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: Z636N

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 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 228
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2714817.920612
FMO2-HF: Nuclear repulsion 2629983.753138
FMO2-HF: Total energy -84834.167474
FMO2-MP2: Total energy -85087.841095


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.
118.89123.3217.327-6.104-5.653-0.034
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 : -0.967 / q_NPA : -0.978
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-1-0.917-0.9561.95434.83738.3427.209-5.683-5.031-0.036
4A27SER0-0.015-0.0092.501-4.034-3.1280.119-0.419-0.6060.002
5A28PRO00.0330.0165.1480.4010.421-0.001-0.002-0.0160.000
6A29ILE00.0330.0168.4460.1130.1130.0000.0000.0000.000
7A30VAL00.0160.0085.287-1.382-1.3820.0000.0000.0000.000
8A31ASN0-0.003-0.0085.1930.1540.1540.0000.0000.0000.000
9A32VAL00.0020.0078.428-1.015-1.0150.0000.0000.0000.000
10A33VAL00.0170.00810.968-1.132-1.1320.0000.0000.0000.000
11A34GLU-1-0.918-0.9548.00628.41528.4150.0000.0000.0000.000
12A35ALA0-0.077-0.03111.154-0.839-0.8390.0000.0000.0000.000
13A36CYS0-0.043-0.03313.643-1.508-1.5080.0000.0000.0000.000
14A37ALA00.0410.01514.974-1.130-1.1300.0000.0000.0000.000
15A38PRO0-0.029-0.01815.583-1.051-1.0510.0000.0000.0000.000
16A39ALA0-0.0060.00718.539-0.690-0.6900.0000.0000.0000.000
17A40VAL0-0.044-0.02019.707-0.838-0.8380.0000.0000.0000.000
18A41VAL0-0.040-0.00622.0150.1910.1910.0000.0000.0000.000
19A42LYS10.7920.90325.007-10.473-10.4730.0000.0000.0000.000
20A43ILE0-0.010-0.03227.322-0.176-0.1760.0000.0000.0000.000
21A44ASP-1-0.793-0.88430.9729.6279.6270.0000.0000.0000.000
22A45VAL00.0010.01133.602-0.104-0.1040.0000.0000.0000.000
23A46VAL00.0140.00637.295-0.082-0.0820.0000.0000.0000.000
24A47LYS10.9350.98140.033-7.011-7.0110.0000.0000.0000.000
25A48THR0-0.045-0.04042.992-0.078-0.0780.0000.0000.0000.000
26A49VAL0-0.014-0.00845.4840.0960.0960.0000.0000.0000.000
27A50LYS10.7850.92841.023-7.279-7.2790.0000.0000.0000.000
28A51THR0-0.068-0.06143.7260.0240.0240.0000.0000.0000.000
29A52SER00.0080.01843.164-0.166-0.1660.0000.0000.0000.000
30A53PHE00.0490.04338.502-0.089-0.0890.0000.0000.0000.000
31A54PHE0-0.057-0.02638.7990.1900.1900.0000.0000.0000.000
32A55ASP-1-0.800-0.91338.3547.5547.5540.0000.0000.0000.000
33A56PRO0-0.007-0.02438.3530.2120.2120.0000.0000.0000.000
34A57TYR0-0.0310.01032.7250.0400.0400.0000.0000.0000.000
35A58PHE00.026-0.00832.2470.2470.2470.0000.0000.0000.000
36A59GLU-1-0.950-0.97433.9028.0838.0830.0000.0000.0000.000
37A60GLN00.0320.01535.6650.1520.1520.0000.0000.0000.000
38A61PHE00.000-0.00226.7630.1310.1310.0000.0000.0000.000
39A62PHE00.017-0.00828.1700.2320.2320.0000.0000.0000.000
40A63LYS10.8290.92131.550-7.710-7.7100.0000.0000.0000.000
41A64LYS10.8750.95431.750-9.146-9.1460.0000.0000.0000.000
42A65TRP0-0.057-0.04627.7290.1010.1010.0000.0000.0000.000
43A66PHE00.0250.02324.0040.3330.3330.0000.0000.0000.000
44A67GLY0-0.0110.01628.825-0.263-0.2630.0000.0000.0000.000
45A68GLU-1-0.882-0.96224.78911.57411.5740.0000.0000.0000.000
46A69LEU0-0.042-0.02329.131-0.046-0.0460.0000.0000.0000.000
47A70PRO0-0.042-0.02332.111-0.236-0.2360.0000.0000.0000.000
48A71PRO00.016-0.00135.002-0.112-0.1120.0000.0000.0000.000
49A72GLY0-0.037-0.01038.268-0.206-0.2060.0000.0000.0000.000
50A73PHE00.0560.02533.421-0.065-0.0650.0000.0000.0000.000
51A74GLU-1-0.753-0.86937.4847.5727.5720.0000.0000.0000.000
52A75ARG10.9040.94839.987-6.755-6.7550.0000.0000.0000.000
53A76GLN0-0.037-0.03539.246-0.144-0.1440.0000.0000.0000.000
54A77VAL0-0.025-0.00334.9040.0260.0260.0000.0000.0000.000
55A78ALA0-0.033-0.01638.325-0.155-0.1550.0000.0000.0000.000
56A79SER0-0.033-0.02135.3640.0410.0410.0000.0000.0000.000
57A80LEU0-0.0080.00029.4700.0400.0400.0000.0000.0000.000
58A81GLY00.0500.02129.232-0.071-0.0710.0000.0000.0000.000
59A82SER0-0.042-0.02324.8180.5210.5210.0000.0000.0000.000
60A83GLY00.0850.05525.820-0.505-0.5050.0000.0000.0000.000
61A84PHE0-0.029-0.01823.7630.4990.4990.0000.0000.0000.000
62A85ILE00.0110.01224.885-0.534-0.5340.0000.0000.0000.000
63A86PHE00.001-0.01425.0400.4380.4380.0000.0000.0000.000
64A87ASP-1-0.802-0.90527.23110.29610.2960.0000.0000.0000.000
65A88PRO0-0.0090.00027.056-0.202-0.2020.0000.0000.0000.000
66A89GLU-1-0.845-0.91328.4449.8919.8910.0000.0000.0000.000
67A90GLY00.0020.00229.872-0.266-0.2660.0000.0000.0000.000
68A91TYR0-0.0110.00330.886-0.302-0.3020.0000.0000.0000.000
69A92ILE0-0.022-0.00928.1460.4080.4080.0000.0000.0000.000
70A93LEU00.0130.03028.631-0.449-0.4490.0000.0000.0000.000
71A94THR00.010-0.02828.8800.2530.2530.0000.0000.0000.000
72A95ASN00.0240.01630.3500.1140.1140.0000.0000.0000.000
73A96TYR0-0.065-0.01532.506-0.041-0.0410.0000.0000.0000.000
74A97HIS0-0.031-0.04732.4260.0450.0450.0000.0000.0000.000
75A98VAL0-0.035-0.00231.065-0.051-0.0510.0000.0000.0000.000
76A99VAL0-0.0020.00733.795-0.137-0.1370.0000.0000.0000.000
77A100GLY00.0510.02036.270-0.209-0.2090.0000.0000.0000.000
78A101GLY0-0.015-0.01539.3070.0000.0000.0000.0000.0000.000
79A102ALA0-0.046-0.01439.371-0.093-0.0930.0000.0000.0000.000
80A103ASP-1-0.794-0.89841.4387.0617.0610.0000.0000.0000.000
81A104ASN00.009-0.03239.2030.0860.0860.0000.0000.0000.000
82A105ILE00.0300.01834.8880.0880.0880.0000.0000.0000.000
83A106THR0-0.035-0.01033.184-0.070-0.0700.0000.0000.0000.000
84A107VAL00.0120.01428.9640.1500.1500.0000.0000.0000.000
85A108THR0-0.047-0.03126.428-0.131-0.1310.0000.0000.0000.000
86A109MET00.0220.01823.5250.0010.0010.0000.0000.0000.000
87A110LEU00.0530.02817.273-0.041-0.0410.0000.0000.0000.000
88A111ASP-1-0.879-0.88821.07013.22113.2210.0000.0000.0000.000
89A112GLY00.0030.00322.161-0.118-0.1180.0000.0000.0000.000
90A113SER0-0.111-0.07525.101-0.717-0.7170.0000.0000.0000.000
91A114LYS10.9250.95127.872-10.001-10.0010.0000.0000.0000.000
92A115TYR0-0.007-0.02327.757-0.279-0.2790.0000.0000.0000.000
93A116ASP-1-0.854-0.92732.8918.4408.4400.0000.0000.0000.000
94A117ALA0-0.026-0.01533.9140.0520.0520.0000.0000.0000.000
95A118GLU-1-0.976-0.98835.7627.4797.4790.0000.0000.0000.000
96A119TYR00.004-0.02038.0200.1570.1570.0000.0000.0000.000
97A120ILE0-0.0210.00137.025-0.181-0.1810.0000.0000.0000.000
98A121GLY00.0320.01938.839-0.230-0.2300.0000.0000.0000.000
99A122GLY0-0.010-0.02538.1990.2660.2660.0000.0000.0000.000
100A123ASP-1-0.873-0.93438.6977.1817.1810.0000.0000.0000.000
101A124GLU-1-0.914-0.96638.8167.2327.2320.0000.0000.0000.000
102A125GLU-1-0.881-0.91939.9437.1177.1170.0000.0000.0000.000
103A126LEU0-0.110-0.05337.0110.0960.0960.0000.0000.0000.000
104A127ASP-1-0.768-0.88234.4288.8588.8580.0000.0000.0000.000
105A128ILE00.0020.01132.9840.3440.3440.0000.0000.0000.000
106A129ALA00.019-0.00833.692-0.291-0.2910.0000.0000.0000.000
107A130VAL0-0.0060.00133.3160.3220.3220.0000.0000.0000.000
108A131ILE0-0.023-0.01732.415-0.265-0.2650.0000.0000.0000.000
109A132LYS10.8890.95833.580-8.844-8.8440.0000.0000.0000.000
110A133ILE00.0250.02030.597-0.248-0.2480.0000.0000.0000.000
111A134LYS10.8070.88933.220-8.372-8.3720.0000.0000.0000.000
112A135ALA00.0560.02531.4920.1770.1770.0000.0000.0000.000
113A136SER0-0.067-0.04132.939-0.048-0.0480.0000.0000.0000.000
114A137ASP-1-0.893-0.92630.68710.03610.0360.0000.0000.0000.000
115A138LYS10.8890.94327.280-11.209-11.2090.0000.0000.0000.000
116A139LYS10.8570.92428.037-10.087-10.0870.0000.0000.0000.000
117A140PHE0-0.0070.00325.6000.2860.2860.0000.0000.0000.000
118A141PRO0-0.016-0.00120.687-0.098-0.0980.0000.0000.0000.000
119A142TYR0-0.077-0.05322.355-0.313-0.3130.0000.0000.0000.000
120A143LEU0-0.0070.00819.3790.5280.5280.0000.0000.0000.000
121A144GLU-1-0.852-0.91321.88912.53412.5340.0000.0000.0000.000
122A145PHE0-0.040-0.02523.2140.1720.1720.0000.0000.0000.000
123A146GLY00.0780.06124.2720.1340.1340.0000.0000.0000.000
124A147ASP-1-0.870-0.95524.9729.2889.2880.0000.0000.0000.000
125A148SER00.0450.00927.2460.0830.0830.0000.0000.0000.000
126A149ASP-1-0.911-0.94328.8808.8058.8050.0000.0000.0000.000
127A150LYS10.8270.92227.353-10.069-10.0690.0000.0000.0000.000
128A151VAL00.0170.03224.6550.2700.2700.0000.0000.0000.000
129A152LYS10.8470.91824.128-11.109-11.1090.0000.0000.0000.000
130A153ILE0-0.010-0.01424.4150.2680.2680.0000.0000.0000.000
131A154GLY0-0.002-0.00523.147-0.107-0.1070.0000.0000.0000.000
132A155GLU-1-0.878-0.92620.04612.67712.6770.0000.0000.0000.000
133A156TRP0-0.003-0.02015.728-0.107-0.1070.0000.0000.0000.000
134A157ALA00.0240.01817.796-0.038-0.0380.0000.0000.0000.000
135A158ILE0-0.043-0.02313.0080.3400.3400.0000.0000.0000.000
136A159ALA00.0230.02817.024-0.305-0.3050.0000.0000.0000.000
137A160ILE0-0.023-0.01615.6010.6240.6240.0000.0000.0000.000
138A161GLY00.0410.01019.169-0.764-0.7640.0000.0000.0000.000
139A162ASN0-0.038-0.04620.4980.6600.6600.0000.0000.0000.000
140A163PRO00.0270.03222.827-0.252-0.2520.0000.0000.0000.000
141A164LEU00.0110.00223.078-0.438-0.4380.0000.0000.0000.000
142A165GLY0-0.046-0.01724.406-0.309-0.3090.0000.0000.0000.000
143A166PHE0-0.028-0.01921.6190.3140.3140.0000.0000.0000.000
144A167GLN0-0.022-0.02116.7350.2420.2420.0000.0000.0000.000
145A168HIS00.0590.04713.137-1.702-1.7020.0000.0000.0000.000
146A169THR0-0.034-0.00916.9670.6970.6970.0000.0000.0000.000
147A170VAL00.009-0.01413.775-0.034-0.0340.0000.0000.0000.000
148A171THR0-0.084-0.04516.6720.0770.0770.0000.0000.0000.000
149A172VAL0-0.003-0.01213.3090.0900.0900.0000.0000.0000.000
150A173GLY00.0370.01516.789-0.371-0.3710.0000.0000.0000.000
151A174VAL0-0.042-0.01018.3970.5780.5780.0000.0000.0000.000
152A175VAL0-0.0060.00920.918-0.487-0.4870.0000.0000.0000.000
153A176SER0-0.012-0.02124.013-0.111-0.1110.0000.0000.0000.000
154A177ALA0-0.027-0.02026.970-0.318-0.3180.0000.0000.0000.000
155A178THR00.0310.02029.0900.1070.1070.0000.0000.0000.000
156A179ASN0-0.011-0.01031.326-0.193-0.1930.0000.0000.0000.000
157A180ARG10.9330.98032.628-8.592-8.5920.0000.0000.0000.000
158A181ARG10.9220.95635.206-7.031-7.0310.0000.0000.0000.000
159A182ILE0-0.036-0.01734.323-0.045-0.0450.0000.0000.0000.000
160A183PRO0-0.0110.00738.494-0.011-0.0110.0000.0000.0000.000
161A184LYS10.9020.94840.079-7.074-7.0740.0000.0000.0000.000
162A185PRO0-0.0100.01039.068-0.186-0.1860.0000.0000.0000.000
163A186ASP-1-0.854-0.89842.1516.6816.6810.0000.0000.0000.000
164A187GLY0-0.047-0.02244.034-0.151-0.1510.0000.0000.0000.000
165A188SER0-0.086-0.08245.561-0.131-0.1310.0000.0000.0000.000
166A189GLY00.0300.00544.434-0.038-0.0380.0000.0000.0000.000
167A190TYR0-0.071-0.04941.4570.0020.0020.0000.0000.0000.000
168A191TYR00.0980.06736.191-0.040-0.0400.0000.0000.0000.000
169A192VAL0-0.052-0.05837.781-0.081-0.0810.0000.0000.0000.000
170A193GLY00.0340.02935.7420.0420.0420.0000.0000.0000.000
171A194LEU0-0.041-0.01531.7250.1910.1910.0000.0000.0000.000
172A195ILE0-0.007-0.00526.149-0.175-0.1750.0000.0000.0000.000
173A196GLN00.0380.01928.342-0.287-0.2870.0000.0000.0000.000
174A197THR00.0190.00822.8940.2090.2090.0000.0000.0000.000
175A198ASP-1-0.872-0.91621.85411.75111.7510.0000.0000.0000.000
176A199ALA00.0300.01720.1680.2110.2110.0000.0000.0000.000
177A200ALA0-0.023-0.02221.527-0.434-0.4340.0000.0000.0000.000
178A201ILE00.0140.02622.6830.4120.4120.0000.0000.0000.000
179A202ASN00.0170.00524.208-0.339-0.3390.0000.0000.0000.000
180A203PRO00.0390.01327.0840.2690.2690.0000.0000.0000.000
181A204GLY00.0060.01325.546-0.017-0.0170.0000.0000.0000.000
182A205ASN0-0.016-0.02921.443-0.016-0.0160.0000.0000.0000.000
183A206SER00.0450.03324.4800.0520.0520.0000.0000.0000.000
184A207GLY0-0.031-0.02327.5960.0330.0330.0000.0000.0000.000
185A208GLY00.0270.01023.5510.0770.0770.0000.0000.0000.000
186A209PRO0-0.034-0.00620.314-0.366-0.3660.0000.0000.0000.000
187A210LEU00.0440.01920.9020.4190.4190.0000.0000.0000.000
188A211LEU0-0.025-0.02616.484-0.270-0.2700.0000.0000.0000.000
189A212ASN00.0260.02118.223-0.161-0.1610.0000.0000.0000.000
190A213ILE0-0.028-0.03313.0920.6940.6940.0000.0000.0000.000
191A214HIS0-0.011-0.02814.1511.1411.1410.0000.0000.0000.000
192A215GLY00.0200.02116.3330.1050.1050.0000.0000.0000.000
193A216GLU-1-0.883-0.92516.94112.69912.6990.0000.0000.0000.000
194A217VAL0-0.011-0.01920.6420.0370.0370.0000.0000.0000.000
195A218ILE00.007-0.00921.954-0.583-0.5830.0000.0000.0000.000
196A219GLY00.003-0.03324.527-0.529-0.5290.0000.0000.0000.000
197A220ILE0-0.0070.00225.0780.4520.4520.0000.0000.0000.000
198A221ASN0-0.028-0.01222.118-0.343-0.3430.0000.0000.0000.000
199A222THR0-0.015-0.00826.281-0.227-0.2270.0000.0000.0000.000
200A223ALA0-0.003-0.00529.315-0.025-0.0250.0000.0000.0000.000
201A224ILE00.0440.03730.902-0.168-0.1680.0000.0000.0000.000
202A225VAL0-0.100-0.01532.635-0.267-0.2670.0000.0000.0000.000
203A226ASN0-0.010-0.02632.7330.1040.1040.0000.0000.0000.000
204A227PRO0-0.0080.00230.8240.1980.1980.0000.0000.0000.000
205A228GLN0-0.019-0.03333.767-0.276-0.2760.0000.0000.0000.000
206A229GLU-1-0.946-0.96634.2357.9247.9240.0000.0000.0000.000
207A230ALA00.0040.02233.368-0.076-0.0760.0000.0000.0000.000
208A231VAL00.005-0.02627.9140.2640.2640.0000.0000.0000.000
209A232ASN0-0.081-0.05523.730-0.334-0.3340.0000.0000.0000.000
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