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: VQV91

Calculation Name: 4NP6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4NP6

Chain ID: A

ChEMBL ID:

UniProt ID: Q9KTB7

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 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 216
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2286147.031678
FMO2-HF: Nuclear repulsion 2204002.154999
FMO2-HF: Total energy -82144.876679
FMO2-MP2: Total energy -82385.0799


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:ASN)


Summations of interaction energy for fragment #1(A:-1:ASN)
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.
-4.896-1.5030.219-1.818-1.7940.001
Interaction energy analysis for fragmet #1(A:-1:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / q_NPA : 0.004
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].
3A1MET0-0.046-0.0233.374-2.4610.9320.219-1.818-1.7940.001
4A2ARG10.8600.9235.632-2.511-2.5110.0000.0000.0000.000
5A3ILE00.008-0.0078.864-0.074-0.0740.0000.0000.0000.000
6A4ILE0-0.0030.02111.8030.1170.1170.0000.0000.0000.000
7A5LEU0-0.025-0.01115.357-0.060-0.0600.0000.0000.0000.000
8A6LEU00.0260.00417.9240.0590.0590.0000.0000.0000.000
9A7GLY00.0630.00421.144-0.049-0.0490.0000.0000.0000.000
10A8ALA00.0160.02124.1510.0160.0160.0000.0000.0000.000
11A9PRO0-0.043-0.02627.929-0.017-0.0170.0000.0000.0000.000
12A10GLY00.027-0.00929.3800.0160.0160.0000.0000.0000.000
13A11ALA0-0.0220.00626.938-0.004-0.0040.0000.0000.0000.000
14A12GLY00.0390.00427.339-0.007-0.0070.0000.0000.0000.000
15A13LYS10.8400.93121.5130.3040.3040.0000.0000.0000.000
16A14GLY00.0170.01321.801-0.045-0.0450.0000.0000.0000.000
17A15THR00.0390.00821.989-0.029-0.0290.0000.0000.0000.000
18A16GLN00.019-0.01018.609-0.104-0.1040.0000.0000.0000.000
19A17ALA0-0.0070.00817.593-0.091-0.0910.0000.0000.0000.000
20A18GLN0-0.054-0.02517.389-0.035-0.0350.0000.0000.0000.000
21A19PHE00.0340.01915.444-0.090-0.0900.0000.0000.0000.000
22A20ILE0-0.004-0.00812.142-0.125-0.1250.0000.0000.0000.000
23A21MET0-0.018-0.00112.979-0.176-0.1760.0000.0000.0000.000
24A22GLU-1-0.912-0.94614.040-0.805-0.8050.0000.0000.0000.000
25A23LYS10.8730.95010.6541.9421.9420.0000.0000.0000.000
26A24PHE0-0.022-0.0307.549-0.224-0.2240.0000.0000.0000.000
27A25GLY00.0090.0249.044-0.403-0.4030.0000.0000.0000.000
28A26ILE0-0.030-0.0088.940-0.107-0.1070.0000.0000.0000.000
29A27PRO00.0170.01611.9160.0960.0960.0000.0000.0000.000
30A28GLN00.009-0.00615.3590.0000.0000.0000.0000.0000.000
31A29ILE0-0.022-0.01115.8450.0600.0600.0000.0000.0000.000
32A30SER00.0250.00519.4530.0270.0270.0000.0000.0000.000
33A31THR00.0340.00521.7770.0270.0270.0000.0000.0000.000
34A32GLY00.0030.01224.0480.0230.0230.0000.0000.0000.000
35A33ASP-1-0.821-0.90725.548-0.168-0.1680.0000.0000.0000.000
36A34MET0-0.0190.01822.2310.0080.0080.0000.0000.0000.000
37A35LEU00.0240.02124.8300.0180.0180.0000.0000.0000.000
38A36ARG10.8340.88427.9550.1550.1550.0000.0000.0000.000
39A37ALA0-0.011-0.00226.3780.0080.0080.0000.0000.0000.000
40A38ALA00.0490.02826.6560.0090.0090.0000.0000.0000.000
41A39ILE0-0.008-0.00928.4620.0110.0110.0000.0000.0000.000
42A40LYS10.8860.93831.8940.0920.0920.0000.0000.0000.000
43A41ALA0-0.0120.00729.1410.0010.0010.0000.0000.0000.000
44A42GLY00.0000.01931.0870.0090.0090.0000.0000.0000.000
45A43THR00.0160.01026.7020.0090.0090.0000.0000.0000.000
46A44GLU-1-0.845-0.91529.3650.0630.0630.0000.0000.0000.000
47A45LEU00.0350.01625.265-0.002-0.0020.0000.0000.0000.000
48A46GLY00.0240.02129.365-0.009-0.0090.0000.0000.0000.000
49A47LYS10.8390.90530.982-0.040-0.0400.0000.0000.0000.000
50A48GLN0-0.042-0.03031.7210.0000.0000.0000.0000.0000.000
51A49ALA00.0410.01830.925-0.003-0.0030.0000.0000.0000.000
52A50LYS10.7650.85933.0670.0110.0110.0000.0000.0000.000
53A51ALA00.0230.00935.954-0.004-0.0040.0000.0000.0000.000
54A52VAL0-0.0010.00635.247-0.001-0.0010.0000.0000.0000.000
55A53ILE0-0.006-0.00933.687-0.005-0.0050.0000.0000.0000.000
56A54ASP-1-0.829-0.88638.009-0.016-0.0160.0000.0000.0000.000
57A55ALA0-0.059-0.02040.868-0.001-0.0010.0000.0000.0000.000
58A56GLY0-0.0080.00441.5080.0020.0020.0000.0000.0000.000
59A57GLN0-0.098-0.05238.8840.0050.0050.0000.0000.0000.000
60A58LEU0-0.003-0.00834.829-0.005-0.0050.0000.0000.0000.000
61A59VAL0-0.014-0.00930.2880.0070.0070.0000.0000.0000.000
62A60SER0-0.014-0.02330.774-0.010-0.0100.0000.0000.0000.000
63A61ASP-1-0.776-0.90326.1430.0380.0380.0000.0000.0000.000
64A62ASP-1-0.852-0.89925.5800.1130.1130.0000.0000.0000.000
65A63ILE00.0350.02225.6230.0120.0120.0000.0000.0000.000
66A64ILE0-0.037-0.01323.793-0.006-0.0060.0000.0000.0000.000
67A65LEU00.014-0.00720.513-0.010-0.0100.0000.0000.0000.000
68A66GLY0-0.0010.00520.9520.0320.0320.0000.0000.0000.000
69A67LEU0-0.001-0.00822.1730.0060.0060.0000.0000.0000.000
70A68ILE00.004-0.00117.293-0.024-0.0240.0000.0000.0000.000
71A69LYS10.9480.96817.544-0.333-0.3330.0000.0000.0000.000
72A70GLU-1-0.906-0.95817.9490.0820.0820.0000.0000.0000.000
73A71ARG10.7430.82216.7090.2440.2440.0000.0000.0000.000
74A72ILE0-0.004-0.03013.190-0.073-0.0730.0000.0000.0000.000
75A73ALA0-0.0020.01613.8010.0610.0610.0000.0000.0000.000
76A74GLN0-0.064-0.01916.0630.0170.0170.0000.0000.0000.000
77A75ALA00.0490.01013.277-0.020-0.0200.0000.0000.0000.000
78A76ASP-1-0.783-0.86111.971-0.459-0.4590.0000.0000.0000.000
79A77CYS0-0.067-0.01411.755-0.205-0.2050.0000.0000.0000.000
80A78GLU-1-0.939-0.9516.523-1.071-1.0710.0000.0000.0000.000
81A79LYS10.8700.9295.3823.0063.0060.0000.0000.0000.000
82A80GLY0-0.0100.0126.568-0.465-0.4650.0000.0000.0000.000
83A81PHE00.024-0.0158.7490.0160.0160.0000.0000.0000.000
84A82LEU00.0130.01211.727-0.039-0.0390.0000.0000.0000.000
85A83LEU0-0.004-0.00114.3860.0670.0670.0000.0000.0000.000
86A84ASP-1-0.817-0.89817.020-0.339-0.3390.0000.0000.0000.000
87A85GLY0-0.028-0.01120.0810.0440.0440.0000.0000.0000.000
88A86PHE0-0.017-0.01019.7220.0360.0360.0000.0000.0000.000
89A87PRO00.0520.02418.669-0.030-0.0300.0000.0000.0000.000
90A88ARG10.8710.91321.6600.0640.0640.0000.0000.0000.000
91A89THR0-0.0050.00724.9370.0040.0040.0000.0000.0000.000
92A90ILE00.0570.02224.3330.0010.0010.0000.0000.0000.000
93A91PRO00.0520.01523.9190.0160.0160.0000.0000.0000.000
94A92GLN0-0.028-0.01622.9240.0040.0040.0000.0000.0000.000
95A93ALA0-0.0010.00019.8810.0180.0180.0000.0000.0000.000
96A94ASP-1-0.825-0.89119.2450.1830.1830.0000.0000.0000.000
97A95GLY00.0490.01920.6420.0490.0490.0000.0000.0000.000
98A96LEU0-0.052-0.03616.8620.0260.0260.0000.0000.0000.000
99A97LYS10.8400.92416.288-0.151-0.1510.0000.0000.0000.000
100A98GLU-1-0.958-0.98117.0780.3610.3610.0000.0000.0000.000
101A99MET0-0.101-0.03217.8170.0020.0020.0000.0000.0000.000
102A100GLY00.0030.00214.5100.0420.0420.0000.0000.0000.000
103A101ILE0-0.052-0.01412.5720.2070.2070.0000.0000.0000.000
104A102ASN0-0.028-0.02211.225-0.261-0.2610.0000.0000.0000.000
105A103VAL0-0.011-0.01310.4190.1080.1080.0000.0000.0000.000
106A104ASP-1-0.760-0.8405.6080.3000.3000.0000.0000.0000.000
107A105TYR0-0.006-0.0226.657-0.262-0.2620.0000.0000.0000.000
108A106VAL0-0.031-0.01310.7550.1010.1010.0000.0000.0000.000
109A107ILE00.0180.01013.157-0.021-0.0210.0000.0000.0000.000
110A108GLU-1-0.788-0.85716.520-0.231-0.2310.0000.0000.0000.000
111A109PHE0-0.032-0.01320.340-0.018-0.0180.0000.0000.0000.000
112A110ASP-1-0.844-0.92522.324-0.225-0.2250.0000.0000.0000.000
113A111VAL0-0.039-0.02025.740-0.015-0.0150.0000.0000.0000.000
114A112ALA00.0520.03229.2100.0120.0120.0000.0000.0000.000
115A113ASP-1-0.774-0.88732.269-0.167-0.1670.0000.0000.0000.000
116A114ASP-1-0.837-0.90534.504-0.147-0.1470.0000.0000.0000.000
117A115VAL00.0210.01333.1070.0010.0010.0000.0000.0000.000
118A116ILE0-0.047-0.01830.210-0.007-0.0070.0000.0000.0000.000
119A117VAL00.005-0.00434.3180.0030.0030.0000.0000.0000.000
120A118GLU-1-0.908-0.95237.339-0.183-0.1830.0000.0000.0000.000
121A119ARG10.8880.96429.6050.2710.2710.0000.0000.0000.000
122A120MET0-0.067-0.02133.2440.0000.0000.0000.0000.0000.000
123A121ALA00.0810.04437.6530.0050.0050.0000.0000.0000.000
124A122GLY00.0160.02239.8970.0080.0080.0000.0000.0000.000
125A123ARG10.8320.90433.4300.1830.1830.0000.0000.0000.000
126A124ARG10.8290.90540.6370.1430.1430.0000.0000.0000.000
127A125ALA00.0150.00442.487-0.007-0.0070.0000.0000.0000.000
128A126HIS10.8460.91244.3660.1050.1050.0000.0000.0000.000
129A127LEU00.0170.00045.716-0.001-0.0010.0000.0000.0000.000
130A128PRO00.0060.00347.2100.0000.0000.0000.0000.0000.000
131A129SER00.0030.00845.6040.0030.0030.0000.0000.0000.000
132A130GLY0-0.0080.01142.609-0.005-0.0050.0000.0000.0000.000
133A131ARG10.8010.87541.4620.1090.1090.0000.0000.0000.000
134A132THR0-0.015-0.00538.5480.0050.0050.0000.0000.0000.000
135A133TYR0-0.016-0.03540.196-0.006-0.0060.0000.0000.0000.000
136A134HIS0-0.031-0.02737.5800.0010.0010.0000.0000.0000.000
137A135VAL00.001-0.00740.100-0.004-0.0040.0000.0000.0000.000
138A136VAL0-0.0060.01337.7850.0020.0020.0000.0000.0000.000
139A137TYR0-0.005-0.01734.704-0.005-0.0050.0000.0000.0000.000
140A138ASN0-0.057-0.03936.457-0.002-0.0020.0000.0000.0000.000
141A139PRO00.0610.06938.8850.0070.0070.0000.0000.0000.000
142A140PRO00.0070.01542.632-0.003-0.0030.0000.0000.0000.000
143A141LYS10.7530.82743.1570.1510.1510.0000.0000.0000.000
144A142VAL00.0030.00347.5080.0030.0030.0000.0000.0000.000
145A143GLU-1-0.915-0.95548.144-0.124-0.1240.0000.0000.0000.000
146A144GLY0-0.001-0.00448.9320.0050.0050.0000.0000.0000.000
147A145LYS10.8150.90050.0370.0930.0930.0000.0000.0000.000
148A146ASP-1-0.696-0.79446.711-0.122-0.1220.0000.0000.0000.000
149A147ASP-1-0.746-0.85345.081-0.133-0.1330.0000.0000.0000.000
150A148VAL0-0.084-0.03745.4780.0000.0000.0000.0000.0000.000
151A149THR0-0.051-0.05248.7750.0050.0050.0000.0000.0000.000
152A150GLY0-0.0030.01351.5250.0040.0040.0000.0000.0000.000
153A151GLU-1-0.832-0.91251.947-0.084-0.0840.0000.0000.0000.000
154A152ASP-1-0.832-0.90751.713-0.092-0.0920.0000.0000.0000.000
155A153LEU0-0.068-0.02345.873-0.001-0.0010.0000.0000.0000.000
156A154VAL0-0.013-0.00446.3550.0020.0020.0000.0000.0000.000
157A155ILE00.018-0.00144.212-0.007-0.0070.0000.0000.0000.000
158A156ARG10.9030.93840.6260.1270.1270.0000.0000.0000.000
159A157GLU-1-0.739-0.86043.795-0.094-0.0940.0000.0000.0000.000
160A158ASP-1-0.900-0.92039.340-0.110-0.1100.0000.0000.0000.000
161A159ASP-1-0.808-0.90538.192-0.157-0.1570.0000.0000.0000.000
162A160LYS10.8240.90340.2930.0920.0920.0000.0000.0000.000
163A161GLU-1-0.800-0.88941.280-0.119-0.1190.0000.0000.0000.000
164A162GLU-1-0.928-0.94841.296-0.084-0.0840.0000.0000.0000.000
165A163THR0-0.004-0.02439.9790.0020.0020.0000.0000.0000.000
166A164VAL0-0.044-0.01536.166-0.003-0.0030.0000.0000.0000.000
167A165ARG10.8430.87136.7440.1250.1250.0000.0000.0000.000
168A166ALA0-0.0150.00937.6550.0010.0010.0000.0000.0000.000
169A167ARG10.8440.90733.6670.1370.1370.0000.0000.0000.000
170A168LEU0-0.006-0.00131.981-0.003-0.0030.0000.0000.0000.000
171A169ASN00.0480.03032.979-0.004-0.0040.0000.0000.0000.000
172A170VAL0-0.0240.00333.1400.0050.0050.0000.0000.0000.000
173A171TYR00.0250.01325.457-0.001-0.0010.0000.0000.0000.000
174A172HIS0-0.007-0.02429.318-0.001-0.0010.0000.0000.0000.000
175A173THR0-0.054-0.03430.2000.0060.0060.0000.0000.0000.000
176A174GLN0-0.044-0.02427.8790.0010.0010.0000.0000.0000.000
177A175THR0-0.015-0.02124.2390.0050.0050.0000.0000.0000.000
178A176ALA00.0360.02725.536-0.004-0.0040.0000.0000.0000.000
179A177PRO0-0.005-0.01626.508-0.001-0.0010.0000.0000.0000.000
180A178LEU00.0030.00421.7450.0150.0150.0000.0000.0000.000
181A179ILE0-0.0140.00821.676-0.005-0.0050.0000.0000.0000.000
182A180GLU-1-0.844-0.91422.327-0.071-0.0710.0000.0000.0000.000
183A181TYR0-0.080-0.06418.9840.0080.0080.0000.0000.0000.000
184A182TYR00.048-0.00216.0670.0020.0020.0000.0000.0000.000
185A183GLY00.0310.02817.915-0.029-0.0290.0000.0000.0000.000
186A184LYS10.8300.90920.0380.0320.0320.0000.0000.0000.000
187A185GLU-1-0.835-0.89816.4080.1800.1800.0000.0000.0000.000
188A186ALA0-0.015-0.00815.3770.0200.0200.0000.0000.0000.000
189A187ALA0-0.037-0.01016.396-0.015-0.0150.0000.0000.0000.000
190A188ALA0-0.071-0.03118.4730.0120.0120.0000.0000.0000.000
191A189GLY0-0.005-0.00614.6120.0620.0620.0000.0000.0000.000
192A190LYS10.8060.89112.695-0.174-0.1740.0000.0000.0000.000
193A191THR0-0.023-0.02610.9380.0370.0370.0000.0000.0000.000
194A192GLN00.0000.0038.8430.0770.0770.0000.0000.0000.000
195A193TYR0-0.019-0.03912.525-0.069-0.0690.0000.0000.0000.000
196A194LEU0-0.032-0.01112.952-0.028-0.0280.0000.0000.0000.000
197A195LYS10.7960.87616.9480.2960.2960.0000.0000.0000.000
198A196PHE0-0.020-0.01715.944-0.017-0.0170.0000.0000.0000.000
199A197ASP-1-0.773-0.86021.747-0.314-0.3140.0000.0000.0000.000
200A198GLY00.018-0.00524.628-0.034-0.0340.0000.0000.0000.000
201A199THR0-0.159-0.12325.9710.0270.0270.0000.0000.0000.000
202A200LYS10.8650.93723.4860.4740.4740.0000.0000.0000.000
203A201GLN00.0380.04826.891-0.024-0.0240.0000.0000.0000.000
204A202VAL00.0620.01523.173-0.032-0.0320.0000.0000.0000.000
205A203SER0-0.013-0.01822.455-0.059-0.0590.0000.0000.0000.000
206A204GLU-1-0.837-0.90821.607-0.464-0.4640.0000.0000.0000.000
207A205VAL00.0010.00920.211-0.051-0.0510.0000.0000.0000.000
208A206SER00.006-0.00818.118-0.062-0.0620.0000.0000.0000.000
209A207ALA0-0.026-0.00316.757-0.124-0.1240.0000.0000.0000.000
210A208ASP-1-0.858-0.93616.719-0.695-0.6950.0000.0000.0000.000
211A209ILE0-0.0120.00014.040-0.063-0.0630.0000.0000.0000.000
212A210ALA0-0.024-0.02212.492-0.181-0.1810.0000.0000.0000.000
213A211LYS10.8330.91712.0380.5210.5210.0000.0000.0000.000
214A212ALA00.0090.01412.727-0.005-0.0050.0000.0000.0000.000
215A213LEU0-0.0490.0018.964-0.103-0.1030.0000.0000.0000.000
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