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: YV3Q2

Calculation Name: 1XKR-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1XKR

Chain ID: A

ChEMBL ID:

UniProt ID: Q9X006

Base Structure: X-ray

Registration Date: 2023-09-24

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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2304698.658292
FMO2-HF: Nuclear repulsion 2224607.517149
FMO2-HF: Total energy -80091.141143
FMO2-MP2: Total energy -80320.513207


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:0:HIS)


Summations of interaction energy for fragment #1(A:0: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.
-17.674-15.436.969-4.486-4.727-0.029
Interaction energy analysis for fragmet #1(A:0:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / q_NPA : -0.002
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].
3A2LYS10.9430.9641.938-13.177-11.1986.968-4.432-4.515-0.029
4A3ILE00.0210.0244.2341.7081.9730.001-0.054-0.2120.000
5A4SER0-0.067-0.0527.0770.4610.4610.0000.0000.0000.000
6A5GLU-1-0.759-0.8919.760-1.727-1.7270.0000.0000.0000.000
7A6ARG10.8710.93312.7561.0421.0420.0000.0000.0000.000
8A7GLN00.0430.03410.302-0.155-0.1550.0000.0000.0000.000
9A8LYS10.8770.9249.6692.1352.1350.0000.0000.0000.000
10A9ASP-1-0.829-0.91013.997-0.678-0.6780.0000.0000.0000.000
11A10LEU0-0.0090.00916.8030.0820.0820.0000.0000.0000.000
12A11LEU00.005-0.00413.6760.0660.0660.0000.0000.0000.000
13A12LYS10.8850.93817.7150.7630.7630.0000.0000.0000.000
14A13GLU-1-0.965-0.97719.832-0.543-0.5430.0000.0000.0000.000
15A14ILE0-0.0010.00119.7560.0570.0570.0000.0000.0000.000
16A15GLY00.0130.00121.6110.0500.0500.0000.0000.0000.000
17A16ASN0-0.062-0.04923.0320.0910.0910.0000.0000.0000.000
18A17ILE00.0010.01825.6880.0470.0470.0000.0000.0000.000
19A18GLY00.0350.02026.3020.0380.0380.0000.0000.0000.000
20A19ALA00.0160.00726.9730.0300.0300.0000.0000.0000.000
21A20GLY00.0520.02828.7420.0310.0310.0000.0000.0000.000
22A21ASN0-0.084-0.05630.5360.0460.0460.0000.0000.0000.000
23A22ALA00.0200.01230.7360.0240.0240.0000.0000.0000.000
24A23ALA0-0.011-0.00832.7630.0210.0210.0000.0000.0000.000
25A24THR0-0.0010.01234.5830.0240.0240.0000.0000.0000.000
26A25ALA00.003-0.00335.9570.0170.0170.0000.0000.0000.000
27A26ILE00.0340.00233.8000.0150.0150.0000.0000.0000.000
28A27SER0-0.027-0.01337.8750.0150.0150.0000.0000.0000.000
29A28TYR0-0.060-0.03840.2950.0170.0170.0000.0000.0000.000
30A29MET0-0.067-0.01339.9490.0070.0070.0000.0000.0000.000
31A30ILE0-0.011-0.01239.3370.0090.0090.0000.0000.0000.000
32A31ASN0-0.075-0.01843.0470.0110.0110.0000.0000.0000.000
33A32LYS10.8290.89742.1560.1730.1730.0000.0000.0000.000
34A33LYS10.7740.89339.5610.2080.2080.0000.0000.0000.000
35A34VAL0-0.002-0.01035.4820.0000.0000.0000.0000.0000.000
36A35GLU-1-0.845-0.90134.019-0.245-0.2450.0000.0000.0000.000
37A36ILE0-0.021-0.01728.961-0.001-0.0010.0000.0000.0000.000
38A37SER0-0.027-0.00327.818-0.010-0.0100.0000.0000.0000.000
39A38VAL00.008-0.00121.655-0.002-0.0020.0000.0000.0000.000
40A39PRO00.0050.00923.438-0.026-0.0260.0000.0000.0000.000
41A40ASN0-0.068-0.04818.360-0.072-0.0720.0000.0000.0000.000
42A41VAL00.0190.02414.7020.0240.0240.0000.0000.0000.000
43A42GLU-1-0.944-0.95613.401-1.060-1.0600.0000.0000.0000.000
44A43ILE0-0.047-0.0329.024-0.051-0.0510.0000.0000.0000.000
45A44VAL00.0130.00910.511-0.192-0.1920.0000.0000.0000.000
46A45PRO00.0130.0099.6400.0010.0010.0000.0000.0000.000
47A46ILE00.0760.02011.6170.1360.1360.0000.0000.0000.000
48A47SER00.0210.02113.7100.0580.0580.0000.0000.0000.000
49A48LYS10.8210.89312.7950.5560.5560.0000.0000.0000.000
50A49VAL00.0640.04215.8670.0260.0260.0000.0000.0000.000
51A50ILE0-0.0160.01217.9890.0410.0410.0000.0000.0000.000
52A51PHE0-0.068-0.04117.5030.0490.0490.0000.0000.0000.000
53A52ILE0-0.0060.01516.8220.0240.0240.0000.0000.0000.000
54A53ALA0-0.0320.00020.9480.0230.0230.0000.0000.0000.000
55A54LYS10.9460.96124.3840.3190.3190.0000.0000.0000.000
56A55ASP-1-0.832-0.92027.282-0.178-0.1780.0000.0000.0000.000
57A56PRO0-0.029-0.01625.166-0.014-0.0140.0000.0000.0000.000
58A57GLU-1-0.916-0.99426.983-0.153-0.1530.0000.0000.0000.000
59A58GLU-1-0.820-0.86930.089-0.246-0.2460.0000.0000.0000.000
60A59ILE0-0.049-0.02330.691-0.012-0.0120.0000.0000.0000.000
61A60VAL0-0.025-0.01728.134-0.002-0.0020.0000.0000.0000.000
62A61VAL0-0.002-0.00331.6070.0110.0110.0000.0000.0000.000
63A62GLY00.0280.01628.526-0.024-0.0240.0000.0000.0000.000
64A63VAL0-0.052-0.02828.3570.0240.0240.0000.0000.0000.000
65A64LYS10.9300.96923.0290.3910.3910.0000.0000.0000.000
66A65MET0-0.0040.00625.7590.0270.0270.0000.0000.0000.000
67A66PRO00.002-0.00324.350-0.046-0.0460.0000.0000.0000.000
68A67VAL0-0.036-0.02421.6700.0200.0200.0000.0000.0000.000
69A68THR0-0.038-0.04223.2110.0000.0000.0000.0000.0000.000
70A69GLY00.0300.01524.0930.0080.0080.0000.0000.0000.000
71A70ASP-1-0.883-0.95121.763-0.534-0.5340.0000.0000.0000.000
72A71ILE0-0.069-0.05117.589-0.094-0.0940.0000.0000.0000.000
73A72GLU-1-0.806-0.85618.723-0.422-0.4220.0000.0000.0000.000
74A73GLY00.0290.01018.136-0.101-0.1010.0000.0000.0000.000
75A74SER0-0.044-0.01719.6660.0890.0890.0000.0000.0000.000
76A75VAL0-0.0070.01320.329-0.077-0.0770.0000.0000.0000.000
77A76LEU0-0.008-0.00522.0900.0630.0630.0000.0000.0000.000
78A77LEU00.0250.00723.706-0.036-0.0360.0000.0000.0000.000
79A78ILE00.000-0.00524.3080.0290.0290.0000.0000.0000.000
80A79MET0-0.004-0.00427.149-0.004-0.0040.0000.0000.0000.000
81A80GLY00.0700.03430.4220.0130.0130.0000.0000.0000.000
82A81THR0-0.018-0.05631.5840.0120.0120.0000.0000.0000.000
83A82THR0-0.032-0.02634.5970.0090.0090.0000.0000.0000.000
84A83VAL00.0170.01331.6940.0090.0090.0000.0000.0000.000
85A84VAL00.0160.01234.0600.0080.0080.0000.0000.0000.000
86A85LYS10.8560.92036.5470.1720.1720.0000.0000.0000.000
87A86LYS10.8490.92738.4560.1850.1850.0000.0000.0000.000
88A87ILE00.0290.01435.0020.0070.0070.0000.0000.0000.000
89A88LEU00.000-0.00739.5110.0080.0080.0000.0000.0000.000
90A89GLU-1-0.924-0.92742.044-0.151-0.1510.0000.0000.0000.000
91A90ILE0-0.036-0.01640.8250.0080.0080.0000.0000.0000.000
92A91LEU0-0.050-0.01441.8090.0050.0050.0000.0000.0000.000
93A92THR0-0.049-0.04844.6440.0080.0080.0000.0000.0000.000
94A93GLY0-0.0040.01147.0080.0080.0080.0000.0000.0000.000
95A94ARG10.7530.83247.3030.1350.1350.0000.0000.0000.000
96A95ALA00.0570.04543.319-0.006-0.0060.0000.0000.0000.000
97A96PRO0-0.0070.01541.7130.0090.0090.0000.0000.0000.000
98A97ASP-1-0.810-0.90043.161-0.129-0.1290.0000.0000.0000.000
99A98ASN0-0.031-0.01041.079-0.006-0.0060.0000.0000.0000.000
100A99LEU00.0690.02335.3720.0020.0020.0000.0000.0000.000
101A100LEU00.0430.01737.653-0.004-0.0040.0000.0000.0000.000
102A101ASN0-0.095-0.05040.2440.0080.0080.0000.0000.0000.000
103A102LEU0-0.0170.01538.5400.0050.0050.0000.0000.0000.000
104A103ASP-1-0.784-0.87642.676-0.152-0.1520.0000.0000.0000.000
105A104GLU-1-0.889-0.95643.306-0.151-0.1510.0000.0000.0000.000
106A105PHE0-0.043-0.00342.993-0.010-0.0100.0000.0000.0000.000
107A106SER00.016-0.02741.867-0.009-0.0090.0000.0000.0000.000
108A107ALA0-0.0030.00838.989-0.013-0.0130.0000.0000.0000.000
109A108SER0-0.027-0.03238.181-0.015-0.0150.0000.0000.0000.000
110A109ALA0-0.0020.00838.889-0.011-0.0110.0000.0000.0000.000
111A110LEU00.0130.00035.663-0.013-0.0130.0000.0000.0000.000
112A111ARG10.8590.93134.3030.2290.2290.0000.0000.0000.000
113A112GLU-1-0.854-0.92034.207-0.281-0.2810.0000.0000.0000.000
114A113ILE00.0220.00233.252-0.013-0.0130.0000.0000.0000.000
115A114GLY00.0200.00030.971-0.021-0.0210.0000.0000.0000.000
116A115ASN0-0.061-0.04430.383-0.041-0.0410.0000.0000.0000.000
117A116ILE0-0.0180.00631.658-0.018-0.0180.0000.0000.0000.000
118A117MET00.0010.00928.249-0.012-0.0120.0000.0000.0000.000
119A118CYS0-0.035-0.01826.667-0.039-0.0390.0000.0000.0000.000
120A119GLY00.0630.03227.000-0.031-0.0310.0000.0000.0000.000
121A120THR0-0.051-0.05229.038-0.018-0.0180.0000.0000.0000.000
122A121TYR0-0.0050.00719.289-0.034-0.0340.0000.0000.0000.000
123A122VAL00.0220.00023.996-0.041-0.0410.0000.0000.0000.000
124A123SER0-0.0120.00225.444-0.007-0.0070.0000.0000.0000.000
125A124ALA00.0000.00725.3950.0020.0020.0000.0000.0000.000
126A125LEU0-0.009-0.01518.730-0.024-0.0240.0000.0000.0000.000
127A126ALA0-0.010-0.00722.718-0.032-0.0320.0000.0000.0000.000
128A127ASP-1-0.893-0.94524.760-0.423-0.4230.0000.0000.0000.000
129A128PHE0-0.058-0.04023.2200.0130.0130.0000.0000.0000.000
130A129LEU0-0.044-0.00918.153-0.031-0.0310.0000.0000.0000.000
131A130GLY0-0.0070.00922.102-0.013-0.0130.0000.0000.0000.000
132A131PHE0-0.088-0.03817.9830.0000.0000.0000.0000.0000.000
133A132LYS10.9110.95124.1210.4100.4100.0000.0000.0000.000
134A133ILE0-0.029-0.02022.172-0.023-0.0230.0000.0000.0000.000
135A134ASP-1-0.895-0.91825.904-0.329-0.3290.0000.0000.0000.000
136A135THR00.002-0.01726.801-0.030-0.0300.0000.0000.0000.000
137A136LEU0-0.042-0.02027.9580.0340.0340.0000.0000.0000.000
138A137PRO0-0.016-0.02730.257-0.007-0.0070.0000.0000.0000.000
139A138PRO00.0310.02930.363-0.008-0.0080.0000.0000.0000.000
140A139GLN0-0.018-0.02028.1740.0160.0160.0000.0000.0000.000
141A140LEU0-0.022-0.00130.363-0.018-0.0180.0000.0000.0000.000
142A141VAL00.0270.01228.8650.0150.0150.0000.0000.0000.000
143A142ILE0-0.022-0.01832.080-0.011-0.0110.0000.0000.0000.000
144A143ASP-1-0.829-0.91030.538-0.198-0.1980.0000.0000.0000.000
145A144MET0-0.098-0.02029.467-0.011-0.0110.0000.0000.0000.000
146A145ILE00.0110.00224.874-0.015-0.0150.0000.0000.0000.000
147A146SER00.013-0.02024.802-0.022-0.0220.0000.0000.0000.000
148A147ALA0-0.0070.00924.944-0.010-0.0100.0000.0000.0000.000
149A148ILE00.0370.02124.520-0.013-0.0130.0000.0000.0000.000
150A149PHE00.016-0.01419.904-0.030-0.0300.0000.0000.0000.000
151A150ALA0-0.0380.01320.851-0.027-0.0270.0000.0000.0000.000
152A151GLU-1-0.927-0.96821.921-0.257-0.2570.0000.0000.0000.000
153A152ALA0-0.016-0.00920.230-0.012-0.0120.0000.0000.0000.000
154A153SER0-0.040-0.05417.392-0.064-0.0640.0000.0000.0000.000
155A154ILE0-0.054-0.02517.409-0.003-0.0030.0000.0000.0000.000
156A155GLU-1-0.812-0.89419.270-0.422-0.4220.0000.0000.0000.000
157A156GLU-1-0.865-0.92114.689-0.662-0.6620.0000.0000.0000.000
158A157LEU0-0.082-0.03611.756-0.036-0.0360.0000.0000.0000.000
159A158GLU-1-0.975-0.96215.319-0.192-0.1920.0000.0000.0000.000
160A159ASP-1-0.951-0.97117.038-0.145-0.1450.0000.0000.0000.000
161A160ASN0-0.088-0.06811.970-0.098-0.0980.0000.0000.0000.000
162A161SER00.002-0.0108.8620.0770.0770.0000.0000.0000.000
163A162GLU-1-0.933-0.9427.445-1.672-1.6720.0000.0000.0000.000
164A163ASP-1-0.772-0.9038.717-1.256-1.2560.0000.0000.0000.000
165A164GLN0-0.119-0.0525.827-1.218-1.2180.0000.0000.0000.000
166A165ILE00.0140.02010.0090.1000.1000.0000.0000.0000.000
167A166VAL0-0.047-0.02113.078-0.198-0.1980.0000.0000.0000.000
168A167PHE00.019-0.00615.0890.1730.1730.0000.0000.0000.000
169A168VAL00.0300.00317.259-0.043-0.0430.0000.0000.0000.000
170A169GLU-1-0.845-0.90820.123-0.426-0.4260.0000.0000.0000.000
171A170THR0-0.050-0.04523.182-0.004-0.0040.0000.0000.0000.000
172A171LEU00.005-0.00426.3330.0270.0270.0000.0000.0000.000
173A172LEU00.0200.01029.1050.0040.0040.0000.0000.0000.000
174A173LYS10.8700.91732.4840.2280.2280.0000.0000.0000.000
175A174VAL00.0420.02935.3790.0010.0010.0000.0000.0000.000
176A175GLU-1-0.860-0.93638.990-0.184-0.1840.0000.0000.0000.000
177A176GLU-1-0.897-0.92241.329-0.155-0.1550.0000.0000.0000.000
178A177GLU-1-0.860-0.94939.531-0.174-0.1740.0000.0000.0000.000
179A178GLU-1-0.947-0.97839.508-0.181-0.1810.0000.0000.0000.000
180A179GLU-1-0.891-0.93835.024-0.220-0.2200.0000.0000.0000.000
181A180PRO0-0.073-0.03531.951-0.001-0.0010.0000.0000.0000.000
182A181LEU0-0.013-0.00532.890-0.003-0.0030.0000.0000.0000.000
183A182THR0-0.023-0.00526.964-0.006-0.0060.0000.0000.0000.000
184A183SER0-0.027-0.01328.0780.0240.0240.0000.0000.0000.000
185A184TYR0-0.035-0.01422.615-0.007-0.0070.0000.0000.0000.000
186A185MET0-0.033-0.00722.7760.0430.0430.0000.0000.0000.000
187A186MET0-0.0180.00518.299-0.059-0.0590.0000.0000.0000.000
188A187MET0-0.0250.00617.3320.0370.0370.0000.0000.0000.000
189A188ILE00.033-0.00116.089-0.161-0.1610.0000.0000.0000.000
190A189PRO0-0.034-0.01312.8650.0910.0910.0000.0000.0000.000
191A190LYS10.8640.91014.3840.5330.5330.0000.0000.0000.000
192A191PRO00.0340.00311.813-0.141-0.1410.0000.0000.0000.000
193A192GLY0-0.014-0.01410.8120.1270.1270.0000.0000.0000.000
194A193TYR0-0.034-0.03211.873-0.065-0.0650.0000.0000.0000.000
195A194LEU00.0610.0439.111-0.035-0.0350.0000.0000.0000.000
196A195VAL0-0.017-0.0197.999-0.179-0.1790.0000.0000.0000.000
197A196LYS10.9440.98410.7300.9370.9370.0000.0000.0000.000
198A197ILE00.0320.02014.3270.1040.1040.0000.0000.0000.000
199A198PHE00.002-0.0339.6360.0520.0520.0000.0000.0000.000
200A199GLU-1-0.961-0.96813.193-0.865-0.8650.0000.0000.0000.000
201A200ARG10.8420.91914.8170.8460.8460.0000.0000.0000.000
202A201MET0-0.0280.01615.0260.0450.0450.0000.0000.0000.000
203A202GLY0-0.0150.00917.0890.0770.0770.0000.0000.0000.000
204A203ILE00.009-0.01015.322-0.113-0.1130.0000.0000.0000.000
205A204GLN0-0.0220.01012.8680.0030.0030.0000.0000.0000.000