-0.005-0.0050.0000.0000.0000.000
194A195ALA00.0290.00918.583-0.018-0.0180.0000.0000.0000.000
195A196LEU00.0110.00013.8850.0010.0010.0000.0000.0000.000
196A197GLU-1-0.871-0.95017.9720.2560.2560.0000.0000.0000.000
197A198MET0-0.084-0.03021.266-0.012-0.0120.0000.0000.0000.000
198A199PHE0-0.0060.00615.859-0.022-0.0220.0000.0000.0000.000
199A200GLY00.0000.00820.0620.0150.0150.0000.0000.0000.000
200A201ILE0-0.064-0.02614.3800.0310.0310.0000.0000.0000.000
201A202ASN00.004-0.00517.955-0.033-0.0330.0000.0000.0000.000
202A203PRO0-0.0070.01415.7930.0690.0690.0000.0000.0000.000
203A204ILE0-0.0010.01214.209-0.072-0.0720.0000.0000.0000.000
204A205VAL0-0.022-0.02317.484-0.026-0.0260.0000.0000.0000.000
205A206VAL00.0080.01516.0740.0040.0040.0000.0000.0000.000
206A207GLU-1-0.860-0.93819.4000.1970.1970.0000.0000.0000.000
207A208CYS0-0.062-0.00721.016-0.011-0.0110.0000.0000.0000.000
208A209SER00.0530.01422.753-0.018-0.0180.0000.0000.0000.000
209A210LYS10.8830.92125.987-0.134-0.1340.0000.0000.0000.000
210A211LYS10.9230.96127.251-0.075-0.0750.0000.0000.0000.000
211A212ASN0-0.030-0.02021.049-0.044-0.0440.0000.0000.0000.000
212A213ILE00.0260.01725.1990.0120.0120.0000.0000.0000.000
213A214LYS10.8660.92824.626-0.029-0.0290.0000.0000.0000.000
214A215ILE0-0.006-0.01426.7520.0020.0020.0000.0000.0000.000
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