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: 4LNLN

Calculation Name: 1G0X-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1G0X

Chain ID: A

ChEMBL ID:

UniProt ID: Q8NHL6

Base Structure: X-ray

Registration Date: 2023-09-26

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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2077431.510038
FMO2-HF: Nuclear repulsion 2000295.050941
FMO2-HF: Total energy -77136.459098
FMO2-MP2: Total energy -77362.15169


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:HIS)


Summations of interaction energy for fragment #1(A:2:HIS)
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.
-5.817-17.99741.026-1.797-27.049-0.028
Interaction energy analysis for fragmet #1(A:2:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.007 / q_NPA : 0.017
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].
3A4PRO00.0140.0103.804-2.4690.018-0.030-1.236-1.2210.002
4A5LYS10.9320.9935.452-0.024-0.0240.0000.0000.0000.000
5A6PRO0-0.022-0.0076.6640.1170.1170.0000.0000.0000.000
6A7THR0-0.025-0.0158.870-0.160-0.1600.0000.0000.0000.000
7A8LEU0-0.032-0.01912.561-0.047-0.0470.0000.0000.0000.000
8A9TRP0-0.050-0.03414.2780.0170.0170.0000.0000.0000.000
9A10ALA00.0180.00218.409-0.046-0.0460.0000.0000.0000.000
10A11GLU-1-0.864-0.89521.417-0.022-0.0220.0000.0000.0000.000
11A12PRO00.025-0.01624.008-0.027-0.0270.0000.0000.0000.000
12A13GLY00.0720.02325.4190.0190.0190.0000.0000.0000.000
13A14SER0-0.014-0.01123.562-0.014-0.0140.0000.0000.0000.000
14A15VAL00.0300.02925.348-0.009-0.0090.0000.0000.0000.000
15A16ILE0-0.035-0.01527.1950.0040.0040.0000.0000.0000.000
16A17THR00.0100.02530.218-0.005-0.0050.0000.0000.0000.000
17A18GLN00.023-0.00232.621-0.005-0.0050.0000.0000.0000.000
18A19GLY0-0.0040.00532.3040.0060.0060.0000.0000.0000.000
19A20SER0-0.044-0.02631.658-0.004-0.0040.0000.0000.0000.000
20A21PRO0-0.031-0.01127.343-0.010-0.0100.0000.0000.0000.000
21A22VAL00.0140.00823.6290.0160.0160.0000.0000.0000.000
22A23THR0-0.035-0.01819.309-0.043-0.0430.0000.0000.0000.000
23A24LEU0-0.0050.00517.9630.0320.0320.0000.0000.0000.000
24A25ARG10.8960.94915.7430.0180.0180.0000.0000.0000.000
25A26CYS0-0.045-0.01310.452-0.034-0.0340.0000.0000.0000.000
26A27GLN00.0170.00810.739-0.174-0.1740.0000.0000.0000.000
27A28GLY00.0850.0256.782-0.012-0.0120.0000.0000.0000.000
28A29GLY0-0.073-0.0526.1380.8970.8970.0000.0000.0000.000
29A30GLN00.007-0.0012.129-2.906-3.1153.238-1.249-1.779-0.015
30A31GLH00.097-0.0132.3402.1992.95412.313-5.962-7.1050.007
31A32THR0-0.069-0.0022.5190.707-10.2445.2919.512-3.852-0.016
32A33GLN00.007-0.0194.4540.2260.333-0.001-0.028-0.0780.000
33A34GLU-1-0.916-0.9362.803-11.404-9.4130.092-0.965-1.119-0.007
34A35TYR00.0380.0204.8930.8040.939-0.001-0.001-0.1330.000
35A36ARG10.9160.9587.4021.3671.3670.0000.0000.0000.000
36A37LEU00.0100.0219.7780.1920.1920.0000.0000.0000.000
37A38TYR0-0.074-0.05411.791-0.046-0.0460.0000.0000.0000.000
38A39ARG10.8020.88015.6240.2710.2710.0000.0000.0000.000
39A40GLU-1-0.843-0.93417.888-0.109-0.1090.0000.0000.0000.000
40A41LYS10.9380.96519.9530.1180.1180.0000.0000.0000.000
41A42LYS11.0061.00622.6320.1860.1860.0000.0000.0000.000
42A43THR00.0500.03719.8220.0020.0020.0000.0000.0000.000
43A44ALA00.0630.03619.9260.0310.0310.0000.0000.0000.000
44A45PRO00.023-0.00520.099-0.040-0.0400.0000.0000.0000.000
45A46TRP00.0150.01619.244-0.048-0.0480.0000.0000.0000.000
46A47ILE00.0310.03315.464-0.020-0.0200.0000.0000.0000.000
47A48THR0-0.088-0.06716.891-0.052-0.0520.0000.0000.0000.000
48A49ARG10.9530.97517.9570.3130.3130.0000.0000.0000.000
49A50ILE0-0.0330.00916.2580.0350.0350.0000.0000.0000.000
50A51PRO00.0650.03616.680-0.088-0.0880.0000.0000.0000.000
51A52GLN00.0700.01010.567-0.282-0.2820.0000.0000.0000.000
52A53GLU-1-0.955-0.98013.012-0.654-0.6540.0000.0000.0000.000
53A54LEU0-0.017-0.01214.8350.0300.0300.0000.0000.0000.000
54A55VAL00.0280.0309.9560.0410.0410.0000.0000.0000.000
55A56LYS10.9480.9809.1641.2991.2990.0000.0000.0000.000
56A57LYS10.9100.9579.7410.4310.4310.0000.0000.0000.000
57A58GLY00.0000.01111.1220.1750.1750.0000.0000.0000.000
58A59GLN0-0.059-0.03611.9460.1580.1580.0000.0000.0000.000
59A60PHE00.012-0.01111.671-0.092-0.0920.0000.0000.0000.000
60A61PRO00.0060.00417.3900.0440.0440.0000.0000.0000.000
61A62ILE0-0.0150.00621.079-0.031-0.0310.0000.0000.0000.000
62A63PRO0-0.024-0.02724.0420.0230.0230.0000.0000.0000.000
63A64SER00.0030.00627.0420.0160.0160.0000.0000.0000.000
64A65ILE0-0.049-0.00826.235-0.014-0.0140.0000.0000.0000.000
65A66THR00.0530.00728.6420.0110.0110.0000.0000.0000.000
66A67TRP00.1230.04229.307-0.004-0.0040.0000.0000.0000.000
67A68GLU-1-0.897-0.94828.051-0.156-0.1560.0000.0000.0000.000
68A69HIS0-0.0280.00723.833-0.004-0.0040.0000.0000.0000.000
69A70ALA00.0600.07824.545-0.008-0.0080.0000.0000.0000.000
70A71GLY0-0.015-0.01923.790-0.016-0.0160.0000.0000.0000.000
71A72ARG10.9210.99020.1600.0360.0360.0000.0000.0000.000
72A73TYR0-0.054-0.07517.235-0.052-0.0520.0000.0000.0000.000
73A74ARG10.8890.94813.3150.0650.0650.0000.0000.0000.000
74A76TYR00.0160.0156.1550.1180.1180.0000.0000.0000.000
75A77TYR0-0.0030.0191.819-3.770-3.85511.600-4.658-6.8560.007
76A78GLY00.0240.0031.956-0.074-1.4407.827-4.386-2.0760.012
77A79SER0-0.073-0.0532.44310.5311.6240.3038.828-0.224-0.003
78A80ASP-1-0.890-0.9465.514-0.683-0.6830.0000.0000.0000.000
79A81THR0-0.060-0.0348.2680.2690.2690.0000.0000.0000.000
80A82ALA0-0.0100.0004.3600.2690.381-0.001-0.010-0.1020.000
81A83GLY00.0440.0514.0791.0771.3010.000-0.044-0.1790.000
82A84ARG10.8430.9122.924-4.480-1.7540.345-1.369-1.703-0.013
83A85SER00.0190.0253.317-0.1510.5200.050-0.213-0.508-0.002
84A86GLU-1-0.897-0.9464.2790.2860.4160.000-0.016-0.1140.000
85A87SER0-0.020-0.0317.653-0.024-0.0240.0000.0000.0000.000
86A88SER00.0200.01910.0880.0480.0480.0000.0000.0000.000
87A89ASP-1-0.871-0.93011.8210.1770.1770.0000.0000.0000.000
88A90PRO0-0.079-0.05615.497-0.026-0.0260.0000.0000.0000.000
89A91LEU00.0360.02417.7560.0210.0210.0000.0000.0000.000
90A92GLU-1-0.928-0.97819.632-0.055-0.0550.0000.0000.0000.000
91A93LEU0-0.043-0.00822.6380.0080.0080.0000.0000.0000.000
92A94VAL00.0250.00024.342-0.010-0.0100.0000.0000.0000.000
93A95VAL0-0.0210.00628.121-0.001-0.0010.0000.0000.0000.000
94A96THR0-0.023-0.01730.6910.0030.0030.0000.0000.0000.000
95A97GLY00.004-0.03034.248-0.006-0.0060.0000.0000.0000.000
96A98ALA0-0.0120.01436.074-0.001-0.0010.0000.0000.0000.000
97A99TYR0-0.0020.00036.9070.0020.0020.0000.0000.0000.000
98A100ILE00.0180.00041.1440.0000.0000.0000.0000.0000.000
99A101LYS10.8520.91442.6340.0340.0340.0000.0000.0000.000
100A102PRO0-0.0090.00741.7880.0010.0010.0000.0000.0000.000
101A103THR0-0.008-0.01844.8580.0000.0000.0000.0000.0000.000
102A104LEU0-0.001-0.00442.1790.0020.0020.0000.0000.0000.000
103A105SER0-0.040-0.01346.0630.0000.0000.0000.0000.0000.000
104A106ALA00.0200.01048.1260.0010.0010.0000.0000.0000.000
105A107GLN0-0.0410.00449.432-0.002-0.0020.0000.0000.0000.000
106A108PRO0-0.015-0.03051.5050.0020.0020.0000.0000.0000.000
107A109SER00.0550.00653.022-0.002-0.0020.0000.0000.0000.000
108A110PRO00.0450.01449.7670.0020.0020.0000.0000.0000.000
109A111VAL0-0.0190.00750.1240.0020.0020.0000.0000.0000.000
110A112VAL00.0080.00948.7300.0000.0000.0000.0000.0000.000
111A113ASN00.000-0.00451.7090.0000.0000.0000.0000.0000.000
112A114SER00.0440.00249.3450.0010.0010.0000.0000.0000.000
113A115GLY0-0.032-0.01547.9400.0000.0000.0000.0000.0000.000
114A116GLY0-0.0080.01048.9280.0010.0010.0000.0000.0000.000
115A117ASN0-0.004-0.01545.8350.0030.0030.0000.0000.0000.000
116A118VAL00.0080.00946.339-0.002-0.0020.0000.0000.0000.000
117A119THR00.0030.00546.4330.0010.0010.0000.0000.0000.000
118A120LEU0-0.0040.00042.550-0.002-0.0020.0000.0000.0000.000
119A121GLN00.018-0.00845.6820.0020.0020.0000.0000.0000.000
120A122CYS0-0.063-0.00838.4500.0000.0000.0000.0000.0000.000
121A123ASP-1-0.856-0.94144.966-0.015-0.0150.0000.0000.0000.000
122A124SER00.0410.00644.770-0.003-0.0030.0000.0000.0000.000
123A125GLN0-0.005-0.00246.9070.0010.0010.0000.0000.0000.000
124A126VAL0-0.022-0.00345.3110.0000.0000.0000.0000.0000.000
125A127ALA0-0.028-0.01045.8380.0020.0020.0000.0000.0000.000
126A128PHE00.003-0.00340.391-0.004-0.0040.0000.0000.0000.000
127A129ASP-1-0.822-0.84238.396-0.031-0.0310.0000.0000.0000.000
128A130GLY00.0290.02637.2480.0050.0050.0000.0000.0000.000
129A131PHE0-0.004-0.02038.118-0.003-0.0030.0000.0000.0000.000
130A132ILE0-0.025-0.00233.2420.0060.0060.0000.0000.0000.000
131A133LEU0-0.0130.00536.518-0.003-0.0030.0000.0000.0000.000
132A134CYS0-0.067-0.02430.630-0.004-0.0040.0000.0000.0000.000
133A135LYS10.9460.97834.984-0.041-0.0410.0000.0000.0000.000
134A136GLU-1-0.906-0.98634.379-0.009-0.0090.0000.0000.0000.000
135A137GLY0-0.056-0.01932.5690.0030.0030.0000.0000.0000.000
136A138GLU-1-1.179-0.93130.2600.0270.0270.0000.0000.0000.000
137A139ASP-1-0.532-0.86634.6580.0460.0460.0000.0000.0000.000
138A140GLU-1-1.024-1.06127.4510.0900.0900.0000.0000.0000.000
139A141HIS0-0.021-0.04424.440-0.006-0.0060.0000.0000.0000.000
140A142PRO0-0.0290.00028.5710.0070.0070.0000.0000.0000.000
141A143GLN0-0.0090.00928.911-0.003-0.0030.0000.0000.0000.000
142A145LEU00.008-0.00631.3290.0050.0050.0000.0000.0000.000
143A146ASN00.0770.04531.987-0.011-0.0110.0000.0000.0000.000
144A147SER0-0.0030.00835.1430.0050.0050.0000.0000.0000.000
145A148GLN00.009-0.00836.5380.0010.0010.0000.0000.0000.000
146A149PRO00.0210.00238.613-0.003-0.0030.0000.0000.0000.000
147A150HIS00.0210.00641.324-0.003-0.0030.0000.0000.0000.000
148A151ALA0-0.050-0.01842.9400.0000.0000.0000.0000.0000.000
149A152ARG10.9030.95838.2660.0000.0000.0000.0000.0000.000
150A153GLY00.0170.01644.4950.0010.0010.0000.0000.0000.000
151A154SER00.022-0.00545.2440.0000.0000.0000.0000.0000.000
152A155SER00.0170.00445.567-0.003-0.0030.0000.0000.0000.000
153A156ARG10.8660.93645.9710.0080.0080.0000.0000.0000.000
154A157ALA00.0020.02342.3610.0010.0010.0000.0000.0000.000
155A158ILE0-0.030-0.00644.395-0.001-0.0010.0000.0000.0000.000
156A159PHE0-0.005-0.00438.2740.0020.0020.0000.0000.0000.000
157A160SER0-0.024-0.00442.656-0.001-0.0010.0000.0000.0000.000
158A161VAL0-0.0030.00840.7360.0030.0030.0000.0000.0000.000
159A162GLY00.0410.01942.018-0.003-0.0030.0000.0000.0000.000
160A163PRO0-0.023-0.02142.3790.0030.0030.0000.0000.0000.000
161A164VAL0-0.0160.00943.3200.0020.0020.0000.0000.0000.000
162A165SER00.021-0.00343.5510.0010.0010.0000.0000.0000.000
163A166PRO00.0230.00944.8580.0000.0000.0000.0000.0000.000
164A167SER0-0.043-0.01343.393-0.002-0.0020.0000.0000.0000.000
165A168ARG10.9410.98336.829-0.050-0.0500.0000.0000.0000.000
166A169ARG10.9841.01238.341-0.015-0.0150.0000.0000.0000.000
167A170TRP0-0.056-0.03540.0030.0040.0040.0000.0000.0000.000
168A171TRP0-0.036-0.03639.153-0.004-0.0040.0000.0000.0000.000
169A172TYR00.0310.00038.9000.0040.0040.0000.0000.0000.000
170A173ARG10.9570.99836.2110.0250.0250.0000.0000.0000.000
171A175TYR00.018-0.00435.271-0.007-0.0070.0000.0000.0000.000
172A176ALA00.0350.02438.4950.0050.0050.0000.0000.0000.000
173A177TYR0-0.088-0.08033.815-0.006-0.0060.0000.0000.0000.000
174A178ASP-1-0.773-0.87736.614-0.049-0.0490.0000.0000.0000.000
175A179SER0-0.054-0.09234.278-0.006-0.0060.0000.0000.0000.000
176A180ASN0-0.067-0.03333.197-0.002-0.0020.0000.0000.0000.000
177A181SER0-0.067-0.03631.675-0.009-0.0090.0000.0000.0000.000
178A182PRO00.0100.00128.9980.0010.0010.0000.0000.0000.000
179A183TYR0-0.082-0.03325.365-0.001-0.0010.0000.0000.0000.000
180A184GLU-1-0.890-0.94629.369-0.114-0.1140.0000.0000.0000.000
181A185TRP0-0.011-0.01730.7410.0090.0090.0000.0000.0000.000
182A186SER00.0200.00935.005-0.005-0.0050.0000.0000.0000.000
183A187LEU00.001-0.00237.5300.0000.0000.0000.0000.0000.000
184A188PRO0-0.027-0.00937.7640.0030.0030.0000.0000.0000.000
185A189SER00.0250.02439.541-0.001-0.0010.0000.0000.0000.000
186A190ASP-1-0.876-0.92142.067-0.028-0.0280.0000.0000.0000.000
187A191LEU0-0.038-0.02840.5850.0020.0020.0000.0000.0000.000
188A192LEU0-0.0060.00443.0600.0000.0000.0000.0000.0000.000
189A193GLU-1-0.868-0.92843.6060.0060.0060.0000.0000.0000.000
190A194LEU0-0.057-0.02244.6370.0000.0000.0000.0000.0000.000
191A195LEU00.0080.01046.6070.0010.0010.0000.0000.0000.000
192A196VAL0-0.014-0.01246.5060.0000.0000.0000.0000.0000.000
193A197LEU00.0130.00449.5850.0000.0000.0000.0000.0000.000
194A198GLY0-0.008-0.00651.5520.0030.0030.0000.0000.0000.000