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: 16N6Z

Calculation Name: 1XWM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1XWM

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-09-27

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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2333058.038642
FMO2-HF: Nuclear repulsion 2250901.145812
FMO2-HF: Total energy -82156.892831
FMO2-MP2: Total energy -82393.9269


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:4:THR)


Summations of interaction energy for fragment #1(A:4:THR)
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.
-14.097-6.881.412-3.834-4.795-0.029
Interaction energy analysis for fragmet #1(A:4:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.008 / q_NPA : -0.017
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].
3A6ALA0-0.030-0.0183.802-1.407-0.032-0.001-0.498-0.8760.001
4A7ASP-1-0.894-0.9532.530-8.224-4.4271.322-2.369-2.750-0.024
5A8ASP-1-0.853-0.8963.253-7.496-5.5970.092-0.941-1.051-0.006
6A9LEU00.006-0.0024.8191.2621.323-0.001-0.003-0.0570.000
7A10ALA00.0150.0177.1290.5770.5770.0000.0000.0000.000
8A11SER0-0.076-0.0556.7970.6050.6050.0000.0000.0000.000
9A12LEU00.0290.0098.7250.3110.3110.0000.0000.0000.000
10A13HIS10.8030.91610.7231.0201.0200.0000.0000.0000.000
11A14ASN00.026-0.01010.3210.2690.2690.0000.0000.0000.000
12A15LYS10.8710.96010.3800.9080.9080.0000.0000.0000.000
13A16LEU00.0390.04114.1720.0860.0860.0000.0000.0000.000
14A17ILE0-0.0120.00516.3900.0690.0690.0000.0000.0000.000
15A18GLU-1-0.835-0.91016.501-0.333-0.3330.0000.0000.0000.000
16A19MET0-0.0190.00118.3280.0390.0390.0000.0000.0000.000
17A20GLY00.0080.00620.5850.0420.0420.0000.0000.0000.000
18A21ARG10.8610.94520.9990.3350.3350.0000.0000.0000.000
19A22LEU0-0.047-0.03521.6720.0360.0360.0000.0000.0000.000
20A23THR00.0830.03324.4990.0280.0280.0000.0000.0000.000
21A24GLU-1-0.906-0.95225.929-0.232-0.2320.0000.0000.0000.000
22A25VAL0-0.051-0.01626.7290.0210.0210.0000.0000.0000.000
23A26ALA00.0370.02028.6940.0170.0170.0000.0000.0000.000
24A27LEU00.0480.00930.1120.0160.0160.0000.0000.0000.000
25A28GLN0-0.0030.01630.6090.0130.0130.0000.0000.0000.000
26A29GLN0-0.026-0.01531.7290.0060.0060.0000.0000.0000.000
27A30ALA00.0320.03134.5660.0100.0100.0000.0000.0000.000
28A31ILE0-0.028-0.00736.3880.0100.0100.0000.0000.0000.000
29A32GLU-1-0.925-0.96237.999-0.103-0.1030.0000.0000.0000.000
30A33ALA0-0.0100.01238.7970.0080.0080.0000.0000.0000.000
31A34PHE00.0450.00540.6130.0070.0070.0000.0000.0000.000
32A35GLN0-0.037-0.03142.2950.0030.0030.0000.0000.0000.000
33A36THR0-0.109-0.08242.8030.0050.0050.0000.0000.0000.000
34A37GLN0-0.0180.00044.8830.0060.0060.0000.0000.0000.000
35A38ASN00.0070.00741.9290.0040.0040.0000.0000.0000.000
36A39ALA00.0670.01041.984-0.004-0.0040.0000.0000.0000.000
37A40ASN00.004-0.01741.088-0.002-0.0020.0000.0000.0000.000
38A41LEU0-0.071-0.01336.266-0.003-0.0030.0000.0000.0000.000
39A42ALA00.020-0.00437.223-0.006-0.0060.0000.0000.0000.000
40A43MET0-0.053-0.02637.276-0.002-0.0020.0000.0000.0000.000
41A44ALA00.0010.01234.227-0.003-0.0030.0000.0000.0000.000
42A45VAL0-0.028-0.01932.870-0.007-0.0070.0000.0000.0000.000
43A46ILE0-0.051-0.02032.414-0.005-0.0050.0000.0000.0000.000
44A47ASP-1-0.908-0.97332.598-0.101-0.1010.0000.0000.0000.000
45A48GLY0-0.071-0.02329.544-0.001-0.0010.0000.0000.0000.000
46A49ASP-1-0.862-0.93128.325-0.187-0.1870.0000.0000.0000.000
47A50GLY00.0360.02727.033-0.013-0.0130.0000.0000.0000.000
48A51SER0-0.046-0.03823.965-0.012-0.0120.0000.0000.0000.000
49A52ILE0-0.006-0.03122.675-0.026-0.0260.0000.0000.0000.000
50A53ASP-1-0.849-0.91122.544-0.207-0.2070.0000.0000.0000.000
51A54ALA0-0.046-0.03021.439-0.009-0.0090.0000.0000.0000.000
52A55LEU0-0.021-0.00818.028-0.024-0.0240.0000.0000.0000.000
53A56GLU-1-0.866-0.94917.923-0.317-0.3170.0000.0000.0000.000
54A57GLU-1-0.957-0.95919.026-0.217-0.2170.0000.0000.0000.000
55A58GLU-1-0.926-0.96714.897-0.478-0.4780.0000.0000.0000.000
56A59VAL0-0.068-0.04514.471-0.100-0.1000.0000.0000.0000.000
57A60ASN00.0050.00115.243-0.066-0.0660.0000.0000.0000.000
58A61ASP-1-0.881-0.93615.515-0.289-0.2890.0000.0000.0000.000
59A62PHE0-0.069-0.0446.5760.0160.0160.0000.0000.0000.000
60A63ALA00.0380.00611.650-0.072-0.0720.0000.0000.0000.000
61A64LEU0-0.003-0.02013.3070.0230.0230.0000.0000.0000.000
62A65TRP0-0.0210.0075.9880.0610.0610.0000.0000.0000.000
63A66LEU0-0.0060.0037.0400.0910.0910.0000.0000.0000.000
64A67ILE0-0.088-0.05510.3790.1300.1300.0000.0000.0000.000
65A68ALA0-0.034-0.01113.2490.0760.0760.0000.0000.0000.000
66A69ALA0-0.066-0.0179.6880.0910.0910.0000.0000.0000.000
67A70GLN0-0.097-0.0883.7431.2141.2990.000-0.023-0.0610.000
68A71GLN0-0.0140.0098.7140.0530.0530.0000.0000.0000.000
69A72PRO00.0340.02710.7870.0370.0370.0000.0000.0000.000
70A73VAL00.0250.02012.2880.0890.0890.0000.0000.0000.000
71A74ALA0-0.008-0.02514.271-0.073-0.0730.0000.0000.0000.000
72A75THR0-0.031-0.03315.1030.0050.0050.0000.0000.0000.000
73A76ASP-1-0.794-0.89810.691-0.792-0.7920.0000.0000.0000.000
74A77LEU0-0.006-0.00813.605-0.057-0.0570.0000.0000.0000.000
75A78ARG10.9130.96315.8400.2970.2970.0000.0000.0000.000
76A79ARG10.8310.89715.0000.5460.5460.0000.0000.0000.000
77A80ILE00.0260.04611.248-0.043-0.0430.0000.0000.0000.000
78A81VAL0-0.014-0.01414.9380.0380.0380.0000.0000.0000.000
79A82ALA0-0.023-0.01618.5870.0210.0210.0000.0000.0000.000
80A83ALA00.002-0.00915.4460.0210.0210.0000.0000.0000.000
81A84ILE00.0210.00717.0470.0130.0130.0000.0000.0000.000
82A85LYS10.8850.94119.2950.2890.2890.0000.0000.0000.000
83A86ILE00.0390.01920.3140.0210.0210.0000.0000.0000.000
84A87ALA00.0320.01518.9930.0160.0160.0000.0000.0000.000
85A88SER00.0490.04421.0760.0250.0250.0000.0000.0000.000
86A89ASP-1-0.806-0.90324.388-0.226-0.2260.0000.0000.0000.000
87A90ILE0-0.038-0.03921.0510.0130.0130.0000.0000.0000.000
88A91GLU-1-0.758-0.85824.406-0.175-0.1750.0000.0000.0000.000
89A92ARG10.7690.87025.9410.1900.1900.0000.0000.0000.000
90A93ILE0-0.026-0.02027.5700.0160.0160.0000.0000.0000.000
91A94ALA0-0.004-0.00227.0630.0140.0140.0000.0000.0000.000
92A95ASP-1-0.832-0.90729.194-0.127-0.1270.0000.0000.0000.000
93A96PHE0-0.076-0.05831.5670.0180.0180.0000.0000.0000.000
94A97ALA00.0360.03131.9820.0120.0120.0000.0000.0000.000
95A98VAL00.0450.03531.9560.0150.0150.0000.0000.0000.000
96A99ASN0-0.055-0.04134.5910.0170.0170.0000.0000.0000.000
97A100ILE0-0.056-0.02137.1540.0100.0100.0000.0000.0000.000
98A101ALA00.0200.01636.8040.0070.0070.0000.0000.0000.000
99A102LYS10.9390.97337.2230.1110.1110.0000.0000.0000.000
100A103ALA0-0.087-0.04840.7920.0070.0070.0000.0000.0000.000
101A104CYS00.0070.02341.7740.0060.0060.0000.0000.0000.000
102A105ILE0-0.0010.01942.2140.0050.0050.0000.0000.0000.000
103A106ARG10.8740.94041.9120.0880.0880.0000.0000.0000.000
104A107ILE0-0.041-0.02246.9250.0040.0040.0000.0000.0000.000
105A108GLY0-0.0240.00048.1320.0030.0030.0000.0000.0000.000
106A109GLY00.0370.00648.699-0.003-0.0030.0000.0000.0000.000
107A110GLN0-0.104-0.04651.0520.0010.0010.0000.0000.0000.000
108A111PRO0-0.023-0.03052.4250.0000.0000.0000.0000.0000.000
109A112PHE00.0650.05647.0260.0020.0020.0000.0000.0000.000
110A113VAL0-0.061-0.02252.6020.0020.0020.0000.0000.0000.000
111A114MET0-0.056-0.03150.9300.0030.0030.0000.0000.0000.000
112A115ASP-1-0.859-0.93651.349-0.074-0.0740.0000.0000.0000.000
113A116ILE0-0.0210.00546.069-0.001-0.0010.0000.0000.0000.000
114A117GLY00.0330.02346.614-0.005-0.0050.0000.0000.0000.000
115A118PRO00.0390.00346.032-0.005-0.0050.0000.0000.0000.000
116A119LEU00.0760.03243.779-0.004-0.0040.0000.0000.0000.000
117A120VAL0-0.029-0.00941.701-0.006-0.0060.0000.0000.0000.000
118A121LEU0-0.049-0.03041.034-0.007-0.0070.0000.0000.0000.000
119A122MET00.0210.03340.875-0.004-0.0040.0000.0000.0000.000
120A123TYR0-0.042-0.05234.691-0.005-0.0050.0000.0000.0000.000
121A124ARG10.9110.95036.5750.1140.1140.0000.0000.0000.000
122A125LEU00.0090.03735.932-0.008-0.0080.0000.0000.0000.000
123A126ALA00.0860.03235.322-0.007-0.0070.0000.0000.0000.000
124A127THR0-0.049-0.04731.885-0.010-0.0100.0000.0000.0000.000
125A128ASP-1-0.880-0.93831.197-0.178-0.1780.0000.0000.0000.000
126A129MET0-0.0490.01831.100-0.013-0.0130.0000.0000.0000.000
127A130VAL00.0160.01827.223-0.016-0.0160.0000.0000.0000.000
128A131SER00.0430.03026.902-0.016-0.0160.0000.0000.0000.000
129A132THR0-0.095-0.06126.306-0.023-0.0230.0000.0000.0000.000
130A133ALA00.0460.01926.613-0.020-0.0200.0000.0000.0000.000
131A134ILE00.0140.00521.660-0.032-0.0320.0000.0000.0000.000
132A135ALA0-0.002-0.01021.960-0.042-0.0420.0000.0000.0000.000
133A136ALA0-0.077-0.05422.664-0.026-0.0260.0000.0000.0000.000
134A137TYR00.0350.01115.676-0.046-0.0460.0000.0000.0000.000
135A138ASP-1-0.902-0.94317.480-0.635-0.6350.0000.0000.0000.000
136A139ARG10.8530.91918.2160.2820.2820.0000.0000.0000.000
137A140GLU-1-0.823-0.88717.266-0.598-0.5980.0000.0000.0000.000
138A141ASP-1-0.865-0.88220.929-0.239-0.2390.0000.0000.0000.000
139A142ALA0-0.005-0.02624.4930.0100.0100.0000.0000.0000.000
140A143SER0-0.181-0.14726.6400.0250.0250.0000.0000.0000.000
141A144LEU00.0390.02226.5160.0110.0110.0000.0000.0000.000
142A145ALA00.0510.02529.5540.0110.0110.0000.0000.0000.000
143A146ALA00.010-0.00230.9470.0080.0080.0000.0000.0000.000
144A147GLN00.0220.02232.9770.0040.0040.0000.0000.0000.000
145A148ILE0-0.025-0.03329.2620.0050.0050.0000.0000.0000.000
146A149ALA00.0100.01533.8870.0050.0050.0000.0000.0000.000
147A150ASP-1-0.888-0.95936.594-0.122-0.1220.0000.0000.0000.000
148A151MET0-0.143-0.06334.7060.0030.0030.0000.0000.0000.000
149A152ASP-1-0.784-0.91237.283-0.135-0.1350.0000.0000.0000.000
150A153HIS00.0120.02738.8960.0080.0080.0000.0000.0000.000
151A154ARG10.8090.90140.9390.1090.1090.0000.0000.0000.000
152A155VAL00.0340.00538.3050.0040.0040.0000.0000.0000.000
153A156ASP-1-0.870-0.92841.646-0.102-0.1020.0000.0000.0000.000
154A157GLU-1-0.997-1.00344.281-0.088-0.0880.0000.0000.0000.000
155A158GLN0-0.0190.00343.5530.0030.0030.0000.0000.0000.000
156A159TYR00.0720.00543.5230.0050.0050.0000.0000.0000.000
157A160GLY00.0430.03846.3600.0040.0040.0000.0000.0000.000
158A161GLU-1-1.032-1.01049.247-0.076-0.0760.0000.0000.0000.000
159A162MET0-0.098-0.04947.2160.0000.0000.0000.0000.0000.000
160A163MET0-0.024-0.02348.5580.0040.0040.0000.0000.0000.000
161A164ALA00.0190.01852.0300.0040.0040.0000.0000.0000.000
162A165SER0-0.046-0.02752.3960.0020.0020.0000.0000.0000.000
163A166LEU00.0070.01150.5840.0020.0020.0000.0000.0000.000
164A167LEU0-0.064-0.03854.4760.0030.0030.0000.0000.0000.000
165A168ALA0-0.0030.01656.7680.0020.0020.0000.0000.0000.000
166A169VAL0-0.056-0.02756.8980.0030.0030.0000.0000.0000.000
167A170ALA00.0300.02159.9190.0000.0000.0000.0000.0000.000
168A171LYS10.9200.92759.2800.0520.0520.0000.0000.0000.000
169A172THR0-0.012-0.01061.502-0.001-0.0010.0000.0000.0000.000
170A173ASP-1-0.826-0.92260.941-0.043-0.0430.0000.0000.0000.000
171A174ALA00.0260.02759.673-0.002-0.0020.0000.0000.0000.000
172A175ALA00.0360.01857.310-0.002-0.0020.0000.0000.0000.000
173A176THR00.025-0.00956.020-0.002-0.0020.0000.0000.0000.000
174A177LEU0-0.0110.00655.895-0.002-0.0020.0000.0000.0000.000
175A178ALA0-0.0310.00753.543-0.003-0.0030.0000.0000.0000.000
176A179GLN00.0140.00951.212-0.003-0.0030.0000.0000.0000.000
177A180MET00.0090.00150.975-0.003-0.0030.0000.0000.0000.000
178A181ASN0-0.064-0.04650.352-0.003-0.0030.0000.0000.0000.000
179A182VAL00.0190.02446.063-0.003-0.0030.0000.0000.0000.000
180A183LEU00.0310.01446.026-0.004-0.0040.0000.0000.0000.000
181A184ALA00.0270.01546.275-0.004-0.0040.0000.0000.0000.000
182A185LEU0-0.073-0.03642.839-0.004-0.0040.0000.0000.0000.000
183A186VAL0-0.009-0.01641.426-0.005-0.0050.0000.0000.0000.000
184A187ALA00.0440.01641.430-0.006-0.0060.0000.0000.0000.000
185A188ARG10.9720.99640.7170.0980.0980.0000.0000.0000.000
186A189TYR0-0.036-0.04036.759-0.001-0.0010.0000.0000.0000.000
187A190ILE00.0060.05936.918-0.009-0.0090.0000.0000.0000.000
188A191GLU-1-0.862-0.93837.416-0.111-0.1110.0000.0000.0000.000
189A192ARG10.8240.92635.5900.1110.1110.0000.0000.0000.000
190A193THR00.014-0.04432.152-0.008-0.0080.0000.0000.0000.000
191A194ALA00.0170.01932.586-0.012-0.0120.0000.0000.0000.000
192A195ASP-1-0.903-0.96033.662-0.155-0.1550.0000.0000.0000.000
193A196HIS0-0.0070.01128.811-0.009-0.0090.0000.0000.0000.000
194A197ALA0-0.0150.01329.015-0.017-0.0170.0000.0000.0000.000
195A198THR00.0400.01129.304-0.017-0.0170.0000.0000.0000.000
196A199ASN0-0.068-0.05028.4430.0020.0020.0000.0000.0000.000
197A200ILE0-0.016-0.01924.106-0.014-0.0140.0000.0000.0000.000
198A201ALA0-0.022-0.01125.631-0.022-0.0220.0000.0000.0000.000
199A202GLU-1-0.782-0.89427.761-0.198-0.1980.0000.0000.0000.000
200A203HIS0-0.047-0.00323.520-0.009-0.0090.0000.0000.0000.000
201A204LEU0-0.0340.01521.686-0.015-0.0150.0000.0000.0000.000
202A205VAL0-0.011-0.01324.132-0.007-0.0070.0000.0000.0000.000
203A206TYR0-0.0020.00123.702-0.002-0.0020.0000.0000.0000.000
204A207LEU0-0.076-0.04019.1540.0040.0040.0000.0000.0000.000
205A208VAL0-0.032-0.01822.1460.0000.0000.0000.0000.0000.000
206A209LYS10.9370.97523.8050.2120.2120.0000.0000.0000.000
207A210GLY0-0.0430.01226.2900.0200.0200.0000.0000.0000.000
208A211LYS10.8460.89027.5820.1490.1490.0000.0000.0000.000
209A212HIS0-0.047-0.04730.2070.0000.0000.0000.0000.0000.000
210A213TYR0-0.0110.01331.3280.0010.0010.0000.0000.0000.000
211A214ASP-1-0.962-0.98432.850-0.123-0.1230.0000.0000.0000.000
212A215PHE0-0.029-0.00636.298-0.003-0.0030.0000.0000.0000.000