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: 9GLZ2

Calculation Name: 1D02-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1D02

Chain ID: A

ChEMBL ID:

UniProt ID: P43642

Base Structure: X-ray

Registration Date: 2023-03-13

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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2225698.440351
FMO2-HF: Nuclear repulsion 2147234.008886
FMO2-HF: Total energy -78464.431465
FMO2-MP2: Total energy -78699.124092


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:6:LEU)


Summations of interaction energy for fragment #1(A:6:LEU)
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.
-15.68-7.9484.021-4.691-7.063-0.027
Interaction energy analysis for fragmet #1(A:6:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : 0.007
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].
3A8GLY00.0970.0403.780-2.288-0.448-0.012-0.944-0.8850.006
4A9ARG10.8860.9436.072-0.610-0.6100.0000.0000.0000.000
5A10LEU00.0320.0218.062-0.035-0.0350.0000.0000.0000.000
6A11ASN0-0.0010.00310.6770.1170.1170.0000.0000.0000.000
7A12TRP00.0570.00012.789-0.045-0.0450.0000.0000.0000.000
8A13GLN0-0.022-0.00715.736-0.017-0.0170.0000.0000.0000.000
9A14ALA00.0660.04415.631-0.016-0.0160.0000.0000.0000.000
10A15LEU0-0.019-0.00517.101-0.021-0.0210.0000.0000.0000.000
11A16ALA0-0.015-0.01518.883-0.012-0.0120.0000.0000.0000.000
12A17GLY00.0330.02020.749-0.005-0.0050.0000.0000.0000.000
13A18LEU0-0.0090.01021.093-0.008-0.0080.0000.0000.0000.000
14A19LYS10.9350.97323.025-0.026-0.0260.0000.0000.0000.000
15A20ALA0-0.025-0.01725.015-0.003-0.0030.0000.0000.0000.000
16A21SER0-0.084-0.04225.864-0.003-0.0030.0000.0000.0000.000
17A22GLY0-0.028-0.01827.675-0.005-0.0050.0000.0000.0000.000
18A23ALA0-0.0080.00526.452-0.005-0.0050.0000.0000.0000.000
19A24GLU-1-0.931-0.95627.862-0.031-0.0310.0000.0000.0000.000
20A25GLN00.0160.00422.969-0.007-0.0070.0000.0000.0000.000
21A26ASN00.0120.00024.388-0.013-0.0130.0000.0000.0000.000
22A27LEU00.0450.00820.2100.0020.0020.0000.0000.0000.000
23A28TYR00.011-0.01620.176-0.007-0.0070.0000.0000.0000.000
24A29ASN00.0180.00119.453-0.010-0.0100.0000.0000.0000.000
25A30VAL00.0190.02219.1340.0110.0110.0000.0000.0000.000
26A31PHE00.016-0.01414.9590.0060.0060.0000.0000.0000.000
27A32ASN0-0.016-0.01214.870-0.034-0.0340.0000.0000.0000.000
28A33ALA00.0370.03415.1330.0060.0060.0000.0000.0000.000
29A34VAL0-0.033-0.01213.4430.0280.0280.0000.0000.0000.000
30A35PHE0-0.008-0.01510.802-0.011-0.0110.0000.0000.0000.000
31A36GLU-1-0.893-0.92610.1960.0220.0220.0000.0000.0000.000
32A37GLY0-0.003-0.0038.3060.0640.0640.0000.0000.0000.000
33A38THR0-0.081-0.0316.2060.1220.1220.0000.0000.0000.000
34A39LYS10.8210.9192.4993.0994.4111.369-0.678-2.003-0.002
35A40TYR0-0.002-0.0064.599-0.438-0.309-0.001-0.013-0.1140.000
36A41VAL00.0340.0298.1420.1300.1300.0000.0000.0000.000
37A42LEU0-0.015-0.00210.860-0.034-0.0340.0000.0000.0000.000
38A43TYR0-0.076-0.06112.5970.0490.0490.0000.0000.0000.000
39A44GLU-1-0.901-0.95717.118-0.128-0.1280.0000.0000.0000.000
40A45LYS10.9000.95120.8250.1360.1360.0000.0000.0000.000
41A46PRO0-0.0110.00718.5790.0000.0000.0000.0000.0000.000
42A47LYS10.9680.95520.3490.2040.2040.0000.0000.0000.000
43A48HIS00.0480.02415.3570.0550.0550.0000.0000.0000.000
44A49LEU00.0380.03520.8400.0050.0050.0000.0000.0000.000
45A50LYS10.8730.93324.0270.1810.1810.0000.0000.0000.000
46A51ASN0-0.001-0.00226.2990.0240.0240.0000.0000.0000.000
47A52LEU0-0.053-0.03025.768-0.008-0.0080.0000.0000.0000.000
48A53TYR00.032-0.01429.5950.0020.0020.0000.0000.0000.000
49A54ALA00.0230.04433.3540.0050.0050.0000.0000.0000.000
50A55GLN00.0310.00729.4680.0120.0120.0000.0000.0000.000
51A56VAL0-0.061-0.02634.200-0.001-0.0010.0000.0000.0000.000
52A57VAL00.0180.01136.1660.0050.0050.0000.0000.0000.000
53A58LEU0-0.027-0.01239.1580.0000.0000.0000.0000.0000.000
54A59PRO00.0180.00542.3170.0020.0020.0000.0000.0000.000
55A60ASP-1-0.834-0.92945.467-0.077-0.0770.0000.0000.0000.000
56A61ASP-1-0.893-0.94648.211-0.061-0.0610.0000.0000.0000.000
57A62VAL0-0.025-0.00844.8740.0020.0020.0000.0000.0000.000
58A63ILE0-0.016-0.00843.6730.0010.0010.0000.0000.0000.000
59A64LYS10.8540.91947.5000.0650.0650.0000.0000.0000.000
60A65GLU-1-0.923-0.95150.266-0.057-0.0570.0000.0000.0000.000
61A66ILE0-0.078-0.01444.4860.0000.0000.0000.0000.0000.000
62A67PHE0-0.025-0.02346.2500.0010.0010.0000.0000.0000.000
63A68ASN0-0.035-0.03045.922-0.007-0.0070.0000.0000.0000.000
64A69PRO0-0.029-0.00743.2930.0020.0020.0000.0000.0000.000
65A70LEU00.0260.01445.190-0.002-0.0020.0000.0000.0000.000
66A71ILE0-0.034-0.02938.770-0.001-0.0010.0000.0000.0000.000
67A72ASP-1-0.748-0.82338.172-0.108-0.1080.0000.0000.0000.000
68A73LEU0-0.005-0.00637.638-0.005-0.0050.0000.0000.0000.000
69A74SER0-0.075-0.04935.489-0.008-0.0080.0000.0000.0000.000
70A75THR0-0.045-0.04433.386-0.009-0.0090.0000.0000.0000.000
71A76THR0-0.063-0.02033.5670.0000.0000.0000.0000.0000.000
72A77GLN0-0.019-0.00827.121-0.010-0.0100.0000.0000.0000.000
73A78TRP00.0170.00031.4080.0030.0030.0000.0000.0000.000
74A79GLY00.0330.01928.825-0.006-0.0060.0000.0000.0000.000
75A80VAL0-0.054-0.02625.9900.0130.0130.0000.0000.0000.000
76A81SER0-0.050-0.04325.399-0.006-0.0060.0000.0000.0000.000
77A82PRO00.0100.03122.1380.0130.0130.0000.0000.0000.000
78A83ALA00.0250.02323.9050.0020.0020.0000.0000.0000.000
79A84PHE00.0250.00518.3400.0080.0080.0000.0000.0000.000
80A85ALA00.0000.00816.541-0.002-0.0020.0000.0000.0000.000
81A86ILE0-0.0030.01812.3410.0170.0170.0000.0000.0000.000
82A87GLU-1-0.791-0.8649.470-0.753-0.7530.0000.0000.0000.000
83A88ASN00.0170.0075.737-0.245-0.2450.0000.0000.0000.000
84A89THR0-0.043-0.0574.728-0.181-0.092-0.001-0.007-0.0810.000
85A90GLU-1-0.877-0.9212.317-15.206-10.9332.666-3.023-3.916-0.031
86A91THR0-0.050-0.0464.1540.2070.2960.000-0.026-0.0640.000
87A92HIS10.8200.9017.3991.4341.4340.0000.0000.0000.000
88A93LYS10.8800.9789.6140.9380.9380.0000.0000.0000.000
89A94ILE0-0.060-0.05211.455-0.029-0.0290.0000.0000.0000.000
90A95LEU00.0080.02014.1670.0390.0390.0000.0000.0000.000
91A96PHE0-0.004-0.01916.7470.0170.0170.0000.0000.0000.000
92A97GLY00.0500.01519.6940.0100.0100.0000.0000.0000.000
93A98GLU-1-0.894-0.95221.927-0.148-0.1480.0000.0000.0000.000
94A99ILE00.0350.01923.7970.0010.0010.0000.0000.0000.000
95A100LYS10.7590.86927.2020.1320.1320.0000.0000.0000.000
96A101ARG10.8650.91627.2940.0950.0950.0000.0000.0000.000
97A102GLN0-0.042-0.04032.932-0.003-0.0030.0000.0000.0000.000
98A103ASP-1-0.800-0.89436.442-0.040-0.0400.0000.0000.0000.000
99A104GLY0-0.013-0.02639.146-0.004-0.0040.0000.0000.0000.000
100A105TRP0-0.086-0.02740.7270.0020.0020.0000.0000.0000.000
101A106VAL00.015-0.00639.610-0.001-0.0010.0000.0000.0000.000
102A107GLU-1-0.773-0.86141.963-0.022-0.0220.0000.0000.0000.000
103A108GLY0-0.007-0.00445.3310.0000.0000.0000.0000.0000.000
104A109LYS10.7740.89041.7650.0350.0350.0000.0000.0000.000
105A110ASP-1-0.825-0.91047.836-0.025-0.0250.0000.0000.0000.000
106A111PRO0-0.006-0.02546.979-0.002-0.0020.0000.0000.0000.000
107A112SER0-0.0070.00346.616-0.003-0.0030.0000.0000.0000.000
108A113ALA00.0020.00744.879-0.002-0.0020.0000.0000.0000.000
109A114GLY00.0440.02942.508-0.002-0.0020.0000.0000.0000.000
110A115ARG10.8670.91743.0270.0390.0390.0000.0000.0000.000
111A116GLY0-0.035-0.00242.014-0.001-0.0010.0000.0000.0000.000
112A117ASN00.006-0.02640.3650.0020.0020.0000.0000.0000.000
113A118ALA00.0510.03438.008-0.004-0.0040.0000.0000.0000.000
114A119HIS0-0.005-0.00134.450-0.007-0.0070.0000.0000.0000.000
115A120GLU-1-0.805-0.89334.391-0.081-0.0810.0000.0000.0000.000
116A121ARG10.9320.96833.6850.0920.0920.0000.0000.0000.000
117A122SER0-0.083-0.05030.084-0.008-0.0080.0000.0000.0000.000
118A123CYS00.0270.01430.633-0.010-0.0100.0000.0000.0000.000
119A124LYS10.9480.98630.6040.1360.1360.0000.0000.0000.000
120A125LEU0-0.032-0.01825.675-0.004-0.0040.0000.0000.0000.000
121A126PHE00.0410.03028.358-0.013-0.0130.0000.0000.0000.000
122A127THR0-0.053-0.02130.8020.0030.0030.0000.0000.0000.000
123A128PRO00.0760.02430.478-0.011-0.0110.0000.0000.0000.000
124A129GLY0-0.020-0.00629.936-0.010-0.0100.0000.0000.0000.000
125A130LEU00.004-0.00827.735-0.011-0.0110.0000.0000.0000.000
126A131LEU00.0240.03326.071-0.020-0.0200.0000.0000.0000.000
127A132LYS10.9930.99424.8790.1550.1550.0000.0000.0000.000
128A133ALA00.0000.01124.563-0.019-0.0190.0000.0000.0000.000
129A134TYR00.033-0.00622.050-0.018-0.0180.0000.0000.0000.000
130A135ARG10.7630.87120.3470.2370.2370.0000.0000.0000.000
131A136THR0-0.071-0.04119.632-0.035-0.0350.0000.0000.0000.000
132A137ILE0-0.055-0.03319.007-0.028-0.0280.0000.0000.0000.000
133A138GLY0-0.0010.01716.464-0.033-0.0330.0000.0000.0000.000
134A139GLY00.0690.03515.061-0.084-0.0840.0000.0000.0000.000
135A140ILE0-0.034-0.01615.442-0.024-0.0240.0000.0000.0000.000
136A141ASN0-0.024-0.03617.4310.0800.0800.0000.0000.0000.000
137A142ASP-1-0.876-0.91818.214-0.277-0.2770.0000.0000.0000.000
138A143GLU-1-0.798-0.90820.210-0.217-0.2170.0000.0000.0000.000
139A144GLU-1-0.897-0.89220.783-0.186-0.1860.0000.0000.0000.000
140A145ILE0-0.073-0.01718.7200.0170.0170.0000.0000.0000.000
141A146LEU0-0.0030.00322.199-0.009-0.0090.0000.0000.0000.000
142A147PRO00.000-0.00920.170-0.015-0.0150.0000.0000.0000.000
143A148PHE0-0.014-0.01120.424-0.020-0.0200.0000.0000.0000.000
144A149TRP00.0190.00918.472-0.001-0.0010.0000.0000.0000.000
145A150VAL0-0.043-0.01622.5740.0010.0010.0000.0000.0000.000
146A151VAL00.0250.02122.7330.0080.0080.0000.0000.0000.000
147A152PHE00.005-0.00925.8850.0040.0040.0000.0000.0000.000
148A153GLU-1-0.746-0.86727.391-0.085-0.0850.0000.0000.0000.000
149A154GLY00.0540.02330.8830.0000.0000.0000.0000.0000.000
150A155ASP-1-0.765-0.87734.422-0.037-0.0370.0000.0000.0000.000
151A156ILE0-0.0320.00234.0130.0010.0010.0000.0000.0000.000
152A157THR0-0.037-0.04431.1580.0010.0010.0000.0000.0000.000
153A158ARG10.7910.85934.1010.0290.0290.0000.0000.0000.000
154A159ASP-1-0.739-0.83436.955-0.043-0.0430.0000.0000.0000.000
155A160PRO0-0.007-0.01038.769-0.003-0.0030.0000.0000.0000.000
156A161LYS10.9660.98540.7080.0420.0420.0000.0000.0000.000
157A162ARG10.8240.88937.4310.0560.0560.0000.0000.0000.000
158A163VAL00.0130.01334.257-0.005-0.0050.0000.0000.0000.000
159A164ARG10.9060.94935.6090.0370.0370.0000.0000.0000.000
160A165GLU-1-0.814-0.87737.674-0.069-0.0690.0000.0000.0000.000
161A166ILE00.0050.00031.866-0.004-0.0040.0000.0000.0000.000
162A167THR0-0.050-0.02232.974-0.004-0.0040.0000.0000.0000.000
163A168PHE0-0.017-0.02033.869-0.004-0.0040.0000.0000.0000.000
164A169TRP0-0.003-0.01633.815-0.005-0.0050.0000.0000.0000.000
165A170TYR0-0.008-0.00827.242-0.010-0.0100.0000.0000.0000.000
166A171ASP-1-0.810-0.85530.693-0.103-0.1030.0000.0000.0000.000
167A172HIS10.8360.89928.2780.1270.1270.0000.0000.0000.000
168A173TYR0-0.0080.00425.3330.0010.0010.0000.0000.0000.000
169A174GLN0-0.021-0.03527.069-0.002-0.0020.0000.0000.0000.000
170A175ASP-1-0.773-0.86622.083-0.127-0.1270.0000.0000.0000.000
171A176ASN0-0.034-0.02321.940-0.006-0.0060.0000.0000.0000.000
172A177TYR0-0.030-0.02524.170-0.001-0.0010.0000.0000.0000.000
173A178PHE00.0060.01323.7590.0020.0020.0000.0000.0000.000
174A179MET0-0.0330.00225.8470.0000.0000.0000.0000.0000.000
175A180TRP0-0.002-0.00125.0150.0000.0000.0000.0000.0000.000
176A181ARG10.8790.92527.8540.0520.0520.0000.0000.0000.000
177A182PRO00.030-0.00230.5970.0020.0020.0000.0000.0000.000
178A183ASN0-0.020-0.01332.0090.0020.0020.0000.0000.0000.000
179A184GLU-1-0.785-0.86027.677-0.011-0.0110.0000.0000.0000.000
180A185SER0-0.032-0.00824.927-0.006-0.0060.0000.0000.0000.000
181A186GLY00.0930.03422.432-0.009-0.0090.0000.0000.0000.000
182A187GLU-1-0.964-0.98920.2520.0260.0260.0000.0000.0000.000
183A188LYS10.8550.91420.5180.0010.0010.0000.0000.0000.000
184A189LEU0-0.0100.01020.497-0.013-0.0130.0000.0000.0000.000
185A190VAL00.001-0.01415.453-0.025-0.0250.0000.0000.0000.000
186A191GLN00.002-0.00317.015-0.037-0.0370.0000.0000.0000.000
187A192HIS00.0150.02118.6420.0040.0040.0000.0000.0000.000
188A193PHE00.0360.00711.790-0.017-0.0170.0000.0000.0000.000
189A194ASN0-0.027-0.02413.036-0.080-0.0800.0000.0000.0000.000
190A195GLU-1-0.961-0.98414.667-0.062-0.0620.0000.0000.0000.000
191A196LYS10.8250.92017.4370.1050.1050.0000.0000.0000.000
192A197LEU0-0.029-0.02116.505-0.017-0.0170.0000.0000.0000.000
193A198LYS10.8480.9309.5290.2900.2900.0000.0000.0000.000
194A199LYS10.9440.98311.3400.1200.1200.0000.0000.0000.000
195A200TYR0-0.046-0.05612.325-0.075-0.0750.0000.0000.0000.000
196A201LEU0-0.014-0.01610.342-0.004-0.0040.0000.0000.0000.000
197A202ASP-1-0.867-0.9136.867-1.820-1.8200.0000.0000.0000.000