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: 9M4Y2

Calculation Name: 4J7R-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4J7R

Chain ID: A

ChEMBL ID:

UniProt ID: Q7X8Q2

Base Structure: X-ray

Registration Date: 2023-09-26

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 800
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -21286006.223704
FMO2-HF: Nuclear repulsion 20972647.184687
FMO2-HF: Total energy -313359.039017
FMO2-MP2: Total energy -314270.450039


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:76:LEU)


Summations of interaction energy for fragment #1(A:76:LEU)
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.
-23.986-20.50812.945-7.94-8.483-0.06
Interaction energy analysis for fragmet #1(A:76:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.039 / q_NPA : 0.002
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].
3A78CYS00.0050.0083.240-2.1300.7750.617-1.462-2.0610.005
4A79GLU-1-0.877-0.9291.833-21.971-21.97912.291-6.312-5.971-0.065
5A80PRO0-0.015-0.0254.6680.1310.175-0.001-0.012-0.0300.000
6A81SER0-0.001-0.0047.226-0.285-0.2850.0000.0000.0000.000
7A82GLY0-0.0100.0068.1690.3120.3120.0000.0000.0000.000
8A83GLN0-0.035-0.01411.3280.0170.0170.0000.0000.0000.000
9A84PRO0-0.021-0.01114.165-0.071-0.0710.0000.0000.0000.000
10A85ALA00.0020.00216.8270.0090.0090.0000.0000.0000.000
11A86SER00.0160.00818.2670.0580.0580.0000.0000.0000.000
12A87THR0-0.043-0.03321.672-0.003-0.0030.0000.0000.0000.000
13A88ALA0-0.017-0.01622.6390.0390.0390.0000.0000.0000.000
14A89TYR00.0760.05117.3090.0440.0440.0000.0000.0000.000
15A90GLY00.0550.03616.0450.0130.0130.0000.0000.0000.000
16A91PRO0-0.041-0.04612.6140.0110.0110.0000.0000.0000.000
17A92ALA00.0160.02512.064-0.058-0.0580.0000.0000.0000.000
18A93LEU0-0.054-0.0197.609-0.233-0.2330.0000.0000.0000.000
19A94THR00.0120.0012.8980.1460.6830.038-0.154-0.4210.000
20A95GLY00.0280.0155.8620.8160.8160.0000.0000.0000.000
21A96ARG10.7850.8596.021-0.150-0.1500.0000.0000.0000.000
22A97PRO00.0240.0117.928-0.112-0.1120.0000.0000.0000.000
23A98ALA0-0.0090.02710.498-0.034-0.0340.0000.0000.0000.000
24A99PRO0-0.024-0.02911.4080.0360.0360.0000.0000.0000.000
25A100LEU0-0.0010.00214.437-0.038-0.0380.0000.0000.0000.000
26A101GLY00.0500.02616.9110.0060.0060.0000.0000.0000.000
27A102ALA0-0.025-0.00216.582-0.029-0.0290.0000.0000.0000.000
28A103SER0-0.053-0.04014.7180.0550.0550.0000.0000.0000.000
29A104ILE0-0.033-0.02015.663-0.056-0.0560.0000.0000.0000.000
30A105ASP-1-0.744-0.82410.330-0.129-0.1290.0000.0000.0000.000
31A106ALA0-0.070-0.03912.888-0.015-0.0150.0000.0000.0000.000
32A107ASP-1-0.955-0.9769.943-0.019-0.0190.0000.0000.0000.000
33A108THR0-0.021-0.0509.323-0.086-0.0860.0000.0000.0000.000
34A109GLY0-0.031-0.00512.464-0.027-0.0270.0000.0000.0000.000
35A110ALA0-0.014-0.00211.9970.0150.0150.0000.0000.0000.000
36A111ILE0-0.009-0.00114.1360.0840.0840.0000.0000.0000.000
37A112ASN00.0330.02010.084-0.277-0.2770.0000.0000.0000.000
38A113PHE00.007-0.00712.9670.1270.1270.0000.0000.0000.000
39A114SER0-0.011-0.01912.898-0.072-0.0720.0000.0000.0000.000
40A115VAL00.0220.01714.5880.0390.0390.0000.0000.0000.000
41A116PHE00.0190.00516.5110.0050.0050.0000.0000.0000.000
42A117SER0-0.033-0.05918.336-0.024-0.0240.0000.0000.0000.000
43A118SER0-0.068-0.04318.7070.0010.0010.0000.0000.0000.000
44A119SER0-0.037-0.04120.794-0.007-0.0070.0000.0000.0000.000
45A120ALA0-0.0110.02119.669-0.013-0.0130.0000.0000.0000.000
46A121GLU-1-0.803-0.90120.092-0.051-0.0510.0000.0000.0000.000
47A122SER0-0.066-0.04918.159-0.045-0.0450.0000.0000.0000.000
48A123VAL00.0100.01816.6090.0310.0310.0000.0000.0000.000
49A124SER00.0090.00817.198-0.069-0.0690.0000.0000.0000.000
50A125LEU00.0100.03015.9230.0490.0490.0000.0000.0000.000
51A126VAL0-0.033-0.01718.373-0.020-0.0200.0000.0000.0000.000
52A127LEU00.005-0.00319.5980.0100.0100.0000.0000.0000.000
53A128PHE00.0360.00923.4550.0040.0040.0000.0000.0000.000
54A129THR00.0440.01327.1860.0090.0090.0000.0000.0000.000
55A130GLU-1-0.806-0.90429.720-0.089-0.0890.0000.0000.0000.000
56A131ALA0-0.007-0.00132.6730.0090.0090.0000.0000.0000.000
57A132ASP-1-0.774-0.83330.417-0.172-0.1720.0000.0000.0000.000
58A133LEU00.0010.01329.7980.0040.0040.0000.0000.0000.000
59A134ASN0-0.058-0.04432.3390.0130.0130.0000.0000.0000.000
60A135ALA0-0.047-0.02034.9700.0060.0060.0000.0000.0000.000
61A136GLY00.0160.02033.9830.0000.0000.0000.0000.0000.000
62A137ARG10.8510.89631.3470.1540.1540.0000.0000.0000.000
63A138ALA00.0420.02625.7900.0020.0020.0000.0000.0000.000
64A139THR0-0.094-0.07226.1570.0090.0090.0000.0000.0000.000
65A140PHE0-0.020-0.02622.029-0.012-0.0120.0000.0000.0000.000
66A141GLU-1-0.809-0.87521.242-0.223-0.2230.0000.0000.0000.000
67A142ILE0-0.036-0.01615.027-0.027-0.0270.0000.0000.0000.000
68A143PRO00.0130.00316.653-0.001-0.0010.0000.0000.0000.000
69A144LEU0-0.039-0.00912.730-0.114-0.1140.0000.0000.0000.000
70A145ASP-1-0.798-0.90210.240-0.663-0.6630.0000.0000.0000.000
71A146PRO0-0.004-0.02311.227-0.017-0.0170.0000.0000.0000.000
72A147TYR0-0.061-0.02410.5900.1680.1680.0000.0000.0000.000
73A148VAL0-0.0310.0015.0550.0810.0810.0000.0000.0000.000
74A149ASN0-0.029-0.0216.586-0.106-0.1060.0000.0000.0000.000
75A150ARG10.9310.9689.0250.1110.1110.0000.0000.0000.000
76A151THR0-0.033-0.0088.0420.1180.1180.0000.0000.0000.000
77A152GLY00.0240.02510.5400.0010.0010.0000.0000.0000.000
78A153ASP-1-0.850-0.91814.1860.0960.0960.0000.0000.0000.000
79A154VAL0-0.028-0.01113.283-0.037-0.0370.0000.0000.0000.000
80A155TRP0-0.009-0.00612.351-0.005-0.0050.0000.0000.0000.000
81A156HIS10.8110.8756.3710.5100.5100.0000.0000.0000.000
82A157ILE00.0060.0109.706-0.181-0.1810.0000.0000.0000.000
83A158MET0-0.0400.0008.2800.2790.2790.0000.0000.0000.000
84A159LEU00.0150.01411.340-0.178-0.1780.0000.0000.0000.000
85A160PRO00.0230.01412.3240.1290.1290.0000.0000.0000.000
86A161ASP-1-0.916-0.97214.760-0.517-0.5170.0000.0000.0000.000
87A162LEU0-0.075-0.02418.0270.0260.0260.0000.0000.0000.000
88A163ARG10.8200.88419.7970.2850.2850.0000.0000.0000.000
89A164ASP-1-0.921-0.96823.486-0.174-0.1740.0000.0000.0000.000
90A165ASP-1-0.890-0.92425.307-0.190-0.1900.0000.0000.0000.000
91A166LEU0-0.052-0.02323.2140.0040.0040.0000.0000.0000.000
92A167LEU0-0.026-0.01425.2470.0110.0110.0000.0000.0000.000
93A168TYR0-0.072-0.07220.158-0.021-0.0210.0000.0000.0000.000
94A169GLY00.0250.01722.3520.0340.0340.0000.0000.0000.000
95A170TYR00.013-0.01717.078-0.047-0.0470.0000.0000.0000.000
96A171ARG10.7850.87521.5590.2190.2190.0000.0000.0000.000
97A172VAL0-0.005-0.00921.110-0.025-0.0250.0000.0000.0000.000
98A173GLU-1-0.810-0.89522.163-0.132-0.1320.0000.0000.0000.000
99A174GLY00.0280.01222.8260.0020.0020.0000.0000.0000.000
100A175VAL0-0.031-0.00225.285-0.001-0.0010.0000.0000.0000.000
101A176HIS00.0300.01328.6720.0090.0090.0000.0000.0000.000
102A177GLN00.0490.02131.6890.0020.0020.0000.0000.0000.000
103A178GLU-1-0.846-0.90334.502-0.019-0.0190.0000.0000.0000.000
104A179GLU-1-0.923-0.94931.287-0.064-0.0640.0000.0000.0000.000
105A180ASP-1-0.829-0.92132.827-0.026-0.0260.0000.0000.0000.000
106A181LYS10.7910.86534.6900.0290.0290.0000.0000.0000.000
107A182ASP-1-0.870-0.92234.1800.0030.0030.0000.0000.0000.000
108A183TYR0-0.065-0.02829.5810.0070.0070.0000.0000.0000.000
109A184PRO00.0170.02332.463-0.005-0.0050.0000.0000.0000.000
110A185GLY00.0720.02132.6830.0070.0070.0000.0000.0000.000
111A186MET0-0.0350.01526.4690.0010.0010.0000.0000.0000.000
112A187ARG10.8090.87229.5080.0140.0140.0000.0000.0000.000
113A188HIS00.0180.02824.296-0.011-0.0110.0000.0000.0000.000
114A189ASP-1-0.773-0.87728.279-0.083-0.0830.0000.0000.0000.000
115A190LYS10.8970.94526.6150.1400.1400.0000.0000.0000.000
116A191ARG10.8500.90327.5630.0700.0700.0000.0000.0000.000
117A192ARG10.8260.90829.0020.0770.0770.0000.0000.0000.000
118A193VAL00.0170.01024.483-0.012-0.0120.0000.0000.0000.000
119A194VAL0-0.0180.01523.7560.0110.0110.0000.0000.0000.000
120A195LEU00.0170.00124.511-0.018-0.0180.0000.0000.0000.000
121A196ASP-1-0.750-0.84920.199-0.068-0.0680.0000.0000.0000.000
122A197PRO00.0320.01322.4110.0050.0050.0000.0000.0000.000
123A198TYR0-0.024-0.04221.0890.0080.0080.0000.0000.0000.000
124A199ALA0-0.061-0.01923.211-0.004-0.0040.0000.0000.0000.000
125A200VAL00.0330.02124.2190.0090.0090.0000.0000.0000.000
126A201ALA00.012-0.00725.9570.0070.0070.0000.0000.0000.000
127A202VAL00.0050.01027.706-0.013-0.0130.0000.0000.0000.000
128A203LEU0-0.021-0.00130.1920.0060.0060.0000.0000.0000.000
129A204ASN00.004-0.02431.859-0.002-0.0020.0000.0000.0000.000
130A205ARG10.7780.87234.6220.0420.0420.0000.0000.0000.000
131A206ARG10.7660.86435.6430.0790.0790.0000.0000.0000.000
132A207ARG10.8560.91439.2000.0480.0480.0000.0000.0000.000
133A208TRP00.0370.01642.817-0.002-0.0020.0000.0000.0000.000
134A209GLY0-0.012-0.01244.2590.0000.0000.0000.0000.0000.000
135A210GLN0-0.055-0.01141.3950.0000.0000.0000.0000.0000.000
136A211MET00.0090.02042.923-0.001-0.0010.0000.0000.0000.000
137A212GLY00.0310.01140.395-0.003-0.0030.0000.0000.0000.000
138A213PRO0-0.0160.00738.4930.0040.0040.0000.0000.0000.000
139A214ASN0-0.026-0.01441.317-0.001-0.0010.0000.0000.0000.000
140A215LEU00.0260.02037.343-0.003-0.0030.0000.0000.0000.000
141A216PRO00.0170.02539.8770.0060.0060.0000.0000.0000.000
142A217TYR0-0.049-0.05737.054-0.004-0.0040.0000.0000.0000.000
143A218GLY0-0.012-0.00838.1380.0060.0060.0000.0000.0000.000
144A219GLU-1-0.991-0.98938.823-0.092-0.0920.0000.0000.0000.000
145A220GLU-1-0.894-0.94432.971-0.131-0.1310.0000.0000.0000.000
146A221GLY0-0.044-0.02832.1880.0000.0000.0000.0000.0000.000
147A222VAL0-0.071-0.02532.474-0.008-0.0080.0000.0000.0000.000
148A223LEU0-0.049-0.01128.8900.0010.0010.0000.0000.0000.000
149A224GLY00.0120.00432.8540.0050.0050.0000.0000.0000.000
150A225VAL0-0.083-0.04534.595-0.001-0.0010.0000.0000.0000.000
151A226MET00.0180.01137.2470.0040.0040.0000.0000.0000.000
152A227PRO00.0370.02539.792-0.001-0.0010.0000.0000.0000.000
153A228THR00.0560.01441.522-0.002-0.0020.0000.0000.0000.000
154A229TRP0-0.041-0.00835.6260.0020.0020.0000.0000.0000.000
155A230PRO00.0320.02336.423-0.004-0.0040.0000.0000.0000.000
156A231GLN00.001-0.02629.0290.0050.0050.0000.0000.0000.000
157A232ALA0-0.015-0.00630.5990.0020.0020.0000.0000.0000.000
158A233ALA0-0.0050.00526.878-0.011-0.0110.0000.0000.0000.000
159A234ALA00.0260.01224.1450.0160.0160.0000.0000.0000.000
160A235ALA0-0.012-0.01825.242-0.022-0.0220.0000.0000.0000.000
161A236LEU00.0450.03020.3020.0040.0040.0000.0000.0000.000
162A237PRO00.0290.02219.1300.0220.0220.0000.0000.0000.000
163A238ALA0-0.009-0.00722.474-0.014-0.0140.0000.0000.0000.000
164A239ALA00.0420.02422.2090.0010.0010.0000.0000.0000.000
165A240ARG10.9810.97618.3150.0340.0340.0000.0000.0000.000
166A241GLY0-0.004-0.00221.826-0.009-0.0090.0000.0000.0000.000
167A242SER0-0.040-0.00925.1230.0040.0040.0000.0000.0000.000
168A243ALA0-0.025-0.02126.603-0.001-0.0010.0000.0000.0000.000
169A244PHE00.0240.01328.434-0.002-0.0020.0000.0000.0000.000
170A245ASP-1-0.855-0.91231.8050.0240.0240.0000.0000.0000.000
171A246TRP00.0340.00131.231-0.003-0.0030.0000.0000.0000.000
172A247GLU-1-0.813-0.88435.5720.0120.0120.0000.0000.0000.000
173A248GLY0-0.034-0.01636.7530.0010.0010.0000.0000.0000.000
174A249ASP-1-0.838-0.89137.1360.0410.0410.0000.0000.0000.000
175A250THR0-0.027-0.02136.2240.0070.0070.0000.0000.0000.000
176A251PRO00.0060.00235.490-0.005-0.0050.0000.0000.0000.000
177A252LEU0-0.038-0.00738.5100.0020.0020.0000.0000.0000.000
178A253ASN0-0.028-0.00340.3240.0060.0060.0000.0000.0000.000
179A254LEU0-0.0040.00842.2200.0010.0010.0000.0000.0000.000
180A255PRO00.0060.00545.5350.0020.0020.0000.0000.0000.000
181A256MET00.0590.04845.378-0.003-0.0030.0000.0000.0000.000
182A257GLU-1-0.840-0.92447.7480.0480.0480.0000.0000.0000.000
183A258SER0-0.091-0.05849.823-0.003-0.0030.0000.0000.0000.000
184A259LEU0-0.045-0.00846.047-0.002-0.0020.0000.0000.0000.000
185A260VAL0-0.020-0.02050.710-0.001-0.0010.0000.0000.0000.000
186A261ILE00.0040.00947.058-0.001-0.0010.0000.0000.0000.000
187A262TYR0-0.051-0.05549.254-0.002-0.0020.0000.0000.0000.000
188A263GLU-1-0.724-0.85447.5040.0170.0170.0000.0000.0000.000
189A264ALA0-0.009-0.01847.115-0.002-0.0020.0000.0000.0000.000
190A265HIS00.0510.02245.1810.0010.0010.0000.0000.0000.000
191A266VAL00.0140.00841.672-0.001-0.0010.0000.0000.0000.000
192A267ARG10.8310.90845.0920.0180.0180.0000.0000.0000.000
193A268GLY00.0450.01347.135-0.001-0.0010.0000.0000.0000.000
194A269PHE0-0.0040.00148.5520.0000.0000.0000.0000.0000.000
195A270THR00.0310.00449.2140.0000.0000.0000.0000.0000.000
196A271ALA00.0330.03150.045-0.002-0.0020.0000.0000.0000.000
197A272HIS0-0.0050.02751.784-0.001-0.0010.0000.0000.0000.000
198A273ALA00.0200.00455.5850.0000.0000.0000.0000.0000.000
199A274SER0-0.041-0.04557.4480.0000.0000.0000.0000.0000.000
200A275SER0-0.019-0.01053.6260.0010.0010.0000.0000.0000.000
201A276GLY00.0120.00655.7260.0010.0010.0000.0000.0000.000
202A277VAL0-0.078-0.01750.3740.0000.0000.0000.0000.0000.000
203A278ALA0-0.037-0.02749.626-0.002-0.0020.0000.0000.0000.000
204A279ALA0-0.039-0.02646.146-0.003-0.0030.0000.0000.0000.000
205A280PRO0-0.0020.00147.7540.0020.0020.0000.0000.0000.000
206A281GLY0-0.0170.01047.785-0.002-0.0020.0000.0000.0000.000
207A282THR0-0.032-0.02943.253-0.002-0.0020.0000.0000.0000.000
208A283TYR00.047-0.00637.4120.0050.0050.0000.0000.0000.000
209A284ALA00.0080.00042.3540.0030.0030.0000.0000.0000.000
210A285GLY00.0110.00544.0150.0020.0020.0000.0000.0000.000
211A286MET0-0.040-0.00944.8510.0020.0020.0000.0000.0000.000
212A287VAL00.0270.00043.1100.0030.0030.0000.0000.0000.000
213A288GLU-1-0.805-0.88746.224-0.009-0.0090.0000.0000.0000.000
214A289ARG10.7650.87449.5170.0060.0060.0000.0000.0000.000
215A290LEU00.0300.02245.2600.0020.0020.0000.0000.0000.000
216A291ASP-1-0.846-0.92149.9020.0100.0100.0000.0000.0000.000
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