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: 5JRVZ

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 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 216
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2284379.476071
FMO2-HF: Nuclear repulsion 2202237.53986
FMO2-HF: Total energy -82141.93621
FMO2-MP2: Total energy -82382.416168


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.
-3.715-1.295-0.01-1.275-1.1340.001
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 : 0.005 / q_NPA : -0.023
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].
3A1MET0-0.053-0.0433.610-1.2821.138-0.010-1.275-1.1340.001
4A2ARG10.8920.9715.798-0.189-0.1890.0000.0000.0000.000
5A3ILE00.018-0.0039.3780.0500.0500.0000.0000.0000.000
6A4ILE00.0170.03312.2120.0650.0650.0000.0000.0000.000
7A5LEU0-0.033-0.01615.995-0.036-0.0360.0000.0000.0000.000
8A6LEU00.0270.01218.3400.0470.0470.0000.0000.0000.000
9A7GLY00.0690.01321.887-0.033-0.0330.0000.0000.0000.000
10A8ALA00.0110.02324.7120.0120.0120.0000.0000.0000.000
11A9PRO0-0.027-0.02628.198-0.012-0.0120.0000.0000.0000.000
12A10GLY00.0350.00129.5140.0110.0110.0000.0000.0000.000
13A11ALA0-0.0040.00227.2660.0010.0010.0000.0000.0000.000
14A12GLY0-0.026-0.01327.218-0.009-0.0090.0000.0000.0000.000
15A13LYS10.9330.97021.8950.2760.2760.0000.0000.0000.000
16A14GLY0-0.023-0.01121.688-0.035-0.0350.0000.0000.0000.000
17A15THR00.0310.00621.533-0.020-0.0200.0000.0000.0000.000
18A16GLN00.0470.00718.631-0.061-0.0610.0000.0000.0000.000
19A17ALA0-0.0280.01017.095-0.067-0.0670.0000.0000.0000.000
20A18GLN00.0460.02316.574-0.050-0.0500.0000.0000.0000.000
21A19PHE00.0230.03315.972-0.036-0.0360.0000.0000.0000.000
22A20ILE0-0.005-0.01111.797-0.067-0.0670.0000.0000.0000.000
23A21MET0-0.065-0.01212.562-0.122-0.1220.0000.0000.0000.000
24A22GLU-1-0.932-0.97313.870-0.561-0.5610.0000.0000.0000.000
25A23LYS10.8750.95010.5991.1311.1310.0000.0000.0000.000
26A24PHE0-0.053-0.0596.8410.0130.0130.0000.0000.0000.000
27A25GLY0-0.0350.0018.785-0.283-0.2830.0000.0000.0000.000
28A26ILE0-0.076-0.0018.516-0.062-0.0620.0000.0000.0000.000
29A27PRO00.0160.01111.5220.1240.1240.0000.0000.0000.000
30A28GLN00.0470.01114.860-0.036-0.0360.0000.0000.0000.000
31A29ILE0-0.0020.00015.7230.0500.0500.0000.0000.0000.000
32A30SER00.0360.03919.1840.0170.0170.0000.0000.0000.000
33A31THR00.0550.01122.3390.0220.0220.0000.0000.0000.000
34A32GLY00.0020.00124.0370.0180.0180.0000.0000.0000.000
35A33ASP-1-0.824-0.90624.530-0.200-0.2000.0000.0000.0000.000
36A34MET0-0.051-0.01622.0570.0050.0050.0000.0000.0000.000
37A35LEU00.0250.01724.5920.0140.0140.0000.0000.0000.000
38A36ARG10.8610.90427.7990.1690.1690.0000.0000.0000.000
39A37ALA0-0.020-0.01726.4020.0110.0110.0000.0000.0000.000
40A38ALA00.0450.03827.2160.0080.0080.0000.0000.0000.000
41A39ILE0-0.0020.00028.8280.0110.0110.0000.0000.0000.000
42A40LYS10.8880.93731.9910.1090.1090.0000.0000.0000.000
43A41ALA0-0.0120.01229.3720.0030.0030.0000.0000.0000.000
44A42GLY0-0.0240.00731.3340.0060.0060.0000.0000.0000.000
45A43THR00.0660.02627.2610.0110.0110.0000.0000.0000.000
46A44GLU-1-0.878-0.94429.467-0.012-0.0120.0000.0000.0000.000
47A45LEU00.0650.01525.7470.0030.0030.0000.0000.0000.000
48A46GLY00.0210.00929.718-0.003-0.0030.0000.0000.0000.000
49A47LYS10.8580.92531.3780.0310.0310.0000.0000.0000.000
50A48GLN00.008-0.00131.463-0.001-0.0010.0000.0000.0000.000
51A49ALA00.0410.03331.4910.0010.0010.0000.0000.0000.000
52A50LYS10.8500.92433.5740.0530.0530.0000.0000.0000.000
53A51ALA0-0.006-0.00736.2880.0010.0010.0000.0000.0000.000
54A52VAL00.0060.01435.6610.0020.0020.0000.0000.0000.000
55A53ILE0-0.023-0.03234.104-0.001-0.0010.0000.0000.0000.000
56A54ASP-1-0.897-0.92438.372-0.046-0.0460.0000.0000.0000.000
57A55ALA0-0.066-0.02941.4610.0010.0010.0000.0000.0000.000
58A56GLY0-0.028-0.00941.5540.0020.0020.0000.0000.0000.000
59A57GLN0-0.064-0.02939.8150.0020.0020.0000.0000.0000.000
60A58LEU00.002-0.01535.773-0.006-0.0060.0000.0000.0000.000
61A59VAL0-0.042-0.01930.8130.0050.0050.0000.0000.0000.000
62A60SER00.0100.02031.811-0.005-0.0050.0000.0000.0000.000
63A61ASP-1-0.836-0.94627.294-0.040-0.0400.0000.0000.0000.000
64A62ASP-1-0.928-0.96026.7760.0070.0070.0000.0000.0000.000
65A63ILE00.0310.01226.645-0.002-0.0020.0000.0000.0000.000
66A64ILE0-0.067-0.03324.273-0.012-0.0120.0000.0000.0000.000
67A65LEU00.011-0.01421.118-0.019-0.0190.0000.0000.0000.000
68A66GLY00.0340.02421.2690.0070.0070.0000.0000.0000.000
69A67LEU00.0610.02522.075-0.006-0.0060.0000.0000.0000.000
70A68ILE00.0370.01917.937-0.026-0.0260.0000.0000.0000.000
71A69LYS10.9500.96617.883-0.093-0.0930.0000.0000.0000.000
72A70GLU-1-0.989-1.00018.241-0.067-0.0670.0000.0000.0000.000
73A71ARG10.8150.91717.1800.3440.3440.0000.0000.0000.000
74A72ILE0-0.029-0.05113.535-0.055-0.0550.0000.0000.0000.000
75A73ALA0-0.0350.00513.956-0.017-0.0170.0000.0000.0000.000
76A74GLN0-0.053-0.01516.2150.0340.0340.0000.0000.0000.000
77A75ALA00.036-0.00113.498-0.035-0.0350.0000.0000.0000.000
78A76ASP-1-0.874-0.93912.088-0.574-0.5740.0000.0000.0000.000
79A77CYS0-0.067-0.02011.445-0.118-0.1180.0000.0000.0000.000
80A78GLU-1-0.946-0.9426.583-1.151-1.1510.0000.0000.0000.000
81A79LYS10.9680.9744.9471.5961.5960.0000.0000.0000.000
82A80GLY0-0.0250.0006.062-0.568-0.5680.0000.0000.0000.000
83A81PHE00.017-0.0398.5110.2150.2150.0000.0000.0000.000
84A82LEU00.0520.03111.285-0.043-0.0430.0000.0000.0000.000
85A83LEU0-0.041-0.02613.9760.0750.0750.0000.0000.0000.000
86A84ASP-1-0.881-0.95016.971-0.292-0.2920.0000.0000.0000.000
87A85GLY0-0.046-0.01920.0130.0340.0340.0000.0000.0000.000
88A86PHE0-0.049-0.03220.1760.0320.0320.0000.0000.0000.000
89A87PRO00.0620.02919.657-0.029-0.0290.0000.0000.0000.000
90A88ARG10.9330.95122.6190.1180.1180.0000.0000.0000.000
91A89THR00.0060.00325.9530.0060.0060.0000.0000.0000.000
92A90ILE00.0690.02825.446-0.004-0.0040.0000.0000.0000.000
93A91PRO00.0600.02725.2950.0070.0070.0000.0000.0000.000
94A92GLN00.0430.04123.842-0.004-0.0040.0000.0000.0000.000
95A93ALA0-0.011-0.00621.3080.0010.0010.0000.0000.0000.000
96A94ASP-1-0.886-0.95920.8380.0570.0570.0000.0000.0000.000
97A95GLY00.0410.01821.8390.0290.0290.0000.0000.0000.000
98A96LEU0-0.053-0.03117.8170.0140.0140.0000.0000.0000.000
99A97LYS10.9560.99617.148-0.081-0.0810.0000.0000.0000.000
100A98GLU-1-0.970-0.98118.0150.1740.1740.0000.0000.0000.000
101A99MET0-0.093-0.02618.967-0.004-0.0040.0000.0000.0000.000
102A100GLY0-0.031-0.01515.7030.0040.0040.0000.0000.0000.000
103A101ILE0-0.083-0.03713.7160.0760.0760.0000.0000.0000.000
104A102ASN0-0.018-0.02811.884-0.164-0.1640.0000.0000.0000.000
105A103VAL0-0.024-0.00511.1550.1000.1000.0000.0000.0000.000
106A104ASP-1-0.747-0.8547.449-0.603-0.6030.0000.0000.0000.000
107A105TYR0-0.006-0.0087.452-0.148-0.1480.0000.0000.0000.000
108A106VAL00.007-0.00412.3700.0400.0400.0000.0000.0000.000
109A107ILE00.0220.01313.6270.0060.0060.0000.0000.0000.000
110A108GLU-1-0.865-0.95717.358-0.209-0.2090.0000.0000.0000.000
111A109PHE0-0.037-0.01921.142-0.005-0.0050.0000.0000.0000.000
112A110ASP-1-0.920-0.96922.937-0.183-0.1830.0000.0000.0000.000
113A111VAL0-0.037-0.02426.438-0.007-0.0070.0000.0000.0000.000
114A112ALA00.0810.03229.4410.0080.0080.0000.0000.0000.000
115A113ASP-1-0.790-0.87332.844-0.143-0.1430.0000.0000.0000.000
116A114ASP-1-0.921-0.97634.869-0.124-0.1240.0000.0000.0000.000
117A115VAL00.0070.01232.8380.0020.0020.0000.0000.0000.000
118A116ILE0-0.027-0.01330.7590.0000.0000.0000.0000.0000.000
119A117VAL00.0340.01334.4670.0020.0020.0000.0000.0000.000
120A118GLU-1-0.911-0.95637.611-0.132-0.1320.0000.0000.0000.000
121A119ARG10.8840.96030.4080.1990.1990.0000.0000.0000.000
122A120MET0-0.072-0.02333.044-0.001-0.0010.0000.0000.0000.000
123A121ALA00.0710.04437.5000.0040.0040.0000.0000.0000.000
124A122GLY00.012-0.00239.5980.0070.0070.0000.0000.0000.000
125A123ARG10.8600.93833.2470.1530.1530.0000.0000.0000.000
126A124ARG10.8140.90640.0480.1130.1130.0000.0000.0000.000
127A125ALA00.012-0.00641.363-0.006-0.0060.0000.0000.0000.000
128A126HIS10.8880.92543.4120.0900.0900.0000.0000.0000.000
129A127LEU00.035-0.00645.144-0.002-0.0020.0000.0000.0000.000
130A128PRO0-0.0030.00546.544-0.001-0.0010.0000.0000.0000.000
131A129SER0-0.0250.00044.1260.0020.0020.0000.0000.0000.000
132A130GLY0-0.0230.00042.105-0.003-0.0030.0000.0000.0000.000
133A131ARG10.8220.90740.5270.0900.0900.0000.0000.0000.000
134A132THR0-0.001-0.01636.8060.0060.0060.0000.0000.0000.000
135A133TYR00.033-0.00439.801-0.001-0.0010.0000.0000.0000.000
136A134HIS00.0040.02437.2330.0000.0000.0000.0000.0000.000
137A135VAL0-0.0080.00039.321-0.001-0.0010.0000.0000.0000.000
138A136VAL0-0.0100.00237.2240.0020.0020.0000.0000.0000.000
139A137TYR0-0.039-0.04534.101-0.002-0.0020.0000.0000.0000.000
140A138ASN0-0.074-0.03935.8950.0000.0000.0000.0000.0000.000
141A139PRO00.0260.03538.1530.0030.0030.0000.0000.0000.000
142A140PRO00.0410.03341.912-0.002-0.0020.0000.0000.0000.000
143A141LYS10.8710.92243.0990.1130.1130.0000.0000.0000.000
144A142VAL00.001-0.00246.7390.0030.0030.0000.0000.0000.000
145A143GLU-1-0.913-0.95547.778-0.093-0.0930.0000.0000.0000.000
146A144GLY0-0.016-0.00648.1210.0040.0040.0000.0000.0000.000
147A145LYS10.8910.95449.4390.0740.0740.0000.0000.0000.000
148A146ASP-1-0.756-0.81746.241-0.098-0.0980.0000.0000.0000.000
149A147ASP-1-0.816-0.92144.731-0.101-0.1010.0000.0000.0000.000
150A148VAL0-0.103-0.04845.3050.0010.0010.0000.0000.0000.000
151A149THR0-0.021-0.05148.3240.0030.0030.0000.0000.0000.000
152A150GLY00.0180.02850.7850.0030.0030.0000.0000.0000.000
153A151GLU-1-0.879-0.92851.239-0.072-0.0720.0000.0000.0000.000
154A152ASP-1-0.838-0.94350.739-0.077-0.0770.0000.0000.0000.000
155A153LEU0-0.099-0.02045.113-0.002-0.0020.0000.0000.0000.000
156A154VAL0-0.037-0.02145.8780.0030.0030.0000.0000.0000.000
157A155ILE0-0.017-0.01643.696-0.005-0.0050.0000.0000.0000.000
158A156ARG10.9480.97740.2310.1110.1110.0000.0000.0000.000
159A157GLU-1-0.824-0.92743.688-0.082-0.0820.0000.0000.0000.000
160A158ASP-1-0.919-0.97539.523-0.101-0.1010.0000.0000.0000.000
161A159ASP-1-0.873-0.94338.617-0.131-0.1310.0000.0000.0000.000
162A160LYS10.9110.95840.3780.0810.0810.0000.0000.0000.000
163A161GLU-1-0.830-0.91141.590-0.097-0.0970.0000.0000.0000.000
164A162GLU-1-0.928-0.95141.746-0.079-0.0790.0000.0000.0000.000
165A163THR00.0150.01640.2330.0010.0010.0000.0000.0000.000
166A164VAL0-0.039-0.02636.211-0.004-0.0040.0000.0000.0000.000
167A165ARG10.9080.92837.4580.1040.1040.0000.0000.0000.000
168A166ALA0-0.0200.00238.626-0.001-0.0010.0000.0000.0000.000
169A167ARG10.8670.93834.1490.1230.1230.0000.0000.0000.000
170A168LEU0-0.009-0.01733.196-0.004-0.0040.0000.0000.0000.000
171A169ASN00.0590.03234.043-0.006-0.0060.0000.0000.0000.000
172A170VAL0-0.0040.03133.5310.0030.0030.0000.0000.0000.000
173A171TYR00.0440.02726.247-0.002-0.0020.0000.0000.0000.000
174A172HIS0-0.007-0.01230.373-0.003-0.0030.0000.0000.0000.000
175A173THR0-0.062-0.04831.4830.0040.0040.0000.0000.0000.000
176A174GLN0-0.070-0.03929.411-0.003-0.0030.0000.0000.0000.000
177A175THR0-0.002-0.02125.6440.0000.0000.0000.0000.0000.000
178A176ALA00.0430.03027.033-0.003-0.0030.0000.0000.0000.000
179A177PRO00.0340.01227.9830.0000.0000.0000.0000.0000.000
180A178LEU00.0140.01123.5160.0090.0090.0000.0000.0000.000
181A179ILE00.0000.00523.190-0.004-0.0040.0000.0000.0000.000
182A180GLU-1-0.950-0.97223.612-0.087-0.0870.0000.0000.0000.000
183A181TYR0-0.056-0.03720.1530.0060.0060.0000.0000.0000.000
184A182TYR00.047-0.00517.7350.0080.0080.0000.0000.0000.000
185A183GLY00.0350.03019.304-0.016-0.0160.0000.0000.0000.000
186A184LYS10.8850.93621.4240.0470.0470.0000.0000.0000.000
187A185GLU-1-0.922-0.97617.3360.0690.0690.0000.0000.0000.000
188A186ALA0-0.035-0.02216.4130.0110.0110.0000.0000.0000.000
189A187ALA0-0.0260.00417.292-0.009-0.0090.0000.0000.0000.000
190A188ALA0-0.080-0.03218.9890.0070.0070.0000.0000.0000.000
191A189GLY0-0.019-0.02315.0960.0460.0460.0000.0000.0000.000
192A190LYS10.8510.94813.344-0.090-0.0900.0000.0000.0000.000
193A191THR0-0.009-0.00712.5460.0180.0180.0000.0000.0000.000
194A192GLN00.0120.01311.131-0.082-0.0820.0000.0000.0000.000
195A193TYR00.0030.01013.720-0.035-0.0350.0000.0000.0000.000
196A194LEU0-0.042-0.02013.263-0.009-0.0090.0000.0000.0000.000
197A195LYS10.9180.97117.7540.2400.2400.0000.0000.0000.000
198A196PHE0-0.014-0.00716.263-0.010-0.0100.0000.0000.0000.000
199A197ASP-1-0.790-0.88921.966-0.233-0.2330.0000.0000.0000.000
200A198GLY00.0160.00024.994-0.018-0.0180.0000.0000.0000.000
201A199THR0-0.120-0.07925.8700.0130.0130.0000.0000.0000.000
202A200LYS10.9320.98524.5100.3170.3170.0000.0000.0000.000
203A201GLN00.0700.04526.804-0.020-0.0200.0000.0000.0000.000
204A202VAL00.0930.03922.536-0.019-0.0190.0000.0000.0000.000
205A203SER0-0.0270.02922.376-0.040-0.0400.0000.0000.0000.000
206A204GLU-1-0.917-0.97122.006-0.312-0.3120.0000.0000.0000.000
207A205VAL0-0.018-0.00620.546-0.033-0.0330.0000.0000.0000.000
208A206SER0-0.037-0.09218.341-0.037-0.0370.0000.0000.0000.000
209A207ALA0-0.032-0.00317.203-0.081-0.0810.0000.0000.0000.000
210A208ASP-1-0.925-0.96516.685-0.524-0.5240.0000.0000.0000.000
211A209ILE0-0.028-0.01114.283-0.067-0.0670.0000.0000.0000.000
212A210ALA0-0.009-0.01312.610-0.147-0.1470.0000.0000.0000.000
213A211LYS10.8760.95111.8750.3750.3750.0000.0000.0000.000
214A212ALA0-0.005-0.00212.560-0.058-0.0580.0000.0000.0000.000
215A213LEU0-0.0600.0048.823-0.081-0.0810.0000.0000.0000.000
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