FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 5J9KZ

Calculation Name: 4NN1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4NN1

Chain ID: A

ChEMBL ID:

UniProt ID: O86312

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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2085893.477285
FMO2-HF: Nuclear repulsion 2006312.528294
FMO2-HF: Total energy -79580.948991
FMO2-MP2: Total energy -79810.698029


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:6:LEU)


Summations of interaction energy for fragment #1(A:6:LEU)
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.
-15.529-10.0751.63-2.712-4.3730.024
Interaction energy analysis for fragmet #1(A:6:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.061 / q_NPA : 0.018
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].
3A8ALA00.0250.0062.686-4.825-1.7561.341-1.808-2.6030.014
4A9HIS00.0700.0342.964-5.900-4.2920.235-0.604-1.2390.008
5A10ALA00.001-0.0024.793-1.406-1.256-0.001-0.025-0.1240.000
6A11ARG11.0181.0176.765-1.483-1.4830.0000.0000.0000.000
7A12ILE0-0.0050.0147.708-0.441-0.4410.0000.0000.0000.000
8A13ARG10.9440.9727.715-0.660-0.6600.0000.0000.0000.000
9A14GLU-1-0.987-0.98710.6260.3640.3640.0000.0000.0000.000
10A15ALA00.0680.02812.455-0.119-0.1190.0000.0000.0000.000
11A16ALA0-0.019-0.01913.745-0.103-0.1030.0000.0000.0000.000
12A17ILE00.0150.01513.893-0.082-0.0820.0000.0000.0000.000
13A18GLU-1-0.859-0.92516.9580.3080.3080.0000.0000.0000.000
14A19GLN0-0.040-0.02718.059-0.077-0.0770.0000.0000.0000.000
15A20PHE0-0.041-0.03817.229-0.035-0.0350.0000.0000.0000.000
16A21GLY00.0310.02520.770-0.033-0.0330.0000.0000.0000.000
17A22ARG10.8920.95321.881-0.294-0.2940.0000.0000.0000.000
18A23HIS0-0.033-0.02223.529-0.033-0.0330.0000.0000.0000.000
19A24GLY00.0400.04224.523-0.014-0.0140.0000.0000.0000.000
20A25PHE00.0650.01120.9260.0230.0230.0000.0000.0000.000
21A26GLY0-0.112-0.05523.2920.0160.0160.0000.0000.0000.000
22A27VAL00.0430.03720.789-0.003-0.0030.0000.0000.0000.000
23A28GLY00.0200.00722.1610.0080.0080.0000.0000.0000.000
24A29LEU00.0810.02017.1220.0250.0250.0000.0000.0000.000
25A30ARG10.9320.96317.463-0.264-0.2640.0000.0000.0000.000
26A31ALA00.0760.04418.9340.0220.0220.0000.0000.0000.000
27A32ILE0-0.0170.00314.3170.0230.0230.0000.0000.0000.000
28A33ALA0-0.041-0.02513.8980.0740.0740.0000.0000.0000.000
29A34GLU-1-0.935-0.97314.6670.4480.4480.0000.0000.0000.000
30A35ALA0-0.026-0.00416.6500.0130.0130.0000.0000.0000.000
31A36ALA0-0.016-0.01311.3420.0190.0190.0000.0000.0000.000
32A37GLY0-0.0210.01712.3740.1030.1030.0000.0000.0000.000
33A38VAL0-0.064-0.0429.4120.1270.1270.0000.0000.0000.000
34A39SER00.0230.01512.855-0.117-0.1170.0000.0000.0000.000
35A40ALA00.0660.00213.3990.0870.0870.0000.0000.0000.000
36A41ALA0-0.009-0.00214.5290.0080.0080.0000.0000.0000.000
37A42LEU00.0240.0117.305-0.085-0.0850.0000.0000.0000.000
38A43VAL00.0490.0199.4690.1970.1970.0000.0000.0000.000
39A44ILE0-0.035-0.02011.255-0.021-0.0210.0000.0000.0000.000
40A45HIS0-0.041-0.0149.547-0.089-0.0890.0000.0000.0000.000
41A46HIS0-0.063-0.0223.044-0.700-0.0730.055-0.275-0.4070.002
42A47PHE0-0.009-0.0178.322-0.174-0.1740.0000.0000.0000.000
43A48GLY00.0180.03411.497-0.118-0.1180.0000.0000.0000.000
44A49SER0-0.019-0.01814.336-0.021-0.0210.0000.0000.0000.000
45A50LYS10.9520.96616.041-0.218-0.2180.0000.0000.0000.000
46A51GLU-1-0.933-0.96018.0720.1810.1810.0000.0000.0000.000
47A52GLY00.000-0.00415.494-0.010-0.0100.0000.0000.0000.000
48A53LEU0-0.0050.00012.2870.0140.0140.0000.0000.0000.000
49A54ARG10.9630.99414.649-0.179-0.1790.0000.0000.0000.000
50A55LYS10.9460.96316.357-0.115-0.1150.0000.0000.0000.000
51A56ALA0-0.0070.00611.319-0.027-0.0270.0000.0000.0000.000
52A57CYS0-0.070-0.03212.7410.0290.0290.0000.0000.0000.000
53A58ASP-1-0.796-0.84714.9120.1510.1510.0000.0000.0000.000
54A59ASP-1-0.918-0.97014.2110.0660.0660.0000.0000.0000.000
55A60PHE00.012-0.00810.567-0.007-0.0070.0000.0000.0000.000
56A61VAL00.0480.02914.016-0.029-0.0290.0000.0000.0000.000
57A62ALA0-0.016-0.01617.352-0.022-0.0220.0000.0000.0000.000
58A63GLU-1-0.858-0.93913.961-0.104-0.1040.0000.0000.0000.000
59A64GLU-1-0.954-0.96913.677-0.019-0.0190.0000.0000.0000.000
60A65ILE0-0.025-0.01517.000-0.010-0.0100.0000.0000.0000.000
61A66ARG10.8240.94017.7830.0670.0670.0000.0000.0000.000
62A67SER0-0.017-0.01716.775-0.008-0.0080.0000.0000.0000.000
63A68SER0-0.0290.00519.415-0.003-0.0030.0000.0000.0000.000
64A69LYS10.9700.96521.606-0.021-0.0210.0000.0000.0000.000
65A70ALA00.0330.00722.588-0.003-0.0030.0000.0000.0000.000
66A71ALA0-0.0230.00122.051-0.007-0.0070.0000.0000.0000.000
67A72ALA0-0.020-0.00324.075-0.002-0.0020.0000.0000.0000.000
68A73LEU0-0.0030.00327.1500.0010.0010.0000.0000.0000.000
69A74LYS10.9320.98624.8260.0910.0910.0000.0000.0000.000
70A75SER0-0.0270.00827.693-0.004-0.0040.0000.0000.0000.000
71A76ASN00.017-0.00329.6480.0080.0080.0000.0000.0000.000
72A77ASP-1-0.866-0.93430.319-0.040-0.0400.0000.0000.0000.000
73A78PRO00.0460.01630.9200.0000.0000.0000.0000.0000.000
74A79THR00.019-0.00330.4900.0060.0060.0000.0000.0000.000
75A80THR0-0.024-0.00826.2820.0050.0050.0000.0000.0000.000
76A81TRP0-0.0050.01227.0260.0080.0080.0000.0000.0000.000
77A82LEU0-0.026-0.01229.4170.0070.0070.0000.0000.0000.000
78A83ALA00.0030.00026.0940.0060.0060.0000.0000.0000.000
79A84GLN00.007-0.02524.0650.0070.0070.0000.0000.0000.000
80A85MET0-0.043-0.02226.0750.0110.0110.0000.0000.0000.000
81A86ALA0-0.0280.00326.9800.0070.0070.0000.0000.0000.000
82A87GLU-1-0.881-0.93922.4920.0380.0380.0000.0000.0000.000
83A88ILE00.0120.05724.0910.0130.0130.0000.0000.0000.000
84A89GLU-1-0.852-0.95225.7510.0810.0810.0000.0000.0000.000
85A90SER0-0.136-0.11820.7000.0160.0160.0000.0000.0000.000
86A91TYR00.0370.01720.4040.0200.0200.0000.0000.0000.000
87A92ALA00.0140.00322.0420.0090.0090.0000.0000.0000.000
88A93PRO0-0.016-0.00518.4930.0080.0080.0000.0000.0000.000
89A94LEU00.0330.00717.0840.0150.0150.0000.0000.0000.000
90A95MET00.0140.01120.0780.0020.0020.0000.0000.0000.000
91A96ALA00.0260.02722.731-0.004-0.0040.0000.0000.0000.000
92A97TYR0-0.055-0.10318.7050.0120.0120.0000.0000.0000.000
93A98LEU0-0.020-0.02521.872-0.006-0.0060.0000.0000.0000.000
94A99VAL00.025-0.00223.555-0.011-0.0110.0000.0000.0000.000
95A100ARG10.8360.93024.217-0.178-0.1780.0000.0000.0000.000
96A101SER0-0.026-0.01022.632-0.003-0.0030.0000.0000.0000.000
97A102MET0-0.0310.00525.403-0.005-0.0050.0000.0000.0000.000
98A103GLN00.0560.01728.9330.0030.0030.0000.0000.0000.000
99A104SER0-0.064-0.01626.819-0.001-0.0010.0000.0000.0000.000
100A105GLY00.0320.03127.7410.0060.0060.0000.0000.0000.000
101A106GLY0-0.072-0.05428.190-0.007-0.0070.0000.0000.0000.000
102A107GLU-1-0.832-0.94327.4450.0740.0740.0000.0000.0000.000
103A108LEU00.003-0.00520.649-0.004-0.0040.0000.0000.0000.000
104A109ALA00.0020.00723.6360.0010.0010.0000.0000.0000.000
105A110LYS10.8890.94725.623-0.071-0.0710.0000.0000.0000.000
106A111MET0-0.017-0.01322.919-0.008-0.0080.0000.0000.0000.000
107A112LEU0-0.0020.02120.544-0.008-0.0080.0000.0000.0000.000
108A113TRP00.0290.01323.702-0.012-0.0120.0000.0000.0000.000
109A114GLN0-0.008-0.00626.673-0.008-0.0080.0000.0000.0000.000
110A115LYS10.9741.01916.988-0.042-0.0420.0000.0000.0000.000
111A116MET0-0.042-0.03122.615-0.007-0.0070.0000.0000.0000.000
112A117ILE0-0.028-0.01324.487-0.008-0.0080.0000.0000.0000.000
113A118ASP-1-0.845-0.92325.236-0.002-0.0020.0000.0000.0000.000
114A119ASN00.000-0.01320.375-0.016-0.0160.0000.0000.0000.000
115A120ALA0-0.0100.00024.531-0.006-0.0060.0000.0000.0000.000
116A121GLU-1-0.873-0.93327.616-0.019-0.0190.0000.0000.0000.000
117A122GLU-1-0.923-0.96223.098-0.068-0.0680.0000.0000.0000.000
118A123TYR00.0720.02023.999-0.002-0.0020.0000.0000.0000.000
119A124LEU0-0.037-0.01626.9530.0000.0000.0000.0000.0000.000
120A125ASP-1-0.887-0.93330.076-0.043-0.0430.0000.0000.0000.000
121A126GLU-1-0.947-0.98324.278-0.078-0.0780.0000.0000.0000.000
122A127GLY00.0270.01629.164-0.004-0.0040.0000.0000.0000.000
123A128VAL0-0.051-0.02631.2750.0010.0010.0000.0000.0000.000
124A129ARG10.8160.90528.1730.0600.0600.0000.0000.0000.000
125A130ALA0-0.048-0.01930.857-0.002-0.0020.0000.0000.0000.000
126A131GLY0-0.0160.00532.9810.0000.0000.0000.0000.0000.000
127A132THR0-0.044-0.02931.9990.0040.0040.0000.0000.0000.000
128A133VAL0-0.021-0.00432.9200.0050.0050.0000.0000.0000.000
129A134LYS11.0031.00036.1040.0080.0080.0000.0000.0000.000
130A135PRO00.0930.05738.0220.0020.0020.0000.0000.0000.000
131A136SER0-0.008-0.01538.3230.0030.0030.0000.0000.0000.000
132A137ARG10.9650.98940.1640.0030.0030.0000.0000.0000.000
133A138ASP-1-0.864-0.94739.199-0.005-0.0050.0000.0000.0000.000
134A139PRO00.0060.00435.2630.0030.0030.0000.0000.0000.000
135A140ARG10.8820.94229.7710.0040.0040.0000.0000.0000.000
136A141ALA00.0140.00934.8720.0040.0040.0000.0000.0000.000
137A142ARG10.7960.88735.5080.0150.0150.0000.0000.0000.000
138A143ALA00.0570.01231.2850.0030.0030.0000.0000.0000.000
139A144ARG10.9310.98232.661-0.019-0.0190.0000.0000.0000.000
140A145PHE00.0180.00433.9550.0050.0050.0000.0000.0000.000
141A146LEU00.0330.02133.5770.0030.0030.0000.0000.0000.000
142A147ALA0-0.0080.01329.8700.0030.0030.0000.0000.0000.000
143A148ILE0-0.047-0.03031.6090.0060.0060.0000.0000.0000.000
144A149THR0-0.021-0.02733.8940.0040.0040.0000.0000.0000.000
145A150GLY00.0400.03532.6650.0030.0030.0000.0000.0000.000
146A151GLY0-0.033-0.02130.3740.0040.0040.0000.0000.0000.000
147A152GLY0-0.022-0.02031.0050.0060.0060.0000.0000.0000.000
148A153GLY00.0220.01633.7960.0020.0020.0000.0000.0000.000
149A154PHE00.0200.00328.0930.0040.0040.0000.0000.0000.000
150A155LEU0-0.036-0.03029.1170.0060.0060.0000.0000.0000.000
151A156LEU0-0.003-0.00632.5240.0030.0030.0000.0000.0000.000
152A157TYR0-0.067-0.03134.2680.0020.0020.0000.0000.0000.000
153A158LEU00.009-0.00429.8720.0010.0010.0000.0000.0000.000
154A159GLN0-0.067-0.03034.3000.0010.0010.0000.0000.0000.000
155A160MET0-0.056-0.03236.3910.0010.0010.0000.0000.0000.000
156A161HIS0-0.018-0.01335.4780.0010.0010.0000.0000.0000.000
157A162GLU-1-0.898-0.94437.7750.0590.0590.0000.0000.0000.000
158A163ASN0-0.009-0.00733.7470.0060.0060.0000.0000.0000.000
159A164PRO00.0270.01233.7890.0060.0060.0000.0000.0000.000
160A165THR0-0.113-0.06330.2650.0080.0080.0000.0000.0000.000
161A166ASP-1-0.901-0.94229.1460.1190.1190.0000.0000.0000.000
162A167LEU0-0.025-0.03226.030-0.007-0.0070.0000.0000.0000.000
163A168ARG10.9450.97123.587-0.123-0.1230.0000.0000.0000.000
164A169ALA00.0480.05028.278-0.008-0.0080.0000.0000.0000.000
165A170ALA00.0340.02030.762-0.007-0.0070.0000.0000.0000.000
166A171LEU0-0.060-0.03125.704-0.006-0.0060.0000.0000.0000.000
167A172ARG10.8670.95830.188-0.056-0.0560.0000.0000.0000.000
168A173ASP-1-0.784-0.88532.3530.0550.0550.0000.0000.0000.000
169A174TYR0-0.0110.01031.941-0.004-0.0040.0000.0000.0000.000
170A175ALA0-0.047-0.03331.856-0.006-0.0060.0000.0000.0000.000
171A176HIS0-0.068-0.02233.806-0.005-0.0050.0000.0000.0000.000
172A177ASP-1-0.862-0.93937.2380.0380.0380.0000.0000.0000.000
173A178MET0-0.051-0.03835.535-0.004-0.0040.0000.0000.0000.000
174A179VAL00.0180.01833.533-0.004-0.0040.0000.0000.0000.000
175A180LEU00.0320.04236.211-0.003-0.0030.0000.0000.0000.000
176A181PRO00.0660.03839.672-0.003-0.0030.0000.0000.0000.000
177A182SER0-0.079-0.06236.718-0.002-0.0020.0000.0000.0000.000
178A183LEU0-0.012-0.01835.395-0.003-0.0030.0000.0000.0000.000
179A184GLU-1-0.913-0.94238.8450.0070.0070.0000.0000.0000.000
180A185VAL00.0180.01741.240-0.002-0.0020.0000.0000.0000.000
181A186TYR0-0.119-0.08035.4790.0000.0000.0000.0000.0000.000
182A187THR0-0.078-0.02239.975-0.004-0.0040.0000.0000.0000.000
183A188GLU-1-0.941-0.97641.910-0.005-0.0050.0000.0000.0000.000
184A189GLY0-0.098-0.02844.098-0.001-0.0010.0000.0000.0000.000
185A190LEU0-0.019-0.02745.3480.0010.0010.0000.0000.0000.000
186A191LEU0-0.044-0.02947.6070.0000.0000.0000.0000.0000.000
187A192ALA00.0400.02850.460-0.001-0.0010.0000.0000.0000.000
188A193ASP-1-0.855-0.94153.3830.0010.0010.0000.0000.0000.000
189A194ARG10.8610.93049.2490.0060.0060.0000.0000.0000.000
190A195ALA00.0730.05952.7710.0000.0000.0000.0000.0000.000
191A196MET00.0300.00452.0680.0000.0000.0000.0000.0000.000
192A197TYR0-0.016-0.01345.5200.0000.0000.0000.0000.0000.000
193A198GLU-1-0.924-0.98050.699-0.003-0.0030.0000.0000.0000.000
194A199ALA00.0000.00953.4920.0000.0000.0000.0000.0000.000
195A200PHE00.018-0.00250.2010.0000.0000.0000.0000.0000.000
196A201LEU0-0.027-0.01647.8090.0000.0000.0000.0000.0000.000
197A202ALA0-0.017-0.00251.042-0.001-0.0010.0000.0000.0000.000
198A203GLU-1-0.923-0.96553.3160.0040.0040.0000.0000.0000.000
199A204ALA0-0.022-0.01849.3230.0000.0000.0000.0000.0000.000
200A205GLN0-0.080-0.03749.566-0.001-0.0010.0000.0000.0000.000
201A206GLN0-0.028-0.01452.3410.0000.0000.0000.0000.0000.000
202A207GLY0-0.007-0.00352.9550.0000.0000.0000.0000.0000.000
203A208GLU-1-0.970-0.98347.265-0.005-0.0050.0000.0000.0000.000
204A209ALA0-0.063-0.01551.605-0.001-0.0010.0000.0000.0000.000
205A210HIS0-0.047-0.01154.9010.0000.0000.0000.0000.0000.000