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: N1RGQ

Calculation Name: 2HZS-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2HZS

Chain ID: H

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 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 230
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2661886.642985
FMO2-HF: Nuclear repulsion 2571253.393853
FMO2-HF: Total energy -90633.249132
FMO2-MP2: Total energy -90895.669819


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(H:2:VAL)


Summations of interaction energy for fragment #1(H: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.
-32.068-20.23614.926-11.955-14.803-0.054
Interaction energy analysis for fragmet #1(H:2:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.078 / 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].
3H4GLN00.0420.0203.248-1.0981.3970.069-1.102-1.462-0.003
4H5LEU00.0020.0024.9310.2240.305-0.001-0.008-0.0710.000
5H6SER0-0.018-0.0298.2270.0130.0130.0000.0000.0000.000
6H7LEU00.0060.01410.9960.0740.0740.0000.0000.0000.000
7H8PHE0-0.006-0.01912.059-0.048-0.0480.0000.0000.0000.000
8H9GLY00.1010.04617.1020.0420.0420.0000.0000.0000.000
9H10SER0-0.078-0.02120.488-0.023-0.0230.0000.0000.0000.000
10H11ILE00.0390.02123.1620.0170.0170.0000.0000.0000.000
11H12GLY00.0630.04026.375-0.013-0.0130.0000.0000.0000.000
12H13ASP-1-0.808-0.92728.630-0.194-0.1940.0000.0000.0000.000
13H14ASP-1-0.924-0.95430.158-0.127-0.1270.0000.0000.0000.000
14H15GLY0-0.046-0.01729.9570.0080.0080.0000.0000.0000.000
15H16TYR0-0.046-0.02425.090-0.009-0.0090.0000.0000.0000.000
16H17ASP-1-0.832-0.92628.146-0.140-0.1400.0000.0000.0000.000
17H18LEU00.0020.01930.1970.0040.0040.0000.0000.0000.000
18H19LEU0-0.0050.02022.9410.0020.0020.0000.0000.0000.000
19H20ILE00.0810.03624.676-0.004-0.0040.0000.0000.0000.000
20H21SER0-0.024-0.00126.3690.0050.0050.0000.0000.0000.000
21H22THR0-0.036-0.02825.8780.0100.0100.0000.0000.0000.000
22H23LEU00.013-0.00220.5200.0050.0050.0000.0000.0000.000
23H24THR0-0.029-0.01923.4130.0000.0000.0000.0000.0000.000
24H25THR0-0.092-0.03325.5960.0110.0110.0000.0000.0000.000
25H26ILE0-0.062-0.02121.6170.0060.0060.0000.0000.0000.000
26H27SER0-0.065-0.04520.5160.0050.0050.0000.0000.0000.000
27H28GLY0-0.003-0.01122.2330.0080.0080.0000.0000.0000.000
28H29ASN0-0.085-0.03321.2250.0120.0120.0000.0000.0000.000
29H30PRO00.0340.01423.677-0.007-0.0070.0000.0000.0000.000
30H31PRO0-0.009-0.00421.811-0.009-0.0090.0000.0000.0000.000
31H32LEU0-0.023-0.00618.2980.0100.0100.0000.0000.0000.000
32H33LEU0-0.0010.00320.048-0.028-0.0280.0000.0000.0000.000
33H34TYR0-0.045-0.02014.8270.0150.0150.0000.0000.0000.000
34H35ASN0-0.016-0.03418.284-0.009-0.0090.0000.0000.0000.000
35H36SER0-0.012-0.00114.413-0.061-0.0610.0000.0000.0000.000
36H37LEU00.0330.02616.4660.0080.0080.0000.0000.0000.000
37H38CYS0-0.053-0.01913.934-0.106-0.1060.0000.0000.0000.000
38H39THR00.0390.01715.9410.0570.0570.0000.0000.0000.000
39H40VAL0-0.016-0.01415.309-0.074-0.0740.0000.0000.0000.000
40H41TRP00.009-0.00216.3780.1010.1010.0000.0000.0000.000
41H42LYS10.8760.92717.1290.2070.2070.0000.0000.0000.000
42H43PRO00.0480.02218.6030.0150.0150.0000.0000.0000.000
43H44ASN0-0.002-0.01421.1910.0060.0060.0000.0000.0000.000
44H45PRO00.0140.00624.6820.0100.0100.0000.0000.0000.000
45H46SER0-0.046-0.00927.0570.0150.0150.0000.0000.0000.000
46H47TYR0-0.096-0.04725.6370.0070.0070.0000.0000.0000.000
47H48ASP-1-0.855-0.94426.686-0.115-0.1150.0000.0000.0000.000
48H49VAL0-0.076-0.02223.3700.0100.0100.0000.0000.0000.000
49H50GLU-1-0.880-0.92825.645-0.035-0.0350.0000.0000.0000.000
50H51ASN0-0.012-0.00421.302-0.015-0.0150.0000.0000.0000.000
51H52VAL0-0.016-0.01621.8060.0190.0190.0000.0000.0000.000
52H53ASN00.0310.01119.4740.0160.0160.0000.0000.0000.000
53H54SER00.0050.01221.8320.0030.0030.0000.0000.0000.000
54H55ARG10.9190.95517.388-0.201-0.2010.0000.0000.0000.000
55H56ASN00.0270.00522.267-0.011-0.0110.0000.0000.0000.000
56H57GLN0-0.054-0.02618.7360.0050.0050.0000.0000.0000.000
57H58LEU00.0390.01219.929-0.016-0.0160.0000.0000.0000.000
58H59VAL0-0.037-0.02515.6040.0290.0290.0000.0000.0000.000
59H60GLU-1-0.876-0.91116.316-0.140-0.1400.0000.0000.0000.000
60H61PRO00.0360.03316.151-0.034-0.0340.0000.0000.0000.000
61H62ASN00.0400.01611.654-0.027-0.0270.0000.0000.0000.000
62H63ARG10.8360.90814.8880.4260.4260.0000.0000.0000.000
63H64ILE0-0.031-0.00712.149-0.097-0.0970.0000.0000.0000.000
64H65LYS10.8850.9349.2271.3841.3840.0000.0000.0000.000
65H66LEU0-0.0010.00311.428-0.126-0.1260.0000.0000.0000.000
66H67SER0-0.072-0.04611.2180.0440.0440.0000.0000.0000.000
67H68LYS10.9020.94213.0280.3250.3250.0000.0000.0000.000
68H69GLU-1-0.887-0.94214.958-0.442-0.4420.0000.0000.0000.000
69H70VAL0-0.0180.00417.3680.0260.0260.0000.0000.0000.000
70H71PRO00.0300.02021.0390.0070.0070.0000.0000.0000.000
71H72PHE00.0980.01621.9150.0070.0070.0000.0000.0000.000
72H73SER0-0.051-0.01325.5060.0030.0030.0000.0000.0000.000
73H74TYR00.011-0.00326.1700.0120.0120.0000.0000.0000.000
74H75LEU0-0.0140.00822.742-0.002-0.0020.0000.0000.0000.000
75H76ILE0-0.003-0.01226.603-0.003-0.0030.0000.0000.0000.000
76H77ASP-1-0.812-0.92129.647-0.162-0.1620.0000.0000.0000.000
77H78GLU-1-0.848-0.92122.889-0.307-0.3070.0000.0000.0000.000
78H79THR0-0.056-0.02425.814-0.017-0.0170.0000.0000.0000.000
79H80MET00.000-0.00727.4100.0060.0060.0000.0000.0000.000
80H81MET0-0.089-0.01531.0870.0040.0040.0000.0000.0000.000
81H82ASP-1-0.843-0.88428.754-0.205-0.2050.0000.0000.0000.000
82H83LYS10.7820.89030.2970.1950.1950.0000.0000.0000.000
83H84PRO0-0.016-0.02733.7100.0040.0040.0000.0000.0000.000
84H85LEU00.1180.04431.2240.0010.0010.0000.0000.0000.000
85H86ASN0-0.108-0.05034.556-0.006-0.0060.0000.0000.0000.000
86H87PHE0-0.0320.01136.6170.0080.0080.0000.0000.0000.000
87H88ARG10.9240.93933.3860.1330.1330.0000.0000.0000.000
88H89ILE0-0.030-0.01033.9070.0080.0080.0000.0000.0000.000
89H160SER00.0240.01723.4170.0080.0080.0000.0000.0000.000
90H161CYS0-0.142-0.07420.489-0.010-0.0100.0000.0000.0000.000
91H162SER00.0450.01319.6170.0160.0160.0000.0000.0000.000
92H163PRO00.021-0.00216.056-0.016-0.0160.0000.0000.0000.000
93H164TRP0-0.003-0.00214.266-0.005-0.0050.0000.0000.0000.000
94H165SER0-0.060-0.0317.832-0.001-0.0010.0000.0000.0000.000
95H166LEU00.010-0.0019.9730.0640.0640.0000.0000.0000.000
96H167GLN0-0.018-0.0395.3340.0450.0450.0000.0000.0000.000
97H168ILE00.0360.0287.1760.3440.3440.0000.0000.0000.000
98H169SER0-0.0180.0027.007-0.456-0.4560.0000.0000.0000.000
99H170ASP-1-0.880-0.9297.500-0.070-0.0700.0000.0000.0000.000
100H171ILE0-0.042-0.0129.527-0.160-0.1600.0000.0000.0000.000
101H172PRO0-0.028-0.01810.5820.0720.0720.0000.0000.0000.000
102H173ALA00.0230.02311.4290.1220.1220.0000.0000.0000.000
103H174ALA0-0.014-0.01412.918-0.043-0.0430.0000.0000.0000.000
104H175GLY00.0370.00816.5700.0380.0380.0000.0000.0000.000
105H176ASN0-0.058-0.01819.087-0.033-0.0330.0000.0000.0000.000
106H177ASN0-0.004-0.02121.6690.0160.0160.0000.0000.0000.000
107H178ARG10.9030.97514.5030.2700.2700.0000.0000.0000.000
108H179SER0-0.026-0.02816.290-0.033-0.0330.0000.0000.0000.000
109H180VAL00.0370.01011.728-0.036-0.0360.0000.0000.0000.000
110H181SER0-0.031-0.01711.7120.0540.0540.0000.0000.0000.000
111H182MET00.0340.0197.923-0.001-0.0010.0000.0000.0000.000
112H183GLN0-0.020-0.0156.9090.1360.1360.0000.0000.0000.000
113H184THR00.0010.0033.608-1.306-1.0170.004-0.111-0.1820.000
114H185ILE0-0.008-0.0102.4250.0311.1921.574-0.843-1.8920.000
115H186ALA0-0.0130.0002.204-9.669-7.5483.586-2.763-2.944-0.040
116H187GLU-1-0.827-0.8934.203-2.626-2.3830.000-0.030-0.2120.000
117H188THR0-0.053-0.0225.5770.3690.3690.0000.0000.0000.000
118H189ILE00.0190.0068.335-0.074-0.0740.0000.0000.0000.000
119H190ILE0-0.0210.00611.2950.1220.1220.0000.0000.0000.000
120H191LEU00.0210.00814.838-0.010-0.0100.0000.0000.0000.000
121H192SER00.0250.01317.2190.0170.0170.0000.0000.0000.000
122H193SER0-0.064-0.04520.541-0.004-0.0040.0000.0000.0000.000
123H194ALA00.0340.00923.1370.0100.0100.0000.0000.0000.000
124H195GLY00.0140.01026.626-0.001-0.0010.0000.0000.0000.000
125H196LYS10.9280.95829.3600.0860.0860.0000.0000.0000.000
126H197ASN00.0230.00727.5520.0040.0040.0000.0000.0000.000
127H198SER00.0360.03125.353-0.011-0.0110.0000.0000.0000.000
128H199SER00.0510.04624.085-0.024-0.0240.0000.0000.0000.000
129H200VAL00.1010.02318.2570.0100.0100.0000.0000.0000.000
130H201SER00.0520.02620.796-0.018-0.0180.0000.0000.0000.000
131H202SER0-0.039-0.01523.0580.0060.0060.0000.0000.0000.000
132H203LEU0-0.010-0.00120.1940.0120.0120.0000.0000.0000.000
133H204MET00.0110.02515.921-0.004-0.0040.0000.0000.0000.000
134H205ASN0-0.030-0.02020.1630.0150.0150.0000.0000.0000.000
135H206GLY0-0.041-0.00923.3730.0160.0160.0000.0000.0000.000
136H207LEU0-0.033-0.02416.4970.0180.0180.0000.0000.0000.000
137H208GLY0-0.0130.00620.5740.0050.0050.0000.0000.0000.000
138H209TYR0-0.084-0.06416.2880.0050.0050.0000.0000.0000.000
139H210VAL0-0.013-0.01121.0160.0210.0210.0000.0000.0000.000
140H211PHE00.0120.01421.291-0.031-0.0310.0000.0000.0000.000
141H212GLU-1-0.797-0.86920.402-0.307-0.3070.0000.0000.0000.000
142H213PHE00.0210.00217.8470.0160.0160.0000.0000.0000.000
143H214GLN00.0370.02119.499-0.061-0.0610.0000.0000.0000.000
144H215TYR0-0.016-0.00813.7750.0170.0170.0000.0000.0000.000
145H216LEU00.0220.01918.621-0.042-0.0420.0000.0000.0000.000
146H217THR0-0.041-0.01515.5020.0310.0310.0000.0000.0000.000
147H218ILE00.0170.00018.833-0.004-0.0040.0000.0000.0000.000
148H219GLY00.0530.02119.5730.0030.0030.0000.0000.0000.000
149H220VAL0-0.0070.00320.3560.0100.0100.0000.0000.0000.000
150H221LYS10.8420.91211.6730.5960.5960.0000.0000.0000.000
151H222PHE00.0360.01416.9620.0300.0300.0000.0000.0000.000
152H223PHE00.0040.00212.297-0.034-0.0340.0000.0000.0000.000
153H224MET00.0340.01415.2020.0370.0370.0000.0000.0000.000
154H225LYS10.9600.97115.6370.0350.0350.0000.0000.0000.000
155H226HIS00.013-0.00613.680-0.001-0.0010.0000.0000.0000.000
156H227GLY00.0260.02110.4500.0280.0280.0000.0000.0000.000
157H228LEU0-0.0240.00110.307-0.089-0.0890.0000.0000.0000.000
158H229ILE0-0.044-0.0169.2940.0230.0230.0000.0000.0000.000
159H230LEU00.024-0.00212.850-0.036-0.0360.0000.0000.0000.000
160H231GLU-1-0.815-0.88212.545-0.741-0.7410.0000.0000.0000.000
161H232LEU00.0160.01916.5520.0020.0020.0000.0000.0000.000
162H233GLN0-0.052-0.04114.179-0.015-0.0150.0000.0000.0000.000
163H234LYS10.8120.89819.6390.2480.2480.0000.0000.0000.000
164H235ILE00.006-0.01517.309-0.027-0.0270.0000.0000.0000.000
165H236TRP0-0.020-0.01921.2590.0290.0290.0000.0000.0000.000
166H237GLN0-0.052-0.02722.594-0.051-0.0510.0000.0000.0000.000
167H238ILE0-0.023-0.02022.8590.0220.0220.0000.0000.0000.000
168H239GLU-1-0.886-0.92825.413-0.236-0.2360.0000.0000.0000.000
169H240GLU-1-0.851-0.93128.263-0.168-0.1680.0000.0000.0000.000
170H241ALA0-0.027-0.01531.6600.0070.0070.0000.0000.0000.000
171H242GLY00.0070.01231.2930.0090.0090.0000.0000.0000.000
172H243ASN00.005-0.01526.947-0.010-0.0100.0000.0000.0000.000
173H244SER00.0140.02027.7270.0030.0030.0000.0000.0000.000
174H245GLN00.0390.00225.608-0.022-0.0220.0000.0000.0000.000
175H246ILE00.0430.02421.5370.0130.0130.0000.0000.0000.000
176H247THR0-0.0090.00521.307-0.003-0.0030.0000.0000.0000.000
177H248SER0-0.030-0.01424.2800.0130.0130.0000.0000.0000.000
178H249GLY00.0020.01128.0370.0030.0030.0000.0000.0000.000
179H250GLY00.0350.01526.8880.0140.0140.0000.0000.0000.000
180H251PHE0-0.0430.00622.379-0.013-0.0130.0000.0000.0000.000
181H252LEU0-0.0070.00416.6490.0110.0110.0000.0000.0000.000
182H253LEU0-0.025-0.01618.681-0.019-0.0190.0000.0000.0000.000
183H254LYS10.8780.9408.7801.0991.0990.0000.0000.0000.000
184H255ALA00.0370.02913.7030.0130.0130.0000.0000.0000.000
185H256TYR0-0.076-0.0867.192-0.103-0.1030.0000.0000.0000.000
186H257ILE00.0610.0436.9830.0800.0800.0000.0000.0000.000
187H258ASN0-0.0050.0152.571-1.309-0.8540.657-0.257-0.8560.002
188H259VAL00.0250.0033.023-0.2520.5860.123-0.245-0.717-0.001
189H260SER00.003-0.0162.607-1.6250.6722.225-2.131-2.391-0.019
190H261ARG11.0171.0041.705-12.867-11.1336.539-4.547-3.7270.008
191H262GLY00.0180.0433.308-1.523-1.4050.1500.082-0.349-0.001
192H263THR0-0.086-0.0795.782-0.773-0.7730.0000.0000.0000.000
193H264ASP-1-0.833-0.9028.3440.5490.5490.0000.0000.0000.000
194H265ILE00.0440.00411.1770.0040.0040.0000.0000.0000.000
195H266ASP-1-0.854-0.90213.2300.3070.3070.0000.0000.0000.000
196H267ARG10.9170.9508.213-1.026-1.0260.0000.0000.0000.000
197H268ILE00.0070.0187.217-0.125-0.1250.0000.0000.0000.000
198H269ASN00.0620.02110.870-0.139-0.1390.0000.0000.0000.000
199H270TYR0-0.067-0.02612.881-0.070-0.0700.0000.0000.0000.000
200H271THR0-0.013-0.0338.310-0.072-0.0720.0000.0000.0000.000
201H272GLU-1-0.863-0.91811.613-0.059-0.0590.0000.0000.0000.000
202H273THR0-0.036-0.01113.554-0.042-0.0420.0000.0000.0000.000
203H274VAL0-0.031-0.00913.457-0.026-0.0260.0000.0000.0000.000
204H275LEU00.0010.00010.763-0.026-0.0260.0000.0000.0000.000
205H276MET0-0.007-0.00714.900-0.019-0.0190.0000.0000.0000.000
206H277ASN0-0.025-0.02218.1560.0000.0000.0000.0000.0000.000
207H278LEU00.0370.03616.332-0.005-0.0050.0000.0000.0000.000
208H279LYS10.8840.92118.6690.1450.1450.0000.0000.0000.000
209H280LYS10.8190.90520.2410.0680.0680.0000.0000.0000.000
210H281GLU-1-0.941-0.97722.207-0.086-0.0860.0000.0000.0000.000
211H282LEU00.0290.02520.774-0.001-0.0010.0000.0000.0000.000
212H283GLN00.0340.01624.5200.0020.0020.0000.0000.0000.000
213H284GLY0-0.069-0.02126.2160.0070.0070.0000.0000.0000.000
214H285TYR0-0.028-0.02227.0040.0010.0010.0000.0000.0000.000
215H286ILE0-0.003-0.00722.531-0.006-0.0060.0000.0000.0000.000
216H287GLU-1-0.960-0.96023.700-0.164-0.1640.0000.0000.0000.000
217H288LEU00.0460.02717.425-0.019-0.0190.0000.0000.0000.000
218H289SER0-0.008-0.02419.4650.0210.0210.0000.0000.0000.000
219H290VAL0-0.028-0.01215.251-0.051-0.0510.0000.0000.0000.000
220H291PRO00.0220.02814.8510.0320.0320.0000.0000.0000.000
221H292ASP-1-0.822-0.92116.997-0.228-0.2280.0000.0000.0000.000
222H293ARG10.9150.95415.1380.1590.1590.0000.0000.0000.000
223H294GLN00.015-0.00815.754-0.041-0.0410.0000.0000.0000.000
224H295SER0-0.054-0.02317.6280.0070.0070.0000.0000.0000.000
225H296MET0-0.082-0.03810.588-0.002-0.0020.0000.0000.0000.000
226H297ASP-1-0.770-0.87212.547-0.472-0.4720.0000.0000.0000.000
227H298SER0-0.015-0.01212.7600.0030.0030.0000.0000.0000.000
228H299ARG10.8060.85814.4920.2630.2630.0000.0000.0000.000
229H300VAL0-0.058-0.02416.5880.0100.0100.0000.0000.0000.000
230H301ALA00.0130.01220.0460.0210.0210.0000.0000.0000.000