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: 16N3Z

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 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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1925163.097586
FMO2-HF: Nuclear repulsion 1850715.637121
FMO2-HF: Total energy -74447.460464
FMO2-MP2: Total energy -74668.514859


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.
-22.006-21.1942.043-0.19-2.664-0.023
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 : 0.911 / q_NPA : 0.951
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].
3A8SER00.0240.0062.363-2.182-1.6092.047-0.168-2.452-0.023
4A9THR00.020-0.0404.6391.4771.468-0.001-0.0080.0180.000
5A10GLU-1-0.927-0.9517.573-19.134-19.1340.0000.0000.0000.000
6A11GLN00.0820.0384.991-2.949-2.839-0.001-0.001-0.1080.000
7A12ILE0-0.039-0.0094.6271.5671.608-0.001-0.002-0.0370.000
8A13LEU0-0.038-0.0368.5511.6211.6210.0000.0000.0000.000
9A14ASP-1-0.787-0.88111.675-17.602-17.6020.0000.0000.0000.000
10A15ALA00.0310.01810.9240.8650.8650.0000.0000.0000.000
11A16ALA0-0.078-0.05012.6951.0681.0680.0000.0000.0000.000
12A17ALA0-0.009-0.01214.4970.9170.9170.0000.0000.0000.000
13A18GLU-1-0.913-0.95315.564-16.580-16.5800.0000.0000.0000.000
14A19LEU0-0.089-0.04815.7640.5330.5330.0000.0000.0000.000
15A20LEU0-0.093-0.04718.4990.6620.6620.0000.0000.0000.000
16A21LEU0-0.023-0.00920.3940.5970.5970.0000.0000.0000.000
17A22ALA00.0350.01122.579-0.138-0.1380.0000.0000.0000.000
18A23GLY0-0.0370.02025.5970.1670.1670.0000.0000.0000.000
19A24ASP-1-0.925-1.01325.632-11.023-11.0230.0000.0000.0000.000
20A25ALA0-0.0320.01223.4520.2710.2710.0000.0000.0000.000
21A26GLU-1-0.884-0.92622.728-11.508-11.5080.0000.0000.0000.000
22A27THR0-0.021-0.01123.476-0.036-0.0360.0000.0000.0000.000
23A28PHE00.0370.01414.864-0.448-0.4480.0000.0000.0000.000
24A29SER0-0.031-0.03118.5240.1310.1310.0000.0000.0000.000
25A30VAL00.0630.02713.108-0.509-0.5090.0000.0000.0000.000
26A31ARG10.9030.95014.02013.92813.9280.0000.0000.0000.000
27A32LYS10.9471.00115.24311.96311.9630.0000.0000.0000.000
28A33LEU00.0510.03111.290-0.514-0.5140.0000.0000.0000.000
29A34ALA0-0.052-0.03710.506-1.218-1.2180.0000.0000.0000.000
30A35ALA0-0.0010.00111.175-1.317-1.3170.0000.0000.0000.000
31A36SER00.0020.01213.545-0.878-0.8780.0000.0000.0000.000
32A37LEU00.0040.0107.569-0.678-0.6780.0000.0000.0000.000
33A38GLY00.0070.0248.588-3.348-3.3480.0000.0000.0000.000
34A39THR0-0.022-0.0086.832-1.747-1.7470.0000.0000.0000.000
35A40ASP-1-0.815-0.9109.054-19.882-19.8820.0000.0000.0000.000
36A41SER00.028-0.0149.996-0.464-0.4640.0000.0000.0000.000
37A42SER0-0.025-0.01911.7170.2940.2940.0000.0000.0000.000
38A43SER0-0.055-0.0426.9390.0630.0630.0000.0000.0000.000
39A44LEU00.0080.0136.814-0.692-0.6920.0000.0000.0000.000
40A45TYR00.004-0.0188.6360.6940.6940.0000.0000.0000.000
41A46ARG10.9560.9839.47521.63821.6380.0000.0000.0000.000
42A47HIS0-0.0050.0443.9511.9202.017-0.001-0.011-0.0850.000
43A48PHE00.0350.0107.8000.3250.3250.0000.0000.0000.000
44A49ARG10.9540.99710.96316.28116.2810.0000.0000.0000.000
45A50ASN00.008-0.01113.4740.5030.5030.0000.0000.0000.000
46A51LYS10.9910.99514.86512.63912.6390.0000.0000.0000.000
47A52THR0-0.018-0.01016.130-0.151-0.1510.0000.0000.0000.000
48A53GLU-1-0.818-0.90415.394-13.103-13.1030.0000.0000.0000.000
49A54LEU0-0.0280.00711.220-0.071-0.0710.0000.0000.0000.000
50A55LEU0-0.040-0.03514.1200.0970.0970.0000.0000.0000.000
51A56ARG10.8420.90717.42512.25312.2530.0000.0000.0000.000
52A57ALA00.0290.02514.3810.2640.2640.0000.0000.0000.000
53A58VAL0-0.005-0.01014.591-0.065-0.0650.0000.0000.0000.000
54A59ALA00.0160.00416.8350.3330.3330.0000.0000.0000.000
55A60ASP-1-0.787-0.86418.648-12.062-12.0620.0000.0000.0000.000
56A61ARG10.8740.92814.51516.37616.3760.0000.0000.0000.000
57A62ILE00.0060.01919.4510.1920.1920.0000.0000.0000.000
58A63LEU00.0140.00422.6710.3620.3620.0000.0000.0000.000
59A64LEU0-0.050-0.03419.6780.2910.2910.0000.0000.0000.000
60A65SER00.009-0.00122.9630.1620.1620.0000.0000.0000.000
61A66ALA0-0.0170.00624.5000.3050.3050.0000.0000.0000.000
62A67MET0-0.066-0.02926.8750.4570.4570.0000.0000.0000.000
63A68ASP-1-0.896-0.92425.401-10.746-10.7460.0000.0000.0000.000
64A69GLY00.0080.00727.6220.2990.2990.0000.0000.0000.000
65A70TYR0-0.118-0.08630.7490.3650.3650.0000.0000.0000.000
66A71ARG10.9300.95332.8558.3278.3270.0000.0000.0000.000
67A72PRO0-0.0160.00936.0700.0830.0830.0000.0000.0000.000
68A73GLU-1-0.959-0.97638.585-6.898-6.8980.0000.0000.0000.000
69A74GLY00.0000.00142.055-0.021-0.0210.0000.0000.0000.000
70A75ASP-1-0.818-0.91844.318-6.459-6.4590.0000.0000.0000.000
71A76TRP00.0530.00942.669-0.231-0.2310.0000.0000.0000.000
72A77LYS10.8690.94042.0425.9905.9900.0000.0000.0000.000
73A78GLN00.0360.02842.380-0.083-0.0830.0000.0000.0000.000
74A79ARG10.8600.93038.1087.2557.2550.0000.0000.0000.000
75A80LEU0-0.027-0.01137.779-0.234-0.2340.0000.0000.0000.000
76A81THR00.000-0.01437.742-0.127-0.1270.0000.0000.0000.000
77A82ALA00.0070.01037.336-0.126-0.1260.0000.0000.0000.000
78A83VAL0-0.0010.00232.353-0.247-0.2470.0000.0000.0000.000
79A84ALA0-0.026-0.01133.308-0.244-0.2440.0000.0000.0000.000
80A85LEU00.0240.00734.299-0.187-0.1870.0000.0000.0000.000
81A86ARG10.8690.92330.6898.8908.8900.0000.0000.0000.000
82A87LEU0-0.038-0.02428.468-0.319-0.3190.0000.0000.0000.000
83A88ARG10.8090.86229.9777.6517.6510.0000.0000.0000.000
84A89GLU-1-0.940-0.96530.734-8.896-8.8960.0000.0000.0000.000
85A90SER0-0.008-0.00726.343-0.297-0.2970.0000.0000.0000.000
86A91PHE0-0.069-0.04024.361-0.455-0.4550.0000.0000.0000.000
87A92GLY00.0300.04027.8000.0410.0410.0000.0000.0000.000
88A93GLN0-0.014-0.01227.038-0.077-0.0770.0000.0000.0000.000
89A94GLN00.0200.00123.156-0.442-0.4420.0000.0000.0000.000
90A95PRO00.1000.05325.871-0.083-0.0830.0000.0000.0000.000
91A96GLN0-0.077-0.04121.471-0.267-0.2670.0000.0000.0000.000
92A97LEU00.000-0.01719.329-0.043-0.0430.0000.0000.0000.000
93A98ALA00.0650.04423.386-0.033-0.0330.0000.0000.0000.000
94A99ALA00.0400.03426.8050.1180.1180.0000.0000.0000.000
95A100VAL0-0.092-0.05420.9880.0680.0680.0000.0000.0000.000
96A101TRP00.0120.01424.4390.0220.0220.0000.0000.0000.000
97A102GLY00.0620.02425.4200.1150.1150.0000.0000.0000.000
98A103ARG10.8800.95926.7439.8789.8780.0000.0000.0000.000
99A104HIS0-0.046-0.03623.5940.1530.1530.0000.0000.0000.000
100A105GLY00.0480.03624.949-0.144-0.1440.0000.0000.0000.000
101A106SER0-0.019-0.04521.395-0.076-0.0760.0000.0000.0000.000
102A107GLY0-0.034-0.01420.329-0.484-0.4840.0000.0000.0000.000
103A108GLY0-0.0040.01319.687-0.237-0.2370.0000.0000.0000.000
104A109THR00.000-0.02220.1230.5520.5520.0000.0000.0000.000
105A110GLY00.0610.03221.5630.4190.4190.0000.0000.0000.000
106A111SER0-0.016-0.03723.2470.6160.6160.0000.0000.0000.000
107A112ARG10.8970.95421.42212.26812.2680.0000.0000.0000.000
108A113LEU00.0280.02024.9370.3420.3420.0000.0000.0000.000
109A114MET00.0000.02027.7200.4360.4360.0000.0000.0000.000
110A115MET0-0.031-0.03728.6460.1900.1900.0000.0000.0000.000
111A116GLU-1-0.879-0.92930.426-8.320-8.3200.0000.0000.0000.000
112A117GLU-1-0.724-0.83032.224-7.620-7.6200.0000.0000.0000.000
113A118VAL0-0.026-0.02033.6070.2870.2870.0000.0000.0000.000
114A119LEU00.000-0.00233.3330.2580.2580.0000.0000.0000.000
115A120GLN0-0.041-0.02636.1770.4550.4550.0000.0000.0000.000
116A121ALA0-0.037-0.00438.1760.2230.2230.0000.0000.0000.000
117A122LEU00.005-0.01638.1800.1810.1810.0000.0000.0000.000
118A123ARG10.9020.96539.3917.3577.3570.0000.0000.0000.000
119A124ALA0-0.063-0.03142.3980.1640.1640.0000.0000.0000.000
120A125SER0-0.049-0.03544.2270.1560.1560.0000.0000.0000.000
121A126GLY00.0320.02446.1890.1350.1350.0000.0000.0000.000
122A127LEU0-0.063-0.02444.6520.0850.0850.0000.0000.0000.000
123A128PRO00.0250.02246.174-0.081-0.0810.0000.0000.0000.000
124A129ASP-1-0.848-0.95042.886-7.020-7.0200.0000.0000.0000.000
125A130ASP-1-0.944-0.97642.685-6.413-6.4130.0000.0000.0000.000
126A131GLU-1-0.833-0.92243.344-6.265-6.2650.0000.0000.0000.000
127A132ILE0-0.0160.01238.941-0.141-0.1410.0000.0000.0000.000
128A133PRO00.0180.00537.244-0.162-0.1620.0000.0000.0000.000
129A134ALA0-0.009-0.01037.697-0.143-0.1430.0000.0000.0000.000
130A135ARG10.8630.93439.8886.2846.2840.0000.0000.0000.000
131A136TYR00.0590.02730.737-0.087-0.0870.0000.0000.0000.000
132A137HIS00.0070.01734.4130.0590.0590.0000.0000.0000.000
133A138ARG10.8900.92036.2886.9686.9680.0000.0000.0000.000
134A139LEU00.0080.03137.2920.0050.0050.0000.0000.0000.000
135A140VAL00.0480.01031.366-0.068-0.0680.0000.0000.0000.000
136A141ILE0-0.0100.01133.844-0.146-0.1460.0000.0000.0000.000
137A142LEU0-0.0060.01635.335-0.060-0.0600.0000.0000.0000.000
138A143ILE00.0340.00433.193-0.031-0.0310.0000.0000.0000.000
139A144SER0-0.001-0.01330.767-0.091-0.0910.0000.0000.0000.000
140A145SER0-0.055-0.03732.545-0.124-0.1240.0000.0000.0000.000
141A146LEU0-0.023-0.00534.8490.0040.0040.0000.0000.0000.000
142A147ILE00.0100.00730.4420.0030.0030.0000.0000.0000.000
143A148THR0-0.064-0.04130.631-0.201-0.2010.0000.0000.0000.000
144A149ALA0-0.064-0.03931.954-0.015-0.0150.0000.0000.0000.000
145A150GLU-1-0.859-0.86234.770-7.696-7.6960.0000.0000.0000.000
146A151GLY00.0370.02731.4210.0260.0260.0000.0000.0000.000
147A152GLY0-0.040-0.02631.008-0.040-0.0400.0000.0000.0000.000
148A168PHE00.015-0.00847.289-0.017-0.0170.0000.0000.0000.000
149A169ARG10.9420.97247.0716.2466.2460.0000.0000.0000.000
150A170VAL00.0130.00550.9490.0140.0140.0000.0000.0000.000
151A171ALA0-0.018-0.00249.561-0.090-0.0900.0000.0000.0000.000
152A172VAL00.0060.00850.589-0.040-0.0400.0000.0000.0000.000
153A173LEU0-0.016-0.00953.6740.0410.0410.0000.0000.0000.000
154A174GLY00.0160.00856.2700.0750.0750.0000.0000.0000.000
155A175ALA0-0.013-0.02958.139-0.077-0.0770.0000.0000.0000.000
156A176ASP-1-0.836-0.92360.508-4.576-4.5760.0000.0000.0000.000
157A177PRO0-0.010-0.00563.751-0.035-0.0350.0000.0000.0000.000
158A178GLU-1-0.890-0.93865.812-4.315-4.3150.0000.0000.0000.000
159A179ARG10.8990.96559.8224.9084.9080.0000.0000.0000.000
160A180PHE0-0.078-0.05659.362-0.070-0.0700.0000.0000.0000.000
161A181PRO00.0730.05562.378-0.046-0.0460.0000.0000.0000.000
162A182ALA00.0160.00061.142-0.001-0.0010.0000.0000.0000.000
163A183LEU00.016-0.00355.896-0.034-0.0340.0000.0000.0000.000
164A184SER0-0.052-0.03459.587-0.032-0.0320.0000.0000.0000.000
165A185HIS0-0.0210.00862.0980.0370.0370.0000.0000.0000.000
166A186PHE00.0500.02457.777-0.006-0.0060.0000.0000.0000.000
167A187ALA0-0.0050.00956.917-0.094-0.0940.0000.0000.0000.000
168A188ARG10.8670.93054.9835.2135.2130.0000.0000.0000.000
169A189GLU-1-0.911-0.96756.027-5.163-5.1630.0000.0000.0000.000
170A190ILE0-0.0170.01451.465-0.093-0.0930.0000.0000.0000.000
171A191ARG10.9830.98647.2126.0436.0430.0000.0000.0000.000
172A192PRO0-0.028-0.02545.774-0.021-0.0210.0000.0000.0000.000
173A193LEU00.0570.02142.196-0.050-0.0500.0000.0000.0000.000
174A194GLY00.0020.00141.385-0.087-0.0870.0000.0000.0000.000
175A195ALA0-0.088-0.04741.482-0.111-0.1110.0000.0000.0000.000
176A196ASP-1-0.900-0.96043.787-6.398-6.3980.0000.0000.0000.000
177A197ARG10.9460.98538.2307.3387.3380.0000.0000.0000.000
178A198GLY00.0300.01539.567-0.041-0.0410.0000.0000.0000.000
179A199ALA00.0760.05240.471-0.033-0.0330.0000.0000.0000.000
180A200ALA00.0450.01842.7370.0340.0340.0000.0000.0000.000
181A201PHE0-0.067-0.03635.791-0.009-0.0090.0000.0000.0000.000
182A202GLU-1-0.924-0.97440.735-6.941-6.9410.0000.0000.0000.000
183A203GLU-1-0.930-0.95742.653-6.139-6.1390.0000.0000.0000.000
184A204ILE0-0.037-0.01942.5720.0820.0820.0000.0000.0000.000
185A205LEU0-0.005-0.00439.0600.0210.0210.0000.0000.0000.000
186A206ALA00.010-0.00142.4470.0470.0470.0000.0000.0000.000
187A207ALA00.0060.01545.6370.0980.0980.0000.0000.0000.000
188A208HIS0-0.014-0.01541.9600.1310.1310.0000.0000.0000.000
189A209LEU0-0.022-0.02641.4810.0390.0390.0000.0000.0000.000
190A210ALA00.0160.01445.3910.0740.0740.0000.0000.0000.000
191A211HIS0-0.014-0.01545.7590.1520.1520.0000.0000.0000.000
192A212LEU0-0.056-0.02242.5360.0300.0300.0000.0000.0000.000
193A213GLU-1-0.872-0.95747.249-5.840-5.8400.0000.0000.0000.000
194A214ALA0-0.047-0.01049.7740.0820.0820.0000.0000.0000.000
195A215ALA0-0.072-0.03549.2500.0830.0830.0000.0000.0000.000
196A216ALA0-0.0100.00749.0220.0040.0040.0000.0000.0000.000
197A217PRO0-0.044-0.01050.4500.0960.0960.0000.0000.0000.000