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

tag_button

FMODB ID: 66MKZ

Calculation Name: 1VJN-A-Xray372

Preferred Name:
Warning: Undefined array key "pref_name" in /home/FMODBwui_src/fmodbwui/detail.php on line 446

Target Type:
Warning: Undefined array key "target_type" in /home/FMODBwui_src/fmodbwui/detail.php on line 447

Ligand Name:
Warning: Undefined variable $Ligand in /home/FMODBwui_src/fmodbwui/detail.php on line 448

Warning: Trying to access array offset on value of type null in /home/FMODBwui_src/fmodbwui/detail.php on line 448

Warning: Trying to access array offset on value of type null in /home/FMODBwui_src/fmodbwui/detail.php on line 448

ligand 3-letter code:
Warning: Undefined variable $Ligand in /home/FMODBwui_src/fmodbwui/detail.php on line 449

Warning: Trying to access array offset on value of type null in /home/FMODBwui_src/fmodbwui/detail.php on line 449

Warning: Trying to access array offset on value of type null in /home/FMODBwui_src/fmodbwui/detail.php on line 449

PDB ID: 1VJN

Chain ID: A

ChEMBL ID:
Warning: Undefined array key "chembl_id" in /home/FMODBwui_src/fmodbwui/detail.php on line 452

Warning: Undefined array key "chembl_id" in /home/FMODBwui_src/fmodbwui/detail.php on line 452

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 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 202
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2390379.919575
FMO2-HF: Nuclear repulsion 2311345.830427
FMO2-HF: Total energy -79034.089147
FMO2-MP2: Total energy -79266.404281


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.
-34.376-28.40620.547-10.929-15.589-0.079
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 : -0.060 / q_NPA : -0.038
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].
3A2LYS10.8170.9093.362-2.6880.9970.027-1.672-2.0400.008
4A3ILE0-0.0080.0115.2340.8670.943-0.001-0.007-0.0680.000
5A4THR0-0.010-0.0088.935-0.470-0.4700.0000.0000.0000.000
6A5TRP0-0.046-0.01410.9760.2230.2230.0000.0000.0000.000
7A6PHE00.026-0.01613.038-0.035-0.0350.0000.0000.0000.000
8A7GLY00.0460.01717.2410.0630.0630.0000.0000.0000.000
9A8HIS10.7930.88620.2190.3660.3660.0000.0000.0000.000
10A9ALA00.0730.04320.628-0.032-0.0320.0000.0000.0000.000
11A10CYS0-0.0480.02618.281-0.001-0.0010.0000.0000.0000.000
12A11PHE00.027-0.00613.486-0.081-0.0810.0000.0000.0000.000
13A12ALA0-0.0040.00411.2410.1230.1230.0000.0000.0000.000
14A13LEU0-0.019-0.0169.490-0.283-0.2830.0000.0000.0000.000
15A14GLU-1-0.850-0.9175.546-0.779-0.7790.0000.0000.0000.000
16A15MET00.0480.0175.7430.2340.2340.0000.0000.0000.000
17A16GLU-1-0.838-0.9205.5310.7470.7470.0000.0000.0000.000
18A17GLY0-0.054-0.0136.940-0.099-0.0990.0000.0000.0000.000
19A18LYS10.7150.8548.850-1.014-1.0140.0000.0000.0000.000
20A19THR00.0350.0079.4940.0950.0950.0000.0000.0000.000
21A20ILE0-0.008-0.00111.4790.0000.0000.0000.0000.0000.000
22A21VAL00.007-0.00813.247-0.111-0.1110.0000.0000.0000.000
23A22THR00.0090.00515.8410.0320.0320.0000.0000.0000.000
24A23ASP-1-0.784-0.86718.270-0.293-0.2930.0000.0000.0000.000
25A24PRO0-0.007-0.01720.032-0.031-0.0310.0000.0000.0000.000
26A25PHE0-0.044-0.02220.5750.0250.0250.0000.0000.0000.000
27A26ASP-1-0.817-0.93623.886-0.201-0.2010.0000.0000.0000.000
28A27GLU-1-0.815-0.86126.424-0.303-0.3030.0000.0000.0000.000
29A28SER0-0.078-0.05728.2790.0180.0180.0000.0000.0000.000
30A29VAL0-0.038-0.03730.080-0.006-0.0060.0000.0000.0000.000
31A30GLY0-0.011-0.00628.0110.0070.0070.0000.0000.0000.000
32A31TYR0-0.040-0.01721.941-0.032-0.0320.0000.0000.0000.000
33A32PRO0-0.0270.00020.9960.0170.0170.0000.0000.0000.000
34A33ILE00.0230.00421.083-0.031-0.0310.0000.0000.0000.000
35A34PRO00.0360.02217.225-0.032-0.0320.0000.0000.0000.000
36A35ASN0-0.0280.00417.2100.1020.1020.0000.0000.0000.000
37A36VAL00.0270.00312.820-0.051-0.0510.0000.0000.0000.000
38A37THR0-0.043-0.02314.1910.0140.0140.0000.0000.0000.000
39A38ALA00.0040.00313.8740.0400.0400.0000.0000.0000.000
40A39ASP-1-0.784-0.88313.7030.3750.3750.0000.0000.0000.000
41A40VAL0-0.009-0.00816.048-0.001-0.0010.0000.0000.0000.000
42A41VAL0-0.0060.01016.925-0.044-0.0440.0000.0000.0000.000
43A42THR00.0170.00218.4430.0210.0210.0000.0000.0000.000
44A43GLU-1-0.849-0.90821.037-0.200-0.2000.0000.0000.0000.000
45A44SER0-0.032-0.03423.5230.0290.0290.0000.0000.0000.000
46A45HIS10.8600.93624.9590.2110.2110.0000.0000.0000.000
47A46GLN00.0300.00728.2580.0020.0020.0000.0000.0000.000
48A47HIS00.012-0.04026.434-0.005-0.0050.0000.0000.0000.000
49A48PHE0-0.041-0.00927.5550.0050.0050.0000.0000.0000.000
50A49ASP-1-0.760-0.87731.170-0.123-0.1230.0000.0000.0000.000
51A50HIS0-0.115-0.05532.4520.0080.0080.0000.0000.0000.000
52A51ASN0-0.058-0.03827.581-0.010-0.0100.0000.0000.0000.000
53A52ALA00.0940.06325.159-0.003-0.0030.0000.0000.0000.000
54A53HIS0-0.033-0.01622.8710.0020.0020.0000.0000.0000.000
55A54HIS10.8340.90523.7620.1600.1600.0000.0000.0000.000
56A55LEU0-0.013-0.00323.6700.0130.0130.0000.0000.0000.000
57A56VAL0-0.0280.01017.910-0.025-0.0250.0000.0000.0000.000
58A57LYS10.9220.95418.3220.2350.2350.0000.0000.0000.000
59A58GLY00.0430.02218.4310.0020.0020.0000.0000.0000.000
60A59ASN0-0.065-0.02719.423-0.037-0.0370.0000.0000.0000.000
61A60PHE0-0.0030.00418.9420.0290.0290.0000.0000.0000.000
62A61ARG10.9030.95220.370-0.036-0.0360.0000.0000.0000.000
63A62VAL00.0340.01421.188-0.014-0.0140.0000.0000.0000.000
64A63ILE0-0.056-0.02619.5940.0210.0210.0000.0000.0000.000
65A64ASP-1-0.756-0.85623.505-0.081-0.0810.0000.0000.0000.000
66A65ARG10.8230.88525.6520.0440.0440.0000.0000.0000.000
67A66PRO00.0390.03124.9580.0010.0010.0000.0000.0000.000
68A67GLY00.0060.01324.4260.0130.0130.0000.0000.0000.000
69A68ALA0-0.014-0.00521.313-0.012-0.0120.0000.0000.0000.000
70A69TYR0-0.046-0.03819.9390.0180.0180.0000.0000.0000.000
71A70THR0-0.032-0.01916.3740.0080.0080.0000.0000.0000.000
72A71VAL0-0.021-0.00516.4660.0020.0020.0000.0000.0000.000
73A72ASN0-0.015-0.01814.989-0.036-0.0360.0000.0000.0000.000
74A73GLY00.0330.01913.0360.0730.0730.0000.0000.0000.000
75A74VAL00.0460.04710.2970.0070.0070.0000.0000.0000.000
76A75LYS10.8520.92312.681-0.164-0.1640.0000.0000.0000.000
77A76ILE00.009-0.00614.329-0.053-0.0530.0000.0000.0000.000
78A77LYS10.8390.91916.8450.0410.0410.0000.0000.0000.000
79A78GLY00.0230.02319.462-0.033-0.0330.0000.0000.0000.000
80A79VAL0-0.003-0.00421.9050.0190.0190.0000.0000.0000.000
81A80GLU-1-0.866-0.94224.374-0.087-0.0870.0000.0000.0000.000
82A81THR0-0.025-0.02625.7750.0060.0060.0000.0000.0000.000
83A82PHE0-0.035-0.01628.6340.0010.0010.0000.0000.0000.000
84A83HIS00.0520.01231.3830.0000.0000.0000.0000.0000.000
85A84ASP-1-0.951-0.93134.146-0.070-0.0700.0000.0000.0000.000
86A92GLY0-0.032-0.02834.443-0.003-0.0030.0000.0000.0000.000
87A93LYS10.8280.90529.2370.0890.0890.0000.0000.0000.000
88A94ASN0-0.024-0.01425.316-0.023-0.0230.0000.0000.0000.000
89A95ILE0-0.072-0.02023.2530.0150.0150.0000.0000.0000.000
90A96VAL00.0190.02520.333-0.021-0.0210.0000.0000.0000.000
91A97PHE00.013-0.00918.1120.0360.0360.0000.0000.0000.000
92A98VAL0-0.014-0.01214.792-0.045-0.0450.0000.0000.0000.000
93A99PHE00.021-0.00911.8660.0630.0630.0000.0000.0000.000
94A100GLU-1-0.840-0.91810.6980.0350.0350.0000.0000.0000.000
95A101GLY00.016-0.0118.1840.1690.1690.0000.0000.0000.000
96A102GLU-1-0.805-0.9053.136-0.828-0.1010.060-0.249-0.539-0.001
97A103GLY0-0.071-0.0274.614-0.0160.077-0.001-0.004-0.0870.000
98A104ILE0-0.021-0.0103.738-0.0040.1770.001-0.034-0.1480.000
99A105LYS10.8670.9297.299-0.004-0.0040.0000.0000.0000.000
100A106VAL00.0190.0049.177-0.049-0.0490.0000.0000.0000.000
101A107CYS0-0.043-0.01111.8310.0970.0970.0000.0000.0000.000
102A108HIS00.0270.01615.619-0.027-0.0270.0000.0000.0000.000
103A109LEU00.035-0.01317.9880.0520.0520.0000.0000.0000.000
104A110GLY00.0310.02021.3590.0310.0310.0000.0000.0000.000
105A111ASP-1-0.878-0.94023.582-0.262-0.2620.0000.0000.0000.000
106A112LEU0-0.026-0.00224.5750.0200.0200.0000.0000.0000.000
107A113GLY00.0730.02127.127-0.011-0.0110.0000.0000.0000.000
108A114HIS10.7600.86529.5790.1260.1260.0000.0000.0000.000
109A115VAL00.0580.02728.063-0.010-0.0100.0000.0000.0000.000
110A116LEU0-0.0150.01122.8720.0120.0120.0000.0000.0000.000
111A117THR00.0330.02027.5470.0060.0060.0000.0000.0000.000
112A118PRO00.0640.00928.000-0.003-0.0030.0000.0000.0000.000
113A119ALA00.0340.03227.7440.0030.0030.0000.0000.0000.000
114A120GLN00.0570.02125.840-0.005-0.0050.0000.0000.0000.000
115A121VAL00.0110.00523.283-0.006-0.0060.0000.0000.0000.000
116A122GLU-1-0.991-0.98122.7440.0020.0020.0000.0000.0000.000
117A123GLU-1-0.933-0.97423.112-0.017-0.0170.0000.0000.0000.000
118A124ILE0-0.027-0.01118.7520.0030.0030.0000.0000.0000.000
119A125GLY0-0.0010.00818.3840.0020.0020.0000.0000.0000.000
120A126GLU-1-0.896-0.94816.357-0.037-0.0370.0000.0000.0000.000
121A127ILE0-0.030-0.01813.949-0.006-0.0060.0000.0000.0000.000
122A128ASP-1-0.808-0.8859.724-0.113-0.1130.0000.0000.0000.000
123A129VAL00.011-0.0089.016-0.065-0.0650.0000.0000.0000.000
124A130LEU0-0.010-0.00512.1280.0560.0560.0000.0000.0000.000
125A131LEU00.0200.01913.723-0.052-0.0520.0000.0000.0000.000
126A132VAL00.000-0.01017.4190.0660.0660.0000.0000.0000.000
127A133PRO0-0.0030.01421.018-0.030-0.0300.0000.0000.0000.000
128A134VAL00.013-0.01623.6410.0170.0170.0000.0000.0000.000
129A135GLY00.0130.00626.4780.0100.0100.0000.0000.0000.000
130A136GLY0-0.036-0.02629.2200.0110.0110.0000.0000.0000.000
131A137THR0-0.053-0.02132.0300.0150.0150.0000.0000.0000.000
132A138TYR0-0.044-0.04731.6560.0150.0150.0000.0000.0000.000
133A139THR0-0.0130.00427.578-0.004-0.0040.0000.0000.0000.000
134A140ILE00.0050.03125.4290.0060.0060.0000.0000.0000.000
135A141GLY00.0400.01729.067-0.019-0.0190.0000.0000.0000.000
136A142PRO00.002-0.00327.472-0.002-0.0020.0000.0000.0000.000
137A143LYS10.9730.96427.5060.1600.1600.0000.0000.0000.000
138A144GLU-1-0.806-0.89728.893-0.168-0.1680.0000.0000.0000.000
139A145ALA00.0080.01024.2100.0030.0030.0000.0000.0000.000
140A146LYS10.8370.90923.9940.1950.1950.0000.0000.0000.000
141A147GLU-1-0.919-0.94824.607-0.129-0.1290.0000.0000.0000.000
142A148VAL00.0150.00322.3200.0140.0140.0000.0000.0000.000
143A149ALA00.005-0.00920.3660.0030.0030.0000.0000.0000.000
144A150ASP-1-0.804-0.88020.585-0.188-0.1880.0000.0000.0000.000
145A151LEU0-0.052-0.01522.7800.0210.0210.0000.0000.0000.000
146A152LEU0-0.0050.00618.7030.0180.0180.0000.0000.0000.000
147A153ASN0-0.044-0.03418.046-0.027-0.0270.0000.0000.0000.000
148A154ALA00.0060.01615.8930.0010.0010.0000.0000.0000.000
149A155LYS10.8670.93612.6760.1260.1260.0000.0000.0000.000
150A156VAL00.0370.02610.171-0.024-0.0240.0000.0000.0000.000
151A157ILE0-0.025-0.01213.4190.0430.0430.0000.0000.0000.000
152A158ILE00.0160.00312.399-0.047-0.0470.0000.0000.0000.000
153A159PRO0-0.0300.00016.9070.0580.0580.0000.0000.0000.000
154A160MET0-0.031-0.01119.658-0.071-0.0710.0000.0000.0000.000
155A161HIS0-0.001-0.02721.7550.0080.0080.0000.0000.0000.000
156A162TYR00.0170.01320.1750.0440.0440.0000.0000.0000.000
157A163LYS10.8040.91126.6550.2500.2500.0000.0000.0000.000
158A164THR00.0500.02825.024-0.022-0.0220.0000.0000.0000.000
159A165LYS10.9440.96227.6600.3240.3240.0000.0000.0000.000
160A166TYR00.029-0.01829.1840.0200.0200.0000.0000.0000.000
161A167LEU00.0360.04928.2040.0180.0180.0000.0000.0000.000
162A168LYS10.9570.95630.1260.2280.2280.0000.0000.0000.000
163A169PHE00.0130.00932.7510.0020.0020.0000.0000.0000.000
164A170ASN00.0180.01834.821-0.004-0.0040.0000.0000.0000.000
165A171LEU00.0300.04629.2880.0000.0000.0000.0000.0000.000
166A172LEU0-0.013-0.00230.636-0.001-0.0010.0000.0000.0000.000
167A173PRO0-0.017-0.01728.697-0.019-0.0190.0000.0000.0000.000
168A174VAL00.1040.05022.2670.0140.0140.0000.0000.0000.000
169A175ASP-1-0.836-0.92425.745-0.391-0.3910.0000.0000.0000.000
170A176ASP-1-0.875-0.93727.473-0.231-0.2310.0000.0000.0000.000
171A177PHE00.006-0.00421.2130.0190.0190.0000.0000.0000.000
172A178LEU0-0.017-0.01421.6830.0070.0070.0000.0000.0000.000
173A179LYS10.8330.91625.2690.2440.2440.0000.0000.0000.000
174A180LEU0-0.103-0.03926.6540.0250.0250.0000.0000.0000.000
175A181PHE0-0.018-0.01822.1830.0150.0150.0000.0000.0000.000
176A182ASP-1-0.893-0.93524.102-0.240-0.2400.0000.0000.0000.000
177A183SER0-0.067-0.03320.844-0.017-0.0170.0000.0000.0000.000
178A184TYR0-0.004-0.00119.1140.0020.0020.0000.0000.0000.000
179A185GLU-1-0.839-0.88512.920-1.256-1.2560.0000.0000.0000.000
180A186ARG10.8570.91516.9740.5510.5510.0000.0000.0000.000
181A187VAL00.0220.01411.518-0.056-0.0560.0000.0000.0000.000
182A188GLY00.0410.03113.0000.1480.1480.0000.0000.0000.000
183A189ASN00.016-0.00213.206-0.047-0.0470.0000.0000.0000.000
184A190ILE00.006-0.0116.8810.1000.1000.0000.0000.0000.000
185A191LEU0-0.0060.0067.9780.0850.0850.0000.0000.0000.000
186A192GLU-1-0.878-0.9351.851-29.465-30.3829.778-4.517-4.344-0.056
187A193LEU0-0.051-0.0254.0090.5381.1550.002-0.202-0.4170.000
188A194PHE00.031-0.0032.277-5.642-3.93710.654-4.885-7.474-0.030
189A195GLU-1-0.921-0.9593.1855.2825.0790.0280.644-0.4700.000
190A196LYS10.8380.9245.078-1.345-1.339-0.001-0.003-0.0020.000
191A197PRO0-0.015-0.0126.7910.0660.0660.0000.0000.0000.000
192A198LYS10.9440.9869.846-0.222-0.2220.0000.0000.0000.000
193A199GLU-1-0.945-0.97912.829-0.157-0.1570.0000.0000.0000.000
194A200ARG10.7850.87614.2520.1900.1900.0000.0000.0000.000
195A201LYS10.8480.90111.3251.1821.1820.0000.0000.0000.000
196A202VAL00.0100.01815.614-0.049-0.0490.0000.0000.0000.000
197A203VAL0-0.002-0.01012.457-0.019-0.0190.0000.0000.0000.000
198A204VAL0-0.011-0.01515.7940.0390.0390.0000.0000.0000.000
199A205MET0-0.0120.00611.412-0.021-0.0210.0000.0000.0000.000
200A206GLU-1-0.961-0.98815.843-0.578-0.5780.0000.0000.0000.000
201A207VAL0-0.038-0.01416.497-0.088-0.0880.0000.0000.0000.000
202A208GLN0-0.0010.00415.3560.0980.0980.0000.0000.0000.000