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: ZYJNN

Calculation Name: 4IYP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4IYP

Chain ID: A

ChEMBL ID:

UniProt ID: P78318

Base Structure: X-ray

Registration Date: 2023-06-20

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 208
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2467193.146624
FMO2-HF: Nuclear repulsion 2381980.239533
FMO2-HF: Total energy -85212.907091
FMO2-MP2: Total energy -85460.343688


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:0:SER)


Summations of interaction energy for fragment #1(A:0: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.
-2.8230.7730.495-1.65-2.4410
Interaction energy analysis for fragmet #1(A:0:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.051 / q_NPA : -0.037
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].
3A2ALA00.0270.0172.955-3.952-1.4510.133-1.202-1.4320.002
4A3ALA0-0.025-0.0312.664-0.8290.0700.363-0.404-0.858-0.002
5A4GLU-1-0.981-0.9774.3981.2761.472-0.001-0.044-0.1510.000
6A5ASP-1-0.945-0.9646.1170.4400.4400.0000.0000.0000.000
7A6GLU-1-0.943-0.9857.1890.0070.0070.0000.0000.0000.000
8A7LEU0-0.108-0.0258.101-0.029-0.0290.0000.0000.0000.000
9A8GLN0-0.018-0.01110.0630.0650.0650.0000.0000.0000.000
10A9LEU0-0.010-0.01012.597-0.025-0.0250.0000.0000.0000.000
11A10PRO00.0010.00015.3290.0050.0050.0000.0000.0000.000
12A11ARG10.9960.99717.452-0.078-0.0780.0000.0000.0000.000
13A12LEU00.0580.02721.132-0.008-0.0080.0000.0000.0000.000
14A13PRO00.0070.00124.383-0.006-0.0060.0000.0000.0000.000
15A14GLU-1-0.913-0.94221.9760.0020.0020.0000.0000.0000.000
16A15LEU0-0.028-0.01220.718-0.007-0.0070.0000.0000.0000.000
17A16PHE0-0.005-0.01324.474-0.005-0.0050.0000.0000.0000.000
18A17GLU-1-0.904-0.95828.1310.0040.0040.0000.0000.0000.000
19A18THR0-0.002-0.00225.438-0.005-0.0050.0000.0000.0000.000
20A19GLY0-0.008-0.01027.616-0.004-0.0040.0000.0000.0000.000
21A20ARG10.9180.96728.804-0.009-0.0090.0000.0000.0000.000
22A21GLN00.0300.01229.963-0.003-0.0030.0000.0000.0000.000
23A22LEU0-0.020-0.00927.194-0.003-0.0030.0000.0000.0000.000
24A23LEU0-0.018-0.01031.659-0.002-0.0020.0000.0000.0000.000
25A24ASP-1-0.908-0.95934.259-0.004-0.0040.0000.0000.0000.000
26A25GLU-1-0.962-0.99732.635-0.019-0.0190.0000.0000.0000.000
27A26VAL0-0.061-0.04233.716-0.001-0.0010.0000.0000.0000.000
28A27GLU-1-0.941-0.93536.676-0.009-0.0090.0000.0000.0000.000
29A28VAL0-0.038-0.01739.4720.0010.0010.0000.0000.0000.000
30A29ALA0-0.0340.00238.083-0.001-0.0010.0000.0000.0000.000
31A30THR0-0.033-0.00940.0370.0000.0000.0000.0000.0000.000
32A31GLU-1-0.929-0.96937.604-0.024-0.0240.0000.0000.0000.000
33A32PRO0-0.003-0.01340.7290.0010.0010.0000.0000.0000.000
34A33ALA00.0890.06339.433-0.001-0.0010.0000.0000.0000.000
35A34GLY00.002-0.01137.688-0.001-0.0010.0000.0000.0000.000
36A35SER0-0.061-0.04737.407-0.003-0.0030.0000.0000.0000.000
37A36ARG10.9660.96930.8170.0540.0540.0000.0000.0000.000
38A37ILE00.0310.01432.260-0.001-0.0010.0000.0000.0000.000
39A38VAL00.0470.03932.8080.0000.0000.0000.0000.0000.000
40A39GLN0-0.014-0.02132.2830.0000.0000.0000.0000.0000.000
41A40GLU-1-0.922-0.96828.211-0.051-0.0510.0000.0000.0000.000
42A41LYS10.9290.97928.1860.0250.0250.0000.0000.0000.000
43A42VAL00.0140.01129.5020.0030.0030.0000.0000.0000.000
44A43PHE0-0.031-0.01422.6850.0020.0020.0000.0000.0000.000
45A44LYS10.9550.98822.1020.0300.0300.0000.0000.0000.000
46A45GLY00.0610.02125.2340.0040.0040.0000.0000.0000.000
47A46LEU0-0.041-0.02827.2330.0050.0050.0000.0000.0000.000
48A47ASP-1-0.801-0.88520.839-0.004-0.0040.0000.0000.0000.000
49A48LEU0-0.063-0.02822.0880.0070.0070.0000.0000.0000.000
50A49LEU00.020-0.00824.0870.0070.0070.0000.0000.0000.000
51A50GLU-1-0.991-0.98121.9910.0060.0060.0000.0000.0000.000
52A51LYS10.8730.92317.516-0.004-0.0040.0000.0000.0000.000
53A52ALA0-0.047-0.01722.0460.0090.0090.0000.0000.0000.000
54A53ALA00.000-0.01224.8660.0050.0050.0000.0000.0000.000
55A54GLU-1-0.876-0.92720.1720.0640.0640.0000.0000.0000.000
56A55MET0-0.052-0.02921.1590.0100.0100.0000.0000.0000.000
57A56LEU0-0.023-0.03223.1730.0030.0030.0000.0000.0000.000
58A57SER0-0.033-0.00525.2740.0010.0010.0000.0000.0000.000
59A58GLN0-0.050-0.02721.0870.0080.0080.0000.0000.0000.000
60A59LEU0-0.098-0.05024.4130.0050.0050.0000.0000.0000.000
61A60ASP-1-0.954-0.95926.6270.0480.0480.0000.0000.0000.000
62A61LEU0-0.040-0.01729.786-0.002-0.0020.0000.0000.0000.000
63A62PHE0-0.034-0.01831.869-0.003-0.0030.0000.0000.0000.000
64A63SER00.0490.05233.9470.0000.0000.0000.0000.0000.000
65A64ARG10.9460.95036.194-0.024-0.0240.0000.0000.0000.000
66A65ASN0-0.134-0.07939.092-0.002-0.0020.0000.0000.0000.000
67A66GLU-1-0.817-0.91237.7090.0370.0370.0000.0000.0000.000
68A67ASP-1-0.861-0.92241.5830.0200.0200.0000.0000.0000.000
69A68LEU00.010-0.00641.1790.0010.0010.0000.0000.0000.000
70A69GLU-1-0.977-1.00442.2750.0210.0210.0000.0000.0000.000
71A70GLU-1-0.971-0.97340.4150.0320.0320.0000.0000.0000.000
72A71ILE0-0.0320.02136.5340.0020.0020.0000.0000.0000.000
73A72ALA00.0550.02935.890-0.002-0.0020.0000.0000.0000.000
74A73SER00.011-0.04637.880-0.001-0.0010.0000.0000.0000.000
75A74THR0-0.048-0.03233.925-0.002-0.0020.0000.0000.0000.000
76A75ASP-1-0.852-0.93032.4780.0390.0390.0000.0000.0000.000
77A76LEU00.0160.01434.382-0.001-0.0010.0000.0000.0000.000
78A77LYS10.8680.94632.162-0.025-0.0250.0000.0000.0000.000
79A78TYR00.0240.00829.429-0.003-0.0030.0000.0000.0000.000
80A79LEU00.0600.04232.806-0.001-0.0010.0000.0000.0000.000
81A80LEU0-0.066-0.04235.224-0.002-0.0020.0000.0000.0000.000
82A81VAL0-0.0100.00828.882-0.003-0.0030.0000.0000.0000.000
83A82PRO00.0310.02132.237-0.003-0.0030.0000.0000.0000.000
84A83ALA00.0250.00833.449-0.003-0.0030.0000.0000.0000.000
85A84PHE0-0.005-0.00332.701-0.003-0.0030.0000.0000.0000.000
86A85GLN00.0230.01427.832-0.001-0.0010.0000.0000.0000.000
87A86GLY00.0270.01932.296-0.003-0.0030.0000.0000.0000.000
88A87ALA0-0.003-0.00535.623-0.002-0.0020.0000.0000.0000.000
89A88LEU00.011-0.01030.673-0.002-0.0020.0000.0000.0000.000
90A89THR0-0.048-0.01632.565-0.003-0.0030.0000.0000.0000.000
91A90MET0-0.042-0.01233.879-0.003-0.0030.0000.0000.0000.000
92A91LYS10.8140.89735.3650.0090.0090.0000.0000.0000.000
93A92GLN00.0010.01430.4060.0000.0000.0000.0000.0000.000
94A93VAL0-0.031-0.00734.9300.0010.0010.0000.0000.0000.000
95A94ASN00.032-0.01032.636-0.003-0.0030.0000.0000.0000.000
96A95PRO00.0520.03736.4500.0010.0010.0000.0000.0000.000
97A96SER0-0.060-0.02436.4280.0010.0010.0000.0000.0000.000
98A97LYS10.9120.94230.9710.0370.0370.0000.0000.0000.000
99A98ARG10.8830.94936.0570.0160.0160.0000.0000.0000.000
100A99LEU00.014-0.00138.6040.0010.0010.0000.0000.0000.000
101A100ASP-1-0.935-0.96632.374-0.018-0.0180.0000.0000.0000.000
102A101HIS00.020-0.00332.3390.0000.0000.0000.0000.0000.000
103A102LEU00.0180.02235.6080.0020.0020.0000.0000.0000.000
104A103GLN00.005-0.00737.1220.0020.0020.0000.0000.0000.000
105A104ARG10.9770.99327.9320.0150.0150.0000.0000.0000.000
106A105ALA00.0290.01834.4700.0020.0020.0000.0000.0000.000
107A106ARG10.7790.87536.3380.0020.0020.0000.0000.0000.000
108A107GLU-1-0.939-0.95834.1350.0050.0050.0000.0000.0000.000
109A108HIS00.0110.01330.0270.0040.0040.0000.0000.0000.000
110A109PHE00.008-0.00535.0940.0020.0020.0000.0000.0000.000
111A110ILE0-0.0070.00538.6190.0010.0010.0000.0000.0000.000
112A111ASN00.0130.00933.1190.0020.0020.0000.0000.0000.000
113A112TYR0-0.041-0.02536.8270.0020.0020.0000.0000.0000.000
114A113LEU0-0.006-0.00537.9010.0010.0010.0000.0000.0000.000
115A114THR0-0.006-0.02239.1440.0010.0010.0000.0000.0000.000
116A115GLN00.0210.01535.1990.0000.0000.0000.0000.0000.000
117A116CYS0-0.030-0.01939.2980.0010.0010.0000.0000.0000.000
118A117HIS0-0.035-0.00741.9380.0010.0010.0000.0000.0000.000
119A118CYS0-0.056-0.02641.3230.0000.0000.0000.0000.0000.000
120A119TYR00.001-0.00337.6790.0000.0000.0000.0000.0000.000
121A120HIS0-0.076-0.03143.324-0.001-0.0010.0000.0000.0000.000
122A121VAL0-0.0060.00442.450-0.001-0.0010.0000.0000.0000.000
123A122ALA0-0.023-0.02845.803-0.001-0.0010.0000.0000.0000.000
124A123GLU-1-0.956-0.96548.7040.0090.0090.0000.0000.0000.000
125A124PHE0-0.068-0.04444.450-0.001-0.0010.0000.0000.0000.000
126A125GLU-1-0.952-0.97150.1080.0050.0050.0000.0000.0000.000
127A126LEU0-0.0160.00243.018-0.001-0.0010.0000.0000.0000.000
128A127PRO0-0.008-0.00544.9940.0000.0000.0000.0000.0000.000
129A142SER00.0250.01345.2800.0010.0010.0000.0000.0000.000
130A143MET00.0740.01740.927-0.001-0.0010.0000.0000.0000.000
131A144ALA0-0.0120.00441.124-0.001-0.0010.0000.0000.0000.000
132A145TYR0-0.0280.01642.9200.0000.0000.0000.0000.0000.000
133A146PRO0-0.057-0.03744.9580.0000.0000.0000.0000.0000.000
134A147SER00.0470.01047.1980.0010.0010.0000.0000.0000.000
135A148LEU0-0.068-0.02748.956-0.001-0.0010.0000.0000.0000.000
136A149VAL00.0810.03952.4390.0010.0010.0000.0000.0000.000
137A150ALA00.0130.00854.699-0.001-0.0010.0000.0000.0000.000
138A151MET0-0.055-0.05658.3400.0000.0000.0000.0000.0000.000
139A152ALA00.0540.02857.3840.0000.0000.0000.0000.0000.000
140A153SER00.0370.01757.8970.0010.0010.0000.0000.0000.000
141A154GLN0-0.044-0.00458.4150.0000.0000.0000.0000.0000.000
142A155ARG11.0081.00157.5570.0020.0020.0000.0000.0000.000
143A156GLN0-0.019-0.01959.0070.0000.0000.0000.0000.0000.000
144A157ALA00.0860.04355.5280.0000.0000.0000.0000.0000.000
145A158LYS11.0011.01152.1790.0030.0030.0000.0000.0000.000
146A159ILE0-0.018-0.01055.6560.0000.0000.0000.0000.0000.000
147A160GLN0-0.021-0.01455.9430.0000.0000.0000.0000.0000.000
148A161ARG10.9520.96450.1910.0000.0000.0000.0000.0000.000
149A162TYR0-0.032-0.00552.7980.0000.0000.0000.0000.0000.000
150A163LYS10.9260.94154.2270.0000.0000.0000.0000.0000.000
151A164GLN00.0270.03151.8680.0000.0000.0000.0000.0000.000
152A165LYS11.0201.00646.4250.0010.0010.0000.0000.0000.000
153A166LYS10.8980.95550.7080.0020.0020.0000.0000.0000.000
154A167GLU-1-0.921-0.95452.8690.0030.0030.0000.0000.0000.000
155A168LEU0-0.024-0.01148.2210.0000.0000.0000.0000.0000.000
156A169GLU-1-0.853-0.94047.107-0.001-0.0010.0000.0000.0000.000
157A170HIS0-0.0050.01449.014-0.001-0.0010.0000.0000.0000.000
158A171ARG10.9951.00350.509-0.005-0.0050.0000.0000.0000.000
159A172LEU00.0180.00444.2820.0000.0000.0000.0000.0000.000
160A173SER0-0.120-0.05846.7410.0000.0000.0000.0000.0000.000
161A174ALA0-0.021-0.00948.1670.0000.0000.0000.0000.0000.000
162A175MET0-0.061-0.02046.4960.0000.0000.0000.0000.0000.000
163A176LYS10.9300.96740.2970.0010.0010.0000.0000.0000.000
164A177SER00.0220.00242.7510.0010.0010.0000.0000.0000.000
165A178ALA00.0220.02243.3470.0000.0000.0000.0000.0000.000
166A179VAL00.0000.01140.0620.0010.0010.0000.0000.0000.000
167A180GLU-1-0.895-0.95538.3390.0040.0040.0000.0000.0000.000
168A181SER0-0.076-0.03738.8080.0000.0000.0000.0000.0000.000
169A182GLY0-0.0030.00040.8000.0000.0000.0000.0000.0000.000
170A183GLN0-0.114-0.06041.4320.0000.0000.0000.0000.0000.000
171A184ALA0-0.019-0.00944.169-0.001-0.0010.0000.0000.0000.000
172A185ASP-1-0.847-0.91544.3600.0150.0150.0000.0000.0000.000
173A186ASP-1-0.812-0.90742.2570.0220.0220.0000.0000.0000.000
174A187GLU-1-0.931-0.95044.6270.0130.0130.0000.0000.0000.000
175A188ARG10.9400.96246.651-0.010-0.0100.0000.0000.0000.000
176A189VAL0-0.038-0.01740.301-0.001-0.0010.0000.0000.0000.000
177A190ARG10.8950.93141.092-0.023-0.0230.0000.0000.0000.000
178A191GLU-1-0.923-0.95243.8030.0090.0090.0000.0000.0000.000
179A192TYR00.002-0.00940.265-0.002-0.0020.0000.0000.0000.000
180A193TYR0-0.012-0.02937.390-0.001-0.0010.0000.0000.0000.000
181A194LEU00.0520.03041.9110.0000.0000.0000.0000.0000.000
182A195LEU0-0.007-0.00544.565-0.001-0.0010.0000.0000.0000.000
183A196HIS0-0.045-0.02240.717-0.001-0.0010.0000.0000.0000.000
184A197LEU00.0420.03539.011-0.001-0.0010.0000.0000.0000.000
185A198GLN00.0470.01842.4120.0000.0000.0000.0000.0000.000
186A199ARG10.8820.95141.840-0.002-0.0020.0000.0000.0000.000
187A200TRP00.018-0.02238.896-0.002-0.0020.0000.0000.0000.000
188A201ILE00.0100.02942.662-0.001-0.0010.0000.0000.0000.000
189A202ASP-1-0.899-0.95544.4810.0030.0030.0000.0000.0000.000
190A203ILE0-0.050-0.02842.124-0.001-0.0010.0000.0000.0000.000
191A204SER00.0260.00141.089-0.001-0.0010.0000.0000.0000.000
192A205LEU0-0.024-0.00642.926-0.001-0.0010.0000.0000.0000.000
193A206GLU-1-1.038-1.01846.293-0.003-0.0030.0000.0000.0000.000
194A207GLU-1-0.886-0.95542.002-0.007-0.0070.0000.0000.0000.000
195A208ILE0-0.0280.00042.139-0.001-0.0010.0000.0000.0000.000
196A209GLU-1-0.893-0.93644.595-0.002-0.0020.0000.0000.0000.000
197A210SER0-0.0080.00045.598-0.001-0.0010.0000.0000.0000.000
198A211ILE00.025-0.00440.528-0.001-0.0010.0000.0000.0000.000
199A212ASP-1-0.763-0.89244.381-0.003-0.0030.0000.0000.0000.000
200A213GLN0-0.066-0.03946.6910.0000.0000.0000.0000.0000.000
201A214GLU-1-0.797-0.88443.878-0.014-0.0140.0000.0000.0000.000
202A215ILE00.011-0.00541.695-0.001-0.0010.0000.0000.0000.000
203A216LYS10.8620.95245.3040.0060.0060.0000.0000.0000.000
204A217ILE0-0.003-0.00548.6500.0000.0000.0000.0000.0000.000
205A218LEU0-0.030-0.01442.993-0.001-0.0010.0000.0000.0000.000
206A219ARG10.8380.92441.8290.0090.0090.0000.0000.0000.000
207A220GLU-1-0.923-0.94646.842-0.009-0.0090.0000.0000.0000.000
208A221ARG10.8860.94842.9260.0170.0170.0000.0000.0000.000