FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: RY888

Calculation Name: 1T72-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1T72

Chain ID: A

ChEMBL ID:

UniProt ID: O67053

Base Structure: X-ray

Registration Date: 2023-09-27

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 215
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2540209.618938
FMO2-HF: Nuclear repulsion 2453062.91627
FMO2-HF: Total energy -87146.702668
FMO2-MP2: Total energy -87397.176041


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:1:GLY)


Summations of interaction energy for fragment #1(A:1:GLY)
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.
-2.183-0.834-0.021-0.73-0.5970
Interaction energy analysis for fragmet #1(A:1:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.006 / q_NPA : -0.017
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].
3A3GLY00.0500.0283.798-0.7060.643-0.021-0.730-0.5970.000
4A4GLY0-0.018-0.0197.042-0.091-0.0910.0000.0000.0000.000
5A5GLY00.0220.00610.3290.0430.0430.0000.0000.0000.000
6A6GLY00.0720.04610.7400.0390.0390.0000.0000.0000.000
7A7MET00.000-0.0179.6920.1240.1240.0000.0000.0000.000
8A8LYS10.8510.94013.8180.1770.1770.0000.0000.0000.000
9A9LEU00.0870.05015.5740.0330.0330.0000.0000.0000.000
10A10PHE0-0.0180.00716.1650.0120.0120.0000.0000.0000.000
11A11LYS10.9780.98317.8290.2000.2000.0000.0000.0000.000
12A12GLU-1-0.793-0.81219.782-0.114-0.1140.0000.0000.0000.000
13A13LEU00.0290.00820.4870.0200.0200.0000.0000.0000.000
14A14GLU-1-0.905-0.96321.452-0.223-0.2230.0000.0000.0000.000
15A15GLU-1-0.929-0.97723.946-0.115-0.1150.0000.0000.0000.000
16A16THR0-0.056-0.02725.4020.0200.0200.0000.0000.0000.000
17A17LYS10.9250.95723.4290.2200.2200.0000.0000.0000.000
18A18GLU-1-0.959-0.98128.025-0.111-0.1110.0000.0000.0000.000
19A19GLN0-0.087-0.03929.8320.0150.0150.0000.0000.0000.000
20A20VAL00.0750.03230.9290.0070.0070.0000.0000.0000.000
21A21ILE00.0040.00731.1020.0060.0060.0000.0000.0000.000
22A22LYS10.8810.94734.2500.0770.0770.0000.0000.0000.000
23A23MET00.0080.00435.8150.0030.0030.0000.0000.0000.000
24A24ALA00.1000.04637.1030.0040.0040.0000.0000.0000.000
25A25LYS10.9050.95438.7480.0700.0700.0000.0000.0000.000
26A26LEU00.0000.00240.3720.0030.0030.0000.0000.0000.000
27A27VAL00.0950.05641.2650.0030.0030.0000.0000.0000.000
28A28GLN0-0.069-0.03840.2640.0040.0040.0000.0000.0000.000
29A29GLU-1-0.985-1.00144.725-0.042-0.0420.0000.0000.0000.000
30A30ALA00.0060.01546.2620.0030.0030.0000.0000.0000.000
31A31ILE00.0220.00146.3840.0020.0020.0000.0000.0000.000
32A32ASP-1-0.928-0.97548.991-0.042-0.0420.0000.0000.0000.000
33A33LYS10.9240.96849.6770.0390.0390.0000.0000.0000.000
34A34ALA00.0240.02452.2470.0020.0020.0000.0000.0000.000
35A35THR00.0440.05753.3750.0020.0020.0000.0000.0000.000
36A36GLU-1-0.959-0.97155.387-0.031-0.0310.0000.0000.0000.000
37A37ALA0-0.010-0.00556.7050.0020.0020.0000.0000.0000.000
38A38LEU00.0160.00558.0220.0020.0020.0000.0000.0000.000
39A39ASN0-0.116-0.08458.4940.0020.0020.0000.0000.0000.000
40A40LYS10.8350.91360.4940.0320.0320.0000.0000.0000.000
41A41GLN0-0.056-0.02563.0180.0020.0020.0000.0000.0000.000
42A42ASN0-0.0170.01559.9130.0020.0020.0000.0000.0000.000
43A43VAL00.0600.01060.059-0.001-0.0010.0000.0000.0000.000
44A44GLU-1-0.946-0.95058.056-0.025-0.0250.0000.0000.0000.000
45A45LEU00.005-0.02254.834-0.001-0.0010.0000.0000.0000.000
46A46ALA00.0260.01255.045-0.002-0.0020.0000.0000.0000.000
47A47GLU-1-0.887-0.96554.902-0.024-0.0240.0000.0000.0000.000
48A48GLU-1-1.000-0.98952.398-0.032-0.0320.0000.0000.0000.000
49A49VAL0-0.016-0.01050.375-0.001-0.0010.0000.0000.0000.000
50A50ILE00.0200.02250.203-0.001-0.0010.0000.0000.0000.000
51A51LYS10.8460.93850.4930.0270.0270.0000.0000.0000.000
52A52GLY0-0.086-0.05447.454-0.001-0.0010.0000.0000.0000.000
53A53ASP-1-0.834-0.92545.866-0.045-0.0450.0000.0000.0000.000
54A54ASP-1-0.859-0.92645.092-0.034-0.0340.0000.0000.0000.000
55A55THR0-0.144-0.07240.970-0.001-0.0010.0000.0000.0000.000
56A56ILE0-0.024-0.02640.734-0.004-0.0040.0000.0000.0000.000
57A57ASP-1-0.758-0.86240.254-0.045-0.0450.0000.0000.0000.000
58A58LEU0-0.133-0.07639.197-0.002-0.0020.0000.0000.0000.000
59A59LEU0-0.032-0.02535.659-0.003-0.0030.0000.0000.0000.000
60A60GLU-1-0.760-0.87135.205-0.065-0.0650.0000.0000.0000.000
61A61VAL00.0170.00934.786-0.004-0.0040.0000.0000.0000.000
62A62ASP-1-0.964-0.96832.304-0.073-0.0730.0000.0000.0000.000
63A63ILE00.022-0.00130.325-0.007-0.0070.0000.0000.0000.000
64A64GLU-1-0.704-0.76729.920-0.076-0.0760.0000.0000.0000.000
65A65ARG10.7170.74429.8340.0400.0400.0000.0000.0000.000
66A66ARG10.8520.93226.9870.0900.0900.0000.0000.0000.000
67A67CYS00.0230.01525.586-0.012-0.0120.0000.0000.0000.000
68A68ILE00.0140.00625.051-0.007-0.0070.0000.0000.0000.000
69A69ARG10.8520.94523.9840.0610.0610.0000.0000.0000.000
70A70MET0-0.037-0.00721.1980.0020.0020.0000.0000.0000.000
71A71ILE00.0250.01720.097-0.023-0.0230.0000.0000.0000.000
72A72ALA0-0.070-0.03520.374-0.003-0.0030.0000.0000.0000.000
73A73LEU0-0.081-0.04718.7110.0120.0120.0000.0000.0000.000
74A74TYR0-0.149-0.17415.4060.0050.0050.0000.0000.0000.000
75A75GLN0-0.056-0.00212.522-0.021-0.0210.0000.0000.0000.000
76A76PRO00.0220.03215.572-0.038-0.0380.0000.0000.0000.000
77A77GLU-1-0.889-0.96112.142-0.472-0.4720.0000.0000.0000.000
78A78ALA0-0.049-0.05016.8940.0100.0100.0000.0000.0000.000
79A79GLY00.0570.03618.9690.0250.0250.0000.0000.0000.000
80A80ASP-1-0.852-0.91916.595-0.367-0.3670.0000.0000.0000.000
81A81LEU0-0.041-0.02819.9200.0320.0320.0000.0000.0000.000
82A82ARG10.9440.96221.7750.2290.2290.0000.0000.0000.000
83A83MET00.0550.05223.2030.0120.0120.0000.0000.0000.000
84A84ILE0-0.0150.00221.2110.0150.0150.0000.0000.0000.000
85A85MET0-0.025-0.01525.3810.0150.0150.0000.0000.0000.000
86A86GLY00.0190.01427.6490.0110.0110.0000.0000.0000.000
87A87ILE00.015-0.00426.7230.0080.0080.0000.0000.0000.000
88A88TYR0-0.073-0.05529.3050.0080.0080.0000.0000.0000.000
89A89LYS10.9630.98231.1580.0920.0920.0000.0000.0000.000
90A90ILE00.0350.01832.4070.0050.0050.0000.0000.0000.000
91A91VAL0-0.041-0.01233.1710.0020.0020.0000.0000.0000.000
92A92SER00.0230.01635.1630.0030.0030.0000.0000.0000.000
93A93ASP-1-0.872-0.91338.065-0.069-0.0690.0000.0000.0000.000
94A94LEU00.002-0.02736.2140.0030.0030.0000.0000.0000.000
95A95GLU-1-0.813-0.89239.811-0.047-0.0470.0000.0000.0000.000
96A96ARG10.7900.89341.4080.0500.0500.0000.0000.0000.000
97A97MET0-0.056-0.01141.9330.0010.0010.0000.0000.0000.000
98A98GLY0-0.036-0.01844.1290.0020.0020.0000.0000.0000.000
99A99ASP-1-0.818-0.89845.633-0.037-0.0370.0000.0000.0000.000
100A100GLU-1-0.851-0.93047.678-0.040-0.0400.0000.0000.0000.000
101A101ALA0-0.044-0.03848.6880.0020.0020.0000.0000.0000.000
102A102GLU-1-0.879-0.92949.575-0.031-0.0310.0000.0000.0000.000
103A103ASN00.0320.00751.4010.0040.0040.0000.0000.0000.000
104A104ILE0-0.101-0.04151.8430.0020.0020.0000.0000.0000.000
105A105ALA0-0.018-0.02153.8960.0020.0020.0000.0000.0000.000
106A106GLU-1-0.815-0.92255.617-0.025-0.0250.0000.0000.0000.000
107A107ARG10.8040.89657.6940.0300.0300.0000.0000.0000.000
108A108ALA0-0.013-0.00158.7290.0010.0010.0000.0000.0000.000
109A109ILE00.0140.01959.2760.0010.0010.0000.0000.0000.000
110A110LEU0-0.023-0.01561.8970.0010.0010.0000.0000.0000.000
111A111LEU0-0.099-0.06261.9070.0010.0010.0000.0000.0000.000
112A112ALA00.0040.00564.2000.0000.0000.0000.0000.0000.000
113A113GLU-1-1.017-0.98866.063-0.020-0.0200.0000.0000.0000.000
114A114GLU-1-0.978-1.02369.143-0.019-0.0190.0000.0000.0000.000
115A115PRO0-0.046-0.00769.413-0.001-0.0010.0000.0000.0000.000
116A116PRO00.0610.04467.5530.0000.0000.0000.0000.0000.000
117A117LEU0-0.0440.01767.9590.0000.0000.0000.0000.0000.000
118A118LYS10.8060.86564.9750.0290.0290.0000.0000.0000.000
119A119PRO0-0.023-0.01766.5950.0000.0000.0000.0000.0000.000
120A120TYR0-0.009-0.01361.7300.0000.0000.0000.0000.0000.000
121A121VAL00.0590.02661.503-0.001-0.0010.0000.0000.0000.000
122A122ASN00.0060.00460.048-0.002-0.0020.0000.0000.0000.000
123A123ILE00.0350.03057.100-0.001-0.0010.0000.0000.0000.000
124A124ASN0-0.045-0.01556.374-0.002-0.0020.0000.0000.0000.000
125A125PHE0-0.007-0.01555.572-0.001-0.0010.0000.0000.0000.000
126A126MET0-0.0380.00053.747-0.001-0.0010.0000.0000.0000.000
127A127SER00.0480.02451.716-0.002-0.0020.0000.0000.0000.000
128A128GLU-1-0.896-0.94750.532-0.050-0.0500.0000.0000.0000.000
129A129ILE0-0.045-0.01549.103-0.002-0.0020.0000.0000.0000.000
130A130VAL00.0740.02847.695-0.003-0.0030.0000.0000.0000.000
131A131LYS10.8240.92746.2090.0460.0460.0000.0000.0000.000
132A132GLU-1-0.966-0.98044.867-0.068-0.0680.0000.0000.0000.000
133A133MET0-0.100-0.03843.382-0.003-0.0030.0000.0000.0000.000
134A134VAL00.0280.01341.234-0.004-0.0040.0000.0000.0000.000
135A135ASN0-0.024-0.00739.575-0.007-0.0070.0000.0000.0000.000
136A136ASP-1-0.862-0.94338.537-0.083-0.0830.0000.0000.0000.000
137A137SER0-0.0040.01237.679-0.007-0.0070.0000.0000.0000.000
138A138VAL00.0880.04134.383-0.008-0.0080.0000.0000.0000.000
139A139ILE0-0.087-0.03833.924-0.009-0.0090.0000.0000.0000.000
140A140SER0-0.101-0.07233.012-0.010-0.0100.0000.0000.0000.000
141A141PHE00.0580.01929.536-0.010-0.0100.0000.0000.0000.000
142A142ILE0-0.038-0.00728.810-0.013-0.0130.0000.0000.0000.000
143A143GLN0-0.076-0.03927.912-0.017-0.0170.0000.0000.0000.000
144A144GLN0-0.0020.00425.1800.0050.0050.0000.0000.0000.000
145A145ASP-1-0.904-0.93830.193-0.115-0.1150.0000.0000.0000.000
146A146THR00.0630.00833.0100.0060.0060.0000.0000.0000.000
147A147LEU0-0.049-0.03535.0790.0070.0070.0000.0000.0000.000
148A148LEU0-0.087-0.04936.6890.0070.0070.0000.0000.0000.000
149A149ALA00.0970.05236.2160.0050.0050.0000.0000.0000.000
150A150LYS10.9500.97337.7170.1000.1000.0000.0000.0000.000
151A151LYS10.9190.97040.3520.0890.0890.0000.0000.0000.000
152A152VAL0-0.033-0.01740.1860.0040.0040.0000.0000.0000.000
153A153ILE00.0430.01740.7850.0030.0030.0000.0000.0000.000
154A154GLU-1-0.996-0.98443.841-0.063-0.0630.0000.0000.0000.000
155A155LYS10.8900.94145.1000.0680.0680.0000.0000.0000.000
156A156ASP-1-0.794-0.90746.383-0.053-0.0530.0000.0000.0000.000
157A157ASP-1-0.788-0.87848.347-0.051-0.0510.0000.0000.0000.000
158A158THR0-0.132-0.05851.0100.0030.0030.0000.0000.0000.000
159A159VAL0-0.009-0.00150.0530.0030.0030.0000.0000.0000.000
160A160ASP-1-0.807-0.88551.678-0.045-0.0450.0000.0000.0000.000
161A161GLU-1-1.025-1.04153.991-0.041-0.0410.0000.0000.0000.000
162A162LEU0-0.114-0.06355.1070.0020.0020.0000.0000.0000.000
163A163TYR0-0.056-0.09155.7680.0020.0020.0000.0000.0000.000
164A164HIS0-0.020-0.02057.2610.0040.0040.0000.0000.0000.000
165A165GLN0-0.059-0.03660.4410.0020.0020.0000.0000.0000.000
166A166LEU0-0.0120.00160.4330.0020.0020.0000.0000.0000.000
167A167GLU-1-0.752-0.80861.229-0.029-0.0290.0000.0000.0000.000
168A168ARG10.8860.94563.8340.0310.0310.0000.0000.0000.000
169A169GLU-1-0.792-0.87865.370-0.028-0.0280.0000.0000.0000.000
170A170LEU00.0030.00163.9240.0010.0010.0000.0000.0000.000
171A171MET0-0.0390.00167.9060.0010.0010.0000.0000.0000.000
172A172THR0-0.009-0.01869.8170.0010.0010.0000.0000.0000.000
173A173TYR00.0390.02169.7040.0010.0010.0000.0000.0000.000
174A174VAL0-0.041-0.02370.3160.0010.0010.0000.0000.0000.000
175A175LEU0-0.071-0.05573.0670.0010.0010.0000.0000.0000.000
176A176GLU-1-0.983-0.97175.499-0.021-0.0210.0000.0000.0000.000
177A177ASP-1-0.831-0.93676.568-0.018-0.0180.0000.0000.0000.000
178A178PRO00.0090.00875.4670.0000.0000.0000.0000.0000.000
179A179ARG10.8820.96674.9210.0170.0170.0000.0000.0000.000
180A180ASN0-0.005-0.01772.1190.0000.0000.0000.0000.0000.000
181A181ILE0-0.060-0.01970.251-0.001-0.0010.0000.0000.0000.000
182A182LYS10.9760.98568.7950.0190.0190.0000.0000.0000.000
183A183ARG10.9971.00567.4100.0210.0210.0000.0000.0000.000
184A184ALA00.0110.00266.204-0.001-0.0010.0000.0000.0000.000
185A185MET0-0.0100.00064.437-0.001-0.0010.0000.0000.0000.000
186A186HIS00.0560.04662.809-0.002-0.0020.0000.0000.0000.000
187A187LEU00.0430.01261.405-0.001-0.0010.0000.0000.0000.000
188A188SER0-0.053-0.02261.016-0.001-0.0010.0000.0000.0000.000
189A189PHE0-0.049-0.03457.481-0.001-0.0010.0000.0000.0000.000
190A190VAL00.0270.03456.928-0.001-0.0010.0000.0000.0000.000
191A191ALA0-0.014-0.01455.866-0.002-0.0020.0000.0000.0000.000
192A192ARG10.8800.92855.5010.0300.0300.0000.0000.0000.000
193A193HIS0-0.003-0.01852.4430.0000.0000.0000.0000.0000.000
194A194TYR0-0.067-0.08651.050-0.001-0.0010.0000.0000.0000.000
195A195GLU-1-0.905-0.97550.557-0.047-0.0470.0000.0000.0000.000
196A196ARG10.9971.01649.1410.0410.0410.0000.0000.0000.000
197A197ILE0-0.031-0.01346.038-0.003-0.0030.0000.0000.0000.000
198A198ALA0-0.059-0.04345.573-0.003-0.0030.0000.0000.0000.000
199A199ASP-1-0.814-0.90545.416-0.059-0.0590.0000.0000.0000.000
200A200HIS0-0.051-0.02042.4910.0000.0000.0000.0000.0000.000
201A201ALA0-0.040-0.04141.319-0.005-0.0050.0000.0000.0000.000
202A202GLU-1-0.916-0.96640.573-0.072-0.0720.0000.0000.0000.000
203A203ASN00.0490.02139.314-0.004-0.0040.0000.0000.0000.000
204A204VAL0-0.042-0.01335.449-0.007-0.0070.0000.0000.0000.000
205A205ALA0-0.015-0.00635.769-0.008-0.0080.0000.0000.0000.000
206A206GLU-1-0.875-0.93836.502-0.086-0.0860.0000.0000.0000.000
207A207ALA0-0.075-0.04233.131-0.008-0.0080.0000.0000.0000.000
208A208ALA0-0.054-0.03032.113-0.010-0.0100.0000.0000.0000.000
209A209ILE00.005-0.00331.893-0.011-0.0110.0000.0000.0000.000
210A210TYR0-0.064-0.00628.342-0.010-0.0100.0000.0000.0000.000
211A211LEU0-0.034-0.03226.735-0.010-0.0100.0000.0000.0000.000
212A212SER0-0.060-0.02127.545-0.012-0.0120.0000.0000.0000.000
213A213GLU-1-0.993-1.00528.638-0.118-0.1180.0000.0000.0000.000
214A214GLY0-0.080-0.02626.764-0.003-0.0030.0000.0000.0000.000
215A215GLU-1-1.071-1.02621.133-0.299-0.2990.0000.0000.0000.000