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: VKKZ1

Calculation Name: 5D19-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5D19

Chain ID: A

ChEMBL ID:

UniProt ID: O07229

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 202
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2137697.676908
FMO2-HF: Nuclear repulsion 2058572.999513
FMO2-HF: Total energy -79124.677395
FMO2-MP2: Total energy -79356.145127


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:12:GLY)


Summations of interaction energy for fragment #1(A:12: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.
-5.344-1.2320.178-1.821-2.4680.008
Interaction energy analysis for fragmet #1(A:12:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.007 / q_NPA : -0.010
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].
3A14ARG10.9751.0013.274-6.615-3.8240.103-1.379-1.5150.008
4A15SER00.0210.0062.896-1.491-0.7380.034-0.238-0.5490.000
5A16ARG10.9441.0164.3872.6712.928-0.001-0.089-0.1670.000
6A17GLU-1-0.792-0.9026.1630.0970.0970.0000.0000.0000.000
7A18SER0-0.052-0.0357.5100.1430.1430.0000.0000.0000.000
8A19ILE00.0260.0018.0490.1260.1260.0000.0000.0000.000
9A20LEU0-0.0200.01810.5050.1320.1320.0000.0000.0000.000
10A21ASP-1-0.774-0.86612.278-0.111-0.1110.0000.0000.0000.000
11A22ALA0-0.044-0.02313.4210.0520.0520.0000.0000.0000.000
12A23THR0-0.039-0.06614.1950.0330.0330.0000.0000.0000.000
13A24GLU-1-0.911-0.96616.485-0.121-0.1210.0000.0000.0000.000
14A25ARG10.9390.96518.0550.1510.1510.0000.0000.0000.000
15A26LEU0-0.082-0.04018.7590.0230.0230.0000.0000.0000.000
16A27MET0-0.0010.02320.3990.0110.0110.0000.0000.0000.000
17A28ALA00.0400.03722.7870.0130.0130.0000.0000.0000.000
18A29THR0-0.063-0.02524.2690.0120.0120.0000.0000.0000.000
19A30LYS10.9340.95622.9190.1590.1590.0000.0000.0000.000
20A31GLY00.0450.02825.734-0.003-0.0030.0000.0000.0000.000
21A32TYR00.0160.00422.900-0.014-0.0140.0000.0000.0000.000
22A33ALA00.008-0.00324.629-0.013-0.0130.0000.0000.0000.000
23A34ALA0-0.049-0.02126.596-0.004-0.0040.0000.0000.0000.000
24A35THR00.0150.02020.747-0.004-0.0040.0000.0000.0000.000
25A36SER0-0.032-0.05521.888-0.005-0.0050.0000.0000.0000.000
26A37ILE00.023-0.01514.932-0.010-0.0100.0000.0000.0000.000
27A38SER0-0.013-0.01017.703-0.027-0.0270.0000.0000.0000.000
28A39ASP-1-0.804-0.87019.597-0.193-0.1930.0000.0000.0000.000
29A40ILE00.000-0.01114.4450.0010.0010.0000.0000.0000.000
30A41ARG10.9490.98214.9920.2410.2410.0000.0000.0000.000
31A42ASP-1-0.937-0.96515.801-0.202-0.2020.0000.0000.0000.000
32A43ALA0-0.063-0.01516.6460.0180.0180.0000.0000.0000.000
33A44CYS0-0.060-0.02311.269-0.010-0.0100.0000.0000.0000.000
34A45GLY00.0250.02311.960-0.023-0.0230.0000.0000.0000.000
35A46LEU0-0.014-0.0197.046-0.040-0.0400.0000.0000.0000.000
36A47ALA00.0130.00711.6460.0630.0630.0000.0000.0000.000
37A48PRO00.0820.06912.248-0.091-0.0910.0000.0000.0000.000
38A49SER00.013-0.01113.096-0.038-0.0380.0000.0000.0000.000
39A50SER0-0.076-0.0698.288-0.016-0.0160.0000.0000.0000.000
40A51ILE00.0550.0238.125-0.235-0.2350.0000.0000.0000.000
41A52TYR0-0.042-0.03810.210-0.043-0.0430.0000.0000.0000.000
42A53TRP0-0.0100.0027.8800.0110.0110.0000.0000.0000.000
43A54HIS0-0.063-0.0183.162-0.511-0.2000.042-0.115-0.2370.000
44A55PHE0-0.002-0.0167.6130.0290.0290.0000.0000.0000.000
45A56GLY00.0530.04111.2760.0720.0720.0000.0000.0000.000
46A57SER0-0.019-0.02014.0080.0550.0550.0000.0000.0000.000
47A58LYS10.9300.97515.4060.1610.1610.0000.0000.0000.000
48A59GLU-1-0.873-0.94917.383-0.231-0.2310.0000.0000.0000.000
49A60GLY00.0260.01415.3330.0080.0080.0000.0000.0000.000
50A61VAL0-0.041-0.01312.644-0.035-0.0350.0000.0000.0000.000
51A62LEU00.011-0.00714.3600.0010.0010.0000.0000.0000.000
52A63ALA00.0060.00916.6790.0240.0240.0000.0000.0000.000
53A64ALA00.0230.01012.2230.0230.0230.0000.0000.0000.000
54A65MET0-0.0360.01114.3400.0310.0310.0000.0000.0000.000
55A66MET00.0330.02715.6340.0490.0490.0000.0000.0000.000
56A67GLU-1-0.798-0.89215.959-0.209-0.2090.0000.0000.0000.000
57A68ARG10.7700.87311.9370.2890.2890.0000.0000.0000.000
58A69GLY0-0.023-0.02715.9680.0430.0430.0000.0000.0000.000
59A70ALA0-0.001-0.00119.1720.0250.0250.0000.0000.0000.000
60A71GLN0-0.021-0.02215.6680.0180.0180.0000.0000.0000.000
61A72ARG10.9420.96815.4680.0980.0980.0000.0000.0000.000
62A73PHE00.0170.02520.4780.0140.0140.0000.0000.0000.000
63A74PHE00.012-0.02723.1010.0100.0100.0000.0000.0000.000
64A75ALA00.0010.01021.4180.0070.0070.0000.0000.0000.000
65A76ALA0-0.0080.01123.5120.0100.0100.0000.0000.0000.000
66A77ILE0-0.0340.00426.0500.0030.0030.0000.0000.0000.000
67A78PRO00.0590.06128.035-0.002-0.0020.0000.0000.0000.000
68A79THR00.016-0.01828.504-0.006-0.0060.0000.0000.0000.000
69A80TRP00.0420.00631.0980.0030.0030.0000.0000.0000.000
70A81ASP-1-0.958-0.99733.2910.0100.0100.0000.0000.0000.000
71A82GLU-1-0.934-0.96327.8930.0250.0250.0000.0000.0000.000
72A83ALA0-0.052-0.00232.6260.0020.0020.0000.0000.0000.000
73A84HIS00.0350.01233.8320.0000.0000.0000.0000.0000.000
74A85GLY0-0.015-0.01337.449-0.003-0.0030.0000.0000.0000.000
75A86PRO00.0120.01940.9170.0010.0010.0000.0000.0000.000
76A87VAL00.042-0.00442.004-0.001-0.0010.0000.0000.0000.000
77A88GLU-1-0.907-0.94643.2220.0060.0060.0000.0000.0000.000
78A89GLN00.015-0.00443.1540.0000.0000.0000.0000.0000.000
79A90ARG10.8890.96437.989-0.013-0.0130.0000.0000.0000.000
80A91SER00.0600.01238.2240.0000.0000.0000.0000.0000.000
81A92GLU-1-0.996-1.00238.831-0.003-0.0030.0000.0000.0000.000
82A93ARG10.8920.95237.134-0.008-0.0080.0000.0000.0000.000
83A94GLN00.0380.02932.553-0.001-0.0010.0000.0000.0000.000
84A95LEU0-0.034-0.01034.376-0.002-0.0020.0000.0000.0000.000
85A96THR00.0220.00036.178-0.002-0.0020.0000.0000.0000.000
86A97GLU-1-0.912-0.95131.2700.0030.0030.0000.0000.0000.000
87A98LEU0-0.039-0.00931.225-0.003-0.0030.0000.0000.0000.000
88A99VAL00.013-0.00132.709-0.004-0.0040.0000.0000.0000.000
89A100SER0-0.0100.00932.776-0.003-0.0030.0000.0000.0000.000
90A101LEU00.0030.00326.926-0.002-0.0020.0000.0000.0000.000
91A102GLN0-0.001-0.02030.194-0.007-0.0070.0000.0000.0000.000
92A103SER0-0.065-0.03532.247-0.002-0.0020.0000.0000.0000.000
93A104GLN0-0.058-0.02328.285-0.004-0.0040.0000.0000.0000.000
94A105HIS0-0.053-0.00430.384-0.001-0.0010.0000.0000.0000.000
95A106PRO0-0.0070.01025.400-0.006-0.0060.0000.0000.0000.000
96A107ASP-1-0.784-0.89623.536-0.124-0.1240.0000.0000.0000.000
97A108PHE0-0.011-0.00521.436-0.011-0.0110.0000.0000.0000.000
98A109LEU00.0190.01823.088-0.010-0.0100.0000.0000.0000.000
99A110ARG10.8870.94125.6310.1090.1090.0000.0000.0000.000
100A111LEU0-0.016-0.00319.873-0.003-0.0030.0000.0000.0000.000
101A112PHE0-0.024-0.02123.828-0.007-0.0070.0000.0000.0000.000
102A113TYR0-0.033-0.07824.875-0.001-0.0010.0000.0000.0000.000
103A114LEU0-0.032-0.01225.6150.0030.0030.0000.0000.0000.000
104A115LEU0-0.020-0.01420.481-0.003-0.0030.0000.0000.0000.000
105A116SER0-0.077-0.03024.8720.0040.0040.0000.0000.0000.000
106A117MET0-0.057-0.02327.2840.0060.0060.0000.0000.0000.000
107A118GLU-1-0.914-0.93725.178-0.133-0.1330.0000.0000.0000.000
108A119ARG10.9030.95327.4960.0960.0960.0000.0000.0000.000
109A120SER00.007-0.00523.0780.0010.0010.0000.0000.0000.000
110A121GLN00.011-0.00122.2120.0000.0000.0000.0000.0000.000
111A122ASP-1-0.835-0.93117.694-0.280-0.2800.0000.0000.0000.000
112A123PRO00.009-0.00221.1800.0030.0030.0000.0000.0000.000
113A124ALA00.0080.00516.8620.0120.0120.0000.0000.0000.000
114A125VAL00.0320.01518.904-0.006-0.0060.0000.0000.0000.000
115A126ALA00.0300.01420.1400.0110.0110.0000.0000.0000.000
116A127ALA0-0.033-0.01819.9510.0150.0150.0000.0000.0000.000
117A128VAL0-0.0140.00216.8820.0150.0150.0000.0000.0000.000
118A129VAL00.0330.02219.8090.0160.0160.0000.0000.0000.000
119A130ARG10.9330.96923.0800.1100.1100.0000.0000.0000.000
120A131ARG10.8440.90616.7320.2120.2120.0000.0000.0000.000
121A132VAL00.0290.01420.7580.0150.0150.0000.0000.0000.000
122A133ARG10.8780.93723.1610.0840.0840.0000.0000.0000.000
123A134ASN0-0.010-0.02925.7880.0110.0110.0000.0000.0000.000
124A135THR0-0.0210.00523.4750.0110.0110.0000.0000.0000.000
125A136ALA00.0430.01725.9930.0090.0090.0000.0000.0000.000
126A137ILE00.0040.00628.5180.0070.0070.0000.0000.0000.000
127A138ALA0-0.020-0.00628.5080.0060.0060.0000.0000.0000.000
128A139ARG10.8010.88825.9640.0260.0260.0000.0000.0000.000
129A140PHE00.0380.01730.6340.0040.0040.0000.0000.0000.000
130A141ARG10.9610.98533.5580.0310.0310.0000.0000.0000.000
131A142ASP-1-0.878-0.93632.944-0.004-0.0040.0000.0000.0000.000
132A143SER0-0.008-0.00934.9290.0020.0020.0000.0000.0000.000
133A144ILE0-0.030-0.02136.9120.0020.0020.0000.0000.0000.000
134A145THR0-0.008-0.01537.8500.0010.0010.0000.0000.0000.000
135A146HIS10.8110.90536.4470.0050.0050.0000.0000.0000.000
136A147LEU0-0.033-0.00940.7900.0010.0010.0000.0000.0000.000
137A148LEU0-0.0250.00243.3750.0000.0000.0000.0000.0000.000
138A149PRO00.0250.01745.6510.0010.0010.0000.0000.0000.000
139A150SER0-0.003-0.01647.8530.0000.0000.0000.0000.0000.000
140A151ASP-1-0.968-0.97348.918-0.003-0.0030.0000.0000.0000.000
141A152ILE0-0.0060.00647.226-0.001-0.0010.0000.0000.0000.000
142A153PRO0-0.028-0.00647.3210.0000.0000.0000.0000.0000.000
143A154PRO00.046-0.01742.642-0.001-0.0010.0000.0000.0000.000
144A155GLY0-0.0160.00644.164-0.001-0.0010.0000.0000.0000.000
145A156LYS10.9600.98146.3150.0090.0090.0000.0000.0000.000
146A157ALA00.0290.02943.478-0.001-0.0010.0000.0000.0000.000
147A158ASP-1-0.889-0.93840.628-0.019-0.0190.0000.0000.0000.000
148A159LEU0-0.025-0.02641.847-0.002-0.0020.0000.0000.0000.000
149A160VAL00.0810.05244.100-0.002-0.0020.0000.0000.0000.000
150A161VAL00.008-0.00438.888-0.001-0.0010.0000.0000.0000.000
151A162ALA0-0.073-0.03138.782-0.002-0.0020.0000.0000.0000.000
152A163GLU-1-0.909-0.94239.477-0.029-0.0290.0000.0000.0000.000
153A164LEU00.0210.00441.761-0.002-0.0020.0000.0000.0000.000
154A165THR0-0.042-0.04235.252-0.001-0.0010.0000.0000.0000.000
155A166ALA0-0.028-0.01336.915-0.003-0.0030.0000.0000.0000.000
156A167PHE00.0070.01537.979-0.003-0.0030.0000.0000.0000.000
157A168ALA00.010-0.00637.578-0.001-0.0010.0000.0000.0000.000
158A169VAL0-0.047-0.02532.930-0.002-0.0020.0000.0000.0000.000
159A170ALA00.0030.00835.090-0.003-0.0030.0000.0000.0000.000
160A171LEU00.001-0.00237.417-0.002-0.0020.0000.0000.0000.000
161A172SER00.005-0.00433.0830.0010.0010.0000.0000.0000.000
162A173ASP-1-0.799-0.85332.131-0.067-0.0670.0000.0000.0000.000
163A174GLY0-0.006-0.00234.291-0.002-0.0020.0000.0000.0000.000
164A175VAL0-0.011-0.00835.7870.0010.0010.0000.0000.0000.000
165A176TYR00.0080.00328.530-0.002-0.0020.0000.0000.0000.000
166A177PHE0-0.029-0.03532.589-0.002-0.0020.0000.0000.0000.000
167A178ALA00.0200.02535.9460.0000.0000.0000.0000.0000.000
168A179GLY00.0280.01636.5700.0020.0020.0000.0000.0000.000
169A180HIS0-0.036-0.01631.8070.0000.0000.0000.0000.0000.000
170A181LEU0-0.067-0.03835.771-0.001-0.0010.0000.0000.0000.000
171A182GLU-1-0.952-0.97239.045-0.038-0.0380.0000.0000.0000.000
172A183PRO0-0.0040.01337.8000.0020.0020.0000.0000.0000.000
173A184ASP-1-0.934-0.95939.594-0.027-0.0270.0000.0000.0000.000
174A185THR0-0.054-0.03642.9720.0020.0020.0000.0000.0000.000
175A186THR0-0.052-0.02539.6270.0020.0020.0000.0000.0000.000
176A187ASP-1-0.867-0.94141.327-0.016-0.0160.0000.0000.0000.000
177A188VAL00.0730.02135.7700.0000.0000.0000.0000.0000.000
178A189GLU-1-0.842-0.92839.098-0.009-0.0090.0000.0000.0000.000
179A190ARG10.8350.91440.6190.0170.0170.0000.0000.0000.000
180A191MET00.0140.00440.6100.0010.0010.0000.0000.0000.000
181A192TYR00.0590.02034.3660.0000.0000.0000.0000.0000.000
182A193ARG10.8580.94440.5150.0130.0130.0000.0000.0000.000
183A194ARG10.8690.91743.7580.0160.0160.0000.0000.0000.000
184A195LEU00.0300.03038.6590.0000.0000.0000.0000.0000.000
185A196ARG10.9490.98741.9530.0090.0090.0000.0000.0000.000
186A197GLN00.0410.01743.6610.0000.0000.0000.0000.0000.000
187A198ALA0-0.0080.00945.4790.0010.0010.0000.0000.0000.000
188A199LEU00.003-0.00740.6680.0000.0000.0000.0000.0000.000
189A200GLU-1-0.907-0.96445.327-0.009-0.0090.0000.0000.0000.000
190A201ALA0-0.030-0.01147.7730.0010.0010.0000.0000.0000.000
191A202LEU0-0.010-0.01946.1550.0000.0000.0000.0000.0000.000
192A203ILE00.0130.01844.8120.0000.0000.0000.0000.0000.000
193A204PRO00.0130.01148.5340.0000.0000.0000.0000.0000.000
194A205VAL0-0.002-0.00251.6420.0000.0000.0000.0000.0000.000
195A206LEU00.0560.01446.4810.0000.0000.0000.0000.0000.000
196A207LEU0-0.036-0.01148.4180.0000.0000.0000.0000.0000.000
197A208GLU-1-0.944-0.96651.622-0.009-0.0090.0000.0000.0000.000
198A209GLU-1-0.973-0.97452.153-0.018-0.0180.0000.0000.0000.000
199A210THR0-0.108-0.07449.6400.0000.0000.0000.0000.0000.000
200A211HIS0-0.096-0.04153.0630.0010.0010.0000.0000.0000.000
201A212HIS0-0.0090.00456.3060.0010.0010.0000.0000.0000.000
202A213HIS0-0.0250.00052.5560.0000.0000.0000.0000.0000.000