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: 98GN2

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 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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2178212.065182
FMO2-HF: Nuclear repulsion 2098084.112866
FMO2-HF: Total energy -80127.952316
FMO2-MP2: Total energy -80357.186342


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.
-0.8251.5370.249-0.953-1.657-0.001
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 : -0.008 / q_NPA : -0.016
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].
3A4ILE00.013-0.0012.697-1.1221.2190.250-0.950-1.641-0.001
4A5ALA00.0180.0224.8950.1140.135-0.001-0.003-0.0160.000
5A6MET00.0540.0028.6140.0720.0720.0000.0000.0000.000
6A7SER0-0.012-0.00911.2510.0390.0390.0000.0000.0000.000
7A8GLY0-0.0010.00911.4220.0560.0560.0000.0000.0000.000
8A9LEU0-0.0310.0088.8720.0300.0300.0000.0000.0000.000
9A10THR00.0740.01212.8830.0280.0280.0000.0000.0000.000
10A11ASN00.030-0.01715.145-0.071-0.0710.0000.0000.0000.000
11A12MET00.0610.04516.824-0.044-0.0440.0000.0000.0000.000
12A13GLN00.0760.05011.625-0.027-0.0270.0000.0000.0000.000
13A14LYS10.8800.94412.2760.2580.2580.0000.0000.0000.000
14A15TYR00.0250.02013.592-0.072-0.0720.0000.0000.0000.000
15A16TRP00.0230.00713.022-0.034-0.0340.0000.0000.0000.000
16A17LEU00.0010.0067.577-0.057-0.0570.0000.0000.0000.000
17A18ILE00.0080.02311.128-0.110-0.1100.0000.0000.0000.000
18A19THR0-0.056-0.03613.800-0.011-0.0110.0000.0000.0000.000
19A20GLY00.007-0.00412.5620.0580.0580.0000.0000.0000.000
20A21SER0-0.073-0.0429.967-0.054-0.0540.0000.0000.0000.000
21A22VAL0-0.0150.00911.9390.0180.0180.0000.0000.0000.000
22A23GLY00.0010.01115.4470.0590.0590.0000.0000.0000.000
23A24PRO00.013-0.00217.803-0.029-0.0290.0000.0000.0000.000
24A25ARG10.7960.89017.4720.4980.4980.0000.0000.0000.000
25A26PRO00.0460.04222.2750.0130.0130.0000.0000.0000.000
26A27ILE0-0.006-0.02925.937-0.011-0.0110.0000.0000.0000.000
27A28ALA00.0250.02028.0570.0130.0130.0000.0000.0000.000
28A29LEU0-0.007-0.00631.012-0.004-0.0040.0000.0000.0000.000
29A30VAL0-0.0130.00133.0770.0090.0090.0000.0000.0000.000
30A31THR00.0320.01935.516-0.001-0.0010.0000.0000.0000.000
31A32SER0-0.018-0.01739.1080.0000.0000.0000.0000.0000.000
32A33LEU00.0300.01041.0460.0010.0010.0000.0000.0000.000
33A34ASN00.0360.01743.8710.0010.0010.0000.0000.0000.000
34A35SER0-0.020-0.02245.1860.0020.0020.0000.0000.0000.000
35A36GLU-1-0.881-0.92848.072-0.075-0.0750.0000.0000.0000.000
36A37GLY0-0.053-0.01848.7480.0020.0020.0000.0000.0000.000
37A38LEU00.0040.01944.626-0.001-0.0010.0000.0000.0000.000
38A39CYS00.0320.01341.882-0.003-0.0030.0000.0000.0000.000
39A40ASN0-0.039-0.00238.8650.0030.0030.0000.0000.0000.000
40A41ALA00.024-0.01237.271-0.001-0.0010.0000.0000.0000.000
41A42ALA0-0.0090.00132.724-0.001-0.0010.0000.0000.0000.000
42A43PRO0-0.0030.00929.219-0.001-0.0010.0000.0000.0000.000
43A44TYR00.009-0.00927.463-0.013-0.0130.0000.0000.0000.000
44A45SER00.0190.00223.223-0.012-0.0120.0000.0000.0000.000
45A46ALA0-0.071-0.02923.174-0.028-0.0280.0000.0000.0000.000
46A47PHE0-0.009-0.00824.1560.0210.0210.0000.0000.0000.000
47A48ASN00.0150.00924.407-0.005-0.0050.0000.0000.0000.000
48A49TYR00.0090.00427.5590.0060.0060.0000.0000.0000.000
49A50MET0-0.106-0.06426.772-0.015-0.0150.0000.0000.0000.000
50A51GLY00.0230.01130.9500.0000.0000.0000.0000.0000.000
51A52GLU-1-0.936-0.97733.839-0.138-0.1380.0000.0000.0000.000
52A53ASP-1-0.971-0.94837.087-0.090-0.0900.0000.0000.0000.000
53A54PRO00.021-0.00438.9970.0010.0010.0000.0000.0000.000
54A55PRO00.0060.00637.524-0.007-0.0070.0000.0000.0000.000
55A56LEU0-0.0070.01835.0490.0000.0000.0000.0000.0000.000
56A57PHE00.005-0.00731.686-0.012-0.0120.0000.0000.0000.000
57A58VAL0-0.0070.00227.6370.0070.0070.0000.0000.0000.000
58A59ILE00.0230.00228.563-0.016-0.0160.0000.0000.0000.000
59A60ALA0-0.071-0.02725.5680.0100.0100.0000.0000.0000.000
60A61VAL00.001-0.00227.643-0.009-0.0090.0000.0000.0000.000
61A62ASP-1-0.833-0.91126.403-0.228-0.2280.0000.0000.0000.000
62A63HIS10.8690.93829.4180.1490.1490.0000.0000.0000.000
63A75LYS10.8410.90132.3600.1460.1460.0000.0000.0000.000
64A76ASP-1-0.844-0.93134.759-0.108-0.1080.0000.0000.0000.000
65A77THR0-0.024-0.00734.6900.0000.0000.0000.0000.0000.000
66A78LEU00.0300.01233.6520.0030.0030.0000.0000.0000.000
67A79LYS10.8710.92836.5810.0900.0900.0000.0000.0000.000
68A80ASN00.017-0.00340.0120.0080.0080.0000.0000.0000.000
69A81ILE0-0.017-0.00536.2850.0030.0030.0000.0000.0000.000
70A82ILE0-0.057-0.03037.9810.0030.0030.0000.0000.0000.000
71A83GLU-1-0.862-0.91741.463-0.081-0.0810.0000.0000.0000.000
72A84ARG10.8890.94144.0330.0860.0860.0000.0000.0000.000
73A85GLU-1-0.938-0.96342.662-0.085-0.0850.0000.0000.0000.000
74A86GLN0-0.011-0.01842.855-0.002-0.0020.0000.0000.0000.000
75A87PHE0-0.034-0.03535.520-0.003-0.0030.0000.0000.0000.000
76A88VAL00.0150.02039.2620.0000.0000.0000.0000.0000.000
77A89VAL0-0.027-0.00233.310-0.007-0.0070.0000.0000.0000.000
78A90ASN0-0.028-0.02235.8640.0100.0100.0000.0000.0000.000
79A91MET00.0000.00633.041-0.016-0.0160.0000.0000.0000.000
80A92VAL00.0340.00130.6660.0080.0080.0000.0000.0000.000
81A93ASP-1-0.784-0.89531.551-0.155-0.1550.0000.0000.0000.000
82A94GLU-1-0.741-0.83332.862-0.164-0.1640.0000.0000.0000.000
83A95ARG10.8100.90634.2550.1280.1280.0000.0000.0000.000
84A96ILE00.001-0.00434.6860.0060.0060.0000.0000.0000.000
85A97ALA00.0100.02030.930-0.003-0.0030.0000.0000.0000.000
86A98GLU-1-0.889-0.94632.010-0.163-0.1630.0000.0000.0000.000
87A99ARG10.8660.91833.6000.1130.1130.0000.0000.0000.000
88A100MET0-0.0140.00728.333-0.004-0.0040.0000.0000.0000.000
89A101VAL0-0.012-0.01728.484-0.008-0.0080.0000.0000.0000.000
90A102LEU00.0140.01730.819-0.001-0.0010.0000.0000.0000.000
91A103CYS0-0.0100.01133.7770.0070.0070.0000.0000.0000.000
92A104GLY0-0.059-0.02230.1070.0010.0010.0000.0000.0000.000
93A105SER0-0.065-0.03730.296-0.007-0.0070.0000.0000.0000.000
94A106ASP-1-0.935-0.98231.342-0.134-0.1340.0000.0000.0000.000
95A107PHE00.0410.00733.2140.0070.0070.0000.0000.0000.000
96A108PRO0-0.0260.03334.8430.0060.0060.0000.0000.0000.000
97A109SER0-0.067-0.05036.9550.0030.0030.0000.0000.0000.000
98A110HIS0-0.057-0.03240.3220.0080.0080.0000.0000.0000.000
99A111ILE0-0.0060.00640.2670.0050.0050.0000.0000.0000.000
100A112SER0-0.022-0.02641.161-0.005-0.0050.0000.0000.0000.000
101A113GLU-1-0.735-0.86536.527-0.125-0.1250.0000.0000.0000.000
102A114ALA0-0.023-0.01639.675-0.001-0.0010.0000.0000.0000.000
103A115GLU-1-0.891-0.94041.421-0.082-0.0820.0000.0000.0000.000
104A116ALA0-0.049-0.01740.3700.0020.0020.0000.0000.0000.000
105A117VAL0-0.065-0.03736.875-0.001-0.0010.0000.0000.0000.000
106A118GLY00.0070.01640.099-0.001-0.0010.0000.0000.0000.000
107A119PHE0-0.082-0.06636.321-0.003-0.0030.0000.0000.0000.000
108A120ASP-1-0.846-0.90642.306-0.084-0.0840.0000.0000.0000.000
109A121LEU0-0.029-0.02342.752-0.006-0.0060.0000.0000.0000.000
110A122THR0-0.042-0.03345.6740.0050.0050.0000.0000.0000.000
111A123PRO0-0.009-0.01346.607-0.004-0.0040.0000.0000.0000.000
112A124SER0-0.038-0.02945.094-0.003-0.0030.0000.0000.0000.000
113A125THR0-0.058-0.03447.5240.0050.0050.0000.0000.0000.000
114A126THR0-0.090-0.08346.4860.0030.0030.0000.0000.0000.000
115A127ILE0-0.103-0.04743.3480.0010.0010.0000.0000.0000.000
116A128ASP-1-0.835-0.91347.829-0.076-0.0760.0000.0000.0000.000
117A129VAL0-0.089-0.02642.0860.0000.0000.0000.0000.0000.000
118A130PRO00.0400.04844.761-0.001-0.0010.0000.0000.0000.000
119A131ARG10.9250.96941.8800.0940.0940.0000.0000.0000.000
120A132ILE00.0230.00237.7850.0040.0040.0000.0000.0000.000
121A133THR00.014-0.00141.733-0.002-0.0020.0000.0000.0000.000
122A134ASP-1-0.823-0.89340.636-0.105-0.1050.0000.0000.0000.000
123A135ALA0-0.036-0.01238.401-0.005-0.0050.0000.0000.0000.000
124A136PRO0-0.054-0.02635.5960.0060.0060.0000.0000.0000.000
125A137ILE00.0300.00036.1110.0050.0050.0000.0000.0000.000
126A138ALA0-0.013-0.00137.626-0.006-0.0060.0000.0000.0000.000
127A139TRP00.0100.00132.6200.0000.0000.0000.0000.0000.000
128A140GLU-1-0.705-0.81939.186-0.095-0.0950.0000.0000.0000.000
129A141CYS0-0.052-0.02538.428-0.003-0.0030.0000.0000.0000.000
130A142LYS11.0121.01340.8240.0900.0900.0000.0000.0000.000
131A143LEU0-0.046-0.01738.068-0.008-0.0080.0000.0000.0000.000
132A144TYR0-0.0070.01837.5880.0030.0030.0000.0000.0000.000
133A145LYS10.9530.95436.2420.1210.1210.0000.0000.0000.000
134A146ILE00.0200.01934.321-0.009-0.0090.0000.0000.0000.000
135A147ILE0-0.044-0.01531.3970.0080.0080.0000.0000.0000.000
136A148ASP-1-0.826-0.89131.638-0.144-0.1440.0000.0000.0000.000
137A149PHE0-0.056-0.02422.283-0.004-0.0040.0000.0000.0000.000
138A150SER0-0.012-0.04526.9220.0010.0010.0000.0000.0000.000
139A151LYS10.9780.97629.0530.1060.1060.0000.0000.0000.000
140A152GLN0-0.0020.01526.8000.0070.0070.0000.0000.0000.000
141A153ARG10.8690.94424.1240.2510.2510.0000.0000.0000.000
142A154SER00.010-0.00928.7630.0070.0070.0000.0000.0000.000
143A155MET0-0.049-0.01727.557-0.018-0.0180.0000.0000.0000.000
144A156VAL00.0300.01830.3300.0130.0130.0000.0000.0000.000
145A157PHE00.010-0.00430.221-0.012-0.0120.0000.0000.0000.000
146A158GLY00.0330.02034.4230.0100.0100.0000.0000.0000.000
147A159GLU-1-0.885-0.96136.417-0.110-0.1100.0000.0000.0000.000
148A160ILE0-0.049-0.03335.7250.0020.0020.0000.0000.0000.000
149A161VAL0-0.020-0.01339.8650.0040.0040.0000.0000.0000.000
150A162ALA00.0090.00642.9160.0040.0040.0000.0000.0000.000
151A163MET0-0.042-0.02038.060-0.007-0.0070.0000.0000.0000.000
152A164TYR00.0090.01441.7590.0070.0070.0000.0000.0000.000
153A165PHE00.029-0.01339.099-0.009-0.0090.0000.0000.0000.000
154A166ARG10.8520.92540.8410.1100.1100.0000.0000.0000.000
155A167GLU-1-0.883-0.93843.566-0.081-0.0810.0000.0000.0000.000
156A168GLU-1-0.798-0.88742.399-0.102-0.1020.0000.0000.0000.000
157A169LEU0-0.077-0.04938.121-0.004-0.0040.0000.0000.0000.000
158A170ILE0-0.0130.00040.586-0.006-0.0060.0000.0000.0000.000
159A171ASP-1-0.851-0.91943.082-0.084-0.0840.0000.0000.0000.000
160A172GLU-1-0.909-0.96844.996-0.079-0.0790.0000.0000.0000.000
161A173GLU-1-0.906-0.94647.415-0.068-0.0680.0000.0000.0000.000
162A174LYS10.8040.89342.8110.0930.0930.0000.0000.0000.000
163A175LEU00.0200.01644.166-0.003-0.0030.0000.0000.0000.000
164A176ARG10.8660.93539.3060.1000.1000.0000.0000.0000.000
165A177VAL00.0610.03936.5420.0030.0030.0000.0000.0000.000
166A178ARG10.8550.93238.6300.0940.0940.0000.0000.0000.000
167A179VAL0-0.008-0.01632.861-0.004-0.0040.0000.0000.0000.000
168A180ASP-1-0.932-0.95634.464-0.143-0.1430.0000.0000.0000.000
169A181LEU0-0.010-0.00735.773-0.003-0.0030.0000.0000.0000.000
170A182PHE00.0270.02832.886-0.003-0.0030.0000.0000.0000.000
171A183GLN0-0.017-0.01032.042-0.012-0.0120.0000.0000.0000.000
172A184PRO0-0.0100.01129.386-0.001-0.0010.0000.0000.0000.000
173A185TYR0-0.053-0.05027.428-0.013-0.0130.0000.0000.0000.000
174A186GLY00.0060.01224.0080.0010.0010.0000.0000.0000.000
175A187ARG10.8290.91221.1130.3350.3350.0000.0000.0000.000
176A188LEU00.0420.01717.160-0.038-0.0380.0000.0000.0000.000
177A189GLY00.0400.02215.5790.0230.0230.0000.0000.0000.000
178A190GLY00.0310.01116.6430.0290.0290.0000.0000.0000.000
179A191PRO0-0.039-0.00518.731-0.002-0.0020.0000.0000.0000.000
180A192ASN0-0.010-0.00818.4150.0520.0520.0000.0000.0000.000
181A193TYR00.0550.00821.676-0.024-0.0240.0000.0000.0000.000
182A194CYS0-0.019-0.00321.656-0.003-0.0030.0000.0000.0000.000
183A195ARG10.9100.93323.6650.1930.1930.0000.0000.0000.000
184A196THR0-0.031-0.02626.340-0.006-0.0060.0000.0000.0000.000
185A197THR00.0430.00828.0760.0110.0110.0000.0000.0000.000
186A198ASP-1-0.957-0.95525.348-0.223-0.2230.0000.0000.0000.000
187A199ARG10.7910.86726.1250.1700.1700.0000.0000.0000.000
188A200VAL00.0380.01424.6460.0120.0120.0000.0000.0000.000
189A201ARG10.9430.97627.8060.1230.1230.0000.0000.0000.000
190A202LEU00.0230.00523.7800.0050.0050.0000.0000.0000.000
191A203THR0-0.024-0.00827.946-0.002-0.0020.0000.0000.0000.000
192A204VAL00.0230.00627.827-0.002-0.0020.0000.0000.0000.000
193A205PRO0-0.039-0.00428.8850.0080.0080.0000.0000.0000.000
194A206THR00.0440.00431.978-0.001-0.0010.0000.0000.0000.000
195A207PHE0-0.039-0.01533.3150.0050.0050.0000.0000.0000.000
196A208LEU00.0250.01230.828-0.006-0.0060.0000.0000.0000.000
197A209PRO00.0040.00926.9170.0070.0070.0000.0000.0000.000
198A210SER00.023-0.00928.7750.0000.0000.0000.0000.0000.000
199A211ALA0-0.040-0.00725.2440.0060.0060.0000.0000.0000.000
200A212GLY00.0120.01726.2900.0120.0120.0000.0000.0000.000