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: ZVL6N

Calculation Name: 3U0J-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3U0J

Chain ID: B

ChEMBL ID:

UniProt ID: Q88A91

Base Structure: X-ray

Registration Date: 2023-09-22

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 OptAll
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 236
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3050277.449179
FMO2-HF: Nuclear repulsion 2954602.908985
FMO2-HF: Total energy -95674.540194
FMO2-MP2: Total energy -95951.147774


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(B:29:GLU)


Summations of interaction energy for fragment #1(B:29:GLU)
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.
129.488132.2341.633-1.067-3.3130.005
Interaction energy analysis for fragmet #1(B:29:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.980 / q_NPA : -0.994
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].
3B31HIS00.0120.0073.8440.9242.523-0.018-0.683-0.8980.003
4B32TYR0-0.053-0.0555.757-4.615-4.6150.0000.0000.0000.000
5B33SER0-0.006-0.0058.9740.5220.5220.0000.0000.0000.000
6B34THR0-0.025-0.03910.646-1.791-1.7910.0000.0000.0000.000
7B35GLY0-0.009-0.02413.017-1.188-1.1880.0000.0000.0000.000
8B36GLN0-0.045-0.02914.609-1.350-1.3500.0000.0000.0000.000
9B37ASP-1-0.754-0.85411.93326.18726.1870.0000.0000.0000.000
10B38ARG10.8780.95014.391-20.872-20.8720.0000.0000.0000.000
11B39HIS0-0.0010.00418.232-1.218-1.2180.0000.0000.0000.000
12B40ASP-1-0.863-0.91616.20617.72017.7200.0000.0000.0000.000
13B41PHE00.000-0.01117.570-0.705-0.7050.0000.0000.0000.000
14B42TYR0-0.049-0.04319.448-0.713-0.7130.0000.0000.0000.000
15B43ARG10.9240.94822.715-12.542-12.5420.0000.0000.0000.000
16B44PHE0-0.032-0.01120.876-0.458-0.4580.0000.0000.0000.000
17B45ALA00.0490.01522.765-0.557-0.5570.0000.0000.0000.000
18B46ALA0-0.048-0.02824.367-0.500-0.5000.0000.0000.0000.000
19B47ARG10.8410.92522.869-13.373-13.3730.0000.0000.0000.000
20B48LEU0-0.0390.00323.967-0.116-0.1160.0000.0000.0000.000
21B49HIS0-0.0120.00328.091-0.513-0.5130.0000.0000.0000.000
22B50VAL00.014-0.00730.5840.2650.2650.0000.0000.0000.000
23B51ASP-1-0.884-0.95932.7258.2018.2010.0000.0000.0000.000
24B52ALA00.0050.00535.325-0.057-0.0570.0000.0000.0000.000
25B53GLN0-0.108-0.05538.668-0.330-0.3300.0000.0000.0000.000
26B54CYS0-0.088-0.03235.757-0.041-0.0410.0000.0000.0000.000
27B55PHE0-0.040-0.02036.865-0.069-0.0690.0000.0000.0000.000
28B56GLY00.0610.02533.8100.1880.1880.0000.0000.0000.000
29B57LEU0-0.046-0.01430.889-0.129-0.1290.0000.0000.0000.000
30B58SER0-0.004-0.02230.6680.3730.3730.0000.0000.0000.000
31B59ILE00.0430.00523.7330.1990.1990.0000.0000.0000.000
32B60ASP-1-0.833-0.90727.62311.08211.0820.0000.0000.0000.000
33B61ASP-1-0.798-0.86329.9529.4609.4600.0000.0000.0000.000
34B62LEU0-0.064-0.02225.6710.0380.0380.0000.0000.0000.000
35B63MET0-0.059-0.03223.1630.4000.4000.0000.0000.0000.000
36B64ASP-1-0.910-0.92527.4129.8129.8120.0000.0000.0000.000
37B65LYS10.9480.98728.306-10.862-10.8620.0000.0000.0000.000
38B66PHE0-0.018-0.00324.5750.0000.0000.0000.0000.0000.000
39B67SER0-0.074-0.05125.3060.5050.5050.0000.0000.0000.000
40B68ASP-1-0.777-0.86927.3749.5589.5580.0000.0000.0000.000
41B69LYS10.8610.91729.404-8.820-8.8200.0000.0000.0000.000
42B70HIS0-0.066-0.05130.537-0.207-0.2070.0000.0000.0000.000
43B71PHE00.0570.04624.046-0.009-0.0090.0000.0000.0000.000
44B72ARG10.8070.87422.142-13.226-13.2260.0000.0000.0000.000
45B73ALA0-0.069-0.02227.0640.0760.0760.0000.0000.0000.000
46B74GLU-1-0.930-0.95930.1429.6869.6860.0000.0000.0000.000
47B75HIS10.8170.90925.599-10.946-10.9460.0000.0000.0000.000
48B76PRO00.0240.01524.8650.4990.4990.0000.0000.0000.000
49B77GLU-1-0.841-0.93121.25712.76412.7640.0000.0000.0000.000
50B78TYR00.021-0.01219.9920.8590.8590.0000.0000.0000.000
51B79ARG10.7430.84321.549-13.806-13.8060.0000.0000.0000.000
52B80ASP-1-0.825-0.88217.93114.98714.9870.0000.0000.0000.000
53B81VAL00.0020.02116.8821.2331.2330.0000.0000.0000.000
54B82TYR0-0.021-0.01115.630-0.675-0.6750.0000.0000.0000.000
55B83PRO00.0370.01019.4890.0420.0420.0000.0000.0000.000
56B84GLU-1-0.810-0.91619.00415.26915.2690.0000.0000.0000.000
57B85GLU-1-0.746-0.82914.20021.28021.2800.0000.0000.0000.000
58B86CYS00.0040.00118.1850.0130.0130.0000.0000.0000.000
59B87SER0-0.001-0.01721.442-0.625-0.6250.0000.0000.0000.000
60B88ALA00.0030.00017.842-0.426-0.4260.0000.0000.0000.000
61B89ILE0-0.001-0.00218.073-0.211-0.2110.0000.0000.0000.000
62B90TYR00.0290.03320.616-0.485-0.4850.0000.0000.0000.000
63B91MET0-0.027-0.02222.540-0.132-0.1320.0000.0000.0000.000
64B92HIS0-0.032-0.00119.114-0.094-0.0940.0000.0000.0000.000
65B93THR0-0.054-0.03422.142-0.170-0.1700.0000.0000.0000.000
66B94ALA0-0.0190.00124.907-0.438-0.4380.0000.0000.0000.000
67B95GLN0-0.029-0.00127.3300.1910.1910.0000.0000.0000.000
68B96ASP-1-0.829-0.89930.0909.9889.9880.0000.0000.0000.000
69B97TYR00.0530.00626.8880.0260.0260.0000.0000.0000.000
70B98SER0-0.037-0.03427.5500.1070.1070.0000.0000.0000.000
71B99SER00.008-0.02125.282-0.251-0.2510.0000.0000.0000.000
72B100HIS0-0.085-0.04827.293-0.354-0.3540.0000.0000.0000.000
73B101LEU00.0300.02330.850-0.027-0.0270.0000.0000.0000.000
74B102VAL0-0.021-0.02134.534-0.076-0.0760.0000.0000.0000.000
75B103ARG10.8750.93337.180-7.510-7.5100.0000.0000.0000.000
76B104GLY0-0.004-0.00640.033-0.131-0.1310.0000.0000.0000.000
77B105GLU-1-0.812-0.88537.7437.8227.8220.0000.0000.0000.000
78B106ILE00.0160.01731.4250.0840.0840.0000.0000.0000.000
79B107GLY0-0.021-0.01231.775-0.193-0.1930.0000.0000.0000.000
80B108THR0-0.037-0.03027.259-0.152-0.1520.0000.0000.0000.000
81B109PRO00.0440.04227.9020.3010.3010.0000.0000.0000.000
82B110LEU00.0520.02721.7710.2310.2310.0000.0000.0000.000
83B111TYR00.0560.01421.8550.3570.3570.0000.0000.0000.000
84B112ARG10.8660.94022.047-10.281-10.2810.0000.0000.0000.000
85B113GLU-1-0.873-0.90423.05912.21112.2110.0000.0000.0000.000
86B114VAL00.0340.01917.4890.3340.3340.0000.0000.0000.000
87B115ASN00.011-0.01618.8721.0931.0930.0000.0000.0000.000
88B116ASN0-0.051-0.03220.1030.1710.1710.0000.0000.0000.000
89B117TYR00.007-0.00515.154-0.233-0.2330.0000.0000.0000.000
90B118LEU00.002-0.00513.7400.2150.2150.0000.0000.0000.000
91B119ARG10.8100.90216.657-12.536-12.5360.0000.0000.0000.000
92B120LEU0-0.053-0.02119.333-0.552-0.5520.0000.0000.0000.000
93B121GLN00.0190.02114.111-0.095-0.0950.0000.0000.0000.000
94B122HIS0-0.064-0.02917.462-0.194-0.1940.0000.0000.0000.000
95B123GLU-1-0.952-0.97416.24815.32515.3250.0000.0000.0000.000
96B124ASN0-0.052-0.02610.7511.7201.7200.0000.0000.0000.000
97B125SER0-0.095-0.0988.310-1.547-1.5470.0000.0000.0000.000
98B126GLY00.019-0.01210.926-0.775-0.7750.0000.0000.0000.000
99B127ARG10.8500.9136.252-22.927-22.9270.0000.0000.0000.000
100B128GLU-1-0.788-0.9084.49134.01734.336-0.001-0.035-0.2830.000
101B129ALA0-0.0040.0062.3583.0364.3051.580-1.166-1.6830.002
102B130GLU-1-0.799-0.8513.23630.23029.7890.0720.817-0.4490.000
103B131ILE0-0.0140.0046.007-3.979-3.9790.0000.0000.0000.000
104B132ASP-1-0.849-0.9238.17829.67729.6770.0000.0000.0000.000
105B133ASN0-0.079-0.0318.651-2.797-2.7970.0000.0000.0000.000
106B134HIS00.0640.06110.835-2.773-2.7730.0000.0000.0000.000
107B135ASP-1-0.776-0.89613.93814.59614.5960.0000.0000.0000.000
108B136GLU-1-0.803-0.90017.18815.30115.3010.0000.0000.0000.000
109B137LYS10.7220.86618.657-14.301-14.3010.0000.0000.0000.000
110B138LEU00.002-0.00318.155-0.293-0.2930.0000.0000.0000.000
111B139SER0-0.004-0.01913.6310.4640.4640.0000.0000.0000.000
112B140PRO0-0.0020.00213.9121.2411.2410.0000.0000.0000.000
113B141HIS00.005-0.00715.4260.6980.6980.0000.0000.0000.000
114B142ILE0-0.0030.00511.5900.3650.3650.0000.0000.0000.000
115B143LYS10.8260.9099.780-26.078-26.0780.0000.0000.0000.000
116B144MET0-0.0140.00411.6251.0131.0130.0000.0000.0000.000
117B145LEU00.0130.00214.448-0.079-0.0790.0000.0000.0000.000
118B146SER0-0.009-0.0299.173-0.129-0.1290.0000.0000.0000.000
119B147SER0-0.016-0.00610.5291.3311.3310.0000.0000.0000.000
120B148ALA0-0.018-0.00311.510-0.187-0.1870.0000.0000.0000.000
121B149LEU0-0.007-0.00412.604-0.680-0.6800.0000.0000.0000.000
122B150ASN0-0.023-0.0347.681-2.021-2.0210.0000.0000.0000.000
123B151ARG10.8250.89710.885-23.845-23.8450.0000.0000.0000.000
124B152LEU0-0.0020.01113.191-0.936-0.9360.0000.0000.0000.000
125B153MET0-0.056-0.02410.996-1.366-1.3660.0000.0000.0000.000
126B154ASP-1-0.797-0.87510.47326.15926.1590.0000.0000.0000.000
127B155VAL0-0.073-0.02613.738-0.665-0.6650.0000.0000.0000.000
128B156ALA0-0.033-0.01917.478-0.951-0.9510.0000.0000.0000.000
129B157ALA0-0.0270.00115.482-0.287-0.2870.0000.0000.0000.000
130B158PHE00.0020.00317.566-0.740-0.7400.0000.0000.0000.000
131B159ARG10.9060.94818.638-12.845-12.8450.0000.0000.0000.000
132B160GLY00.0150.00920.796-0.534-0.5340.0000.0000.0000.000
133B161THR0-0.048-0.03623.1410.4160.4160.0000.0000.0000.000
134B162VAL00.0120.03022.456-0.129-0.1290.0000.0000.0000.000
135B163TYR0-0.032-0.02425.614-0.269-0.2690.0000.0000.0000.000
136B164ARG10.8950.95422.719-11.899-11.8990.0000.0000.0000.000
137B165GLY00.0120.00927.306-0.250-0.2500.0000.0000.0000.000
138B166ILE0-0.024-0.00426.8470.2420.2420.0000.0000.0000.000
139B167ARG10.9550.96330.820-8.163-8.1630.0000.0000.0000.000
140B168GLY0-0.009-0.00733.0160.2070.2070.0000.0000.0000.000
141B169ASP-1-0.893-0.94134.0428.2448.2440.0000.0000.0000.000
142B170LEU00.013-0.00935.0210.1490.1490.0000.0000.0000.000
143B171ASP-1-0.780-0.85032.5769.2439.2430.0000.0000.0000.000
144B172THR00.0230.00829.3720.3060.3060.0000.0000.0000.000
145B173ILE0-0.016-0.00630.9770.2170.2170.0000.0000.0000.000
146B174ALA00.000-0.00132.7500.1010.1010.0000.0000.0000.000
147B175ARG10.8050.87626.875-9.743-9.7430.0000.0000.0000.000
148B176LEU0-0.008-0.00126.6010.3150.3150.0000.0000.0000.000
149B177TYR0-0.037-0.03429.0380.1310.1310.0000.0000.0000.000
150B178HIS00.0410.02828.750-0.118-0.1180.0000.0000.0000.000
151B179LEU0-0.038-0.00623.8160.1140.1140.0000.0000.0000.000
152B180PHE0-0.0090.00127.0010.1210.1210.0000.0000.0000.000
153B181ASP-1-0.912-0.96428.5598.7638.7630.0000.0000.0000.000
154B182THR0-0.121-0.08028.026-0.026-0.0260.0000.0000.0000.000
155B183GLY0-0.0190.00125.7630.1960.1960.0000.0000.0000.000
156B184GLY0-0.047-0.01423.2600.5110.5110.0000.0000.0000.000
157B185ARG10.8590.90614.581-15.856-15.8560.0000.0000.0000.000
158B186TYR0-0.009-0.01420.456-0.356-0.3560.0000.0000.0000.000
159B187VAL0-0.020-0.02915.5360.6080.6080.0000.0000.0000.000
160B188GLU-1-0.749-0.84817.01012.57812.5780.0000.0000.0000.000
161B189PRO00.017-0.02214.6300.8260.8260.0000.0000.0000.000
162B190ALA0-0.0370.00014.4590.8360.8360.0000.0000.0000.000
163B191PHE00.0170.00712.413-0.230-0.2300.0000.0000.0000.000
164B192MET0-0.055-0.00816.703-1.091-1.0910.0000.0000.0000.000
165B193SER0-0.002-0.01319.3430.2250.2250.0000.0000.0000.000
166B194THR0-0.058-0.05121.611-0.342-0.3420.0000.0000.0000.000
167B195THR00.0470.01024.1090.0500.0500.0000.0000.0000.000
168B196ARG10.7930.86224.786-11.389-11.3890.0000.0000.0000.000
169B197ILE0-0.033-0.00428.218-0.280-0.2800.0000.0000.0000.000
170B198LYS10.8540.93531.709-8.775-8.7750.0000.0000.0000.000
171B199ASP-1-0.856-0.93133.1578.2588.2580.0000.0000.0000.000
172B200SER00.0310.00731.824-0.205-0.2050.0000.0000.0000.000
173B201ALA0-0.0100.00730.4320.1240.1240.0000.0000.0000.000
174B202GLN0-0.063-0.02431.960-0.227-0.2270.0000.0000.0000.000
175B203VAL0-0.008-0.01532.2970.0070.0070.0000.0000.0000.000
176B204PHE00.0250.00131.522-0.133-0.1330.0000.0000.0000.000
177B205GLU-1-0.796-0.87637.3027.9397.9390.0000.0000.0000.000
178B206PRO0-0.0090.00040.7380.0190.0190.0000.0000.0000.000
179B207GLY0-0.025-0.00743.185-0.108-0.1080.0000.0000.0000.000
180B208THR0-0.070-0.05738.338-0.015-0.0150.0000.0000.0000.000
181B209PRO00.0440.01036.813-0.013-0.0130.0000.0000.0000.000
182B210ASN0-0.0340.00432.7320.0210.0210.0000.0000.0000.000
183B211ASN00.010-0.01235.041-0.033-0.0330.0000.0000.0000.000
184B212ILE00.0000.01330.277-0.097-0.0970.0000.0000.0000.000
185B213ALA00.0270.01431.2050.2380.2380.0000.0000.0000.000
186B214PHE00.0290.00425.4860.0990.0990.0000.0000.0000.000
187B215GLN00.021-0.00327.770-0.237-0.2370.0000.0000.0000.000
188B216ILE00.0010.00621.242-0.017-0.0170.0000.0000.0000.000
189B217SER0-0.011-0.01023.0090.0840.0840.0000.0000.0000.000
190B218LEU00.0110.00418.1420.4850.4850.0000.0000.0000.000
191B219LYS10.7980.87316.357-14.563-14.5630.0000.0000.0000.000
192B220ARG10.7850.85310.304-23.137-23.1370.0000.0000.0000.000
193B221GLY00.0530.03714.7880.6030.6030.0000.0000.0000.000
194B222ALA00.0310.02015.504-0.204-0.2040.0000.0000.0000.000
195B223ASP-1-0.751-0.84317.36511.85511.8550.0000.0000.0000.000
196B224ILE00.0310.00518.8380.3250.3250.0000.0000.0000.000
197B225SER0-0.048-0.03821.568-0.434-0.4340.0000.0000.0000.000
198B226GLY00.0220.00524.637-0.401-0.4010.0000.0000.0000.000
199B227SER0-0.035-0.03922.533-0.137-0.1370.0000.0000.0000.000
200B228SER0-0.004-0.02224.692-0.130-0.1300.0000.0000.0000.000
201B229GLN0-0.032-0.03925.603-0.357-0.3570.0000.0000.0000.000
202B230ALA00.0110.01328.363-0.427-0.4270.0000.0000.0000.000
203B231PRO00.0100.00628.5400.0320.0320.0000.0000.0000.000
204B232SER0-0.023-0.01729.6140.0410.0410.0000.0000.0000.000
205B233GLU-1-0.947-0.96729.2639.7729.7720.0000.0000.0000.000
206B234GLU-1-0.891-0.92627.86910.26610.2660.0000.0000.0000.000
207B235GLU-1-0.789-0.86423.15912.59312.5930.0000.0000.0000.000
208B236ILE0-0.045-0.01619.7100.3290.3290.0000.0000.0000.000
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