FMO DATABASE

FMODB ID: 2N73R

Calculation Name: 2P9R-A-Xray372

Preferred Name: Alpha-2-macroglobulin

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2P9R

Chain ID: A

ChEMBL ID: CHEMBL4295690

UniProt ID: P01023

Base Structure: X-ray

Registration Date: 2023-09-20

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	102
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-767678.823837
FMO2-HF: Nuclear repulsion	727607.130584
FMO2-HF: Total energy	-40071.693253
FMO2-MP2: Total energy	-40191.424416

3D Structure

Snapshot

Ligand structure

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/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:103:ASP)

Summations of interaction energy for fragment #1(A:103:ASP)

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.
-150.875	-156.874	27.115	-11.997	-9.121	0.148

Interaction energy analysis for fragmet #1(A:103:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.803 / q_NPA : -0.898

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 ES EX CT+mix DI(MP2)

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].
3	A	105	LEU	0	0.019	0.012	3.893	8.822	11.013	-0.006	-1.076	-1.110	0.001
4	A	106	VAL	0	-0.030	-0.016	5.875	-6.200	-6.200	0.000	0.000	0.000	0.000
5	A	107	PHE	0	-0.043	-0.029	7.806	-0.979	-0.979	0.000	0.000	0.000	0.000
6	A	108	VAL	0	0.003	-0.009	11.240	-0.714	-0.714	0.000	0.000	0.000	0.000
7	A	109	GLN	0	0.041	0.031	14.719	-0.627	-0.627	0.000	0.000	0.000	0.000
8	A	110	THR	0	0.017	-0.004	18.344	0.294	0.294	0.000	0.000	0.000	0.000
9	A	111	ASP	-1	-0.812	-0.887	21.862	11.795	11.795	0.000	0.000	0.000	0.000
10	A	112	LYS	1	0.848	0.935	25.232	-11.758	-11.758	0.000	0.000	0.000	0.000
11	A	113	SER	0	0.040	0.033	24.342	0.440	0.440	0.000	0.000	0.000	0.000
12	A	114	ILE	0	0.004	0.011	25.768	0.160	0.160	0.000	0.000	0.000	0.000
13	A	115	TYR	0	-0.065	-0.054	25.461	0.035	0.035	0.000	0.000	0.000	0.000
14	A	116	LYS	1	0.861	0.916	30.773	-8.959	-8.959	0.000	0.000	0.000	0.000
15	A	117	PRO	0	0.036	0.005	33.640	0.245	0.245	0.000	0.000	0.000	0.000
16	A	118	GLY	0	0.002	0.014	35.344	-0.151	-0.151	0.000	0.000	0.000	0.000
17	A	119	GLN	0	-0.027	-0.003	32.094	0.310	0.310	0.000	0.000	0.000	0.000
18	A	120	THR	0	-0.026	-0.015	28.969	0.283	0.283	0.000	0.000	0.000	0.000
19	A	121	VAL	0	0.036	0.016	23.974	0.017	0.017	0.000	0.000	0.000	0.000
20	A	122	LYS	1	0.923	0.967	24.785	-10.866	-10.866	0.000	0.000	0.000	0.000
21	A	123	PHE	0	0.007	-0.002	17.620	0.128	0.128	0.000	0.000	0.000	0.000
22	A	124	ARG	1	0.877	0.936	17.949	-16.934	-16.934	0.000	0.000	0.000	0.000
23	A	125	VAL	0	-0.005	0.000	13.114	0.424	0.424	0.000	0.000	0.000	0.000
24	A	126	VAL	0	0.001	-0.006	12.611	-1.407	-1.407	0.000	0.000	0.000	0.000
25	A	127	SER	0	-0.025	-0.038	7.334	2.924	2.924	0.000	0.000	0.000	0.000
26	A	128	MET	0	-0.006	0.017	8.621	-3.746	-3.746	0.000	0.000	0.000	0.000
27	A	129	ASP	-1	-0.785	-0.892	6.897	30.748	30.748	0.000	0.000	0.000	0.000
28	A	130	GLU	-1	-0.851	-0.932	6.017	33.714	33.714	0.000	0.000	0.000	0.000
29	A	131	ASN	0	-0.092	-0.055	9.337	-2.345	-2.345	0.000	0.000	0.000	0.000
30	A	132	PHE	0	-0.016	-0.018	11.542	-1.669	-1.669	0.000	0.000	0.000	0.000
31	A	133	HIS	1	0.859	0.940	11.197	-22.203	-22.203	0.000	0.000	0.000	0.000
32	A	134	PRO	0	0.019	0.018	11.451	1.918	1.918	0.000	0.000	0.000	0.000
33	A	135	LEU	0	0.018	0.010	6.900	-0.319	-0.319	0.000	0.000	0.000	0.000
34	A	136	ASN	0	0.009	0.006	10.966	0.395	0.395	0.000	0.000	0.000	0.000
35	A	137	GLU	-1	-0.805	-0.875	6.203	49.397	49.397	0.000	0.000	0.000	0.000
36	A	138	LEU	0	-0.023	-0.016	9.809	-2.167	-2.167	0.000	0.000	0.000	0.000
37	A	139	ILE	0	0.002	0.004	8.735	2.733	2.733	0.000	0.000	0.000	0.000
38	A	140	PRO	0	-0.020	-0.012	10.023	-2.715	-2.715	0.000	0.000	0.000	0.000
39	A	141	LEU	0	-0.038	-0.011	12.575	-2.364	-2.364	0.000	0.000	0.000	0.000
40	A	142	VAL	0	0.003	0.009	13.223	1.879	1.879	0.000	0.000	0.000	0.000
41	A	143	TYR	0	-0.003	-0.009	15.786	-0.972	-0.972	0.000	0.000	0.000	0.000
42	A	144	ILE	0	0.029	0.020	18.666	0.657	0.657	0.000	0.000	0.000	0.000
43	A	145	GLN	0	-0.083	-0.068	21.006	0.376	0.376	0.000	0.000	0.000	0.000
44	A	146	ASP	-1	-0.702	-0.847	22.995	11.615	11.615	0.000	0.000	0.000	0.000
45	A	147	PRO	0	0.001	-0.006	26.244	0.234	0.234	0.000	0.000	0.000	0.000
46	A	148	LYS	1	0.806	0.926	28.344	-10.362	-10.362	0.000	0.000	0.000	0.000
47	A	149	GLY	0	0.025	0.029	25.085	0.007	0.007	0.000	0.000	0.000	0.000
48	A	150	ASN	0	-0.060	-0.031	24.996	0.437	0.437	0.000	0.000	0.000	0.000
49	A	151	ARG	1	0.888	0.932	17.751	-16.881	-16.881	0.000	0.000	0.000	0.000
50	A	152	ILE	0	-0.012	0.000	24.007	-0.183	-0.183	0.000	0.000	0.000	0.000
51	A	153	ALA	0	0.018	0.019	24.000	-0.405	-0.405	0.000	0.000	0.000	0.000
52	A	154	GLN	0	-0.002	-0.011	19.435	0.941	0.941	0.000	0.000	0.000	0.000
53	A	155	TRP	0	0.014	0.011	18.971	-0.502	-0.502	0.000	0.000	0.000	0.000
54	A	156	GLN	0	0.036	0.000	16.880	0.515	0.515	0.000	0.000	0.000	0.000
55	A	157	SER	0	-0.044	-0.020	15.349	-0.346	-0.346	0.000	0.000	0.000	0.000
56	A	158	PHE	0	0.029	0.028	14.152	-0.952	-0.952	0.000	0.000	0.000	0.000
57	A	159	GLN	0	0.000	-0.005	13.566	1.207	1.207	0.000	0.000	0.000	0.000
58	A	160	LEU	0	-0.044	-0.004	11.241	-1.337	-1.337	0.000	0.000	0.000	0.000
59	A	161	GLU	-1	-0.809	-0.899	14.887	16.183	16.183	0.000	0.000	0.000	0.000
60	A	162	GLY	0	0.010	0.001	17.039	-0.228	-0.228	0.000	0.000	0.000	0.000
61	A	163	GLY	0	0.016	0.005	13.187	-0.205	-0.205	0.000	0.000	0.000	0.000
62	A	164	LEU	0	-0.032	-0.018	13.588	1.412	1.412	0.000	0.000	0.000	0.000
63	A	165	LYS	1	0.814	0.895	15.665	-17.491	-17.491	0.000	0.000	0.000	0.000
64	A	166	GLN	0	-0.023	-0.015	17.692	0.484	0.484	0.000	0.000	0.000	0.000
65	A	167	PHE	0	0.003	0.013	16.989	-0.323	-0.323	0.000	0.000	0.000	0.000
66	A	168	SER	0	-0.065	-0.041	22.193	-0.374	-0.374	0.000	0.000	0.000	0.000
67	A	169	PHE	0	0.041	0.017	25.123	0.093	0.093	0.000	0.000	0.000	0.000
68	A	170	PRO	0	0.012	-0.001	27.101	-0.054	-0.054	0.000	0.000	0.000	0.000
69	A	171	LEU	0	-0.002	0.020	28.825	0.065	0.065	0.000	0.000	0.000	0.000
70	A	172	SER	0	0.002	-0.007	31.919	-0.207	-0.207	0.000	0.000	0.000	0.000
71	A	173	SER	0	-0.015	-0.043	35.241	0.170	0.170	0.000	0.000	0.000	0.000
72	A	174	GLU	-1	-0.845	-0.885	38.100	7.947	7.947	0.000	0.000	0.000	0.000
73	A	175	PRO	0	-0.054	-0.013	32.707	0.109	0.109	0.000	0.000	0.000	0.000
74	A	176	PHE	0	0.019	-0.016	31.468	-0.198	-0.198	0.000	0.000	0.000	0.000
75	A	177	GLN	0	0.112	0.067	31.978	0.370	0.370	0.000	0.000	0.000	0.000
76	A	178	GLY	0	0.019	0.008	30.993	-0.079	-0.079	0.000	0.000	0.000	0.000
77	A	179	SER	0	-0.013	-0.014	25.634	0.037	0.037	0.000	0.000	0.000	0.000
78	A	180	TYR	0	-0.047	-0.044	24.419	-0.068	-0.068	0.000	0.000	0.000	0.000
79	A	181	LYS	1	0.842	0.907	18.414	-16.931	-16.931	0.000	0.000	0.000	0.000
80	A	182	VAL	0	0.016	0.021	16.910	-0.310	-0.310	0.000	0.000	0.000	0.000
81	A	183	VAL	0	-0.052	-0.023	14.314	0.803	0.803	0.000	0.000	0.000	0.000
82	A	184	VAL	0	0.034	0.013	9.714	-0.943	-0.943	0.000	0.000	0.000	0.000
83	A	185	GLN	0	-0.023	-0.017	9.653	0.287	0.287	0.000	0.000	0.000	0.000
84	A	186	LYS	1	0.829	0.923	1.726	-119.920	-124.017	12.981	-4.902	-3.983	0.076
85	A	187	LYS	1	0.999	0.990	6.221	-32.265	-32.265	0.000	0.000	0.000	0.000
86	A	188	SER	0	-0.065	-0.048	1.705	-29.675	-33.805	14.141	-6.012	-4.000	0.071
87	A	189	GLY	0	0.005	0.006	4.968	-0.528	-0.491	-0.001	-0.007	-0.028	0.000
88	A	190	GLY	0	0.013	0.014	5.608	-4.853	-4.853	0.000	0.000	0.000	0.000
89	A	191	ARG	1	0.822	0.887	6.627	-26.118	-26.118	0.000	0.000	0.000	0.000
90	A	192	THR	0	0.000	0.005	9.314	0.254	0.254	0.000	0.000	0.000	0.000
91	A	193	GLU	-1	-0.765	-0.863	11.029	18.503	18.503	0.000	0.000	0.000	0.000
92	A	194	HIS	0	0.006	-0.001	14.838	0.805	0.805	0.000	0.000	0.000	0.000
93	A	195	PRO	0	0.013	0.003	17.384	-0.635	-0.635	0.000	0.000	0.000	0.000
94	A	196	PHE	0	-0.039	-0.011	21.020	-0.026	-0.026	0.000	0.000	0.000	0.000
95	A	197	THR	0	-0.018	-0.040	24.178	0.073	0.073	0.000	0.000	0.000	0.000
96	A	198	VAL	0	-0.013	-0.007	27.871	0.001	0.001	0.000	0.000	0.000	0.000
97	A	199	GLU	-1	-0.891	-0.929	30.823	10.164	10.164	0.000	0.000	0.000	0.000
98	A	200	GLU	-1	-0.841	-0.916	34.140	8.553	8.553	0.000	0.000	0.000	0.000
99	A	201	PHE	0	-0.024	-0.005	35.783	-0.253	-0.253	0.000	0.000	0.000	0.000
100	A	202	VAL	0	0.017	0.001	40.031	-0.028	-0.028	0.000	0.000	0.000	0.000
101	A	203	LEU	0	-0.024	-0.008	43.686	-0.213	-0.213	0.000	0.000	0.000	0.000
102	A	204	PRO	0	0.001	0.017	44.065	0.150	0.150	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:103:ASP)