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: NN27Q

Calculation Name: 4M9C-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4M9C

Chain ID: A

ChEMBL ID:

UniProt ID: B0V6J7

Base Structure: X-ray

Registration Date: 2023-09-22

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 216
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2343232.200348
FMO2-HF: Nuclear repulsion 2262615.700214
FMO2-HF: Total energy -80616.500135
FMO2-MP2: Total energy -80851.198555


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-10.646-2.4873.523-4.508-7.175-0.022
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.042 / 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].
3A3MET0-0.025-0.0023.838-1.0402.165-0.019-1.663-1.5220.003
4A4ILE0-0.0190.0013.152-1.311-0.9600.019-0.102-0.268-0.001
5A5ILE00.0200.0015.6800.3890.3890.0000.0000.0000.000
6A6GLY00.005-0.0029.3720.1230.1230.0000.0000.0000.000
7A7VAL0-0.016-0.01911.851-0.041-0.0410.0000.0000.0000.000
8A8TYR00.014-0.00315.3760.0530.0530.0000.0000.0000.000
9A9GLY00.0120.00417.705-0.019-0.0190.0000.0000.0000.000
10A10ALA00.0120.02419.363-0.024-0.0240.0000.0000.0000.000
11A11SER0-0.021-0.02620.530-0.017-0.0170.0000.0000.0000.000
12A12GLY0-0.006-0.00723.812-0.010-0.0100.0000.0000.0000.000
13A13PHE00.0120.00124.7840.0020.0020.0000.0000.0000.000
14A14GLY00.0950.05820.646-0.020-0.0200.0000.0000.0000.000
15A15LYS10.8700.91719.989-0.042-0.0420.0000.0000.0000.000
16A16GLU-1-0.816-0.88621.656-0.102-0.1020.0000.0000.0000.000
17A17VAL00.0370.00218.425-0.020-0.0200.0000.0000.0000.000
18A18MET0-0.0100.01913.344-0.064-0.0640.0000.0000.0000.000
19A19PRO0-0.019-0.01616.796-0.051-0.0510.0000.0000.0000.000
20A20LEU00.0090.01718.972-0.029-0.0290.0000.0000.0000.000
21A21VAL00.0560.02114.187-0.033-0.0330.0000.0000.0000.000
22A22ARG10.8210.91812.3140.4490.4490.0000.0000.0000.000
23A23GLN0-0.058-0.03915.419-0.043-0.0430.0000.0000.0000.000
24A24GLN00.0140.02916.6730.0220.0220.0000.0000.0000.000
25A25PHE0-0.026-0.02112.651-0.031-0.0310.0000.0000.0000.000
26A26PRO00.0350.01912.999-0.089-0.0890.0000.0000.0000.000
27A27THR0-0.023-0.01711.4980.0590.0590.0000.0000.0000.000
28A28LEU0-0.0400.0067.502-0.126-0.1260.0000.0000.0000.000
29A29SER00.011-0.0207.3880.1400.1400.0000.0000.0000.000
30A30LYS10.8490.9318.531-0.014-0.0140.0000.0000.0000.000
31A31GLU-1-0.859-0.9256.637-0.336-0.3360.0000.0000.0000.000
32A32GLN0-0.029-0.0054.0970.6840.862-0.001-0.022-0.1560.000
33A33PHE0-0.009-0.0056.1150.0330.0330.0000.0000.0000.000
34A34ALA00.0180.0019.3390.1830.1830.0000.0000.0000.000
35A35PHE0-0.041-0.01011.332-0.073-0.0730.0000.0000.0000.000
36A36ILE00.0100.01712.6900.0740.0740.0000.0000.0000.000
37A37ASP-1-0.861-0.97615.5880.0800.0800.0000.0000.0000.000
38A38ASP-1-0.799-0.91018.9870.2910.2910.0000.0000.0000.000
39A39GLY0-0.0160.00620.5400.0170.0170.0000.0000.0000.000
40A40LEU0-0.055-0.03020.810-0.001-0.0010.0000.0000.0000.000
41A41SER00.0160.00617.8570.0290.0290.0000.0000.0000.000
42A42GLY00.0030.01217.002-0.012-0.0120.0000.0000.0000.000
43A43THR0-0.0260.00018.099-0.002-0.0020.0000.0000.0000.000
44A44THR0-0.032-0.02315.9510.0210.0210.0000.0000.0000.000
45A45LEU0-0.003-0.00817.324-0.026-0.0260.0000.0000.0000.000
46A46ASN00.009-0.00417.704-0.002-0.0020.0000.0000.0000.000
47A47GLY00.0350.01317.271-0.038-0.0380.0000.0000.0000.000
48A48TYR0-0.005-0.00412.252-0.017-0.0170.0000.0000.0000.000
49A49PRO00.0780.03710.3530.0010.0010.0000.0000.0000.000
50A50VAL0-0.028-0.00813.539-0.072-0.0720.0000.0000.0000.000
51A51LEU0-0.020-0.0099.6980.0770.0770.0000.0000.0000.000
52A52SER00.0390.02314.357-0.079-0.0790.0000.0000.0000.000
53A53TYR00.002-0.04614.6150.0580.0580.0000.0000.0000.000
54A54LEU00.0220.00314.3480.0490.0490.0000.0000.0000.000
55A55ASP-1-0.819-0.89512.5730.9450.9450.0000.0000.0000.000
56A56PHE0-0.012-0.0149.0000.3040.3040.0000.0000.0000.000
57A57ILE00.0380.0129.5480.1720.1720.0000.0000.0000.000
58A58SER0-0.092-0.05010.6150.1670.1670.0000.0000.0000.000
59A59LYS10.8380.9315.926-1.062-1.0620.0000.0000.0000.000
60A60PRO00.0090.0193.377-1.781-1.0180.326-0.269-0.8210.002
61A61ALA00.020-0.0282.5890.8073.1941.479-1.625-2.242-0.009
62A62ASP-1-0.931-0.9442.592-7.863-6.7101.720-0.819-2.053-0.017
63A63HIS0-0.023-0.0085.1170.4620.584-0.001-0.008-0.1130.000
64A64LYS10.8610.9376.728-1.565-1.5650.0000.0000.0000.000
65A65ALA00.0310.0178.9600.0430.0430.0000.0000.0000.000
66A66VAL00.0070.00411.3150.0130.0130.0000.0000.0000.000
67A67THR00.0020.02314.0180.0040.0040.0000.0000.0000.000
68A68ILE00.0230.00317.0330.0330.0330.0000.0000.0000.000
69A69ALA00.0270.01419.686-0.009-0.0090.0000.0000.0000.000
70A70ILE0-0.050-0.02321.4980.0050.0050.0000.0000.0000.000
71A71ALA00.0810.04424.209-0.006-0.0060.0000.0000.0000.000
72A72ASN0-0.032-0.01927.603-0.005-0.0050.0000.0000.0000.000
73A73SER00.1120.05727.8930.0050.0050.0000.0000.0000.000
74A74VAL00.0310.02028.9530.0000.0000.0000.0000.0000.000
75A75VAL0-0.011-0.01924.9800.0050.0050.0000.0000.0000.000
76A76ARG10.7990.90423.6550.0670.0670.0000.0000.0000.000
77A77GLU-1-0.768-0.86824.297-0.007-0.0070.0000.0000.0000.000
78A78LYS10.8030.89225.750-0.020-0.0200.0000.0000.0000.000
79A79LEU0-0.004-0.00120.8230.0100.0100.0000.0000.0000.000
80A80VAL00.0330.02920.8790.0080.0080.0000.0000.0000.000
81A81SER0-0.033-0.01821.570-0.002-0.0020.0000.0000.0000.000
82A82LEU0-0.067-0.03219.4610.0090.0090.0000.0000.0000.000
83A83LEU00.010-0.00915.6350.0250.0250.0000.0000.0000.000
84A84GLU-1-0.854-0.90817.615-0.087-0.0870.0000.0000.0000.000
85A85LYS10.7960.90718.390-0.232-0.2320.0000.0000.0000.000
86A86ASP-1-0.866-0.91514.8460.3010.3010.0000.0000.0000.000
87A87GLY00.0070.01314.6210.0200.0200.0000.0000.0000.000
88A88VAL0-0.073-0.03112.407-0.046-0.0460.0000.0000.0000.000
89A89GLN00.0210.01813.210-0.073-0.0730.0000.0000.0000.000
90A90HIS0-0.019-0.03514.754-0.013-0.0130.0000.0000.0000.000
91A91LEU0-0.056-0.02912.652-0.036-0.0360.0000.0000.0000.000
92A92ALA0-0.0080.00316.9720.0480.0480.0000.0000.0000.000
93A93VAL0-0.047-0.03217.841-0.038-0.0380.0000.0000.0000.000
94A94GLN00.0130.01420.5180.0220.0220.0000.0000.0000.000
95A95SER00.0170.00422.478-0.010-0.0100.0000.0000.0000.000
96A96THR00.021-0.00524.568-0.003-0.0030.0000.0000.0000.000
97A97ASN0-0.022-0.00926.041-0.002-0.0020.0000.0000.0000.000
98A98THR0-0.0220.00527.6780.0080.0080.0000.0000.0000.000
99A99VAL0-0.0090.00329.567-0.007-0.0070.0000.0000.0000.000
100A100ILE0-0.007-0.01728.2000.0060.0060.0000.0000.0000.000
101A101LEU0-0.046-0.01232.592-0.004-0.0040.0000.0000.0000.000
102A102ASP-1-0.861-0.91934.714-0.124-0.1240.0000.0000.0000.000
103A103GLU-1-0.927-0.95935.921-0.117-0.1170.0000.0000.0000.000
104A104VAL0-0.040-0.01731.9520.0080.0080.0000.0000.0000.000
105A105GLU-1-0.911-0.95431.519-0.128-0.1280.0000.0000.0000.000
106A106ILE0-0.031-0.03427.3750.0110.0110.0000.0000.0000.000
107A107GLY0-0.0110.00927.370-0.012-0.0120.0000.0000.0000.000
108A108GLU-1-0.906-0.96521.823-0.171-0.1710.0000.0000.0000.000
109A109GLY00.0380.00920.8620.0230.0230.0000.0000.0000.000
110A110SER0-0.0210.00021.8950.0140.0140.0000.0000.0000.000
111A111LEU0-0.006-0.00721.296-0.021-0.0210.0000.0000.0000.000
112A112LEU0-0.022-0.01223.8840.0210.0210.0000.0000.0000.000
113A113CYS0-0.031-0.00225.499-0.015-0.0150.0000.0000.0000.000
114A114PRO00.0420.02525.8580.0010.0010.0000.0000.0000.000
115A115PHE0-0.014-0.03528.6660.0120.0120.0000.0000.0000.000
116A116THR0-0.026-0.00729.1170.0050.0050.0000.0000.0000.000
117A117CYS0-0.022-0.01831.916-0.007-0.0070.0000.0000.0000.000
118A118LEU0-0.0130.00330.5350.0080.0080.0000.0000.0000.000
119A119THR00.002-0.01234.426-0.003-0.0030.0000.0000.0000.000
120A120SER00.0670.01236.619-0.007-0.0070.0000.0000.0000.000
121A121ASN0-0.022-0.01438.1840.0070.0070.0000.0000.0000.000
122A122ILE0-0.056-0.00734.6240.0070.0070.0000.0000.0000.000
123A123LYS10.9160.98833.0690.0860.0860.0000.0000.0000.000
124A124ILE0-0.009-0.02029.8560.0100.0100.0000.0000.0000.000
125A125GLY0-0.043-0.01130.856-0.008-0.0080.0000.0000.0000.000
126A126LYS10.8780.91726.0540.0770.0770.0000.0000.0000.000
127A127PHE00.004-0.00220.9960.0180.0180.0000.0000.0000.000
128A128PHE00.0400.02825.5520.0150.0150.0000.0000.0000.000
129A129HIS00.002-0.00723.122-0.003-0.0030.0000.0000.0000.000
130A130ALA00.0260.02627.6630.0120.0120.0000.0000.0000.000
131A131ASN00.023-0.01127.404-0.007-0.0070.0000.0000.0000.000
132A132ILE00.0440.02429.1030.0000.0000.0000.0000.0000.000
133A133TYR0-0.025-0.02231.2340.0120.0120.0000.0000.0000.000
134A134SER0-0.105-0.04132.1290.0040.0040.0000.0000.0000.000
135A135TYR0-0.016-0.03733.972-0.006-0.0060.0000.0000.0000.000
136A136VAL00.003-0.00334.2090.0070.0070.0000.0000.0000.000
137A137ALA0-0.004-0.00836.891-0.006-0.0060.0000.0000.0000.000
138A138HIS00.005-0.01639.5680.0010.0010.0000.0000.0000.000
139A139ASP-1-0.786-0.88640.987-0.067-0.0670.0000.0000.0000.000
140A140CYS0-0.114-0.03338.4290.0070.0070.0000.0000.0000.000
141A141VAL00.0210.00637.674-0.006-0.0060.0000.0000.0000.000
142A142ILE0-0.023-0.01933.4660.0070.0070.0000.0000.0000.000
143A143GLY00.0190.01234.128-0.007-0.0070.0000.0000.0000.000
144A144ASP-1-0.793-0.87730.148-0.083-0.0830.0000.0000.0000.000
145A145TYR00.009-0.00725.5180.0080.0080.0000.0000.0000.000
146A146VAL0-0.0060.01729.7830.0090.0090.0000.0000.0000.000
147A147THR0-0.031-0.02529.938-0.010-0.0100.0000.0000.0000.000
148A148PHE0-0.016-0.01231.3260.0080.0080.0000.0000.0000.000
149A149ALA00.0010.00231.703-0.005-0.0050.0000.0000.0000.000
150A150PRO00.0560.01731.765-0.003-0.0030.0000.0000.0000.000
151A151GLY0-0.0040.00833.8960.0070.0070.0000.0000.0000.000
152A152ALA0-0.0300.00835.6960.0030.0030.0000.0000.0000.000
153A153LYS10.9040.94337.2080.0510.0510.0000.0000.0000.000
154A154CYS0-0.0010.01938.1800.0060.0060.0000.0000.0000.000
155A155ASN0-0.027-0.01640.143-0.008-0.0080.0000.0000.0000.000
156A156GLY00.1110.05642.295-0.001-0.0010.0000.0000.0000.000
157A157ASN0-0.046-0.01543.6280.0060.0060.0000.0000.0000.000
158A158ILE0-0.026-0.02741.6700.0050.0050.0000.0000.0000.000
159A159HIS00.0370.01840.631-0.005-0.0050.0000.0000.0000.000
160A160ILE0-0.032-0.02436.9760.0060.0060.0000.0000.0000.000
161A161GLU-1-0.811-0.91237.305-0.037-0.0370.0000.0000.0000.000
162A162ASP-1-0.809-0.91534.188-0.042-0.0420.0000.0000.0000.000
163A163HIS0-0.055-0.05230.5920.0060.0060.0000.0000.0000.000
164A164ALA0-0.0130.02934.2090.0050.0050.0000.0000.0000.000
165A165TYR00.000-0.00232.865-0.004-0.0040.0000.0000.0000.000
166A166ILE0-0.019-0.01435.5060.0040.0040.0000.0000.0000.000
167A167GLY00.0550.02236.145-0.003-0.0030.0000.0000.0000.000
168A168THR0-0.040-0.03936.106-0.003-0.0030.0000.0000.0000.000
169A169GLY00.021-0.00337.6980.0040.0040.0000.0000.0000.000
170A170ALA0-0.0360.00439.9530.0010.0010.0000.0000.0000.000
171A171VAL0-0.021-0.01541.166-0.005-0.0050.0000.0000.0000.000
172A172ILE0-0.009-0.00140.2890.0050.0050.0000.0000.0000.000
173A173LYS10.9450.97944.4120.0310.0310.0000.0000.0000.000
174A174GLN00.0070.01346.2260.0000.0000.0000.0000.0000.000
175A175GLY0-0.017-0.00346.7670.0040.0040.0000.0000.0000.000
176A176THR0-0.074-0.05248.567-0.001-0.0010.0000.0000.0000.000
177A177PRO00.0870.02548.4540.0000.0000.0000.0000.0000.000
178A178ASP-1-0.911-0.93049.538-0.043-0.0430.0000.0000.0000.000
179A179LYS10.7940.88849.6500.0370.0370.0000.0000.0000.000
180A180PRO00.0740.05745.5790.0010.0010.0000.0000.0000.000
181A181LEU0-0.081-0.01945.1560.0040.0040.0000.0000.0000.000
182A182ILE00.004-0.00543.477-0.002-0.0020.0000.0000.0000.000
183A183ILE0-0.029-0.01440.4240.0040.0040.0000.0000.0000.000
184A184GLY00.0350.01341.223-0.002-0.0020.0000.0000.0000.000
185A185LYS10.9090.93235.9940.0260.0260.0000.0000.0000.000
186A186GLY0-0.006-0.00937.3230.0050.0050.0000.0000.0000.000
187A187ALA0-0.073-0.01138.3560.0040.0040.0000.0000.0000.000
188A188ILE00.003-0.00638.282-0.002-0.0020.0000.0000.0000.000
189A189VAL0-0.016-0.01039.7700.0020.0020.0000.0000.0000.000
190A190GLY00.0180.00940.172-0.001-0.0010.0000.0000.0000.000
191A191MET00.011-0.01439.749-0.002-0.0020.0000.0000.0000.000
192A192GLY0-0.025-0.00741.2560.0030.0030.0000.0000.0000.000
193A193ALA0-0.076-0.01943.6410.0010.0010.0000.0000.0000.000
194A194VAL00.0190.00944.944-0.003-0.0030.0000.0000.0000.000
195A195VAL00.012-0.00444.3380.0030.0030.0000.0000.0000.000
196A196THR0-0.011-0.01347.347-0.002-0.0020.0000.0000.0000.000
197A197LYS10.9520.96649.4040.0190.0190.0000.0000.0000.000
198A198SER00.0630.02047.256-0.001-0.0010.0000.0000.0000.000
199A199VAL0-0.039-0.00544.5820.0030.0030.0000.0000.0000.000
200A200PRO0-0.001-0.00545.414-0.002-0.0020.0000.0000.0000.000
201A201ALA00.0690.02742.9080.0000.0000.0000.0000.0000.000
202A202GLY0-0.0050.00641.7970.0020.0020.0000.0000.0000.000
203A203VAL0-0.095-0.02242.8370.0030.0030.0000.0000.0000.000
204A204THR00.026-0.00942.324-0.003-0.0030.0000.0000.0000.000
205A205VAL0-0.018-0.01344.2690.0010.0010.0000.0000.0000.000
206A206VAL00.0540.02244.848-0.001-0.0010.0000.0000.0000.000
207A207GLY00.0260.01446.9490.0000.0000.0000.0000.0000.000
208A208ASN00.0300.03848.846-0.003-0.0030.0000.0000.0000.000
209A209PRO00.039-0.00151.1850.0010.0010.0000.0000.0000.000
210A210ALA00.0020.01147.6970.0020.0020.0000.0000.0000.000
211A211ARG10.8230.90649.6160.0130.0130.0000.0000.0000.000
212A212ILE00.020-0.00248.6760.0000.0000.0000.0000.0000.000
213A213LEU0-0.0190.00146.4630.0010.0010.0000.0000.0000.000
214A214GLU-1-0.829-0.88444.3450.0060.0060.0000.0000.0000.000
215A215ARG10.8820.92846.7140.0010.0010.0000.0000.0000.000
216A216LYS10.9861.00346.995-0.006-0.0060.0000.0000.0000.000