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: 4J6KN

Calculation Name: 1NKV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1NKV

Chain ID: A

ChEMBL ID:

UniProt ID: P39367

Base Structure: X-ray

Registration Date: 2023-09-23

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 245
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3051964.007324
FMO2-HF: Nuclear repulsion 2956266.293732
FMO2-HF: Total energy -95697.713592
FMO2-MP2: Total energy -95974.027845


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:4:PRO)


Summations of interaction energy for fragment #1(A:4:PRO)
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.
-4.991.132.534-3.051-5.6030.004
Interaction energy analysis for fragmet #1(A:4:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.047 / q_NPA : 0.014
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].
3A6ILE00.0310.0082.266-3.6380.1912.066-2.370-3.5250.007
4A7PHE00.0040.0132.663-1.1690.1040.402-0.417-1.258-0.002
5A8THR00.023-0.0014.090-0.0590.1700.002-0.053-0.1790.000
6A9ILE0-0.057-0.0176.7470.3460.3460.0000.0000.0000.000
7A10SER00.001-0.0216.6970.1350.1350.0000.0000.0000.000
8A11GLU-1-0.749-0.8558.127-0.927-0.9270.0000.0000.0000.000
9A12SER0-0.047-0.05110.143-0.015-0.0150.0000.0000.0000.000
10A13GLU-1-0.900-0.93312.189-0.338-0.3380.0000.0000.0000.000
11A14HIS0-0.099-0.03412.5520.0360.0360.0000.0000.0000.000
12A15ARG10.7960.87714.8050.2590.2590.0000.0000.0000.000
13A16ILE0-0.007-0.00816.206-0.003-0.0030.0000.0000.0000.000
14A17HIS10.8110.88810.2580.8440.8440.0000.0000.0000.000
15A18ASN00.030-0.00411.872-0.009-0.0090.0000.0000.0000.000
16A19PRO00.0140.01613.9490.0290.0290.0000.0000.0000.000
17A20PHE0-0.0420.00016.7740.0420.0420.0000.0000.0000.000
18A21THR00.046-0.01318.996-0.013-0.0130.0000.0000.0000.000
19A22GLU-1-0.795-0.87121.549-0.244-0.2440.0000.0000.0000.000
20A23GLU-1-0.859-0.92023.760-0.181-0.1810.0000.0000.0000.000
21A24LYS10.8000.91022.8260.1890.1890.0000.0000.0000.000
22A25TYR00.0830.03117.429-0.003-0.0030.0000.0000.0000.000
23A26ALA00.0070.02423.7040.0120.0120.0000.0000.0000.000
24A27THR0-0.074-0.05127.2040.0170.0170.0000.0000.0000.000
25A28LEU00.0030.01722.2690.0090.0090.0000.0000.0000.000
26A29GLY00.0700.02926.3500.0100.0100.0000.0000.0000.000
27A30ARG10.9370.96827.7590.1290.1290.0000.0000.0000.000
28A31VAL0-0.109-0.04628.8520.0100.0100.0000.0000.0000.000
29A32LEU00.0520.02626.4550.0070.0070.0000.0000.0000.000
30A33ARG10.7710.89630.4450.0950.0950.0000.0000.0000.000
31A34MET00.0290.03928.0200.0010.0010.0000.0000.0000.000
32A35LYS10.9450.97032.9940.0690.0690.0000.0000.0000.000
33A36PRO00.0280.02534.223-0.003-0.0030.0000.0000.0000.000
34A37GLY00.0280.00633.5770.0060.0060.0000.0000.0000.000
35A38THR0-0.089-0.05129.7870.0030.0030.0000.0000.0000.000
36A39ARG10.8200.88828.8280.0770.0770.0000.0000.0000.000
37A40ILE0-0.029-0.03523.3130.0030.0030.0000.0000.0000.000
38A41LEU00.0020.00121.0590.0030.0030.0000.0000.0000.000
39A42ASP-1-0.877-0.94517.555-0.315-0.3150.0000.0000.0000.000
40A43LEU0-0.011-0.01515.629-0.007-0.0070.0000.0000.0000.000
41A44GLY00.0440.01412.475-0.025-0.0250.0000.0000.0000.000
42A45SER0-0.023-0.00113.131-0.033-0.0330.0000.0000.0000.000
43A46GLY00.0520.03112.4060.0100.0100.0000.0000.0000.000
44A47SER0-0.067-0.04913.309-0.001-0.0010.0000.0000.0000.000
45A48GLY00.018-0.00616.2840.0500.0500.0000.0000.0000.000
46A49GLU-1-0.706-0.81618.372-0.229-0.2290.0000.0000.0000.000
47A50MET0-0.0170.01419.4920.0290.0290.0000.0000.0000.000
48A51LEU00.000-0.00420.9920.0240.0240.0000.0000.0000.000
49A52CYS0-0.022-0.00622.0320.0240.0240.0000.0000.0000.000
50A53THR00.001-0.01123.7470.0230.0230.0000.0000.0000.000
51A54TRP00.0440.00823.3550.0160.0160.0000.0000.0000.000
52A55ALA00.0140.01926.9940.0150.0150.0000.0000.0000.000
53A56ARG10.8090.85927.8650.1710.1710.0000.0000.0000.000
54A57ASP-1-0.826-0.86429.721-0.137-0.1370.0000.0000.0000.000
55A58HIS0-0.072-0.04929.2970.0020.0020.0000.0000.0000.000
56A59GLY0-0.0100.00532.2680.0070.0070.0000.0000.0000.000
57A60ILE0-0.065-0.01626.4320.0070.0070.0000.0000.0000.000
58A61THR00.016-0.00928.8850.0000.0000.0000.0000.0000.000
59A62GLY00.0530.02625.2750.0010.0010.0000.0000.0000.000
60A63THR0-0.058-0.03122.871-0.001-0.0010.0000.0000.0000.000
61A64GLY00.0500.01919.0390.0000.0000.0000.0000.0000.000
62A65ILE0-0.041-0.00415.187-0.004-0.0040.0000.0000.0000.000
63A66ASP-1-0.804-0.91710.937-0.841-0.8410.0000.0000.0000.000
64A67MET00.0950.0488.7140.0330.0330.0000.0000.0000.000
65A68SER0-0.0350.0108.9460.0470.0470.0000.0000.0000.000
66A69SER00.0280.01310.2720.0760.0760.0000.0000.0000.000
67A70LEU00.0120.00111.8430.0700.0700.0000.0000.0000.000
68A71PHE00.0240.0018.8270.0600.0600.0000.0000.0000.000
69A72THR00.0490.02513.9560.0910.0910.0000.0000.0000.000
70A73ALA0-0.050-0.02916.0850.0570.0570.0000.0000.0000.000
71A74GLN0-0.014-0.01914.8180.0090.0090.0000.0000.0000.000
72A75ALA00.0380.03817.8290.0280.0280.0000.0000.0000.000
73A76LYS10.8670.93819.5760.2300.2300.0000.0000.0000.000
74A77ARG10.9260.96718.8870.3040.3040.0000.0000.0000.000
75A78ARG10.7920.87021.5270.2520.2520.0000.0000.0000.000
76A79ALA00.040-0.00923.4490.0170.0170.0000.0000.0000.000
77A80GLU-1-0.910-0.92925.576-0.121-0.1210.0000.0000.0000.000
78A81GLU-1-0.917-0.93025.059-0.195-0.1950.0000.0000.0000.000
79A82LEU0-0.088-0.05126.0340.0110.0110.0000.0000.0000.000
80A83GLY0-0.0080.00829.3800.0090.0090.0000.0000.0000.000
81A84VAL0-0.039-0.03027.9400.0090.0090.0000.0000.0000.000
82A85SER0-0.047-0.05527.379-0.001-0.0010.0000.0000.0000.000
83A86GLU-1-0.975-0.97028.332-0.093-0.0930.0000.0000.0000.000
84A87ARG10.8470.92130.0980.1170.1170.0000.0000.0000.000
85A88VAL0-0.034-0.00924.383-0.001-0.0010.0000.0000.0000.000
86A89HIS00.0100.00224.273-0.007-0.0070.0000.0000.0000.000
87A90PHE00.0190.03319.032-0.007-0.0070.0000.0000.0000.000
88A91ILE0-0.045-0.02218.7840.0150.0150.0000.0000.0000.000
89A92HIS0-0.025-0.01112.0060.0090.0090.0000.0000.0000.000
90A93ASN0-0.031-0.02414.7650.0610.0610.0000.0000.0000.000
91A94ASP-1-0.756-0.90212.434-0.083-0.0830.0000.0000.0000.000
92A95ALA0-0.050-0.04413.2050.0070.0070.0000.0000.0000.000
93A96ALA00.0080.00612.6540.0040.0040.0000.0000.0000.000
94A97GLY00.0200.01314.4170.0210.0210.0000.0000.0000.000
95A98TYR0-0.069-0.02117.9270.0030.0030.0000.0000.0000.000
96A99VAL00.0480.01319.543-0.002-0.0020.0000.0000.0000.000
97A100ALA0-0.039-0.00723.1370.0010.0010.0000.0000.0000.000
98A101ASN00.0040.00225.3510.0130.0130.0000.0000.0000.000
99A102GLU-1-0.892-0.92828.577-0.066-0.0660.0000.0000.0000.000
100A103LYS10.9500.97228.6310.0380.0380.0000.0000.0000.000
101A104CYS0-0.057-0.03226.515-0.003-0.0030.0000.0000.0000.000
102A105ASP-1-0.810-0.89528.662-0.078-0.0780.0000.0000.0000.000
103A106VAL00.0280.00424.7770.0020.0020.0000.0000.0000.000
104A107ALA0-0.0130.01422.799-0.008-0.0080.0000.0000.0000.000
105A108ALA00.007-0.01620.2520.0050.0050.0000.0000.0000.000
106A109CYS00.0090.02714.610-0.010-0.0100.0000.0000.0000.000
107A110VAL0-0.006-0.00616.0090.0070.0070.0000.0000.0000.000
108A111GLY00.0270.02112.493-0.050-0.0500.0000.0000.0000.000
109A112ALA0-0.0360.0059.737-0.043-0.0430.0000.0000.0000.000
110A113THR00.051-0.02810.7630.0760.0760.0000.0000.0000.000
111A114TRP0-0.055-0.0223.063-0.753-0.1450.063-0.174-0.497-0.001
112A115ILE0-0.057-0.0239.2810.1010.1010.0000.0000.0000.000
113A116ALA00.0130.00810.8460.0750.0750.0000.0000.0000.000
114A117GLY0-0.015-0.00312.6540.0520.0520.0000.0000.0000.000
115A118GLY0-0.016-0.01012.7300.0060.0060.0000.0000.0000.000
116A119PHE00.0680.04414.385-0.042-0.0420.0000.0000.0000.000
117A120ALA00.0150.01317.0730.0030.0030.0000.0000.0000.000
118A121GLY00.0340.02717.6170.0090.0090.0000.0000.0000.000
119A122ALA0-0.018-0.02316.0600.0000.0000.0000.0000.0000.000
120A123GLU-1-0.890-0.92717.855-0.054-0.0540.0000.0000.0000.000
121A124GLU-1-0.867-0.93721.2300.0120.0120.0000.0000.0000.000
122A125LEU0-0.0320.00516.4740.0000.0000.0000.0000.0000.000
123A126LEU00.0160.01618.8510.0000.0000.0000.0000.0000.000
124A127ALA00.0540.03222.0220.0030.0030.0000.0000.0000.000
125A128GLN0-0.101-0.05723.3670.0130.0130.0000.0000.0000.000
126A129SER0-0.123-0.07024.044-0.001-0.0010.0000.0000.0000.000
127A130LEU0-0.0090.02526.063-0.008-0.0080.0000.0000.0000.000
128A131LYS10.7880.87327.8890.0810.0810.0000.0000.0000.000
129A132PRO00.0310.01231.311-0.002-0.0020.0000.0000.0000.000
130A133GLY00.0030.00132.958-0.001-0.0010.0000.0000.0000.000
131A134GLY0-0.0040.00930.191-0.002-0.0020.0000.0000.0000.000
132A135ILE00.000-0.01326.8610.0000.0000.0000.0000.0000.000
133A136MET00.0000.01022.891-0.007-0.0070.0000.0000.0000.000
134A137LEU0-0.020-0.00821.2340.0000.0000.0000.0000.0000.000
135A138ILE00.0490.01717.977-0.010-0.0100.0000.0000.0000.000
136A139GLY0-0.031-0.01216.7480.0100.0100.0000.0000.0000.000
137A140GLU-1-0.841-0.93115.140-0.246-0.2460.0000.0000.0000.000
138A141PRO0-0.055-0.02512.8770.0120.0120.0000.0000.0000.000
139A142TYR00.0160.00516.1170.0310.0310.0000.0000.0000.000
140A143TRP0-0.015-0.04916.174-0.023-0.0230.0000.0000.0000.000
141A144ARG10.7880.88620.2440.1400.1400.0000.0000.0000.000
142A145GLN0-0.065-0.06121.8050.0100.0100.0000.0000.0000.000
143A146LEU0-0.0100.01121.699-0.003-0.0030.0000.0000.0000.000
144A147PRO00.0070.01019.2310.0080.0080.0000.0000.0000.000
145A148ALA0-0.003-0.00222.4920.0060.0060.0000.0000.0000.000
146A149THR0-0.003-0.01523.1330.0050.0050.0000.0000.0000.000
147A150GLU-1-0.670-0.78719.376-0.009-0.0090.0000.0000.0000.000
148A151GLU-1-0.906-0.94018.3350.0280.0280.0000.0000.0000.000
149A152ILE0-0.003-0.00318.164-0.009-0.0090.0000.0000.0000.000
150A153ALA00.0310.01717.061-0.018-0.0180.0000.0000.0000.000
151A154GLN00.008-0.00314.465-0.004-0.0040.0000.0000.0000.000
152A155ALA0-0.116-0.04213.868-0.002-0.0020.0000.0000.0000.000
153A156CYS0-0.127-0.06814.289-0.016-0.0160.0000.0000.0000.000
154A157GLY0-0.049-0.02710.226-0.053-0.0530.0000.0000.0000.000
155A158VAL0-0.051-0.0029.251-0.074-0.0740.0000.0000.0000.000
156A159SER0-0.032-0.03611.5990.0490.0490.0000.0000.0000.000
157A160SER0-0.025-0.02713.3430.0150.0150.0000.0000.0000.000
158A161THR0-0.066-0.08116.375-0.027-0.0270.0000.0000.0000.000
159A162SER0-0.061-0.02718.894-0.010-0.0100.0000.0000.0000.000
160A163ASP-1-0.802-0.88413.020-0.019-0.0190.0000.0000.0000.000
161A164PHE00.0030.00411.632-0.025-0.0250.0000.0000.0000.000
162A165LEU00.0700.04217.5750.0200.0200.0000.0000.0000.000
163A166THR00.0060.01020.858-0.015-0.0150.0000.0000.0000.000
164A167LEU00.0470.02823.5660.0000.0000.0000.0000.0000.000
165A168PRO00.017-0.01824.9770.0010.0010.0000.0000.0000.000
166A169GLY00.002-0.00225.4980.0060.0060.0000.0000.0000.000
167A170LEU0-0.0030.00719.9700.0050.0050.0000.0000.0000.000
168A171VAL0-0.021-0.01923.5690.0010.0010.0000.0000.0000.000
169A172GLY0-0.0010.00226.4420.0040.0040.0000.0000.0000.000
170A173ALA00.0290.02123.7390.0060.0060.0000.0000.0000.000
171A174PHE00.008-0.02020.6940.0030.0030.0000.0000.0000.000
172A175ASP-1-0.842-0.89525.845-0.041-0.0410.0000.0000.0000.000
173A176ASP-1-0.935-0.95027.819-0.026-0.0260.0000.0000.0000.000
174A177LEU0-0.074-0.03723.5560.0060.0060.0000.0000.0000.000
175A178GLY0-0.066-0.02728.1360.0000.0000.0000.0000.0000.000
176A179TYR0-0.079-0.07226.655-0.005-0.0050.0000.0000.0000.000
177A180ASP-1-0.833-0.89129.700-0.051-0.0510.0000.0000.0000.000
178A181VAL0-0.010-0.01527.094-0.005-0.0050.0000.0000.0000.000
179A182VAL0-0.042-0.02029.3180.0020.0020.0000.0000.0000.000
180A183GLU-1-0.853-0.94528.437-0.103-0.1030.0000.0000.0000.000
181A184MET0-0.0240.00625.574-0.006-0.0060.0000.0000.0000.000
182A185VAL0-0.034-0.00124.3530.0040.0040.0000.0000.0000.000
183A186LEU0-0.002-0.00622.815-0.019-0.0190.0000.0000.0000.000
184A187ALA0-0.018-0.02719.9350.0040.0040.0000.0000.0000.000
185A188ASP-1-0.804-0.91521.918-0.163-0.1630.0000.0000.0000.000
186A189GLN0-0.043-0.04221.191-0.012-0.0120.0000.0000.0000.000
187A190GLU-1-0.826-0.88121.015-0.199-0.1990.0000.0000.0000.000
188A191GLY00.0560.00920.576-0.011-0.0110.0000.0000.0000.000
189A192TRP00.0040.00013.146-0.047-0.0470.0000.0000.0000.000
190A193ASP-1-0.821-0.84916.822-0.221-0.2210.0000.0000.0000.000
191A194ARG10.8170.89117.7950.1990.1990.0000.0000.0000.000
192A195TYR0-0.013-0.0119.1960.0030.0030.0000.0000.0000.000
193A196GLU-1-0.811-0.91311.294-0.574-0.5740.0000.0000.0000.000
194A197ALA0-0.017-0.02013.989-0.001-0.0010.0000.0000.0000.000
195A198ALA0-0.0100.01014.8120.0110.0110.0000.0000.0000.000
196A199LYS10.8510.9228.4360.7930.7930.0000.0000.0000.000
197A200TRP0-0.018-0.01012.3310.0480.0480.0000.0000.0000.000
198A201LEU0-0.036-0.01214.6880.0390.0390.0000.0000.0000.000
199A202THR00.0080.00812.5960.0550.0550.0000.0000.0000.000
200A203MET00.0180.0209.6010.0070.0070.0000.0000.0000.000
201A204ARG10.7910.87112.7570.1540.1540.0000.0000.0000.000
202A205ARG10.9000.93816.2140.2030.2030.0000.0000.0000.000
203A206TRP00.0440.02311.2720.0060.0060.0000.0000.0000.000
204A207LEU0-0.002-0.00512.9670.0260.0260.0000.0000.0000.000
205A208GLU-1-0.891-0.90915.638-0.075-0.0750.0000.0000.0000.000
206A209ALA0-0.042-0.01617.7610.0120.0120.0000.0000.0000.000
207A210ASN0-0.043-0.02315.069-0.026-0.0260.0000.0000.0000.000
208A211PRO0-0.034-0.00715.8160.0050.0050.0000.0000.0000.000
209A212ASP-1-0.910-0.96017.692-0.002-0.0020.0000.0000.0000.000
210A213ASP-1-0.790-0.85311.656-0.128-0.1280.0000.0000.0000.000
211A214ASP-1-0.869-0.94511.7200.1380.1380.0000.0000.0000.000
212A215PHE0-0.078-0.0383.843-0.197-0.0160.001-0.037-0.1440.000
213A216ALA00.0130.0089.489-0.030-0.0300.0000.0000.0000.000
214A217ALA0-0.015-0.00912.100-0.021-0.0210.0000.0000.0000.000
215A218GLU-1-0.828-0.9296.9710.4370.4370.0000.0000.0000.000
216A219VAL00.0020.0037.998-0.060-0.0600.0000.0000.0000.000
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