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

tag_button

FMODB ID: QYVMY

Calculation Name: 1GDT-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1GDT

Chain ID: A

ChEMBL ID:

UniProt ID: P03012

Base Structure: X-ray

Registration Date: 2023-06-22

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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1590329.682804
FMO2-HF: Nuclear repulsion 1518178.796683
FMO2-HF: Total energy -72150.886121
FMO2-MP2: Total energy -72358.783802


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-18.458-9.6074.994-4.918-8.927-0.029
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.026 / q_NPA : 0.039
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].
3A3LEU00.0400.0252.670-5.937-2.3901.004-1.547-3.0030.004
4A4PHE0-0.049-0.0524.2030.3360.4770.001-0.020-0.1230.000
5A5GLY00.0390.0257.561-0.037-0.0370.0000.0000.0000.000
6A6TYR0-0.069-0.06410.430-0.002-0.0020.0000.0000.0000.000
7A7ALA00.0160.00113.6940.0280.0280.0000.0000.0000.000
8A8ARG10.8820.97417.1910.2540.2540.0000.0000.0000.000
9A9VAL0-0.055-0.03820.4260.0120.0120.0000.0000.0000.000
10A10SER00.0710.03623.350-0.004-0.0040.0000.0000.0000.000
11A11THR0-0.001-0.00726.6330.0040.0040.0000.0000.0000.000
12A12SER00.0450.00927.826-0.002-0.0020.0000.0000.0000.000
13A13GLN00.025-0.01025.822-0.002-0.0020.0000.0000.0000.000
14A14GLN00.0920.05925.958-0.004-0.0040.0000.0000.0000.000
15A15SER00.006-0.00725.8800.0070.0070.0000.0000.0000.000
16A16LEU0-0.050-0.02121.030-0.004-0.0040.0000.0000.0000.000
17A17ASP-1-0.855-0.92421.373-0.052-0.0520.0000.0000.0000.000
18A18ILE00.0320.01921.1970.0080.0080.0000.0000.0000.000
19A19GLN0-0.021-0.01518.664-0.009-0.0090.0000.0000.0000.000
20A20VAL00.017-0.00116.866-0.006-0.0060.0000.0000.0000.000
21A21ARG10.7830.88816.766-0.034-0.0340.0000.0000.0000.000
22A22ALA00.0360.01117.3000.0230.0230.0000.0000.0000.000
23A23LEU00.0060.00211.8890.0140.0140.0000.0000.0000.000
24A24LYS10.9220.96312.373-0.035-0.0350.0000.0000.0000.000
25A25ASP-1-0.842-0.90314.1290.1240.1240.0000.0000.0000.000
26A26ALA0-0.049-0.00911.4680.0180.0180.0000.0000.0000.000
27A27GLY00.0350.02310.1430.0550.0550.0000.0000.0000.000
28A28VAL0-0.056-0.0138.2710.1460.1460.0000.0000.0000.000
29A29LYS10.9820.9859.292-0.450-0.4500.0000.0000.0000.000
30A30ALA00.046-0.00111.284-0.094-0.0940.0000.0000.0000.000
31A31ASN00.001-0.00113.2240.0110.0110.0000.0000.0000.000
32A32ARG10.8280.9396.6340.3520.3520.0000.0000.0000.000
33A33ILE00.0320.02110.530-0.076-0.0760.0000.0000.0000.000
34A34PHE0-0.0280.00011.4490.0120.0120.0000.0000.0000.000
35A35THR0-0.008-0.00915.2140.0030.0030.0000.0000.0000.000
36A36ASP-1-0.762-0.87618.380-0.239-0.2390.0000.0000.0000.000
37A37LYS10.9040.95921.2650.1050.1050.0000.0000.0000.000
38A38ALA0-0.013-0.01624.704-0.005-0.0050.0000.0000.0000.000
39A39SER00.004-0.00325.9340.0090.0090.0000.0000.0000.000
40A40GLY0-0.0220.01828.0460.0090.0090.0000.0000.0000.000
41A41SER0-0.036-0.03029.975-0.002-0.0020.0000.0000.0000.000
42A42SER0-0.026-0.02329.6280.0060.0060.0000.0000.0000.000
43A43SER0-0.037-0.02626.644-0.009-0.0090.0000.0000.0000.000
44A44ASP-1-0.816-0.88525.565-0.151-0.1510.0000.0000.0000.000
45A45ARG10.8160.89520.6430.2250.2250.0000.0000.0000.000
46A46LYS11.0331.01520.7650.1280.1280.0000.0000.0000.000
47A47GLY00.0180.00818.632-0.014-0.0140.0000.0000.0000.000
48A48LEU00.007-0.00714.975-0.033-0.0330.0000.0000.0000.000
49A49ASP-1-0.798-0.87816.010-0.327-0.3270.0000.0000.0000.000
50A50LEU0-0.043-0.00415.842-0.003-0.0030.0000.0000.0000.000
51A51LEU0-0.032-0.0109.754-0.035-0.0350.0000.0000.0000.000
52A52ARG10.7550.80411.5240.2560.2560.0000.0000.0000.000
53A53MET0-0.0190.00712.9590.0110.0110.0000.0000.0000.000
54A54LYS10.8800.9429.1720.4510.4510.0000.0000.0000.000
55A55VAL0-0.060-0.0287.192-0.148-0.1480.0000.0000.0000.000
56A56GLU-1-0.813-0.8744.921-0.670-0.6700.0000.0000.0000.000
57A57GLU-1-0.905-0.9645.480-0.740-0.7400.0000.0000.0000.000
58A58GLY00.0110.0093.6810.0770.4430.007-0.091-0.2830.000
59A59ASP-1-0.824-0.9202.680-11.937-7.5431.783-2.763-3.414-0.029
60A60VAL00.0200.0082.4070.0000.3582.200-0.497-2.060-0.004
61A61ILE0-0.044-0.0074.2110.6870.732-0.0010.000-0.0440.000
62A62LEU0-0.0030.0076.1540.0620.0620.0000.0000.0000.000
63A63VAL0-0.009-0.0259.1600.0640.0640.0000.0000.0000.000
64A64LYS10.7710.87812.9500.1190.1190.0000.0000.0000.000
65A65LYS10.9200.94215.9380.1530.1530.0000.0000.0000.000
66A66LEU00.0980.04617.574-0.011-0.0110.0000.0000.0000.000
67A67ASP-1-0.803-0.88018.761-0.174-0.1740.0000.0000.0000.000
68A68ARG10.8020.89817.7440.1610.1610.0000.0000.0000.000
69A69LEU00.0170.00214.466-0.005-0.0050.0000.0000.0000.000
70A70GLY00.0100.00317.577-0.013-0.0130.0000.0000.0000.000
71A71ARG10.7650.86820.9160.2030.2030.0000.0000.0000.000
72A72ASP-1-0.799-0.89824.696-0.148-0.1480.0000.0000.0000.000
73A73THR00.0200.00223.998-0.015-0.0150.0000.0000.0000.000
74A74ALA00.017-0.00223.366-0.021-0.0210.0000.0000.0000.000
75A75ASP-1-0.836-0.90222.736-0.240-0.2400.0000.0000.0000.000
76A76MET0-0.0080.00419.350-0.027-0.0270.0000.0000.0000.000
77A77ILE0-0.0010.00918.979-0.033-0.0330.0000.0000.0000.000
78A78GLN00.027-0.00519.555-0.024-0.0240.0000.0000.0000.000
79A79LEU00.0160.02616.191-0.022-0.0220.0000.0000.0000.000
80A80ILE0-0.005-0.00914.523-0.052-0.0520.0000.0000.0000.000
81A81LYS10.9200.95914.9400.2250.2250.0000.0000.0000.000
82A82GLU-1-0.849-0.86515.378-0.410-0.4100.0000.0000.0000.000
83A83PHE0-0.012-0.03010.897-0.006-0.0060.0000.0000.0000.000
84A84ASP-1-0.797-0.90711.173-0.740-0.7400.0000.0000.0000.000
85A85ALA0-0.055-0.01212.443-0.019-0.0190.0000.0000.0000.000
86A86GLN0-0.058-0.0229.8370.1050.1050.0000.0000.0000.000
87A87GLY00.0570.0179.207-0.054-0.0540.0000.0000.0000.000
88A88VAL0-0.100-0.0366.716-0.342-0.3420.0000.0000.0000.000
89A89SER00.0240.0225.9940.3490.3490.0000.0000.0000.000
90A90ILE0-0.005-0.0237.428-0.170-0.1700.0000.0000.0000.000
91A91ARG10.8890.9298.6900.4650.4650.0000.0000.0000.000
92A92PHE0-0.010-0.01410.3020.0390.0390.0000.0000.0000.000
93A93ILE00.027-0.01110.3770.0380.0380.0000.0000.0000.000
94A94ASP-1-0.850-0.90613.791-0.090-0.0900.0000.0000.0000.000
95A95ASP-1-0.824-0.92716.325-0.195-0.1950.0000.0000.0000.000
96A96GLY0-0.072-0.00615.0750.0060.0060.0000.0000.0000.000
97A97ILE00.009-0.01114.488-0.040-0.0400.0000.0000.0000.000
98A98SER00.0430.0149.6500.0060.0060.0000.0000.0000.000
99A99THR0-0.061-0.01811.4310.0240.0240.0000.0000.0000.000
100A100ASP-1-0.887-0.9688.889-0.905-0.9050.0000.0000.0000.000
101A101GLY00.0930.05010.2760.1450.1450.0000.0000.0000.000
102A102GLU-1-0.844-0.91512.017-0.292-0.2920.0000.0000.0000.000
103A103MET0-0.0350.00112.7740.0410.0410.0000.0000.0000.000
104A104GLY00.0500.03914.1290.0390.0390.0000.0000.0000.000
105A105LYS10.8710.91715.1990.4070.4070.0000.0000.0000.000
106A106MET00.0070.01718.3660.0400.0400.0000.0000.0000.000
107A107VAL0-0.012-0.01016.1100.0310.0310.0000.0000.0000.000
108A108VAL00.016-0.00218.2090.0340.0340.0000.0000.0000.000
109A109THR0-0.028-0.01820.7970.0310.0310.0000.0000.0000.000
110A110ILE00.0140.00922.8420.0220.0220.0000.0000.0000.000
111A111LEU0-0.0170.01020.0420.0190.0190.0000.0000.0000.000
112A112SER0-0.014-0.02424.2940.0140.0140.0000.0000.0000.000
113A113ALA0-0.0260.00426.7670.0140.0140.0000.0000.0000.000
114A114VAL00.009-0.02527.4630.0130.0130.0000.0000.0000.000
115A115ALA00.0120.02428.1650.0100.0100.0000.0000.0000.000
116A116GLN00.0450.02030.0590.0110.0110.0000.0000.0000.000
117A117ALA0-0.0080.01032.1420.0090.0090.0000.0000.0000.000
118A118GLU-1-0.855-0.93832.825-0.085-0.0850.0000.0000.0000.000
119A119ARG10.8920.93533.7820.1100.1100.0000.0000.0000.000
120A120GLN0-0.025-0.01536.1390.0020.0020.0000.0000.0000.000
121A121ARG10.9000.95233.3740.0980.0980.0000.0000.0000.000
122A122ILE0-0.036-0.01437.3350.0050.0050.0000.0000.0000.000
123A123LEU0-0.018-0.01140.5530.0040.0040.0000.0000.0000.000
124A124GLU-1-0.871-0.93242.076-0.062-0.0620.0000.0000.0000.000
125A125ARG10.9300.96040.4160.0690.0690.0000.0000.0000.000
126A126THR0-0.062-0.03744.5070.0030.0030.0000.0000.0000.000
127A127ASN0-0.0060.00046.5370.0020.0020.0000.0000.0000.000
128A128GLU-1-0.864-0.91448.190-0.042-0.0420.0000.0000.0000.000
129A129GLY00.0180.00651.0740.0020.0020.0000.0000.0000.000
130A130ARG10.8700.92847.0610.0570.0570.0000.0000.0000.000
131A131GLN00.0310.00851.0490.0000.0000.0000.0000.0000.000
132A132GLU-1-0.816-0.87753.594-0.036-0.0360.0000.0000.0000.000
133A133ALA00.0450.00955.0990.0010.0010.0000.0000.0000.000
134A134MET0-0.072-0.03854.1280.0010.0010.0000.0000.0000.000
135A135ALA0-0.032-0.01256.3900.0010.0010.0000.0000.0000.000
136A136LYS10.8060.88259.1820.0360.0360.0000.0000.0000.000
137A137GLY00.0440.03460.0070.0010.0010.0000.0000.0000.000
138A138VAL0-0.086-0.02956.8960.0000.0000.0000.0000.0000.000
139A139VAL00.0020.00757.988-0.001-0.0010.0000.0000.0000.000
140A140PHE00.0140.00751.672-0.002-0.0020.0000.0000.0000.000
141A141GLY0-0.006-0.00351.9880.0000.0000.0000.0000.0000.000
142A142ARG10.9150.95451.4610.0490.0490.0000.0000.0000.000
143A143LYS11.0341.01753.5150.0400.0400.0000.0000.0000.000
144A144ARG10.8720.92156.7520.0360.0360.0000.0000.0000.000
145A145LYS10.9750.97155.8470.0390.0390.0000.0000.0000.000
146A146ILE0-0.041-0.01358.9330.0010.0010.0000.0000.0000.000
147A147ASP-1-0.816-0.89861.671-0.029-0.0290.0000.0000.0000.000
148A148ARG10.8370.86660.3850.0360.0360.0000.0000.0000.000
149A149ASP-1-0.835-0.89466.386-0.027-0.0270.0000.0000.0000.000
150A150ALA00.0240.01468.6040.0010.0010.0000.0000.0000.000
151A151VAL0-0.063-0.05064.7970.0000.0000.0000.0000.0000.000
152A152LEU00.005-0.00168.2510.0000.0000.0000.0000.0000.000
153A153ASN00.0570.03870.5790.0010.0010.0000.0000.0000.000
154A154MET0-0.005-0.00769.2030.0000.0000.0000.0000.0000.000
155A155TRP0-0.009-0.01069.4600.0000.0000.0000.0000.0000.000
156A156GLN0-0.016-0.00272.1390.0010.0010.0000.0000.0000.000
157A157GLN0-0.085-0.03175.1560.0010.0010.0000.0000.0000.000
158A158GLY00.0250.01875.4340.0010.0010.0000.0000.0000.000
159A159LEU0-0.067-0.02272.0360.0000.0000.0000.0000.0000.000
160A160GLY00.0780.03070.261-0.001-0.0010.0000.0000.0000.000
161A161ALA00.0610.00864.9230.0000.0000.0000.0000.0000.000
162A162SER0-0.005-0.02564.506-0.001-0.0010.0000.0000.0000.000
163A163HIS00.0600.05665.478-0.001-0.0010.0000.0000.0000.000
164A164ILE00.0590.03465.8160.0000.0000.0000.0000.0000.000
165A165SER0-0.047-0.03661.6630.0000.0000.0000.0000.0000.000
166A166LYS10.8860.95162.9980.0270.0270.0000.0000.0000.000
167A167THR0-0.024-0.02864.2900.0000.0000.0000.0000.0000.000
168A168MET0-0.0130.00364.8770.0000.0000.0000.0000.0000.000
169A169ASN0-0.044-0.00859.927-0.001-0.0010.0000.0000.0000.000
170A170ILE0-0.0250.01259.333-0.002-0.0020.0000.0000.0000.000
171A171ALA00.0170.00256.1830.0000.0000.0000.0000.0000.000
172A172ARG11.0290.99158.1970.0350.0350.0000.0000.0000.000
173A173SER00.0270.01755.8210.0010.0010.0000.0000.0000.000
174A174THR0-0.022-0.01657.2760.0000.0000.0000.0000.0000.000
175A175VAL00.0430.03859.7030.0000.0000.0000.0000.0000.000
176A176TYR00.0560.01561.6830.0010.0010.0000.0000.0000.000
177A177LYS10.8830.96656.6780.0410.0410.0000.0000.0000.000
178A178VAL0-0.034-0.04061.4030.0000.0000.0000.0000.0000.000
179A179ILE00.0050.02063.8160.0010.0010.0000.0000.0000.000
180A180ASN0-0.025-0.03463.6720.0010.0010.0000.0000.0000.000
181A181GLU-1-0.800-0.87960.968-0.037-0.0370.0000.0000.0000.000
182A182SER0-0.015-0.00364.9100.0010.0010.0000.0000.0000.000
183A183ASN0-0.0150.02568.1660.0020.0020.0000.0000.0000.000