FMO DATABASE

FMODB ID: MN61Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-770113.443475
FMO2-HF: Nuclear repulsion	730042.956968
FMO2-HF: Total energy	-40070.486506
FMO2-MP2: Total energy	-40190.321886

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.
-50.331	-47.014	0.097	-1.31	-2.104	0.007

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 : -1.021 / q_NPA : -1.016

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	0.014	0.001	3.819	2.211	4.606	-0.016	-0.986	-1.392	0.005
4	A	106	VAL	0	-0.019	-0.014	5.949	-5.867	-5.867	0.000	0.000	0.000	0.000
5	A	107	PHE	0	-0.032	-0.029	8.862	-0.136	-0.136	0.000	0.000	0.000	0.000
6	A	108	VAL	0	0.005	-0.009	12.005	-1.046	-1.046	0.000	0.000	0.000	0.000
7	A	109	GLN	0	0.073	0.053	15.718	0.338	0.338	0.000	0.000	0.000	0.000
8	A	110	THR	0	0.016	-0.001	18.845	0.105	0.105	0.000	0.000	0.000	0.000
9	A	111	ASP	-1	-0.829	-0.873	22.483	11.851	11.851	0.000	0.000	0.000	0.000
10	A	112	LYS	1	0.865	0.932	25.361	-10.633	-10.633	0.000	0.000	0.000	0.000
11	A	113	SER	0	0.032	0.036	25.013	0.350	0.350	0.000	0.000	0.000	0.000
12	A	114	ILE	0	0.027	0.017	26.562	0.126	0.126	0.000	0.000	0.000	0.000
13	A	115	TYR	0	-0.119	-0.114	26.338	-0.063	-0.063	0.000	0.000	0.000	0.000
14	A	116	LYS	1	0.978	0.980	31.715	-9.021	-9.021	0.000	0.000	0.000	0.000
15	A	117	PRO	0	0.032	0.008	34.930	0.225	0.225	0.000	0.000	0.000	0.000
16	A	118	GLY	0	0.029	0.023	36.319	-0.142	-0.142	0.000	0.000	0.000	0.000
17	A	119	GLN	0	-0.001	0.037	33.040	0.277	0.277	0.000	0.000	0.000	0.000
18	A	120	THR	0	-0.030	-0.015	30.160	0.261	0.261	0.000	0.000	0.000	0.000
19	A	121	VAL	0	0.030	0.017	25.082	0.072	0.072	0.000	0.000	0.000	0.000
20	A	122	LYS	1	0.950	0.979	25.394	-10.661	-10.661	0.000	0.000	0.000	0.000
21	A	123	PHE	0	0.027	0.012	18.335	0.170	0.170	0.000	0.000	0.000	0.000
22	A	124	ARG	1	0.827	0.902	17.918	-16.663	-16.663	0.000	0.000	0.000	0.000
23	A	125	VAL	0	-0.028	-0.007	13.936	0.508	0.508	0.000	0.000	0.000	0.000
24	A	126	VAL	0	0.001	-0.013	12.795	-0.939	-0.939	0.000	0.000	0.000	0.000
25	A	127	SER	0	-0.012	-0.019	8.139	2.210	2.210	0.000	0.000	0.000	0.000
26	A	128	MET	0	-0.013	0.011	8.506	-3.511	-3.511	0.000	0.000	0.000	0.000
27	A	129	ASP	-1	-0.755	-0.869	6.397	33.438	33.438	0.000	0.000	0.000	0.000
28	A	130	GLU	-1	-0.824	-0.926	4.456	48.924	49.082	-0.001	-0.011	-0.147	0.000
29	A	131	ASN	0	-0.093	-0.054	8.269	-3.043	-3.043	0.000	0.000	0.000	0.000
30	A	132	PHE	0	-0.040	-0.038	10.558	-2.326	-2.326	0.000	0.000	0.000	0.000
31	A	133	HIS	1	0.845	0.941	11.159	-24.330	-24.330	0.000	0.000	0.000	0.000
32	A	134	PRO	0	0.022	0.019	11.061	1.919	1.919	0.000	0.000	0.000	0.000
33	A	135	LEU	0	0.016	0.009	6.581	-0.203	-0.203	0.000	0.000	0.000	0.000
34	A	136	ASN	0	0.035	0.023	10.732	0.069	0.069	0.000	0.000	0.000	0.000
35	A	137	GLU	-1	-0.825	-0.880	6.894	38.130	38.130	0.000	0.000	0.000	0.000
36	A	138	LEU	0	-0.016	-0.005	10.376	-1.860	-1.860	0.000	0.000	0.000	0.000
37	A	139	ILE	0	-0.017	-0.008	9.994	1.982	1.982	0.000	0.000	0.000	0.000
38	A	140	PRO	0	-0.013	-0.015	10.897	-1.880	-1.880	0.000	0.000	0.000	0.000
39	A	141	LEU	0	-0.037	-0.016	13.655	-1.593	-1.593	0.000	0.000	0.000	0.000
40	A	142	VAL	0	0.033	0.028	14.511	1.358	1.358	0.000	0.000	0.000	0.000
41	A	143	TYR	0	-0.019	-0.021	16.978	-0.797	-0.797	0.000	0.000	0.000	0.000
42	A	144	ILE	0	0.045	0.036	19.966	0.619	0.619	0.000	0.000	0.000	0.000
43	A	145	GLN	0	-0.039	-0.031	22.760	-0.336	-0.336	0.000	0.000	0.000	0.000
44	A	146	ASP	-1	-0.737	-0.878	24.405	10.869	10.869	0.000	0.000	0.000	0.000
45	A	147	PRO	0	0.013	-0.013	27.602	0.195	0.195	0.000	0.000	0.000	0.000
46	A	148	LYS	1	0.848	0.941	29.744	-9.418	-9.418	0.000	0.000	0.000	0.000
47	A	149	GLY	0	0.005	0.022	26.659	-0.029	-0.029	0.000	0.000	0.000	0.000
48	A	150	ASN	0	-0.074	-0.033	26.965	0.205	0.205	0.000	0.000	0.000	0.000
49	A	151	ARG	1	0.892	0.953	19.739	-14.265	-14.265	0.000	0.000	0.000	0.000
50	A	152	ILE	0	-0.003	0.006	25.607	-0.238	-0.238	0.000	0.000	0.000	0.000
51	A	153	ALA	0	0.010	0.009	24.825	-0.295	-0.295	0.000	0.000	0.000	0.000
52	A	154	GLN	0	-0.022	-0.026	20.766	0.451	0.451	0.000	0.000	0.000	0.000
53	A	155	TRP	0	0.009	0.022	19.828	-0.355	-0.355	0.000	0.000	0.000	0.000
54	A	156	GLN	0	0.002	-0.029	18.299	1.047	1.047	0.000	0.000	0.000	0.000
55	A	157	SER	0	-0.054	-0.021	16.225	-0.358	-0.358	0.000	0.000	0.000	0.000
56	A	158	PHE	0	0.033	0.035	15.084	-0.830	-0.830	0.000	0.000	0.000	0.000
57	A	159	GLN	0	0.003	-0.020	13.995	1.212	1.212	0.000	0.000	0.000	0.000
58	A	160	LEU	0	-0.085	-0.024	11.790	-1.106	-1.106	0.000	0.000	0.000	0.000
59	A	161	GLU	-1	-0.934	-0.961	15.321	14.023	14.023	0.000	0.000	0.000	0.000
60	A	162	GLY	0	-0.005	-0.004	16.809	-0.388	-0.388	0.000	0.000	0.000	0.000
61	A	163	GLY	0	0.021	0.009	13.402	0.067	0.067	0.000	0.000	0.000	0.000
62	A	164	LEU	0	-0.035	-0.031	13.891	1.182	1.182	0.000	0.000	0.000	0.000
63	A	165	LYS	1	0.969	0.997	16.155	-15.400	-15.400	0.000	0.000	0.000	0.000
64	A	166	GLN	0	-0.010	-0.004	18.444	0.654	0.654	0.000	0.000	0.000	0.000
65	A	167	PHE	0	-0.021	-0.010	17.824	-0.347	-0.347	0.000	0.000	0.000	0.000
66	A	168	SER	0	-0.044	-0.034	22.946	-0.202	-0.202	0.000	0.000	0.000	0.000
67	A	169	PHE	0	0.012	-0.009	26.162	0.032	0.032	0.000	0.000	0.000	0.000
68	A	170	PRO	0	0.011	-0.003	27.959	-0.009	-0.009	0.000	0.000	0.000	0.000
69	A	171	LEU	0	0.010	0.024	29.974	0.002	0.002	0.000	0.000	0.000	0.000
70	A	172	SER	0	0.007	-0.003	32.789	-0.293	-0.293	0.000	0.000	0.000	0.000
71	A	173	SER	0	0.036	0.001	36.167	0.125	0.125	0.000	0.000	0.000	0.000
72	A	174	GLU	-1	-0.916	-0.942	39.059	7.604	7.604	0.000	0.000	0.000	0.000
73	A	175	PRO	0	-0.090	-0.028	33.771	0.072	0.072	0.000	0.000	0.000	0.000
74	A	176	PHE	0	0.059	0.014	32.898	-0.151	-0.151	0.000	0.000	0.000	0.000
75	A	177	GLN	0	0.072	0.057	33.406	0.303	0.303	0.000	0.000	0.000	0.000
76	A	178	GLY	0	0.026	0.013	31.996	-0.059	-0.059	0.000	0.000	0.000	0.000
77	A	179	SER	0	-0.036	-0.028	26.510	0.053	0.053	0.000	0.000	0.000	0.000
78	A	180	TYR	0	-0.034	-0.037	25.533	-0.035	-0.035	0.000	0.000	0.000	0.000
79	A	181	LYS	1	0.872	0.929	20.411	-14.950	-14.950	0.000	0.000	0.000	0.000
80	A	182	VAL	0	-0.003	0.017	17.986	-0.304	-0.304	0.000	0.000	0.000	0.000
81	A	183	VAL	0	-0.034	-0.016	15.472	0.805	0.805	0.000	0.000	0.000	0.000
82	A	184	VAL	0	0.020	0.011	11.233	-0.850	-0.850	0.000	0.000	0.000	0.000
83	A	185	GLN	0	-0.024	-0.019	11.155	1.928	1.928	0.000	0.000	0.000	0.000
84	A	186	LYS	1	0.931	0.982	2.852	-62.530	-61.939	0.113	-0.244	-0.460	0.002
85	A	187	LYS	1	1.041	1.000	7.201	-27.948	-27.948	0.000	0.000	0.000	0.000
86	A	188	SER	0	-0.036	-0.020	4.092	-1.462	-1.289	0.001	-0.069	-0.105	0.000
87	A	189	GLY	0	0.033	0.025	6.064	0.174	0.174	0.000	0.000	0.000	0.000
88	A	190	GLY	0	-0.017	0.012	6.912	-1.387	-1.387	0.000	0.000	0.000	0.000
89	A	191	ARG	1	0.919	0.944	7.866	-22.569	-22.569	0.000	0.000	0.000	0.000
90	A	192	THR	0	0.005	0.010	10.778	0.315	0.315	0.000	0.000	0.000	0.000
91	A	193	GLU	-1	-0.882	-0.956	12.495	16.397	16.397	0.000	0.000	0.000	0.000
92	A	194	HIS	0	0.008	0.003	16.294	0.924	0.924	0.000	0.000	0.000	0.000
93	A	195	PRO	0	0.014	0.002	18.374	-0.615	-0.615	0.000	0.000	0.000	0.000
94	A	196	PHE	0	-0.014	-0.003	22.062	0.041	0.041	0.000	0.000	0.000	0.000
95	A	197	THR	0	0.003	-0.003	25.086	-0.144	-0.144	0.000	0.000	0.000	0.000
96	A	198	VAL	0	0.009	0.007	28.744	-0.012	-0.012	0.000	0.000	0.000	0.000
97	A	199	GLU	-1	-0.942	-0.991	31.892	9.410	9.410	0.000	0.000	0.000	0.000
98	A	200	GLU	-1	-0.944	-0.989	35.198	8.227	8.227	0.000	0.000	0.000	0.000
99	A	201	PHE	0	-0.014	0.006	37.102	-0.168	-0.168	0.000	0.000	0.000	0.000
100	A	202	VAL	0	-0.001	0.005	41.152	-0.086	-0.086	0.000	0.000	0.000	0.000
101	A	203	LEU	0	-0.012	-0.005	44.657	-0.125	-0.125	0.000	0.000	0.000	0.000
102	A	204	PRO	0	0.018	0.021	44.648	0.187	0.187	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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