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: VQ9J1

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 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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2475498.484235
FMO2-HF: Nuclear repulsion 2388656.226868
FMO2-HF: Total energy -86842.257367
FMO2-MP2: Total energy -87093.437881


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.
-27.268-20.3235.164-5.761-6.3490.018
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 : -0.015 / 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].
3A1CYS0-0.049-0.0243.945-0.8580.6540.039-0.749-0.8020.002
4A2PHE00.0230.0025.7890.2990.2990.0000.0000.0000.000
5A3ALA00.0830.0369.3120.1080.1080.0000.0000.0000.000
6A4LYS10.9870.99812.4820.2740.2740.0000.0000.0000.000
7A5GLY00.0030.00513.998-0.005-0.0050.0000.0000.0000.000
8A6THR0-0.095-0.05511.7650.0250.0250.0000.0000.0000.000
9A7ASN00.0070.00713.2810.0610.0610.0000.0000.0000.000
10A8VAL00.0100.00210.270-0.104-0.1040.0000.0000.0000.000
11A9LEU0-0.031-0.00713.4900.0590.0590.0000.0000.0000.000
12A10MET00.0350.02912.8710.0670.0670.0000.0000.0000.000
13A11ALA0-0.037-0.04215.916-0.046-0.0460.0000.0000.0000.000
14A12ASP-1-0.865-0.92017.5770.2060.2060.0000.0000.0000.000
15A13GLY0-0.050-0.02319.604-0.030-0.0300.0000.0000.0000.000
16A14SER0-0.059-0.02519.948-0.051-0.0510.0000.0000.0000.000
17A15ILE0-0.032-0.04117.390-0.001-0.0010.0000.0000.0000.000
18A16GLU-1-0.819-0.91214.3770.1350.1350.0000.0000.0000.000
19A17CYS0-0.050-0.00914.469-0.075-0.0750.0000.0000.0000.000
20A18ILE00.011-0.0047.1060.1010.1010.0000.0000.0000.000
21A19GLU-1-0.880-0.95110.456-0.197-0.1970.0000.0000.0000.000
22A20ASN0-0.050-0.03212.2800.0730.0730.0000.0000.0000.000
23A21ILE0-0.0300.0129.7190.1020.1020.0000.0000.0000.000
24A22GLU-1-0.941-0.97511.2390.5650.5650.0000.0000.0000.000
25A23VAL0-0.029-0.0289.8590.1670.1670.0000.0000.0000.000
26A24GLY00.0190.01211.661-0.216-0.2160.0000.0000.0000.000
27A25ASN0-0.029-0.00412.330-0.196-0.1960.0000.0000.0000.000
28A26LYS10.9630.96512.545-0.684-0.6840.0000.0000.0000.000
29A27VAL00.0530.0389.882-0.154-0.1540.0000.0000.0000.000
30A28MET0-0.038-0.01712.9620.0700.0700.0000.0000.0000.000
31A29GLY00.0660.02212.660-0.059-0.0590.0000.0000.0000.000
32A30LYS10.9280.95712.7260.0300.0300.0000.0000.0000.000
33A31ASP-1-0.856-0.93214.8410.2330.2330.0000.0000.0000.000
34A32GLY0-0.066-0.04017.050-0.003-0.0030.0000.0000.0000.000
35A33ARG10.8800.95416.879-0.275-0.2750.0000.0000.0000.000
36A34PRO00.0360.00515.5300.0070.0070.0000.0000.0000.000
37A35ARG10.7870.90910.169-0.605-0.6050.0000.0000.0000.000
38A36GLU-1-0.945-0.95811.5371.2891.2890.0000.0000.0000.000
39A37VAL00.0080.0147.1850.6910.6910.0000.0000.0000.000
40A38ILE00.0420.0126.995-0.447-0.4470.0000.0000.0000.000
41A39LYS10.9040.9434.748-8.491-8.387-0.001-0.012-0.0900.000
42A40LEU00.0070.0145.6340.4950.4950.0000.0000.0000.000
43A41PRO0-0.045-0.0022.395-1.408-0.9011.243-0.662-1.0890.002
44A42ARG10.9610.9725.411-0.807-0.8070.0000.0000.0000.000
45A43GLY00.0070.0138.0720.1770.1770.0000.0000.0000.000
46A44SER00.0200.02910.295-0.064-0.0640.0000.0000.0000.000
47A45GLU-1-0.857-0.9178.912-2.228-2.2280.0000.0000.0000.000
48A46THR00.0170.01212.5030.0520.0520.0000.0000.0000.000
49A47MET0-0.0020.01811.126-0.287-0.2870.0000.0000.0000.000
50A48TYR00.022-0.00213.3610.1300.1300.0000.0000.0000.000
51A49SER0-0.0150.00514.445-0.079-0.0790.0000.0000.0000.000
52A50VAL00.0390.01914.0420.0350.0350.0000.0000.0000.000
53A51VAL0-0.026-0.02417.2020.0520.0520.0000.0000.0000.000
54A52GLN00.0480.02420.710-0.001-0.0010.0000.0000.0000.000
55A53LYS10.8420.94422.2270.4270.4270.0000.0000.0000.000
56A54SER0-0.001-0.00825.2350.0050.0050.0000.0000.0000.000
57A67MET0-0.004-0.01631.0470.0040.0040.0000.0000.0000.000
58A68PRO0-0.040-0.01727.8830.0060.0060.0000.0000.0000.000
59A69GLU-1-0.911-0.95125.998-0.244-0.2440.0000.0000.0000.000
60A70LEU0-0.051-0.02324.191-0.010-0.0100.0000.0000.0000.000
61A71LEU00.0020.00619.600-0.011-0.0110.0000.0000.0000.000
62A72LYS10.9370.95518.7550.3730.3730.0000.0000.0000.000
63A73PHE0-0.002-0.00111.2590.0590.0590.0000.0000.0000.000
64A74THR0-0.004-0.00114.0980.0480.0480.0000.0000.0000.000
65A75CYS0-0.0060.0189.0160.0430.0430.0000.0000.0000.000
66A76ASN00.1030.0386.449-0.087-0.0870.0000.0000.0000.000
67A77ALA0-0.010-0.0159.634-0.144-0.1440.0000.0000.0000.000
68A78THR0-0.056-0.0557.059-0.083-0.0830.0000.0000.0000.000
69A79HIS00.0270.0395.565-1.567-1.5670.0000.0000.0000.000
70A80GLU-1-0.895-0.9495.516-2.242-2.2420.0000.0000.0000.000
71A81LEU0-0.047-0.0307.1730.0630.0630.0000.0000.0000.000
72A82VAL00.0400.0249.1140.0470.0470.0000.0000.0000.000
73A83VAL0-0.048-0.02811.2310.1680.1680.0000.0000.0000.000
74A84ARG10.9050.95214.6670.4200.4200.0000.0000.0000.000
75A85THR0-0.001-0.00617.913-0.022-0.0220.0000.0000.0000.000
76A86PRO0-0.0150.02120.8890.0200.0200.0000.0000.0000.000
77A87ARG10.9280.95724.0800.2140.2140.0000.0000.0000.000
78A88SER0-0.051-0.02925.8380.0320.0320.0000.0000.0000.000
79A89VAL00.0150.01228.5040.0000.0000.0000.0000.0000.000
80A90ARG10.9250.96531.8030.2200.2200.0000.0000.0000.000
81A91ARG10.9280.97134.4510.1280.1280.0000.0000.0000.000
82A92LEU0-0.056-0.02936.177-0.004-0.0040.0000.0000.0000.000
83A93SER00.0770.05939.8750.0020.0020.0000.0000.0000.000
84A94ARG10.8460.90736.5660.1690.1690.0000.0000.0000.000
85A95THR00.0500.02643.8610.0060.0060.0000.0000.0000.000
86A96ILE0-0.012-0.00543.012-0.004-0.0040.0000.0000.0000.000
87A97LYS10.9420.95945.6270.1170.1170.0000.0000.0000.000
88A98GLY00.0270.01549.7520.0040.0040.0000.0000.0000.000
89A99VAL00.0050.02448.1370.0040.0040.0000.0000.0000.000
90A100GLU-1-0.911-0.95647.198-0.105-0.1050.0000.0000.0000.000
91A101TYR0-0.030-0.01943.0020.0030.0030.0000.0000.0000.000
92A102PHE00.0420.01642.062-0.004-0.0040.0000.0000.0000.000
93A103GLU-1-0.786-0.85536.644-0.172-0.1720.0000.0000.0000.000
94A104VAL0-0.055-0.04734.483-0.001-0.0010.0000.0000.0000.000
95A105ILE0-0.016-0.00530.832-0.003-0.0030.0000.0000.0000.000
96A106THR0-0.031-0.03629.1900.0020.0020.0000.0000.0000.000
97A107PHE0-0.0210.00724.315-0.014-0.0140.0000.0000.0000.000
98A108GLU-1-0.849-0.91624.402-0.205-0.2050.0000.0000.0000.000
99A109MET00.0080.01217.118-0.040-0.0400.0000.0000.0000.000
100A110GLY00.0160.00120.5140.0500.0500.0000.0000.0000.000
101A111GLN00.0250.02019.354-0.026-0.0260.0000.0000.0000.000
102A112LYS10.8390.91219.4380.5330.5330.0000.0000.0000.000
103A113LYS10.9501.00819.3220.3080.3080.0000.0000.0000.000
104A114ALA00.0370.01717.8420.0200.0200.0000.0000.0000.000
105A115PRO0-0.016-0.02619.9360.0430.0430.0000.0000.0000.000
106A116ASP-1-0.795-0.87817.120-0.641-0.6410.0000.0000.0000.000
107A117GLY0-0.090-0.05720.7730.0350.0350.0000.0000.0000.000
108A118ARG10.8070.86913.1840.9940.9940.0000.0000.0000.000
109A119ILE0-0.023-0.01117.4240.0020.0020.0000.0000.0000.000
110A120VAL00.0260.01913.939-0.043-0.0430.0000.0000.0000.000
111A121GLU-1-0.915-0.95614.481-0.471-0.4710.0000.0000.0000.000
112A122LEU0-0.023-0.02215.148-0.092-0.0920.0000.0000.0000.000
113A123VAL00.0260.01717.5620.0770.0770.0000.0000.0000.000
114A124LYS10.8630.91820.4880.3520.3520.0000.0000.0000.000
115A125GLU-1-0.872-0.93623.846-0.258-0.2580.0000.0000.0000.000
116A126VAL0-0.0190.01227.3850.0000.0000.0000.0000.0000.000
117A127SER0-0.051-0.06129.9090.0080.0080.0000.0000.0000.000
118A128LYS10.9410.96433.6550.1370.1370.0000.0000.0000.000
119A129SER00.005-0.00236.594-0.001-0.0010.0000.0000.0000.000
120A130TYR00.0200.01437.7470.0050.0050.0000.0000.0000.000
121A131PRO00.0450.00943.192-0.003-0.0030.0000.0000.0000.000
122A132VAL00.0300.01146.7390.0030.0030.0000.0000.0000.000
123A133SER0-0.005-0.01448.3540.0020.0020.0000.0000.0000.000
124A134GLU-1-1.022-1.00847.973-0.070-0.0700.0000.0000.0000.000
125A135GLY00.0330.05249.3470.0020.0020.0000.0000.0000.000
126A136PRO0-0.057-0.04145.718-0.004-0.0040.0000.0000.0000.000
127A137GLU-1-0.868-0.94344.246-0.079-0.0790.0000.0000.0000.000
128A138ARG11.0351.02142.7320.0740.0740.0000.0000.0000.000
129A139ALA0-0.010-0.01040.188-0.006-0.0060.0000.0000.0000.000
130A140ASN0-0.014-0.01639.210-0.013-0.0130.0000.0000.0000.000
131A141GLU-1-0.830-0.91239.311-0.083-0.0830.0000.0000.0000.000
132A142LEU0-0.0540.00233.954-0.003-0.0030.0000.0000.0000.000
133A143VAL0-0.038-0.02734.927-0.009-0.0090.0000.0000.0000.000
134A144GLU-1-0.926-0.95534.408-0.097-0.0970.0000.0000.0000.000
135A145SER0-0.029-0.03834.205-0.003-0.0030.0000.0000.0000.000
136A146TYR0-0.029-0.05526.5680.0000.0000.0000.0000.0000.000
137A147ARG10.9300.95429.8080.1300.1300.0000.0000.0000.000
138A148LYS10.9341.01030.6810.1040.1040.0000.0000.0000.000
139A149ALA0-0.096-0.04128.3390.0090.0090.0000.0000.0000.000
140A150SER0-0.026-0.02424.224-0.005-0.0050.0000.0000.0000.000
141A151ASN00.0510.02322.918-0.014-0.0140.0000.0000.0000.000
142A152LYS10.9691.00618.2890.1960.1960.0000.0000.0000.000
143A153ALA00.0490.01524.128-0.006-0.0060.0000.0000.0000.000
144A154TYR0-0.056-0.03219.0490.0080.0080.0000.0000.0000.000
145A155PHE0-0.008-0.00418.6630.0290.0290.0000.0000.0000.000
146A156GLU-1-0.885-0.95814.400-0.363-0.3630.0000.0000.0000.000
147A157TRP0-0.009-0.02813.3090.0310.0310.0000.0000.0000.000
148A158THR00.0150.0098.4400.1660.1660.0000.0000.0000.000
149A159ILE0-0.0140.00310.5460.1480.1480.0000.0000.0000.000
150A160GLU-1-0.772-0.8698.137-2.068-2.0680.0000.0000.0000.000
151A161ALA00.0140.00710.1490.3820.3820.0000.0000.0000.000
152A162ARG10.8570.91711.1841.5891.5890.0000.0000.0000.000
153A163ASP-1-0.802-0.88113.255-0.958-0.9580.0000.0000.0000.000
154A164LEU0-0.015-0.00315.1570.1390.1390.0000.0000.0000.000
155A165SER0-0.020-0.01216.6100.0900.0900.0000.0000.0000.000
156A166LEU0-0.023-0.00317.0890.1000.1000.0000.0000.0000.000
157A167LEU0-0.0090.00917.9200.0700.0700.0000.0000.0000.000
158A168GLY00.0310.01921.1950.0260.0260.0000.0000.0000.000
159A169SER00.0330.00524.341-0.020-0.0200.0000.0000.0000.000
160A170HIS0-0.083-0.06526.306-0.004-0.0040.0000.0000.0000.000
161A171VAL00.0330.02221.2450.0030.0030.0000.0000.0000.000
162A172ARG10.9100.96220.3270.5810.5810.0000.0000.0000.000
163A173LYS10.9380.97022.2510.2720.2720.0000.0000.0000.000
164A174ALA0-0.019-0.01324.2480.0080.0080.0000.0000.0000.000
165A175THR0-0.005-0.00117.6750.0070.0070.0000.0000.0000.000
166A176TYR0-0.088-0.02419.3690.0070.0070.0000.0000.0000.000
167A177GLN00.0710.03813.661-0.134-0.1340.0000.0000.0000.000
168A178THR00.008-0.02615.7830.1110.1110.0000.0000.0000.000
169A179TYR00.0350.02416.525-0.043-0.0430.0000.0000.0000.000
170A180ALA0-0.003-0.00617.9920.0240.0240.0000.0000.0000.000
171A181PRO0-0.0290.00819.8180.0330.0330.0000.0000.0000.000
172A182ILE00.013-0.01223.0830.0120.0120.0000.0000.0000.000
173A183GLY0-0.0060.02525.039-0.013-0.0130.0000.0000.0000.000
174A410ALA00.002-0.00327.8050.0140.0140.0000.0000.0000.000
175A411ALA0-0.027-0.03629.4590.0010.0010.0000.0000.0000.000
176A412PHE0-0.027-0.01527.9820.0100.0100.0000.0000.0000.000
177A413ALA00.0400.04824.2430.0170.0170.0000.0000.0000.000
178A414ARG10.9300.95719.304-0.002-0.0020.0000.0000.0000.000
179A415GLU-1-0.866-0.91722.451-0.100-0.1000.0000.0000.0000.000
180A416CYS0-0.036-0.02318.660-0.027-0.0270.0000.0000.0000.000
181A417ARG10.8720.92721.1710.1720.1720.0000.0000.0000.000
182A418GLY00.0360.01220.696-0.039-0.0390.0000.0000.0000.000
183A419PHE0-0.036-0.02316.9470.0440.0440.0000.0000.0000.000
184A420TYR00.0390.02920.345-0.050-0.0500.0000.0000.0000.000
185A421PHE00.012-0.00616.6460.0110.0110.0000.0000.0000.000
186A422GLU-1-0.897-0.95020.964-0.486-0.4860.0000.0000.0000.000
187A423LEU00.0070.00514.769-0.027-0.0270.0000.0000.0000.000
188A424GLN0-0.053-0.01818.6520.0700.0700.0000.0000.0000.000
189A425GLU-1-0.931-0.95817.280-0.762-0.7620.0000.0000.0000.000
190A426LEU0-0.067-0.03916.8530.1030.1030.0000.0000.0000.000
191A427LYS10.9680.97518.8510.4700.4700.0000.0000.0000.000
192A428GLU-1-0.930-0.97515.868-0.608-0.6080.0000.0000.0000.000
193A429ASP-1-0.881-0.92114.894-0.490-0.4900.0000.0000.0000.000
194A430ASP-1-0.940-0.98013.148-0.581-0.5810.0000.0000.0000.000
195A431TYR0-0.072-0.0475.657-0.221-0.2210.0000.0000.0000.000
196A432TYR0-0.006-0.0238.2330.2680.2680.0000.0000.0000.000
197A433GLY00.0470.0033.951-0.558-0.530-0.001-0.016-0.0100.000
198A434ILE0-0.060-0.0173.5011.0961.4930.003-0.115-0.2850.000
199A435THR0-0.030-0.0262.286-12.981-9.2253.858-3.953-3.6610.013
200A436LEU00.004-0.0043.839-4.200-3.8060.023-0.179-0.2380.001
201A437SER00.0040.0025.9351.0801.0800.0000.0000.0000.000
202A438ASP-1-0.849-0.9227.0262.7892.7890.0000.0000.0000.000
203A439ASP-1-0.942-0.9639.1660.8310.8310.0000.0000.0000.000
204A440SER0-0.138-0.07810.657-0.297-0.2970.0000.0000.0000.000
205A441ASP-1-0.850-0.9089.1360.3780.3780.0000.0000.0000.000
206A442HIS00.0360.0054.403-1.211-1.041-0.001-0.025-0.1450.000
207A443GLN0-0.024-0.0236.609-0.095-0.0950.0000.0000.0000.000
208A444PHE0-0.019-0.0136.7200.2040.2040.0000.0000.0000.000
209A445LEU0-0.034-0.00111.275-0.240-0.2400.0000.0000.0000.000
210A446LEU00.0380.02210.9450.0690.0690.0000.0000.0000.000
211A447ALA00.0290.01114.1910.0680.0680.0000.0000.0000.000
212A448ASN0-0.026-0.00817.0620.0380.0380.0000.0000.0000.000
213A449GLN0-0.004-0.02917.9110.0330.0330.0000.0000.0000.000
214A450VAL0-0.009-0.00213.9310.0250.0250.0000.0000.0000.000
215A451VAL0-0.0010.00512.1080.0290.0290.0000.0000.0000.000
216A452VAL0-0.055-0.0169.023-0.218-0.2180.0000.0000.0000.000
217A453HIS00.0460.0224.0960.9611.0380.001-0.050-0.0290.000