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: GY541

Calculation Name: 2HXI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2HXI

Chain ID: A

ChEMBL ID:

UniProt ID: O87854

Base Structure: X-ray

Registration Date: 2023-09-27

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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1925066.037227
FMO2-HF: Nuclear repulsion 1850617.613612
FMO2-HF: Total energy -74448.423615
FMO2-MP2: Total energy -74669.347084


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:6:ARG)


Summations of interaction energy for fragment #1(A:6: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.
-21.204-20.0822.091-0.388-2.827-0.024
Interaction energy analysis for fragmet #1(A:6:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.942 / q_NPA : 0.975
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].
3A8SER00.017-0.0042.330-1.826-0.9692.095-0.359-2.593-0.024
4A9THR00.027-0.0214.5650.8460.845-0.001-0.0100.0110.000
5A10GLU-1-0.919-0.9567.529-19.661-19.6610.0000.0000.0000.000
6A11GLN00.0890.0534.870-3.016-2.911-0.001-0.002-0.1020.000
7A12ILE0-0.039-0.0094.6151.4701.512-0.001-0.003-0.0380.000
8A13LEU0-0.035-0.0318.5691.5931.5930.0000.0000.0000.000
9A14ASP-1-0.777-0.86511.661-17.002-17.0020.0000.0000.0000.000
10A15ALA00.0280.01910.9430.8280.8280.0000.0000.0000.000
11A16ALA0-0.080-0.05212.7281.0861.0860.0000.0000.0000.000
12A17ALA0-0.008-0.00814.5300.9290.9290.0000.0000.0000.000
13A18GLU-1-0.906-0.94815.175-16.845-16.8450.0000.0000.0000.000
14A19LEU0-0.086-0.04415.5970.5480.5480.0000.0000.0000.000
15A20LEU0-0.094-0.05118.5460.6810.6810.0000.0000.0000.000
16A21LEU0-0.011-0.00120.5910.6330.6330.0000.0000.0000.000
17A22ALA00.0250.00222.610-0.129-0.1290.0000.0000.0000.000
18A23GLY0-0.0410.02225.6360.1660.1660.0000.0000.0000.000
19A24ASP-1-0.938-1.01225.712-10.991-10.9910.0000.0000.0000.000
20A25ALA0-0.0230.01023.5090.2790.2790.0000.0000.0000.000
21A26GLU-1-0.782-0.86923.099-11.614-11.6140.0000.0000.0000.000
22A27THR0-0.015-0.00123.573-0.036-0.0360.0000.0000.0000.000
23A28PHE00.0370.01214.821-0.462-0.4620.0000.0000.0000.000
24A29SER0-0.011-0.02118.6040.1190.1190.0000.0000.0000.000
25A30VAL00.0560.02213.005-0.598-0.5980.0000.0000.0000.000
26A31ARG10.9070.95114.08814.20514.2050.0000.0000.0000.000
27A32LYS10.8450.93015.32611.71911.7190.0000.0000.0000.000
28A33LEU00.0490.02811.306-0.550-0.5500.0000.0000.0000.000
29A34ALA0-0.050-0.04010.587-1.340-1.3400.0000.0000.0000.000
30A35ALA00.0010.00411.147-1.448-1.4480.0000.0000.0000.000
31A36SER00.0280.02313.402-0.314-0.3140.0000.0000.0000.000
32A37LEU0-0.043-0.0147.754-0.673-0.6730.0000.0000.0000.000
33A38GLY00.0150.0278.444-3.551-3.5510.0000.0000.0000.000
34A39THR0-0.033-0.0186.355-1.914-1.9140.0000.0000.0000.000
35A40ASP-1-0.788-0.8698.609-18.990-18.9900.0000.0000.0000.000
36A41SER00.0310.0049.935-0.514-0.5140.0000.0000.0000.000
37A42SER0-0.048-0.05011.7700.5180.5180.0000.0000.0000.000
38A43SER0-0.027-0.0386.6700.0370.0370.0000.0000.0000.000
39A44LEU00.0060.0206.707-0.591-0.5910.0000.0000.0000.000
40A45TYR0-0.003-0.0238.6760.7700.7700.0000.0000.0000.000
41A46ARG10.9280.9599.35621.80021.8000.0000.0000.0000.000
42A47HIS0-0.0050.0293.8272.1702.289-0.001-0.014-0.1050.000
43A48PHE00.0210.0037.7830.5440.5440.0000.0000.0000.000
44A49ARG10.8740.94210.94215.96015.9600.0000.0000.0000.000
45A50ASN00.010-0.00613.4510.4950.4950.0000.0000.0000.000
46A51LYS11.0060.99814.86512.55312.5530.0000.0000.0000.000
47A52THR0-0.010-0.00316.147-0.160-0.1600.0000.0000.0000.000
48A53GLU-1-0.798-0.87115.360-13.118-13.1180.0000.0000.0000.000
49A54LEU0-0.0040.01411.000-0.076-0.0760.0000.0000.0000.000
50A55LEU0-0.035-0.02914.1220.0800.0800.0000.0000.0000.000
51A56ARG10.8570.91217.43712.11012.1100.0000.0000.0000.000
52A57ALA00.0200.02714.2700.2640.2640.0000.0000.0000.000
53A58VAL00.006-0.00814.671-0.070-0.0700.0000.0000.0000.000
54A59ALA00.0160.00216.8410.3340.3340.0000.0000.0000.000
55A60ASP-1-0.784-0.85718.652-11.930-11.9300.0000.0000.0000.000
56A61ARG10.8450.89814.53116.33816.3380.0000.0000.0000.000
57A62ILE00.0110.02219.4430.1910.1910.0000.0000.0000.000
58A63LEU00.0110.00822.6730.3640.3640.0000.0000.0000.000
59A64LEU0-0.052-0.03619.7610.2890.2890.0000.0000.0000.000
60A65SER00.001-0.00222.9490.1390.1390.0000.0000.0000.000
61A66ALA0-0.0080.00824.4920.3000.3000.0000.0000.0000.000
62A67MET0-0.067-0.02126.8530.4550.4550.0000.0000.0000.000
63A68ASP-1-0.882-0.92125.633-10.669-10.6690.0000.0000.0000.000
64A69GLY00.0020.00727.5570.2990.2990.0000.0000.0000.000
65A70TYR0-0.113-0.08630.6860.3540.3540.0000.0000.0000.000
66A71ARG10.9280.95632.7898.3328.3320.0000.0000.0000.000
67A72PRO0-0.0230.00236.0080.0850.0850.0000.0000.0000.000
68A73GLU-1-0.960-0.97638.553-6.886-6.8860.0000.0000.0000.000
69A74GLY00.0100.00542.027-0.021-0.0210.0000.0000.0000.000
70A75ASP-1-0.810-0.90644.287-6.448-6.4480.0000.0000.0000.000
71A76TRP00.0470.00942.640-0.235-0.2350.0000.0000.0000.000
72A77LYS10.8080.88842.0165.9555.9550.0000.0000.0000.000
73A78GLN00.0390.03242.362-0.072-0.0720.0000.0000.0000.000
74A79ARG10.8350.89637.8057.2697.2690.0000.0000.0000.000
75A80LEU0-0.021-0.00937.754-0.237-0.2370.0000.0000.0000.000
76A81THR0-0.006-0.02037.727-0.129-0.1290.0000.0000.0000.000
77A82ALA00.0060.01237.398-0.130-0.1300.0000.0000.0000.000
78A83VAL00.0070.00332.343-0.249-0.2490.0000.0000.0000.000
79A84ALA0-0.036-0.01533.298-0.247-0.2470.0000.0000.0000.000
80A85LEU00.0200.00634.298-0.192-0.1920.0000.0000.0000.000
81A86ARG10.8590.91230.4268.9438.9430.0000.0000.0000.000
82A87LEU0-0.033-0.01528.496-0.335-0.3350.0000.0000.0000.000
83A88ARG10.8300.88029.9847.6917.6910.0000.0000.0000.000
84A89GLU-1-0.943-0.96531.167-8.822-8.8220.0000.0000.0000.000
85A90SER0-0.018-0.02126.400-0.283-0.2830.0000.0000.0000.000
86A91PHE0-0.065-0.04024.267-0.466-0.4660.0000.0000.0000.000
87A92GLY00.0300.04027.8170.0440.0440.0000.0000.0000.000
88A93GLN0-0.018-0.01226.934-0.077-0.0770.0000.0000.0000.000
89A94GLN00.014-0.00323.158-0.505-0.5050.0000.0000.0000.000
90A95PRO00.1020.05425.904-0.060-0.0600.0000.0000.0000.000
91A96GLN0-0.073-0.03721.498-0.360-0.3600.0000.0000.0000.000
92A97LEU0-0.004-0.01819.362-0.036-0.0360.0000.0000.0000.000
93A98ALA00.0640.04223.407-0.020-0.0200.0000.0000.0000.000
94A99ALA00.0450.03326.8200.1340.1340.0000.0000.0000.000
95A100VAL0-0.097-0.05520.9530.0770.0770.0000.0000.0000.000
96A101TRP00.0290.01724.4480.0380.0380.0000.0000.0000.000
97A102GLY00.0580.02625.4180.1180.1180.0000.0000.0000.000
98A103ARG10.8850.96226.9419.8439.8430.0000.0000.0000.000
99A104HIS0-0.058-0.04123.7270.1470.1470.0000.0000.0000.000
100A105GLY00.0470.03824.928-0.136-0.1360.0000.0000.0000.000
101A106SER0-0.004-0.04821.368-0.079-0.0790.0000.0000.0000.000
102A107GLY0-0.033-0.01020.303-0.482-0.4820.0000.0000.0000.000
103A108GLY0-0.0110.00419.643-0.218-0.2180.0000.0000.0000.000
104A109THR00.002-0.02020.0800.5350.5350.0000.0000.0000.000
105A110GLY00.0590.03521.5300.4020.4020.0000.0000.0000.000
106A111SER0-0.018-0.04223.2170.5970.5970.0000.0000.0000.000
107A112ARG10.9020.96020.60912.25712.2570.0000.0000.0000.000
108A113LEU00.0230.01624.8230.3360.3360.0000.0000.0000.000
109A114MET00.0040.01927.6820.4300.4300.0000.0000.0000.000
110A115MET0-0.032-0.03728.4270.1840.1840.0000.0000.0000.000
111A116GLU-1-0.865-0.91530.388-8.194-8.1940.0000.0000.0000.000
112A117GLU-1-0.715-0.80232.186-7.591-7.5910.0000.0000.0000.000
113A118VAL0-0.018-0.01633.6820.2800.2800.0000.0000.0000.000
114A119LEU0-0.006-0.00333.3430.2530.2530.0000.0000.0000.000
115A120GLN0-0.053-0.03636.2010.4530.4530.0000.0000.0000.000
116A121ALA0-0.039-0.01038.1370.2250.2250.0000.0000.0000.000
117A122LEU00.007-0.01138.1300.1790.1790.0000.0000.0000.000
118A123ARG10.8370.90039.6927.3017.3010.0000.0000.0000.000
119A124ALA0-0.057-0.02842.3560.1670.1670.0000.0000.0000.000
120A125SER0-0.051-0.03844.1890.1520.1520.0000.0000.0000.000
121A126GLY00.0220.01846.1520.1360.1360.0000.0000.0000.000
122A127LEU0-0.067-0.02744.9290.0910.0910.0000.0000.0000.000
123A128PRO00.0420.02846.129-0.079-0.0790.0000.0000.0000.000
124A129ASP-1-0.778-0.88242.616-7.038-7.0380.0000.0000.0000.000
125A130ASP-1-0.949-0.97742.636-6.381-6.3810.0000.0000.0000.000
126A131GLU-1-0.803-0.88443.299-6.244-6.2440.0000.0000.0000.000
127A132ILE0-0.0220.01138.901-0.140-0.1400.0000.0000.0000.000
128A133PRO00.0220.00337.092-0.152-0.1520.0000.0000.0000.000
129A134ALA0-0.022-0.01037.662-0.144-0.1440.0000.0000.0000.000
130A135ARG10.8490.90339.8606.2226.2220.0000.0000.0000.000
131A136TYR00.0540.02430.622-0.103-0.1030.0000.0000.0000.000
132A137HIS00.0070.01534.2860.0440.0440.0000.0000.0000.000
133A138ARG10.8940.92936.2696.9276.9270.0000.0000.0000.000
134A139LEU00.0080.03037.2050.0040.0040.0000.0000.0000.000
135A140VAL00.0550.01431.338-0.069-0.0690.0000.0000.0000.000
136A141ILE0-0.0130.01533.835-0.150-0.1500.0000.0000.0000.000
137A142LEU00.0000.02435.326-0.062-0.0620.0000.0000.0000.000
138A143ILE00.0290.00433.299-0.036-0.0360.0000.0000.0000.000
139A144SER00.004-0.01630.796-0.093-0.0930.0000.0000.0000.000
140A145SER0-0.051-0.03132.546-0.144-0.1440.0000.0000.0000.000
141A146LEU0-0.026-0.00934.857-0.002-0.0020.0000.0000.0000.000
142A147ILE00.0260.01230.4670.0020.0020.0000.0000.0000.000
143A148THR0-0.080-0.05730.271-0.201-0.2010.0000.0000.0000.000
144A149ALA0-0.056-0.03331.973-0.016-0.0160.0000.0000.0000.000
145A150GLU-1-0.872-0.89334.782-7.659-7.6590.0000.0000.0000.000
146A151GLY00.0730.05331.4530.0170.0170.0000.0000.0000.000
147A152GLY0-0.074-0.04731.237-0.118-0.1180.0000.0000.0000.000
148A168PHE00.0440.00547.159-0.013-0.0130.0000.0000.0000.000
149A169ARG10.9320.96547.0466.2776.2770.0000.0000.0000.000
150A170VAL00.0190.00650.9970.0150.0150.0000.0000.0000.000
151A171ALA0-0.018-0.00149.604-0.090-0.0900.0000.0000.0000.000
152A172VAL00.0030.00550.631-0.041-0.0410.0000.0000.0000.000
153A173LEU0-0.023-0.01053.7170.0420.0420.0000.0000.0000.000
154A174GLY00.0230.01256.3180.0760.0760.0000.0000.0000.000
155A175ALA0-0.002-0.02358.182-0.077-0.0770.0000.0000.0000.000
156A176ASP-1-0.825-0.90560.549-4.580-4.5800.0000.0000.0000.000
157A177PRO00.0020.00263.792-0.035-0.0350.0000.0000.0000.000
158A178GLU-1-0.906-0.95165.849-4.304-4.3040.0000.0000.0000.000
159A179ARG10.8930.96459.8904.9224.9220.0000.0000.0000.000
160A180PHE0-0.082-0.05958.780-0.069-0.0690.0000.0000.0000.000
161A181PRO00.0750.05462.411-0.047-0.0470.0000.0000.0000.000
162A182ALA00.014-0.00361.250-0.002-0.0020.0000.0000.0000.000
163A183LEU00.0140.00055.850-0.034-0.0340.0000.0000.0000.000
164A184SER0-0.052-0.04859.619-0.030-0.0300.0000.0000.0000.000
165A185HIS0-0.0320.00362.1350.0530.0530.0000.0000.0000.000
166A186PHE00.0260.01457.945-0.006-0.0060.0000.0000.0000.000
167A187ALA0-0.0060.01756.956-0.095-0.0950.0000.0000.0000.000
168A188ARG10.8250.90854.7205.2745.2740.0000.0000.0000.000
169A189GLU-1-0.882-0.95256.085-5.157-5.1570.0000.0000.0000.000
170A190ILE0-0.0200.01151.575-0.091-0.0910.0000.0000.0000.000
171A191ARG10.8760.90847.7596.0836.0830.0000.0000.0000.000
172A192PRO0-0.031-0.02945.778-0.019-0.0190.0000.0000.0000.000
173A193LEU00.0490.01742.061-0.051-0.0510.0000.0000.0000.000
174A194GLY0-0.005-0.00241.422-0.086-0.0860.0000.0000.0000.000
175A195ALA0-0.059-0.02441.518-0.132-0.1320.0000.0000.0000.000
176A196ASP-1-0.801-0.87743.878-6.308-6.3080.0000.0000.0000.000
177A197ARG10.9220.96837.6347.4207.4200.0000.0000.0000.000
178A198GLY00.0430.02739.576-0.029-0.0290.0000.0000.0000.000
179A199ALA00.0580.03040.492-0.006-0.0060.0000.0000.0000.000
180A200ALA00.0370.02042.7350.0480.0480.0000.0000.0000.000
181A201PHE0-0.037-0.02535.8410.0020.0020.0000.0000.0000.000
182A202GLU-1-0.925-0.97440.746-6.957-6.9570.0000.0000.0000.000
183A203GLU-1-0.943-0.96142.659-6.094-6.0940.0000.0000.0000.000
184A204ILE0-0.031-0.01842.5290.0820.0820.0000.0000.0000.000
185A205LEU0-0.006-0.00439.0580.0230.0230.0000.0000.0000.000
186A206ALA00.008-0.00242.4440.0490.0490.0000.0000.0000.000
187A207ALA00.0090.01645.6310.0980.0980.0000.0000.0000.000
188A208HIS0-0.010-0.01441.7080.1440.1440.0000.0000.0000.000
189A209LEU0-0.012-0.01841.4100.0390.0390.0000.0000.0000.000
190A210ALA00.0190.01845.3750.0750.0750.0000.0000.0000.000
191A211HIS0-0.028-0.02645.1280.1390.1390.0000.0000.0000.000
192A212LEU0-0.055-0.01842.5440.0370.0370.0000.0000.0000.000
193A213GLU-1-0.804-0.91147.226-5.922-5.9220.0000.0000.0000.000
194A214ALA0-0.055-0.01649.7490.0850.0850.0000.0000.0000.000
195A215ALA0-0.075-0.03849.1980.0830.0830.0000.0000.0000.000
196A216ALA0-0.0050.01449.0080.0070.0070.0000.0000.0000.000
197A217PRO0-0.039-0.00950.4040.0910.0910.0000.0000.0000.000