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: 6Y7NZ

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 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 236
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3045532.463172
FMO2-HF: Nuclear repulsion 2949858.683872
FMO2-HF: Total energy -95673.7793
FMO2-MP2: Total energy -95950.43082


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.
131.889135.0420.752-1.112-2.7940.006
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 : -0.986 / q_NPA : -1.000
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].
3B31HIS00.0120.0033.777-0.0851.603-0.021-0.618-1.0490.005
4B32TYR0-0.076-0.0735.852-5.535-5.5350.0000.0000.0000.000
5B33SER0-0.002-0.0058.6070.9230.9230.0000.0000.0000.000
6B34THR0-0.043-0.05710.062-1.341-1.3410.0000.0000.0000.000
7B35GLY00.004-0.02012.614-1.206-1.2060.0000.0000.0000.000
8B36GLN0-0.029-0.02414.600-1.387-1.3870.0000.0000.0000.000
9B37ASP-1-0.735-0.83611.54027.18527.1850.0000.0000.0000.000
10B38ARG10.8630.94113.954-21.313-21.3130.0000.0000.0000.000
11B39HIS0-0.007-0.00217.594-1.318-1.3180.0000.0000.0000.000
12B40ASP-1-0.872-0.92016.13717.86617.8660.0000.0000.0000.000
13B41PHE0-0.008-0.02017.720-0.896-0.8960.0000.0000.0000.000
14B42TYR0-0.044-0.03519.580-0.660-0.6600.0000.0000.0000.000
15B43ARG10.9320.95222.507-12.793-12.7930.0000.0000.0000.000
16B44PHE0-0.058-0.02620.863-0.522-0.5220.0000.0000.0000.000
17B45ALA00.0420.00022.830-0.527-0.5270.0000.0000.0000.000
18B46ALA0-0.044-0.01824.352-0.536-0.5360.0000.0000.0000.000
19B47ARG10.8690.93522.727-13.509-13.5090.0000.0000.0000.000
20B48LEU0-0.0430.00723.902-0.199-0.1990.0000.0000.0000.000
21B49HIS0-0.0170.00528.052-0.496-0.4960.0000.0000.0000.000
22B50VAL00.015-0.00830.6610.2350.2350.0000.0000.0000.000
23B51ASP-1-0.884-0.95532.5998.3068.3060.0000.0000.0000.000
24B52ALA00.0290.01735.089-0.052-0.0520.0000.0000.0000.000
25B53GLN0-0.149-0.06638.415-0.304-0.3040.0000.0000.0000.000
26B54CYS0-0.068-0.03235.549-0.028-0.0280.0000.0000.0000.000
27B55PHE0-0.040-0.02236.769-0.105-0.1050.0000.0000.0000.000
28B56GLY00.0540.02234.0320.2000.2000.0000.0000.0000.000
29B57LEU0-0.038-0.01030.866-0.100-0.1000.0000.0000.0000.000
30B58SER00.007-0.01530.4270.4130.4130.0000.0000.0000.000
31B59ILE00.0640.02023.9530.1700.1700.0000.0000.0000.000
32B60ASP-1-0.837-0.89327.83111.03711.0370.0000.0000.0000.000
33B61ASP-1-0.775-0.86030.2899.5369.5360.0000.0000.0000.000
34B62LEU0-0.071-0.02825.8590.0700.0700.0000.0000.0000.000
35B63MET0-0.068-0.02622.8240.3190.3190.0000.0000.0000.000
36B64ASP-1-0.922-0.93027.1269.9449.9440.0000.0000.0000.000
37B65LYS10.9901.00228.395-10.974-10.9740.0000.0000.0000.000
38B66PHE0-0.049-0.03324.5040.0070.0070.0000.0000.0000.000
39B67SER0-0.078-0.04325.2620.4680.4680.0000.0000.0000.000
40B68ASP-1-0.802-0.88127.1739.5819.5810.0000.0000.0000.000
41B69LYS10.8740.92929.267-8.838-8.8380.0000.0000.0000.000
42B70HIS0-0.056-0.04830.317-0.177-0.1770.0000.0000.0000.000
43B71PHE00.0450.03623.889-0.058-0.0580.0000.0000.0000.000
44B72ARG10.8280.88221.843-13.497-13.4970.0000.0000.0000.000
45B73ALA0-0.071-0.02926.6820.0480.0480.0000.0000.0000.000
46B74GLU-1-0.929-0.94429.9009.5589.5580.0000.0000.0000.000
47B75HIS10.7990.89725.748-10.903-10.9030.0000.0000.0000.000
48B76PRO00.0460.02224.8580.4950.4950.0000.0000.0000.000
49B77GLU-1-0.833-0.91921.02912.85212.8520.0000.0000.0000.000
50B78TYR00.008-0.01920.0140.8960.8960.0000.0000.0000.000
51B79ARG10.8590.94721.316-13.213-13.2130.0000.0000.0000.000
52B80ASP-1-0.931-0.97817.47115.42815.4280.0000.0000.0000.000
53B81VAL00.0050.01916.7301.2331.2330.0000.0000.0000.000
54B82TYR0-0.017-0.01215.337-0.679-0.6790.0000.0000.0000.000
55B83PRO00.0530.01619.3060.0730.0730.0000.0000.0000.000
56B84GLU-1-0.820-0.92618.81215.44315.4430.0000.0000.0000.000
57B85GLU-1-0.743-0.83514.17221.62821.6280.0000.0000.0000.000
58B86CYS0-0.0110.00518.231-0.090-0.0900.0000.0000.0000.000
59B87SER00.014-0.01221.352-0.563-0.5630.0000.0000.0000.000
60B88ALA00.0150.01717.936-0.390-0.3900.0000.0000.0000.000
61B89ILE0-0.012-0.01117.968-0.195-0.1950.0000.0000.0000.000
62B90TYR00.0300.01820.507-0.481-0.4810.0000.0000.0000.000
63B91MET0-0.041-0.02522.745-0.141-0.1410.0000.0000.0000.000
64B92HIS0-0.0140.00419.119-0.170-0.1700.0000.0000.0000.000
65B93THR0-0.069-0.03222.262-0.232-0.2320.0000.0000.0000.000
66B94ALA00.0000.02624.780-0.454-0.4540.0000.0000.0000.000
67B95GLN0-0.026-0.01327.2980.2020.2020.0000.0000.0000.000
68B96ASP-1-0.800-0.89729.9529.9789.9780.0000.0000.0000.000
69B97TYR00.0360.00626.724-0.012-0.0120.0000.0000.0000.000
70B98SER0-0.025-0.02527.6270.1260.1260.0000.0000.0000.000
71B99SER0-0.005-0.03125.353-0.289-0.2890.0000.0000.0000.000
72B100HIS0-0.082-0.05127.358-0.388-0.3880.0000.0000.0000.000
73B101LEU00.0370.03530.842-0.026-0.0260.0000.0000.0000.000
74B102VAL0-0.031-0.03534.371-0.051-0.0510.0000.0000.0000.000
75B103ARG10.8610.91536.898-7.599-7.5990.0000.0000.0000.000
76B104GLY00.0090.02039.6780.0390.0390.0000.0000.0000.000
77B105GLU-1-0.795-0.89337.5617.9007.9000.0000.0000.0000.000
78B106ILE00.0030.02431.6540.0910.0910.0000.0000.0000.000
79B107GLY0-0.025-0.01831.833-0.174-0.1740.0000.0000.0000.000
80B108THR0-0.039-0.02227.485-0.199-0.1990.0000.0000.0000.000
81B109PRO00.0360.03427.5760.2930.2930.0000.0000.0000.000
82B110LEU00.0680.02921.5310.2110.2110.0000.0000.0000.000
83B111TYR00.0320.00721.7800.3880.3880.0000.0000.0000.000
84B112ARG10.8700.93322.020-10.396-10.3960.0000.0000.0000.000
85B113GLU-1-0.870-0.89022.87012.49712.4970.0000.0000.0000.000
86B114VAL00.0280.01217.4020.3840.3840.0000.0000.0000.000
87B115ASN00.022-0.00418.7691.1221.1220.0000.0000.0000.000
88B116ASN0-0.020-0.02419.6240.3160.3160.0000.0000.0000.000
89B117TYR0-0.004-0.01015.076-0.315-0.3150.0000.0000.0000.000
90B118LEU00.006-0.00313.4890.2560.2560.0000.0000.0000.000
91B119ARG10.7700.86816.693-12.817-12.8170.0000.0000.0000.000
92B120LEU0-0.045-0.01719.136-0.302-0.3020.0000.0000.0000.000
93B121GLN00.0410.03714.1500.1180.1180.0000.0000.0000.000
94B122HIS0-0.064-0.03017.361-0.203-0.2030.0000.0000.0000.000
95B123GLU-1-0.955-0.98216.07015.81315.8130.0000.0000.0000.000
96B124ASN0-0.078-0.04110.6401.8191.8190.0000.0000.0000.000
97B125SER0-0.064-0.0698.498-1.397-1.3970.0000.0000.0000.000
98B126GLY0-0.024-0.02110.791-1.266-1.2660.0000.0000.0000.000
99B127ARG10.8860.9316.460-23.172-23.1720.0000.0000.0000.000
100B128GLU-1-0.802-0.9194.32234.99335.245-0.001-0.025-0.2260.000
101B129ALA0-0.008-0.0042.4634.3165.4730.754-0.798-1.1140.001
102B130GLU-1-0.834-0.8843.43032.84232.8980.0200.329-0.4050.000
103B131ILE00.0060.0175.890-4.404-4.4040.0000.0000.0000.000
104B132ASP-1-0.859-0.9357.40030.54030.5400.0000.0000.0000.000
105B133ASN0-0.070-0.0138.569-2.611-2.6110.0000.0000.0000.000
106B134HIS00.0770.06810.525-2.938-2.9380.0000.0000.0000.000
107B135ASP-1-0.780-0.88613.94814.81614.8160.0000.0000.0000.000
108B136GLU-1-0.818-0.91217.17315.62215.6220.0000.0000.0000.000
109B137LYS10.7260.85818.151-14.494-14.4940.0000.0000.0000.000
110B138LEU00.0430.01017.946-0.119-0.1190.0000.0000.0000.000
111B139SER0-0.003-0.00413.6720.4230.4230.0000.0000.0000.000
112B140PRO00.0100.01114.1851.1281.1280.0000.0000.0000.000
113B141HIS0-0.009-0.01815.8150.4750.4750.0000.0000.0000.000
114B142ILE0-0.0160.00011.6120.3390.3390.0000.0000.0000.000
115B143LYS10.8160.9109.581-28.786-28.7860.0000.0000.0000.000
116B144MET0-0.0160.01111.6511.1081.1080.0000.0000.0000.000
117B145LEU00.006-0.00314.2370.0490.0490.0000.0000.0000.000
118B146SER0-0.015-0.0259.170-0.059-0.0590.0000.0000.0000.000
119B147SER00.000-0.00710.2851.1541.1540.0000.0000.0000.000
120B148ALA0-0.031-0.00711.272-0.385-0.3850.0000.0000.0000.000
121B149LEU00.000-0.00912.801-0.661-0.6610.0000.0000.0000.000
122B150ASN0-0.024-0.0237.576-2.300-2.3000.0000.0000.0000.000
123B151ARG10.8410.90610.992-24.682-24.6820.0000.0000.0000.000
124B152LEU0-0.018-0.00313.314-0.892-0.8920.0000.0000.0000.000
125B153MET0-0.059-0.02810.985-1.344-1.3440.0000.0000.0000.000
126B154ASP-1-0.813-0.88510.53625.87425.8740.0000.0000.0000.000
127B155VAL0-0.075-0.02113.772-0.689-0.6890.0000.0000.0000.000
128B156ALA0-0.041-0.02917.402-0.938-0.9380.0000.0000.0000.000
129B157ALA0-0.0340.00215.672-0.322-0.3220.0000.0000.0000.000
130B158PHE0-0.0080.00817.598-0.894-0.8940.0000.0000.0000.000
131B159ARG10.9280.95718.842-12.674-12.6740.0000.0000.0000.000
132B160GLY00.0050.00120.951-0.521-0.5210.0000.0000.0000.000
133B161THR0-0.039-0.02623.4420.4150.4150.0000.0000.0000.000
134B162VAL0-0.0020.01922.787-0.161-0.1610.0000.0000.0000.000
135B163TYR0-0.016-0.02525.998-0.225-0.2250.0000.0000.0000.000
136B164ARG10.9380.97022.825-12.015-12.0150.0000.0000.0000.000
137B165GLY00.0230.00827.740-0.259-0.2590.0000.0000.0000.000
138B166ILE0-0.062-0.02326.5840.2210.2210.0000.0000.0000.000
139B167ARG10.9430.95230.630-8.268-8.2680.0000.0000.0000.000
140B168GLY0-0.021-0.01432.8120.2030.2030.0000.0000.0000.000
141B169ASP-1-0.915-0.94933.9398.3328.3320.0000.0000.0000.000
142B170LEU00.0430.00735.4430.0940.0940.0000.0000.0000.000
143B171ASP-1-0.820-0.87832.6229.2829.2820.0000.0000.0000.000
144B172THR00.028-0.00729.7460.3000.3000.0000.0000.0000.000
145B173ILE0-0.021-0.01031.2320.2060.2060.0000.0000.0000.000
146B174ALA00.0100.00032.8490.0930.0930.0000.0000.0000.000
147B175ARG10.8480.91926.887-9.834-9.8340.0000.0000.0000.000
148B176LEU0-0.0070.01026.9830.2670.2670.0000.0000.0000.000
149B177TYR0-0.017-0.02929.4070.1320.1320.0000.0000.0000.000
150B178HIS00.0400.03228.927-0.176-0.1760.0000.0000.0000.000
151B179LEU0-0.040-0.02724.0860.1030.1030.0000.0000.0000.000
152B180PHE0-0.036-0.02727.3810.1410.1410.0000.0000.0000.000
153B181ASP-1-0.914-0.95129.0548.7078.7070.0000.0000.0000.000
154B182THR0-0.136-0.07828.6540.0080.0080.0000.0000.0000.000
155B183GLY0-0.0120.00826.5210.1810.1810.0000.0000.0000.000
156B184GLY0-0.051-0.01423.4860.4990.4990.0000.0000.0000.000
157B185ARG10.8610.90615.218-15.667-15.6670.0000.0000.0000.000
158B186TYR0-0.017-0.00320.760-0.302-0.3020.0000.0000.0000.000
159B187VAL0-0.008-0.01615.5810.5200.5200.0000.0000.0000.000
160B188GLU-1-0.800-0.88317.20312.96012.9600.0000.0000.0000.000
161B189PRO00.043-0.00214.8380.7670.7670.0000.0000.0000.000
162B190ALA0-0.0330.00014.4620.8910.8910.0000.0000.0000.000
163B191PHE00.0290.01412.5540.1590.1590.0000.0000.0000.000
164B192MET0-0.068-0.01816.689-1.070-1.0700.0000.0000.0000.000
165B193SER00.0030.01519.2710.2070.2070.0000.0000.0000.000
166B194THR0-0.051-0.05221.833-0.463-0.4630.0000.0000.0000.000
167B195THR00.0600.01724.305-0.005-0.0050.0000.0000.0000.000
168B196ARG10.8190.88324.949-11.453-11.4530.0000.0000.0000.000
169B197ILE0-0.0300.00028.254-0.273-0.2730.0000.0000.0000.000
170B198LYS10.9120.95831.843-8.555-8.5550.0000.0000.0000.000
171B199ASP-1-0.868-0.93533.3858.2028.2020.0000.0000.0000.000
172B200SER00.0230.00731.718-0.213-0.2130.0000.0000.0000.000
173B201ALA0-0.043-0.00830.7510.1350.1350.0000.0000.0000.000
174B202GLN0-0.018-0.01031.966-0.220-0.2200.0000.0000.0000.000
175B203VAL0-0.0010.00332.577-0.026-0.0260.0000.0000.0000.000
176B204PHE00.002-0.00932.315-0.157-0.1570.0000.0000.0000.000
177B205GLU-1-0.858-0.91037.6897.8827.8820.0000.0000.0000.000
178B206PRO0-0.0050.02241.0060.0650.0650.0000.0000.0000.000
179B207GLY0-0.005-0.01043.298-0.075-0.0750.0000.0000.0000.000
180B208THR0-0.042-0.03638.3680.0190.0190.0000.0000.0000.000
181B209PRO00.0310.00636.877-0.038-0.0380.0000.0000.0000.000
182B210ASN0-0.0220.00732.668-0.033-0.0330.0000.0000.0000.000
183B211ASN00.0300.01335.3460.0270.0270.0000.0000.0000.000
184B212ILE00.0050.01030.581-0.089-0.0890.0000.0000.0000.000
185B213ALA00.0450.02731.5270.1950.1950.0000.0000.0000.000
186B214PHE0-0.003-0.01425.9660.0400.0400.0000.0000.0000.000
187B215GLN00.002-0.00528.235-0.151-0.1510.0000.0000.0000.000
188B216ILE00.0130.01421.6160.0510.0510.0000.0000.0000.000
189B217SER00.0080.01922.835-0.241-0.2410.0000.0000.0000.000
190B218LEU0-0.013-0.01218.5750.3870.3870.0000.0000.0000.000
191B219LYS10.8580.90216.338-14.869-14.8690.0000.0000.0000.000
192B220ARG10.7890.85610.609-22.597-22.5970.0000.0000.0000.000
193B221GLY00.0450.03015.5040.4360.4360.0000.0000.0000.000
194B222ALA00.0470.02415.668-0.085-0.0850.0000.0000.0000.000
195B223ASP-1-0.744-0.82517.59511.83911.8390.0000.0000.0000.000
196B224ILE00.0230.00219.0940.2470.2470.0000.0000.0000.000
197B225SER0-0.037-0.03821.725-0.417-0.4170.0000.0000.0000.000
198B226GLY0-0.003-0.00624.544-0.384-0.3840.0000.0000.0000.000
199B227SER0-0.031-0.03822.335-0.186-0.1860.0000.0000.0000.000
200B228SER0-0.004-0.01624.453-0.149-0.1490.0000.0000.0000.000
201B229GLN0-0.044-0.04625.799-0.343-0.3430.0000.0000.0000.000
202B230ALA00.0010.00228.444-0.472-0.4720.0000.0000.0000.000
203B231PRO00.0300.02428.4040.0740.0740.0000.0000.0000.000
204B232SER0-0.023-0.00929.4870.0660.0660.0000.0000.0000.000
205B233GLU-1-0.956-0.96929.0299.9099.9090.0000.0000.0000.000
206B234GLU-1-0.918-0.96527.96710.26710.2670.0000.0000.0000.000
207B235GLU-1-0.837-0.91623.54812.53112.5310.0000.0000.0000.000
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