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: YV942

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 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 -2284272.926038
FMO2-HF: Nuclear repulsion 2202129.188388
FMO2-HF: Total energy -82143.73765
FMO2-MP2: Total energy -82384.066717


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.
-2.7660.442-0.015-1.676-1.5170.006
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 : 0.008 / q_NPA : -0.003
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].
3A1MET0-0.024-0.0343.803-1.3281.880-0.015-1.676-1.5170.006
4A2ARG10.8810.9606.256-2.535-2.5350.0000.0000.0000.000
5A3ILE00.000-0.0089.602-0.010-0.0100.0000.0000.0000.000
6A4ILE00.0050.02812.5880.0390.0390.0000.0000.0000.000
7A5LEU0-0.022-0.01216.159-0.057-0.0570.0000.0000.0000.000
8A6LEU00.0230.01318.7050.0410.0410.0000.0000.0000.000
9A7GLY00.0730.01221.998-0.040-0.0400.0000.0000.0000.000
10A8ALA00.0060.02124.9410.0160.0160.0000.0000.0000.000
11A9PRO0-0.025-0.01728.534-0.015-0.0150.0000.0000.0000.000
12A10GLY00.0440.00029.8320.0080.0080.0000.0000.0000.000
13A11ALA0-0.020-0.00427.511-0.004-0.0040.0000.0000.0000.000
14A12GLY0-0.026-0.01427.450-0.013-0.0130.0000.0000.0000.000
15A13LYS10.9100.95921.9980.1910.1910.0000.0000.0000.000
16A14GLY0-0.007-0.00521.916-0.034-0.0340.0000.0000.0000.000
17A15THR00.0240.00121.705-0.021-0.0210.0000.0000.0000.000
18A16GLN00.039-0.00218.735-0.077-0.0770.0000.0000.0000.000
19A17ALA0-0.0320.00717.313-0.068-0.0680.0000.0000.0000.000
20A18GLN0-0.024-0.01116.740-0.030-0.0300.0000.0000.0000.000
21A19PHE00.0480.03215.629-0.061-0.0610.0000.0000.0000.000
22A20ILE0-0.001-0.01011.910-0.104-0.1040.0000.0000.0000.000
23A21MET0-0.051-0.00812.620-0.148-0.1480.0000.0000.0000.000
24A22GLU-1-0.913-0.94813.802-0.651-0.6510.0000.0000.0000.000
25A23LYS10.8850.95810.7231.4101.4100.0000.0000.0000.000
26A24PHE0-0.016-0.0377.056-0.123-0.1230.0000.0000.0000.000
27A25GLY0-0.0090.0108.743-0.409-0.4090.0000.0000.0000.000
28A26ILE0-0.067-0.0078.616-0.049-0.0490.0000.0000.0000.000
29A27PRO00.0300.01911.6780.0880.0880.0000.0000.0000.000
30A28GLN00.013-0.00715.137-0.004-0.0040.0000.0000.0000.000
31A29ILE00.0040.00215.8950.0360.0360.0000.0000.0000.000
32A30SER00.0180.01919.5410.0230.0230.0000.0000.0000.000
33A31THR00.0700.02922.4370.0170.0170.0000.0000.0000.000
34A32GLY00.0140.00724.3950.0140.0140.0000.0000.0000.000
35A33ASP-1-0.815-0.90324.982-0.132-0.1320.0000.0000.0000.000
36A34MET0-0.054-0.01422.3240.0060.0060.0000.0000.0000.000
37A35LEU00.0250.01524.8070.0110.0110.0000.0000.0000.000
38A36ARG10.8540.90827.9770.1020.1020.0000.0000.0000.000
39A37ALA0-0.023-0.01926.5840.0050.0050.0000.0000.0000.000
40A38ALA00.0530.03727.2260.0040.0040.0000.0000.0000.000
41A39ILE0-0.011-0.00528.9810.0060.0060.0000.0000.0000.000
42A40LYS10.8970.94232.1940.0650.0650.0000.0000.0000.000
43A41ALA0-0.0080.01629.627-0.002-0.0020.0000.0000.0000.000
44A42GLY0-0.0040.01631.6130.0050.0050.0000.0000.0000.000
45A43THR00.0570.02527.3150.0080.0080.0000.0000.0000.000
46A44GLU-1-0.849-0.91729.6820.0590.0590.0000.0000.0000.000
47A45LEU00.0650.02425.6290.0000.0000.0000.0000.0000.000
48A46GLY00.0120.00529.769-0.005-0.0050.0000.0000.0000.000
49A47LYS10.8220.89931.411-0.035-0.0350.0000.0000.0000.000
50A48GLN0-0.007-0.02031.8790.0010.0010.0000.0000.0000.000
51A49ALA00.0370.02831.367-0.001-0.0010.0000.0000.0000.000
52A50LYS10.7830.86933.4980.0000.0000.0000.0000.0000.000
53A51ALA0-0.016-0.01136.314-0.003-0.0030.0000.0000.0000.000
54A52VAL0-0.0070.00535.355-0.001-0.0010.0000.0000.0000.000
55A53ILE0-0.010-0.02833.989-0.004-0.0040.0000.0000.0000.000
56A54ASP-1-0.828-0.86538.281-0.003-0.0030.0000.0000.0000.000
57A55ALA0-0.055-0.02441.263-0.002-0.0020.0000.0000.0000.000
58A56GLY0-0.025-0.00841.4340.0010.0010.0000.0000.0000.000
59A57GLN0-0.071-0.03039.3250.0050.0050.0000.0000.0000.000
60A58LEU00.003-0.01435.502-0.004-0.0040.0000.0000.0000.000
61A59VAL0-0.044-0.02230.6100.0050.0050.0000.0000.0000.000
62A60SER0-0.016-0.01831.244-0.004-0.0040.0000.0000.0000.000
63A61ASP-1-0.773-0.90126.4910.0770.0770.0000.0000.0000.000
64A62ASP-1-0.887-0.91526.1750.1210.1210.0000.0000.0000.000
65A63ILE00.0160.00526.2920.0060.0060.0000.0000.0000.000
66A64ILE0-0.049-0.02323.793-0.007-0.0070.0000.0000.0000.000
67A65LEU00.021-0.01120.651-0.007-0.0070.0000.0000.0000.000
68A66GLY00.0420.03121.0110.0300.0300.0000.0000.0000.000
69A67LEU00.0550.02322.1260.0020.0020.0000.0000.0000.000
70A68ILE00.0350.01817.493-0.020-0.0200.0000.0000.0000.000
71A69LYS10.9560.96817.903-0.280-0.2800.0000.0000.0000.000
72A70GLU-1-0.964-0.98618.2910.0770.0770.0000.0000.0000.000
73A71ARG10.7270.83616.8390.1840.1840.0000.0000.0000.000
74A72ILE0-0.022-0.04113.536-0.064-0.0640.0000.0000.0000.000
75A73ALA0-0.0220.00914.0060.0210.0210.0000.0000.0000.000
76A74GLN0-0.060-0.02016.3070.0030.0030.0000.0000.0000.000
77A75ALA00.0440.00413.626-0.001-0.0010.0000.0000.0000.000
78A76ASP-1-0.794-0.86812.350-0.419-0.4190.0000.0000.0000.000
79A77CYS0-0.061-0.02011.824-0.144-0.1440.0000.0000.0000.000
80A78GLU-1-0.943-0.9406.714-1.059-1.0590.0000.0000.0000.000
81A79LYS10.8810.9345.2592.5802.5800.0000.0000.0000.000
82A80GLY0-0.0170.0026.348-0.134-0.1340.0000.0000.0000.000
83A81PHE00.015-0.0348.7300.0350.0350.0000.0000.0000.000
84A82LEU00.0340.02211.6930.0060.0060.0000.0000.0000.000
85A83LEU0-0.040-0.02814.3580.0400.0400.0000.0000.0000.000
86A84ASP-1-0.846-0.92217.420-0.218-0.2180.0000.0000.0000.000
87A85GLY0-0.049-0.02620.4200.0280.0280.0000.0000.0000.000
88A86PHE0-0.039-0.02520.0760.0190.0190.0000.0000.0000.000
89A87PRO00.0520.02519.402-0.008-0.0080.0000.0000.0000.000
90A88ARG10.9090.94022.3050.0020.0020.0000.0000.0000.000
91A89THR0-0.010-0.00225.4930.0000.0000.0000.0000.0000.000
92A90ILE00.0610.02624.7400.0080.0080.0000.0000.0000.000
93A91PRO00.0680.03524.3760.0190.0190.0000.0000.0000.000
94A92GLN0-0.021-0.01823.3220.0070.0070.0000.0000.0000.000
95A93ALA0-0.015-0.00620.4500.0220.0220.0000.0000.0000.000
96A94ASP-1-0.848-0.91619.9310.2300.2300.0000.0000.0000.000
97A95GLY00.0450.01621.0190.0420.0420.0000.0000.0000.000
98A96LEU0-0.055-0.02816.8680.0290.0290.0000.0000.0000.000
99A97LYS10.9010.95916.348-0.251-0.2510.0000.0000.0000.000
100A98GLU-1-0.976-0.97917.2970.3600.3600.0000.0000.0000.000
101A99MET0-0.099-0.02918.284-0.019-0.0190.0000.0000.0000.000
102A100GLY0-0.036-0.01715.0500.0180.0180.0000.0000.0000.000
103A101ILE0-0.073-0.03212.8790.1810.1810.0000.0000.0000.000
104A102ASN0-0.021-0.02511.246-0.250-0.2500.0000.0000.0000.000
105A103VAL0-0.024-0.00510.2440.2570.2570.0000.0000.0000.000
106A104ASP-1-0.771-0.8616.6701.1591.1590.0000.0000.0000.000
107A105TYR00.014-0.0047.013-0.277-0.2770.0000.0000.0000.000
108A106VAL0-0.008-0.01011.5260.0650.0650.0000.0000.0000.000
109A107ILE00.0230.01713.550-0.028-0.0280.0000.0000.0000.000
110A108GLU-1-0.805-0.87917.033-0.136-0.1360.0000.0000.0000.000
111A109PHE0-0.015-0.01420.851-0.018-0.0180.0000.0000.0000.000
112A110ASP-1-0.857-0.92523.044-0.145-0.1450.0000.0000.0000.000
113A111VAL0-0.027-0.01426.323-0.014-0.0140.0000.0000.0000.000
114A112ALA00.0550.02329.5290.0110.0110.0000.0000.0000.000
115A113ASP-1-0.759-0.87132.743-0.111-0.1110.0000.0000.0000.000
116A114ASP-1-0.862-0.93434.889-0.105-0.1050.0000.0000.0000.000
117A115VAL00.0050.00533.0970.0000.0000.0000.0000.0000.000
118A116ILE0-0.017-0.00230.938-0.002-0.0020.0000.0000.0000.000
119A117VAL00.0190.00634.7450.0010.0010.0000.0000.0000.000
120A118GLU-1-0.922-0.95937.715-0.133-0.1330.0000.0000.0000.000
121A119ARG10.9270.97830.2820.1940.1940.0000.0000.0000.000
122A120MET0-0.054-0.01433.295-0.001-0.0010.0000.0000.0000.000
123A121ALA00.0680.04937.7470.0040.0040.0000.0000.0000.000
124A122GLY00.0050.00439.8060.0060.0060.0000.0000.0000.000
125A123ARG10.8430.91733.4830.1300.1300.0000.0000.0000.000
126A124ARG10.8090.89140.2530.1060.1060.0000.0000.0000.000
127A125ALA00.009-0.00341.556-0.006-0.0060.0000.0000.0000.000
128A126HIS10.8640.92143.6100.0810.0810.0000.0000.0000.000
129A127LEU00.0350.00045.346-0.002-0.0020.0000.0000.0000.000
130A128PRO0-0.0020.00846.7760.0000.0000.0000.0000.0000.000
131A129SER0-0.006-0.00144.5540.0010.0010.0000.0000.0000.000
132A130GLY0-0.0220.00242.318-0.003-0.0030.0000.0000.0000.000
133A131ARG10.8210.90640.7230.0850.0850.0000.0000.0000.000
134A132THR0-0.009-0.01537.7870.0040.0040.0000.0000.0000.000
135A133TYR00.003-0.03839.869-0.003-0.0030.0000.0000.0000.000
136A134HIS0-0.0060.01537.3980.0010.0010.0000.0000.0000.000
137A135VAL0-0.009-0.00239.467-0.002-0.0020.0000.0000.0000.000
138A136VAL0-0.0050.00437.6170.0010.0010.0000.0000.0000.000
139A137TYR0-0.020-0.03034.210-0.003-0.0030.0000.0000.0000.000
140A138ASN0-0.062-0.03435.951-0.002-0.0020.0000.0000.0000.000
141A139PRO00.0410.05238.2220.0050.0050.0000.0000.0000.000
142A140PRO00.0200.01641.987-0.003-0.0030.0000.0000.0000.000
143A141LYS10.7650.85242.7460.1200.1200.0000.0000.0000.000
144A142VAL00.0080.00046.7730.0030.0030.0000.0000.0000.000
145A143GLU-1-0.899-0.94647.706-0.094-0.0940.0000.0000.0000.000
146A144GLY0-0.012-0.00648.2530.0040.0040.0000.0000.0000.000
147A145LYS10.8500.91249.5420.0720.0720.0000.0000.0000.000
148A146ASP-1-0.726-0.82046.299-0.094-0.0940.0000.0000.0000.000
149A147ASP-1-0.777-0.88544.787-0.105-0.1050.0000.0000.0000.000
150A148VAL0-0.093-0.04245.2960.0000.0000.0000.0000.0000.000
151A149THR0-0.038-0.04848.4020.0030.0030.0000.0000.0000.000
152A150GLY00.0090.02050.8870.0030.0030.0000.0000.0000.000
153A151GLU-1-0.855-0.91251.339-0.065-0.0650.0000.0000.0000.000
154A152ASP-1-0.825-0.90350.883-0.071-0.0710.0000.0000.0000.000
155A153LEU0-0.080-0.02145.388-0.001-0.0010.0000.0000.0000.000
156A154VAL0-0.022-0.01446.0960.0030.0030.0000.0000.0000.000
157A155ILE00.006-0.00643.841-0.005-0.0050.0000.0000.0000.000
158A156ARG10.9580.98240.3350.0930.0930.0000.0000.0000.000
159A157GLU-1-0.721-0.85443.982-0.066-0.0660.0000.0000.0000.000
160A158ASP-1-0.914-0.95239.855-0.076-0.0760.0000.0000.0000.000
161A159ASP-1-0.827-0.91638.530-0.112-0.1120.0000.0000.0000.000
162A160LYS10.8030.89440.6790.0640.0640.0000.0000.0000.000
163A161GLU-1-0.804-0.88941.910-0.083-0.0830.0000.0000.0000.000
164A162GLU-1-0.921-0.94642.101-0.055-0.0550.0000.0000.0000.000
165A163THR0-0.005-0.01240.9380.0030.0030.0000.0000.0000.000
166A164VAL0-0.053-0.02636.591-0.001-0.0010.0000.0000.0000.000
167A165ARG10.8410.87037.7950.0880.0880.0000.0000.0000.000
168A166ALA0-0.0310.00038.6910.0010.0010.0000.0000.0000.000
169A167ARG10.8380.90634.5750.0910.0910.0000.0000.0000.000
170A168LEU0-0.011-0.00933.1000.0010.0010.0000.0000.0000.000
171A169ASN00.0350.02333.944-0.002-0.0020.0000.0000.0000.000
172A170VAL0-0.0100.01633.8490.0060.0060.0000.0000.0000.000
173A171TYR00.0460.03226.2710.0040.0040.0000.0000.0000.000
174A172HIS00.0120.00530.0770.0070.0070.0000.0000.0000.000
175A173THR0-0.053-0.03830.8610.0070.0070.0000.0000.0000.000
176A174GLN0-0.071-0.03728.7300.0020.0020.0000.0000.0000.000
177A175THR0-0.014-0.04125.0500.0080.0080.0000.0000.0000.000
178A176ALA00.0490.03826.2230.0050.0050.0000.0000.0000.000
179A177PRO00.0250.00427.0470.0020.0020.0000.0000.0000.000
180A178LEU00.0150.01722.3340.0160.0160.0000.0000.0000.000
181A179ILE0-0.0090.00622.2410.0060.0060.0000.0000.0000.000
182A180GLU-1-0.869-0.92222.717-0.011-0.0110.0000.0000.0000.000
183A181TYR0-0.093-0.07619.4170.0150.0150.0000.0000.0000.000
184A182TYR00.042-0.01216.8400.0070.0070.0000.0000.0000.000
185A183GLY00.0430.03618.460-0.011-0.0110.0000.0000.0000.000
186A184LYS10.8280.90020.670-0.028-0.0280.0000.0000.0000.000
187A185GLU-1-0.866-0.93016.5250.2670.2670.0000.0000.0000.000
188A186ALA0-0.030-0.01915.6880.0140.0140.0000.0000.0000.000
189A187ALA0-0.0270.00616.668-0.021-0.0210.0000.0000.0000.000
190A188ALA0-0.079-0.03318.442-0.004-0.0040.0000.0000.0000.000
191A189GLY0-0.012-0.01914.5470.0550.0550.0000.0000.0000.000
192A190LYS10.8230.91212.782-0.220-0.2200.0000.0000.0000.000
193A191THR0-0.024-0.01811.7130.0570.0570.0000.0000.0000.000
194A192GLN00.0190.0189.766-0.090-0.0900.0000.0000.0000.000
195A193TYR0-0.020-0.03512.931-0.013-0.0130.0000.0000.0000.000
196A194LEU0-0.045-0.02112.986-0.035-0.0350.0000.0000.0000.000
197A195LYS10.7990.87817.2790.1950.1950.0000.0000.0000.000
198A196PHE0-0.015-0.01115.897-0.024-0.0240.0000.0000.0000.000
199A197ASP-1-0.810-0.88421.847-0.230-0.2300.0000.0000.0000.000
200A198GLY00.012-0.00824.952-0.023-0.0230.0000.0000.0000.000
201A199THR0-0.132-0.09725.9290.0120.0120.0000.0000.0000.000
202A200LYS10.9060.97023.2020.3680.3680.0000.0000.0000.000
203A201GLN00.0410.04326.772-0.023-0.0230.0000.0000.0000.000
204A202VAL00.0800.02922.838-0.024-0.0240.0000.0000.0000.000
205A203SER0-0.024-0.01522.388-0.045-0.0450.0000.0000.0000.000
206A204GLU-1-0.880-0.94721.949-0.355-0.3550.0000.0000.0000.000
207A205VAL0-0.036-0.01520.489-0.040-0.0400.0000.0000.0000.000
208A206SER00.013-0.02518.377-0.043-0.0430.0000.0000.0000.000
209A207ALA0-0.041-0.00617.190-0.096-0.0960.0000.0000.0000.000
210A208ASP-1-0.893-0.95016.642-0.565-0.5650.0000.0000.0000.000
211A209ILE0-0.0150.00014.429-0.062-0.0620.0000.0000.0000.000
212A210ALA0-0.002-0.01112.559-0.141-0.1410.0000.0000.0000.000
213A211LYS10.8770.95111.8380.4170.4170.0000.0000.0000.000
214A212ALA00.0020.00312.519-0.072-0.0720.0000.0000.0000.000
215A213LEU0-0.0590.0048.868-0.080-0.0800.0000.0000.0000.000
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