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: G5JZ1

Calculation Name: 1GPP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1GPP

Chain ID: A

ChEMBL ID:

UniProt ID: P17255

Base Structure: X-ray

Registration Date: 2023-09-23

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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2477353.565556
FMO2-HF: Nuclear repulsion 2390508.850191
FMO2-HF: Total energy -86844.715365
FMO2-MP2: Total energy -87095.987346


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.
-40.412-41.41926.164-12.121-13.034-0.024
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 : -0.016 / 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].
3A1CYS0-0.042-0.0143.3320.3262.1310.042-0.856-0.9930.002
4A2PHE00.000-0.0225.7170.4320.4320.0000.0000.0000.000
5A3ALA00.0780.0319.4070.1930.1930.0000.0000.0000.000
6A4LYS10.9460.97912.7420.2670.2670.0000.0000.0000.000
7A5GLY00.0130.01114.3800.0080.0080.0000.0000.0000.000
8A6THR0-0.074-0.04511.8050.0450.0450.0000.0000.0000.000
9A7ASN0-0.038-0.02912.8530.0440.0440.0000.0000.0000.000
10A8VAL0-0.029-0.0119.708-0.144-0.1440.0000.0000.0000.000
11A9LEU0-0.021-0.00512.8060.1230.1230.0000.0000.0000.000
12A10MET00.0500.02912.909-0.018-0.0180.0000.0000.0000.000
13A11ALA0-0.046-0.03514.406-0.024-0.0240.0000.0000.0000.000
14A12ASP-1-0.844-0.89815.8110.0550.0550.0000.0000.0000.000
15A13GLY0-0.033-0.01618.107-0.012-0.0120.0000.0000.0000.000
16A14SER0-0.072-0.05119.209-0.045-0.0450.0000.0000.0000.000
17A15ILE0-0.032-0.03516.714-0.034-0.0340.0000.0000.0000.000
18A16GLU-1-0.793-0.86714.330-0.077-0.0770.0000.0000.0000.000
19A17CYS0-0.048-0.01814.108-0.132-0.1320.0000.0000.0000.000
20A18ILE00.0230.0016.8010.0850.0850.0000.0000.0000.000
21A19GLU-1-0.843-0.93110.198-0.406-0.4060.0000.0000.0000.000
22A20ASN0-0.069-0.04912.4450.1400.1400.0000.0000.0000.000
23A21ILE0-0.0270.0119.3720.0880.0880.0000.0000.0000.000
24A22GLU-1-0.862-0.93410.6220.4940.4940.0000.0000.0000.000
25A23VAL0-0.043-0.0389.5960.1540.1540.0000.0000.0000.000
26A24GLY00.0170.02011.321-0.199-0.1990.0000.0000.0000.000
27A25ASN0-0.051-0.01911.615-0.235-0.2350.0000.0000.0000.000
28A26LYS10.8210.87111.879-0.577-0.5770.0000.0000.0000.000
29A27VAL00.0050.0148.194-0.136-0.1360.0000.0000.0000.000
30A28MET0-0.0100.01011.6120.1110.1110.0000.0000.0000.000
31A29GLY00.0800.03210.999-0.140-0.1400.0000.0000.0000.000
32A30LYS10.8110.88711.5240.2370.2370.0000.0000.0000.000
33A31ASP-1-0.823-0.89313.4710.0660.0660.0000.0000.0000.000
34A32GLY0-0.034-0.02615.7160.0210.0210.0000.0000.0000.000
35A33ARG10.8490.92915.842-0.146-0.1460.0000.0000.0000.000
36A34PRO00.0360.00514.124-0.025-0.0250.0000.0000.0000.000
37A35ARG10.7590.8678.908-0.320-0.3200.0000.0000.0000.000
38A36GLU-1-0.760-0.85010.6890.8520.8520.0000.0000.0000.000
39A37VAL00.0030.0076.7020.6610.6610.0000.0000.0000.000
40A38ILE00.0260.0036.756-0.418-0.4180.0000.0000.0000.000
41A39LYS10.8940.9394.520-11.121-10.934-0.001-0.064-0.1220.000
42A40LEU00.0070.0165.2320.3950.3950.0000.0000.0000.000
43A41PRO0-0.051-0.0092.147-0.791-0.7221.818-0.756-1.1310.000
44A42ARG10.8790.9315.319-0.967-0.989-0.0010.0000.0240.000
45A43GLY00.0100.0178.1840.2790.2790.0000.0000.0000.000
46A44SER00.0090.02210.598-0.096-0.0960.0000.0000.0000.000
47A45GLU-1-0.815-0.8999.622-1.473-1.4730.0000.0000.0000.000
48A46THR0-0.001-0.00213.0730.0120.0120.0000.0000.0000.000
49A47MET00.0180.03610.840-0.202-0.2020.0000.0000.0000.000
50A48TYR0-0.049-0.06413.7690.1310.1310.0000.0000.0000.000
51A49SER0-0.0100.00614.686-0.120-0.1200.0000.0000.0000.000
52A50VAL0-0.007-0.00813.8410.0340.0340.0000.0000.0000.000
53A51VAL00.0200.00817.1650.0290.0290.0000.0000.0000.000
54A52GLN00.0390.02620.381-0.002-0.0020.0000.0000.0000.000
55A53LYS10.7870.87021.8810.4620.4620.0000.0000.0000.000
56A54SER00.0060.00425.1650.0070.0070.0000.0000.0000.000
57A67MET0-0.006-0.01730.7380.0040.0040.0000.0000.0000.000
58A68PRO0-0.018-0.01226.7190.0050.0050.0000.0000.0000.000
59A69GLU-1-0.794-0.89025.300-0.376-0.3760.0000.0000.0000.000
60A70LEU0-0.070-0.02023.720-0.017-0.0170.0000.0000.0000.000
61A71LEU00.0180.00418.628-0.016-0.0160.0000.0000.0000.000
62A72LYS10.8120.89118.4910.4470.4470.0000.0000.0000.000
63A73PHE00.0260.01711.144-0.012-0.0120.0000.0000.0000.000
64A74THR0-0.001-0.01013.8550.1450.1450.0000.0000.0000.000
65A75CYS0-0.0410.0009.263-0.034-0.0340.0000.0000.0000.000
66A76ASN00.0830.0256.989-0.089-0.0890.0000.0000.0000.000
67A77ALA00.0100.00210.485-0.164-0.1640.0000.0000.0000.000
68A78THR0-0.044-0.0437.941-0.076-0.0760.0000.0000.0000.000
69A79HIS00.0150.0275.931-1.356-1.3560.0000.0000.0000.000
70A80GLU-1-0.833-0.8895.743-1.900-1.9000.0000.0000.0000.000
71A81LEU0-0.046-0.0207.567-0.161-0.1610.0000.0000.0000.000
72A82VAL00.0250.0148.3270.1070.1070.0000.0000.0000.000
73A83VAL0-0.033-0.01710.6840.1770.1770.0000.0000.0000.000
74A84ARG10.8510.91014.2800.5150.5150.0000.0000.0000.000
75A85THR00.009-0.00117.508-0.016-0.0160.0000.0000.0000.000
76A86PRO00.0020.01120.7230.0210.0210.0000.0000.0000.000
77A87ARG10.8710.94124.0830.2200.2200.0000.0000.0000.000
78A88SER0-0.042-0.02525.9470.0270.0270.0000.0000.0000.000
79A89VAL0-0.0040.00528.5180.0000.0000.0000.0000.0000.000
80A90ARG10.8110.89431.1930.2340.2340.0000.0000.0000.000
81A91ARG10.8800.92834.5550.1260.1260.0000.0000.0000.000
82A92LEU0-0.038-0.01937.051-0.004-0.0040.0000.0000.0000.000
83A93SER00.0320.02040.5180.0020.0020.0000.0000.0000.000
84A94ARG10.8210.89037.2890.1560.1560.0000.0000.0000.000
85A95THR00.0540.02444.4550.0030.0030.0000.0000.0000.000
86A96ILE0-0.031-0.01543.643-0.002-0.0020.0000.0000.0000.000
87A97LYS10.9320.94847.0240.1000.1000.0000.0000.0000.000
88A98GLY00.0450.03350.6640.0040.0040.0000.0000.0000.000
89A99VAL00.0060.02448.8830.0020.0020.0000.0000.0000.000
90A100GLU-1-0.860-0.92547.347-0.103-0.1030.0000.0000.0000.000
91A101TYR0-0.017-0.01243.7420.0040.0040.0000.0000.0000.000
92A102PHE00.0700.02842.527-0.006-0.0060.0000.0000.0000.000
93A103GLU-1-0.786-0.85737.059-0.159-0.1590.0000.0000.0000.000
94A104VAL0-0.045-0.04035.062-0.001-0.0010.0000.0000.0000.000
95A105ILE0-0.035-0.00331.341-0.002-0.0020.0000.0000.0000.000
96A106THR0-0.029-0.04529.496-0.001-0.0010.0000.0000.0000.000
97A107PHE0-0.0150.00324.357-0.012-0.0120.0000.0000.0000.000
98A108GLU-1-0.833-0.90224.814-0.189-0.1890.0000.0000.0000.000
99A109MET00.0060.01417.276-0.032-0.0320.0000.0000.0000.000
100A110GLY00.0120.00320.9180.0450.0450.0000.0000.0000.000
101A111GLN0-0.0010.00019.875-0.026-0.0260.0000.0000.0000.000
102A112LYS10.8270.90320.5780.4520.4520.0000.0000.0000.000
103A113LYS10.9110.97920.4260.2560.2560.0000.0000.0000.000
104A114ALA00.0490.03618.2240.0020.0020.0000.0000.0000.000
105A115PRO0-0.006-0.02120.3400.0480.0480.0000.0000.0000.000
106A116ASP-1-0.796-0.89717.276-0.474-0.4740.0000.0000.0000.000
107A117GLY0-0.022-0.01520.7890.0410.0410.0000.0000.0000.000
108A118ARG10.7280.82413.2780.7620.7620.0000.0000.0000.000
109A119ILE0-0.0130.00318.262-0.010-0.0100.0000.0000.0000.000
110A120VAL00.0200.01114.797-0.037-0.0370.0000.0000.0000.000
111A121GLU-1-0.862-0.93215.567-0.312-0.3120.0000.0000.0000.000
112A122LEU0-0.029-0.02815.821-0.092-0.0920.0000.0000.0000.000
113A123VAL0-0.0140.00518.0860.0710.0710.0000.0000.0000.000
114A124LYS10.8860.93520.7410.2830.2830.0000.0000.0000.000
115A125GLU-1-0.815-0.89724.125-0.252-0.2520.0000.0000.0000.000
116A126VAL0-0.0180.00727.7370.0020.0020.0000.0000.0000.000
117A127SER0-0.039-0.05030.2500.0030.0030.0000.0000.0000.000
118A128LYS10.9330.97334.0290.1260.1260.0000.0000.0000.000
119A129SER00.0220.00637.184-0.003-0.0030.0000.0000.0000.000
120A130TYR00.0140.01439.0610.0020.0020.0000.0000.0000.000
121A131PRO00.0290.01743.852-0.003-0.0030.0000.0000.0000.000
122A132VAL0-0.007-0.00947.2370.0020.0020.0000.0000.0000.000
123A133SER0-0.056-0.05548.8450.0010.0010.0000.0000.0000.000
124A134GLU-1-0.918-0.93347.945-0.068-0.0680.0000.0000.0000.000
125A135GLY00.0390.04449.2380.0020.0020.0000.0000.0000.000
126A136PRO0-0.066-0.04245.525-0.004-0.0040.0000.0000.0000.000
127A137GLU-1-0.840-0.92544.052-0.079-0.0790.0000.0000.0000.000
128A138ARG10.9100.92842.9620.0680.0680.0000.0000.0000.000
129A139ALA00.0110.00740.406-0.005-0.0050.0000.0000.0000.000
130A140ASN0-0.0040.00139.298-0.013-0.0130.0000.0000.0000.000
131A141GLU-1-0.758-0.86038.934-0.084-0.0840.0000.0000.0000.000
132A142LEU0-0.0410.01834.256-0.002-0.0020.0000.0000.0000.000
133A143VAL00.002-0.00734.821-0.009-0.0090.0000.0000.0000.000
134A144GLU-1-0.941-0.97634.364-0.104-0.1040.0000.0000.0000.000
135A145SER0-0.046-0.05434.632-0.004-0.0040.0000.0000.0000.000
136A146TYR0-0.016-0.04126.8320.0000.0000.0000.0000.0000.000
137A147ARG10.9350.97029.9570.1320.1320.0000.0000.0000.000
138A148LYS10.9260.98230.2380.0980.0980.0000.0000.0000.000
139A149ALA0-0.068-0.03528.6100.0110.0110.0000.0000.0000.000
140A150SER0-0.032-0.02324.313-0.005-0.0050.0000.0000.0000.000
141A151ASN00.0270.01322.952-0.012-0.0120.0000.0000.0000.000
142A152LYS10.9050.96717.6270.3080.3080.0000.0000.0000.000
143A153ALA00.0300.01324.000-0.004-0.0040.0000.0000.0000.000
144A154TYR0-0.072-0.04818.3360.0140.0140.0000.0000.0000.000
145A155PHE00.0200.01418.7230.0230.0230.0000.0000.0000.000
146A156GLU-1-0.780-0.88914.464-0.450-0.4500.0000.0000.0000.000
147A157TRP0-0.019-0.01613.0550.0530.0530.0000.0000.0000.000
148A158THR00.005-0.0208.1360.1410.1410.0000.0000.0000.000
149A159ILE0-0.014-0.00310.8340.1880.1880.0000.0000.0000.000
150A160GLU-1-0.739-0.8319.228-1.424-1.4240.0000.0000.0000.000
151A161ALA00.0120.00410.6270.3090.3090.0000.0000.0000.000
152A162ARG10.8470.90411.8961.1631.1630.0000.0000.0000.000
153A163ASP-1-0.786-0.86714.119-0.705-0.7050.0000.0000.0000.000
154A164LEU00.0230.01515.7560.0970.0970.0000.0000.0000.000
155A165SER0-0.055-0.03617.3630.1010.1010.0000.0000.0000.000
156A166LEU0-0.039-0.01417.8310.0880.0880.0000.0000.0000.000
157A167LEU00.0190.02518.5430.0610.0610.0000.0000.0000.000
158A168GLY00.0310.02421.9070.0280.0280.0000.0000.0000.000
159A169SER00.022-0.00125.078-0.019-0.0190.0000.0000.0000.000
160A170HIS0-0.037-0.03226.768-0.002-0.0020.0000.0000.0000.000
161A171VAL00.0420.02421.844-0.003-0.0030.0000.0000.0000.000
162A172ARG10.8490.92220.8670.5550.5550.0000.0000.0000.000
163A173LYS10.9360.96922.5490.2630.2630.0000.0000.0000.000
164A174ALA00.0040.00024.5460.0020.0020.0000.0000.0000.000
165A175THR0-0.020-0.01617.8750.0050.0050.0000.0000.0000.000
166A176TYR0-0.086-0.03119.3190.0000.0000.0000.0000.0000.000
167A177GLN00.0760.04113.698-0.158-0.1580.0000.0000.0000.000
168A178THR00.013-0.01915.0240.0810.0810.0000.0000.0000.000
169A179TYR00.0430.02215.381-0.076-0.0760.0000.0000.0000.000
170A180ALA00.0260.01616.2630.0480.0480.0000.0000.0000.000
171A181PRO0-0.0260.01018.0270.0230.0230.0000.0000.0000.000
172A182ILE00.0060.00021.1160.0130.0130.0000.0000.0000.000
173A183GLY00.0270.02123.054-0.010-0.0100.0000.0000.0000.000
174A410ALA0-0.015-0.02126.0820.0180.0180.0000.0000.0000.000
175A411ALA0-0.033-0.02828.014-0.001-0.0010.0000.0000.0000.000
176A412PHE0-0.009-0.00126.3510.0120.0120.0000.0000.0000.000
177A413ALA00.0260.03523.4470.0050.0050.0000.0000.0000.000
178A414ARG10.8560.90517.8260.2030.2030.0000.0000.0000.000
179A415GLU-1-0.819-0.88320.899-0.200-0.2000.0000.0000.0000.000
180A416CYS0-0.060-0.03817.445-0.042-0.0420.0000.0000.0000.000
181A417ARG10.8390.90619.9840.2760.2760.0000.0000.0000.000
182A418GLY00.0360.00919.647-0.056-0.0560.0000.0000.0000.000
183A419PHE0-0.021-0.01716.1280.0610.0610.0000.0000.0000.000
184A420TYR00.0240.01619.912-0.043-0.0430.0000.0000.0000.000
185A421PHE0-0.0030.01017.1420.0040.0040.0000.0000.0000.000
186A422GLU-1-0.808-0.87320.916-0.489-0.4890.0000.0000.0000.000
187A423LEU00.0150.01214.603-0.052-0.0520.0000.0000.0000.000
188A424GLN0-0.063-0.02318.8950.0920.0920.0000.0000.0000.000
189A425GLU-1-0.827-0.87418.240-0.669-0.6690.0000.0000.0000.000
190A426LEU0-0.030-0.00816.9940.0770.0770.0000.0000.0000.000
191A427LYS10.8450.89919.1230.5420.5420.0000.0000.0000.000
192A428GLU-1-0.912-0.95816.261-0.512-0.5120.0000.0000.0000.000
193A429ASP-1-0.889-0.93015.203-0.502-0.5020.0000.0000.0000.000
194A430ASP-1-0.889-0.92513.599-0.435-0.4350.0000.0000.0000.000
195A431TYR0-0.039-0.0355.729-0.099-0.0990.0000.0000.0000.000
196A432TYR0-0.006-0.0508.6640.2940.2940.0000.0000.0000.000
197A433GLY00.0580.0104.636-0.600-0.605-0.001-0.0060.0120.000
198A434ILE0-0.036-0.0053.4390.6851.7780.003-0.521-0.574-0.001
199A435THR0-0.021-0.0231.881-23.286-28.54022.853-9.756-7.843-0.021
200A436LEU00.0100.0073.157-4.107-4.1360.1390.564-0.6730.004
201A437SER0-0.057-0.0675.1801.6531.722-0.0010.000-0.0680.000
202A438ASP-1-0.853-0.9207.1902.3852.3850.0000.0000.0000.000
203A439ASP-1-0.886-0.8989.1120.9690.9690.0000.0000.0000.000
204A440SER0-0.097-0.06610.746-0.319-0.3190.0000.0000.0000.000
205A441ASP-1-0.786-0.8669.5850.1510.1510.0000.0000.0000.000
206A442HIS00.0150.0024.266-1.219-1.028-0.001-0.014-0.1760.000
207A443GLN0-0.065-0.0415.382-0.447-0.4470.0000.0000.0000.000
208A444PHE00.0030.0004.4070.2770.346-0.001-0.003-0.0650.000
209A445LEU0-0.047-0.0079.385-0.248-0.2480.0000.0000.0000.000
210A446LEU00.0580.02910.2800.0530.0530.0000.0000.0000.000
211A447ALA00.0270.01012.8570.1230.1230.0000.0000.0000.000
212A448ASN0-0.043-0.02516.1090.0290.0290.0000.0000.0000.000
213A449GLN00.019-0.01015.8990.0570.0570.0000.0000.0000.000
214A450VAL00.0010.00512.8570.0410.0410.0000.0000.0000.000
215A451VAL0-0.006-0.00410.658-0.028-0.0280.0000.0000.0000.000
216A452VAL0-0.036-0.0117.561-0.176-0.1760.0000.0000.0000.000
217A453HIS00.0430.0082.580-1.873-1.0531.315-0.709-1.425-0.008