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

tag_button

FMODB ID: MN36Z

Calculation Name: 4Z85-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4Z85

Chain ID: A

ChEMBL ID:

UniProt ID: A4UVY1

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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2179159.547769
FMO2-HF: Nuclear repulsion 2099031.400516
FMO2-HF: Total energy -80128.147253
FMO2-MP2: Total energy -80357.392129


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.
-0.411.4020.04-0.721-1.1320.001
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 : -0.005 / q_NPA : -0.014
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].
3A4ILE00.021-0.0013.097-0.4881.3240.040-0.721-1.1320.001
4A5ALA00.0240.0235.4010.0590.0590.0000.0000.0000.000
5A6MET00.0420.0068.3980.0920.0920.0000.0000.0000.000
6A7SER0-0.007-0.00911.4780.0340.0340.0000.0000.0000.000
7A8GLY00.0070.01811.9710.0550.0550.0000.0000.0000.000
8A9LEU0-0.034-0.0028.8000.0060.0060.0000.0000.0000.000
9A10THR00.050-0.00113.0150.0080.0080.0000.0000.0000.000
10A11ASN00.032-0.01615.016-0.063-0.0630.0000.0000.0000.000
11A12MET00.0590.05016.783-0.042-0.0420.0000.0000.0000.000
12A13GLN00.0780.05011.470-0.020-0.0200.0000.0000.0000.000
13A14LYS10.8770.94112.1600.2040.2040.0000.0000.0000.000
14A15TYR00.0320.02613.362-0.068-0.0680.0000.0000.0000.000
15A16TRP00.0190.01913.053-0.030-0.0300.0000.0000.0000.000
16A17LEU00.0020.0027.499-0.051-0.0510.0000.0000.0000.000
17A18ILE00.0090.02810.895-0.103-0.1030.0000.0000.0000.000
18A19THR0-0.045-0.03913.613-0.018-0.0180.0000.0000.0000.000
19A20GLY00.0070.00012.6740.0590.0590.0000.0000.0000.000
20A21SER0-0.088-0.05410.058-0.092-0.0920.0000.0000.0000.000
21A22VAL0-0.0030.01111.9760.0050.0050.0000.0000.0000.000
22A23GLY00.0100.00515.5500.0640.0640.0000.0000.0000.000
23A24PRO00.0010.00417.552-0.041-0.0410.0000.0000.0000.000
24A25ARG10.7780.88517.7110.4610.4610.0000.0000.0000.000
25A26PRO00.0380.02922.2260.0120.0120.0000.0000.0000.000
26A27ILE0-0.016-0.03425.796-0.011-0.0110.0000.0000.0000.000
27A28ALA00.0370.02928.2030.0130.0130.0000.0000.0000.000
28A29LEU0-0.003-0.00231.056-0.002-0.0020.0000.0000.0000.000
29A30VAL0-0.0170.00233.1110.0080.0080.0000.0000.0000.000
30A31THR00.0180.00635.454-0.001-0.0010.0000.0000.0000.000
31A32SER00.001-0.01238.8000.0010.0010.0000.0000.0000.000
32A33LEU00.0190.01140.8090.0010.0010.0000.0000.0000.000
33A34ASN00.0220.00843.4710.0010.0010.0000.0000.0000.000
34A35SER0-0.018-0.03744.6220.0020.0020.0000.0000.0000.000
35A36GLU-1-0.885-0.93347.818-0.066-0.0660.0000.0000.0000.000
36A37GLY0-0.021-0.00648.0800.0020.0020.0000.0000.0000.000
37A38LEU0-0.0160.00944.438-0.001-0.0010.0000.0000.0000.000
38A39CYS00.0120.00241.708-0.003-0.0030.0000.0000.0000.000
39A40ASN0-0.036-0.00338.3930.0030.0030.0000.0000.0000.000
40A41ALA00.021-0.01437.400-0.001-0.0010.0000.0000.0000.000
41A42ALA00.0150.01532.426-0.001-0.0010.0000.0000.0000.000
42A43PRO0-0.0140.00329.120-0.003-0.0030.0000.0000.0000.000
43A44TYR00.0350.01827.447-0.006-0.0060.0000.0000.0000.000
44A45SER00.013-0.00123.162-0.013-0.0130.0000.0000.0000.000
45A46ALA0-0.057-0.02923.146-0.031-0.0310.0000.0000.0000.000
46A47PHE0-0.001-0.00524.1840.0180.0180.0000.0000.0000.000
47A48ASN00.0100.00724.786-0.008-0.0080.0000.0000.0000.000
48A49TYR00.0120.00727.6880.0070.0070.0000.0000.0000.000
49A50MET0-0.100-0.05827.113-0.014-0.0140.0000.0000.0000.000
50A51GLY00.0150.01731.2530.0000.0000.0000.0000.0000.000
51A52GLU-1-0.940-0.97834.256-0.140-0.1400.0000.0000.0000.000
52A53ASP-1-0.956-0.95237.419-0.088-0.0880.0000.0000.0000.000
53A54PRO00.0270.00239.2290.0000.0000.0000.0000.0000.000
54A55PRO0-0.0010.01337.867-0.008-0.0080.0000.0000.0000.000
55A56LEU0-0.0150.00635.060-0.001-0.0010.0000.0000.0000.000
56A57PHE0-0.002-0.01831.955-0.012-0.0120.0000.0000.0000.000
57A58VAL0-0.012-0.00227.9610.0080.0080.0000.0000.0000.000
58A59ILE00.0180.00428.645-0.016-0.0160.0000.0000.0000.000
59A60ALA0-0.051-0.02025.2740.0110.0110.0000.0000.0000.000
60A61VAL0-0.011-0.00927.133-0.011-0.0110.0000.0000.0000.000
61A62ASP-1-0.846-0.91626.507-0.193-0.1930.0000.0000.0000.000
62A63HIS10.8560.94129.3510.1270.1270.0000.0000.0000.000
63A75LYS10.8210.88632.0490.1300.1300.0000.0000.0000.000
64A76ASP-1-0.853-0.93234.634-0.094-0.0940.0000.0000.0000.000
65A77THR0-0.023-0.01834.1010.0050.0050.0000.0000.0000.000
66A78LEU00.0180.01133.6110.0010.0010.0000.0000.0000.000
67A79LYS10.8680.92436.3770.0790.0790.0000.0000.0000.000
68A80ASN0-0.011-0.02139.8070.0070.0070.0000.0000.0000.000
69A81ILE0-0.009-0.00436.0090.0020.0020.0000.0000.0000.000
70A82ILE0-0.045-0.02937.9480.0030.0030.0000.0000.0000.000
71A83GLU-1-0.835-0.88741.478-0.071-0.0710.0000.0000.0000.000
72A84ARG10.8570.93843.7670.0770.0770.0000.0000.0000.000
73A85GLU-1-0.922-0.94642.829-0.076-0.0760.0000.0000.0000.000
74A86GLN0-0.037-0.02742.801-0.003-0.0030.0000.0000.0000.000
75A87PHE0-0.037-0.03735.401-0.003-0.0030.0000.0000.0000.000
76A88VAL00.0290.03039.2090.0010.0010.0000.0000.0000.000
77A89VAL0-0.015-0.00133.386-0.006-0.0060.0000.0000.0000.000
78A90ASN0-0.015-0.02236.1710.0070.0070.0000.0000.0000.000
79A91MET0-0.025-0.00233.092-0.015-0.0150.0000.0000.0000.000
80A92VAL00.028-0.00430.6710.0080.0080.0000.0000.0000.000
81A93ASP-1-0.765-0.87431.658-0.151-0.1510.0000.0000.0000.000
82A94GLU-1-0.720-0.80732.783-0.158-0.1580.0000.0000.0000.000
83A95ARG10.7820.87434.4680.1250.1250.0000.0000.0000.000
84A96ILE00.0030.00134.6210.0060.0060.0000.0000.0000.000
85A97ALA0-0.0090.01531.017-0.002-0.0020.0000.0000.0000.000
86A98GLU-1-0.863-0.93531.960-0.147-0.1470.0000.0000.0000.000
87A99ARG10.8500.89633.4680.1050.1050.0000.0000.0000.000
88A100MET0-0.0240.00328.471-0.002-0.0020.0000.0000.0000.000
89A101VAL0-0.012-0.01728.296-0.007-0.0070.0000.0000.0000.000
90A102LEU00.0090.01930.5940.0000.0000.0000.0000.0000.000
91A103CYS00.0020.02033.4820.0060.0060.0000.0000.0000.000
92A104GLY0-0.050-0.02429.8040.0000.0000.0000.0000.0000.000
93A105SER0-0.076-0.04430.341-0.004-0.0040.0000.0000.0000.000
94A106ASP-1-0.923-0.97030.967-0.113-0.1130.0000.0000.0000.000
95A107PHE00.0460.00732.9030.0060.0060.0000.0000.0000.000
96A108PRO0-0.0310.03134.6440.0060.0060.0000.0000.0000.000
97A109SER0-0.062-0.05436.6920.0020.0020.0000.0000.0000.000
98A110HIS0-0.066-0.03840.2880.0070.0070.0000.0000.0000.000
99A111ILE0-0.0050.00640.1090.0040.0040.0000.0000.0000.000
100A112SER0-0.016-0.02040.883-0.005-0.0050.0000.0000.0000.000
101A113GLU-1-0.743-0.86336.048-0.112-0.1120.0000.0000.0000.000
102A114ALA0-0.004-0.01139.222-0.001-0.0010.0000.0000.0000.000
103A115GLU-1-0.909-0.95441.163-0.074-0.0740.0000.0000.0000.000
104A116ALA0-0.037-0.01339.9830.0010.0010.0000.0000.0000.000
105A117VAL0-0.067-0.03136.685-0.001-0.0010.0000.0000.0000.000
106A118GLY00.0150.02439.944-0.001-0.0010.0000.0000.0000.000
107A119PHE0-0.071-0.05836.309-0.004-0.0040.0000.0000.0000.000
108A120ASP-1-0.848-0.91842.281-0.080-0.0800.0000.0000.0000.000
109A121LEU0-0.023-0.01442.719-0.006-0.0060.0000.0000.0000.000
110A122THR0-0.049-0.03645.6990.0050.0050.0000.0000.0000.000
111A123PRO0-0.005-0.01446.635-0.003-0.0030.0000.0000.0000.000
112A124SER0-0.033-0.02745.259-0.003-0.0030.0000.0000.0000.000
113A125THR0-0.057-0.04347.7040.0040.0040.0000.0000.0000.000
114A126THR0-0.081-0.06746.6680.0030.0030.0000.0000.0000.000
115A127ILE0-0.057-0.03343.6180.0000.0000.0000.0000.0000.000
116A128ASP-1-0.845-0.91447.809-0.071-0.0710.0000.0000.0000.000
117A129VAL0-0.076-0.02042.0250.0000.0000.0000.0000.0000.000
118A130PRO00.0470.04844.622-0.002-0.0020.0000.0000.0000.000
119A131ARG10.9240.97441.8460.0910.0910.0000.0000.0000.000
120A132ILE00.0200.00537.7920.0040.0040.0000.0000.0000.000
121A133THR00.009-0.00241.778-0.002-0.0020.0000.0000.0000.000
122A134ASP-1-0.816-0.89440.554-0.100-0.1000.0000.0000.0000.000
123A135ALA0-0.0250.00738.582-0.005-0.0050.0000.0000.0000.000
124A136PRO0-0.043-0.01435.5530.0060.0060.0000.0000.0000.000
125A137ILE00.032-0.00236.0830.0040.0040.0000.0000.0000.000
126A138ALA0-0.0120.00037.477-0.005-0.0050.0000.0000.0000.000
127A139TRP00.0190.00532.6120.0000.0000.0000.0000.0000.000
128A140GLU-1-0.696-0.80839.271-0.090-0.0900.0000.0000.0000.000
129A141CYS0-0.075-0.03938.376-0.003-0.0030.0000.0000.0000.000
130A142LYS10.9450.97840.7600.0860.0860.0000.0000.0000.000
131A143LEU0-0.031-0.02237.866-0.007-0.0070.0000.0000.0000.000
132A144TYR00.0090.02637.3240.0030.0030.0000.0000.0000.000
133A145LYS10.9270.94635.9830.1110.1110.0000.0000.0000.000
134A146ILE00.0340.02534.076-0.008-0.0080.0000.0000.0000.000
135A147ILE0-0.027-0.00931.3250.0080.0080.0000.0000.0000.000
136A148ASP-1-0.800-0.88731.203-0.128-0.1280.0000.0000.0000.000
137A149PHE0-0.045-0.01421.950-0.001-0.0010.0000.0000.0000.000
138A150SER0-0.018-0.04626.791-0.001-0.0010.0000.0000.0000.000
139A151LYS10.9850.98028.9190.0800.0800.0000.0000.0000.000
140A152GLN00.0170.03127.0810.0070.0070.0000.0000.0000.000
141A153ARG10.8450.93724.2930.2170.2170.0000.0000.0000.000
142A154SER0-0.006-0.02828.8560.0070.0070.0000.0000.0000.000
143A155MET0-0.051-0.02127.353-0.020-0.0200.0000.0000.0000.000
144A156VAL00.0350.01730.0640.0110.0110.0000.0000.0000.000
145A157PHE00.001-0.01230.144-0.011-0.0110.0000.0000.0000.000
146A158GLY00.0240.01234.3440.0090.0090.0000.0000.0000.000
147A159GLU-1-0.883-0.95736.530-0.105-0.1050.0000.0000.0000.000
148A160ILE0-0.035-0.02335.7490.0030.0030.0000.0000.0000.000
149A161VAL0-0.008-0.00440.0120.0030.0030.0000.0000.0000.000
150A162ALA00.0170.01143.0660.0040.0040.0000.0000.0000.000
151A163MET0-0.051-0.02538.232-0.007-0.0070.0000.0000.0000.000
152A164TYR00.0050.00441.4260.0070.0070.0000.0000.0000.000
153A165PHE00.020-0.01739.270-0.009-0.0090.0000.0000.0000.000
154A166ARG10.8490.92740.8120.1070.1070.0000.0000.0000.000
155A167GLU-1-0.881-0.93843.380-0.081-0.0810.0000.0000.0000.000
156A168GLU-1-0.799-0.88942.248-0.101-0.1010.0000.0000.0000.000
157A169LEU0-0.070-0.04238.060-0.006-0.0060.0000.0000.0000.000
158A170ILE0-0.0100.00540.458-0.006-0.0060.0000.0000.0000.000
159A171ASP-1-0.853-0.92343.092-0.089-0.0890.0000.0000.0000.000
160A172GLU-1-0.899-0.95544.985-0.079-0.0790.0000.0000.0000.000
161A173GLU-1-0.896-0.94547.363-0.071-0.0710.0000.0000.0000.000
162A174LYS10.8180.90343.3710.0960.0960.0000.0000.0000.000
163A175LEU00.0070.00844.084-0.004-0.0040.0000.0000.0000.000
164A176ARG10.8540.93039.7510.1030.1030.0000.0000.0000.000
165A177VAL00.0760.04236.3520.0030.0030.0000.0000.0000.000
166A178ARG10.8240.92038.7460.0950.0950.0000.0000.0000.000
167A179VAL00.006-0.01133.108-0.003-0.0030.0000.0000.0000.000
168A180ASP-1-0.922-0.94634.485-0.152-0.1520.0000.0000.0000.000
169A181LEU0-0.0050.00735.585-0.002-0.0020.0000.0000.0000.000
170A182PHE00.0270.01332.745-0.002-0.0020.0000.0000.0000.000
171A183GLN0-0.041-0.02431.944-0.013-0.0130.0000.0000.0000.000
172A184PRO0-0.0090.01229.4960.0010.0010.0000.0000.0000.000
173A185TYR0-0.051-0.05327.547-0.015-0.0150.0000.0000.0000.000
174A186GLY00.0200.01624.2390.0040.0040.0000.0000.0000.000
175A187ARG10.8160.90821.2930.2950.2950.0000.0000.0000.000
176A188LEU00.0350.01617.071-0.035-0.0350.0000.0000.0000.000
177A189GLY00.0840.04215.4550.0170.0170.0000.0000.0000.000
178A190GLY00.0290.00016.5320.0300.0300.0000.0000.0000.000
179A191PRO0-0.024-0.01118.2880.0000.0000.0000.0000.0000.000
180A192ASN0-0.031-0.00517.8230.0450.0450.0000.0000.0000.000
181A193TYR00.0460.00821.207-0.020-0.0200.0000.0000.0000.000
182A194CYS0-0.029-0.01621.746-0.007-0.0070.0000.0000.0000.000
183A195ARG10.8870.91923.8120.1860.1860.0000.0000.0000.000
184A196THR0-0.018-0.01726.209-0.010-0.0100.0000.0000.0000.000
185A197THR00.0360.00227.7380.0090.0090.0000.0000.0000.000
186A198ASP-1-0.933-0.94925.529-0.235-0.2350.0000.0000.0000.000
187A199ARG10.7770.85526.5710.1780.1780.0000.0000.0000.000
188A200VAL00.0340.02124.6740.0110.0110.0000.0000.0000.000
189A201ARG10.9520.97527.9940.1380.1380.0000.0000.0000.000
190A202LEU00.0070.00023.7280.0130.0130.0000.0000.0000.000
191A203THR0-0.028-0.00827.952-0.001-0.0010.0000.0000.0000.000
192A204VAL00.0370.01227.755-0.001-0.0010.0000.0000.0000.000
193A205PRO0-0.0330.00029.0460.0100.0100.0000.0000.0000.000
194A206THR00.0460.00232.1270.0000.0000.0000.0000.0000.000
195A207PHE0-0.046-0.01532.9960.0060.0060.0000.0000.0000.000
196A208LEU00.0320.01430.915-0.007-0.0070.0000.0000.0000.000
197A209PRO0-0.0080.00626.9510.0080.0080.0000.0000.0000.000
198A210SER00.023-0.00928.790-0.001-0.0010.0000.0000.0000.000
199A211ALA0-0.041-0.01825.4160.0080.0080.0000.0000.0000.000
200A212GLY00.0050.02226.4380.0090.0090.0000.0000.0000.000