Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 1N8QZ

Calculation Name: 4GJ1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4GJ1

Chain ID: A

ChEMBL ID:

UniProt ID: Q9PM74

Base Structure: X-ray

Registration Date: 2023-09-23

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 234
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2891758.415121
FMO2-HF: Nuclear repulsion 2801706.081884
FMO2-HF: Total energy -90052.333237
FMO2-MP2: Total energy -90314.149442


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:THR)


Summations of interaction energy for fragment #1(A:2:THR)
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.
-32.695-28.01124.709-12.848-16.546-0.045
Interaction energy analysis for fragmet #1(A:2:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.029 / q_NPA : -0.030
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].
3A4ILE00.0190.0093.643-1.6930.397-0.003-0.924-1.1630.001
4A5ILE0-0.014-0.0105.2520.3480.379-0.001-0.001-0.0290.000
5A6PRO0-0.0080.0038.2370.0800.0800.0000.0000.0000.000
6A7ALA0-0.0030.00011.2180.0570.0570.0000.0000.0000.000
7A8LEU0-0.074-0.03513.8350.0340.0340.0000.0000.0000.000
8A9ASP-1-0.821-0.89917.608-0.396-0.3960.0000.0000.0000.000
9A10LEU0-0.021-0.02420.1130.0170.0170.0000.0000.0000.000
10A11ILE0-0.006-0.01123.5540.0000.0000.0000.0000.0000.000
11A12ASP-1-0.845-0.90127.073-0.137-0.1370.0000.0000.0000.000
12A13GLY0-0.018-0.01127.5420.0070.0070.0000.0000.0000.000
13A14GLU-1-0.890-0.93627.046-0.160-0.1600.0000.0000.0000.000
14A15VAL0-0.008-0.01120.912-0.013-0.0130.0000.0000.0000.000
15A16VAL0-0.020-0.01422.8320.0130.0130.0000.0000.0000.000
16A17ARG10.8390.90815.2370.4160.4160.0000.0000.0000.000
17A18LEU00.0150.01621.5630.0200.0200.0000.0000.0000.000
18A19VAL0-0.032-0.01621.294-0.033-0.0330.0000.0000.0000.000
19A20LYS10.8650.89819.3960.3620.3620.0000.0000.0000.000
20A21GLY00.0340.01723.456-0.006-0.0060.0000.0000.0000.000
21A22ASP-1-0.931-0.94825.020-0.158-0.1580.0000.0000.0000.000
22A23TYR0-0.016-0.02028.2940.0100.0100.0000.0000.0000.000
23A24GLU-1-0.962-0.96425.690-0.212-0.2120.0000.0000.0000.000
24A25GLN0-0.016-0.01126.4130.0190.0190.0000.0000.0000.000
25A26LYS10.8900.95225.7920.1490.1490.0000.0000.0000.000
26A27LYS10.8370.93422.4710.2540.2540.0000.0000.0000.000
27A28VAL00.0230.00325.048-0.019-0.0190.0000.0000.0000.000
28A29TYR0-0.071-0.06920.7600.0040.0040.0000.0000.0000.000
29A30LYS11.0030.99125.6300.1690.1690.0000.0000.0000.000
30A31TYR0-0.058-0.02221.4510.0170.0170.0000.0000.0000.000
31A32ASN00.0630.02525.021-0.001-0.0010.0000.0000.0000.000
32A33PRO00.0800.03322.316-0.007-0.0070.0000.0000.0000.000
33A34LEU00.0440.02921.647-0.017-0.0170.0000.0000.0000.000
34A35LYS10.9310.95622.4840.1210.1210.0000.0000.0000.000
35A36LYS10.8120.90518.3430.2950.2950.0000.0000.0000.000
36A37PHE00.0730.02415.737-0.020-0.0200.0000.0000.0000.000
37A38LYS10.8050.88117.8570.1240.1240.0000.0000.0000.000
38A39GLU-1-0.869-0.90518.685-0.275-0.2750.0000.0000.0000.000
39A40TYR00.0560.00214.032-0.010-0.0100.0000.0000.0000.000
40A41GLU-1-0.748-0.86214.651-0.190-0.1900.0000.0000.0000.000
41A42LYS10.8950.94816.3390.1560.1560.0000.0000.0000.000
42A43ALA0-0.0110.00214.8550.0230.0230.0000.0000.0000.000
43A44GLY0-0.008-0.00513.320-0.018-0.0180.0000.0000.0000.000
44A45ALA0-0.023-0.01510.692-0.033-0.0330.0000.0000.0000.000
45A46LYS10.9430.9639.8990.2640.2640.0000.0000.0000.000
46A47GLU-1-0.775-0.8548.154-0.065-0.0650.0000.0000.0000.000
47A48LEU0-0.021-0.00710.981-0.129-0.1290.0000.0000.0000.000
48A49HIS00.0570.03412.1660.0400.0400.0000.0000.0000.000
49A50LEU00.0250.01114.0590.0060.0060.0000.0000.0000.000
50A51VAL00.0080.00416.9390.0110.0110.0000.0000.0000.000
51A52ASP-1-0.736-0.86719.469-0.165-0.1650.0000.0000.0000.000
52A53LEU0-0.003-0.02121.7210.0080.0080.0000.0000.0000.000
53A54THR00.002-0.01524.6750.0040.0040.0000.0000.0000.000
54A55GLY00.0210.00626.9090.0110.0110.0000.0000.0000.000
55A56ALA0-0.112-0.04524.0120.0050.0050.0000.0000.0000.000
56A57LYS10.8970.95326.0780.1850.1850.0000.0000.0000.000
57A58ASP-1-0.789-0.87229.272-0.099-0.0990.0000.0000.0000.000
58A59PRO00.0080.01329.745-0.002-0.0020.0000.0000.0000.000
59A60SER0-0.090-0.05730.7910.0050.0050.0000.0000.0000.000
60A61LYS10.8750.92232.4960.1000.1000.0000.0000.0000.000
61A62ARG10.8280.91124.9300.1570.1570.0000.0000.0000.000
62A63GLN0-0.037-0.02426.0780.0140.0140.0000.0000.0000.000
63A64PHE00.0500.00127.402-0.008-0.0080.0000.0000.0000.000
64A65ALA00.0290.02428.427-0.001-0.0010.0000.0000.0000.000
65A66LEU0-0.019-0.00625.4120.0020.0020.0000.0000.0000.000
66A67ILE00.0160.00122.880-0.007-0.0070.0000.0000.0000.000
67A68GLU-1-0.826-0.89824.385-0.080-0.0800.0000.0000.0000.000
68A69LYS10.7810.87326.2120.1070.1070.0000.0000.0000.000
69A70LEU0-0.061-0.03621.768-0.001-0.0010.0000.0000.0000.000
70A71ALA00.005-0.00621.504-0.005-0.0050.0000.0000.0000.000
71A72LYS10.8440.92422.3170.0780.0780.0000.0000.0000.000
72A73GLU-1-0.820-0.88024.507-0.091-0.0910.0000.0000.0000.000
73A74VAL0-0.072-0.02017.977-0.001-0.0010.0000.0000.0000.000
74A75SER0-0.019-0.00919.9590.0150.0150.0000.0000.0000.000
75A76VAL0-0.091-0.02914.3240.0300.0300.0000.0000.0000.000
76A77ASN0-0.017-0.01911.8820.0060.0060.0000.0000.0000.000
77A78LEU00.0210.01914.343-0.072-0.0720.0000.0000.0000.000
78A79GLN00.008-0.00711.3150.0720.0720.0000.0000.0000.000
79A80VAL00.0310.01115.677-0.030-0.0300.0000.0000.0000.000
80A81GLY00.0440.02318.2210.0040.0040.0000.0000.0000.000
81A82GLY00.0190.00219.0350.0070.0070.0000.0000.0000.000
82A83GLY0-0.0010.00022.0380.0220.0220.0000.0000.0000.000
83A84ILE0-0.049-0.00621.0860.0180.0180.0000.0000.0000.000
84A85ARG10.8960.93723.9520.1400.1400.0000.0000.0000.000
85A86SER00.0220.00126.6690.0120.0120.0000.0000.0000.000
86A87LYS10.9030.93927.3150.0450.0450.0000.0000.0000.000
87A88GLU-1-0.859-0.93528.279-0.072-0.0720.0000.0000.0000.000
88A89GLU-1-0.790-0.87526.537-0.141-0.1410.0000.0000.0000.000
89A90VAL0-0.001-0.00722.728-0.006-0.0060.0000.0000.0000.000
90A91LYS10.8580.92024.6870.0460.0460.0000.0000.0000.000
91A92ALA00.0280.01827.1690.0040.0040.0000.0000.0000.000
92A93LEU0-0.020-0.01922.748-0.002-0.0020.0000.0000.0000.000
93A94LEU0-0.017-0.00920.401-0.002-0.0020.0000.0000.0000.000
94A95ASP-1-0.838-0.89423.677-0.039-0.0390.0000.0000.0000.000
95A96CYS0-0.121-0.05425.1100.0040.0040.0000.0000.0000.000
96A97GLY00.0240.00823.3900.0000.0000.0000.0000.0000.000
97A98VAL0-0.077-0.02819.035-0.007-0.0070.0000.0000.0000.000
98A99LYS10.8620.94214.566-0.013-0.0130.0000.0000.0000.000
99A100ARG10.7750.85910.8080.3130.3130.0000.0000.0000.000
100A101VAL00.0140.01016.628-0.034-0.0340.0000.0000.0000.000
101A102VAL0-0.038-0.02514.993-0.006-0.0060.0000.0000.0000.000
102A103ILE00.0360.02317.6470.0170.0170.0000.0000.0000.000
103A104GLY00.0920.02318.793-0.032-0.0320.0000.0000.0000.000
104A105SER0-0.0100.00620.7400.0050.0050.0000.0000.0000.000
105A106MET00.008-0.00123.7740.0070.0070.0000.0000.0000.000
106A107ALA00.0330.02421.5410.0130.0130.0000.0000.0000.000
107A108ILE00.0270.00823.5990.0100.0100.0000.0000.0000.000
108A109LYS10.8580.93526.4070.1660.1660.0000.0000.0000.000
109A110ASP-1-0.790-0.89728.057-0.076-0.0760.0000.0000.0000.000
110A111ALA00.0370.02426.492-0.004-0.0040.0000.0000.0000.000
111A112THR0-0.026-0.01727.1300.0040.0040.0000.0000.0000.000
112A113LEU00.0430.03027.7950.0040.0040.0000.0000.0000.000
113A114CYS0-0.045-0.01323.337-0.007-0.0070.0000.0000.0000.000
114A115LEU0-0.011-0.00724.0810.0040.0040.0000.0000.0000.000
115A116GLU-1-0.898-0.93725.681-0.042-0.0420.0000.0000.0000.000
116A117ILE0-0.016-0.00522.8550.0070.0070.0000.0000.0000.000
117A118LEU0-0.009-0.01119.0000.0060.0060.0000.0000.0000.000
118A119LYS10.8710.93222.7920.0180.0180.0000.0000.0000.000
119A120GLU-1-0.918-0.93725.373-0.034-0.0340.0000.0000.0000.000
120A121PHE00.020-0.00422.6160.0060.0060.0000.0000.0000.000
121A122GLY00.0260.02621.1220.0120.0120.0000.0000.0000.000
122A123SER00.008-0.01416.925-0.014-0.0140.0000.0000.0000.000
123A124GLU-1-0.838-0.90113.2200.1150.1150.0000.0000.0000.000
124A125ALA00.0230.01115.176-0.024-0.0240.0000.0000.0000.000
125A126ILE0-0.0040.00517.242-0.035-0.0350.0000.0000.0000.000
126A127VAL0-0.036-0.01412.759-0.005-0.0050.0000.0000.0000.000
127A128LEU0-0.005-0.00315.3140.0160.0160.0000.0000.0000.000
128A129ALA0-0.025-0.01715.009-0.067-0.0670.0000.0000.0000.000
129A130LEU0-0.037-0.02515.4660.0620.0620.0000.0000.0000.000
130A131ASP-1-0.840-0.90615.853-0.449-0.4490.0000.0000.0000.000
131A132THR0-0.070-0.05815.9830.0420.0420.0000.0000.0000.000
132A133ILE00.0310.00918.422-0.024-0.0240.0000.0000.0000.000
133A134LEU0-0.0150.00120.0950.0070.0070.0000.0000.0000.000
134A135LYS10.9230.97121.9200.1410.1410.0000.0000.0000.000
135A136GLU-1-0.915-0.95725.599-0.115-0.1150.0000.0000.0000.000
136A137ASP-1-0.836-0.93722.249-0.134-0.1340.0000.0000.0000.000
137A138TYR00.0140.00217.367-0.024-0.0240.0000.0000.0000.000
138A139VAL0-0.006-0.00220.9870.0130.0130.0000.0000.0000.000
139A140VAL0-0.023-0.00520.420-0.029-0.0290.0000.0000.0000.000
140A141ALA0-0.017-0.00421.5710.0180.0180.0000.0000.0000.000
141A150ASP-1-0.900-0.95026.336-0.120-0.1200.0000.0000.0000.000
142A151LYS10.8330.90825.3040.1070.1070.0000.0000.0000.000
143A152LYS10.9270.94823.3360.0720.0720.0000.0000.0000.000
144A153LEU00.0290.00915.7090.0040.0040.0000.0000.0000.000
145A154MET00.0410.01317.801-0.021-0.0210.0000.0000.0000.000
146A155GLU-1-0.799-0.87119.578-0.075-0.0750.0000.0000.0000.000
147A156VAL0-0.035-0.01820.5140.0130.0130.0000.0000.0000.000
148A157LEU0-0.015-0.01515.1510.0020.0020.0000.0000.0000.000
149A158ASP-1-0.856-0.93418.885-0.033-0.0330.0000.0000.0000.000
150A159PHE0-0.054-0.01920.8900.0220.0220.0000.0000.0000.000
151A160TYR0-0.017-0.04519.7520.0160.0160.0000.0000.0000.000
152A161SER00.0100.01917.7820.0120.0120.0000.0000.0000.000
153A162ASN0-0.082-0.03819.0040.0440.0440.0000.0000.0000.000
154A163LYS10.8600.92821.8040.0310.0310.0000.0000.0000.000
155A164GLY00.0050.01219.572-0.002-0.0020.0000.0000.0000.000
156A165LEU0-0.0120.00115.9220.0100.0100.0000.0000.0000.000
157A166LYS10.9020.95310.919-0.266-0.2660.0000.0000.0000.000
158A167HIS0-0.016-0.0189.885-0.148-0.1480.0000.0000.0000.000
159A168ILE00.0290.01811.1310.0560.0560.0000.0000.0000.000
160A169LEU0-0.032-0.01510.364-0.187-0.1870.0000.0000.0000.000
161A170CYS0-0.029-0.00510.7250.1380.1380.0000.0000.0000.000
162A171THR00.0370.01911.462-0.168-0.1680.0000.0000.0000.000
163A172ASP-1-0.778-0.86913.980-0.291-0.2910.0000.0000.0000.000
164A173ILE0-0.019-0.01115.986-0.009-0.0090.0000.0000.0000.000
165A174SER00.008-0.00918.3580.0480.0480.0000.0000.0000.000
166A175LYS10.7820.90314.9380.3680.3680.0000.0000.0000.000
167A176ASP-1-0.812-0.90515.764-0.380-0.3800.0000.0000.0000.000
168A177GLY00.0440.03615.765-0.053-0.0530.0000.0000.0000.000
169A178THR0-0.017-0.02618.2790.0120.0120.0000.0000.0000.000
170A179MET0-0.062-0.02617.1800.0240.0240.0000.0000.0000.000
171A180GLN00.0250.00216.611-0.017-0.0170.0000.0000.0000.000
172A181GLY00.0470.05613.5870.0080.0080.0000.0000.0000.000
173A182VAL00.0130.0018.3600.0170.0170.0000.0000.0000.000
174A183ASN0-0.054-0.03911.6550.0920.0920.0000.0000.0000.000
175A184VAL00.023-0.0048.945-0.045-0.0450.0000.0000.0000.000
176A185ARG10.9340.96710.7000.0840.0840.0000.0000.0000.000
177A186LEU00.0340.02812.8990.0260.0260.0000.0000.0000.000
178A187TYR00.011-0.0338.182-0.058-0.0580.0000.0000.0000.000
179A188LYS10.9250.9539.130-0.134-0.1340.0000.0000.0000.000
180A189LEU00.0250.03210.4310.0800.0800.0000.0000.0000.000
181A190ILE00.0200.00511.3470.0300.0300.0000.0000.0000.000
182A191HIS0-0.025-0.0127.502-0.043-0.0430.0000.0000.0000.000
183A192GLU-1-0.976-0.98210.3490.1110.1110.0000.0000.0000.000
184A193ILE0-0.019-0.00413.2260.0520.0520.0000.0000.0000.000
185A194PHE0-0.041-0.02013.5050.0330.0330.0000.0000.0000.000
186A195PRO00.0290.01511.194-0.066-0.0660.0000.0000.0000.000
187A196ASN0-0.045-0.02610.6400.1050.1050.0000.0000.0000.000
188A197ILE0-0.025-0.00110.9730.0300.0300.0000.0000.0000.000
189A198CYS0-0.071-0.0307.7540.0610.0610.0000.0000.0000.000
190A199ILE00.0380.0126.901-0.050-0.0500.0000.0000.0000.000
191A200GLN00.0120.0105.693-0.959-0.9590.0000.0000.0000.000
192A201ALA00.0500.0175.8410.3530.3530.0000.0000.0000.000
193A202SER0-0.020-0.0187.563-0.048-0.0480.0000.0000.0000.000
194A203GLY00.0300.01710.4880.0850.0850.0000.0000.0000.000
195A204GLY0-0.020-0.02212.234-0.036-0.0360.0000.0000.0000.000
196A205VAL0-0.048-0.0218.7020.0250.0250.0000.0000.0000.000
197A206ALA0-0.014-0.00111.3790.0350.0350.0000.0000.0000.000
198A207SER0-0.043-0.02812.0360.0660.0660.0000.0000.0000.000
199A208LEU00.0830.0259.823-0.085-0.0850.0000.0000.0000.000
200A209LYS10.8650.9248.8220.0430.0430.0000.0000.0000.000
201A210ASP-1-0.803-0.9038.886-0.458-0.4580.0000.0000.0000.000
202A211LEU00.012-0.0064.918-0.105-0.1050.0000.0000.0000.000
203A212GLU-1-0.863-0.9164.294-0.0510.064-0.001-0.015-0.1000.000
204A213ASN0-0.045-0.0256.4690.5440.5440.0000.0000.0000.000
205A214LEU0-0.017-0.0123.741-0.0780.1300.004-0.038-0.1730.000
206A215LYS10.8330.9212.599-3.603-1.1621.540-1.618-2.3640.007
207A216GLY0-0.046-0.0181.998-6.560-7.9565.462-1.643-2.4230.026
208A217ILE0-0.049-0.0163.741-2.258-1.8580.003-0.066-0.3380.000
209A218CYS0-0.0060.0183.182-0.4160.6000.051-0.400-0.6680.000
210A219SER0-0.0110.0031.723-15.340-18.91813.519-5.692-4.249-0.058
211A220GLY00.003-0.0072.640-1.1410.6921.364-1.645-1.551-0.018
212A221VAL00.0070.0062.636-0.477-0.0390.776-0.201-1.013-0.001
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