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: 6N76Z

Calculation Name: 1VHK-B-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: 1VHK

Chain ID: B

ChEMBL ID:
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UniProt ID: P54461

Base Structure: X-ray

Registration Date: 2023-06-22

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 202
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2278038.504117
FMO2-HF: Nuclear repulsion 2197842.793925
FMO2-HF: Total energy -80195.710192
FMO2-MP2: Total energy -80428.238266


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(B:2:GLN)


Summations of interaction energy for fragment #1(B:2:GLN)
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.
-10.199-4.456.975-4.638-8.085-0.003
Interaction energy analysis for fragmet #1(B:2:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.002 / q_NPA : 0.000
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].
3B4TYR00.0260.0152.505-8.043-2.8193.802-3.448-5.578-0.003
4B5PHE0-0.002-0.0016.000-0.417-0.4170.0000.0000.0000.000
5B6ILE0-0.057-0.0349.3370.3020.3020.0000.0000.0000.000
6B7GLU-1-0.887-0.96111.8330.0160.0160.0000.0000.0000.000
7B8LEU0-0.075-0.01814.703-0.015-0.0150.0000.0000.0000.000
8B9THR0-0.029-0.03016.014-0.067-0.0670.0000.0000.0000.000
9B10LYS10.8370.91717.7020.3710.3710.0000.0000.0000.000
10B40GLN0-0.030-0.0246.2050.3460.3460.0000.0000.0000.000
11B41ILE0-0.024-0.0041.975-0.643-1.0993.171-0.960-1.7550.000
12B42ILE0-0.005-0.0093.5100.4031.1640.005-0.210-0.5570.000
13B43CYS0-0.038-0.0075.3360.0810.082-0.001-0.0090.0090.000
14B44CYS00.0030.0108.083-0.050-0.0500.0000.0000.0000.000
15B45SER0-0.029-0.03210.9460.1850.1850.0000.0000.0000.000
16B46GLN00.0980.05514.1240.0000.0000.0000.0000.0000.000
17B47ASP-1-0.815-0.85716.418-0.374-0.3740.0000.0000.0000.000
18B48GLY00.0050.01715.4330.0040.0040.0000.0000.0000.000
19B49PHE0-0.025-0.02615.467-0.051-0.0510.0000.0000.0000.000
20B50GLU-1-0.708-0.8488.774-2.488-2.4880.0000.0000.0000.000
21B51ALA00.003-0.01410.1320.1490.1490.0000.0000.0000.000
22B52LYS10.9360.9837.0421.9791.9790.0000.0000.0000.000
23B53CYS0-0.0190.0107.5550.4370.4370.0000.0000.0000.000
24B65CYS0-0.027-0.0378.9790.0200.0200.0000.0000.0000.000
25B66LEU00.0180.01211.7170.0600.0600.0000.0000.0000.000
26B67VAL00.0230.00911.874-0.158-0.1580.0000.0000.0000.000
27B68ILE0-0.046-0.01910.8910.1140.1140.0000.0000.0000.000
28B69GLU-1-0.927-0.97811.747-1.159-1.1590.0000.0000.0000.000
29B70TRP0-0.033-0.00412.285-0.217-0.2170.0000.0000.0000.000
30B71THR00.0320.0089.9340.1490.1490.0000.0000.0000.000
31B72ASN0-0.049-0.02613.3030.1140.1140.0000.0000.0000.000
32B73GLU-1-0.935-0.93711.456-1.434-1.4340.0000.0000.0000.000
33B74ASN0-0.040-0.03314.253-0.032-0.0320.0000.0000.0000.000
34B75ARG10.8420.8959.9391.6451.6450.0000.0000.0000.000
35B76GLU-1-0.763-0.84115.547-0.451-0.4510.0000.0000.0000.000
36B77LEU00.0300.02818.1640.0100.0100.0000.0000.0000.000
37B78PRO0-0.085-0.04321.4040.0220.0220.0000.0000.0000.000
38B79ILE0-0.034-0.01824.4200.0210.0210.0000.0000.0000.000
39B80LYS10.9190.96424.5600.2010.2010.0000.0000.0000.000
40B81VAL00.0290.02224.4880.0220.0220.0000.0000.0000.000
41B82TYR0-0.006-0.01124.6880.0100.0100.0000.0000.0000.000
42B83ILE00.0170.00624.3430.0050.0050.0000.0000.0000.000
43B84ALA00.0470.03226.9850.0190.0190.0000.0000.0000.000
44B85SER0-0.038-0.02827.9690.0000.0000.0000.0000.0000.000
45B86GLY00.0040.00730.4220.0100.0100.0000.0000.0000.000
46B87LEU0-0.006-0.01229.6720.0050.0050.0000.0000.0000.000
47B88PRO00.0040.04828.394-0.004-0.0040.0000.0000.0000.000
48B89LYS10.9310.95130.906-0.080-0.0800.0000.0000.0000.000
49B90GLY0-0.029-0.01828.9490.0010.0010.0000.0000.0000.000
50B91ASP-1-0.846-0.91823.4420.2860.2860.0000.0000.0000.000
51B92LYS10.8360.90223.888-0.094-0.0940.0000.0000.0000.000
52B93LEU00.0410.01124.540-0.014-0.0140.0000.0000.0000.000
53B94GLU-1-0.924-0.97720.4080.3870.3870.0000.0000.0000.000
54B95TRP0-0.005-0.00619.946-0.019-0.0190.0000.0000.0000.000
55B96ILE00.0050.00320.404-0.023-0.0230.0000.0000.0000.000
56B97ILE0-0.0290.00018.287-0.035-0.0350.0000.0000.0000.000
57B98GLN00.0490.03713.941-0.113-0.1130.0000.0000.0000.000
58B99LYS10.9200.94916.331-0.144-0.1440.0000.0000.0000.000
59B100GLY00.0400.01918.547-0.056-0.0560.0000.0000.0000.000
60B101THR0-0.060-0.03214.382-0.041-0.0410.0000.0000.0000.000
61B102GLU-1-0.929-0.94414.210-0.221-0.2210.0000.0000.0000.000
62B103LEU0-0.059-0.02815.447-0.071-0.0710.0000.0000.0000.000
63B104GLY00.0780.03717.8400.0030.0030.0000.0000.0000.000
64B105ALA0-0.062-0.02819.2430.0110.0110.0000.0000.0000.000
65B106HIS0-0.052-0.02219.7480.0090.0090.0000.0000.0000.000
66B107ALA00.003-0.01221.6900.0190.0190.0000.0000.0000.000
67B108PHE0-0.0100.01719.5000.0000.0000.0000.0000.0000.000
68B109ILE0-0.012-0.04024.7430.0140.0140.0000.0000.0000.000
69B110PRO00.0140.02726.819-0.008-0.0080.0000.0000.0000.000
70B111PHE00.0200.00129.5290.0000.0000.0000.0000.0000.000
71B112GLN00.006-0.01233.3410.0140.0140.0000.0000.0000.000
72B113ALA00.0170.01436.261-0.008-0.0080.0000.0000.0000.000
73B114ALA00.000-0.00737.9090.0070.0070.0000.0000.0000.000
74B115ARG10.8520.92839.142-0.023-0.0230.0000.0000.0000.000
75B116SER0-0.062-0.06334.6010.0020.0020.0000.0000.0000.000
76B117VAL0-0.051-0.01936.3860.0000.0000.0000.0000.0000.000
77B118VAL0-0.020-0.00332.2590.0120.0120.0000.0000.0000.000
78B129ARG10.9020.94622.349-0.213-0.2130.0000.0000.0000.000
79B130GLU-1-0.805-0.91721.2200.3240.3240.0000.0000.0000.000
80B131ARG10.8700.94218.828-0.410-0.4100.0000.0000.0000.000
81B132TRP00.032-0.00118.2060.0460.0460.0000.0000.0000.000
82B133THR00.0770.05017.813-0.034-0.0340.0000.0000.0000.000
83B134LYS10.9430.98213.792-0.846-0.8460.0000.0000.0000.000
84B135ILE0-0.031-0.01913.8970.1070.1070.0000.0000.0000.000
85B136ALA00.0290.02214.681-0.010-0.0100.0000.0000.0000.000
86B137LYS10.9810.98910.617-1.054-1.0540.0000.0000.0000.000
87B138GLU-1-0.934-0.9618.7531.1351.1350.0000.0000.0000.000
88B139ALA00.0400.0179.759-0.083-0.0830.0000.0000.0000.000
89B140ALA0-0.022-0.01011.247-0.210-0.2100.0000.0000.0000.000
90B141GLU-1-0.986-1.0016.3281.7281.7280.0000.0000.0000.000
91B142GLN0-0.011-0.0095.080-0.331-0.250-0.0010.000-0.0790.000
92B143SER0-0.034-0.0247.559-0.371-0.3710.0000.0000.0000.000
93B144TYR0-0.088-0.0484.347-0.908-0.770-0.001-0.011-0.1250.000
94B145ARG10.7990.8809.2950.4400.4400.0000.0000.0000.000
95B146ASN0-0.064-0.04211.277-0.200-0.2000.0000.0000.0000.000
96B147GLU-1-0.865-0.94113.674-0.166-0.1660.0000.0000.0000.000
97B148VAL0-0.011-0.00113.0660.0140.0140.0000.0000.0000.000
98B149PRO00.0390.05015.4920.0220.0220.0000.0000.0000.000
99B150ARG10.9920.98518.7160.0690.0690.0000.0000.0000.000
100B151VAL0-0.060-0.03220.839-0.018-0.0180.0000.0000.0000.000
101B152MET0-0.057-0.02823.4200.0170.0170.0000.0000.0000.000
102B153ASP-1-0.852-0.93026.9340.1470.1470.0000.0000.0000.000
103B154VAL0-0.050-0.00929.447-0.013-0.0130.0000.0000.0000.000
104B155HIS0-0.037-0.02130.829-0.013-0.0130.0000.0000.0000.000
105B156SER00.009-0.01034.2800.0010.0010.0000.0000.0000.000
106B157PHE00.0640.01337.318-0.003-0.0030.0000.0000.0000.000
107B158GLN00.007-0.00839.119-0.010-0.0100.0000.0000.0000.000
108B159GLN00.0510.03936.352-0.001-0.0010.0000.0000.0000.000
109B160LEU0-0.0140.00133.629-0.006-0.0060.0000.0000.0000.000
110B161LEU00.0360.00236.487-0.007-0.0070.0000.0000.0000.000
111B162GLN0-0.052-0.02539.222-0.003-0.0030.0000.0000.0000.000
112B163ARG10.9430.98030.635-0.009-0.0090.0000.0000.0000.000
113B164MET0-0.034-0.01535.568-0.004-0.0040.0000.0000.0000.000
114B165GLN0-0.0050.00337.055-0.011-0.0110.0000.0000.0000.000
115B166ASP-1-0.924-0.94833.823-0.041-0.0410.0000.0000.0000.000
116B167PHE0-0.122-0.06229.801-0.009-0.0090.0000.0000.0000.000
117B168ASP-1-0.757-0.86533.169-0.119-0.1190.0000.0000.0000.000
118B169LYS10.9200.95434.2670.0800.0800.0000.0000.0000.000
119B170CYS00.0260.02834.139-0.001-0.0010.0000.0000.0000.000
120B171VAL00.0020.00333.8210.0010.0010.0000.0000.0000.000
121B172VAL00.006-0.00334.9100.0060.0060.0000.0000.0000.000
122B173ALA0-0.040-0.02133.665-0.004-0.0040.0000.0000.0000.000
123B174TYR0-0.028-0.02535.7600.0110.0110.0000.0000.0000.000
124B175GLU-1-0.890-0.95239.202-0.049-0.0490.0000.0000.0000.000
125B176GLU-1-0.850-0.93342.036-0.010-0.0100.0000.0000.0000.000
126B177SER0-0.058-0.02245.6270.0000.0000.0000.0000.0000.000
127B178SER0-0.024-0.02444.6470.0000.0000.0000.0000.0000.000
128B179LYS10.8470.94638.2330.0350.0350.0000.0000.0000.000
129B180GLN0-0.029-0.05441.226-0.004-0.0040.0000.0000.0000.000
130B181GLY0-0.015-0.00639.7440.0010.0010.0000.0000.0000.000
131B182GLU-1-0.903-0.93940.753-0.060-0.0600.0000.0000.0000.000
132B183ILE00.0180.01543.042-0.003-0.0030.0000.0000.0000.000
133B184SER0-0.0250.00938.0120.0000.0000.0000.0000.0000.000
134B185ALA00.0640.02739.896-0.007-0.0070.0000.0000.0000.000
135B186PHE00.013-0.00530.257-0.007-0.0070.0000.0000.0000.000
136B187SER00.026-0.00734.396-0.006-0.0060.0000.0000.0000.000
137B188ALA00.0070.01335.452-0.009-0.0090.0000.0000.0000.000
138B189ILE00.010-0.00134.560-0.005-0.0050.0000.0000.0000.000
139B190VAL00.0080.00029.956-0.007-0.0070.0000.0000.0000.000
140B191SER0-0.056-0.02932.098-0.015-0.0150.0000.0000.0000.000
141B192SER0-0.045-0.01833.926-0.007-0.0070.0000.0000.0000.000
142B193LEU0-0.0340.00731.3860.0050.0050.0000.0000.0000.000
143B194PRO0-0.0030.00531.984-0.016-0.0160.0000.0000.0000.000
144B195LYS10.9630.96625.8850.3160.3160.0000.0000.0000.000
145B196GLY0-0.020-0.00627.4120.0070.0070.0000.0000.0000.000
146B197SER0-0.0190.00428.4180.0120.0120.0000.0000.0000.000
147B198SER0-0.008-0.01228.883-0.016-0.0160.0000.0000.0000.000
148B199LEU0-0.042-0.02929.1790.0080.0080.0000.0000.0000.000
149B200LEU00.0040.02429.261-0.001-0.0010.0000.0000.0000.000
150B201ILE0-0.007-0.00428.891-0.003-0.0030.0000.0000.0000.000
151B202VAL0-0.007-0.00930.9460.0100.0100.0000.0000.0000.000
152B203PHE00.0400.00828.947-0.005-0.0050.0000.0000.0000.000
153B204GLY00.0270.02233.1600.0100.0100.0000.0000.0000.000
154B205PRO00.0500.04833.1750.0000.0000.0000.0000.0000.000
155B206GLU-1-0.808-0.91932.0650.0840.0840.0000.0000.0000.000
156B207GLY0-0.032-0.01835.2670.0020.0020.0000.0000.0000.000
157B208GLY0-0.012-0.00737.351-0.005-0.0050.0000.0000.0000.000
158B209LEU00.002-0.00136.7060.0060.0060.0000.0000.0000.000
159B210THR0-0.060-0.01439.673-0.001-0.0010.0000.0000.0000.000
160B211GLU-1-0.797-0.91043.3670.0080.0080.0000.0000.0000.000
161B212ALA00.0520.01446.018-0.002-0.0020.0000.0000.0000.000
162B213GLU-1-0.868-0.93840.7540.0280.0280.0000.0000.0000.000
163B214VAL00.001-0.00541.659-0.003-0.0030.0000.0000.0000.000
164B215GLU-1-0.934-0.95543.099-0.008-0.0080.0000.0000.0000.000
165B216ARG10.9840.99144.219-0.016-0.0160.0000.0000.0000.000
166B217LEU0-0.069-0.04838.065-0.001-0.0010.0000.0000.0000.000
167B218THR0-0.030-0.01141.840-0.006-0.0060.0000.0000.0000.000
168B219GLU-1-0.951-0.98144.144-0.009-0.0090.0000.0000.0000.000
169B220GLN0-0.047-0.01741.659-0.003-0.0030.0000.0000.0000.000
170B221ASP-1-0.887-0.93541.609-0.047-0.0470.0000.0000.0000.000
171B222GLY0-0.118-0.05639.135-0.007-0.0070.0000.0000.0000.000
172B223VAL0-0.013-0.02038.9740.0010.0010.0000.0000.0000.000
173B224THR00.0150.01638.812-0.001-0.0010.0000.0000.0000.000
174B225CYS0-0.068-0.01836.710-0.008-0.0080.0000.0000.0000.000
175B226GLY00.0580.03737.2830.0040.0040.0000.0000.0000.000
176B227LEU0-0.016-0.01931.857-0.008-0.0080.0000.0000.0000.000
177B228GLY00.0220.02434.494-0.001-0.0010.0000.0000.0000.000
178B229PRO00.0500.01936.7320.0070.0070.0000.0000.0000.000
179B230ARG10.9440.96733.7530.0710.0710.0000.0000.0000.000
180B231ILE0-0.002-0.00636.081-0.002-0.0020.0000.0000.0000.000
181B232LEU00.0030.01531.0440.0040.0040.0000.0000.0000.000
182B233ARG10.9450.96830.196-0.034-0.0340.0000.0000.0000.000
183B234THR0-0.005-0.00529.953-0.006-0.0060.0000.0000.0000.000
184B235GLU-1-0.822-0.92825.5080.0600.0600.0000.0000.0000.000
185B236THR0-0.057-0.03325.844-0.007-0.0070.0000.0000.0000.000
186B237ALA0-0.0030.00827.376-0.017-0.0170.0000.0000.0000.000
187B238PRO00.0600.01925.479-0.018-0.0180.0000.0000.0000.000
188B239LEU00.0220.00922.031-0.020-0.0200.0000.0000.0000.000
189B240TYR0-0.017-0.00424.750-0.028-0.0280.0000.0000.0000.000
190B241ALA00.0090.00727.603-0.017-0.0170.0000.0000.0000.000
191B242LEU00.0200.01221.802-0.007-0.0070.0000.0000.0000.000
192B243SER00.0240.01723.479-0.038-0.0380.0000.0000.0000.000
193B244ALA0-0.046-0.02224.492-0.018-0.0180.0000.0000.0000.000
194B245ILE0-0.020-0.01425.382-0.010-0.0100.0000.0000.0000.000
195B246SER00.0210.01121.399-0.002-0.0020.0000.0000.0000.000
196B247TYR00.0220.01423.825-0.012-0.0120.0000.0000.0000.000
197B248GLN0-0.023-0.01926.115-0.012-0.0120.0000.0000.0000.000
198B249THR0-0.071-0.06825.474-0.012-0.0120.0000.0000.0000.000
199B250GLU-1-0.819-0.91420.601-0.447-0.4470.0000.0000.0000.000
200B251LEU0-0.057-0.02421.744-0.018-0.0180.0000.0000.0000.000
201B252LEU0-0.053-0.00925.2560.0110.0110.0000.0000.0000.000
202B253ARG10.8910.97825.5380.2400.2400.0000.0000.0000.000