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: R9R98

Calculation Name: 1L1J-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1L1J

Chain ID: A

ChEMBL ID:

UniProt ID: Q9WZ41

Base Structure: X-ray

Registration Date: 2023-09-20

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 228
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2712629.768699
FMO2-HF: Nuclear repulsion 2627794.096497
FMO2-HF: Total energy -84835.672202
FMO2-MP2: Total energy -85089.134711


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:24:ASP)


Summations of interaction energy for fragment #1(A:24:ASP)
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.
118.829119.90710.218-6.074-5.222-0.04
Interaction energy analysis for fragmet #1(A:24:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.907 / q_NPA : -0.948
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].
3A26GLU-1-0.928-0.9601.86335.91336.33610.194-5.814-4.803-0.041
4A27SER0-0.011-0.0102.878-3.571-2.9830.025-0.228-0.3850.001
5A28PRO00.0300.0075.5710.4720.4720.0000.0000.0000.000
6A29ILE00.0290.0108.745-0.206-0.2060.0000.0000.0000.000
7A30VAL00.0290.0215.503-1.385-1.3850.0000.0000.0000.000
8A31ASN0-0.020-0.0064.7520.6760.743-0.001-0.032-0.0340.000
9A32VAL0-0.0170.0038.230-1.036-1.0360.0000.0000.0000.000
10A33VAL00.003-0.00710.541-1.306-1.3060.0000.0000.0000.000
11A34GLU-1-0.901-0.9638.01627.96727.9670.0000.0000.0000.000
12A35ALA0-0.074-0.02510.897-0.995-0.9950.0000.0000.0000.000
13A36CYS0-0.032-0.02013.089-1.623-1.6230.0000.0000.0000.000
14A37ALA00.0340.01414.700-1.209-1.2090.0000.0000.0000.000
15A38PRO0-0.016-0.01515.216-1.061-1.0610.0000.0000.0000.000
16A39ALA0-0.0070.01118.200-0.726-0.7260.0000.0000.0000.000
17A40VAL0-0.031-0.00919.571-0.868-0.8680.0000.0000.0000.000
18A41VAL0-0.047-0.02021.6840.2760.2760.0000.0000.0000.000
19A42LYS10.8060.90324.497-10.617-10.6170.0000.0000.0000.000
20A43ILE0-0.002-0.01826.879-0.150-0.1500.0000.0000.0000.000
21A44ASP-1-0.799-0.89330.5229.7349.7340.0000.0000.0000.000
22A45VAL00.0160.02433.390-0.115-0.1150.0000.0000.0000.000
23A46VAL00.0220.01137.175-0.065-0.0650.0000.0000.0000.000
24A47LYS10.8950.94739.743-7.041-7.0410.0000.0000.0000.000
25A48THR0-0.030-0.03242.550-0.148-0.1480.0000.0000.0000.000
26A49VAL0-0.040-0.00545.6070.0620.0620.0000.0000.0000.000
27A50LYS10.8170.91440.911-7.302-7.3020.0000.0000.0000.000
28A51THR0-0.078-0.06843.5720.0220.0220.0000.0000.0000.000
29A52SER0-0.0080.01143.090-0.156-0.1560.0000.0000.0000.000
30A53PHE00.0840.04338.526-0.075-0.0750.0000.0000.0000.000
31A54PHE0-0.046-0.00438.9050.1910.1910.0000.0000.0000.000
32A55ASP-1-0.790-0.90237.9757.6317.6310.0000.0000.0000.000
33A56PRO0-0.020-0.02438.3270.1930.1930.0000.0000.0000.000
34A57TYR0-0.048-0.04632.9880.1850.1850.0000.0000.0000.000
35A58PHE00.003-0.00932.0420.2680.2680.0000.0000.0000.000
36A59GLU-1-0.892-0.94133.8958.0958.0950.0000.0000.0000.000
37A60GLN00.0170.01135.2200.2210.2210.0000.0000.0000.000
38A61PHE00.0150.00027.0330.1510.1510.0000.0000.0000.000
39A62PHE00.000-0.01628.1580.2520.2520.0000.0000.0000.000
40A63LYS10.7900.89431.357-7.762-7.7620.0000.0000.0000.000
41A64LYS10.8180.92131.210-9.322-9.3220.0000.0000.0000.000
42A65TRP0-0.038-0.02827.4810.0850.0850.0000.0000.0000.000
43A66PHE00.0300.02923.6570.3530.3530.0000.0000.0000.000
44A67GLY00.0050.00628.465-0.323-0.3230.0000.0000.0000.000
45A68GLU-1-0.880-0.95724.72411.48911.4890.0000.0000.0000.000
46A69LEU0-0.045-0.01029.057-0.081-0.0810.0000.0000.0000.000
47A70PRO00.0030.00032.077-0.201-0.2010.0000.0000.0000.000
48A71PRO00.007-0.00834.994-0.122-0.1220.0000.0000.0000.000
49A72GLY0-0.022-0.00138.104-0.231-0.2310.0000.0000.0000.000
50A73PHE00.0240.01133.633-0.139-0.1390.0000.0000.0000.000
51A74GLU-1-0.742-0.87337.6337.7027.7020.0000.0000.0000.000
52A75ARG10.8720.93340.202-6.846-6.8460.0000.0000.0000.000
53A76GLN0-0.022-0.02539.180-0.141-0.1410.0000.0000.0000.000
54A77VAL0-0.0190.00934.9720.0090.0090.0000.0000.0000.000
55A78ALA0-0.027-0.02138.426-0.126-0.1260.0000.0000.0000.000
56A79SER0-0.031-0.03235.133-0.033-0.0330.0000.0000.0000.000
57A80LEU0-0.023-0.01129.6120.0110.0110.0000.0000.0000.000
58A81GLY00.0380.02129.007-0.112-0.1120.0000.0000.0000.000
59A82SER0-0.022-0.00224.5570.4510.4510.0000.0000.0000.000
60A83GLY00.0510.03525.855-0.496-0.4960.0000.0000.0000.000
61A84PHE0-0.017-0.01223.3980.5490.5490.0000.0000.0000.000
62A85ILE00.0010.01124.323-0.579-0.5790.0000.0000.0000.000
63A86PHE0-0.014-0.01524.4910.4620.4620.0000.0000.0000.000
64A87ASP-1-0.819-0.90626.73810.32010.3200.0000.0000.0000.000
65A88PRO00.0130.01426.168-0.078-0.0780.0000.0000.0000.000
66A89GLU-1-0.834-0.91527.75810.03510.0350.0000.0000.0000.000
67A90GLY00.0020.01729.055-0.250-0.2500.0000.0000.0000.000
68A91TYR0-0.0110.00230.100-0.369-0.3690.0000.0000.0000.000
69A92ILE0-0.007-0.01427.7290.4300.4300.0000.0000.0000.000
70A93LEU0-0.0020.00728.345-0.443-0.4430.0000.0000.0000.000
71A94THR00.003-0.02228.5330.2750.2750.0000.0000.0000.000
72A95ASN0-0.0020.00430.183-0.001-0.0010.0000.0000.0000.000
73A96TYR0-0.069-0.02932.4610.0060.0060.0000.0000.0000.000
74A97HIS0-0.026-0.05532.3090.0650.0650.0000.0000.0000.000
75A98VAL0-0.0160.01130.753-0.061-0.0610.0000.0000.0000.000
76A99VAL0-0.035-0.00533.8550.0220.0220.0000.0000.0000.000
77A100GLY00.0220.01236.519-0.209-0.2090.0000.0000.0000.000
78A101GLY0-0.0030.00039.6290.0230.0230.0000.0000.0000.000
79A102ALA0-0.031-0.01339.513-0.120-0.1200.0000.0000.0000.000
80A103ASP-1-0.809-0.89741.4717.1867.1860.0000.0000.0000.000
81A104ASN00.005-0.01338.328-0.006-0.0060.0000.0000.0000.000
82A105ILE00.0360.02134.5420.0410.0410.0000.0000.0000.000
83A106THR0-0.051-0.01733.217-0.066-0.0660.0000.0000.0000.000
84A107VAL00.0560.02828.4820.1200.1200.0000.0000.0000.000
85A108THR0-0.087-0.05425.885-0.218-0.2180.0000.0000.0000.000
86A109MET00.0240.03123.192-0.032-0.0320.0000.0000.0000.000
87A110LEU00.0410.02316.966-0.106-0.1060.0000.0000.0000.000
88A111ASP-1-0.858-0.88620.44113.67913.6790.0000.0000.0000.000
89A112GLY0-0.009-0.00421.806-0.233-0.2330.0000.0000.0000.000
90A113SER0-0.099-0.06924.813-0.782-0.7820.0000.0000.0000.000
91A114LYS10.9110.93727.417-10.219-10.2190.0000.0000.0000.000
92A115TYR00.005-0.01027.365-0.284-0.2840.0000.0000.0000.000
93A116ASP-1-0.842-0.90232.6818.5618.5610.0000.0000.0000.000
94A117ALA0-0.043-0.02233.5240.0180.0180.0000.0000.0000.000
95A118GLU-1-0.964-0.97235.4437.6267.6260.0000.0000.0000.000
96A119TYR00.030-0.00337.1350.2330.2330.0000.0000.0000.000
97A120ILE0-0.026-0.00736.848-0.191-0.1910.0000.0000.0000.000
98A121GLY00.0240.00938.498-0.223-0.2230.0000.0000.0000.000
99A122GLY00.003-0.01237.9090.2750.2750.0000.0000.0000.000
100A123ASP-1-0.903-0.94238.4557.1747.1740.0000.0000.0000.000
101A124GLU-1-0.877-0.93638.6647.2297.2290.0000.0000.0000.000
102A125GLU-1-0.876-0.91440.0327.1007.1000.0000.0000.0000.000
103A126LEU0-0.095-0.05836.9940.1030.1030.0000.0000.0000.000
104A127ASP-1-0.758-0.87733.9178.9678.9670.0000.0000.0000.000
105A128ILE0-0.0070.00933.1270.3350.3350.0000.0000.0000.000
106A129ALA00.0170.00233.678-0.315-0.3150.0000.0000.0000.000
107A130VAL0-0.018-0.00333.1450.3510.3510.0000.0000.0000.000
108A131ILE0-0.005-0.00332.530-0.284-0.2840.0000.0000.0000.000
109A132LYS10.8490.92533.336-8.988-8.9880.0000.0000.0000.000
110A133ILE00.0280.01129.948-0.185-0.1850.0000.0000.0000.000
111A134LYS10.8070.87632.968-8.546-8.5460.0000.0000.0000.000
112A135ALA00.0410.02231.3160.1610.1610.0000.0000.0000.000
113A136SER0-0.060-0.04532.237-0.216-0.2160.0000.0000.0000.000
114A137ASP-1-0.899-0.93630.53010.10210.1020.0000.0000.0000.000
115A138LYS10.8790.94426.674-11.360-11.3600.0000.0000.0000.000
116A139LYS10.8490.91427.622-10.324-10.3240.0000.0000.0000.000
117A140PHE00.0000.00425.1930.3240.3240.0000.0000.0000.000
118A141PRO0-0.0110.00120.288-0.066-0.0660.0000.0000.0000.000
119A142TYR0-0.090-0.07421.842-0.390-0.3900.0000.0000.0000.000
120A143LEU0-0.0110.00618.8040.6430.6430.0000.0000.0000.000
121A144GLU-1-0.845-0.90721.78812.54512.5450.0000.0000.0000.000
122A145PHE0-0.050-0.03023.0680.2610.2610.0000.0000.0000.000
123A146GLY00.0930.06324.1330.0330.0330.0000.0000.0000.000
124A147ASP-1-0.875-0.95824.8839.3649.3640.0000.0000.0000.000
125A148SER00.0460.01327.551-0.009-0.0090.0000.0000.0000.000
126A149ASP-1-0.904-0.92528.7838.7298.7290.0000.0000.0000.000
127A150LYS10.8410.91827.504-10.001-10.0010.0000.0000.0000.000
128A151VAL00.0070.02024.7490.1600.1600.0000.0000.0000.000
129A152LYS10.8270.91924.270-11.197-11.1970.0000.0000.0000.000
130A153ILE00.0000.00224.5680.3050.3050.0000.0000.0000.000
131A154GLY0-0.022-0.01323.728-0.163-0.1630.0000.0000.0000.000
132A155GLU-1-0.862-0.92620.38312.52112.5210.0000.0000.0000.000
133A156TRP0-0.021-0.02315.818-0.105-0.1050.0000.0000.0000.000
134A157ALA00.0070.00217.9010.0980.0980.0000.0000.0000.000
135A158ILE0-0.027-0.02013.0360.2530.2530.0000.0000.0000.000
136A159ALA00.0200.02716.946-0.225-0.2250.0000.0000.0000.000
137A160ILE0-0.012-0.00815.2390.5740.5740.0000.0000.0000.000
138A161GLY00.0350.00219.013-0.765-0.7650.0000.0000.0000.000
139A162ASN0-0.018-0.02920.1940.6870.6870.0000.0000.0000.000
140A163PRO00.0110.02522.436-0.325-0.3250.0000.0000.0000.000
141A164LEU00.0300.01122.403-0.480-0.4800.0000.0000.0000.000
142A165GLY0-0.045-0.01324.223-0.274-0.2740.0000.0000.0000.000
143A166PHE0-0.016-0.01921.3240.3910.3910.0000.0000.0000.000
144A167GLN0-0.025-0.02116.0900.1320.1320.0000.0000.0000.000
145A168HIS00.0360.03712.790-1.784-1.7840.0000.0000.0000.000
146A169THR0-0.038-0.02217.2440.5380.5380.0000.0000.0000.000
147A170VAL00.010-0.01113.8320.0510.0510.0000.0000.0000.000
148A171THR0-0.084-0.04616.899-0.062-0.0620.0000.0000.0000.000
149A172VAL00.001-0.00913.4130.1970.1970.0000.0000.0000.000
150A173GLY00.0060.00116.831-0.371-0.3710.0000.0000.0000.000
151A174VAL0-0.031-0.00618.4150.5340.5340.0000.0000.0000.000
152A175VAL00.0170.01821.099-0.400-0.4000.0000.0000.0000.000
153A176SER0-0.006-0.02524.057-0.184-0.1840.0000.0000.0000.000
154A177ALA0-0.060-0.03426.837-0.363-0.3630.0000.0000.0000.000
155A178THR00.0400.01428.9210.1650.1650.0000.0000.0000.000
156A179ASN0-0.019-0.01031.295-0.241-0.2410.0000.0000.0000.000
157A180ARG10.8710.94332.569-8.597-8.5970.0000.0000.0000.000
158A181ARG10.8950.96435.090-6.993-6.9930.0000.0000.0000.000
159A182ILE0-0.016-0.01334.4330.0210.0210.0000.0000.0000.000
160A183PRO0-0.028-0.00238.615-0.025-0.0250.0000.0000.0000.000
161A184LYS10.8880.92540.295-6.952-6.9520.0000.0000.0000.000
162A185PRO0-0.010-0.00438.842-0.181-0.1810.0000.0000.0000.000
163A186ASP-1-0.869-0.90042.0276.6586.6580.0000.0000.0000.000
164A187GLY0-0.024-0.00844.049-0.149-0.1490.0000.0000.0000.000
165A188SER0-0.066-0.06345.206-0.112-0.1120.0000.0000.0000.000
166A189GLY00.007-0.00844.936-0.062-0.0620.0000.0000.0000.000
167A190TYR0-0.053-0.03841.4200.0210.0210.0000.0000.0000.000
168A191TYR00.1130.05636.261-0.049-0.0490.0000.0000.0000.000
169A192VAL0-0.027-0.04637.603-0.105-0.1050.0000.0000.0000.000
170A193GLY00.0460.02635.8430.1090.1090.0000.0000.0000.000
171A194LEU0-0.0330.00231.5840.1870.1870.0000.0000.0000.000
172A195ILE00.0070.00125.923-0.153-0.1530.0000.0000.0000.000
173A196GLN00.0230.01028.364-0.376-0.3760.0000.0000.0000.000
174A197THR0-0.004-0.01122.9620.1580.1580.0000.0000.0000.000
175A198ASP-1-0.814-0.88321.94511.73711.7370.0000.0000.0000.000
176A199ALA00.0300.02520.1880.0960.0960.0000.0000.0000.000
177A200ALA00.0050.00121.629-0.398-0.3980.0000.0000.0000.000
178A201ILE0-0.0280.01722.9560.4040.4040.0000.0000.0000.000
179A202ASN00.0280.01524.150-0.336-0.3360.0000.0000.0000.000
180A203PRO00.0600.02127.0470.2860.2860.0000.0000.0000.000
181A204GLY00.0120.01425.2590.0510.0510.0000.0000.0000.000
182A205ASN0-0.005-0.01921.4690.0600.0600.0000.0000.0000.000
183A206SER00.0250.01424.1550.0770.0770.0000.0000.0000.000
184A207GLY00.0040.00927.4510.0490.0490.0000.0000.0000.000
185A208GLY00.0250.01223.5530.0730.0730.0000.0000.0000.000
186A209PRO0-0.027-0.00120.367-0.402-0.4020.0000.0000.0000.000
187A210LEU00.0280.00720.7470.3870.3870.0000.0000.0000.000
188A211LEU0-0.005-0.01316.375-0.355-0.3550.0000.0000.0000.000
189A212ASN00.003-0.01018.268-0.141-0.1410.0000.0000.0000.000
190A213ILE0-0.004-0.02113.3750.6840.6840.0000.0000.0000.000
191A214HIS0-0.012-0.01313.8561.3381.3380.0000.0000.0000.000
192A215GLY00.0140.00916.1130.2720.2720.0000.0000.0000.000
193A216GLU-1-0.885-0.92516.62312.78712.7870.0000.0000.0000.000
194A217VAL00.0160.00820.3210.1160.1160.0000.0000.0000.000
195A218ILE00.007-0.00521.965-0.548-0.5480.0000.0000.0000.000
196A219GLY0-0.001-0.02524.219-0.588-0.5880.0000.0000.0000.000
197A220ILE00.0080.01924.9160.4480.4480.0000.0000.0000.000
198A221ASN0-0.030-0.00622.313-0.401-0.4010.0000.0000.0000.000
199A222THR0-0.020-0.01626.497-0.190-0.1900.0000.0000.0000.000
200A223ALA00.009-0.00129.359-0.078-0.0780.0000.0000.0000.000
201A224ILE00.0350.02730.954-0.176-0.1760.0000.0000.0000.000
202A225VAL0-0.082-0.01732.314-0.311-0.3110.0000.0000.0000.000
203A226ASN0-0.0110.00432.3600.0490.0490.0000.0000.0000.000
204A227PRO00.0100.00930.7860.1820.1820.0000.0000.0000.000
205A228GLN0-0.033-0.02633.652-0.316-0.3160.0000.0000.0000.000
206A229GLU-1-0.893-0.93234.0408.0098.0090.0000.0000.0000.000
207A230ALA0-0.0270.00733.4890.0270.0270.0000.0000.0000.000
208A231VAL00.001-0.01628.1650.2270.2270.0000.0000.0000.000
209A232ASN0-0.098-0.06723.733-0.320-0.3200.0000.0000.0000.000
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