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: 2JYRR

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 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 227
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2821835.988958
FMO2-HF: Nuclear repulsion 2732091.743111
FMO2-HF: Total energy -89744.245847
FMO2-MP2: Total energy -90007.994911


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.
-28.348-18.83710.053-9.041-10.525-0.045
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 : -0.102 / q_NPA : -0.042
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].
3A4LYS10.8540.9262.729-7.731-4.9090.044-1.340-1.5270.004
4A5TYR00.0220.0136.0670.4780.4780.0000.0000.0000.000
5A6VAL0-0.009-0.0038.863-0.064-0.0640.0000.0000.0000.000
6A7ILE00.0230.02712.3160.0470.0470.0000.0000.0000.000
7A8ILE0-0.014-0.01614.8270.0180.0180.0000.0000.0000.000
8A9PRO0-0.049-0.01818.3530.0190.0190.0000.0000.0000.000
9A10ALA00.0470.04520.9430.0280.0280.0000.0000.0000.000
10A11ALA0-0.039-0.04324.576-0.018-0.0180.0000.0000.0000.000
11A12GLY00.0470.01126.9250.0160.0160.0000.0000.0000.000
12A13ILE0-0.0250.05226.5280.0110.0110.0000.0000.0000.000
13A14GLY00.033-0.01230.6010.0000.0000.0000.0000.0000.000
14A15THR0-0.020-0.04232.213-0.008-0.0080.0000.0000.0000.000
15A16ARG10.8010.91932.7540.1230.1230.0000.0000.0000.000
16A17MET00.1050.07732.019-0.009-0.0090.0000.0000.0000.000
17A18GLN0-0.045-0.05132.1650.0100.0100.0000.0000.0000.000
18A19LEU00.0240.01033.651-0.008-0.0080.0000.0000.0000.000
19A20ASP-1-0.882-0.92935.336-0.061-0.0610.0000.0000.0000.000
20A21ILE00.0120.00534.2730.0000.0000.0000.0000.0000.000
21A22PRO0-0.028-0.00629.9810.0000.0000.0000.0000.0000.000
22A23LYS10.9640.96631.0080.0990.0990.0000.0000.0000.000
23A24GLN0-0.026-0.01026.583-0.002-0.0020.0000.0000.0000.000
24A25TYR00.0460.00427.3000.0000.0000.0000.0000.0000.000
25A26TYR00.0070.00531.2810.0080.0080.0000.0000.0000.000
26A27LYS10.9430.97232.1270.0140.0140.0000.0000.0000.000
27A28LEU00.0000.01130.5380.0010.0010.0000.0000.0000.000
28A29ASN00.0460.02133.2320.0070.0070.0000.0000.0000.000
29A30ASN00.003-0.00632.5950.0040.0040.0000.0000.0000.000
30A31GLY00.0110.01034.1340.0030.0030.0000.0000.0000.000
31A32LYS10.9560.99228.201-0.042-0.0420.0000.0000.0000.000
32A33THR0-0.0030.00728.542-0.005-0.0050.0000.0000.0000.000
33A34ILE0-0.065-0.00427.5410.0020.0020.0000.0000.0000.000
34A35LEU00.0510.02723.377-0.003-0.0030.0000.0000.0000.000
35A36ASP-1-0.802-0.92523.920-0.030-0.0300.0000.0000.0000.000
36A37ASN0-0.062-0.05624.3060.0230.0230.0000.0000.0000.000
37A38THR0-0.071-0.02720.3900.0130.0130.0000.0000.0000.000
38A39LEU00.013-0.00519.1910.0020.0020.0000.0000.0000.000
39A40VAL00.0250.02319.6520.0180.0180.0000.0000.0000.000
40A41LYS10.8320.91719.0370.0180.0180.0000.0000.0000.000
41A42PHE0-0.011-0.00513.8780.0210.0210.0000.0000.0000.000
42A43ILE0-0.0120.00215.4700.0390.0390.0000.0000.0000.000
43A44ASP-1-0.914-0.95417.1310.2080.2080.0000.0000.0000.000
44A45ASN0-0.038-0.03313.4900.1150.1150.0000.0000.0000.000
45A46PRO00.006-0.00612.171-0.038-0.0380.0000.0000.0000.000
46A47LEU0-0.0340.0117.8570.2150.2150.0000.0000.0000.000
47A48PHE0-0.021-0.0268.4040.0380.0380.0000.0000.0000.000
48A49ASP-1-0.799-0.8886.4690.8730.8730.0000.0000.0000.000
49A50LYS10.8970.9499.686-0.005-0.0050.0000.0000.0000.000
50A51ILE0-0.023-0.01311.522-0.104-0.1040.0000.0000.0000.000
51A52PHE00.0220.00610.7960.0350.0350.0000.0000.0000.000
52A53VAL0-0.0010.00115.770-0.018-0.0180.0000.0000.0000.000
53A54ALA00.003-0.00119.3880.0090.0090.0000.0000.0000.000
54A55ILE0-0.014-0.02021.2260.0110.0110.0000.0000.0000.000
55A56ALA00.0210.02725.052-0.006-0.0060.0000.0000.0000.000
56A57ALA00.0500.01827.5560.0130.0130.0000.0000.0000.000
57A58SER0-0.065-0.04629.3580.0070.0070.0000.0000.0000.000
58A59ASP-1-0.858-0.92329.698-0.110-0.1100.0000.0000.0000.000
59A60ASN0-0.080-0.03124.3040.0200.0200.0000.0000.0000.000
60A61PHE00.0090.00528.7130.0050.0050.0000.0000.0000.000
61A62TRP00.032-0.00423.343-0.003-0.0030.0000.0000.0000.000
62A63ASN0-0.0040.00028.0890.0060.0060.0000.0000.0000.000
63A64ASN0-0.046-0.05729.7780.0130.0130.0000.0000.0000.000
64A65SER00.0160.05627.1290.0000.0000.0000.0000.0000.000
65A66LEU00.006-0.01729.2970.0010.0010.0000.0000.0000.000
66A67TYR0-0.097-0.04226.4140.0070.0070.0000.0000.0000.000
67A68TYR00.0310.01422.6470.0090.0090.0000.0000.0000.000
68A69ASN0-0.031-0.00323.737-0.027-0.0270.0000.0000.0000.000
69A70HIS00.0410.02318.426-0.008-0.0080.0000.0000.0000.000
70A71ASP-1-0.806-0.89417.5550.1470.1470.0000.0000.0000.000
71A72LYS10.7820.88713.335-0.311-0.3110.0000.0000.0000.000
72A73ILE0-0.064-0.02315.289-0.063-0.0630.0000.0000.0000.000
73A74VAL00.0390.03415.0670.0170.0170.0000.0000.0000.000
74A75VAL0-0.0010.00917.804-0.033-0.0330.0000.0000.0000.000
75A76CYS0-0.020-0.00218.841-0.022-0.0220.0000.0000.0000.000
76A77ASN00.013-0.00320.8680.0250.0250.0000.0000.0000.000
77A78GLY00.0440.01722.657-0.028-0.0280.0000.0000.0000.000
78A79GLY00.002-0.02223.9760.0080.0080.0000.0000.0000.000
79A80GLU-1-0.955-0.96725.728-0.182-0.1820.0000.0000.0000.000
80A81THR00.023-0.00925.9420.0010.0010.0000.0000.0000.000
81A82ARG10.9190.94819.3930.2990.2990.0000.0000.0000.000
82A83PHE00.0360.02620.755-0.019-0.0190.0000.0000.0000.000
83A84ASN00.0440.01420.599-0.023-0.0230.0000.0000.0000.000
84A85SER00.0390.02220.7080.0020.0020.0000.0000.0000.000
85A86VAL0-0.034-0.01815.745-0.006-0.0060.0000.0000.0000.000
86A87TYR0-0.050-0.06416.479-0.028-0.0280.0000.0000.0000.000
87A88ASN0-0.031-0.02917.273-0.044-0.0440.0000.0000.0000.000
88A89ALA00.020-0.00615.466-0.004-0.0040.0000.0000.0000.000
89A90LEU0-0.022-0.00511.724-0.040-0.0400.0000.0000.0000.000
90A91ASN00.002-0.01213.330-0.093-0.0930.0000.0000.0000.000
91A92VAL0-0.037-0.01815.1610.0430.0430.0000.0000.0000.000
92A93ILE0-0.090-0.0278.9170.0240.0240.0000.0000.0000.000
93A94ASP-1-0.902-0.95211.617-0.410-0.4100.0000.0000.0000.000
94A95GLU-1-0.960-0.9869.450-0.120-0.1200.0000.0000.0000.000
95A96ARG10.7980.9397.4540.6610.6610.0000.0000.0000.000
96A97LYS10.9260.9601.8930.3650.8812.206-1.569-1.1540.000
97A98ASN00.003-0.0325.720-0.639-0.6390.0000.0000.0000.000
98A99ASP-1-0.909-0.9523.071-6.550-4.7080.207-0.990-1.059-0.010
99A100ASP-1-0.727-0.8651.900-19.730-16.1286.619-5.797-4.425-0.041
100A101TRP0-0.058-0.0212.606-0.846-0.9480.8880.974-1.7600.002
101A102VAL00.0220.0165.0030.6260.633-0.001-0.001-0.0050.000
102A103PHE00.0130.0077.5980.0840.0840.0000.0000.0000.000
103A104VAL00.0420.03111.3350.0910.0910.0000.0000.0000.000
104A105HIS00.0690.01814.7380.0160.0160.0000.0000.0000.000
105A106ASP-1-0.855-0.94117.423-0.223-0.2230.0000.0000.0000.000
106A107ALA00.0440.00821.2340.0230.0230.0000.0000.0000.000
107A108ALA0-0.028-0.01422.8920.0210.0210.0000.0000.0000.000
108A109ARG10.8490.92021.4820.1670.1670.0000.0000.0000.000
109A110PRO00.0500.03422.326-0.001-0.0010.0000.0000.0000.000
110A111CYS00.000-0.00723.9790.0220.0220.0000.0000.0000.000
111A112VAL0-0.0140.01818.3880.0070.0070.0000.0000.0000.000
112A113SER00.0180.00821.2140.0180.0180.0000.0000.0000.000
113A114ILE00.0810.02515.684-0.024-0.0240.0000.0000.0000.000
114A115ASP-1-0.875-0.94117.0120.1230.1230.0000.0000.0000.000
115A116SER0-0.019-0.00617.740-0.009-0.0090.0000.0000.0000.000
116A117ILE0-0.0020.00612.992-0.042-0.0420.0000.0000.0000.000
117A118ILE00.006-0.00213.033-0.028-0.0280.0000.0000.0000.000
118A119ASP-1-0.864-0.92313.120-0.006-0.0060.0000.0000.0000.000
119A120LEU0-0.032-0.01112.148-0.031-0.0310.0000.0000.0000.000
120A121TYR00.016-0.0084.513-0.0560.013-0.001-0.009-0.0580.000
121A122GLU-1-0.877-0.9499.3280.3560.3560.0000.0000.0000.000
122A123GLN0-0.017-0.02111.310-0.099-0.0990.0000.0000.0000.000
123A124THR0-0.020-0.0108.980-0.066-0.0660.0000.0000.0000.000
124A125LYS10.8740.9566.324-1.048-1.0480.0000.0000.0000.000
125A126SER0-0.055-0.0188.549-0.053-0.0530.0000.0000.0000.000
126A127SER0-0.047-0.01911.5100.0200.0200.0000.0000.0000.000
127A128HIS00.0180.00112.259-0.093-0.0930.0000.0000.0000.000
128A129SER0-0.076-0.10013.456-0.056-0.0560.0000.0000.0000.000
129A130GLN0-0.030-0.0037.488-0.655-0.6550.0000.0000.0000.000
130A131ALA00.040-0.0029.453-0.257-0.2570.0000.0000.0000.000
131A132GLY00.0270.01511.9070.1190.1190.0000.0000.0000.000
132A133ILE0-0.029-0.00113.938-0.041-0.0410.0000.0000.0000.000
133A134LEU00.0130.01716.4490.0450.0450.0000.0000.0000.000
134A135ALA00.0160.00318.543-0.012-0.0120.0000.0000.0000.000
135A136VAL0-0.017-0.01222.1270.0230.0230.0000.0000.0000.000
136A137ARG10.9901.00225.6760.0980.0980.0000.0000.0000.000
137A138ALA0-0.046-0.03328.2170.0080.0080.0000.0000.0000.000
138A139TYR00.0060.00130.9300.0010.0010.0000.0000.0000.000
139A140GLU-1-0.905-0.94533.610-0.078-0.0780.0000.0000.0000.000
140A141THR0-0.051-0.03735.278-0.005-0.0050.0000.0000.0000.000
141A142VAL00.0520.03432.4290.0020.0020.0000.0000.0000.000
142A143LYS10.8960.94535.8000.0850.0850.0000.0000.0000.000
143A144GLN00.003-0.00334.600-0.005-0.0050.0000.0000.0000.000
144A145VAL00.0200.02038.5760.0060.0060.0000.0000.0000.000
145A146THR00.0120.01040.745-0.005-0.0050.0000.0000.0000.000
146A147LYS10.9440.96243.2920.0810.0810.0000.0000.0000.000
147A148ASN00.0250.00444.1650.0000.0000.0000.0000.0000.000
148A149ILE00.0570.04445.3200.0030.0030.0000.0000.0000.000
149A150VAL0-0.013-0.01142.489-0.005-0.0050.0000.0000.0000.000
150A151VAL0-0.012-0.00842.2090.0020.0020.0000.0000.0000.000
151A152LYS10.9500.97039.4430.1150.1150.0000.0000.0000.000
152A153THR00.028-0.00639.4680.0020.0020.0000.0000.0000.000
153A154LEU00.0060.01633.150-0.001-0.0010.0000.0000.0000.000
154A155ALA0-0.029-0.00737.1300.0060.0060.0000.0000.0000.000
155A156ARG10.9650.99335.3940.0680.0680.0000.0000.0000.000
156A157ASP-1-0.835-0.95233.687-0.098-0.0980.0000.0000.0000.000
157A158ASN0-0.0420.00628.8180.0030.0030.0000.0000.0000.000
158A159ILE0-0.008-0.00729.048-0.013-0.0130.0000.0000.0000.000
159A160TRP00.0300.00523.8200.0100.0100.0000.0000.0000.000
160A161LEU0-0.029-0.00926.475-0.009-0.0090.0000.0000.0000.000
161A162ALA00.0630.03621.3000.0070.0070.0000.0000.0000.000
162A163GLN0-0.060-0.03621.2350.0210.0210.0000.0000.0000.000
163A164THR0-0.013-0.00317.861-0.017-0.0170.0000.0000.0000.000
164A165PRO0-0.016-0.04314.0140.0480.0480.0000.0000.0000.000
165A166GLN0-0.084-0.03614.7290.0070.0070.0000.0000.0000.000
166A167LEU00.0230.0257.589-0.035-0.0350.0000.0000.0000.000
167A168SER00.0690.0379.4640.1180.1180.0000.0000.0000.000
168A169ARG10.8290.9132.8534.5885.3430.091-0.309-0.5370.000
169A170LEU00.0390.0186.1930.7010.7010.0000.0000.0000.000
170A171GLY00.0390.0177.8120.4920.4920.0000.0000.0000.000
171A172GLN0-0.116-0.0619.8730.3110.3110.0000.0000.0000.000
172A173LEU00.0240.02010.9860.2110.2110.0000.0000.0000.000
173A174GLU-1-0.819-0.93011.626-0.861-0.8610.0000.0000.0000.000
174A175LYS10.9320.97912.4041.2211.2210.0000.0000.0000.000
175A176ALA00.0180.02215.6130.0980.0980.0000.0000.0000.000
176A177PHE00.002-0.01516.5600.0930.0930.0000.0000.0000.000
177A178ASP-1-0.810-0.85217.713-0.517-0.5170.0000.0000.0000.000
178A179PHE0-0.034-0.01919.7710.0610.0610.0000.0000.0000.000
179A180CYS0-0.021-0.01820.8670.0520.0520.0000.0000.0000.000
180A181TYR0-0.016-0.00422.3670.0450.0450.0000.0000.0000.000
181A182SER0-0.073-0.03623.7630.0390.0390.0000.0000.0000.000
182A183ASN0-0.039-0.01125.1500.0440.0440.0000.0000.0000.000
183A184ASN0-0.060-0.02827.5080.0120.0120.0000.0000.0000.000
184A185LEU00.008-0.00925.0230.0160.0160.0000.0000.0000.000
185A186VAL00.0320.01024.449-0.004-0.0040.0000.0000.0000.000
186A187ALA0-0.0010.00426.3170.0000.0000.0000.0000.0000.000
187A188LYS10.8830.94826.6780.2720.2720.0000.0000.0000.000
188A189VAL0-0.016-0.00121.634-0.005-0.0050.0000.0000.0000.000
189A190THR0-0.082-0.03323.7080.0250.0250.0000.0000.0000.000
190A191ASP-1-0.840-0.91419.922-0.345-0.3450.0000.0000.0000.000
191A192GLU-1-0.863-0.95013.278-0.831-0.8310.0000.0000.0000.000
192A193ALA00.0200.00717.237-0.045-0.0450.0000.0000.0000.000
193A194SER00.0070.00318.1550.0030.0030.0000.0000.0000.000
194A195ALA00.009-0.00418.2350.0180.0180.0000.0000.0000.000
195A196LEU00.007-0.00913.548-0.012-0.0120.0000.0000.0000.000
196A197GLU-1-0.896-0.94517.678-0.348-0.3480.0000.0000.0000.000
197A198MET0-0.121-0.04620.7490.0280.0280.0000.0000.0000.000
198A199PHE0-0.028-0.00516.0730.0100.0100.0000.0000.0000.000
199A200GLY0-0.016-0.00120.239-0.007-0.0070.0000.0000.0000.000
200A201ILE0-0.072-0.04014.048-0.007-0.0070.0000.0000.0000.000
201A202ASN00.0360.01017.7080.0180.0180.0000.0000.0000.000
202A203PRO00.0040.05815.339-0.019-0.0190.0000.0000.0000.000
203A204ILE00.0100.02014.0570.0690.0690.0000.0000.0000.000
204A205VAL0-0.016-0.01416.920-0.023-0.0230.0000.0000.0000.000
205A206VAL00.0170.01415.5700.0200.0200.0000.0000.0000.000
206A207GLU-1-0.961-0.97518.767-0.090-0.0900.0000.0000.0000.000
207A208CYS0-0.0060.02520.5040.0110.0110.0000.0000.0000.000
208A209SER00.0050.00822.1540.0090.0090.0000.0000.0000.000
209A210LYS10.9740.96225.5150.0730.0730.0000.0000.0000.000
210A211LYS10.9770.98626.986-0.004-0.0040.0000.0000.0000.000
211A212ASN0-0.019-0.01120.9600.0110.0110.0000.0000.0000.000
212A213ILE00.0300.02125.014-0.018-0.0180.0000.0000.0000.000
213A214LYS10.9120.96024.8150.1720.1720.0000.0000.0000.000
214A215ILE00.021-0.00227.0000.0050.0050.0000.0000.0000.000
215A216THR0-0.074-0.02729.805-0.003-0.0030.0000.0000.0000.000
216A217THR00.0170.00832.0960.0050.0050.0000.0000.0000.000
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