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: 6N9NZ

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 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 228
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2716089.76998
FMO2-HF: Nuclear repulsion 2631257.366556
FMO2-HF: Total energy -84832.403424
FMO2-MP2: Total energy -85086.30339


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.
125.451131.3120.34-3.034-3.168-0.015
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 : -0.999 / q_NPA : -0.997
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-1-0.952-0.9792.73436.93642.5080.339-2.997-2.915-0.015
4A27SER0-0.002-0.0034.314-1.568-1.2790.001-0.037-0.2530.000
5A28PRO00.003-0.0105.8710.0480.0480.0000.0000.0000.000
6A29ILE00.0520.0199.2460.0060.0060.0000.0000.0000.000
7A30VAL0-0.0040.0045.866-1.657-1.6570.0000.0000.0000.000
8A31ASN00.0330.0216.3121.6971.6970.0000.0000.0000.000
9A32VAL0-0.0020.0078.873-1.249-1.2490.0000.0000.0000.000
10A33VAL00.0220.01211.583-1.270-1.2700.0000.0000.0000.000
11A34GLU-1-0.940-0.9667.96029.38529.3850.0000.0000.0000.000
12A35ALA0-0.060-0.02511.186-0.944-0.9440.0000.0000.0000.000
13A36CYS0-0.044-0.03413.667-1.510-1.5100.0000.0000.0000.000
14A37ALA00.0370.01715.079-1.141-1.1410.0000.0000.0000.000
15A38PRO0-0.035-0.02615.572-1.042-1.0420.0000.0000.0000.000
16A39ALA0-0.0040.00518.563-0.703-0.7030.0000.0000.0000.000
17A40VAL0-0.042-0.01719.344-0.827-0.8270.0000.0000.0000.000
18A41VAL0-0.0260.00522.0760.2090.2090.0000.0000.0000.000
19A42LYS10.8790.95525.045-10.489-10.4890.0000.0000.0000.000
20A43ILE0-0.022-0.03227.372-0.176-0.1760.0000.0000.0000.000
21A44ASP-1-0.870-0.94231.0869.5439.5430.0000.0000.0000.000
22A45VAL00.0320.02133.681-0.103-0.1030.0000.0000.0000.000
23A46VAL0-0.0010.00337.403-0.088-0.0880.0000.0000.0000.000
24A47LYS10.9450.98440.074-7.006-7.0060.0000.0000.0000.000
25A48THR0-0.035-0.03443.163-0.098-0.0980.0000.0000.0000.000
26A49VAL0-0.044-0.01845.5800.0930.0930.0000.0000.0000.000
27A50LYS10.7760.91541.296-7.324-7.3240.0000.0000.0000.000
28A51THR0-0.049-0.04643.8110.0530.0530.0000.0000.0000.000
29A52SER00.0080.01543.686-0.161-0.1610.0000.0000.0000.000
30A53PHE00.0500.05139.116-0.089-0.0890.0000.0000.0000.000
31A54PHE0-0.079-0.03639.4880.2000.2000.0000.0000.0000.000
32A55ASP-1-0.837-0.92839.3807.5347.5340.0000.0000.0000.000
33A56PRO00.012-0.01039.2880.2250.2250.0000.0000.0000.000
34A57TYR0-0.0070.02134.0270.0170.0170.0000.0000.0000.000
35A58PHE00.026-0.01233.9730.2430.2430.0000.0000.0000.000
36A59GLU-1-0.929-0.96034.7528.0568.0560.0000.0000.0000.000
37A60GLN00.0400.01036.4350.1930.1930.0000.0000.0000.000
38A61PHE0-0.0030.00127.4580.1360.1360.0000.0000.0000.000
39A62PHE00.020-0.00728.8930.2340.2340.0000.0000.0000.000
40A63LYS10.8730.94732.286-7.819-7.8190.0000.0000.0000.000
41A64LYS10.8950.95232.421-9.121-9.1210.0000.0000.0000.000
42A65TRP0-0.058-0.03528.2300.1000.1000.0000.0000.0000.000
43A66PHE00.0180.01924.8900.3650.3650.0000.0000.0000.000
44A67GLY0-0.0110.01429.321-0.275-0.2750.0000.0000.0000.000
45A68GLU-1-0.885-0.96225.30111.58111.5810.0000.0000.0000.000
46A69LEU0-0.050-0.03029.300-0.054-0.0540.0000.0000.0000.000
47A70PRO0-0.028-0.01732.312-0.232-0.2320.0000.0000.0000.000
48A71PRO00.0100.00035.044-0.106-0.1060.0000.0000.0000.000
49A72GLY0-0.028-0.01238.367-0.206-0.2060.0000.0000.0000.000
50A73PHE00.0400.02433.437-0.061-0.0610.0000.0000.0000.000
51A74GLU-1-0.792-0.90737.7077.4997.4990.0000.0000.0000.000
52A75ARG10.9160.95140.375-6.781-6.7810.0000.0000.0000.000
53A76GLN0-0.060-0.03939.261-0.115-0.1150.0000.0000.0000.000
54A77VAL0-0.0180.00335.2400.0270.0270.0000.0000.0000.000
55A78ALA0-0.026-0.00738.574-0.150-0.1500.0000.0000.0000.000
56A79SER00.014-0.00335.6980.0040.0040.0000.0000.0000.000
57A80LEU0-0.050-0.00129.9040.0410.0410.0000.0000.0000.000
58A81GLY00.0310.01129.812-0.071-0.0710.0000.0000.0000.000
59A82SER0-0.018-0.01125.2840.5030.5030.0000.0000.0000.000
60A83GLY00.0800.06926.140-0.516-0.5160.0000.0000.0000.000
61A84PHE0-0.037-0.01924.0210.5280.5280.0000.0000.0000.000
62A85ILE00.0270.01624.667-0.516-0.5160.0000.0000.0000.000
63A86PHE0-0.021-0.02625.0690.4470.4470.0000.0000.0000.000
64A87ASP-1-0.801-0.88727.26610.49110.4910.0000.0000.0000.000
65A88PRO0-0.023-0.00827.222-0.185-0.1850.0000.0000.0000.000
66A89GLU-1-0.889-0.96728.4579.8729.8720.0000.0000.0000.000
67A90GLY0-0.011-0.01629.892-0.262-0.2620.0000.0000.0000.000
68A91TYR0-0.0070.00530.906-0.294-0.2940.0000.0000.0000.000
69A92ILE0-0.020-0.00728.3140.4080.4080.0000.0000.0000.000
70A93LEU00.0000.02229.060-0.447-0.4470.0000.0000.0000.000
71A94THR00.002-0.04929.2450.2900.2900.0000.0000.0000.000
72A95ASN0-0.012-0.01030.8840.0310.0310.0000.0000.0000.000
73A96TYR0-0.047-0.00733.242-0.066-0.0660.0000.0000.0000.000
74A97HIS0-0.044-0.04533.4430.0800.0800.0000.0000.0000.000
75A98VAL0-0.051-0.01631.735-0.045-0.0450.0000.0000.0000.000
76A99VAL0-0.016-0.00334.159-0.123-0.1230.0000.0000.0000.000
77A100GLY00.0430.01336.661-0.211-0.2110.0000.0000.0000.000
78A101GLY0-0.022-0.02139.818-0.002-0.0020.0000.0000.0000.000
79A102ALA0-0.041-0.01139.596-0.096-0.0960.0000.0000.0000.000
80A103ASP-1-0.755-0.89941.6507.1727.1720.0000.0000.0000.000
81A104ASN0-0.009-0.02339.8390.1410.1410.0000.0000.0000.000
82A105ILE00.0390.01434.9360.0900.0900.0000.0000.0000.000
83A106THR0-0.0090.01032.888-0.065-0.0650.0000.0000.0000.000
84A107VAL00.0130.01528.8110.1590.1590.0000.0000.0000.000
85A108THR0-0.059-0.03526.545-0.130-0.1300.0000.0000.0000.000
86A109MET00.0380.01023.1910.0570.0570.0000.0000.0000.000
87A110LEU00.0510.03517.289-0.034-0.0340.0000.0000.0000.000
88A111ASP-1-0.908-0.88321.09113.09413.0940.0000.0000.0000.000
89A112GLY00.0130.00322.175-0.115-0.1150.0000.0000.0000.000
90A113SER0-0.109-0.08625.119-0.715-0.7150.0000.0000.0000.000
91A114LYS10.9350.95227.888-10.123-10.1230.0000.0000.0000.000
92A115TYR0-0.052-0.03027.748-0.291-0.2910.0000.0000.0000.000
93A116ASP-1-0.928-0.96232.9138.3658.3650.0000.0000.0000.000
94A117ALA0-0.006-0.03533.8020.0640.0640.0000.0000.0000.000
95A118GLU-1-0.988-0.98335.7917.4537.4530.0000.0000.0000.000
96A119TYR0-0.009-0.01638.0520.1740.1740.0000.0000.0000.000
97A120ILE0-0.0360.00536.786-0.181-0.1810.0000.0000.0000.000
98A121GLY00.0320.00539.058-0.232-0.2320.0000.0000.0000.000
99A122GLY0-0.007-0.03338.6110.2630.2630.0000.0000.0000.000
100A123ASP-1-0.869-0.94039.3547.2237.2230.0000.0000.0000.000
101A124GLU-1-0.934-0.98439.6307.2787.2780.0000.0000.0000.000
102A125GLU-1-0.956-0.95940.9297.0717.0710.0000.0000.0000.000
103A126LEU0-0.140-0.06637.9430.1110.1110.0000.0000.0000.000
104A127ASP-1-0.727-0.86135.8768.8608.8600.0000.0000.0000.000
105A128ILE0-0.0040.02733.8090.3610.3610.0000.0000.0000.000
106A129ALA00.010-0.01534.284-0.292-0.2920.0000.0000.0000.000
107A130VAL0-0.0120.00133.4090.3340.3340.0000.0000.0000.000
108A131ILE00.006-0.00632.519-0.272-0.2720.0000.0000.0000.000
109A132LYS10.8570.95133.611-8.908-8.9080.0000.0000.0000.000
110A133ILE00.0280.03530.544-0.242-0.2420.0000.0000.0000.000
111A134LYS10.9150.94333.238-8.385-8.3850.0000.0000.0000.000
112A135ALA00.0550.02731.5350.1770.1770.0000.0000.0000.000
113A136SER0-0.081-0.04732.960-0.044-0.0440.0000.0000.0000.000
114A137ASP-1-0.896-0.93130.87610.08510.0850.0000.0000.0000.000
115A138LYS10.9170.95927.380-11.171-11.1710.0000.0000.0000.000
116A139LYS10.9420.98028.149-10.191-10.1910.0000.0000.0000.000
117A140PHE00.0050.00625.6050.2740.2740.0000.0000.0000.000
118A141PRO0-0.028-0.00420.721-0.111-0.1110.0000.0000.0000.000
119A142TYR0-0.021-0.01822.374-0.227-0.2270.0000.0000.0000.000
120A143LEU0-0.0120.00419.6140.5310.5310.0000.0000.0000.000
121A144GLU-1-0.895-0.93922.13812.83712.8370.0000.0000.0000.000
122A145PHE0-0.058-0.03523.7120.1240.1240.0000.0000.0000.000
123A146GLY00.0860.06225.0780.1290.1290.0000.0000.0000.000
124A147ASP-1-0.895-0.97725.7179.3559.3550.0000.0000.0000.000
125A148SER00.035-0.00328.0730.1020.1020.0000.0000.0000.000
126A149ASP-1-0.929-0.95529.7498.8758.8750.0000.0000.0000.000
127A150LYS10.8250.91328.100-10.254-10.2540.0000.0000.0000.000
128A151VAL00.0410.04225.3390.3000.3000.0000.0000.0000.000
129A152LYS10.8660.93524.721-11.245-11.2450.0000.0000.0000.000
130A153ILE00.007-0.00625.1000.2900.2900.0000.0000.0000.000
131A154GLY0-0.0090.00023.754-0.116-0.1160.0000.0000.0000.000
132A155GLU-1-0.934-0.96520.64713.24713.2470.0000.0000.0000.000
133A156TRP0-0.001-0.02016.155-0.118-0.1180.0000.0000.0000.000
134A157ALA00.0390.02618.651-0.046-0.0460.0000.0000.0000.000
135A158ILE0-0.056-0.03214.0580.3990.3990.0000.0000.0000.000
136A159ALA00.0260.02918.019-0.345-0.3450.0000.0000.0000.000
137A160ILE0-0.016-0.01216.4420.6720.6720.0000.0000.0000.000
138A161GLY00.0350.00620.010-0.780-0.7800.0000.0000.0000.000
139A162ASN0-0.043-0.04120.9380.5510.5510.0000.0000.0000.000
140A163PRO00.0410.04123.113-0.274-0.2740.0000.0000.0000.000
141A164LEU00.005-0.00323.350-0.445-0.4450.0000.0000.0000.000
142A165GLY0-0.046-0.02024.459-0.321-0.3210.0000.0000.0000.000
143A166PHE0-0.028-0.02321.8720.3170.3170.0000.0000.0000.000
144A167GLN0-0.026-0.02616.8860.2170.2170.0000.0000.0000.000
145A168HIS00.0450.04413.297-1.771-1.7710.0000.0000.0000.000
146A169THR0-0.021-0.00417.3860.7120.7120.0000.0000.0000.000
147A170VAL00.014-0.01214.699-0.047-0.0470.0000.0000.0000.000
148A171THR0-0.097-0.05117.6410.0840.0840.0000.0000.0000.000
149A172VAL00.000-0.01214.3750.1290.1290.0000.0000.0000.000
150A173GLY00.0310.01017.766-0.372-0.3720.0000.0000.0000.000
151A174VAL0-0.041-0.02019.3220.6110.6110.0000.0000.0000.000
152A175VAL0-0.013-0.00121.824-0.527-0.5270.0000.0000.0000.000
153A176SER0-0.015-0.02224.926-0.099-0.0990.0000.0000.0000.000
154A177ALA0-0.025-0.02327.853-0.319-0.3190.0000.0000.0000.000
155A178THR00.0430.03230.2430.1270.1270.0000.0000.0000.000
156A179ASN0-0.012-0.01232.250-0.144-0.1440.0000.0000.0000.000
157A180ARG10.9200.97233.551-8.738-8.7380.0000.0000.0000.000
158A181ARG10.9330.96136.166-7.124-7.1240.0000.0000.0000.000
159A182ILE0-0.033-0.01335.495-0.037-0.0370.0000.0000.0000.000
160A183PRO0-0.0230.00739.481-0.014-0.0140.0000.0000.0000.000
161A184LYS11.0191.00941.023-7.232-7.2320.0000.0000.0000.000
162A185PRO0-0.0240.00940.235-0.187-0.1870.0000.0000.0000.000
163A186ASP-1-0.871-0.92343.1426.6736.6730.0000.0000.0000.000
164A187GLY0-0.032-0.01445.032-0.147-0.1470.0000.0000.0000.000
165A188SER0-0.070-0.06446.575-0.129-0.1290.0000.0000.0000.000
166A189GLY00.0500.01945.436-0.036-0.0360.0000.0000.0000.000
167A190TYR0-0.076-0.05742.437-0.033-0.0330.0000.0000.0000.000
168A191TYR00.0990.07637.178-0.007-0.0070.0000.0000.0000.000
169A192VAL0-0.052-0.05838.716-0.076-0.0760.0000.0000.0000.000
170A193GLY00.0150.01636.7060.0380.0380.0000.0000.0000.000
171A194LEU0-0.030-0.00732.7430.1870.1870.0000.0000.0000.000
172A195ILE00.0070.00727.025-0.192-0.1920.0000.0000.0000.000
173A196GLN00.0220.01529.309-0.266-0.2660.0000.0000.0000.000
174A197THR00.014-0.00323.1130.2310.2310.0000.0000.0000.000
175A198ASP-1-0.869-0.89422.86512.05512.0550.0000.0000.0000.000
176A199ALA00.0120.00521.1500.2210.2210.0000.0000.0000.000
177A200ALA0-0.031-0.02122.495-0.449-0.4490.0000.0000.0000.000
178A201ILE00.0210.03323.6710.4090.4090.0000.0000.0000.000
179A202ASN00.0140.00125.411-0.268-0.2680.0000.0000.0000.000
180A203PRO00.0360.01228.0620.2710.2710.0000.0000.0000.000
181A204GLY00.0030.01326.455-0.022-0.0220.0000.0000.0000.000
182A205ASN0-0.025-0.03122.7620.0140.0140.0000.0000.0000.000
183A206SER00.0740.04325.3810.1180.1180.0000.0000.0000.000
184A207GLY0-0.019-0.02228.3370.0240.0240.0000.0000.0000.000
185A208GLY00.0360.01524.2530.0710.0710.0000.0000.0000.000
186A209PRO0-0.035-0.00821.102-0.361-0.3610.0000.0000.0000.000
187A210LEU00.0470.02522.0330.4560.4560.0000.0000.0000.000
188A211LEU0-0.035-0.03117.436-0.269-0.2690.0000.0000.0000.000
189A212ASN00.0670.05819.107-0.139-0.1390.0000.0000.0000.000
190A213ILE0-0.030-0.03613.7900.7470.7470.0000.0000.0000.000
191A214HIS0-0.021-0.03614.9141.0681.0680.0000.0000.0000.000
192A215GLY00.0270.02917.1480.0700.0700.0000.0000.0000.000
193A216GLU-1-0.907-0.95417.60512.92312.9230.0000.0000.0000.000
194A217VAL00.001-0.01121.3530.0570.0570.0000.0000.0000.000
195A218ILE00.014-0.01122.965-0.629-0.6290.0000.0000.0000.000
196A219GLY0-0.005-0.03525.443-0.537-0.5370.0000.0000.0000.000
197A220ILE0-0.019-0.00126.0400.4620.4620.0000.0000.0000.000
198A221ASN0-0.015-0.01523.122-0.376-0.3760.0000.0000.0000.000
199A222THR0-0.039-0.01127.278-0.257-0.2570.0000.0000.0000.000
200A223ALA0-0.007-0.00730.366-0.017-0.0170.0000.0000.0000.000
201A224ILE00.0110.02431.901-0.183-0.1830.0000.0000.0000.000
202A225VAL0-0.097-0.01433.563-0.259-0.2590.0000.0000.0000.000
203A226ASN0-0.005-0.01633.7270.1800.1800.0000.0000.0000.000
204A227PRO0-0.008-0.01631.8140.1980.1980.0000.0000.0000.000
205A228GLN0-0.039-0.04434.746-0.226-0.2260.0000.0000.0000.000
206A229GLU-1-0.949-0.96635.1737.8547.8540.0000.0000.0000.000
207A230ALA00.0080.02534.299-0.074-0.0740.0000.0000.0000.000
208A231VAL00.016-0.01628.6400.2700.2700.0000.0000.0000.000
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210A233LEU0-0.0170.01428.0160.0900.0900.0000.0000.0000.000
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