Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: LZ8R9

Calculation Name: 1YAC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YAC

Chain ID: A

ChEMBL ID:

UniProt ID: P21367

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 OptHSide
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 204
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2283968.878403
FMO2-HF: Nuclear repulsion 2205745.945117
FMO2-HF: Total energy -78222.933286
FMO2-MP2: Total energy -78453.262425


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:THR)


Summations of interaction energy for fragment #1(A:2:THR)
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.
-0.2171.1290.001-0.47-0.8760.002
Interaction energy analysis for fragmet #1(A:2:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.009 / q_NPA : -0.022
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].
3A4PRO00.0280.0133.7820.3791.7250.001-0.470-0.8760.002
4A5TYR0-0.051-0.0475.5190.3900.3900.0000.0000.0000.000
5A6VAL00.0000.0018.3230.0160.0160.0000.0000.0000.000
6A7ARG10.9620.99411.3600.2740.2740.0000.0000.0000.000
7A8LEU00.0240.01214.058-0.028-0.0280.0000.0000.0000.000
8A9ASP-1-0.825-0.90417.455-0.228-0.2280.0000.0000.0000.000
9A10LYS10.9580.98219.2310.1060.1060.0000.0000.0000.000
10A11ASN0-0.014-0.00322.0060.0200.0200.0000.0000.0000.000
11A12ASP-1-0.857-0.93619.510-0.329-0.3290.0000.0000.0000.000
12A13ALA00.0110.02221.084-0.022-0.0220.0000.0000.0000.000
13A14ALA00.0510.02822.9050.0200.0200.0000.0000.0000.000
14A15VAL0-0.033-0.01625.305-0.008-0.0080.0000.0000.0000.000
15A16LEU0-0.010-0.01127.1000.0060.0060.0000.0000.0000.000
16A17LEU0-0.024-0.01529.0840.0030.0030.0000.0000.0000.000
17A18VAL0-0.011-0.02430.2580.0030.0030.0000.0000.0000.000
18A19ASP-1-0.686-0.80932.913-0.076-0.0760.0000.0000.0000.000
19A20HIS00.0150.03231.4330.0040.0040.0000.0000.0000.000
20A21GLN0-0.040-0.04836.582-0.002-0.0020.0000.0000.0000.000
21A22ALA0-0.013-0.01340.2190.0020.0020.0000.0000.0000.000
22A23GLY00.0300.02643.0230.0030.0030.0000.0000.0000.000
23A24LEU0-0.0010.00537.9140.0030.0030.0000.0000.0000.000
24A25LEU00.0100.00536.9570.0010.0010.0000.0000.0000.000
25A26SER0-0.089-0.03839.3490.0040.0040.0000.0000.0000.000
26A27LEU0-0.039-0.03338.3830.0030.0030.0000.0000.0000.000
27A28VAL0-0.074-0.01034.3180.0000.0000.0000.0000.0000.000
28A29ARG10.8970.94236.0420.0180.0180.0000.0000.0000.000
29A30ASP-1-0.802-0.88030.456-0.022-0.0220.0000.0000.0000.000
30A31ILE0-0.0190.00629.2720.0060.0060.0000.0000.0000.000
31A32GLU-1-0.821-0.89433.567-0.001-0.0010.0000.0000.0000.000
32A33PRO00.0720.00636.328-0.002-0.0020.0000.0000.0000.000
33A34ASP-1-0.896-0.92538.320-0.009-0.0090.0000.0000.0000.000
34A35LYS10.8350.89631.534-0.009-0.0090.0000.0000.0000.000
35A36PHE00.001-0.00531.514-0.004-0.0040.0000.0000.0000.000
36A37LYS10.9250.96134.2800.0210.0210.0000.0000.0000.000
37A38ASN0-0.020-0.00932.944-0.005-0.0050.0000.0000.0000.000
38A39ASN0-0.007-0.01729.5060.0010.0010.0000.0000.0000.000
39A40VAL00.0100.01531.049-0.007-0.0070.0000.0000.0000.000
40A41LEU0-0.042-0.03032.945-0.005-0.0050.0000.0000.0000.000
41A42ALA0-0.0190.00930.667-0.002-0.0020.0000.0000.0000.000
42A43LEU00.013-0.00326.802-0.004-0.0040.0000.0000.0000.000
43A44GLY00.0340.01929.893-0.008-0.0080.0000.0000.0000.000
44A45ASP-1-0.789-0.88532.838-0.044-0.0440.0000.0000.0000.000
45A46LEU0-0.045-0.01725.959-0.002-0.0020.0000.0000.0000.000
46A47ALA00.0020.01128.969-0.006-0.0060.0000.0000.0000.000
47A48LYS10.8490.92229.9400.0670.0670.0000.0000.0000.000
48A49TYR0-0.107-0.06628.838-0.001-0.0010.0000.0000.0000.000
49A50PHE0-0.048-0.03526.0160.0010.0010.0000.0000.0000.000
50A51ASN0-0.088-0.03428.635-0.008-0.0080.0000.0000.0000.000
51A52LEU00.0180.02225.313-0.008-0.0080.0000.0000.0000.000
52A53PRO0-0.0010.00627.5540.0100.0100.0000.0000.0000.000
53A54THR0-0.020-0.01929.265-0.007-0.0070.0000.0000.0000.000
54A55ILE0-0.0190.00130.2630.0040.0040.0000.0000.0000.000
55A56LEU00.0010.01332.8790.0010.0010.0000.0000.0000.000
56A57THR0-0.051-0.03133.863-0.002-0.0020.0000.0000.0000.000
57A58THR0-0.017-0.02936.6630.0020.0020.0000.0000.0000.000
58A59SER00.0130.01338.020-0.002-0.0020.0000.0000.0000.000
59A60ALA00.0280.01139.9630.0040.0040.0000.0000.0000.000
60A61GLU-1-0.775-0.85742.979-0.054-0.0540.0000.0000.0000.000
61A62THR0-0.065-0.01344.5450.0020.0020.0000.0000.0000.000
62A63GLY00.0440.00947.5230.0010.0010.0000.0000.0000.000
63A64PRO0-0.017-0.01746.0800.0000.0000.0000.0000.0000.000
64A65ASN00.000-0.00341.6200.0040.0040.0000.0000.0000.000
65A66GLY00.0260.02643.1230.0000.0000.0000.0000.0000.000
66A67PRO00.0340.01943.654-0.003-0.0030.0000.0000.0000.000
67A68LEU00.0310.01137.4010.0020.0020.0000.0000.0000.000
68A69VAL0-0.019-0.00638.6000.0030.0030.0000.0000.0000.000
69A70PRO00.016-0.01541.058-0.003-0.0030.0000.0000.0000.000
70A71GLU-1-0.833-0.90839.653-0.036-0.0360.0000.0000.0000.000
71A72LEU00.0440.02334.964-0.002-0.0020.0000.0000.0000.000
72A73LYS10.8980.95538.5280.0500.0500.0000.0000.0000.000
73A74ALA0-0.024-0.00941.368-0.001-0.0010.0000.0000.0000.000
74A75GLN0-0.023-0.00835.894-0.003-0.0030.0000.0000.0000.000
75A76PHE0-0.053-0.03333.233-0.004-0.0040.0000.0000.0000.000
76A77PRO0-0.0010.00638.522-0.002-0.0020.0000.0000.0000.000
77A78ASP-1-0.906-0.95539.376-0.068-0.0680.0000.0000.0000.000
78A79ALA0-0.065-0.01235.913-0.005-0.0050.0000.0000.0000.000
79A80PRO0-0.003-0.00434.6300.0040.0040.0000.0000.0000.000
80A81TYR0-0.020-0.04636.9620.0010.0010.0000.0000.0000.000
81A82ILE0-0.025-0.01035.6350.0030.0030.0000.0000.0000.000
82A83ALA00.0300.03838.9140.0000.0000.0000.0000.0000.000
83A84ARG10.7150.81235.7430.0870.0870.0000.0000.0000.000
84A85PRO0-0.014-0.02540.5660.0030.0030.0000.0000.0000.000
85A86GLY0-0.007-0.01041.6780.0040.0040.0000.0000.0000.000
86A87ASN0-0.045-0.02136.7470.0060.0060.0000.0000.0000.000
87A88ILE00.0440.03334.558-0.001-0.0010.0000.0000.0000.000
88A89ASN00.0390.00629.733-0.001-0.0010.0000.0000.0000.000
89A90ALA00.011-0.00831.7310.0000.0000.0000.0000.0000.000
90A91TRP0-0.012-0.02726.0620.0020.0020.0000.0000.0000.000
91A92ASP-1-0.834-0.90231.281-0.120-0.1200.0000.0000.0000.000
92A93ASN0-0.083-0.03034.2850.0040.0040.0000.0000.0000.000
93A94GLU-1-0.858-0.94535.158-0.113-0.1130.0000.0000.0000.000
94A95ASP-1-0.873-0.92635.615-0.103-0.1030.0000.0000.0000.000
95A96PHE0-0.013-0.01229.984-0.003-0.0030.0000.0000.0000.000
96A97VAL00.0550.03229.726-0.007-0.0070.0000.0000.0000.000
97A98LYS10.8510.92031.0150.0990.0990.0000.0000.0000.000
98A99ALA0-0.0030.00532.548-0.005-0.0050.0000.0000.0000.000
99A100VAL00.024-0.00427.066-0.004-0.0040.0000.0000.0000.000
100A101LYS10.8350.89527.0760.1960.1960.0000.0000.0000.000
101A102ALA0-0.047-0.01128.735-0.007-0.0070.0000.0000.0000.000
102A103THR0-0.063-0.03527.444-0.001-0.0010.0000.0000.0000.000
103A104GLY0-0.010-0.00226.6460.0000.0000.0000.0000.0000.000
104A105LYS10.7140.85423.3630.2200.2200.0000.0000.0000.000
105A106LYS10.8700.92915.8050.5700.5700.0000.0000.0000.000
106A107GLN0-0.011-0.01415.7590.0260.0260.0000.0000.0000.000
107A108LEU00.0130.01120.1400.0360.0360.0000.0000.0000.000
108A109ILE00.0060.00321.831-0.007-0.0070.0000.0000.0000.000
109A110ILE0-0.008-0.00923.5570.0140.0140.0000.0000.0000.000
110A111ALA00.0120.00925.3320.0050.0050.0000.0000.0000.000
111A112GLY00.0530.00528.088-0.003-0.0030.0000.0000.0000.000
112A113VAL0-0.075-0.01531.1270.0060.0060.0000.0000.0000.000
113A114VAL00.0220.00832.786-0.002-0.0020.0000.0000.0000.000
114A115THR00.052-0.01826.634-0.008-0.0080.0000.0000.0000.000
115A116GLU-1-0.771-0.87727.906-0.064-0.0640.0000.0000.0000.000
116A117VAL0-0.055-0.02328.985-0.003-0.0030.0000.0000.0000.000
117A118CYS0-0.036-0.02730.278-0.009-0.0090.0000.0000.0000.000
118A119VAL00.0000.02925.461-0.008-0.0080.0000.0000.0000.000
119A120ALA00.024-0.01625.028-0.015-0.0150.0000.0000.0000.000
120A121PHE0-0.046-0.01525.442-0.012-0.0120.0000.0000.0000.000
121A122PRO00.0490.03326.918-0.012-0.0120.0000.0000.0000.000
122A123ALA0-0.0010.00422.377-0.018-0.0180.0000.0000.0000.000
123A124LEU0-0.021-0.02321.408-0.025-0.0250.0000.0000.0000.000
124A125SER00.0140.01023.060-0.012-0.0120.0000.0000.0000.000
125A126ALA00.0220.01223.349-0.013-0.0130.0000.0000.0000.000
126A127ILE0-0.029-0.01617.824-0.024-0.0240.0000.0000.0000.000
127A128GLU-1-0.999-0.98520.044-0.248-0.2480.0000.0000.0000.000
128A129GLU-1-0.832-0.88922.172-0.226-0.2260.0000.0000.0000.000
129A130GLY0-0.0160.00919.131-0.007-0.0070.0000.0000.0000.000
130A131PHE0-0.049-0.02518.642-0.040-0.0400.0000.0000.0000.000
131A132ASP-1-0.887-0.92315.361-0.647-0.6470.0000.0000.0000.000
132A133VAL00.005-0.00717.5270.0470.0470.0000.0000.0000.000
133A134PHE0-0.016-0.01615.373-0.020-0.0200.0000.0000.0000.000
134A135VAL00.0200.00619.5340.0190.0190.0000.0000.0000.000
135A136VAL00.0120.00721.5950.0100.0100.0000.0000.0000.000
136A137THR0-0.049-0.04021.9740.0130.0130.0000.0000.0000.000
137A138ASP-1-0.809-0.90024.767-0.029-0.0290.0000.0000.0000.000
138A139ALA00.0180.01227.3720.0060.0060.0000.0000.0000.000
139A140SER0-0.006-0.01327.100-0.010-0.0100.0000.0000.0000.000
140A141GLY00.0130.02029.4780.0070.0070.0000.0000.0000.000
141A142THR0-0.066-0.06730.161-0.004-0.0040.0000.0000.0000.000
142A143PHE00.0520.02933.1070.0060.0060.0000.0000.0000.000
143A144ASN00.000-0.00933.4130.0050.0050.0000.0000.0000.000
144A145GLU-1-0.764-0.89329.7180.0100.0100.0000.0000.0000.000
145A146ILE0-0.0080.01528.836-0.001-0.0010.0000.0000.0000.000
146A147THR0-0.015-0.00829.033-0.002-0.0020.0000.0000.0000.000
147A148ARG10.8100.88226.253-0.001-0.0010.0000.0000.0000.000
148A149HIS0-0.017-0.01324.685-0.009-0.0090.0000.0000.0000.000
149A150SER0-0.005-0.00723.919-0.003-0.0030.0000.0000.0000.000
150A151ALA0-0.0020.00624.357-0.011-0.0110.0000.0000.0000.000
151A152TRP0-0.003-0.01621.056-0.014-0.0140.0000.0000.0000.000
152A153ASP-1-0.899-0.93619.799-0.071-0.0710.0000.0000.0000.000
153A154ARG10.9560.97519.5040.0910.0910.0000.0000.0000.000
154A155MET0-0.017-0.00420.309-0.022-0.0220.0000.0000.0000.000
155A156SER00.0170.00914.870-0.026-0.0260.0000.0000.0000.000
156A157GLN0-0.120-0.04515.211-0.050-0.0500.0000.0000.0000.000
157A158ALA0-0.025-0.01416.011-0.028-0.0280.0000.0000.0000.000
158A159GLY0-0.0010.00413.845-0.048-0.0480.0000.0000.0000.000
159A160ALA0-0.029-0.00314.734-0.041-0.0410.0000.0000.0000.000
160A161GLN0-0.058-0.03112.3190.0060.0060.0000.0000.0000.000
161A162LEU0-0.036-0.01615.8160.0210.0210.0000.0000.0000.000
162A163MET00.0120.01416.6940.0050.0050.0000.0000.0000.000
163A164THR00.0050.00619.6690.0040.0040.0000.0000.0000.000
164A165TRP00.035-0.00622.567-0.006-0.0060.0000.0000.0000.000
165A166PHE00.0110.01723.457-0.005-0.0050.0000.0000.0000.000
166A167GLY00.0450.02420.3970.0020.0020.0000.0000.0000.000
167A168VAL00.0130.00020.218-0.011-0.0110.0000.0000.0000.000
168A169ALA00.007-0.00121.623-0.011-0.0110.0000.0000.0000.000
169A170CYS0-0.045-0.02520.8870.0010.0010.0000.0000.0000.000
170A171GLU-1-0.832-0.88714.993-0.180-0.1800.0000.0000.0000.000
171A172LEU0-0.0090.00518.970-0.019-0.0190.0000.0000.0000.000
172A173HIS00.0210.00721.665-0.014-0.0140.0000.0000.0000.000
173A174ARG10.7340.86017.3630.1960.1960.0000.0000.0000.000
174A175ASP-1-0.847-0.91621.0260.0190.0190.0000.0000.0000.000
175A176TRP00.0610.03023.906-0.011-0.0110.0000.0000.0000.000
176A177ARG10.8300.86624.591-0.010-0.0100.0000.0000.0000.000
177A178ASN0-0.077-0.02224.316-0.004-0.0040.0000.0000.0000.000
178A179ASP-1-0.794-0.88328.702-0.040-0.0400.0000.0000.0000.000
179A180ILE0-0.0150.00430.6130.0010.0010.0000.0000.0000.000
180A181ALA00.0490.02131.9440.0010.0010.0000.0000.0000.000
181A182GLY00.0350.03033.2290.0010.0010.0000.0000.0000.000
182A183LEU00.0020.00626.150-0.001-0.0010.0000.0000.0000.000
183A184ALA00.002-0.00630.5270.0030.0030.0000.0000.0000.000
184A185THR0-0.025-0.01832.7030.0040.0040.0000.0000.0000.000
185A186LEU0-0.0170.00628.8970.0020.0020.0000.0000.0000.000
186A187PHE00.000-0.02625.7400.0020.0020.0000.0000.0000.000
187A188SER00.0160.01131.6530.0030.0030.0000.0000.0000.000
188A189ASN0-0.033-0.02435.2390.0050.0050.0000.0000.0000.000
189A190HIS10.7790.88132.2880.0250.0250.0000.0000.0000.000
190A191ILE00.0280.03428.7750.0010.0010.0000.0000.0000.000
191A192PRO00.0360.01433.2050.0020.0020.0000.0000.0000.000
192A193ASP-1-0.885-0.94232.9460.0300.0300.0000.0000.0000.000
193A194TYR00.016-0.00530.0240.0040.0040.0000.0000.0000.000
194A195ARG10.9270.95333.6350.0030.0030.0000.0000.0000.000
195A196ASN0-0.0090.00436.970-0.002-0.0020.0000.0000.0000.000
196A197LEU0-0.016-0.00432.8240.0010.0010.0000.0000.0000.000
197A198MET0-0.0120.00135.2740.0000.0000.0000.0000.0000.000
198A199THR00.0070.01237.707-0.001-0.0010.0000.0000.0000.000
199A200SER0-0.026-0.01839.9000.0000.0000.0000.0000.0000.000
200A201TYR0-0.019-0.00637.4490.0030.0030.0000.0000.0000.000
201A202ASP-1-0.870-0.93839.9200.0110.0110.0000.0000.0000.000
202A203THR0-0.119-0.06542.0350.0000.0000.0000.0000.0000.000
203A204LEU0-0.062-0.02142.0940.0000.0000.0000.0000.0000.000
204A205THR0-0.107-0.04440.447-0.002-0.0020.0000.0000.0000.000