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: 9M4K2

Calculation Name: 5GJ7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5GJ7

Chain ID: A

ChEMBL ID:

UniProt ID: C8WV06

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 388
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -6484986.413586
FMO2-HF: Nuclear repulsion 6334767.939074
FMO2-HF: Total energy -150218.474512
FMO2-MP2: Total energy -150658.432293


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:-2:SER)


Summations of interaction energy for fragment #1(A:-2:SER)
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.
-20.265-17.92915.979-8.966-9.348-0.072
Interaction energy analysis for fragmet #1(A:-2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.069 / q_NPA : -0.024
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].
3A0ALA00.0350.0012.7271.0943.9360.062-1.515-1.3880.004
4A1MET0-0.061-0.0214.133-0.428-0.313-0.001-0.040-0.0740.000
5A2TYR00.0820.0456.7990.6090.6090.0000.0000.0000.000
6A3ASP-1-0.824-0.8817.969-1.125-1.1250.0000.0000.0000.000
7A4ILE0-0.056-0.0198.9550.2600.2600.0000.0000.0000.000
8A5TYR0-0.028-0.0235.4220.4640.4640.0000.0000.0000.000
9A6GLY00.0250.0248.8630.1910.1910.0000.0000.0000.000
10A7GLU-1-0.817-0.9019.115-1.758-1.7580.0000.0000.0000.000
11A8ALA0-0.075-0.03210.562-0.045-0.0450.0000.0000.0000.000
12A9ALA00.0090.0116.4590.2240.2240.0000.0000.0000.000
13A10LEU0-0.0150.0155.756-0.353-0.3530.0000.0000.0000.000
14A11PRO00.0330.0185.8140.6710.6710.0000.0000.0000.000
15A12ALA00.011-0.0188.861-0.112-0.1120.0000.0000.0000.000
16A13ASP-1-0.800-0.88510.475-1.241-1.2410.0000.0000.0000.000
17A14VAL00.0170.0186.9730.0380.0380.0000.0000.0000.000
18A15ARG10.8940.94410.2001.3151.3150.0000.0000.0000.000
19A16GLU-1-0.794-0.85512.236-0.588-0.5880.0000.0000.0000.000
20A17ARG10.7410.82110.2861.4111.4110.0000.0000.0000.000
21A18LEU0-0.001-0.0169.7560.0250.0250.0000.0000.0000.000
22A19ARG10.7330.84314.1560.7130.7130.0000.0000.0000.000
23A20ILE00.0070.01017.4560.0720.0720.0000.0000.0000.000
24A21THR00.004-0.02314.7120.0630.0630.0000.0000.0000.000
25A22ARG10.8100.87612.5221.4161.4160.0000.0000.0000.000
26A23ASP-1-0.855-0.92018.601-0.532-0.5320.0000.0000.0000.000
27A24LEU0-0.041-0.01520.0810.0490.0490.0000.0000.0000.000
28A25ALA0-0.0080.00119.1570.0460.0460.0000.0000.0000.000
29A26GLN0-0.059-0.04821.3030.0190.0190.0000.0000.0000.000
30A27ALA00.0430.01824.0390.0380.0380.0000.0000.0000.000
31A28PHE0-0.016-0.02721.8860.0250.0250.0000.0000.0000.000
32A29HIS00.000-0.00824.4590.0280.0280.0000.0000.0000.000
33A30GLU-1-0.943-0.95726.328-0.313-0.3130.0000.0000.0000.000
34A31ARG10.8240.90128.4510.3380.3380.0000.0000.0000.000
35A32ALA0-0.0140.00827.4630.0160.0160.0000.0000.0000.000
36A33PRO0-0.061-0.03329.6080.0140.0140.0000.0000.0000.000
37A34GLU-1-0.894-0.95332.511-0.201-0.2010.0000.0000.0000.000
38A35HIS00.025-0.00430.896-0.001-0.0010.0000.0000.0000.000
39A36ASP-1-0.774-0.86031.072-0.194-0.1940.0000.0000.0000.000
40A37ARG10.9080.95032.9430.1650.1650.0000.0000.0000.000
41A38ALA0-0.048-0.02436.6160.0120.0120.0000.0000.0000.000
42A39GLY0-0.038-0.01234.8860.0100.0100.0000.0000.0000.000
43A40ASP-1-0.861-0.91335.516-0.189-0.1890.0000.0000.0000.000
44A41PHE00.0370.00629.500-0.016-0.0160.0000.0000.0000.000
45A42PRO00.0130.02828.8110.0050.0050.0000.0000.0000.000
46A43PHE0-0.008-0.04129.976-0.020-0.0200.0000.0000.0000.000
47A44GLU-1-0.898-0.93730.883-0.252-0.2520.0000.0000.0000.000
48A45ASN00.0120.00026.117-0.014-0.0140.0000.0000.0000.000
49A46ILE0-0.035-0.01526.166-0.032-0.0320.0000.0000.0000.000
50A47GLU-1-0.818-0.89027.463-0.253-0.2530.0000.0000.0000.000
51A48ASP-1-0.756-0.86226.014-0.352-0.3520.0000.0000.0000.000
52A49LEU0-0.041-0.00621.374-0.038-0.0380.0000.0000.0000.000
53A50LYS10.8100.88923.6700.2240.2240.0000.0000.0000.000
54A51ALA0-0.030-0.00625.965-0.005-0.0050.0000.0000.0000.000
55A52SER0-0.039-0.04521.771-0.016-0.0160.0000.0000.0000.000
56A53GLY0-0.011-0.00721.725-0.040-0.0400.0000.0000.0000.000
57A54TYR0-0.010-0.01915.862-0.037-0.0370.0000.0000.0000.000
58A55VAL0-0.0130.00119.501-0.016-0.0160.0000.0000.0000.000
59A56ARG10.9410.97421.2510.3700.3700.0000.0000.0000.000
60A57TRP0-0.003-0.00315.009-0.025-0.0250.0000.0000.0000.000
61A58THR0-0.030-0.02614.699-0.030-0.0300.0000.0000.0000.000
62A59VAL00.0420.03916.7730.0540.0540.0000.0000.0000.000
63A60PRO00.0220.00318.588-0.037-0.0370.0000.0000.0000.000
64A61VAL00.0330.00817.1530.0080.0080.0000.0000.0000.000
65A62GLU-1-0.899-0.92820.166-0.079-0.0790.0000.0000.0000.000
66A63TYR0-0.052-0.04923.2280.0160.0160.0000.0000.0000.000
67A64GLY00.0180.01323.427-0.002-0.0020.0000.0000.0000.000
68A65GLY00.0160.00520.345-0.021-0.0210.0000.0000.0000.000
69A66LEU0-0.077-0.03815.5010.0100.0100.0000.0000.0000.000
70A67GLY0-0.027-0.00714.865-0.046-0.0460.0000.0000.0000.000
71A68LEU0-0.040-0.01411.1540.0320.0320.0000.0000.0000.000
72A69SER0-0.024-0.0227.102-0.065-0.0650.0000.0000.0000.000
73A70LEU00.026-0.0129.682-0.168-0.1680.0000.0000.0000.000
74A71GLU-1-0.732-0.8691.916-19.913-20.0539.724-5.006-4.578-0.080
75A72GLU-1-0.690-0.8276.795-2.040-2.0400.0000.0000.0000.000
76A73MET0-0.0060.0148.3120.2360.2360.0000.0000.0000.000
77A74LEU0-0.042-0.0219.1560.1300.1300.0000.0000.0000.000
78A75MET0-0.0270.0176.364-0.424-0.4240.0000.0000.0000.000
79A76HIS00.0150.0089.7110.2420.2420.0000.0000.0000.000
80A77GLN0-0.0160.00413.2290.1410.1410.0000.0000.0000.000
81A78GLU-1-0.776-0.83910.503-1.329-1.3290.0000.0000.0000.000
82A79VAL0-0.019-0.01612.8460.0950.0950.0000.0000.0000.000
83A80LEU00.0050.00115.2690.1100.1100.0000.0000.0000.000
84A81ALA0-0.015-0.01817.5420.0740.0740.0000.0000.0000.000
85A82LYS10.7830.89415.8860.8210.8210.0000.0000.0000.000
86A83GLY00.0020.01519.6780.0460.0460.0000.0000.0000.000
87A84ASP-1-0.768-0.88822.258-0.282-0.2820.0000.0000.0000.000
88A85GLY00.0240.01221.498-0.025-0.0250.0000.0000.0000.000
89A86SER0-0.003-0.01522.5510.0090.0090.0000.0000.0000.000
90A87THR0-0.001-0.02923.8990.0120.0120.0000.0000.0000.000
91A88ALA0-0.0090.01319.107-0.005-0.0050.0000.0000.0000.000
92A89LEU00.0230.00320.386-0.017-0.0170.0000.0000.0000.000
93A90ALA0-0.024-0.00321.7560.0130.0130.0000.0000.0000.000
94A91ILE00.0300.00720.1160.0160.0160.0000.0000.0000.000
95A92GLY00.0300.00918.617-0.018-0.0180.0000.0000.0000.000
96A93TRP0-0.037-0.02619.4220.0110.0110.0000.0000.0000.000
97A94HIS00.0250.02721.8210.0420.0420.0000.0000.0000.000
98A95VAL00.005-0.00117.0710.0180.0180.0000.0000.0000.000
99A96GLY00.0670.03017.551-0.004-0.0040.0000.0000.0000.000
100A97ILE0-0.052-0.02318.5780.0430.0430.0000.0000.0000.000
101A98LEU00.0210.01120.4370.0350.0350.0000.0000.0000.000
102A99LEU00.0060.01313.2390.0270.0270.0000.0000.0000.000
103A100HIS10.7960.87417.8690.1210.1210.0000.0000.0000.000
104A101LEU0-0.0240.00820.0100.0400.0400.0000.0000.0000.000
105A102ARG10.7730.87413.2260.3680.3680.0000.0000.0000.000
106A103GLU-1-0.802-0.88615.474-0.025-0.0250.0000.0000.0000.000
107A104THR0-0.042-0.03318.6820.0450.0450.0000.0000.0000.000
108A105GLY00.0050.00322.2510.0190.0190.0000.0000.0000.000
109A106ALA0-0.054-0.02724.9620.0080.0080.0000.0000.0000.000
110A107PHE00.0240.01127.003-0.003-0.0030.0000.0000.0000.000
111A108PRO00.0540.02629.0260.0080.0080.0000.0000.0000.000
112A109ASP-1-0.821-0.88328.371-0.036-0.0360.0000.0000.0000.000
113A110GLU-1-0.832-0.90829.808-0.073-0.0730.0000.0000.0000.000
114A111LEU0-0.0180.00731.717-0.011-0.0110.0000.0000.0000.000
115A112PHE00.002-0.01522.032-0.014-0.0140.0000.0000.0000.000
116A113ARG10.8780.94627.4950.0540.0540.0000.0000.0000.000
117A114MET00.0010.01428.852-0.017-0.0170.0000.0000.0000.000
118A115VAL00.0230.00926.813-0.011-0.0110.0000.0000.0000.000
119A116CYS0-0.052-0.02324.558-0.023-0.0230.0000.0000.0000.000
120A117GLU-1-0.844-0.91826.239-0.146-0.1460.0000.0000.0000.000
121A118SER00.0070.01328.744-0.011-0.0110.0000.0000.0000.000
122A119VAL0-0.054-0.02923.785-0.011-0.0110.0000.0000.0000.000
123A120VAL0-0.066-0.03623.748-0.029-0.0290.0000.0000.0000.000
124A121LYS10.8200.90726.1670.1330.1330.0000.0000.0000.000
125A122GLU-1-0.888-0.95729.797-0.167-0.1670.0000.0000.0000.000
126A123GLY0-0.0050.01427.188-0.006-0.0060.0000.0000.0000.000
127A124ALA0-0.028-0.01228.231-0.003-0.0030.0000.0000.0000.000
128A125LEU00.013-0.00925.773-0.023-0.0230.0000.0000.0000.000
129A126ILE0-0.004-0.01625.2980.0270.0270.0000.0000.0000.000
130A127ASN00.0680.02325.967-0.025-0.0250.0000.0000.0000.000
131A128SER0-0.0300.00526.9890.0190.0190.0000.0000.0000.000
132A129CYS0-0.029-0.02828.807-0.012-0.0120.0000.0000.0000.000
133A130ALA00.0340.01730.9420.0090.0090.0000.0000.0000.000
134A131THR0-0.006-0.00331.1470.0080.0080.0000.0000.0000.000
135A132GLU-1-0.706-0.82333.632-0.062-0.0620.0000.0000.0000.000
136A133PRO0-0.064-0.02437.3280.0020.0020.0000.0000.0000.000
137A144PRO0-0.040-0.03637.2690.0000.0000.0000.0000.0000.000
138A145GLU-1-0.861-0.90139.894-0.042-0.0420.0000.0000.0000.000
139A146THR0-0.078-0.05739.524-0.002-0.0020.0000.0000.0000.000
140A147THR0-0.016-0.00341.5700.0040.0040.0000.0000.0000.000
141A148ALA0-0.024-0.01741.959-0.004-0.0040.0000.0000.0000.000
142A149VAL00.0290.01344.0920.0050.0050.0000.0000.0000.000
143A150LYS10.8320.92445.5640.0290.0290.0000.0000.0000.000
144A151VAL0-0.0050.00047.6090.0010.0010.0000.0000.0000.000
145A152PRO00.009-0.02448.7720.0010.0010.0000.0000.0000.000
146A153GLY00.0050.00847.422-0.003-0.0030.0000.0000.0000.000
147A154GLY00.0110.01244.333-0.003-0.0030.0000.0000.0000.000
148A155TYR0-0.050-0.04142.3300.0060.0060.0000.0000.0000.000
149A156ARG10.8220.92344.7300.0490.0490.0000.0000.0000.000
150A157ILE00.0240.01039.8710.0030.0030.0000.0000.0000.000
151A158THR0-0.055-0.04143.740-0.003-0.0030.0000.0000.0000.000
152A159GLY00.0480.02942.5560.0040.0040.0000.0000.0000.000
153A160ARG10.8130.89940.2190.0820.0820.0000.0000.0000.000
154A161LYS10.7470.87835.0700.0750.0750.0000.0000.0000.000
155A162THR0-0.020-0.03934.785-0.004-0.0040.0000.0000.0000.000
156A163PHE0-0.004-0.01130.599-0.001-0.0010.0000.0000.0000.000
157A164SER00.0000.00330.120-0.013-0.0130.0000.0000.0000.000
158A165THR00.005-0.01426.707-0.004-0.0040.0000.0000.0000.000
159A166LEU00.0360.02425.529-0.007-0.0070.0000.0000.0000.000
160A167SER0-0.022-0.02829.041-0.002-0.0020.0000.0000.0000.000
161A168PRO00.0290.01532.1870.0060.0060.0000.0000.0000.000
162A169ALA00.0030.00030.5350.0060.0060.0000.0000.0000.000
163A170LEU0-0.071-0.00128.476-0.006-0.0060.0000.0000.0000.000
164A171THR00.0010.00131.1230.0030.0030.0000.0000.0000.000
165A172TRP00.006-0.01530.0030.0230.0230.0000.0000.0000.000
166A173ILE00.034-0.00330.975-0.013-0.0130.0000.0000.0000.000
167A174MET0-0.0510.00026.9650.0070.0070.0000.0000.0000.000
168A175VAL00.0200.01131.661-0.002-0.0020.0000.0000.0000.000
169A176THR00.022-0.00432.9010.0040.0040.0000.0000.0000.000
170A177ALA00.001-0.00535.595-0.004-0.0040.0000.0000.0000.000
171A178THR00.023-0.00239.3680.0040.0040.0000.0000.0000.000
172A179VAL0-0.029-0.01441.617-0.003-0.0030.0000.0000.0000.000
173A180ALA00.0360.00344.0850.0040.0040.0000.0000.0000.000
174A181ASP-1-0.950-0.98047.739-0.018-0.0180.0000.0000.0000.000
175A182GLU-1-0.864-0.89445.905-0.010-0.0100.0000.0000.0000.000
176A183ASP-1-0.963-0.97045.478-0.009-0.0090.0000.0000.0000.000
177A184VAL0-0.0140.00741.0430.0040.0040.0000.0000.0000.000
178A185VAL00.0120.00936.278-0.005-0.0050.0000.0000.0000.000
179A186GLY00.0240.01136.9790.0050.0050.0000.0000.0000.000
180A187GLN0-0.043-0.02829.484-0.013-0.0130.0000.0000.0000.000
181A188PHE00.0290.01134.8590.0040.0040.0000.0000.0000.000
182A189LEU00.0130.01731.049-0.007-0.0070.0000.0000.0000.000
183A190VAL00.0120.01034.5050.0040.0040.0000.0000.0000.000
184A191ARG10.8020.87935.0440.0880.0880.0000.0000.0000.000
185A192LYS10.8510.92434.5440.1630.1630.0000.0000.0000.000
186A193GLU-1-0.871-0.94036.613-0.106-0.1060.0000.0000.0000.000
187A194ASP-1-0.846-0.89939.771-0.085-0.0850.0000.0000.0000.000
188A195VAL0-0.048-0.03237.6260.0060.0060.0000.0000.0000.000
189A196GLU-1-0.812-0.88940.945-0.086-0.0860.0000.0000.0000.000
190A197ILE00.012-0.00336.3340.0010.0010.0000.0000.0000.000
191A198VAL0-0.056-0.02739.2480.0040.0040.0000.0000.0000.000
192A199GLU-1-0.853-0.92338.525-0.135-0.1350.0000.0000.0000.000
193A200THR0-0.070-0.04137.5640.0070.0070.0000.0000.0000.000
194A201TRP0-0.025-0.01439.148-0.003-0.0030.0000.0000.0000.000
195A202ASP-1-0.796-0.87536.307-0.136-0.1360.0000.0000.0000.000
196A203THR0-0.027-0.03331.8700.0080.0080.0000.0000.0000.000
197A204LEU0-0.037-0.01931.566-0.002-0.0020.0000.0000.0000.000
198A205GLY00.0940.03329.714-0.002-0.0020.0000.0000.0000.000
199A206MET0-0.094-0.02923.2080.0020.0020.0000.0000.0000.000
200A207ARG10.7910.88428.7890.1580.1580.0000.0000.0000.000
201A208ALA00.0300.04029.7450.0070.0070.0000.0000.0000.000
202A209THR0-0.015-0.00327.299-0.002-0.0020.0000.0000.0000.000
203A210GLY00.0090.01430.5380.0110.0110.0000.0000.0000.000
204A211SER0-0.073-0.04331.880-0.009-0.0090.0000.0000.0000.000
205A212HIS00.0280.02433.3340.0130.0130.0000.0000.0000.000
206A213ASP-1-0.760-0.82634.650-0.102-0.1020.0000.0000.0000.000
207A214ILE0-0.014-0.00435.137-0.004-0.0040.0000.0000.0000.000
208A215VAL0-0.020-0.01938.3580.0070.0070.0000.0000.0000.000
209A216LEU0-0.014-0.00238.643-0.002-0.0020.0000.0000.0000.000
210A217LYS10.8450.89142.7440.0800.0800.0000.0000.0000.000
211A218ASP-1-0.841-0.91346.470-0.056-0.0560.0000.0000.0000.000
212A219VAL00.0190.02540.6240.0000.0000.0000.0000.0000.000
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