FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

tag_button

FMODB ID: 2NN3R

Calculation Name: 5X15-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5X15

Chain ID: A

ChEMBL ID:

UniProt ID: Q9FBS9

Base Structure: X-ray

Registration Date: 2023-09-21

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 198
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2075028.596582
FMO2-HF: Nuclear repulsion 1999693.017243
FMO2-HF: Total energy -75335.579339
FMO2-MP2: Total energy -75555.758465


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:34:ARG)


Summations of interaction energy for fragment #1(A:34:ARG)
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.
-131.253-128.56.327-4.687-4.394-0.012
Interaction energy analysis for fragmet #1(A:34:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.951 / q_NPA : 0.976
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].
3A36ASP-1-0.801-0.9023.844-28.014-26.273-0.016-0.913-0.8130.003
4A37GLY00.005-0.0036.3021.9391.9390.0000.0000.0000.000
5A38GLU-1-0.954-0.9887.438-15.465-15.4650.0000.0000.0000.000
6A39LEU00.0000.0049.5941.4711.4710.0000.0000.0000.000
7A40VAL00.0100.0107.3601.1091.1090.0000.0000.0000.000
8A41ARG10.8970.94810.50420.84620.8460.0000.0000.0000.000
9A42SER00.0190.01213.3710.8280.8280.0000.0000.0000.000
10A43LEU00.038-0.00512.2920.9210.9210.0000.0000.0000.000
11A44ASN00.001-0.00214.9011.1521.1520.0000.0000.0000.000
12A45ARG10.8540.94116.37713.21013.2100.0000.0000.0000.000
13A46VAL00.0460.04218.2970.6140.6140.0000.0000.0000.000
14A47SER00.0350.04519.753-0.398-0.3980.0000.0000.0000.000
15A48SER00.0530.03220.555-0.087-0.0870.0000.0000.0000.000
16A49ALA00.0560.02921.533-0.096-0.0960.0000.0000.0000.000
17A50THR0-0.015-0.01323.3600.3810.3810.0000.0000.0000.000
18A51ALA00.018-0.00718.455-0.045-0.0450.0000.0000.0000.000
19A52CYS0-0.063-0.03120.307-0.140-0.1400.0000.0000.0000.000
20A53ALA00.0100.00022.0600.1170.1170.0000.0000.0000.000
21A54LYS10.8360.90121.92711.30511.3050.0000.0000.0000.000
22A55LEU00.019-0.00217.049-0.168-0.1680.0000.0000.0000.000
23A56HIS00.0000.00021.039-0.191-0.1910.0000.0000.0000.000
24A57GLU-1-0.941-0.96424.530-10.132-10.1320.0000.0000.0000.000
25A58LEU0-0.0290.00119.094-0.080-0.0800.0000.0000.0000.000
26A59GLY0-0.035-0.00823.0600.0290.0290.0000.0000.0000.000
27A60ILE0-0.085-0.04818.279-0.283-0.2830.0000.0000.0000.000
28A61ARG11.0071.01422.41010.28710.2870.0000.0000.0000.000
29A62ARG10.7200.89422.32411.95411.9540.0000.0000.0000.000
30A63SER00.1210.05818.967-0.347-0.3470.0000.0000.0000.000
31A64TYR00.0390.03919.376-0.314-0.3140.0000.0000.0000.000
32A65LEU0-0.036-0.02917.8390.3420.3420.0000.0000.0000.000
33A66SER0-0.024-0.00921.7380.3500.3500.0000.0000.0000.000
34A67GLY00.0430.00925.467-0.009-0.0090.0000.0000.0000.000
35A68PRO0-0.076-0.03121.3520.2740.2740.0000.0000.0000.000
36A69THR0-0.032-0.01524.1370.1630.1630.0000.0000.0000.000
37A70ALA00.0420.02124.099-0.283-0.2830.0000.0000.0000.000
38A71LEU0-0.044-0.02124.5470.4920.4920.0000.0000.0000.000
39A72ASP-1-0.925-0.97625.089-10.657-10.6570.0000.0000.0000.000
40A73LEU0-0.031-0.02225.993-0.224-0.2240.0000.0000.0000.000
41A74GLY0-0.0280.00126.310-0.005-0.0050.0000.0000.0000.000
42A75ASN0-0.040-0.02120.979-0.374-0.3740.0000.0000.0000.000
43A76LYS10.8840.92918.22113.01413.0140.0000.0000.0000.000
44A77VAL0-0.043-0.01413.753-0.289-0.2890.0000.0000.0000.000
45A78THR0-0.0410.00612.639-0.179-0.1790.0000.0000.0000.000
46A79GLY00.0350.0078.835-0.254-0.2540.0000.0000.0000.000
47A80PRO0-0.0180.0064.4281.0831.176-0.001-0.005-0.0870.000
48A81ALA00.0270.0177.2261.1721.1720.0000.0000.0000.000
49A82ARG10.8710.9294.64634.53034.620-0.0010.000-0.0890.000
50A83THR0-0.034-0.01910.3031.8041.8040.0000.0000.0000.000
51A84LEU00.0320.01712.919-0.103-0.1030.0000.0000.0000.000
52A85GLN0-0.008-0.00116.1100.6480.6480.0000.0000.0000.000
53A86PHE0-0.007-0.02318.8440.0740.0740.0000.0000.0000.000
54A87MET0-0.004-0.00122.3270.1770.1770.0000.0000.0000.000
55A88PRO00.037-0.00424.9630.1460.1460.0000.0000.0000.000
56A89GLN0-0.092-0.04628.693-0.314-0.3140.0000.0000.0000.000
57A90ARG10.9100.96330.29010.14510.1450.0000.0000.0000.000
58A91GLU-1-0.920-0.95031.928-9.289-9.2890.0000.0000.0000.000
59A92ASP-1-0.903-0.94932.250-8.940-8.9400.0000.0000.0000.000
60A93VAL0-0.088-0.05128.3730.0950.0950.0000.0000.0000.000
61A105SER00.0350.00023.5330.1310.1310.0000.0000.0000.000
62A106THR0-0.015-0.02819.992-0.277-0.2770.0000.0000.0000.000
63A107ALA00.0510.04518.541-0.606-0.6060.0000.0000.0000.000
64A108LEU00.026-0.00217.186-0.901-0.9010.0000.0000.0000.000
65A109TRP0-0.029-0.03017.315-0.276-0.2760.0000.0000.0000.000
66A110ALA00.0090.01713.955-0.302-0.3020.0000.0000.0000.000
67A111VAL00.0360.03912.298-1.339-1.3390.0000.0000.0000.000
68A112LEU00.0120.00512.304-1.211-1.2110.0000.0000.0000.000
69A113GLU-1-1.032-1.03213.132-17.989-17.9890.0000.0000.0000.000
70A114GLU-1-0.925-0.9457.742-33.297-33.2970.0000.0000.0000.000
71A115VAL0-0.072-0.0238.332-2.565-2.5650.0000.0000.0000.000
72A116GLN0-0.039-0.0282.195-9.410-8.5816.345-3.769-3.405-0.015
73A117PRO0-0.038-0.0296.9620.5290.5290.0000.0000.0000.000
74A118GLY00.0010.0047.630-1.117-1.1170.0000.0000.0000.000
75A119ASP-1-0.857-0.9345.896-33.289-33.2890.0000.0000.0000.000
76A120VAL0-0.016-0.0028.4392.3692.3690.0000.0000.0000.000
77A121LEU0-0.0350.00410.978-1.136-1.1360.0000.0000.0000.000
78A122VAL00.0150.00912.9791.2841.2840.0000.0000.0000.000
79A123VAL00.020-0.00515.367-0.473-0.4730.0000.0000.0000.000
80A124GLN00.0280.00618.344-0.047-0.0470.0000.0000.0000.000
81A125ALA00.014-0.00820.6300.0300.0300.0000.0000.0000.000
82A126TYR0-0.044-0.02823.8220.4650.4650.0000.0000.0000.000
83A127GLY00.0320.01725.9300.3930.3930.0000.0000.0000.000
84A128SER0-0.064-0.06827.7980.5020.5020.0000.0000.0000.000
85A129ALA0-0.042-0.03329.610-0.150-0.1500.0000.0000.0000.000
86A130PHE00.004-0.00631.6500.2960.2960.0000.0000.0000.000
87A131THR00.024-0.00227.494-0.105-0.1050.0000.0000.0000.000
88A132GLY0-0.0150.01527.472-0.103-0.1030.0000.0000.0000.000
89A133CYS0-0.049-0.01922.024-0.095-0.0950.0000.0000.0000.000
90A134LEU00.0280.00818.466-0.362-0.3620.0000.0000.0000.000
91A135GLY00.005-0.00223.1600.4860.4860.0000.0000.0000.000
92A136ASP-1-0.821-0.92924.287-11.111-11.1110.0000.0000.0000.000
93A137MET0-0.027-0.01425.051-0.130-0.1300.0000.0000.0000.000
94A138LEU0-0.016-0.02120.620-0.292-0.2920.0000.0000.0000.000
95A139VAL00.0840.05719.582-0.775-0.7750.0000.0000.0000.000
96A140ARG10.9460.98119.70411.20211.2020.0000.0000.0000.000
97A141TYR0-0.014-0.02415.759-0.616-0.6160.0000.0000.0000.000
98A142PHE00.0460.04212.758-0.801-0.8010.0000.0000.0000.000
99A143LYN00.0730.05415.077-0.686-0.6860.0000.0000.0000.000
100A144ARG10.8880.94316.78015.34015.3400.0000.0000.0000.000
101A145LYS10.8490.93712.50320.57120.5710.0000.0000.0000.000
102A146GLY00.0090.01812.138-1.397-1.3970.0000.0000.0000.000
103A147GLY0-0.002-0.00411.250-1.455-1.4550.0000.0000.0000.000
104A148ALA0-0.020-0.00611.4571.1271.1270.0000.0000.0000.000
105A149GLY00.0580.01613.2101.1781.1780.0000.0000.0000.000
106A150ILE0-0.045-0.01714.366-0.953-0.9530.0000.0000.0000.000
107A151VAL00.0230.01616.0140.8200.8200.0000.0000.0000.000
108A152VAL0-0.014-0.01118.246-0.549-0.5490.0000.0000.0000.000
109A153ASP-1-0.819-0.89821.030-11.586-11.5860.0000.0000.0000.000
110A154GLY00.0480.01923.1650.2380.2380.0000.0000.0000.000
111A155ARG10.9051.02625.5499.6619.6610.0000.0000.0000.000
112A156ILE00.0440.01921.941-0.385-0.3850.0000.0000.0000.000
113A157ARG10.9130.95426.13410.69810.6980.0000.0000.0000.000
114A158ASP-1-0.955-0.98227.584-9.925-9.9250.0000.0000.0000.000
115A159ALA00.0300.01228.905-0.188-0.1880.0000.0000.0000.000
116A160PRO0-0.012-0.02329.905-0.082-0.0820.0000.0000.0000.000
117A161ARG10.9500.97829.2499.2399.2390.0000.0000.0000.000
118A162VAL00.0130.00724.148-0.154-0.1540.0000.0000.0000.000
119A163ARG10.9530.98125.5509.3179.3170.0000.0000.0000.000
120A164GLU-1-0.942-0.94627.218-9.469-9.4690.0000.0000.0000.000
121A165LEU0-0.111-0.06123.312-0.198-0.1980.0000.0000.0000.000
122A166GLY00.018-0.01022.2980.0500.0500.0000.0000.0000.000
123A167VAL0-0.052-0.02117.445-0.476-0.4760.0000.0000.0000.000
124A168PRO00.0550.06017.9970.4120.4120.0000.0000.0000.000
125A169ILE0-0.018-0.03418.807-0.786-0.7860.0000.0000.0000.000
126A170TRP00.008-0.00218.4130.3150.3150.0000.0000.0000.000
127A171CYS0-0.058-0.02021.682-0.358-0.3580.0000.0000.0000.000
128A172THR00.015-0.02624.4500.3400.3400.0000.0000.0000.000
129A173GLY00.015-0.01027.7690.4550.4550.0000.0000.0000.000
130A174THR0-0.049-0.01328.305-0.233-0.2330.0000.0000.0000.000
131A175THR00.001-0.00830.0570.2780.2780.0000.0000.0000.000
132A176PRO00.0400.01231.425-0.208-0.2080.0000.0000.0000.000
133A177HIS0-0.030-0.01132.0450.1410.1410.0000.0000.0000.000
134A178TYR0-0.0120.00028.494-0.223-0.2230.0000.0000.0000.000
135A179ALA00.0060.00124.9500.1400.1400.0000.0000.0000.000
136A180SER00.0430.01326.9850.1190.1190.0000.0000.0000.000
137A181GLN0-0.0100.00528.9110.0930.0930.0000.0000.0000.000
138A182SER0-0.001-0.01431.3150.4390.4390.0000.0000.0000.000
139A183GLU-1-0.783-0.85430.966-9.928-9.9280.0000.0000.0000.000
140A184LEU0-0.052-0.00526.124-0.251-0.2510.0000.0000.0000.000
141A185PHE00.0180.00525.4970.1290.1290.0000.0000.0000.000
142A186PRO0-0.042-0.02120.916-0.182-0.1820.0000.0000.0000.000
143A187TRP00.0030.01319.8870.4970.4970.0000.0000.0000.000
144A188ALA0-0.009-0.00515.810-0.354-0.3540.0000.0000.0000.000
145A189TYR0-0.036-0.0409.3141.9421.9420.0000.0000.0000.000
146A190ASP-1-0.803-0.9008.739-32.047-32.0470.0000.0000.0000.000
147A191VAL0-0.053-0.01210.771-0.975-0.9750.0000.0000.0000.000
148A192PRO00.016-0.00612.9850.1430.1430.0000.0000.0000.000
149A193VAL00.0130.02514.8170.6990.6990.0000.0000.0000.000
150A194ALA0-0.048-0.02317.1280.0170.0170.0000.0000.0000.000
151A195ALA00.0230.01818.5210.6190.6190.0000.0000.0000.000
152A196GLY00.0110.00520.215-0.250-0.2500.0000.0000.0000.000
153A197GLY0-0.057-0.06322.7910.1670.1670.0000.0000.0000.000
154A198VAL0-0.046-0.02217.6910.2280.2280.0000.0000.0000.000
155A199LEU00.0060.00715.757-0.062-0.0620.0000.0000.0000.000
156A200THR00.0090.00312.664-0.301-0.3010.0000.0000.0000.000
157A201LEU0-0.019-0.01411.1080.1980.1980.0000.0000.0000.000
158A202PRO0-0.0010.0017.615-0.252-0.2520.0000.0000.0000.000
159A203GLY0-0.020-0.0025.001-2.435-2.4350.0000.0000.0000.000
160A204ASP-1-0.875-0.9545.856-23.967-23.9670.0000.0000.0000.000
161A205LEU0-0.013-0.0127.827-0.652-0.6520.0000.0000.0000.000
162A206VAL0-0.011-0.00110.4651.4361.4360.0000.0000.0000.000
163A207VAL00.002-0.00613.586-0.185-0.1850.0000.0000.0000.000
164A208ALA0-0.044-0.02616.0700.7830.7830.0000.0000.0000.000
165A209ASP-1-0.836-0.92218.188-11.777-11.7770.0000.0000.0000.000
166A210ASP-1-0.815-0.93321.660-10.806-10.8060.0000.0000.0000.000
167A211ASP-1-0.937-0.95624.848-10.185-10.1850.0000.0000.0000.000
168A212GLY0-0.055-0.02923.4720.1720.1720.0000.0000.0000.000
169A213ALA0-0.010-0.00518.162-0.345-0.3450.0000.0000.0000.000
170A214VAL00.001-0.01817.8340.4610.4610.0000.0000.0000.000
171A215VAL0-0.034-0.01013.351-0.636-0.6360.0000.0000.0000.000
172A216VAL00.007-0.00813.3700.7510.7510.0000.0000.0000.000
173A217PRO00.0190.01511.531-1.449-1.4490.0000.0000.0000.000
174A218VAL00.030-0.0016.2030.7170.7170.0000.0000.0000.000
175A219SER0-0.097-0.0309.5450.6040.6040.0000.0000.0000.000
176A220LYS10.9720.97612.33516.14316.1430.0000.0000.0000.000
177A221ALA00.0730.04611.4590.7430.7430.0000.0000.0000.000
178A222GLN0-0.005-0.01213.3290.0260.0260.0000.0000.0000.000
179A223GLU-1-0.927-0.95615.373-13.657-13.6570.0000.0000.0000.000
180A224ILE0-0.022-0.01117.1780.8850.8850.0000.0000.0000.000
181A225VAL0-0.040-0.02215.1590.6280.6280.0000.0000.0000.000
182A226ASP-1-0.859-0.93918.203-14.035-14.0350.0000.0000.0000.000
183A227SER0-0.0120.01320.9640.6360.6360.0000.0000.0000.000
184A228ALA0-0.018-0.03221.3910.5490.5490.0000.0000.0000.000
185A229PHE00.0210.01119.5470.3950.3950.0000.0000.0000.000
186A230ASP-1-0.907-0.94524.204-10.533-10.5330.0000.0000.0000.000
187A231HIS0-0.0060.01426.2030.2670.2670.0000.0000.0000.000
188A232GLU-1-0.863-0.96324.234-10.843-10.8430.0000.0000.0000.000
189A233GLN0-0.028-0.00227.5050.2410.2410.0000.0000.0000.000
190A234TRP0-0.004-0.00529.7810.4920.4920.0000.0000.0000.000
191A235GLU-1-0.920-0.96729.833-9.191-9.1910.0000.0000.0000.000
192A236GLU-1-0.849-0.91330.722-8.743-8.7430.0000.0000.0000.000
193A237PHE0-0.061-0.02232.6880.3420.3420.0000.0000.0000.000
194A238SER0-0.091-0.07035.4990.2310.2310.0000.0000.0000.000
195A239ARG10.8970.94529.1809.4809.4800.0000.0000.0000.000
196A240MET00.0080.01236.8670.1490.1490.0000.0000.0000.000
197A241ARG10.8300.92938.9347.2967.2960.0000.0000.0000.000
198A242ILE0-0.0170.00740.2230.1580.1580.0000.0000.0000.000