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: YY2Y2

Calculation Name: 1G62-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1G62

Chain ID: A

ChEMBL ID:

UniProt ID: Q12522

Base Structure: X-ray

Registration Date: 2023-06-21

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 224
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2669081.373093
FMO2-HF: Nuclear repulsion 2583955.511066
FMO2-HF: Total energy -85125.862027
FMO2-MP2: Total energy -85373.728372


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.
-26.536-12.367.1-8.583-12.695-0.082
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 : -0.004 / q_NPA : 0.022
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].
3A3THR00.0250.0102.677-4.640-0.8210.659-2.041-2.437-0.004
4A4ARG10.7960.9255.3171.7841.842-0.001-0.002-0.0540.000
5A5THR0-0.045-0.0218.555-0.042-0.0420.0000.0000.0000.000
6A6GLN0-0.018-0.03511.9950.0760.0760.0000.0000.0000.000
7A7PHE00.0100.03115.625-0.002-0.0020.0000.0000.0000.000
8A8GLU-1-0.967-0.99118.432-0.332-0.3320.0000.0000.0000.000
9A9ASN0-0.018-0.01319.462-0.032-0.0320.0000.0000.0000.000
10A10SER00.0020.00919.6140.0060.0060.0000.0000.0000.000
11A11ASN00.0210.00115.328-0.139-0.1390.0000.0000.0000.000
12A12GLU-1-0.931-0.95915.266-0.476-0.4760.0000.0000.0000.000
13A13ILE00.0240.01312.3960.0680.0680.0000.0000.0000.000
14A14GLY00.0400.03315.4900.0070.0070.0000.0000.0000.000
15A15VAL0-0.029-0.02316.3940.0720.0720.0000.0000.0000.000
16A16PHE0-0.050-0.03418.4010.0590.0590.0000.0000.0000.000
17A17SER0-0.014-0.02014.427-0.056-0.0560.0000.0000.0000.000
18A18LYS10.9020.96315.5510.4450.4450.0000.0000.0000.000
19A19LEU00.0220.0257.8460.0390.0390.0000.0000.0000.000
20A20THR00.0360.03412.6010.0730.0730.0000.0000.0000.000
21A21ASN00.0230.00910.270-0.241-0.2410.0000.0000.0000.000
22A22THR0-0.071-0.03612.0250.0210.0210.0000.0000.0000.000
23A23TYR00.0080.00014.0550.0110.0110.0000.0000.0000.000
24A24CYS00.0090.02912.218-0.052-0.0520.0000.0000.0000.000
25A25LEU0-0.0270.00414.2690.0640.0640.0000.0000.0000.000
26A26VAL00.0630.01814.938-0.057-0.0570.0000.0000.0000.000
27A27ALA00.0390.01917.7410.0740.0740.0000.0000.0000.000
28A28VAL0-0.0130.00620.618-0.028-0.0280.0000.0000.0000.000
29A29GLY0-0.034-0.01823.2230.0070.0070.0000.0000.0000.000
30A30GLY00.0030.00719.8360.0080.0080.0000.0000.0000.000
31A31SER0-0.011-0.00918.8250.0130.0130.0000.0000.0000.000
32A32GLU-1-0.821-0.92216.969-0.686-0.6860.0000.0000.0000.000
33A33ASN0-0.039-0.02013.750-0.094-0.0940.0000.0000.0000.000
34A34PHE00.013-0.00213.391-0.132-0.1320.0000.0000.0000.000
35A35TYR00.006-0.03813.365-0.100-0.1000.0000.0000.0000.000
36A36SER00.0380.01512.511-0.089-0.0890.0000.0000.0000.000
37A37ALA0-0.0360.0089.204-0.160-0.1600.0000.0000.0000.000
38A38PHE0-0.031-0.0128.032-0.510-0.5100.0000.0000.0000.000
39A39GLU-1-0.877-0.9708.873-0.875-0.8750.0000.0000.0000.000
40A40ALA0-0.074-0.0418.7000.1300.1300.0000.0000.0000.000
41A41GLU-1-0.909-0.9672.586-13.505-10.3920.927-1.987-2.054-0.024
42A42LEU0-0.061-0.0196.0740.1650.1650.0000.0000.0000.000
43A43GLY00.0260.0178.5410.3130.3130.0000.0000.0000.000
44A44ASP-1-0.986-0.99711.281-0.362-0.3620.0000.0000.0000.000
45A45ALA0-0.074-0.02310.5600.1010.1010.0000.0000.0000.000
46A46ILE0-0.053-0.02310.7470.0930.0930.0000.0000.0000.000
47A47PRO00.002-0.00213.743-0.071-0.0710.0000.0000.0000.000
48A48ILE00.0550.03612.106-0.037-0.0370.0000.0000.0000.000
49A49VAL0-0.013-0.00715.8310.0480.0480.0000.0000.0000.000
50A50HIS10.8750.94617.8580.5140.5140.0000.0000.0000.000
51A51THR00.028-0.01020.8850.0530.0530.0000.0000.0000.000
52A52THR0-0.044-0.03023.500-0.028-0.0280.0000.0000.0000.000
53A53ILE00.0200.01724.1660.0070.0070.0000.0000.0000.000
54A54ALA0-0.006-0.00127.0950.0000.0000.0000.0000.0000.000
55A55GLY0-0.040-0.01530.0310.0090.0090.0000.0000.0000.000
56A56THR0-0.084-0.03627.516-0.015-0.0150.0000.0000.0000.000
57A57ARG10.9880.97624.0670.3570.3570.0000.0000.0000.000
58A58ILE0-0.0040.02322.877-0.039-0.0390.0000.0000.0000.000
59A59ILE00.006-0.01718.5240.0190.0190.0000.0000.0000.000
60A60GLY00.0000.03018.9960.0100.0100.0000.0000.0000.000
61A61ARG10.8440.91618.7320.4010.4010.0000.0000.0000.000
62A62MET0-0.032-0.01122.5850.0360.0360.0000.0000.0000.000
63A63THR00.0030.00821.0660.0170.0170.0000.0000.0000.000
64A64ALA00.0150.00120.535-0.025-0.0250.0000.0000.0000.000
65A65GLY00.0150.01519.6300.0170.0170.0000.0000.0000.000
66A66ASN00.0140.01716.849-0.038-0.0380.0000.0000.0000.000
67A67ARG10.9300.95915.2680.0330.0330.0000.0000.0000.000
68A68ARG10.8250.89317.4660.0430.0430.0000.0000.0000.000
69A69GLY00.0420.02421.0090.0110.0110.0000.0000.0000.000
70A70LEU0-0.045-0.02020.129-0.023-0.0230.0000.0000.0000.000
71A71LEU00.0070.00222.7020.0210.0210.0000.0000.0000.000
72A72VAL0-0.006-0.01524.667-0.025-0.0250.0000.0000.0000.000
73A73PRO00.0650.04027.0050.0200.0200.0000.0000.0000.000
74A74THR00.0360.00829.987-0.001-0.0010.0000.0000.0000.000
75A75GLN0-0.031-0.02332.758-0.003-0.0030.0000.0000.0000.000
76A76THR0-0.025-0.00828.532-0.013-0.0130.0000.0000.0000.000
77A77THR00.010-0.01131.0730.0140.0140.0000.0000.0000.000
78A78ASP-1-0.826-0.93031.789-0.138-0.1380.0000.0000.0000.000
79A79GLN00.003-0.00432.6610.0010.0010.0000.0000.0000.000
80A80GLU-1-0.726-0.84327.878-0.234-0.2340.0000.0000.0000.000
81A81LEU00.0220.01427.649-0.013-0.0130.0000.0000.0000.000
82A82GLN0-0.057-0.02128.5350.0030.0030.0000.0000.0000.000
83A83HIS0-0.007-0.00624.0820.0180.0180.0000.0000.0000.000
84A84LEU00.0050.00922.610-0.015-0.0150.0000.0000.0000.000
85A85ARG10.8510.91624.4270.1520.1520.0000.0000.0000.000
86A86ASN0-0.061-0.03026.1930.0060.0060.0000.0000.0000.000
87A87SER00.0050.00821.8960.0000.0000.0000.0000.0000.000
88A88LEU0-0.042-0.01619.735-0.019-0.0190.0000.0000.0000.000
89A89PRO00.0400.01718.8590.0260.0260.0000.0000.0000.000
90A90ASP-1-0.874-0.95322.018-0.120-0.1200.0000.0000.0000.000
91A91SER0-0.106-0.05221.289-0.001-0.0010.0000.0000.0000.000
92A92VAL0-0.0130.03320.8870.0090.0090.0000.0000.0000.000
93A93LYS10.8760.94723.0190.0760.0760.0000.0000.0000.000
94A94ILE00.0160.00924.498-0.014-0.0140.0000.0000.0000.000
95A95GLN0-0.021-0.00426.5690.0160.0160.0000.0000.0000.000
96A96ARG10.8230.91028.3610.1300.1300.0000.0000.0000.000
97A97VAL00.021-0.00228.6130.0120.0120.0000.0000.0000.000
98A98GLU-1-0.859-0.90831.378-0.127-0.1270.0000.0000.0000.000
99A99GLU-1-0.790-0.91030.194-0.142-0.1420.0000.0000.0000.000
100A100ARG10.7870.86332.8820.1100.1100.0000.0000.0000.000
101A101LEU0-0.0080.02531.7910.0000.0000.0000.0000.0000.000
102A102SER0-0.041-0.03529.182-0.010-0.0100.0000.0000.0000.000
103A103ALA00.0130.02626.2400.0020.0020.0000.0000.0000.000
104A104LEU00.0890.03525.221-0.005-0.0050.0000.0000.0000.000
105A105GLY0-0.027-0.00322.1690.0050.0050.0000.0000.0000.000
106A106ASN0-0.030-0.03522.013-0.039-0.0390.0000.0000.0000.000
107A107VAL0-0.046-0.00524.5470.0140.0140.0000.0000.0000.000
108A108ILE00.0310.00922.3600.0180.0180.0000.0000.0000.000
109A109CYS0-0.0320.00919.010-0.026-0.0260.0000.0000.0000.000
110A110CYS0-0.038-0.00518.4060.0280.0280.0000.0000.0000.000
111A111ASN00.1300.09115.592-0.063-0.0630.0000.0000.0000.000
112A112ASP-1-0.829-0.93915.322-0.129-0.1290.0000.0000.0000.000
113A113TYR0-0.032-0.01416.8040.0270.0270.0000.0000.0000.000
114A114VAL00.0150.00820.2890.0010.0010.0000.0000.0000.000
115A115ALA00.011-0.00920.820-0.024-0.0240.0000.0000.0000.000
116A116LEU0-0.0030.00322.7530.0150.0150.0000.0000.0000.000
117A117VAL0-0.016-0.01724.644-0.024-0.0240.0000.0000.0000.000
118A118HIS00.0450.00927.3590.0140.0140.0000.0000.0000.000
119A119PRO0-0.010-0.02429.6440.0050.0050.0000.0000.0000.000
120A120ASP-1-0.921-0.96032.466-0.066-0.0660.0000.0000.0000.000
121A121ILE0-0.090-0.02830.247-0.001-0.0010.0000.0000.0000.000
122A122ASP-1-0.833-0.87433.907-0.069-0.0690.0000.0000.0000.000
123A123ARG10.9420.95234.9950.0330.0330.0000.0000.0000.000
124A124GLU-1-0.863-0.92935.457-0.046-0.0460.0000.0000.0000.000
125A125THR0-0.036-0.07431.417-0.004-0.0040.0000.0000.0000.000
126A126GLU-1-0.921-0.97030.687-0.054-0.0540.0000.0000.0000.000
127A127GLU-1-0.929-0.97230.789-0.036-0.0360.0000.0000.0000.000
128A128LEU0-0.0200.00130.9380.0000.0000.0000.0000.0000.000
129A129ILE0-0.022-0.01225.939-0.007-0.0070.0000.0000.0000.000
130A130SER0-0.028-0.00926.824-0.003-0.0030.0000.0000.0000.000
131A131ASP-1-0.870-0.93427.597-0.052-0.0520.0000.0000.0000.000
132A132VAL0-0.092-0.06525.5160.0010.0010.0000.0000.0000.000
133A133LEU0-0.029-0.00921.872-0.010-0.0100.0000.0000.0000.000
134A134GLY00.0080.01123.2070.0060.0060.0000.0000.0000.000
135A135VAL0-0.080-0.02721.6700.0110.0110.0000.0000.0000.000
136A136GLU-1-0.934-0.95024.7350.0350.0350.0000.0000.0000.000
137A137VAL0-0.016-0.01725.423-0.008-0.0080.0000.0000.0000.000
138A138PHE00.0260.01226.2580.0090.0090.0000.0000.0000.000
139A139ARG10.9070.98027.8020.0300.0300.0000.0000.0000.000
140A140GLN00.0380.00527.1100.0050.0050.0000.0000.0000.000
141A141THR0-0.026-0.00628.379-0.012-0.0120.0000.0000.0000.000
142A142ILE00.0250.03022.8620.0110.0110.0000.0000.0000.000
143A143SER0-0.003-0.02025.907-0.010-0.0100.0000.0000.0000.000
144A144GLY0-0.0140.00227.816-0.007-0.0070.0000.0000.0000.000
145A145ASN0-0.065-0.02026.937-0.011-0.0110.0000.0000.0000.000
146A146ILE00.0950.02928.5060.0030.0030.0000.0000.0000.000
147A147LEU0-0.051-0.01426.190-0.003-0.0030.0000.0000.0000.000
148A148VAL00.0910.02123.762-0.019-0.0190.0000.0000.0000.000
149A149GLY0-0.0080.01721.036-0.007-0.0070.0000.0000.0000.000
150A150SER0-0.049-0.04220.268-0.048-0.0480.0000.0000.0000.000
151A151TYR0-0.099-0.05021.298-0.026-0.0260.0000.0000.0000.000
152A152CYS00.002-0.02118.8380.0370.0370.0000.0000.0000.000
153A153SER0-0.0060.02012.972-0.030-0.0300.0000.0000.0000.000
154A154LEU00.007-0.01514.4770.0670.0670.0000.0000.0000.000
155A155SER00.0760.05210.018-0.046-0.0460.0000.0000.0000.000
156A156ASN0-0.058-0.05912.1080.0100.0100.0000.0000.0000.000
157A157GLN0-0.053-0.0229.3490.2080.2080.0000.0000.0000.000
158A158GLY00.0760.03112.2040.0910.0910.0000.0000.0000.000
159A159GLY00.005-0.01313.704-0.099-0.0990.0000.0000.0000.000
160A160LEU0-0.042-0.00312.6110.0440.0440.0000.0000.0000.000
161A161VAL00.0280.00915.924-0.051-0.0510.0000.0000.0000.000
162A162HIS00.0730.03619.2810.0070.0070.0000.0000.0000.000
163A163PRO00.0040.00319.7530.0270.0270.0000.0000.0000.000
164A164GLN0-0.052-0.04121.1790.0040.0040.0000.0000.0000.000
165A165THR0-0.0070.00123.1090.0050.0050.0000.0000.0000.000
166A166SER00.0160.02824.6920.0160.0160.0000.0000.0000.000
167A167VAL00.0620.00324.5960.0000.0000.0000.0000.0000.000
168A168GLN00.0340.02026.1850.0070.0070.0000.0000.0000.000
169A169ASP-1-0.821-0.91426.8680.0030.0030.0000.0000.0000.000
170A170GLN0-0.076-0.04621.3210.0190.0190.0000.0000.0000.000
171A171GLU-1-0.954-0.97223.2160.1270.1270.0000.0000.0000.000
172A172GLU-1-0.939-0.97625.3410.0480.0480.0000.0000.0000.000
173A173LEU0-0.022-0.02322.980-0.002-0.0020.0000.0000.0000.000
174A174SER0-0.0020.00321.0320.0110.0110.0000.0000.0000.000
175A175SER0-0.062-0.03422.0430.0160.0160.0000.0000.0000.000
176A176LEU0-0.061-0.01924.6600.0020.0020.0000.0000.0000.000
177A177LEU0-0.012-0.02319.663-0.011-0.0110.0000.0000.0000.000
178A178GLN0-0.053-0.01819.9270.0220.0220.0000.0000.0000.000
179A179VAL0-0.0300.00215.8040.0400.0400.0000.0000.0000.000
180A180PRO0-0.040-0.02115.520-0.034-0.0340.0000.0000.0000.000
181A181LEU0-0.0150.02116.171-0.015-0.0150.0000.0000.0000.000
182A182VAL00.0070.00415.3670.0220.0220.0000.0000.0000.000
183A183ALA0-0.0340.00117.448-0.043-0.0430.0000.0000.0000.000
184A184GLY0-0.006-0.01915.7870.0310.0310.0000.0000.0000.000
185A185THR0-0.092-0.08315.4670.0000.0000.0000.0000.0000.000
186A186VAL00.0300.01611.993-0.020-0.0200.0000.0000.0000.000
187A187ASN0-0.070-0.03613.102-0.024-0.0240.0000.0000.0000.000
188A188ARG10.8200.89114.3470.4840.4840.0000.0000.0000.000
189A189GLY00.0060.00316.1620.0310.0310.0000.0000.0000.000
190A190SER0-0.0240.00717.8230.0470.0470.0000.0000.0000.000
191A191SER00.0390.00118.175-0.010-0.0100.0000.0000.0000.000
192A192VAL00.0060.01520.2520.0240.0240.0000.0000.0000.000
193A193VAL00.029-0.00915.923-0.057-0.0570.0000.0000.0000.000
194A194GLY0-0.0220.01716.116-0.057-0.0570.0000.0000.0000.000
195A195ALA0-0.007-0.01217.190-0.047-0.0470.0000.0000.0000.000
196A196GLY0-0.035-0.02516.257-0.048-0.0480.0000.0000.0000.000
197A197MET0-0.046-0.01510.170-0.055-0.0550.0000.0000.0000.000
198A198VAL0-0.0040.01810.1200.1690.1690.0000.0000.0000.000
199A199VAL0-0.034-0.0337.235-0.287-0.2870.0000.0000.0000.000
200A200ASN0-0.005-0.0066.811-0.015-0.0150.0000.0000.0000.000
201A201ASP-1-0.845-0.9607.2640.0160.0160.0000.0000.0000.000
202A202TYR0-0.064-0.0274.5890.4150.595-0.001-0.029-0.1500.000
203A203LEU00.0340.0322.455-4.868-2.5981.087-1.453-1.905-0.015
204A204ALA0-0.0010.0053.7041.9682.3010.001-0.087-0.2470.000
205A205VAL00.0160.0275.976-0.693-0.6930.0000.0000.0000.000
206A206THR00.009-0.0197.9330.5580.5580.0000.0000.0000.000
207A207GLY00.0940.02910.432-0.113-0.1130.0000.0000.0000.000
208A208LEU0-0.033-0.03611.180-0.052-0.0520.0000.0000.0000.000
209A209ASP-1-0.812-0.90212.222-0.499-0.4990.0000.0000.0000.000
210A210THR0-0.0450.0089.5010.1010.1010.0000.0000.0000.000
211A211THR0-0.016-0.01610.513-0.061-0.0610.0000.0000.0000.000
212A212ALA00.0360.0078.709-0.098-0.0980.0000.0000.0000.000
213A213PRO00.019-0.0078.728-0.004-0.0040.0000.0000.0000.000
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