Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

tag_button

FMODB ID: JL2Z9

Calculation Name: 4TZO-G-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4TZO

Chain ID: G

ChEMBL ID:

UniProt ID: G5EBG0

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 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 236
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3112745.563165
FMO2-HF: Nuclear repulsion 3017219.829161
FMO2-HF: Total energy -95525.734004
FMO2-MP2: Total energy -95799.927466


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(G:17:ASP)


Summations of interaction energy for fragment #1(G:17:ASP)
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.
-114.021-136.82963.577-25.907-14.8630.218
Interaction energy analysis for fragmet #1(G:17:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.783 / q_NPA : -0.835
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].
3G19ILE00.0130.0373.893-3.618-1.695-0.020-0.987-0.9160.002
4G20ASP-1-0.820-0.8887.11827.89927.8990.0000.0000.0000.000
5G21ASP-1-0.751-0.8569.45718.05518.0550.0000.0000.0000.000
6G22LYS10.8280.87612.498-18.304-18.3040.0000.0000.0000.000
7G23LYS10.8050.91315.456-16.377-16.3770.0000.0000.0000.000
8G24TRP00.0800.0338.799-2.130-2.1300.0000.0000.0000.000
9G25SER00.0140.00512.651-0.629-0.6290.0000.0000.0000.000
10G26LYS10.8800.95913.629-15.405-15.4050.0000.0000.0000.000
11G27LEU0-0.071-0.03815.582-1.104-1.1040.0000.0000.0000.000
12G28PHE00.0390.00711.161-0.638-0.6380.0000.0000.0000.000
13G29PRO00.0260.0158.894-0.475-0.4750.0000.0000.0000.000
14G30ARG10.8400.9058.051-25.776-25.7760.0000.0000.0000.000
15G31ILE00.0070.0063.7320.1270.7370.008-0.277-0.3420.001
16G32VAL00.005-0.0034.046-8.922-8.646-0.001-0.091-0.1840.000
17G33SER00.0510.0011.594-28.059-36.73420.874-8.214-3.9840.068
18G34ASP-1-0.810-0.8774.49429.05829.1770.000-0.060-0.0600.000
19G35PRO00.0880.0147.851-0.002-0.0020.0000.0000.0000.000
20G36ASP-1-0.783-0.86811.33119.54019.5400.0000.0000.0000.000
21G37ARG10.8620.9067.112-38.234-38.2340.0000.0000.0000.000
22G38SER0-0.003-0.0148.6660.9730.9730.0000.0000.0000.000
23G39SER00.0650.0339.719-1.753-1.7530.0000.0000.0000.000
24G40ASN0-0.074-0.05013.043-2.169-2.1690.0000.0000.0000.000
25G41PHE0-0.012-0.0179.904-0.922-0.9220.0000.0000.0000.000
26G42MET0-0.0020.02311.980-1.426-1.4260.0000.0000.0000.000
27G43THR0-0.008-0.01114.482-0.983-0.9830.0000.0000.0000.000
28G44ARG10.8180.92914.507-18.474-18.4740.0000.0000.0000.000
29G45ALA0-0.001-0.01114.062-1.029-1.0290.0000.0000.0000.000
30G46ILE00.0550.03416.085-0.910-0.9100.0000.0000.0000.000
31G47TYR00.003-0.01619.458-0.596-0.5960.0000.0000.0000.000
32G48VAL0-0.043-0.01617.748-0.854-0.8540.0000.0000.0000.000
33G49ALA00.0190.00718.894-0.717-0.7170.0000.0000.0000.000
34G50PHE00.0700.02120.740-0.650-0.6500.0000.0000.0000.000
35G51SER0-0.060-0.03623.335-0.803-0.8030.0000.0000.0000.000
36G52ALA0-0.018-0.01023.046-0.534-0.5340.0000.0000.0000.000
37G53VAL00.0220.02324.615-0.465-0.4650.0000.0000.0000.000
38G54LEU00.0230.01126.947-0.470-0.4700.0000.0000.0000.000
39G55ARG10.7650.87528.268-10.182-10.1820.0000.0000.0000.000
40G56ASN0-0.045-0.03927.062-0.006-0.0060.0000.0000.0000.000
41G57ARG10.8040.86630.082-9.690-9.6900.0000.0000.0000.000
42G58ASN0-0.046-0.01732.475-0.345-0.3450.0000.0000.0000.000
43G59ILE00.0730.06631.584-0.204-0.2040.0000.0000.0000.000
44G60LEU0-0.057-0.01831.135-0.146-0.1460.0000.0000.0000.000
45G61GLY00.0930.04833.5400.1690.1690.0000.0000.0000.000
46G62GLN00.006-0.00932.7510.4710.4710.0000.0000.0000.000
47G63GLU-1-0.840-0.93532.6749.1099.1090.0000.0000.0000.000
48G64TYR00.0040.02331.9760.0050.0050.0000.0000.0000.000
49G65PHE0-0.007-0.00927.0470.4740.4740.0000.0000.0000.000
50G66THR0-0.035-0.00425.634-0.257-0.2570.0000.0000.0000.000
51G67LYS10.9360.95526.176-10.810-10.8100.0000.0000.0000.000
52G68ASN0-0.026-0.02721.3370.2500.2500.0000.0000.0000.000
53G69TYR0-0.027-0.02819.328-0.853-0.8530.0000.0000.0000.000
54G70ILE00.0580.03815.2590.2360.2360.0000.0000.0000.000
55G71THR00.0610.02813.5400.9820.9820.0000.0000.0000.000
56G72GLU-1-0.885-0.94715.46916.87716.8770.0000.0000.0000.000
57G73LYS10.9540.97816.745-17.858-17.8580.0000.0000.0000.000
58G74LEU00.0120.02818.026-0.622-0.6220.0000.0000.0000.000
59G75LYS10.8830.95419.955-12.332-12.3320.0000.0000.0000.000
60G76CYS00.0250.01821.1390.0790.0790.0000.0000.0000.000
61G77MET0-0.023-0.00623.185-0.313-0.3130.0000.0000.0000.000
62G78THR00.0670.02221.1940.3580.3580.0000.0000.0000.000
63G79LEU00.0400.03824.449-0.422-0.4220.0000.0000.0000.000
64G80CYS0-0.057-0.00226.3080.3600.3600.0000.0000.0000.000
65G81PHE00.0650.02922.740-0.327-0.3270.0000.0000.0000.000
66G82ARG10.9080.94728.684-10.899-10.8990.0000.0000.0000.000
67G83ASN0-0.010-0.00231.927-0.416-0.4160.0000.0000.0000.000
68G84LEU00.0430.02332.7910.2800.2800.0000.0000.0000.000
69G85ARG11.0391.02033.864-8.612-8.6120.0000.0000.0000.000
70G86SER00.026-0.00529.8730.0440.0440.0000.0000.0000.000
71G87ASN0-0.026-0.01329.0660.8080.8080.0000.0000.0000.000
72G88GLN00.0280.00929.2450.2670.2670.0000.0000.0000.000
73G89ILE00.0450.02928.1100.1810.1810.0000.0000.0000.000
74G90ALA0-0.034-0.02125.2880.4270.4270.0000.0000.0000.000
75G91GLN0-0.042-0.00725.0210.3410.3410.0000.0000.0000.000
76G92LEU00.0460.03726.5650.2990.2990.0000.0000.0000.000
77G93LEU0-0.018-0.01023.1290.3410.3410.0000.0000.0000.000
78G94ARG10.7960.88519.211-15.067-15.0670.0000.0000.0000.000
79G95ASN0-0.037-0.03822.3750.9080.9080.0000.0000.0000.000
80G96ALA00.0360.01624.0860.1380.1380.0000.0000.0000.000
81G97GLY0-0.002-0.00919.8860.3460.3460.0000.0000.0000.000
82G98ASP-1-0.794-0.88619.08217.18417.1840.0000.0000.0000.000
83G99ALA00.0230.02120.4540.2380.2380.0000.0000.0000.000
84G100THR0-0.062-0.03016.015-0.065-0.0650.0000.0000.0000.000
85G101LYS10.8290.89717.042-17.466-17.4660.0000.0000.0000.000
86G102ASP-1-0.928-0.96717.77015.77815.7780.0000.0000.0000.000
87G103GLY00.0210.01119.775-0.135-0.1350.0000.0000.0000.000
88G104PHE0-0.0190.00320.610-0.442-0.4420.0000.0000.0000.000
89G105LEU00.0190.01720.797-0.704-0.7040.0000.0000.0000.000
90G106LYS10.8320.92421.798-10.734-10.7340.0000.0000.0000.000
91G107GLU-1-0.791-0.87122.83112.34912.3490.0000.0000.0000.000
92G108VAL0-0.028-0.00823.123-0.347-0.3470.0000.0000.0000.000
93G109SER0-0.005-0.04124.5380.5890.5890.0000.0000.0000.000
94G110LEU0-0.071-0.01427.274-0.276-0.2760.0000.0000.0000.000
95G111VAL00.0150.00529.3770.0550.0550.0000.0000.0000.000
96G112ILE0-0.016-0.01232.303-0.096-0.0960.0000.0000.0000.000
97G113THR0-0.036-0.02235.4600.0400.0400.0000.0000.0000.000
98G114ASN00.006-0.00439.092-0.041-0.0410.0000.0000.0000.000
99G115ASN0-0.042-0.04342.686-0.149-0.1490.0000.0000.0000.000
100G116GLU-1-0.945-0.94740.4158.0698.0690.0000.0000.0000.000
101G117GLY00.033-0.01040.212-0.164-0.1640.0000.0000.0000.000
102G118ASP-1-0.816-0.87340.6607.5097.5090.0000.0000.0000.000
103G119LEU00.025-0.00138.8830.2550.2550.0000.0000.0000.000
104G120GLU-1-0.826-0.89137.9628.2068.2060.0000.0000.0000.000
105G121ALA0-0.045-0.02135.287-0.059-0.0590.0000.0000.0000.000
106G122ILE0-0.0180.00037.312-0.065-0.0650.0000.0000.0000.000
107G123GLU-1-0.755-0.84632.4329.6579.6570.0000.0000.0000.000
108G124VAL00.0120.00929.0250.0040.0040.0000.0000.0000.000
109G125PHE0-0.046-0.01825.9800.3150.3150.0000.0000.0000.000
110G126SER00.0270.00625.4120.0430.0430.0000.0000.0000.000
111G127MET0-0.062-0.03417.9260.4460.4460.0000.0000.0000.000
112G128LYS10.8970.95821.091-12.718-12.7180.0000.0000.0000.000
113G129PHE00.004-0.02116.9541.1071.1070.0000.0000.0000.000
114G130ILE0-0.0120.01617.192-0.839-0.8390.0000.0000.0000.000
115G131TYR0-0.006-0.01615.8161.7901.7900.0000.0000.0000.000
116G132PHE0-0.005-0.01313.357-0.491-0.4910.0000.0000.0000.000
117G133GLU-1-0.842-0.89415.08816.57216.5720.0000.0000.0000.000
118G134ASN0-0.005-0.02014.3761.2081.2080.0000.0000.0000.000
119G135GLY0-0.037-0.02211.014-0.182-0.1820.0000.0000.0000.000
120G136GLY00.0430.02510.0352.2282.2280.0000.0000.0000.000
121G137VAL0-0.061-0.01311.1100.2420.2420.0000.0000.0000.000
122G138VAL00.0180.00313.438-0.716-0.7160.0000.0000.0000.000
123G139ALA00.0080.00916.9930.3310.3310.0000.0000.0000.000
124G140ARG10.8120.88118.311-16.427-16.4270.0000.0000.0000.000
125G141LEU0-0.023-0.01321.0860.1220.1220.0000.0000.0000.000
126G142SER0-0.060-0.04422.8700.0020.0020.0000.0000.0000.000
127G143THR00.0090.00424.861-0.083-0.0830.0000.0000.0000.000
128G144ASP-1-0.794-0.89228.6589.5779.5770.0000.0000.0000.000
129G145LYS10.8150.88331.686-10.035-10.0350.0000.0000.0000.000
130G146ASN0-0.096-0.04734.718-0.413-0.4130.0000.0000.0000.000
131G147GLY0-0.026-0.01032.955-0.144-0.1440.0000.0000.0000.000
132G148GLN0-0.035-0.01532.0600.0400.0400.0000.0000.0000.000
133G149GLU-1-0.851-0.93825.97612.55112.5510.0000.0000.0000.000
134G150ASP-1-0.749-0.84225.71511.66111.6610.0000.0000.0000.000
135G151PRO00.010-0.01526.1670.4400.4400.0000.0000.0000.000
136G152HIS0-0.036-0.01520.769-0.285-0.2850.0000.0000.0000.000
137G153PHE0-0.018-0.01621.2630.9640.9640.0000.0000.0000.000
138G154ALA00.0460.02820.8150.8960.8960.0000.0000.0000.000
139G155LYS10.8540.92218.545-15.370-15.3700.0000.0000.0000.000
140G156LEU0-0.017-0.01715.9420.9640.9640.0000.0000.0000.000
141G157ALA0-0.0020.00415.9691.5061.5060.0000.0000.0000.000
142G158GLN0-0.033-0.01417.2140.0630.0630.0000.0000.0000.000
143G159LEU0-0.047-0.00112.8350.6470.6470.0000.0000.0000.000
144G160VAL00.0370.01810.0030.6410.6410.0000.0000.0000.000
145G161TYR0-0.055-0.0611.556-24.828-37.11426.868-9.874-4.7090.083
146G162GLU-1-0.955-0.9736.96029.96529.9650.0000.0000.0000.000
147G163GLY00.0030.0132.825-1.960-0.5140.649-1.209-0.8860.010
148G164GLY00.013-0.0101.733-22.604-29.23115.109-5.065-3.4170.049
149G165ASP-1-0.830-0.9223.55120.70021.1060.090-0.130-0.3650.005
150G166SER00.005-0.0036.244-7.044-7.0440.0000.0000.0000.000
151G167VAL00.0080.0095.801-4.470-4.4700.0000.0000.0000.000
152G168ARG10.7130.8157.981-32.719-32.7190.0000.0000.0000.000
153G169ASP-1-0.809-0.8829.98521.79221.7920.0000.0000.0000.000
154G170GLN00.0530.0459.388-2.162-2.1620.0000.0000.0000.000
155G171MET00.0000.02012.200-2.547-2.5470.0000.0000.0000.000
156G172VAL0-0.073-0.05313.984-2.018-2.0180.0000.0000.0000.000
157G173THR0-0.029-0.02715.663-1.689-1.6890.0000.0000.0000.000
158G174ILE00.0160.02315.784-1.148-1.1480.0000.0000.0000.000
159G175VAL00.031-0.00118.310-1.032-1.0320.0000.0000.0000.000
160G176ARG10.8510.91719.160-15.925-15.9250.0000.0000.0000.000
161G177SER00.0080.02621.318-1.025-1.0250.0000.0000.0000.000
162G178VAL00.0330.02022.534-0.630-0.6300.0000.0000.0000.000
163G179GLN0-0.033-0.02023.317-0.509-0.5090.0000.0000.0000.000
164G180PHE0-0.0050.00525.747-0.587-0.5870.0000.0000.0000.000
165G181LEU00.0570.02226.336-0.477-0.4770.0000.0000.0000.000
166G182CYS0-0.046-0.03228.141-0.396-0.3960.0000.0000.0000.000
167G183THR0-0.075-0.03929.996-0.368-0.3680.0000.0000.0000.000
168G184LYS10.8220.90130.991-9.660-9.6600.0000.0000.0000.000
169G185VAL0-0.0110.00730.634-0.112-0.1120.0000.0000.0000.000
170G186LEU00.0220.02630.283-0.073-0.0730.0000.0000.0000.000
171G187GLU-1-0.810-0.86334.3687.8547.8540.0000.0000.0000.000
172G188PRO0-0.062-0.03037.0470.2420.2420.0000.0000.0000.000
173G189LEU00.0110.00835.020-0.055-0.0550.0000.0000.0000.000
174G190PRO00.006-0.00339.076-0.127-0.1270.0000.0000.0000.000
175G191GLU-1-0.975-0.98641.9426.8786.8780.0000.0000.0000.000
176G192GLU-1-0.982-0.97944.0516.7756.7750.0000.0000.0000.000
177G193PHE0-0.040-0.02636.4100.1380.1380.0000.0000.0000.000
178G194THR0-0.0070.00438.337-0.055-0.0550.0000.0000.0000.000
179G195ALA00.009-0.00133.7800.1400.1400.0000.0000.0000.000
180G196ASN00.0020.01133.596-0.063-0.0630.0000.0000.0000.000
181G197PHE0-0.006-0.00926.5430.1650.1650.0000.0000.0000.000
182G198ARG10.8110.89529.791-9.318-9.3180.0000.0000.0000.000
183G199LEU0-0.023-0.01826.6570.4550.4550.0000.0000.0000.000
184G200GLU-1-0.758-0.84827.26610.16010.1600.0000.0000.0000.000
185G201TYR00.0470.01626.4610.6710.6710.0000.0000.0000.000
186G202THR0-0.031-0.02523.021-0.402-0.4020.0000.0000.0000.000
187G203ASN0-0.022-0.03026.373-0.467-0.4670.0000.0000.0000.000
188G204ASP-1-0.838-0.90823.63013.36713.3670.0000.0000.0000.000
189G205ALA0-0.035-0.00726.8650.0050.0050.0000.0000.0000.000
190G206PRO0-0.0020.00727.993-0.460-0.4600.0000.0000.0000.000
191G207SER00.008-0.00631.2490.1080.1080.0000.0000.0000.000
192G208ASN0-0.056-0.03032.022-0.028-0.0280.0000.0000.0000.000
193G209PHE00.0000.00325.4410.0770.0770.0000.0000.0000.000
194G210ARG10.8410.87930.165-9.589-9.5890.0000.0000.0000.000
195G211ILE0-0.0220.01025.6950.2870.2870.0000.0000.0000.000
196G212ASP-1-0.879-0.94328.85910.11510.1150.0000.0000.0000.000
197G213GLY0-0.047-0.03529.9330.2990.2990.0000.0000.0000.000
198G214PHE0-0.046-0.03027.9690.0010.0010.0000.0000.0000.000
199G215GLU-1-0.933-0.95732.4628.4508.4500.0000.0000.0000.000
200G216ASP-1-0.837-0.88434.8049.3699.3690.0000.0000.0000.000
201G217SER00.007-0.01535.829-0.372-0.3720.0000.0000.0000.000
202G218SER0-0.042-0.01636.4970.2040.2040.0000.0000.0000.000
203G219THR0-0.048-0.01837.679-0.042-0.0420.0000.0000.0000.000
204G220PHE00.0470.02128.5980.1300.1300.0000.0000.0000.000
205G221TYR0-0.068-0.05928.913-0.101-0.1010.0000.0000.0000.000
206G222THR0-0.054-0.04335.5070.0720.0720.0000.0000.0000.000
207G223LEU0-0.013-0.02032.4190.1410.1410.0000.0000.0000.000
208G224PRO00.0610.03937.172-0.029-0.0290.0000.0000.0000.000
209G225ASP-1-0.924-0.96338.6887.8967.8960.0000.0000.0000.000
210G226ASP-1-0.943-0.97039.6057.8337.8330.0000.0000.0000.000
211G227ILE0-0.061-0.00634.7290.1380.1380.0000.0000.0000.000
212G228GLN0-0.033-0.01634.7340.2600.2600.0000.0000.0000.000
213G229SER00.031-0.01529.4980.0730.0730.0000.0000.0000.000
214G230ALA00.0090.00127.489-0.033-0.0330.0000.0000.0000.000
215G231THR0-0.024-0.01021.4760.2050.2050.0000.0000.0000.000
216G232ILE0-0.042-0.00720.7890.1470.1470.0000.0000.0000.000
217G233GLY00.000-0.02718.3850.3530.3530.0000.0000.0000.000
218G234HIS00.0060.00814.017-1.579-1.5790.0000.0000.0000.000
219G235LEU0-0.055-0.02612.1110.9500.9500.0000.0000.0000.000
220G236ARG10.8340.9069.282-30.541-30.5410.0000.0000.0000.000
221G237PRO0-0.0090.0016.6924.9534.9530.0000.0000.0000.000
222G238GLY00.0240.0106.600-2.033-2.0330.0000.0000.0000.000
223G239CYS0-0.060-0.0317.269-3.593-3.5930.0000.0000.0000.000
224G240HIS00.0160.03910.731-0.640-0.6400.0000.0000.0000.000
225G241ALA00.0030.00411.4462.2062.2060.0000.0000.0000.000
226G242ALA00.009-0.00413.859-1.252-1.2520.0000.0000.0000.000
227G243ASN00.0120.01616.2231.2381.2380.0000.0000.0000.000
228G244MET0-0.021-0.00419.066-0.214-0.2140.0000.0000.0000.000
229G245GLU-1-0.813-0.91020.99213.03613.0360.0000.0000.0000.000
230G246CYS0-0.033-0.00224.560-0.208-0.2080.0000.0000.0000.000
231G247TRP00.0780.02326.9010.2030.2030.0000.0000.0000.000
232G248SER0-0.033-0.05931.341-0.136-0.1360.0000.0000.0000.000
233G249MET00.0410.03234.564-0.082-0.0820.0000.0000.0000.000
234G250LEU0-0.0200.00436.485-0.192-0.1920.0000.0000.0000.000
235G251MET0-0.098-0.02730.2990.2280.2280.0000.0000.0000.000
236G252SER0-0.086-0.06735.575-0.162-0.1620.0000.0000.0000.000