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

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FMODB ID: G5531

Calculation Name: 1XTZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1XTZ

Chain ID: A

ChEMBL ID:

UniProt ID: Q12189

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 OptAll
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 246
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3146039.669071
FMO2-HF: Nuclear repulsion 3051865.003119
FMO2-HF: Total energy -94174.665953
FMO2-MP2: Total energy -94455.914247


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:19:GLU)


Summations of interaction energy for fragment #1(A:19:GLU)
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.
-184.74-193.38249.071-22.222-18.2080.193
Interaction energy analysis for fragmet #1(A:19:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.795 / q_NPA : -0.866
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].
3A21ALA0-0.010-0.0123.437-3.103-1.5750.006-0.587-0.9470.002
4A22LYS10.7620.8601.686-148.543-151.97425.672-12.009-10.2310.132
5A23ARG10.8980.9433.788-36.220-35.7670.001-0.183-0.2720.001
6A24ALA00.0160.0175.561-3.871-3.8710.0000.0000.0000.000
7A25ALA00.000-0.0097.793-2.882-2.8820.0000.0000.0000.000
8A26ALA0-0.009-0.0187.689-2.674-2.6740.0000.0000.0000.000
9A27TYR0-0.055-0.0559.342-3.042-3.0420.0000.0000.0000.000
10A28ARG10.8360.89911.602-19.839-19.8390.0000.0000.0000.000
11A29ALA0-0.0070.01212.376-1.378-1.3780.0000.0000.0000.000
12A30VAL00.0110.01713.203-1.242-1.2420.0000.0000.0000.000
13A31ASP-1-0.766-0.84215.47817.07817.0780.0000.0000.0000.000
14A32GLU-1-0.808-0.85417.34815.69415.6940.0000.0000.0000.000
15A33ASN0-0.080-0.05917.290-1.453-1.4530.0000.0000.0000.000
16A34LEU0-0.011-0.00118.059-0.446-0.4460.0000.0000.0000.000
17A35LYS10.8240.91320.658-11.317-11.3170.0000.0000.0000.000
18A36PHE00.018-0.01420.499-0.165-0.1650.0000.0000.0000.000
19A37ASP-1-0.925-0.95025.47110.66910.6690.0000.0000.0000.000
20A38ASP-1-0.855-0.91627.27910.50610.5060.0000.0000.0000.000
21A39HIS0-0.061-0.03123.4660.2790.2790.0000.0000.0000.000
22A40LYS10.9390.97125.846-10.652-10.6520.0000.0000.0000.000
23A41ILE0-0.0150.00024.8020.3230.3230.0000.0000.0000.000
24A42ILE00.0370.01618.7310.1330.1330.0000.0000.0000.000
25A43GLY00.0190.00419.5490.1230.1230.0000.0000.0000.000
26A44ILE0-0.015-0.01313.8100.8880.8880.0000.0000.0000.000
27A45GLY00.0600.04413.798-0.471-0.4710.0000.0000.0000.000
28A46SER00.0260.01512.5980.8120.8120.0000.0000.0000.000
29A47GLY0-0.0050.0149.7261.3801.3800.0000.0000.0000.000
30A48SER00.014-0.0104.6762.5812.651-0.001-0.011-0.0580.000
31A49THR00.006-0.0044.07018.91919.2650.002-0.038-0.3100.000
32A50VAL0-0.0060.0066.172-1.736-1.7360.0000.0000.0000.000
33A51VAL00.0170.0125.325-3.787-3.7870.0000.0000.0000.000
34A52TYR0-0.002-0.0411.609-35.748-43.41223.392-9.391-6.3380.058
35A53VAL0-0.0040.0117.555-3.257-3.2570.0000.0000.0000.000
36A54ALA00.003-0.00110.747-2.485-2.4850.0000.0000.0000.000
37A55GLU-1-0.771-0.8397.89629.05229.0520.0000.0000.0000.000
38A56ARG10.7670.86111.409-20.952-20.9520.0000.0000.0000.000
39A57ILE00.019-0.00713.114-1.626-1.6260.0000.0000.0000.000
40A58GLY00.0580.02815.055-1.276-1.2760.0000.0000.0000.000
41A59GLN0-0.042-0.01811.904-2.127-2.1270.0000.0000.0000.000
42A60TYR0-0.057-0.05316.842-1.304-1.3040.0000.0000.0000.000
43A61LEU0-0.0230.00019.313-0.824-0.8240.0000.0000.0000.000
44A62HIS0-0.062-0.04418.632-0.899-0.8990.0000.0000.0000.000
45A63ASP-1-0.798-0.87521.17912.27512.2750.0000.0000.0000.000
46A64PRO00.017-0.00122.726-0.183-0.1830.0000.0000.0000.000
47A65LYS10.7690.87823.881-12.659-12.6590.0000.0000.0000.000
48A66PHE00.0140.00022.931-0.186-0.1860.0000.0000.0000.000
49A67TYR00.0400.04424.5320.0220.0220.0000.0000.0000.000
50A68GLU-1-0.854-0.91825.47210.26010.2600.0000.0000.0000.000
51A69VAL0-0.0300.00125.906-0.266-0.2660.0000.0000.0000.000
52A70ALA00.0580.02521.8720.0720.0720.0000.0000.0000.000
53A71SER0-0.021-0.02923.7210.3730.3730.0000.0000.0000.000
54A72LYS10.7520.86725.806-10.677-10.6770.0000.0000.0000.000
55A73PHE00.0040.00720.807-0.220-0.2200.0000.0000.0000.000
56A74ILE0-0.039-0.01424.266-0.119-0.1190.0000.0000.0000.000
57A75CYS0-0.0100.00918.9180.3130.3130.0000.0000.0000.000
58A76ILE0-0.007-0.01520.705-0.397-0.3970.0000.0000.0000.000
59A77PRO0-0.003-0.00418.1360.7650.7650.0000.0000.0000.000
60A78THR0-0.004-0.03215.542-0.596-0.5960.0000.0000.0000.000
61A79GLY00.1010.04617.3540.3320.3320.0000.0000.0000.000
62A80PHE0-0.042-0.02717.1300.3490.3490.0000.0000.0000.000
63A81GLN0-0.029-0.01510.1150.5410.5410.0000.0000.0000.000
64A82SER0-0.008-0.00313.2310.1630.1630.0000.0000.0000.000
65A83ARG10.9960.99114.386-14.919-14.9190.0000.0000.0000.000
66A84ASN0-0.005-0.00213.574-1.511-1.5110.0000.0000.0000.000
67A85LEU00.0010.0018.9790.0130.0130.0000.0000.0000.000
68A86ILE00.0010.00913.002-0.234-0.2340.0000.0000.0000.000
69A87LEU0-0.006-0.00316.383-0.580-0.5800.0000.0000.0000.000
70A88ASP-1-0.904-0.94613.95619.78319.7830.0000.0000.0000.000
71A89ASN0-0.049-0.04111.824-0.263-0.2630.0000.0000.0000.000
72A90LYS10.8150.90215.929-18.116-18.1160.0000.0000.0000.000
73A91LEU00.0190.02416.799-0.877-0.8770.0000.0000.0000.000
74A92GLN0-0.039-0.02620.439-0.171-0.1710.0000.0000.0000.000
75A93LEU0-0.019-0.00219.9860.4110.4110.0000.0000.0000.000
76A94GLY00.0000.00122.661-0.719-0.7190.0000.0000.0000.000
77A95SER0-0.062-0.06223.7730.4600.4600.0000.0000.0000.000
78A96ILE00.0640.02024.223-0.324-0.3240.0000.0000.0000.000
79A97GLU-1-0.854-0.92326.63011.55511.5550.0000.0000.0000.000
80A98GLN0-0.042-0.00129.408-0.374-0.3740.0000.0000.0000.000
81A99TYR0-0.025-0.02427.080-0.291-0.2910.0000.0000.0000.000
82A100PRO00.0130.02727.6820.3980.3980.0000.0000.0000.000
83A101ARG10.8760.91728.874-10.026-10.0260.0000.0000.0000.000
84A102ILE00.0720.04222.420-0.147-0.1470.0000.0000.0000.000
85A103ASP-1-0.810-0.86625.03011.44411.4440.0000.0000.0000.000
86A104ILE0-0.0170.00019.690-0.095-0.0950.0000.0000.0000.000
87A105ALA00.0080.01219.1350.1930.1930.0000.0000.0000.000
88A106PHE00.0350.01413.9480.1350.1350.0000.0000.0000.000
89A107ASP-1-0.749-0.87612.86025.56525.5650.0000.0000.0000.000
90A108GLY0-0.0060.00910.5880.7280.7280.0000.0000.0000.000
91A109ALA0-0.007-0.00611.483-2.575-2.5750.0000.0000.0000.000
92A110ASP-1-0.826-0.92211.51830.86030.8600.0000.0000.0000.000
93A111GLU-1-0.743-0.87213.34818.29418.2940.0000.0000.0000.000
94A112VAL0-0.0110.00215.061-0.410-0.4100.0000.0000.0000.000
95A113ASP-1-0.772-0.88717.69213.88413.8840.0000.0000.0000.000
96A114GLU-1-0.783-0.87220.92712.23612.2360.0000.0000.0000.000
97A115ASN0-0.092-0.04722.933-0.650-0.6500.0000.0000.0000.000
98A116LEU0-0.050-0.01219.350-0.209-0.2090.0000.0000.0000.000
99A117GLN0-0.033-0.02721.814-0.019-0.0190.0000.0000.0000.000
100A118LEU0-0.014-0.02517.4310.8590.8590.0000.0000.0000.000
101A119ILE0-0.0210.00817.209-0.947-0.9470.0000.0000.0000.000
102A120LYS10.7720.86814.537-20.577-20.5770.0000.0000.0000.000
103A121GLY00.0880.04115.104-1.452-1.4520.0000.0000.0000.000
104A122GLY00.004-0.00112.911-0.852-0.8520.0000.0000.0000.000
105A123GLY0-0.027-0.01813.192-0.128-0.1280.0000.0000.0000.000
106A124ALA0-0.027-0.01313.671-0.723-0.7230.0000.0000.0000.000
107A125CYS0-0.046-0.01816.279-0.717-0.7170.0000.0000.0000.000
108A126LEU0-0.007-0.00318.091-0.300-0.3000.0000.0000.0000.000
109A127PHE00.0190.01119.667-0.262-0.2620.0000.0000.0000.000
110A128GLN0-0.011-0.01220.0690.0830.0830.0000.0000.0000.000
111A129GLU-1-0.835-0.92815.34321.80321.8030.0000.0000.0000.000
112A130LYS10.8020.89318.829-14.186-14.1860.0000.0000.0000.000
113A131LEU0-0.0230.02122.018-0.504-0.5040.0000.0000.0000.000
114A132VAL00.0130.01219.355-0.524-0.5240.0000.0000.0000.000
115A133SER0-0.031-0.03419.813-0.312-0.3120.0000.0000.0000.000
116A134THR0-0.041-0.03321.571-0.525-0.5250.0000.0000.0000.000
117A135SER0-0.039-0.01624.970-0.773-0.7730.0000.0000.0000.000
118A136ALA0-0.032-0.01323.134-0.251-0.2510.0000.0000.0000.000
119A137LYS10.7830.87225.105-11.511-11.5110.0000.0000.0000.000
120A138THR0-0.047-0.02221.545-0.242-0.2420.0000.0000.0000.000
121A139PHE0-0.0020.00517.0850.3990.3990.0000.0000.0000.000
122A140ILE0-0.0070.00715.102-0.325-0.3250.0000.0000.0000.000
123A141VAL00.0210.00713.7861.0141.0140.0000.0000.0000.000
124A142VAL00.0050.0038.988-0.411-0.4110.0000.0000.0000.000
125A143ALA0-0.038-0.0178.3393.0203.0200.0000.0000.0000.000
126A144ASP-1-0.745-0.8385.35841.40841.464-0.001-0.003-0.0520.000
127A145SER00.030-0.0157.343-1.922-1.9220.0000.0000.0000.000
128A146ARG10.8300.8836.449-41.475-41.4750.0000.0000.0000.000
129A147LYS10.7630.8848.934-34.819-34.8190.0000.0000.0000.000
130A148LYS10.8470.93112.418-20.141-20.1410.0000.0000.0000.000
131A149SER00.011-0.01115.223-0.327-0.3270.0000.0000.0000.000
132A150PRO0-0.058-0.03918.258-0.383-0.3830.0000.0000.0000.000
133A151LYS10.7980.89020.790-12.312-12.3120.0000.0000.0000.000
134A152HIS00.0150.00023.021-0.213-0.2130.0000.0000.0000.000
135A153LEU0-0.0180.01119.5160.6970.6970.0000.0000.0000.000
136A154GLY00.0440.03619.967-0.752-0.7520.0000.0000.0000.000
137A155LYS10.7980.90420.086-13.997-13.9970.0000.0000.0000.000
138A156ASN0-0.021-0.03914.956-1.202-1.2020.0000.0000.0000.000
139A157TRP0-0.065-0.02711.7931.6251.6250.0000.0000.0000.000
140A158ARG10.7810.84516.826-15.220-15.2200.0000.0000.0000.000
141A159GLN0-0.0070.00114.096-1.278-1.2780.0000.0000.0000.000
142A160GLY00.0220.02419.154-0.610-0.6100.0000.0000.0000.000
143A161VAL0-0.010-0.02119.5941.0581.0580.0000.0000.0000.000
144A162PRO0-0.0010.02217.742-0.607-0.6070.0000.0000.0000.000
145A163ILE0-0.014-0.01520.887-0.381-0.3810.0000.0000.0000.000
146A164GLU-1-0.723-0.82523.19514.36314.3630.0000.0000.0000.000
147A165ILE0-0.006-0.00925.062-0.483-0.4830.0000.0000.0000.000
148A166VAL00.0740.03528.5650.1500.1500.0000.0000.0000.000
149A167PRO00.0160.02729.407-0.222-0.2220.0000.0000.0000.000
150A168SER0-0.001-0.01131.2140.0510.0510.0000.0000.0000.000
151A169SER0-0.061-0.03832.280-0.176-0.1760.0000.0000.0000.000
152A170TYR00.0220.00230.306-0.055-0.0550.0000.0000.0000.000
153A171VAL00.0120.01431.8920.1350.1350.0000.0000.0000.000
154A172ARG10.8720.92434.725-8.597-8.5970.0000.0000.0000.000
155A173VAL00.0390.01730.089-0.065-0.0650.0000.0000.0000.000
156A174LYS10.8930.93329.357-10.756-10.7560.0000.0000.0000.000
157A175ASN0-0.040-0.04032.0170.1450.1450.0000.0000.0000.000
158A176ASP-1-0.752-0.86534.7998.7908.7900.0000.0000.0000.000
159A177LEU0-0.027-0.02628.4390.0160.0160.0000.0000.0000.000
160A178LEU0-0.028-0.00931.3660.0950.0950.0000.0000.0000.000
161A179GLU-1-0.914-0.93733.9578.2678.2670.0000.0000.0000.000
162A180GLN0-0.086-0.04336.278-0.316-0.3160.0000.0000.0000.000
163A181LEU0-0.081-0.04931.952-0.025-0.0250.0000.0000.0000.000
164A182HIS0-0.0390.00033.0960.2540.2540.0000.0000.0000.000
165A183ALA0-0.0100.00428.8950.1230.1230.0000.0000.0000.000
166A184GLU-1-0.918-0.95727.92511.20111.2010.0000.0000.0000.000
167A185LYS10.8670.91623.991-13.150-13.1500.0000.0000.0000.000
168A186VAL00.0320.02226.7260.3740.3740.0000.0000.0000.000
169A187ASP-1-0.892-0.92524.83711.59611.5960.0000.0000.0000.000
170A188ILE00.0140.01825.0280.3600.3600.0000.0000.0000.000
171A189ARG10.7600.86116.188-18.695-18.6950.0000.0000.0000.000
172A190GLN0-0.016-0.02522.372-0.550-0.5500.0000.0000.0000.000
173A191GLY00.0220.00720.1940.8290.8290.0000.0000.0000.000
174A192GLY0-0.012-0.00619.6190.6060.6060.0000.0000.0000.000
175A193SER0-0.017-0.02418.995-0.408-0.4080.0000.0000.0000.000
176A194ALA0-0.0010.01718.079-0.379-0.3790.0000.0000.0000.000
177A195LYS10.8290.89820.233-13.352-13.3520.0000.0000.0000.000
178A196ALA00.0570.04123.1640.0760.0760.0000.0000.0000.000
179A197GLY00.0180.01725.924-0.206-0.2060.0000.0000.0000.000
180A198PRO0-0.0010.00624.8690.5940.5940.0000.0000.0000.000
181A199VAL00.0120.00119.6970.0120.0120.0000.0000.0000.000
182A200VAL0-0.036-0.02322.591-0.628-0.6280.0000.0000.0000.000
183A201THR0-0.011-0.01221.2660.4480.4480.0000.0000.0000.000
184A202ASP-1-0.821-0.91819.28016.97516.9750.0000.0000.0000.000
185A203ASN0-0.050-0.03722.283-0.528-0.5280.0000.0000.0000.000
186A204ASN0-0.058-0.02725.452-0.562-0.5620.0000.0000.0000.000
187A205ASN0-0.035-0.01925.786-0.900-0.9000.0000.0000.0000.000
188A206PHE00.0030.00125.2750.4040.4040.0000.0000.0000.000
189A207ILE00.0170.00320.2960.0780.0780.0000.0000.0000.000
190A208ILE0-0.035-0.01723.647-0.307-0.3070.0000.0000.0000.000
191A209ASP-1-0.770-0.85119.69417.42017.4200.0000.0000.0000.000
192A210ALA00.012-0.01222.652-0.579-0.5790.0000.0000.0000.000
193A211ASP-1-0.782-0.86123.98013.87013.8700.0000.0000.0000.000
194A212PHE0-0.003-0.02124.904-0.534-0.5340.0000.0000.0000.000
195A213GLY00.0930.07325.686-0.290-0.2900.0000.0000.0000.000
196A214GLU-1-0.884-0.92024.08913.29513.2950.0000.0000.0000.000
197A215ILE00.003-0.00423.396-0.560-0.5600.0000.0000.0000.000
198A216SER0-0.004-0.00926.3390.2710.2710.0000.0000.0000.000
199A217ASP-1-0.843-0.92428.86910.45510.4550.0000.0000.0000.000
200A218PRO00.0180.00225.143-0.144-0.1440.0000.0000.0000.000
201A219ARG10.8960.93427.260-11.005-11.0050.0000.0000.0000.000
202A220LYS10.7840.86829.527-9.729-9.7290.0000.0000.0000.000
203A221LEU00.0460.02926.897-0.118-0.1180.0000.0000.0000.000
204A222HIS00.0170.02427.0500.1600.1600.0000.0000.0000.000
205A223ARG10.9250.95928.696-9.527-9.5270.0000.0000.0000.000
206A224GLU-1-0.814-0.88832.3249.4159.4150.0000.0000.0000.000
207A225ILE00.0450.01427.186-0.155-0.1550.0000.0000.0000.000
208A226LYS10.7870.90328.985-11.013-11.0130.0000.0000.0000.000
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