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: JQQ89

Calculation Name: 3L7O-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3L7O

Chain ID: A

ChEMBL ID:

UniProt ID: Q8DTT9

Base Structure: X-ray

Registration Date: 2023-09-21

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 224
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2614879.763724
FMO2-HF: Nuclear repulsion 2529401.384465
FMO2-HF: Total energy -85478.37926
FMO2-MP2: Total energy -85729.723133


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:2:GLU)


Summations of interaction energy for fragment #1(A:2: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.
-35.109-22.889.577-10.564-11.2390.114
Interaction energy analysis for fragmet #1(A:2:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.821 / q_NPA : -0.918
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].
3A4LEU00.0100.0193.168-4.831-2.3900.138-1.088-1.4900.006
4A5LYS10.8650.9282.581-103.321-95.7371.639-4.203-5.0190.048
5A6LYS10.9940.9934.048-37.603-37.2130.000-0.128-0.2620.000
6A7ILE00.0080.0076.107-4.862-4.8620.0000.0000.0000.000
7A8ALA00.002-0.0027.538-3.203-3.2030.0000.0000.0000.000
8A9GLY0-0.013-0.0118.126-2.915-2.9150.0000.0000.0000.000
9A10VAL00.0320.0129.910-2.345-2.3450.0000.0000.0000.000
10A11ARG10.9050.96111.690-19.696-19.6960.0000.0000.0000.000
11A12ALA0-0.012-0.01812.872-1.825-1.8250.0000.0000.0000.000
12A13ALA00.0400.01814.454-1.246-1.2460.0000.0000.0000.000
13A14GLN0-0.034-0.03316.329-1.484-1.4840.0000.0000.0000.000
14A15TYR0-0.026-0.01617.639-0.434-0.4340.0000.0000.0000.000
15A16VAL0-0.0050.01518.995-0.508-0.5080.0000.0000.0000.000
16A17GLU-1-0.935-0.99021.44012.20112.2010.0000.0000.0000.000
17A18ASP-1-0.817-0.93024.82411.61611.6160.0000.0000.0000.000
18A19GLY0-0.086-0.04826.965-0.299-0.2990.0000.0000.0000.000
19A20MET0-0.0450.02324.7140.0310.0310.0000.0000.0000.000
20A21ILE00.0000.01225.7500.1660.1660.0000.0000.0000.000
21A22VAL0-0.032-0.03919.3940.2430.2430.0000.0000.0000.000
22A23GLY00.0260.00820.625-0.012-0.0120.0000.0000.0000.000
23A24LEU0-0.053-0.03616.6310.9800.9800.0000.0000.0000.000
24A25GLY00.0770.03115.464-0.541-0.5410.0000.0000.0000.000
25A26THR0-0.065-0.02511.9670.9640.9640.0000.0000.0000.000
26A27GLY00.1200.0399.946-0.935-0.9350.0000.0000.0000.000
27A28SER0-0.070-0.0234.2413.9174.029-0.001-0.034-0.0770.000
28A29THR00.0160.0054.73011.42811.582-0.001-0.002-0.1500.000
29A30ALA00.0560.0246.870-1.107-1.1070.0000.0000.0000.000
30A31TYR00.0110.0166.455-2.224-2.2240.0000.0000.0000.000
31A32TYR0-0.011-0.0401.850-31.277-29.7297.802-5.109-4.2410.060
32A33PHE0-0.0040.0218.288-2.335-2.3350.0000.0000.0000.000
33A34VAL00.0060.00511.595-1.960-1.9600.0000.0000.0000.000
34A35GLU-1-0.897-0.9469.11524.47324.4730.0000.0000.0000.000
35A36GLU-1-0.831-0.88312.13019.11619.1160.0000.0000.0000.000
36A37VAL0-0.014-0.01613.837-1.619-1.6190.0000.0000.0000.000
37A38GLY00.016-0.00115.672-1.179-1.1790.0000.0000.0000.000
38A39ARG10.8200.88614.199-18.996-18.9960.0000.0000.0000.000
39A40ARG10.8620.95117.074-16.473-16.4730.0000.0000.0000.000
40A41VAL0-0.041-0.01619.699-0.819-0.8190.0000.0000.0000.000
41A42GLN0-0.067-0.02817.982-0.210-0.2100.0000.0000.0000.000
42A43GLU-1-0.980-1.00019.03113.84413.8440.0000.0000.0000.000
43A44GLU-1-0.961-0.98020.10914.70714.7070.0000.0000.0000.000
44A45GLY0-0.0140.00323.604-0.381-0.3810.0000.0000.0000.000
45A46LEU0-0.0220.01920.872-0.353-0.3530.0000.0000.0000.000
46A47GLN0-0.079-0.05524.653-0.096-0.0960.0000.0000.0000.000
47A48VAL00.0390.01821.574-0.052-0.0520.0000.0000.0000.000
48A49ILE0-0.047-0.02025.070-0.259-0.2590.0000.0000.0000.000
49A50GLY00.0060.00921.5180.2060.2060.0000.0000.0000.000
50A51VAL00.0400.01721.867-0.550-0.5500.0000.0000.0000.000
51A52THR0-0.043-0.02418.9500.5030.5030.0000.0000.0000.000
52A53THR00.0400.03017.316-0.495-0.4950.0000.0000.0000.000
53A54SER00.0310.01016.917-0.123-0.1230.0000.0000.0000.000
54A55SER00.0440.01518.9260.4430.4430.0000.0000.0000.000
55A56ARG10.9560.95914.063-19.754-19.7540.0000.0000.0000.000
56A57THR00.0490.01814.6600.5160.5160.0000.0000.0000.000
57A58THR00.0140.02316.128-0.127-0.1270.0000.0000.0000.000
58A59ALA0-0.017-0.00617.544-0.361-0.3610.0000.0000.0000.000
59A60GLN0-0.066-0.03210.592-0.980-0.9800.0000.0000.0000.000
60A61ALA00.0560.00915.683-0.067-0.0670.0000.0000.0000.000
61A62GLN0-0.029-0.01917.982-0.398-0.3980.0000.0000.0000.000
62A63ALA0-0.058-0.01917.017-0.553-0.5530.0000.0000.0000.000
63A64LEU0-0.044-0.01914.047-0.461-0.4610.0000.0000.0000.000
64A65GLY0-0.0170.01118.470-0.460-0.4600.0000.0000.0000.000
65A66ILE0-0.019-0.00817.077-0.402-0.4020.0000.0000.0000.000
66A67PRO0-0.014-0.00421.584-0.118-0.1180.0000.0000.0000.000
67A68LEU0-0.035-0.01520.6980.4190.4190.0000.0000.0000.000
68A69LYS10.9570.97624.847-10.810-10.8100.0000.0000.0000.000
69A70SER0-0.0140.00525.9610.5140.5140.0000.0000.0000.000
70A71ILE00.026-0.01826.025-0.096-0.0960.0000.0000.0000.000
71A72ASP-1-0.892-0.93228.4029.7319.7310.0000.0000.0000.000
72A73GLU-1-1.045-1.00930.62110.02010.0200.0000.0000.0000.000
73A74VAL0-0.063-0.03528.197-0.043-0.0430.0000.0000.0000.000
74A75ASP-1-0.867-0.93331.4679.1739.1730.0000.0000.0000.000
75A76SER0-0.120-0.08830.381-0.186-0.1860.0000.0000.0000.000
76A77VAL00.0270.02623.518-0.035-0.0350.0000.0000.0000.000
77A78ASP-1-0.868-0.92425.74311.31411.3140.0000.0000.0000.000
78A79VAL00.0190.01519.8620.1230.1230.0000.0000.0000.000
79A80THR0-0.012-0.01118.9550.1470.1470.0000.0000.0000.000
80A81VAL0-0.024-0.00113.7740.2500.2500.0000.0000.0000.000
81A82ASP-1-0.810-0.91514.59820.71820.7180.0000.0000.0000.000
82A83GLY0-0.0030.00212.2140.9250.9250.0000.0000.0000.000
83A84ALA0-0.032-0.01112.899-2.170-2.1700.0000.0000.0000.000
84A85ASP-1-0.869-0.94113.34224.03124.0310.0000.0000.0000.000
85A86GLU-1-0.800-0.90614.57617.64517.6450.0000.0000.0000.000
86A87VAL0-0.026-0.02115.805-0.632-0.6320.0000.0000.0000.000
87A88ASP-1-0.780-0.88718.09814.14114.1410.0000.0000.0000.000
88A89PRO0-0.004-0.01120.9110.1200.1200.0000.0000.0000.000
89A90ASN0-0.097-0.04522.224-0.601-0.6010.0000.0000.0000.000
90A91PHE0-0.058-0.02520.317-0.261-0.2610.0000.0000.0000.000
91A92ASN00.0060.00722.742-0.344-0.3440.0000.0000.0000.000
92A93GLY00.0450.01220.1230.6780.6780.0000.0000.0000.000
93A94ILE0-0.051-0.00319.218-1.017-1.0170.0000.0000.0000.000
94A95LYS10.8210.91416.442-17.791-17.7910.0000.0000.0000.000
95A96GLY00.1110.04317.845-0.987-0.9870.0000.0000.0000.000
96A97GLY00.0160.01016.382-0.679-0.6790.0000.0000.0000.000
97A98GLY0-0.080-0.04615.6040.0730.0730.0000.0000.0000.000
98A99GLY0-0.051-0.02816.350-0.360-0.3600.0000.0000.0000.000
99A100ALA00.0010.00718.329-0.884-0.8840.0000.0000.0000.000
100A101LEU00.0330.01620.251-0.208-0.2080.0000.0000.0000.000
101A102LEU00.0210.03221.946-0.207-0.2070.0000.0000.0000.000
102A103MET00.015-0.00522.619-0.336-0.3360.0000.0000.0000.000
103A104GLU-1-0.864-0.94817.35918.17718.1770.0000.0000.0000.000
104A105LYS10.8200.90621.394-12.428-12.4280.0000.0000.0000.000
105A106ILE0-0.0200.00524.462-0.363-0.3630.0000.0000.0000.000
106A107VAL00.0200.00321.985-0.279-0.2790.0000.0000.0000.000
107A108GLY0-0.0060.00623.211-0.145-0.1450.0000.0000.0000.000
108A109THR0-0.054-0.03523.849-0.331-0.3310.0000.0000.0000.000
109A110LEU0-0.039-0.00127.179-0.363-0.3630.0000.0000.0000.000
110A111THR0-0.047-0.03622.8790.1370.1370.0000.0000.0000.000
111A112LYS10.8590.95526.073-10.799-10.7990.0000.0000.0000.000
112A113ASP-1-0.876-0.92122.89714.13714.1370.0000.0000.0000.000
113A114TYR00.023-0.00719.7170.7060.7060.0000.0000.0000.000
114A115ILE00.0130.00316.0470.0710.0710.0000.0000.0000.000
115A116TRP00.0150.00915.4240.6510.6510.0000.0000.0000.000
116A117VAL0-0.011-0.00110.074-0.007-0.0070.0000.0000.0000.000
117A118VAL0-0.006-0.0019.7812.0792.0790.0000.0000.0000.000
118A119ASP-1-0.780-0.8896.17341.52541.5250.0000.0000.0000.000
119A120GLU-1-0.691-0.8518.10519.60419.6040.0000.0000.0000.000
120A121SER0-0.111-0.0698.598-2.516-2.5160.0000.0000.0000.000
121A122LYS10.8640.9358.393-35.696-35.6960.0000.0000.0000.000
122A123MET0-0.0380.01112.882-1.319-1.3190.0000.0000.0000.000
123A124VAL0-0.020-0.00915.0160.0600.0600.0000.0000.0000.000
124A125ASP-1-0.883-0.95017.98513.83713.8370.0000.0000.0000.000
125A126THR0-0.101-0.06121.386-0.826-0.8260.0000.0000.0000.000
126A127LEU00.0210.02620.6110.4040.4040.0000.0000.0000.000
127A128GLY0-0.020-0.03621.449-0.854-0.8540.0000.0000.0000.000
128A129ALA0-0.0260.00919.191-0.308-0.3080.0000.0000.0000.000
129A130PHE0-0.052-0.01414.6260.3790.3790.0000.0000.0000.000
130A131ARG10.9350.95419.092-14.986-14.9860.0000.0000.0000.000
131A132LEU00.0440.02220.9250.6240.6240.0000.0000.0000.000
132A133PRO00.0020.01620.502-0.657-0.6570.0000.0000.0000.000
133A134VAL00.0140.00023.654-0.228-0.2280.0000.0000.0000.000
134A135GLU-1-0.755-0.83626.00812.33512.3350.0000.0000.0000.000
135A136VAL0-0.043-0.03727.976-0.436-0.4360.0000.0000.0000.000
136A137VAL00.0610.02431.5780.0640.0640.0000.0000.0000.000
137A138GLN0-0.012-0.01332.771-0.262-0.2620.0000.0000.0000.000
138A139TYR0-0.047-0.02635.119-0.152-0.1520.0000.0000.0000.000
139A140GLY00.0300.01438.837-0.045-0.0450.0000.0000.0000.000
140A141ALA00.0640.03733.5850.0080.0080.0000.0000.0000.000
141A142GLU-1-0.850-0.93235.1949.0369.0360.0000.0000.0000.000
142A143ARG10.8210.90636.820-7.968-7.9680.0000.0000.0000.000
143A144LEU00.0640.04634.152-0.122-0.1220.0000.0000.0000.000
144A145PHE00.0570.03830.5120.0460.0460.0000.0000.0000.000
145A146ARG10.9590.97634.552-8.217-8.2170.0000.0000.0000.000
146A147GLU-1-0.918-0.93237.6238.2918.2910.0000.0000.0000.000
147A148PHE00.0780.01631.691-0.059-0.0590.0000.0000.0000.000
148A149GLU-1-0.920-0.96834.2879.2559.2550.0000.0000.0000.000
149A150LYS10.8520.92935.207-8.008-8.0080.0000.0000.0000.000
150A151LYS10.8020.89135.890-8.733-8.7330.0000.0000.0000.000
151A152GLY00.0010.01434.7620.0490.0490.0000.0000.0000.000
152A153TYR0-0.025-0.03130.5530.1750.1750.0000.0000.0000.000
153A154LYS10.9520.98128.102-10.991-10.9910.0000.0000.0000.000
154A155PRO00.0290.03128.1750.4670.4670.0000.0000.0000.000
155A156SER0-0.003-0.00625.597-0.077-0.0770.0000.0000.0000.000
156A157PHE0-0.053-0.03126.8830.0840.0840.0000.0000.0000.000
157A158ARG10.7830.85919.248-15.927-15.9270.0000.0000.0000.000
158A159GLU-1-0.942-0.97423.78512.68412.6840.0000.0000.0000.000
159A160TYR00.0120.02118.2290.6420.6420.0000.0000.0000.000
160A161ASP-1-0.921-0.94822.27014.30314.3030.0000.0000.0000.000
161A162GLY0-0.006-0.00224.606-0.569-0.5690.0000.0000.0000.000
162A163VAL0-0.070-0.04026.506-0.613-0.6130.0000.0000.0000.000
163A164ARG10.8170.92426.433-9.776-9.7760.0000.0000.0000.000
164A165PHE00.003-0.02321.869-0.097-0.0970.0000.0000.0000.000
165A166VAL0-0.042-0.01925.797-0.404-0.4040.0000.0000.0000.000
166A167THR0-0.029-0.02124.8030.2200.2200.0000.0000.0000.000
167A168ASP-1-0.811-0.91323.12813.48913.4890.0000.0000.0000.000
168A169MET0-0.097-0.05326.151-0.617-0.6170.0000.0000.0000.000
169A170LYS10.8550.93528.871-11.161-11.1610.0000.0000.0000.000
170A171ASN00.001-0.00129.118-0.868-0.8680.0000.0000.0000.000
171A172PHE0-0.011-0.00528.4330.1410.1410.0000.0000.0000.000
172A173ILE00.0620.03322.856-0.024-0.0240.0000.0000.0000.000
173A174ILE0-0.083-0.03726.797-0.147-0.1470.0000.0000.0000.000
174A175ASP-1-0.773-0.87422.39014.91714.9170.0000.0000.0000.000
175A176LEU00.005-0.00425.118-0.479-0.4790.0000.0000.0000.000
176A177ASP-1-0.959-0.97524.80313.68113.6810.0000.0000.0000.000
177A178LEU00.006-0.02025.645-0.537-0.5370.0000.0000.0000.000
178A179GLY0-0.0190.01624.873-0.436-0.4360.0000.0000.0000.000
179A180SER0-0.050-0.03224.6420.4480.4480.0000.0000.0000.000
180A181ILE0-0.006-0.01324.789-0.503-0.5030.0000.0000.0000.000
181A182PRO00.0090.01327.4230.1760.1760.0000.0000.0000.000
182A183ASP-1-0.882-0.95229.1349.8339.8330.0000.0000.0000.000
183A184PRO00.0420.01226.558-0.210-0.2100.0000.0000.0000.000
184A185ILE0-0.0180.01128.845-0.013-0.0130.0000.0000.0000.000
185A186ALA0-0.010-0.01031.407-0.190-0.1900.0000.0000.0000.000
186A187PHE00.010-0.00129.718-0.198-0.1980.0000.0000.0000.000
187A188GLY00.0190.00630.433-0.043-0.0430.0000.0000.0000.000
188A189ASN00.0300.01930.962-0.039-0.0390.0000.0000.0000.000
189A190MET0-0.068-0.01933.651-0.342-0.3420.0000.0000.0000.000
190A191LEU0-0.060-0.04529.528-0.164-0.1640.0000.0000.0000.000
191A192ASP-1-0.832-0.90632.31310.15510.1550.0000.0000.0000.000
192A193HIS0-0.075-0.03034.516-0.302-0.3020.0000.0000.0000.000
193A194GLN0-0.115-0.04635.426-0.317-0.3170.0000.0000.0000.000
194A195VAL00.012-0.00436.6520.1510.1510.0000.0000.0000.000
195A196GLY00.0280.00336.802-0.022-0.0220.0000.0000.0000.000
196A197VAL0-0.024-0.00931.1420.2610.2610.0000.0000.0000.000
197A198VAL0-0.081-0.03930.235-0.240-0.2400.0000.0000.0000.000
198A199GLU-1-0.788-0.86326.72511.44711.4470.0000.0000.0000.000
199A200HIS0-0.011-0.03426.7470.5450.5450.0000.0000.0000.000
200A201GLY00.0600.01722.9390.0990.0990.0000.0000.0000.000
201A202LEU0-0.0280.00122.5740.6650.6650.0000.0000.0000.000
202A203PHE0-0.055-0.03821.895-0.426-0.4260.0000.0000.0000.000
203A204ASN00.047-0.00724.0790.7470.7470.0000.0000.0000.000
204A205GLY00.0460.02826.366-0.330-0.3300.0000.0000.0000.000
205A206MET0-0.066-0.02524.336-0.194-0.1940.0000.0000.0000.000
206A207VAL0-0.018-0.00519.198-0.242-0.2420.0000.0000.0000.000
207A208ASN00.0330.01822.377-0.389-0.3890.0000.0000.0000.000
208A209ARG10.7990.88118.270-14.924-14.9240.0000.0000.0000.000
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