FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: MNGYZ

Calculation Name: 4OO8-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4OO8

Chain ID: D

ChEMBL ID:

UniProt ID: Q99ZW2

Base Structure: X-ray

Registration Date: 2023-09-24

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 1172
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -36521182.350027
FMO2-HF: Nuclear repulsion 36053206.061
FMO2-HF: Total energy -467976.289027
FMO2-MP2: Total energy -469368.352931


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(D:3:LYS)


Summations of interaction energy for fragment #1(D:3:LYS)
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.
72.5270.52238.336-16.559-19.78-0.173
Interaction energy analysis for fragmet #1(D:3:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.819 / q_NPA : 0.913
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].
3D5TYR0-0.053-0.0682.554-4.4071.6730.876-2.787-4.169-0.012
4D6SER00.0450.0194.6041.8131.867-0.001-0.011-0.0420.000
5D7ILE0-0.054-0.0317.814-0.838-0.8380.0000.0000.0000.000
6D8GLY00.0180.0369.7941.5631.5630.0000.0000.0000.000
7D9LEU0-0.050-0.05113.324-0.094-0.0940.0000.0000.0000.000
8D10ALA00.0320.01016.0100.7070.7070.0000.0000.0000.000
9D11ILE0-0.023-0.01019.1850.2370.2370.0000.0000.0000.000
10D12GLY00.0670.03421.6580.5110.5110.0000.0000.0000.000
11D13THR0-0.049-0.03525.110-0.192-0.1920.0000.0000.0000.000
12D14ASN0-0.019-0.00727.0700.2760.2760.0000.0000.0000.000
13D15SER00.0060.00222.7740.0760.0760.0000.0000.0000.000
14D16VAL0-0.0140.00117.3720.0160.0160.0000.0000.0000.000
15D17GLY00.0220.02918.010-0.392-0.3920.0000.0000.0000.000
16D18TRP0-0.011-0.01911.085-0.979-0.9790.0000.0000.0000.000
17D19ALA00.0280.00711.6430.5840.5840.0000.0000.0000.000
18D20VAL0-0.0120.0014.945-1.076-1.0760.0000.0000.0000.000
19D21ILE00.003-0.0018.1261.2901.2900.0000.0000.0000.000
20D22THR0-0.058-0.0684.724-4.365-4.311-0.001-0.007-0.0460.000
21D23ASP-1-0.748-0.8556.454-31.623-31.6230.0000.0000.0000.000
22D24GLU-1-0.804-0.8838.186-25.651-25.6510.0000.0000.0000.000
23D25TYR0-0.019-0.01110.5420.7960.7960.0000.0000.0000.000
24D26LYS10.9280.9979.51921.99521.9950.0000.0000.0000.000
25D27VAL00.0250.0078.895-2.528-2.5280.0000.0000.0000.000
26D28PRO0-0.0180.0155.2661.4291.4290.0000.0000.0000.000
27D29SER00.0530.0197.9791.4271.4270.0000.0000.0000.000
28D30LYS10.8590.9234.10545.52745.640-0.001-0.006-0.1060.000
29D31LYS10.9570.9629.99325.54625.5460.0000.0000.0000.000
30D32PHE00.0050.0199.509-1.120-1.1200.0000.0000.0000.000
31D33LYS10.9860.97913.74616.41416.4140.0000.0000.0000.000
32D34VAL0-0.037-0.02016.607-0.291-0.2910.0000.0000.0000.000
33D35LEU0-0.045-0.02419.8540.4440.4440.0000.0000.0000.000
34D36GLY00.0420.00322.4000.1040.1040.0000.0000.0000.000
35D37ASN0-0.0130.00126.088-0.282-0.2820.0000.0000.0000.000
36D38THR00.0240.02126.2560.2310.2310.0000.0000.0000.000
37D39ASP-1-0.824-0.91827.243-10.463-10.4630.0000.0000.0000.000
38D40ARG10.8710.93922.47512.29912.2990.0000.0000.0000.000
39D41HIS10.9690.99021.68311.94811.9480.0000.0000.0000.000
40D42SER0-0.0250.00317.181-0.585-0.5850.0000.0000.0000.000
41D43ILE00.0110.01316.7310.7660.7660.0000.0000.0000.000
42D44LYS10.9040.95312.79919.67819.6780.0000.0000.0000.000
43D45LYS10.7620.87113.51518.38518.3850.0000.0000.0000.000
44D46ASN00.022-0.00412.073-2.510-2.5100.0000.0000.0000.000
45D47LEU0-0.037-0.0126.0170.3740.3740.0000.0000.0000.000
46D48ILE00.0440.00810.130-1.036-1.0360.0000.0000.0000.000
47D49GLY00.0110.00513.0140.8690.8690.0000.0000.0000.000
48D50ALA00.0110.00916.053-0.168-0.1680.0000.0000.0000.000
49D51LEU0-0.052-0.00218.6340.4660.4660.0000.0000.0000.000
50D52LEU00.0340.01020.3700.3190.3190.0000.0000.0000.000
51D53PHE0-0.075-0.04823.2850.1520.1520.0000.0000.0000.000
52D54ASP-1-0.743-0.83326.438-9.850-9.8500.0000.0000.0000.000
53D55SER00.004-0.01629.650-0.204-0.2040.0000.0000.0000.000
54D56GLY0-0.0050.01531.1140.0950.0950.0000.0000.0000.000
55D57GLU-1-0.918-0.95532.168-8.286-8.2860.0000.0000.0000.000
56D58THR0-0.005-0.01835.494-0.098-0.0980.0000.0000.0000.000
57D59ALA00.0260.00537.5910.0750.0750.0000.0000.0000.000
58D60GLU-1-0.803-0.87239.525-7.083-7.0830.0000.0000.0000.000
59D61ALA00.0860.03742.7020.1930.1930.0000.0000.0000.000
60D62THR00.008-0.00940.2450.2020.2020.0000.0000.0000.000
61D63ARG10.8270.88243.3887.3347.3340.0000.0000.0000.000
62D64LEU00.0450.02145.2670.1590.1590.0000.0000.0000.000
63D65LYS10.8720.90946.5116.9706.9700.0000.0000.0000.000
64D66ARG10.8800.96542.8827.4967.4960.0000.0000.0000.000
65D67THR0-0.004-0.01248.1100.1550.1550.0000.0000.0000.000
66D68ALA00.0080.00951.0000.1420.1420.0000.0000.0000.000
67D69ARG10.9800.99545.8166.9106.9100.0000.0000.0000.000
68D70ARG10.9480.98447.1586.7506.7500.0000.0000.0000.000
69D71ARG10.9981.00053.8605.9715.9710.0000.0000.0000.000
70D72TYR00.0000.00255.3310.1500.1500.0000.0000.0000.000
71D73THR0-0.049-0.02455.3130.0810.0810.0000.0000.0000.000
72D74ARG10.9900.98554.3295.9205.9200.0000.0000.0000.000
73D75ARG10.9070.96959.8765.3055.3050.0000.0000.0000.000
74D76LYS10.9630.98059.1425.4885.4880.0000.0000.0000.000
75D77ASN00.0420.00659.7930.0720.0720.0000.0000.0000.000
76D78ARG10.9270.98862.1085.1285.1280.0000.0000.0000.000
77D79ILE0-0.010-0.00366.1650.0610.0610.0000.0000.0000.000
78D80LEU00.0120.00663.8730.0440.0440.0000.0000.0000.000
79D81TYR00.0140.00563.436-0.006-0.0060.0000.0000.0000.000
80D82LEU00.0010.00969.0280.0500.0500.0000.0000.0000.000
81D83GLN0-0.050-0.03970.4590.0390.0390.0000.0000.0000.000
82D84GLU-1-0.952-0.96569.521-4.605-4.6050.0000.0000.0000.000
83D85ILE0-0.027-0.01072.5940.0530.0530.0000.0000.0000.000
84D86PHE00.0270.00075.4280.0570.0570.0000.0000.0000.000
85D87SER0-0.047-0.02174.7320.0680.0680.0000.0000.0000.000
86D88ASN00.0100.00776.8560.0830.0830.0000.0000.0000.000
87D89GLU-1-0.782-0.89579.809-3.805-3.8050.0000.0000.0000.000
88D90MET0-0.073-0.02678.3140.0310.0310.0000.0000.0000.000
89D91ALA00.0340.01679.8670.0300.0300.0000.0000.0000.000
90D92LYS10.8030.90181.5233.8963.8960.0000.0000.0000.000
91D93VAL0-0.059-0.01384.1400.0430.0430.0000.0000.0000.000
92D94ASP-1-0.807-0.92781.575-3.975-3.9750.0000.0000.0000.000
93D95ASP-1-0.855-0.91680.550-4.042-4.0420.0000.0000.0000.000
94D96SER0-0.017-0.00377.810-0.059-0.0590.0000.0000.0000.000
95D97PHE00.0030.00177.686-0.044-0.0440.0000.0000.0000.000
96D98PHE00.001-0.02873.154-0.044-0.0440.0000.0000.0000.000
97D99HIS00.0280.02172.880-0.078-0.0780.0000.0000.0000.000
98D100ARG10.8450.94173.0834.0354.0350.0000.0000.0000.000
99D101LEU0-0.043-0.00972.263-0.041-0.0410.0000.0000.0000.000
100D102GLU-1-0.982-0.97967.946-4.835-4.8350.0000.0000.0000.000
101D103GLU-1-0.771-0.87168.620-4.549-4.5490.0000.0000.0000.000
102D104SER0-0.045-0.02870.729-0.013-0.0130.0000.0000.0000.000
103D105PHE0-0.088-0.04764.033-0.016-0.0160.0000.0000.0000.000
104D106LEU0-0.010-0.00566.587-0.033-0.0330.0000.0000.0000.000
105D107VAL0-0.015-0.03069.2510.0610.0610.0000.0000.0000.000
106D108GLU-1-0.841-0.91871.651-4.124-4.1240.0000.0000.0000.000
107D109GLU-1-0.853-0.91972.339-4.522-4.5220.0000.0000.0000.000
108D110ASP-1-0.789-0.85768.415-4.731-4.7310.0000.0000.0000.000
109D111LYS10.7900.92871.4804.4054.4050.0000.0000.0000.000
110D112LYS10.8750.92170.1774.6014.6010.0000.0000.0000.000
111D113HIS0-0.046-0.02474.5120.0730.0730.0000.0000.0000.000
112D114GLU-1-0.814-0.91977.915-3.991-3.9910.0000.0000.0000.000
113D115ARG10.8290.89877.2983.9673.9670.0000.0000.0000.000
114D116HIS0-0.046-0.01477.570-0.068-0.0680.0000.0000.0000.000
115D117PRO0-0.019-0.00975.6200.0030.0030.0000.0000.0000.000
116D118ILE0-0.047-0.02477.708-0.006-0.0060.0000.0000.0000.000
117D119PHE0-0.023-0.02480.0860.0180.0180.0000.0000.0000.000
118D120GLY00.0460.02082.342-0.033-0.0330.0000.0000.0000.000
119D121ASN0-0.034-0.03283.882-0.019-0.0190.0000.0000.0000.000
120D122ILE00.0360.01184.704-0.027-0.0270.0000.0000.0000.000
121D123VAL0-0.006-0.01085.989-0.008-0.0080.0000.0000.0000.000
122D124ASP-1-0.825-0.90486.729-3.673-3.6730.0000.0000.0000.000
123D125GLU-1-0.790-0.90380.225-4.067-4.0670.0000.0000.0000.000
124D126VAL0-0.007-0.01484.344-0.028-0.0280.0000.0000.0000.000
125D127ALA00.0180.01586.1930.0090.0090.0000.0000.0000.000
126D128TYR0-0.038-0.02980.4030.0150.0150.0000.0000.0000.000
127D129HIS00.004-0.00879.070-0.011-0.0110.0000.0000.0000.000
128D130GLU-1-0.935-0.94583.876-3.729-3.7290.0000.0000.0000.000
129D131LYS10.8900.95287.2233.6613.6610.0000.0000.0000.000
130D132TYR0-0.082-0.05483.2150.0270.0270.0000.0000.0000.000
131D133PRO00.0580.05982.461-0.056-0.0560.0000.0000.0000.000
132D134THR0-0.061-0.05278.198-0.093-0.0930.0000.0000.0000.000
133D135ILE00.021-0.00975.0880.0310.0310.0000.0000.0000.000
134D136TYR00.024-0.01173.128-0.027-0.0270.0000.0000.0000.000
135D137HIS00.1060.09079.588-0.010-0.0100.0000.0000.0000.000
136D138LEU0-0.0280.00280.3210.0420.0420.0000.0000.0000.000
137D139ARG10.7890.85974.0064.3414.3410.0000.0000.0000.000
138D140LYS10.8650.91481.2703.8063.8060.0000.0000.0000.000
139D141LYS10.9630.99183.9503.7153.7150.0000.0000.0000.000
140D142LEU0-0.0020.01082.0470.0440.0440.0000.0000.0000.000
141D143VAL0-0.019-0.00382.292-0.004-0.0040.0000.0000.0000.000
142D144ASP-1-0.872-0.91385.377-3.709-3.7090.0000.0000.0000.000
143D145SER0-0.047-0.04288.9320.0510.0510.0000.0000.0000.000
144D146THR00.0050.00389.982-0.030-0.0300.0000.0000.0000.000
145D147ASP-1-0.904-0.94392.304-3.469-3.4690.0000.0000.0000.000
146D148LYS10.9200.99289.2003.6093.6090.0000.0000.0000.000
147D149ALA0-0.014-0.00186.4640.0110.0110.0000.0000.0000.000
148D150ASP-1-0.758-0.86084.880-3.843-3.8430.0000.0000.0000.000
149D151LEU00.0660.02981.742-0.037-0.0370.0000.0000.0000.000
150D152ARG10.8280.88480.5263.8103.8100.0000.0000.0000.000
151D153LEU0-0.022-0.02079.942-0.060-0.0600.0000.0000.0000.000
152D154ILE00.0170.01880.719-0.047-0.0470.0000.0000.0000.000
153D155TYR00.0230.01471.905-0.077-0.0770.0000.0000.0000.000
154D156LEU00.0140.00975.366-0.078-0.0780.0000.0000.0000.000
155D157ALA00.0000.00675.620-0.068-0.0680.0000.0000.0000.000
156D158LEU00.0590.02975.868-0.056-0.0560.0000.0000.0000.000
157D159ALA00.010-0.00472.115-0.084-0.0840.0000.0000.0000.000
158D160HIS0-0.050-0.01371.125-0.097-0.0970.0000.0000.0000.000
159D161MET00.0070.01871.359-0.070-0.0700.0000.0000.0000.000
160D162ILE00.0260.03368.570-0.090-0.0900.0000.0000.0000.000
161D163LYS10.8760.93765.9384.7494.7490.0000.0000.0000.000
162D164PHE0-0.129-0.09765.682-0.138-0.1380.0000.0000.0000.000
163D165ARG10.8630.93262.5855.0765.0760.0000.0000.0000.000
164D166GLY00.0460.04467.2520.0440.0440.0000.0000.0000.000
165D167HIS0-0.059-0.01664.211-0.125-0.1250.0000.0000.0000.000
166D168PHE0-0.012-0.03163.3180.0270.0270.0000.0000.0000.000
167D169LEU0-0.058-0.04461.652-0.079-0.0790.0000.0000.0000.000
168D170ILE0-0.004-0.00364.941-0.017-0.0170.0000.0000.0000.000
169D171GLU-1-0.938-0.95066.776-4.851-4.8510.0000.0000.0000.000
170D172GLY00.0690.04568.7880.0320.0320.0000.0000.0000.000
171D173ASP-1-0.946-0.96672.446-4.385-4.3850.0000.0000.0000.000
172D174LEU0-0.064-0.03475.6240.0040.0040.0000.0000.0000.000
173D175ASN0-0.018-0.02277.5780.0380.0380.0000.0000.0000.000
174D176PRO0-0.056-0.02681.353-0.003-0.0030.0000.0000.0000.000
175D177ASP-1-0.887-0.94683.060-3.774-3.7740.0000.0000.0000.000
176D178ASN0-0.059-0.03082.2340.0880.0880.0000.0000.0000.000
177D179SER0-0.029-0.02083.261-0.038-0.0380.0000.0000.0000.000
178D180ASP-1-0.816-0.88285.238-3.637-3.6370.0000.0000.0000.000
179D181VAL00.033-0.00283.378-0.001-0.0010.0000.0000.0000.000
180D182ASP-1-0.841-0.92785.997-3.682-3.6820.0000.0000.0000.000
181D183LYS10.8360.87889.2253.5863.5860.0000.0000.0000.000
182D184LEU0-0.021-0.00284.6350.0140.0140.0000.0000.0000.000
183D185PHE0-0.008-0.00485.067-0.027-0.0270.0000.0000.0000.000
184D186ILE00.0120.00487.1000.0000.0000.0000.0000.0000.000
185D187GLN00.0260.02387.484-0.024-0.0240.0000.0000.0000.000
186D188LEU0-0.0030.01282.749-0.002-0.0020.0000.0000.0000.000
187D189VAL0-0.024-0.01286.881-0.006-0.0060.0000.0000.0000.000
188D190GLN0-0.016-0.02389.107-0.001-0.0010.0000.0000.0000.000
189D191THR0-0.007-0.00787.0810.0260.0260.0000.0000.0000.000
190D192TYR0-0.003-0.01884.008-0.034-0.0340.0000.0000.0000.000
191D193ASN0-0.006-0.02788.122-0.031-0.0310.0000.0000.0000.000
192D194GLN0-0.0320.00291.5610.0330.0330.0000.0000.0000.000
193D195LEU0-0.022-0.00386.1460.0120.0120.0000.0000.0000.000
194D196PHE0-0.057-0.03084.373-0.026-0.0260.0000.0000.0000.000
195D197GLU-1-0.863-0.93490.414-3.410-3.4100.0000.0000.0000.000
196D198GLU-1-0.962-0.96091.980-3.444-3.4440.0000.0000.0000.000
197D199ASN0-0.142-0.07889.760-0.018-0.0180.0000.0000.0000.000
198D200PRO00.0350.03990.285-0.048-0.0480.0000.0000.0000.000
199D201ILE0-0.015-0.01786.676-0.008-0.0080.0000.0000.0000.000
200D202ASN0-0.016-0.00791.098-0.005-0.0050.0000.0000.0000.000
201D203ALA00.021-0.00491.365-0.034-0.0340.0000.0000.0000.000
202D204SER0-0.006-0.00692.8960.0470.0470.0000.0000.0000.000
203D205GLY0-0.007-0.00594.537-0.007-0.0070.0000.0000.0000.000
204D206VAL0-0.0130.00589.237-0.017-0.0170.0000.0000.0000.000
205D207ASP-1-0.805-0.89988.908-3.697-3.6970.0000.0000.0000.000
206D208ALA00.0260.00286.294-0.054-0.0540.0000.0000.0000.000
207D209LYS10.8860.95284.9503.7223.7220.0000.0000.0000.000
208D210ALA0-0.0370.00584.519-0.068-0.0680.0000.0000.0000.000
209D211ILE0-0.026-0.01782.184-0.069-0.0690.0000.0000.0000.000
210D212LEU00.0320.01580.148-0.074-0.0740.0000.0000.0000.000
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1156D1350GLN00.008-0.01020.432-0.281-0.2810.0000.0000.0000.000
1157D1351SER0-0.022-0.02715.5610.4840.4840.0000.0000.0000.000
1158D1352ILE0-0.023-0.00915.8060.4420.4420.0000.0000.0000.000
1159D1353THR0-0.004-0.03112.1940.1980.1980.0000.0000.0000.000
1160D1354GLY00.0150.00215.355-0.017-0.0170.0000.0000.0000.000
1161D1355LEU0-0.0260.00310.4510.4130.4130.0000.0000.0000.000
1162D1356TYR0-0.020-0.01110.517-0.270-0.2700.0000.0000.0000.000
1163D1357GLU-1-0.781-0.87216.274-13.977-13.9770.0000.0000.0000.000
1164D1358THR0-0.029-0.02419.884-0.063-0.0630.0000.0000.0000.000
1165D1359ARG10.7370.83922.91912.89412.8940.0000.0000.0000.000
1166D1360ILE00.005-0.01325.5240.0480.0480.0000.0000.0000.000
1167D1361ASP-1-0.789-0.83829.148-9.180-9.1800.0000.0000.0000.000
1168D1362LEU0-0.010-0.01731.8880.1380.1380.0000.0000.0000.000
1169D1363SER0-0.062-0.06035.0210.3700.3700.0000.0000.0000.000
1170D1364GLN0-0.007-0.02733.9090.0110.0110.0000.0000.0000.000
1171D1365LEU0-0.050-0.01834.7470.1470.1470.0000.0000.0000.000
1172D1366GLY0-0.0210.00238.6130.2400.2400.0000.0000.0000.000