Manual

About

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: 66JVZ

Calculation Name: 2HZS-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2HZS

Chain ID: B

ChEMBL ID:

UniProt ID: P32585

Base Structure: X-ray

Registration Date: 2023-06-21

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 238
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2794493.637574
FMO2-HF: Nuclear repulsion 2700849.78759
FMO2-HF: Total energy -93643.849984
FMO2-MP2: Total energy -93915.634706


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:VAL)


Summations of interaction energy for fragment #1(B:2:VAL)
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.
-10.97-0.7562.414-4.668-7.953-0.027
Interaction energy analysis for fragmet #1(B:2:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / q_NPA : -0.004
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].
3B4GLN00.0400.0253.204-1.1920.9870.191-0.724-1.6450.000
4B5LEU0-0.0020.0064.3960.0190.0990.000-0.015-0.0650.000
5B6SER0-0.023-0.0327.9070.0190.0190.0000.0000.0000.000
6B7LEU00.0000.00110.6060.0390.0390.0000.0000.0000.000
7B8PHE00.008-0.01011.467-0.026-0.0260.0000.0000.0000.000
8B9GLY00.0790.03316.5370.0300.0300.0000.0000.0000.000
9B10SER0-0.080-0.02320.049-0.017-0.0170.0000.0000.0000.000
10B11ILE00.0540.03022.6630.0130.0130.0000.0000.0000.000
11B12GLY00.0480.03025.916-0.010-0.0100.0000.0000.0000.000
12B13ASP-1-0.820-0.92528.509-0.127-0.1270.0000.0000.0000.000
13B14ASP-1-0.898-0.95329.602-0.083-0.0830.0000.0000.0000.000
14B15GLY0-0.092-0.03729.2220.0050.0050.0000.0000.0000.000
15B16TYR0-0.028-0.02024.2200.0010.0010.0000.0000.0000.000
16B17ASP-1-0.833-0.92527.655-0.086-0.0860.0000.0000.0000.000
17B18LEU0-0.0140.00629.6830.0030.0030.0000.0000.0000.000
18B19LEU0-0.0080.00522.5520.0030.0030.0000.0000.0000.000
19B20ILE00.0550.02723.891-0.001-0.0010.0000.0000.0000.000
20B21SER0-0.035-0.00726.0780.0050.0050.0000.0000.0000.000
21B22THR0-0.011-0.01525.6210.0070.0070.0000.0000.0000.000
22B23LEU00.0050.00120.6490.0040.0040.0000.0000.0000.000
23B24THR00.000-0.00223.4640.0030.0030.0000.0000.0000.000
24B25THR0-0.096-0.04625.5860.0070.0070.0000.0000.0000.000
25B26ILE0-0.015-0.00822.1480.0050.0050.0000.0000.0000.000
26B27SER0-0.069-0.03720.5530.0060.0060.0000.0000.0000.000
27B28GLY0-0.014-0.00122.4260.0070.0070.0000.0000.0000.000
28B29ASN0-0.071-0.03121.3960.0080.0080.0000.0000.0000.000
29B30PRO00.0310.01423.812-0.005-0.0050.0000.0000.0000.000
30B31PRO0-0.0060.00321.645-0.004-0.0040.0000.0000.0000.000
31B32LEU0-0.015-0.00518.4230.0060.0060.0000.0000.0000.000
32B33LEU0-0.005-0.00519.612-0.019-0.0190.0000.0000.0000.000
33B34TYR0-0.050-0.01914.6340.0130.0130.0000.0000.0000.000
34B35ASN0-0.015-0.03018.152-0.013-0.0130.0000.0000.0000.000
35B36SER00.0070.00614.593-0.037-0.0370.0000.0000.0000.000
36B37LEU00.0530.03316.5840.0100.0100.0000.0000.0000.000
37B38CYS0-0.044-0.02313.993-0.076-0.0760.0000.0000.0000.000
38B39THR00.0320.01216.1670.0440.0440.0000.0000.0000.000
39B40VAL0-0.006-0.00815.600-0.060-0.0600.0000.0000.0000.000
40B41TRP0-0.012-0.00817.0110.0800.0800.0000.0000.0000.000
41B42LYS10.9500.98617.8100.1690.1690.0000.0000.0000.000
42B43PRO00.0580.02518.9410.0160.0160.0000.0000.0000.000
43B44ASN00.001-0.00421.4930.0100.0100.0000.0000.0000.000
44B45PRO00.0260.00225.1200.0070.0070.0000.0000.0000.000
45B46SER0-0.043-0.01827.3750.0120.0120.0000.0000.0000.000
46B47TYR0-0.102-0.04325.6810.0070.0070.0000.0000.0000.000
47B48ASP-1-0.891-0.94626.967-0.118-0.1180.0000.0000.0000.000
48B49VAL0-0.039-0.00923.0140.0090.0090.0000.0000.0000.000
49B50GLU-1-0.904-0.94625.632-0.049-0.0490.0000.0000.0000.000
50B51ASN0-0.047-0.03621.681-0.022-0.0220.0000.0000.0000.000
51B52VAL00.0010.01121.7360.0080.0080.0000.0000.0000.000
52B53ASN0-0.050-0.01217.5870.0230.0230.0000.0000.0000.000
53B54SER00.0580.02521.2690.0020.0020.0000.0000.0000.000
54B55ARG10.9340.94516.473-0.115-0.1150.0000.0000.0000.000
55B56ASN00.0290.00423.4610.0000.0000.0000.0000.0000.000
56B57GLN0-0.051-0.02218.4530.0140.0140.0000.0000.0000.000
57B58LEU00.0650.02320.452-0.011-0.0110.0000.0000.0000.000
58B59VAL0-0.0230.00015.8660.0110.0110.0000.0000.0000.000
59B60GLU-1-0.891-0.94815.598-0.166-0.1660.0000.0000.0000.000
60B61PRO0-0.0050.01716.112-0.040-0.0400.0000.0000.0000.000
61B62ASN00.0930.04212.1580.0140.0140.0000.0000.0000.000
62B63ARG10.7780.86714.9780.3720.3720.0000.0000.0000.000
63B64ILE0-0.0150.00712.874-0.088-0.0880.0000.0000.0000.000
64B65LYS10.9270.9549.5551.0201.0200.0000.0000.0000.000
65B66LEU00.0120.01012.021-0.101-0.1010.0000.0000.0000.000
66B67SER0-0.076-0.03911.6330.0390.0390.0000.0000.0000.000
67B68LYS10.9930.99713.5820.2360.2360.0000.0000.0000.000
68B69GLU-1-0.889-0.93115.387-0.300-0.3000.0000.0000.0000.000
69B70VAL00.0050.00417.5740.0120.0120.0000.0000.0000.000
70B71PRO00.0220.01921.2840.0070.0070.0000.0000.0000.000
71B72PHE00.0700.00721.881-0.001-0.0010.0000.0000.0000.000
72B73SER0-0.035-0.01525.6840.0030.0030.0000.0000.0000.000
73B74TYR00.0260.00626.2120.0090.0090.0000.0000.0000.000
74B75LEU00.0140.01922.976-0.004-0.0040.0000.0000.0000.000
75B76ILE00.0120.02126.590-0.004-0.0040.0000.0000.0000.000
76B77ASP-1-0.752-0.90329.647-0.121-0.1210.0000.0000.0000.000
77B78GLU-1-0.930-0.96123.751-0.210-0.2100.0000.0000.0000.000
78B79THR0-0.074-0.04424.938-0.008-0.0080.0000.0000.0000.000
79B80MET0-0.053-0.03327.4230.0040.0040.0000.0000.0000.000
80B81MET0-0.081-0.03531.0990.0050.0050.0000.0000.0000.000
81B82ASP-1-0.861-0.90928.494-0.165-0.1650.0000.0000.0000.000
82B83LYS10.9170.95429.7810.1540.1540.0000.0000.0000.000
83B84PRO00.0440.04933.0960.0040.0040.0000.0000.0000.000
84B85LEU00.0360.02032.3630.0030.0030.0000.0000.0000.000
85B86ASN0-0.088-0.06934.637-0.003-0.0030.0000.0000.0000.000
86B87PHE0-0.071-0.02336.6420.0070.0070.0000.0000.0000.000
87B88ARG10.9250.96433.0220.1050.1050.0000.0000.0000.000
88B89ILE0-0.019-0.01833.6000.0070.0070.0000.0000.0000.000
89B90LEU0-0.111-0.03630.7410.0070.0070.0000.0000.0000.000
90B159GLU-1-0.965-0.99829.014-0.094-0.0940.0000.0000.0000.000
91B160SER0-0.039-0.01124.105-0.001-0.0010.0000.0000.0000.000
92B161CYS0-0.109-0.04020.267-0.003-0.0030.0000.0000.0000.000
93B162SER00.006-0.00320.4270.0100.0100.0000.0000.0000.000
94B163PRO00.0410.01016.355-0.015-0.0150.0000.0000.0000.000
95B164TRP0-0.003-0.00115.047-0.001-0.0010.0000.0000.0000.000
96B165SER0-0.0250.0118.820-0.043-0.0430.0000.0000.0000.000
97B166LEU00.014-0.00310.4310.0500.0500.0000.0000.0000.000
98B167GLN0-0.012-0.0206.366-0.220-0.2200.0000.0000.0000.000
99B168ILE00.0340.0297.8580.3260.3260.0000.0000.0000.000
100B169SER0-0.030-0.0067.127-0.433-0.4330.0000.0000.0000.000
101B170ASP-1-0.867-0.9207.646-0.309-0.3090.0000.0000.0000.000
102B171ILE0-0.043-0.0139.344-0.096-0.0960.0000.0000.0000.000
103B172PRO0-0.022-0.0159.9550.0510.0510.0000.0000.0000.000
104B173ALA00.0460.03210.6810.0910.0910.0000.0000.0000.000
105B174ALA0-0.032-0.02112.495-0.020-0.0200.0000.0000.0000.000
106B175GLY00.0360.00916.2850.0330.0330.0000.0000.0000.000
107B176ASN0-0.024-0.01618.609-0.029-0.0290.0000.0000.0000.000
108B177ASN0-0.045-0.02421.1810.0070.0070.0000.0000.0000.000
109B178ARG10.9631.01113.4950.2140.2140.0000.0000.0000.000
110B179SER0-0.027-0.01916.414-0.025-0.0250.0000.0000.0000.000
111B180VAL00.0650.00611.530-0.017-0.0170.0000.0000.0000.000
112B181SER0-0.058-0.02011.3520.0190.0190.0000.0000.0000.000
113B182MET00.0480.0157.7670.0020.0020.0000.0000.0000.000
114B183GLN0-0.052-0.0435.9230.1100.1100.0000.0000.0000.000
115B184THR00.0220.0113.561-1.065-0.6980.003-0.131-0.2390.000
116B185ILE0-0.040-0.0352.266-0.4041.1690.968-0.730-1.811-0.001
117B186ALA00.0020.0122.646-6.024-3.5590.774-1.551-1.687-0.019
118B187GLU-1-0.881-0.9754.546-1.458-1.299-0.001-0.007-0.1500.000
119B188THR0-0.059-0.0166.1140.2510.2510.0000.0000.0000.000
120B189ILE00.0100.0058.808-0.036-0.0360.0000.0000.0000.000
121B190ILE0-0.028-0.00411.6860.0830.0830.0000.0000.0000.000
122B191LEU00.0160.00015.2470.0050.0050.0000.0000.0000.000
123B192SER0-0.027-0.01217.5080.0200.0200.0000.0000.0000.000
124B193SER00.008-0.01120.865-0.007-0.0070.0000.0000.0000.000
125B194ALA00.0520.01223.5380.0100.0100.0000.0000.0000.000
126B195GLY00.0030.00627.061-0.003-0.0030.0000.0000.0000.000
127B196LYS10.9210.95429.7930.0820.0820.0000.0000.0000.000
128B197ASN00.0190.00828.0340.0040.0040.0000.0000.0000.000
129B198SER00.0480.03525.840-0.009-0.0090.0000.0000.0000.000
130B199SER00.0960.07624.564-0.017-0.0170.0000.0000.0000.000
131B200VAL00.0950.02818.9700.0050.0050.0000.0000.0000.000
132B201SER00.0080.00321.431-0.017-0.0170.0000.0000.0000.000
133B202SER0-0.001-0.01223.6740.0050.0050.0000.0000.0000.000
134B203LEU0-0.009-0.00620.8070.0050.0050.0000.0000.0000.000
135B204MET00.0190.02816.503-0.006-0.0060.0000.0000.0000.000
136B205ASN0-0.036-0.03120.7720.0140.0140.0000.0000.0000.000
137B206GLY0-0.050-0.01524.0350.0100.0100.0000.0000.0000.000
138B207LEU0-0.039-0.02417.0930.0120.0120.0000.0000.0000.000
139B208GLY0-0.032-0.00620.8700.0020.0020.0000.0000.0000.000
140B209TYR0-0.075-0.05516.3060.0030.0030.0000.0000.0000.000
141B210VAL0-0.021-0.00221.7010.0200.0200.0000.0000.0000.000
142B211PHE0-0.0010.00021.811-0.024-0.0240.0000.0000.0000.000
143B212GLU-1-0.857-0.90020.494-0.270-0.2700.0000.0000.0000.000
144B213PHE00.0300.00117.4030.0160.0160.0000.0000.0000.000
145B214GLN00.0460.01419.639-0.045-0.0450.0000.0000.0000.000
146B215TYR0-0.023-0.01013.7840.0120.0120.0000.0000.0000.000
147B216LEU00.0320.02618.645-0.027-0.0270.0000.0000.0000.000
148B217THR0-0.073-0.02715.3230.0170.0170.0000.0000.0000.000
149B218ILE00.0290.00118.608-0.001-0.0010.0000.0000.0000.000
150B219GLY00.0390.01019.1180.0020.0020.0000.0000.0000.000
151B220VAL0-0.0140.00819.7280.0080.0080.0000.0000.0000.000
152B221LYS10.9340.97011.9600.3020.3020.0000.0000.0000.000
153B222PHE00.0350.01016.6620.0200.0200.0000.0000.0000.000
154B223PHE00.007-0.00112.996-0.021-0.0210.0000.0000.0000.000
155B224MET00.0270.01815.4690.0190.0190.0000.0000.0000.000
156B225LYS10.9590.96315.866-0.013-0.0130.0000.0000.0000.000
157B226HIS00.0140.01114.0760.0060.0060.0000.0000.0000.000
158B227GLY00.0350.03310.8720.0260.0260.0000.0000.0000.000
159B228LEU0-0.0290.00610.482-0.050-0.0500.0000.0000.0000.000
160B229ILE0-0.041-0.0179.7670.0110.0110.0000.0000.0000.000
161B230LEU00.023-0.00712.891-0.027-0.0270.0000.0000.0000.000
162B231GLU-1-0.933-0.97412.194-0.456-0.4560.0000.0000.0000.000
163B232LEU00.0040.01415.8550.0000.0000.0000.0000.0000.000
164B233GLN0-0.029-0.03413.543-0.003-0.0030.0000.0000.0000.000
165B234LYS10.8170.92519.1410.1700.1700.0000.0000.0000.000
166B235ILE00.008-0.00317.266-0.017-0.0170.0000.0000.0000.000
167B236TRP0-0.002-0.01120.9260.0210.0210.0000.0000.0000.000
168B237GLN00.0090.01322.310-0.026-0.0260.0000.0000.0000.000
169B238ILE0-0.023-0.01423.1240.0160.0160.0000.0000.0000.000
170B239GLU-1-0.910-0.96025.463-0.181-0.1810.0000.0000.0000.000
171B240GLU-1-0.908-0.96328.520-0.116-0.1160.0000.0000.0000.000
172B241ALA0-0.054-0.01731.9220.0070.0070.0000.0000.0000.000
173B242GLY00.0090.00531.3590.0070.0070.0000.0000.0000.000
174B243ASN0-0.010-0.01526.749-0.010-0.0100.0000.0000.0000.000
175B244SER0-0.0040.01226.7220.0110.0110.0000.0000.0000.000
176B245GLN00.002-0.01825.193-0.017-0.0170.0000.0000.0000.000
177B246ILE00.0250.01821.2510.0100.0100.0000.0000.0000.000
178B247THR0-0.003-0.00321.064-0.002-0.0020.0000.0000.0000.000
179B248SER0-0.061-0.02524.1030.0110.0110.0000.0000.0000.000
180B249GLY00.0390.02927.8730.0010.0010.0000.0000.0000.000
181B250GLY00.0390.01626.6130.0110.0110.0000.0000.0000.000
182B251PHE0-0.048-0.01321.801-0.010-0.0100.0000.0000.0000.000
183B252LEU0-0.0070.00316.0850.0090.0090.0000.0000.0000.000
184B253LEU0-0.019-0.01818.218-0.009-0.0090.0000.0000.0000.000
185B254LYS10.8780.9508.5450.7240.7240.0000.0000.0000.000
186B255ALA00.0210.02513.4700.0140.0140.0000.0000.0000.000
187B256TYR0-0.034-0.0396.998-0.058-0.0580.0000.0000.0000.000
188B257ILE00.0610.0347.3750.0490.0490.0000.0000.0000.000
189B258ASN00.0080.0023.304-1.083-0.3260.051-0.212-0.5940.001
190B259VAL00.001-0.0053.406-0.2130.3210.010-0.128-0.4150.000
191B260SER0-0.018-0.0202.820-1.7920.1070.415-1.184-1.129-0.008
192B261ARG00.0470.0233.8140.7160.9170.0030.014-0.2180.000
193B262GLY0-0.0040.0176.7710.3380.3380.0000.0000.0000.000
194B263THR00.003-0.0499.5540.0060.0060.0000.0000.0000.000
195B264ASP-1-0.980-0.9569.7900.6320.6320.0000.0000.0000.000
196B265ILE00.0760.02110.933-0.012-0.0120.0000.0000.0000.000
197B266ASP-1-0.873-0.93212.8840.2910.2910.0000.0000.0000.000
198B267ARG00.0370.0329.1860.1630.1630.0000.0000.0000.000
199B268ILE00.0050.0187.182-0.064-0.0640.0000.0000.0000.000
200B269ASN00.0640.02410.938-0.093-0.0930.0000.0000.0000.000
201B270TYR0-0.084-0.04813.462-0.056-0.0560.0000.0000.0000.000
202B271THR0-0.007-0.0388.582-0.051-0.0510.0000.0000.0000.000
203B272GLU-1-0.922-0.96311.8650.0090.0090.0000.0000.0000.000
204B273THR0-0.047-0.02113.604-0.035-0.0350.0000.0000.0000.000
205B274VAL00.0050.01013.658-0.021-0.0210.0000.0000.0000.000
206B275LEU0-0.007-0.00410.478-0.020-0.0200.0000.0000.0000.000
207B276MET0-0.0060.00214.913-0.019-0.0190.0000.0000.0000.000
208B277ASN0-0.062-0.03918.1230.0070.0070.0000.0000.0000.000
209B278LEU00.0780.05616.416-0.004-0.0040.0000.0000.0000.000
210B279LYS10.9080.95718.6860.0770.0770.0000.0000.0000.000
211B280LYS10.8160.90920.2440.0280.0280.0000.0000.0000.000
212B281GLU-1-0.962-0.99722.504-0.032-0.0320.0000.0000.0000.000
213B282LEU00.0250.03020.792-0.002-0.0020.0000.0000.0000.000
214B283GLN00.005-0.00124.3300.0010.0010.0000.0000.0000.000
215B284GLY0-0.061-0.02326.0620.0060.0060.0000.0000.0000.000
216B285TYR0-0.042-0.02026.961-0.001-0.0010.0000.0000.0000.000
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