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: 1NN1Z

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 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 246
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3139791.066007
FMO2-HF: Nuclear repulsion 3045617.113652
FMO2-HF: Total energy -94173.952354
FMO2-MP2: Total energy -94455.321498


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.
-178.331-184.07340.98-19.274-15.9640.186
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 : -0.809 / q_NPA : -0.883
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].
3A21ALA0-0.014-0.0023.189-2.629-0.9590.009-0.593-1.0860.001
4A22LYS10.7900.8631.690-144.745-146.90122.511-11.092-9.2630.131
5A23ARG10.9570.9704.075-34.736-34.441-0.001-0.083-0.2120.000
6A24ALA00.0050.0146.027-3.915-3.9150.0000.0000.0000.000
7A25ALA0-0.002-0.0058.094-2.788-2.7880.0000.0000.0000.000
8A26ALA0-0.010-0.0148.435-2.552-2.5520.0000.0000.0000.000
9A27TYR0-0.013-0.0399.610-2.709-2.7090.0000.0000.0000.000
10A28ARG10.8570.91112.339-19.195-19.1950.0000.0000.0000.000
11A29ALA0-0.0170.01113.364-1.385-1.3850.0000.0000.0000.000
12A30VAL00.0220.01614.111-1.238-1.2380.0000.0000.0000.000
13A31ASP-1-0.771-0.83316.21816.77416.7740.0000.0000.0000.000
14A32GLU-1-0.816-0.86117.92415.23115.2310.0000.0000.0000.000
15A33ASN0-0.090-0.06018.003-1.441-1.4410.0000.0000.0000.000
16A34LEU0-0.0120.00118.896-0.421-0.4210.0000.0000.0000.000
17A35LYS10.8820.94621.348-11.458-11.4580.0000.0000.0000.000
18A36PHE00.006-0.01121.059-0.266-0.2660.0000.0000.0000.000
19A37ASP-1-0.928-0.95426.17810.45310.4530.0000.0000.0000.000
20A38ASP-1-0.888-0.94028.09010.35410.3540.0000.0000.0000.000
21A39HIS0-0.077-0.03724.0030.2640.2640.0000.0000.0000.000
22A40LYS10.9710.97526.144-10.415-10.4150.0000.0000.0000.000
23A41ILE0-0.048-0.01524.9030.2810.2810.0000.0000.0000.000
24A42ILE00.0510.01718.8640.0990.0990.0000.0000.0000.000
25A43GLY0-0.007-0.01119.7680.1030.1030.0000.0000.0000.000
26A44ILE00.012-0.00713.9760.8870.8870.0000.0000.0000.000
27A45GLY00.0670.04114.300-0.565-0.5650.0000.0000.0000.000
28A46SER00.0090.00312.9380.7620.7620.0000.0000.0000.000
29A47GLY0-0.035-0.0189.4321.3431.3430.0000.0000.0000.000
30A48SER00.0340.0224.8691.0461.116-0.001-0.008-0.0610.000
31A49THR0-0.002-0.0024.02118.08018.4580.002-0.043-0.3370.000
32A50VAL00.0410.0266.060-2.886-2.8860.0000.0000.0000.000
33A51VAL00.0150.0245.441-3.300-3.3000.0000.0000.0000.000
34A52TYR00.004-0.0371.638-33.281-39.32718.461-7.445-4.9690.054
35A53VAL0-0.0070.0018.208-3.071-3.0710.0000.0000.0000.000
36A54ALA0-0.0030.00611.142-2.185-2.1850.0000.0000.0000.000
37A55GLU-1-0.835-0.8738.30029.36529.3650.0000.0000.0000.000
38A56ARG10.7830.86311.935-20.863-20.8630.0000.0000.0000.000
39A57ILE00.005-0.01513.699-1.618-1.6180.0000.0000.0000.000
40A58GLY00.0680.02815.454-1.200-1.2000.0000.0000.0000.000
41A59GLN0-0.040-0.01911.813-2.198-2.1980.0000.0000.0000.000
42A60TYR0-0.065-0.05216.927-1.212-1.2120.0000.0000.0000.000
43A61LEU0-0.0240.00219.787-0.892-0.8920.0000.0000.0000.000
44A62HIS0-0.076-0.04918.550-0.797-0.7970.0000.0000.0000.000
45A63ASP-1-0.801-0.87321.34312.33012.3300.0000.0000.0000.000
46A64PRO00.008-0.00523.130-0.227-0.2270.0000.0000.0000.000
47A65LYS10.7740.88324.024-12.592-12.5920.0000.0000.0000.000
48A66PHE00.022-0.00323.388-0.239-0.2390.0000.0000.0000.000
49A67TYR00.0160.03824.932-0.105-0.1050.0000.0000.0000.000
50A68GLU-1-0.824-0.90825.88110.17210.1720.0000.0000.0000.000
51A69VAL0-0.008-0.00226.629-0.130-0.1300.0000.0000.0000.000
52A70ALA00.0370.00522.3150.0790.0790.0000.0000.0000.000
53A71SER0-0.031-0.03123.7840.3910.3910.0000.0000.0000.000
54A72LYS10.7630.88026.016-10.528-10.5280.0000.0000.0000.000
55A73PHE00.0020.02221.330-0.158-0.1580.0000.0000.0000.000
56A74ILE0-0.040-0.01124.294-0.009-0.0090.0000.0000.0000.000
57A75CYS0-0.0170.00919.1040.3100.3100.0000.0000.0000.000
58A76ILE0-0.010-0.00920.847-0.341-0.3410.0000.0000.0000.000
59A77PRO00.0040.00818.1980.7670.7670.0000.0000.0000.000
60A78THR0-0.021-0.03315.865-0.656-0.6560.0000.0000.0000.000
61A79GLY00.0840.04818.1890.0670.0670.0000.0000.0000.000
62A80PHE00.000-0.00817.4920.3900.3900.0000.0000.0000.000
63A81GLN0-0.008-0.00510.2770.1270.1270.0000.0000.0000.000
64A82SER0-0.0020.00513.2110.4550.4550.0000.0000.0000.000
65A83ARG11.0090.98914.533-14.806-14.8060.0000.0000.0000.000
66A84ASN0-0.040-0.02813.456-1.555-1.5550.0000.0000.0000.000
67A85LEU00.0230.0189.2550.0020.0020.0000.0000.0000.000
68A86ILE00.0030.01713.347-0.150-0.1500.0000.0000.0000.000
69A87LEU0-0.021-0.00716.625-0.611-0.6110.0000.0000.0000.000
70A88ASP-1-0.896-0.94213.72620.33720.3370.0000.0000.0000.000
71A89ASN0-0.046-0.03412.050-0.271-0.2710.0000.0000.0000.000
72A90LYS10.7850.88716.187-17.978-17.9780.0000.0000.0000.000
73A91LEU00.0160.02216.756-0.750-0.7500.0000.0000.0000.000
74A92GLN0-0.029-0.03120.520-0.249-0.2490.0000.0000.0000.000
75A93LEU0-0.010-0.00320.1560.4500.4500.0000.0000.0000.000
76A94GLY0-0.010-0.00922.921-0.709-0.7090.0000.0000.0000.000
77A95SER0-0.060-0.06923.9890.4160.4160.0000.0000.0000.000
78A96ILE00.0780.02724.685-0.297-0.2970.0000.0000.0000.000
79A97GLU-1-0.856-0.90826.63311.48711.4870.0000.0000.0000.000
80A98GLN0-0.056-0.01029.535-0.457-0.4570.0000.0000.0000.000
81A99TYR0-0.054-0.04727.236-0.291-0.2910.0000.0000.0000.000
82A100PRO00.0300.02527.7580.3360.3360.0000.0000.0000.000
83A101ARG10.8900.94329.067-9.585-9.5850.0000.0000.0000.000
84A102ILE00.0580.02922.777-0.023-0.0230.0000.0000.0000.000
85A103ASP-1-0.800-0.87025.44011.36111.3610.0000.0000.0000.000
86A104ILE0-0.025-0.00220.274-0.075-0.0750.0000.0000.0000.000
87A105ALA00.0090.02419.3140.2180.2180.0000.0000.0000.000
88A106PHE00.0190.01214.3380.1200.1200.0000.0000.0000.000
89A107ASP-1-0.751-0.88513.35224.11724.1170.0000.0000.0000.000
90A108GLY00.0010.01211.0580.6110.6110.0000.0000.0000.000
91A109ALA0-0.004-0.01411.919-2.562-2.5620.0000.0000.0000.000
92A110ASP-1-0.864-0.93412.05528.72028.7200.0000.0000.0000.000
93A111GLU-1-0.763-0.89013.58618.18618.1860.0000.0000.0000.000
94A112VAL0-0.020-0.00415.169-0.481-0.4810.0000.0000.0000.000
95A113ASP-1-0.764-0.89417.87513.81513.8150.0000.0000.0000.000
96A114GLU-1-0.790-0.86921.12212.11512.1150.0000.0000.0000.000
97A115ASN0-0.108-0.05623.202-0.698-0.6980.0000.0000.0000.000
98A116LEU0-0.048-0.01619.352-0.147-0.1470.0000.0000.0000.000
99A117GLN0-0.044-0.02421.743-0.142-0.1420.0000.0000.0000.000
100A118LEU0-0.022-0.02017.6410.7960.7960.0000.0000.0000.000
101A119ILE00.0020.01717.616-0.953-0.9530.0000.0000.0000.000
102A120LYS10.7620.87314.977-19.926-19.9260.0000.0000.0000.000
103A121GLY00.0930.03615.700-1.234-1.2340.0000.0000.0000.000
104A122GLY00.0090.01013.637-0.680-0.6800.0000.0000.0000.000
105A123GLY0-0.032-0.01813.4250.1600.1600.0000.0000.0000.000
106A124ALA0-0.055-0.02914.032-0.641-0.6410.0000.0000.0000.000
107A125CYS0-0.0140.00116.253-0.653-0.6530.0000.0000.0000.000
108A126LEU00.0330.01118.159-0.103-0.1030.0000.0000.0000.000
109A127PHE0-0.0030.00219.711-0.390-0.3900.0000.0000.0000.000
110A128GLN00.008-0.01020.627-0.011-0.0110.0000.0000.0000.000
111A129GLU-1-0.813-0.92315.71421.29021.2900.0000.0000.0000.000
112A130LYS10.8050.89919.346-13.870-13.8700.0000.0000.0000.000
113A131LEU0-0.0340.01822.439-0.512-0.5120.0000.0000.0000.000
114A132VAL00.0160.01119.899-0.507-0.5070.0000.0000.0000.000
115A133SER0-0.006-0.02520.070-0.358-0.3580.0000.0000.0000.000
116A134THR0-0.079-0.05421.942-0.503-0.5030.0000.0000.0000.000
117A135SER0-0.020-0.01225.060-0.769-0.7690.0000.0000.0000.000
118A136ALA0-0.066-0.02223.271-0.283-0.2830.0000.0000.0000.000
119A137LYS10.8130.89025.277-11.465-11.4650.0000.0000.0000.000
120A138THR0-0.060-0.02321.921-0.209-0.2090.0000.0000.0000.000
121A139PHE00.0290.01717.4890.4400.4400.0000.0000.0000.000
122A140ILE0-0.017-0.00915.646-0.243-0.2430.0000.0000.0000.000
123A141VAL00.0280.01113.7610.9800.9800.0000.0000.0000.000
124A142VAL0-0.0050.0069.156-0.425-0.4250.0000.0000.0000.000
125A143ALA0-0.049-0.0298.8242.3962.3960.0000.0000.0000.000
126A144ASP-1-0.757-0.8445.93142.31042.3100.0000.0000.0000.000
127A145SER00.027-0.0038.000-1.586-1.5860.0000.0000.0000.000
128A146ARG10.8300.8806.851-41.342-41.3420.0000.0000.0000.000
129A147LYS10.7900.8909.235-34.103-34.1030.0000.0000.0000.000
130A148LYS10.8620.94812.986-19.485-19.4850.0000.0000.0000.000
131A149SER0-0.010-0.02915.576-0.412-0.4120.0000.0000.0000.000
132A150PRO0-0.058-0.03618.536-0.441-0.4410.0000.0000.0000.000
133A151LYS10.8040.89221.091-12.108-12.1080.0000.0000.0000.000
134A152HIS00.0090.00623.590-0.293-0.2930.0000.0000.0000.000
135A153LEU00.0030.02019.9930.6600.6600.0000.0000.0000.000
136A154GLY00.0420.02720.494-0.809-0.8090.0000.0000.0000.000
137A155LYS10.8030.91220.406-13.812-13.8120.0000.0000.0000.000
138A156ASN0-0.015-0.03715.809-0.967-0.9670.0000.0000.0000.000
139A157TRP0-0.071-0.01112.2921.8321.8320.0000.0000.0000.000
140A158ARG10.8080.86117.007-15.393-15.3930.0000.0000.0000.000
141A159GLN0-0.005-0.00414.670-1.152-1.1520.0000.0000.0000.000
142A160GLY00.0600.04519.176-0.556-0.5560.0000.0000.0000.000
143A161VAL0-0.030-0.02019.8371.0721.0720.0000.0000.0000.000
144A162PRO0-0.0020.02118.039-0.626-0.6260.0000.0000.0000.000
145A163ILE0-0.009-0.00821.267-0.251-0.2510.0000.0000.0000.000
146A164GLU-1-0.752-0.83723.34014.07014.0700.0000.0000.0000.000
147A165ILE00.008-0.00125.340-0.484-0.4840.0000.0000.0000.000
148A166VAL00.0540.01928.7710.1490.1490.0000.0000.0000.000
149A167PRO00.0400.03329.531-0.165-0.1650.0000.0000.0000.000
150A168SER0-0.018-0.01131.4620.0290.0290.0000.0000.0000.000
151A169SER0-0.064-0.03832.551-0.223-0.2230.0000.0000.0000.000
152A170TYR00.0380.01330.452-0.006-0.0060.0000.0000.0000.000
153A171VAL00.0100.00632.1440.1060.1060.0000.0000.0000.000
154A172ARG10.8870.93735.025-8.570-8.5700.0000.0000.0000.000
155A173VAL00.0380.02030.486-0.039-0.0390.0000.0000.0000.000
156A174LYS10.9010.93929.758-10.621-10.6210.0000.0000.0000.000
157A175ASN0-0.051-0.04232.4370.1670.1670.0000.0000.0000.000
158A176ASP-1-0.754-0.86535.2458.6318.6310.0000.0000.0000.000
159A177LEU0-0.028-0.01628.8800.0110.0110.0000.0000.0000.000
160A178LEU0-0.031-0.01431.7310.0750.0750.0000.0000.0000.000
161A179GLU-1-0.912-0.93934.2848.1878.1870.0000.0000.0000.000
162A180GLN0-0.084-0.05236.803-0.286-0.2860.0000.0000.0000.000
163A181LEU0-0.086-0.04532.282-0.002-0.0020.0000.0000.0000.000
164A182HIS0-0.0300.00533.5150.2310.2310.0000.0000.0000.000
165A183ALA0-0.042-0.01629.2850.2080.2080.0000.0000.0000.000
166A184GLU-1-0.896-0.95428.25311.03111.0310.0000.0000.0000.000
167A185LYS10.8400.90424.234-13.015-13.0150.0000.0000.0000.000
168A186VAL00.0180.01427.0140.3230.3230.0000.0000.0000.000
169A187ASP-1-0.864-0.90724.49011.89611.8960.0000.0000.0000.000
170A188ILE00.0020.01325.0610.3010.3010.0000.0000.0000.000
171A189ARG10.7570.84016.252-18.492-18.4920.0000.0000.0000.000
172A190GLN0-0.034-0.03722.154-0.595-0.5950.0000.0000.0000.000
173A191GLY00.0210.00420.2000.8010.8010.0000.0000.0000.000
174A192GLY0-0.028-0.00219.0610.7320.7320.0000.0000.0000.000
175A193SER00.002-0.02018.482-0.415-0.4150.0000.0000.0000.000
176A194ALA0-0.0050.00918.132-0.562-0.5620.0000.0000.0000.000
177A195LYS10.8490.91320.237-13.386-13.3860.0000.0000.0000.000
178A196ALA00.0450.03623.1350.1310.1310.0000.0000.0000.000
179A197GLY00.0190.01025.979-0.271-0.2710.0000.0000.0000.000
180A198PRO0-0.0050.00924.6250.6050.6050.0000.0000.0000.000
181A199VAL00.0260.00819.505-0.006-0.0060.0000.0000.0000.000
182A200VAL0-0.038-0.01722.579-0.566-0.5660.0000.0000.0000.000
183A201THR0-0.034-0.02821.5990.4140.4140.0000.0000.0000.000
184A202ASP-1-0.818-0.92219.67716.53916.5390.0000.0000.0000.000
185A203ASN0-0.092-0.06322.991-0.536-0.5360.0000.0000.0000.000
186A204ASN0-0.061-0.02625.788-0.452-0.4520.0000.0000.0000.000
187A205ASN0-0.020-0.01325.996-0.942-0.9420.0000.0000.0000.000
188A206PHE00.000-0.00225.4540.3610.3610.0000.0000.0000.000
189A207ILE00.0340.01220.3700.0520.0520.0000.0000.0000.000
190A208ILE0-0.029-0.01123.687-0.204-0.2040.0000.0000.0000.000
191A209ASP-1-0.763-0.84820.02817.10517.1050.0000.0000.0000.000
192A210ALA00.004-0.01622.758-0.469-0.4690.0000.0000.0000.000
193A211ASP-1-0.796-0.87924.22413.84513.8450.0000.0000.0000.000
194A212PHE00.003-0.01625.098-0.541-0.5410.0000.0000.0000.000
195A213GLY00.0990.07925.936-0.324-0.3240.0000.0000.0000.000
196A214GLU-1-0.883-0.93524.35013.21713.2170.0000.0000.0000.000
197A215ILE0-0.019-0.01323.816-0.531-0.5310.0000.0000.0000.000
198A216SER00.0300.00926.9900.1970.1970.0000.0000.0000.000
199A217ASP-1-0.895-0.95129.66810.17110.1710.0000.0000.0000.000
200A218PRO00.0270.00525.922-0.132-0.1320.0000.0000.0000.000
201A219ARG10.9030.93527.911-10.822-10.8220.0000.0000.0000.000
202A220LYS10.7880.88330.180-9.518-9.5180.0000.0000.0000.000
203A221LEU00.0590.03327.081-0.134-0.1340.0000.0000.0000.000
204A222HIS00.0140.02027.4980.1470.1470.0000.0000.0000.000
205A223ARG10.9210.95429.149-9.371-9.3710.0000.0000.0000.000
206A224GLU-1-0.822-0.89332.7229.2439.2430.0000.0000.0000.000
207A225ILE00.0370.01527.598-0.143-0.1430.0000.0000.0000.000
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