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

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FMODB ID: R5ZY8

Calculation Name: 4IYP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4IYP

Chain ID: A

ChEMBL ID:

UniProt ID: P78318

Base Structure: X-ray

Registration Date: 2023-06-20

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 OptHSide
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 208
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2467906.971631
FMO2-HF: Nuclear repulsion 2382692.653893
FMO2-HF: Total energy -85214.317738
FMO2-MP2: Total energy -85461.711269


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:0:SER)


Summations of interaction energy for fragment #1(A:0: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.
-8.036-4.2710.519-1.876-2.4080.005
Interaction energy analysis for fragmet #1(A:0:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.020 / 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].
3A2ALA00.0250.0183.166-1.6051.0030.132-1.296-1.4440.005
4A3ALA0-0.018-0.0252.657-2.796-1.7830.388-0.548-0.8530.000
5A4GLU-1-0.974-0.9764.364-3.848-3.704-0.001-0.032-0.1110.000
6A5ASP-1-0.936-0.9656.1140.0430.0430.0000.0000.0000.000
7A6GLU-1-0.952-0.9857.7120.5170.5170.0000.0000.0000.000
8A7LEU0-0.115-0.0267.7530.1370.1370.0000.0000.0000.000
9A8GLN00.0030.00010.049-0.047-0.0470.0000.0000.0000.000
10A9LEU0-0.002-0.00512.1930.0510.0510.0000.0000.0000.000
11A10PRO0-0.0020.00215.3310.0070.0070.0000.0000.0000.000
12A11ARG10.9480.97417.0700.1610.1610.0000.0000.0000.000
13A12LEU00.0700.02920.9380.0140.0140.0000.0000.0000.000
14A13PRO00.0130.00423.9210.0090.0090.0000.0000.0000.000
15A14GLU-1-0.892-0.94221.655-0.067-0.0670.0000.0000.0000.000
16A15LEU0-0.0230.00419.9950.0130.0130.0000.0000.0000.000
17A16PHE00.012-0.00524.0570.0090.0090.0000.0000.0000.000
18A17GLU-1-0.845-0.91427.629-0.032-0.0320.0000.0000.0000.000
19A18THR0-0.025-0.02525.1600.0090.0090.0000.0000.0000.000
20A19GLY00.007-0.00427.1780.0060.0060.0000.0000.0000.000
21A20ARG10.8140.89728.2730.0380.0380.0000.0000.0000.000
22A21GLN0-0.005-0.00430.3220.0060.0060.0000.0000.0000.000
23A22LEU0-0.016-0.00626.8010.0040.0040.0000.0000.0000.000
24A23LEU0-0.021-0.01131.2900.0040.0040.0000.0000.0000.000
25A24ASP-1-0.907-0.96033.665-0.020-0.0200.0000.0000.0000.000
26A25GLU-1-0.905-0.94832.350-0.001-0.0010.0000.0000.0000.000
27A26VAL0-0.061-0.04333.0980.0030.0030.0000.0000.0000.000
28A27GLU-1-0.894-0.91636.166-0.014-0.0140.0000.0000.0000.000
29A28VAL0-0.046-0.02439.1540.0010.0010.0000.0000.0000.000
30A29ALA0-0.0310.00637.6970.0020.0020.0000.0000.0000.000
31A30THR0-0.042-0.01039.7140.0000.0000.0000.0000.0000.000
32A31GLU-1-0.918-0.96737.1460.0080.0080.0000.0000.0000.000
33A32PRO00.000-0.01140.422-0.002-0.0020.0000.0000.0000.000
34A33ALA00.0820.04338.8750.0010.0010.0000.0000.0000.000
35A34GLY00.004-0.00837.057-0.001-0.0010.0000.0000.0000.000
36A35SER0-0.054-0.02636.8210.0030.0030.0000.0000.0000.000
37A36ARG10.9740.97630.467-0.039-0.0390.0000.0000.0000.000
38A37ILE00.0220.01131.7870.0000.0000.0000.0000.0000.000
39A38VAL00.0480.03532.462-0.002-0.0020.0000.0000.0000.000
40A39GLN0-0.027-0.03831.784-0.004-0.0040.0000.0000.0000.000
41A40GLU-1-0.913-0.96727.6540.0280.0280.0000.0000.0000.000
42A41LYS10.8590.93327.601-0.006-0.0060.0000.0000.0000.000
43A42VAL00.0140.00928.878-0.006-0.0060.0000.0000.0000.000
44A43PHE0-0.030-0.01122.078-0.006-0.0060.0000.0000.0000.000
45A44LYS10.9630.99022.1550.0180.0180.0000.0000.0000.000
46A45GLY00.0550.01824.496-0.010-0.0100.0000.0000.0000.000
47A46LEU0-0.032-0.02226.458-0.008-0.0080.0000.0000.0000.000
48A47ASP-1-0.788-0.87119.880-0.087-0.0870.0000.0000.0000.000
49A48LEU0-0.036-0.02321.388-0.015-0.0150.0000.0000.0000.000
50A49LEU00.018-0.00423.299-0.013-0.0130.0000.0000.0000.000
51A50GLU-1-0.987-0.97921.484-0.095-0.0950.0000.0000.0000.000
52A51LYS10.8190.88917.2030.1010.1010.0000.0000.0000.000
53A52ALA0-0.047-0.01621.279-0.014-0.0140.0000.0000.0000.000
54A53ALA00.008-0.01124.092-0.006-0.0060.0000.0000.0000.000
55A54GLU-1-0.857-0.90719.668-0.194-0.1940.0000.0000.0000.000
56A55MET0-0.040-0.02720.497-0.019-0.0190.0000.0000.0000.000
57A56LEU0-0.033-0.03122.4470.0020.0020.0000.0000.0000.000
58A57SER0-0.039-0.00624.4090.0060.0060.0000.0000.0000.000
59A58GLN0-0.068-0.05120.387-0.002-0.0020.0000.0000.0000.000
60A59LEU0-0.092-0.04523.780-0.002-0.0020.0000.0000.0000.000
61A60ASP-1-0.961-0.96425.975-0.097-0.0970.0000.0000.0000.000
62A61LEU0-0.042-0.01928.8470.0060.0060.0000.0000.0000.000
63A62PHE0-0.038-0.01931.1900.0070.0070.0000.0000.0000.000
64A63SER00.0300.01133.292-0.002-0.0020.0000.0000.0000.000
65A64ARG10.9430.94535.5600.0570.0570.0000.0000.0000.000
66A65ASN0-0.123-0.07538.4590.0030.0030.0000.0000.0000.000
67A66GLU-1-0.755-0.84636.852-0.070-0.0700.0000.0000.0000.000
68A67ASP-1-0.887-0.93240.939-0.040-0.0400.0000.0000.0000.000
69A68LEU00.015-0.00240.502-0.003-0.0030.0000.0000.0000.000
70A69GLU-1-0.893-0.96041.561-0.039-0.0390.0000.0000.0000.000
71A70GLU-1-0.987-0.98139.839-0.051-0.0510.0000.0000.0000.000
72A71ILE0-0.0520.00735.975-0.004-0.0040.0000.0000.0000.000
73A72ALA00.0400.02235.3770.0050.0050.0000.0000.0000.000
74A73SER00.016-0.05437.324-0.001-0.0010.0000.0000.0000.000
75A74THR0-0.043-0.02233.6510.0020.0020.0000.0000.0000.000
76A75ASP-1-0.856-0.93632.136-0.077-0.0770.0000.0000.0000.000
77A76LEU00.0230.02133.800-0.002-0.0020.0000.0000.0000.000
78A77LYS10.8680.93731.4240.0600.0600.0000.0000.0000.000
79A78TYR0-0.009-0.00129.3610.0020.0020.0000.0000.0000.000
80A79LEU00.0590.04432.043-0.002-0.0020.0000.0000.0000.000
81A80LEU0-0.062-0.04234.4890.0020.0020.0000.0000.0000.000
82A81VAL0-0.0040.00928.0690.0030.0030.0000.0000.0000.000
83A82PRO00.0380.01831.4660.0030.0030.0000.0000.0000.000
84A83ALA00.0250.01332.7040.0040.0040.0000.0000.0000.000
85A84PHE0-0.004-0.00531.6460.0040.0040.0000.0000.0000.000
86A85GLN00.0300.01926.9980.0030.0030.0000.0000.0000.000
87A86GLY00.0240.02831.5460.0040.0040.0000.0000.0000.000
88A87ALA0-0.007-0.00734.8900.0040.0040.0000.0000.0000.000
89A88LEU00.011-0.00529.7520.0040.0040.0000.0000.0000.000
90A89THR0-0.040-0.02632.0440.0030.0030.0000.0000.0000.000
91A90MET0-0.057-0.02033.1740.0040.0040.0000.0000.0000.000
92A91LYS10.7900.88834.7280.0180.0180.0000.0000.0000.000
93A92GLN00.0020.02129.9690.0000.0000.0000.0000.0000.000
94A93VAL0-0.029-0.00234.3020.0000.0000.0000.0000.0000.000
95A94ASN00.017-0.01332.3480.0030.0030.0000.0000.0000.000
96A95PRO00.0510.03336.062-0.002-0.0020.0000.0000.0000.000
97A96SER0-0.054-0.02035.917-0.002-0.0020.0000.0000.0000.000
98A97LYS10.9110.94231.284-0.004-0.0040.0000.0000.0000.000
99A98ARG10.8600.91135.7070.0090.0090.0000.0000.0000.000
100A99LEU00.0220.00238.189-0.002-0.0020.0000.0000.0000.000
101A100ASP-1-0.877-0.91932.447-0.026-0.0260.0000.0000.0000.000
102A101HIS00.002-0.01731.8850.0000.0000.0000.0000.0000.000
103A102LEU0-0.0020.02035.136-0.003-0.0030.0000.0000.0000.000
104A103GLN0-0.008-0.00536.606-0.001-0.0010.0000.0000.0000.000
105A104ARG10.9570.96327.9690.0360.0360.0000.0000.0000.000
106A105ALA00.0240.01833.965-0.004-0.0040.0000.0000.0000.000
107A106ARG10.7520.82935.7030.0270.0270.0000.0000.0000.000
108A107GLU-1-0.944-0.96233.154-0.053-0.0530.0000.0000.0000.000
109A108HIS00.0130.01329.214-0.004-0.0040.0000.0000.0000.000
110A109PHE00.013-0.00234.391-0.002-0.0020.0000.0000.0000.000
111A110ILE0-0.0070.00137.9010.0000.0000.0000.0000.0000.000
112A111ASN00.0120.02133.123-0.001-0.0010.0000.0000.0000.000
113A112TYR0-0.021-0.00836.135-0.002-0.0020.0000.0000.0000.000
114A113LEU0-0.010-0.00737.1730.0000.0000.0000.0000.0000.000
115A114THR0-0.016-0.03738.4110.0010.0010.0000.0000.0000.000
116A115GLN00.0270.02034.7690.0030.0030.0000.0000.0000.000
117A116CYS0-0.014-0.01538.5980.0010.0010.0000.0000.0000.000
118A117HIS0-0.060-0.02341.2130.0000.0000.0000.0000.0000.000
119A118CYS0-0.072-0.03440.5990.0010.0010.0000.0000.0000.000
120A119TYR00.0000.00037.1850.0000.0000.0000.0000.0000.000
121A120HIS0-0.099-0.04842.6230.0030.0030.0000.0000.0000.000
122A121VAL00.0030.01041.6520.0020.0020.0000.0000.0000.000
123A122ALA0-0.027-0.02645.0630.0020.0020.0000.0000.0000.000
124A123GLU-1-0.950-0.96247.975-0.026-0.0260.0000.0000.0000.000
125A124PHE0-0.065-0.04343.7120.0010.0010.0000.0000.0000.000
126A125GLU-1-0.952-0.96949.404-0.024-0.0240.0000.0000.0000.000
127A126LEU0-0.0080.00542.4080.0000.0000.0000.0000.0000.000
128A127PRO0-0.007-0.00644.2520.0010.0010.0000.0000.0000.000
129A142SER00.0280.01244.656-0.002-0.0020.0000.0000.0000.000
130A143MET00.0770.02640.4270.0000.0000.0000.0000.0000.000
131A144ALA0-0.0120.00540.588-0.001-0.0010.0000.0000.0000.000
132A145TYR0-0.0190.01642.4940.0020.0020.0000.0000.0000.000
133A146PRO0-0.069-0.03644.5350.0000.0000.0000.0000.0000.000
134A147SER00.0610.00646.649-0.001-0.0010.0000.0000.0000.000
135A148LEU0-0.078-0.02948.4250.0010.0010.0000.0000.0000.000
136A149VAL00.0730.02951.8560.0000.0000.0000.0000.0000.000
137A150ALA00.0210.01354.1030.0010.0010.0000.0000.0000.000
138A151MET0-0.055-0.05057.7500.0000.0000.0000.0000.0000.000
139A152ALA00.0410.02256.7650.0000.0000.0000.0000.0000.000
140A153SER00.0430.01757.220-0.001-0.0010.0000.0000.0000.000
141A154GLN0-0.036-0.00257.7070.0000.0000.0000.0000.0000.000
142A155ARG11.0000.99456.8350.0100.0100.0000.0000.0000.000
143A156GLN00.003-0.00558.2620.0000.0000.0000.0000.0000.000
144A157ALA00.0760.03754.8420.0000.0000.0000.0000.0000.000
145A158LYS10.8860.94750.8010.0150.0150.0000.0000.0000.000
146A159ILE0-0.032-0.01254.8930.0000.0000.0000.0000.0000.000
147A160GLN0-0.042-0.02155.6230.0000.0000.0000.0000.0000.000
148A161ARG10.8450.88849.0440.0190.0190.0000.0000.0000.000
149A162TYR0-0.034-0.00752.0210.0000.0000.0000.0000.0000.000
150A163LYS10.9310.94453.4420.0120.0120.0000.0000.0000.000
151A164GLN00.0200.02951.0910.0000.0000.0000.0000.0000.000
152A165LYS10.9710.98146.6730.0180.0180.0000.0000.0000.000
153A166LYS10.8360.91449.8070.0120.0120.0000.0000.0000.000
154A167GLU-1-0.814-0.88252.312-0.015-0.0150.0000.0000.0000.000
155A168LEU0-0.007-0.00447.4600.0000.0000.0000.0000.0000.000
156A169GLU-1-0.813-0.89846.543-0.016-0.0160.0000.0000.0000.000
157A170HIS0-0.0120.01148.5030.0010.0010.0000.0000.0000.000
158A171ARG10.8910.93650.0670.0190.0190.0000.0000.0000.000
159A172LEU00.0200.00543.9440.0000.0000.0000.0000.0000.000
160A173SER0-0.121-0.06146.5430.0000.0000.0000.0000.0000.000
161A174ALA0-0.031-0.01447.9850.0010.0010.0000.0000.0000.000
162A175MET0-0.048-0.01646.4060.0000.0000.0000.0000.0000.000
163A176LYS10.9250.97439.3640.0180.0180.0000.0000.0000.000
164A177SER0-0.008-0.00742.750-0.001-0.0010.0000.0000.0000.000
165A178ALA00.0430.02543.3430.0000.0000.0000.0000.0000.000
166A179VAL00.0180.01940.117-0.001-0.0010.0000.0000.0000.000
167A180GLU-1-0.850-0.93738.190-0.025-0.0250.0000.0000.0000.000
168A181SER0-0.089-0.04838.8010.0000.0000.0000.0000.0000.000
169A182GLY0-0.003-0.00340.7890.0010.0010.0000.0000.0000.000
170A183GLN0-0.094-0.04541.4220.0010.0010.0000.0000.0000.000
171A184ALA0-0.019-0.00344.0440.0010.0010.0000.0000.0000.000
172A185ASP-1-0.851-0.91644.352-0.025-0.0250.0000.0000.0000.000
173A186ASP-1-0.799-0.89042.102-0.038-0.0380.0000.0000.0000.000
174A187GLU-1-0.920-0.94444.533-0.025-0.0250.0000.0000.0000.000
175A188ARG10.8550.89346.7190.0200.0200.0000.0000.0000.000
176A189VAL0-0.036-0.01840.2100.0000.0000.0000.0000.0000.000
177A190ARG10.8490.90940.6370.0410.0410.0000.0000.0000.000
178A191GLU-1-0.835-0.88843.394-0.023-0.0230.0000.0000.0000.000
179A192TYR0-0.016-0.01840.0060.0010.0010.0000.0000.0000.000
180A193TYR0-0.002-0.02236.921-0.001-0.0010.0000.0000.0000.000
181A194LEU00.0490.02641.386-0.001-0.0010.0000.0000.0000.000
182A195LEU0-0.020-0.01043.8710.0010.0010.0000.0000.0000.000
183A196HIS0-0.034-0.01640.0510.0000.0000.0000.0000.0000.000
184A197LEU00.0410.03338.0980.0010.0010.0000.0000.0000.000
185A198GLN00.0390.01441.6360.0000.0000.0000.0000.0000.000
186A199ARG10.8850.93641.4890.0230.0230.0000.0000.0000.000
187A200TRP00.021-0.01638.1220.0020.0020.0000.0000.0000.000
188A201ILE00.0110.03441.8850.0000.0000.0000.0000.0000.000
189A202ASP-1-0.885-0.95243.722-0.022-0.0220.0000.0000.0000.000
190A203ILE0-0.076-0.04341.4370.0010.0010.0000.0000.0000.000
191A204SER00.0400.00440.4150.0000.0000.0000.0000.0000.000
192A205LEU0-0.021-0.00542.1810.0010.0010.0000.0000.0000.000
193A206GLU-1-0.854-0.91145.560-0.015-0.0150.0000.0000.0000.000
194A207GLU-1-0.862-0.95341.353-0.017-0.0170.0000.0000.0000.000
195A208ILE0-0.0100.00641.2620.0010.0010.0000.0000.0000.000
196A209GLU-1-0.805-0.87043.907-0.017-0.0170.0000.0000.0000.000
197A210SER0-0.032-0.00644.9390.0020.0020.0000.0000.0000.000
198A211ILE00.038-0.00139.8010.0010.0010.0000.0000.0000.000
199A212ASP-1-0.725-0.84843.791-0.022-0.0220.0000.0000.0000.000
200A213GLN0-0.058-0.03046.1660.0010.0010.0000.0000.0000.000
201A214GLU-1-0.768-0.84942.879-0.010-0.0100.0000.0000.0000.000
202A215ILE0-0.005-0.00741.2600.0010.0010.0000.0000.0000.000
203A216LYS10.7870.88744.9040.0120.0120.0000.0000.0000.000
204A217ILE0-0.0060.00148.3340.0010.0010.0000.0000.0000.000
205A218LEU0-0.020-0.00942.1070.0010.0010.0000.0000.0000.000
206A219ARG10.8420.92441.5560.0200.0200.0000.0000.0000.000
207A220GLU-1-0.848-0.88846.618-0.010-0.0100.0000.0000.0000.000
208A221ARG10.8600.93143.2100.0060.0060.0000.0000.0000.000