FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: ZYJKN

Calculation Name: 1VJN-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 1VJN

Chain ID: A

ChEMBL ID:
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UniProt ID: Q9WY50

Base Structure: X-ray

Registration Date: 2023-06-20

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 202
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2393986.3176
FMO2-HF: Nuclear repulsion 2314951.695507
FMO2-HF: Total energy -79034.622093
FMO2-MP2: Total energy -79267.029903


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:0:HIS)


Summations of interaction energy for fragment #1(A:0:HIS)
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.
-37.737-31.3221.526-11.603-16.339-0.083
Interaction energy analysis for fragmet #1(A:0:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.065 / q_NPA : -0.041
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].
3A2LYS10.8180.9043.759-2.7360.8430.066-1.646-1.9980.007
4A3ILE00.0010.0125.4211.1471.1470.0000.0000.0000.000
5A4THR0-0.036-0.0368.716-0.418-0.4180.0000.0000.0000.000
6A5TRP0-0.0300.00711.1470.2470.2470.0000.0000.0000.000
7A6PHE00.030-0.00813.656-0.022-0.0220.0000.0000.0000.000
8A7GLY00.0530.01817.8650.0840.0840.0000.0000.0000.000
9A8HIS10.7890.88420.4340.4160.4160.0000.0000.0000.000
10A9ALA00.0780.04420.827-0.026-0.0260.0000.0000.0000.000
11A10CYS0-0.0570.01218.723-0.011-0.0110.0000.0000.0000.000
12A11PHE00.032-0.01013.582-0.089-0.0890.0000.0000.0000.000
13A12ALA00.0070.01411.7000.1290.1290.0000.0000.0000.000
14A13LEU0-0.026-0.0199.987-0.294-0.2940.0000.0000.0000.000
15A14GLU-1-0.845-0.9095.673-1.072-1.0720.0000.0000.0000.000
16A15MET00.0330.0046.104-0.059-0.0590.0000.0000.0000.000
17A16GLU-1-0.835-0.9246.0370.6920.6920.0000.0000.0000.000
18A17GLY0-0.042-0.0067.0750.1010.1010.0000.0000.0000.000
19A18LYS10.7010.8428.652-0.844-0.8440.0000.0000.0000.000
20A19THR00.0490.0189.8460.0360.0360.0000.0000.0000.000
21A20ILE0-0.0050.00411.7360.0490.0490.0000.0000.0000.000
22A21VAL00.005-0.01013.608-0.132-0.1320.0000.0000.0000.000
23A22THR00.0360.01616.2740.0400.0400.0000.0000.0000.000
24A23ASP-1-0.800-0.87818.712-0.379-0.3790.0000.0000.0000.000
25A24PRO00.007-0.00220.686-0.033-0.0330.0000.0000.0000.000
26A25PHE0-0.043-0.02720.8330.0240.0240.0000.0000.0000.000
27A26ASP-1-0.790-0.90724.381-0.250-0.2500.0000.0000.0000.000
28A27GLU-1-0.824-0.87327.055-0.347-0.3470.0000.0000.0000.000
29A28SER0-0.081-0.06828.8070.0190.0190.0000.0000.0000.000
30A29VAL0-0.023-0.02030.498-0.004-0.0040.0000.0000.0000.000
31A30GLY0-0.010-0.00328.5820.0080.0080.0000.0000.0000.000
32A31TYR0-0.045-0.01922.360-0.032-0.0320.0000.0000.0000.000
33A32PRO0-0.015-0.00421.0020.0220.0220.0000.0000.0000.000
34A33ILE00.0450.02121.303-0.036-0.0360.0000.0000.0000.000
35A34PRO00.0310.01217.612-0.035-0.0350.0000.0000.0000.000
36A35ASN0-0.0380.00417.7030.1090.1090.0000.0000.0000.000
37A36VAL00.0040.00313.281-0.038-0.0380.0000.0000.0000.000
38A37THR0-0.031-0.02014.6270.0360.0360.0000.0000.0000.000
39A38ALA0-0.011-0.00714.039-0.008-0.0080.0000.0000.0000.000
40A39ASP-1-0.754-0.85914.0570.3330.3330.0000.0000.0000.000
41A40VAL0-0.031-0.02116.5770.0120.0120.0000.0000.0000.000
42A41VAL0-0.0090.00617.426-0.053-0.0530.0000.0000.0000.000
43A42THR0-0.015-0.00618.9200.0260.0260.0000.0000.0000.000
44A43GLU-1-0.818-0.90721.379-0.269-0.2690.0000.0000.0000.000
45A44SER0-0.034-0.04124.0100.0380.0380.0000.0000.0000.000
46A45HIS10.8580.92725.3460.2810.2810.0000.0000.0000.000
47A46GLN00.0280.01328.495-0.001-0.0010.0000.0000.0000.000
48A47HIS0-0.033-0.03926.6570.0000.0000.0000.0000.0000.000
49A48PHE0-0.010-0.00527.9450.0010.0010.0000.0000.0000.000
50A49ASP-1-0.808-0.90231.906-0.156-0.1560.0000.0000.0000.000
51A50HIS0-0.097-0.05132.8910.0110.0110.0000.0000.0000.000
52A51ASN0-0.040-0.02727.792-0.013-0.0130.0000.0000.0000.000
53A52ALA00.0710.04725.9220.0000.0000.0000.0000.0000.000
54A53HIS00.015-0.00423.093-0.004-0.0040.0000.0000.0000.000
55A54HIS10.7950.89323.9260.2020.2020.0000.0000.0000.000
56A55LEU0-0.010-0.00423.7510.0140.0140.0000.0000.0000.000
57A56VAL0-0.0350.00518.333-0.024-0.0240.0000.0000.0000.000
58A57LYS10.9140.95218.6750.2920.2920.0000.0000.0000.000
59A58GLY00.0370.01318.774-0.003-0.0030.0000.0000.0000.000
60A59ASN0-0.043-0.02319.867-0.036-0.0360.0000.0000.0000.000
61A60PHE0-0.0050.00719.0710.0240.0240.0000.0000.0000.000
62A61ARG10.8970.94120.5810.0130.0130.0000.0000.0000.000
63A62VAL00.0540.02821.578-0.023-0.0230.0000.0000.0000.000
64A63ILE0-0.055-0.02120.2820.0310.0310.0000.0000.0000.000
65A64ASP-1-0.733-0.83024.058-0.136-0.1360.0000.0000.0000.000
66A65ARG10.8160.86825.9580.0900.0900.0000.0000.0000.000
67A66PRO00.0400.03925.288-0.005-0.0050.0000.0000.0000.000
68A67GLY00.0160.01924.9910.0170.0170.0000.0000.0000.000
69A68ALA0-0.015-0.01221.614-0.019-0.0190.0000.0000.0000.000
70A69TYR0-0.043-0.03620.1820.0240.0240.0000.0000.0000.000
71A70THR0-0.030-0.02716.0880.0090.0090.0000.0000.0000.000
72A71VAL0-0.031-0.00916.4200.0050.0050.0000.0000.0000.000
73A72ASN0-0.074-0.04715.196-0.013-0.0130.0000.0000.0000.000
74A73GLY00.0600.03612.7150.0970.0970.0000.0000.0000.000
75A74VAL00.0270.03010.274-0.010-0.0100.0000.0000.0000.000
76A75LYS10.8530.92412.601-0.096-0.0960.0000.0000.0000.000
77A76ILE0-0.005-0.01314.289-0.069-0.0690.0000.0000.0000.000
78A77LYS10.8080.90316.9310.1170.1170.0000.0000.0000.000
79A78GLY00.0360.02719.698-0.043-0.0430.0000.0000.0000.000
80A79VAL00.003-0.00122.2680.0260.0260.0000.0000.0000.000
81A80GLU-1-0.855-0.94924.690-0.142-0.1420.0000.0000.0000.000
82A81THR0-0.026-0.02326.2060.0030.0030.0000.0000.0000.000
83A82PHE0-0.038-0.01729.0450.0010.0010.0000.0000.0000.000
84A83HIS00.0370.00131.825-0.004-0.0040.0000.0000.0000.000
85A84ASP-1-0.941-0.93134.581-0.104-0.1040.0000.0000.0000.000
86A92GLY0-0.017-0.01435.279-0.005-0.0050.0000.0000.0000.000
87A93LYS10.8200.90329.8990.1370.1370.0000.0000.0000.000
88A94ASN0-0.022-0.01626.105-0.023-0.0230.0000.0000.0000.000
89A95ILE0-0.071-0.01323.7300.0140.0140.0000.0000.0000.000
90A96VAL0-0.0030.01420.797-0.027-0.0270.0000.0000.0000.000
91A97PHE00.021-0.00218.5960.0390.0390.0000.0000.0000.000
92A98VAL00.000-0.00315.280-0.053-0.0530.0000.0000.0000.000
93A99PHE00.017-0.00112.2480.0680.0680.0000.0000.0000.000
94A100GLU-1-0.833-0.90410.606-0.036-0.0360.0000.0000.0000.000
95A101GLY00.0550.0258.2960.1990.1990.0000.0000.0000.000
96A102GLU-1-0.810-0.9032.183-0.9680.0050.970-0.666-1.2760.001
97A103GLY0-0.047-0.0074.7620.1350.242-0.001-0.003-0.1020.000
98A104ILE0-0.056-0.0343.812-0.0060.1480.000-0.027-0.1280.000
99A105LYS10.8730.9257.5940.1130.1130.0000.0000.0000.000
100A106VAL00.0290.0109.447-0.070-0.0700.0000.0000.0000.000
101A107CYS0-0.050-0.02812.1170.1320.1320.0000.0000.0000.000
102A108HIS00.0050.00715.932-0.047-0.0470.0000.0000.0000.000
103A109LEU00.0340.00218.6480.0600.0600.0000.0000.0000.000
104A110GLY00.0640.03122.1000.0400.0400.0000.0000.0000.000
105A111ASP-1-0.864-0.92524.207-0.329-0.3290.0000.0000.0000.000
106A112LEU0-0.036-0.00325.2330.0220.0220.0000.0000.0000.000
107A113GLY00.0590.01727.770-0.013-0.0130.0000.0000.0000.000
108A114HIS10.7690.86330.1270.1890.1890.0000.0000.0000.000
109A115VAL00.0450.02528.400-0.014-0.0140.0000.0000.0000.000
110A116LEU0-0.0190.02023.4050.0150.0150.0000.0000.0000.000
111A117THR00.0260.00928.0580.0080.0080.0000.0000.0000.000
112A118PRO00.0460.00428.405-0.005-0.0050.0000.0000.0000.000
113A119ALA00.0650.03827.8560.0000.0000.0000.0000.0000.000
114A120GLN00.0280.01626.313-0.007-0.0070.0000.0000.0000.000
115A121VAL0-0.005-0.00423.560-0.013-0.0130.0000.0000.0000.000
116A122GLU-1-0.964-0.97822.941-0.049-0.0490.0000.0000.0000.000
117A123GLU-1-0.924-0.97023.418-0.072-0.0720.0000.0000.0000.000
118A124ILE0-0.036-0.00818.8240.0050.0050.0000.0000.0000.000
119A125GLY00.0040.00818.6180.0020.0020.0000.0000.0000.000
120A126GLU-1-0.841-0.91716.336-0.152-0.1520.0000.0000.0000.000
121A127ILE0-0.034-0.02014.147-0.009-0.0090.0000.0000.0000.000
122A128ASP-1-0.797-0.8799.766-0.307-0.3070.0000.0000.0000.000
123A129VAL00.010-0.0069.201-0.112-0.1120.0000.0000.0000.000
124A130LEU0-0.0060.00012.5350.0610.0610.0000.0000.0000.000
125A131LEU00.0070.00713.921-0.040-0.0400.0000.0000.0000.000
126A132VAL00.010-0.00617.5780.0830.0830.0000.0000.0000.000
127A133PRO00.0000.01421.229-0.031-0.0310.0000.0000.0000.000
128A134VAL00.000-0.02223.8770.0190.0190.0000.0000.0000.000
129A135GLY00.0400.02326.6340.0170.0170.0000.0000.0000.000
130A136GLY0-0.027-0.02929.2550.0130.0130.0000.0000.0000.000
131A137THR0-0.056-0.02732.3850.0200.0200.0000.0000.0000.000
132A138TYR0-0.062-0.06231.5210.0160.0160.0000.0000.0000.000
133A139THR0-0.0130.00327.758-0.007-0.0070.0000.0000.0000.000
134A140ILE0-0.0200.01725.6710.0090.0090.0000.0000.0000.000
135A141GLY00.0260.01529.583-0.020-0.0200.0000.0000.0000.000
136A142PRO0-0.001-0.00127.555-0.003-0.0030.0000.0000.0000.000
137A143LYS10.9710.96527.5070.2040.2040.0000.0000.0000.000
138A144GLU-1-0.760-0.88428.758-0.222-0.2220.0000.0000.0000.000
139A145ALA00.0160.01524.4890.0000.0000.0000.0000.0000.000
140A146LYS10.8170.90324.0630.2590.2590.0000.0000.0000.000
141A147GLU-1-0.916-0.95624.812-0.184-0.1840.0000.0000.0000.000
142A148VAL00.003-0.00722.6440.0130.0130.0000.0000.0000.000
143A149ALA00.0220.00320.622-0.001-0.0010.0000.0000.0000.000
144A150ASP-1-0.818-0.87320.814-0.280-0.2800.0000.0000.0000.000
145A151LEU0-0.034-0.01422.9630.0210.0210.0000.0000.0000.000
146A152LEU0-0.0020.00319.0760.0200.0200.0000.0000.0000.000
147A153ASN0-0.075-0.05518.413-0.042-0.0420.0000.0000.0000.000
148A154ALA00.0170.02316.403-0.009-0.0090.0000.0000.0000.000
149A155LYS10.8410.92712.8630.2400.2400.0000.0000.0000.000
150A156VAL00.0210.00410.308-0.023-0.0230.0000.0000.0000.000
151A157ILE0-0.034-0.01113.5670.0660.0660.0000.0000.0000.000
152A158ILE00.0130.00512.243-0.057-0.0570.0000.0000.0000.000
153A159PRO0-0.032-0.00316.8840.0650.0650.0000.0000.0000.000
154A160MET0-0.021-0.00119.540-0.076-0.0760.0000.0000.0000.000
155A161HIS0-0.003-0.03321.6750.0130.0130.0000.0000.0000.000
156A162TYR00.0000.01420.0870.0570.0570.0000.0000.0000.000
157A163LYS10.8040.90926.3930.2930.2930.0000.0000.0000.000
158A164THR00.0340.01225.266-0.023-0.0230.0000.0000.0000.000
159A165LYS10.9670.97327.7940.3690.3690.0000.0000.0000.000
160A166TYR00.0080.00129.1360.0240.0240.0000.0000.0000.000
161A167LEU00.0730.04927.7070.0230.0230.0000.0000.0000.000
162A168LYS10.9180.94029.7820.2610.2610.0000.0000.0000.000
163A169PHE00.0360.01432.3790.0030.0030.0000.0000.0000.000
164A170ASN00.0160.01634.544-0.007-0.0070.0000.0000.0000.000
165A171LEU00.0160.05328.9580.0010.0010.0000.0000.0000.000
166A172LEU00.0120.00230.3220.0030.0030.0000.0000.0000.000
167A173PRO0-0.020-0.00828.353-0.022-0.0220.0000.0000.0000.000
168A174VAL00.1050.04521.8610.0140.0140.0000.0000.0000.000
169A175ASP-1-0.797-0.90125.313-0.473-0.4730.0000.0000.0000.000
170A176ASP-1-0.872-0.93626.967-0.273-0.2730.0000.0000.0000.000
171A177PHE0-0.018-0.01321.1430.0230.0230.0000.0000.0000.000
172A178LEU0-0.018-0.01421.4770.0080.0080.0000.0000.0000.000
173A179LYS10.8110.90224.9330.3000.3000.0000.0000.0000.000
174A180LEU0-0.082-0.02926.6910.0340.0340.0000.0000.0000.000
175A181PHE00.000-0.01622.2200.0110.0110.0000.0000.0000.000
176A182ASP-1-0.897-0.93623.886-0.301-0.3010.0000.0000.0000.000
177A183SER0-0.064-0.03120.778-0.014-0.0140.0000.0000.0000.000
178A184TYR0-0.019-0.00319.100-0.002-0.0020.0000.0000.0000.000
179A185GLU-1-0.814-0.88012.791-1.492-1.4920.0000.0000.0000.000
180A186ARG10.8220.88416.7940.6490.6490.0000.0000.0000.000
181A187VAL00.0080.01311.607-0.031-0.0310.0000.0000.0000.000
182A188GLY00.0640.03113.3000.1470.1470.0000.0000.0000.000
183A189ASN00.0180.00413.345-0.116-0.1160.0000.0000.0000.000
184A190ILE0-0.009-0.0177.0200.0680.0680.0000.0000.0000.000
185A191LEU0-0.0040.0027.8440.2030.2030.0000.0000.0000.000
186A192GLU-1-0.867-0.9301.807-31.061-32.91011.481-5.000-4.632-0.060
187A193LEU0-0.028-0.0143.5861.0021.6070.005-0.191-0.4190.000
188A194PHE00.023-0.0052.334-7.267-4.4088.991-4.384-7.467-0.031
189A195GLU-1-0.894-0.9443.3934.1004.0890.0140.314-0.3170.000
190A196LYS10.8370.9095.410-1.035-1.0350.0000.0000.0000.000
191A197PRO0-0.022-0.0217.2060.1080.1080.0000.0000.0000.000
192A198LYS10.8580.94110.1330.0290.0290.0000.0000.0000.000
193A199GLU-1-0.882-0.93212.949-0.155-0.1550.0000.0000.0000.000
194A200ARG10.7750.87514.2990.2810.2810.0000.0000.0000.000
195A201LYS10.8300.89810.9561.4971.4970.0000.0000.0000.000
196A202VAL00.0160.01615.392-0.074-0.0740.0000.0000.0000.000
197A203VAL00.001-0.01012.423-0.004-0.0040.0000.0000.0000.000
198A204VAL0-0.018-0.01915.7290.0210.0210.0000.0000.0000.000
199A205MET0-0.0070.01911.204-0.014-0.0140.0000.0000.0000.000
200A206GLU-1-0.877-0.93515.636-0.643-0.6430.0000.0000.0000.000
201A207VAL0-0.049-0.01316.425-0.098-0.0980.0000.0000.0000.000
202A208GLN0-0.077-0.04015.3180.0960.0960.0000.0000.0000.000