FMO DATABASE

FMODB ID: 763VK

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

Total energy (hartree)

FMO2-HF: Electronic energy	-770023.265616
FMO2-HF: Nuclear repulsion	729951.930384
FMO2-HF: Total energy	-40071.335232
FMO2-MP2: Total energy	-40191.082722

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.
-74.605	-69.767	0.175	-2.306	-2.707	0.016

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 : -0.981 / q_NPA : -1.005

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	0.013	-0.007	3.731	7.686	10.029	-0.001	-1.018	-1.325	0.004
4	A	106	VAL	0	-0.021	-0.017	6.208	-5.670	-5.670	0.000	0.000	0.000	0.000
5	A	107	PHE	0	-0.036	-0.024	8.497	-0.063	-0.063	0.000	0.000	0.000	0.000
6	A	108	VAL	0	0.012	-0.007	11.569	-1.083	-1.083	0.000	0.000	0.000	0.000
7	A	109	GLN	0	0.042	0.034	15.135	-0.210	-0.210	0.000	0.000	0.000	0.000
8	A	110	THR	0	0.027	0.013	18.481	0.136	0.136	0.000	0.000	0.000	0.000
9	A	111	ASP	-1	-0.842	-0.900	22.006	11.860	11.860	0.000	0.000	0.000	0.000
10	A	112	LYS	1	0.885	0.948	25.062	-10.945	-10.945	0.000	0.000	0.000	0.000
11	A	113	SER	0	0.027	0.028	24.649	0.397	0.397	0.000	0.000	0.000	0.000
12	A	114	ILE	0	0.014	0.012	26.118	0.127	0.127	0.000	0.000	0.000	0.000
13	A	115	TYR	0	-0.088	-0.071	25.749	-0.068	-0.068	0.000	0.000	0.000	0.000
14	A	116	LYS	1	0.883	0.926	31.042	-8.773	-8.773	0.000	0.000	0.000	0.000
15	A	117	PRO	0	0.024	-0.003	34.307	0.210	0.210	0.000	0.000	0.000	0.000
16	A	118	GLY	0	0.029	0.025	35.816	-0.155	-0.155	0.000	0.000	0.000	0.000
17	A	119	GLN	0	-0.026	0.009	32.571	0.326	0.326	0.000	0.000	0.000	0.000
18	A	120	THR	0	-0.025	-0.018	30.222	0.282	0.282	0.000	0.000	0.000	0.000
19	A	121	VAL	0	0.021	0.016	24.647	0.055	0.055	0.000	0.000	0.000	0.000
20	A	122	LYS	1	0.945	0.978	25.184	-10.756	-10.756	0.000	0.000	0.000	0.000
21	A	123	PHE	0	0.021	0.008	18.341	0.160	0.160	0.000	0.000	0.000	0.000
22	A	124	ARG	1	0.850	0.920	18.303	-16.633	-16.633	0.000	0.000	0.000	0.000
23	A	125	VAL	0	-0.017	-0.002	13.790	0.606	0.606	0.000	0.000	0.000	0.000
24	A	126	VAL	0	-0.009	-0.013	13.177	-1.009	-1.009	0.000	0.000	0.000	0.000
25	A	127	SER	0	-0.013	-0.031	7.843	2.587	2.587	0.000	0.000	0.000	0.000
26	A	128	MET	0	-0.018	0.006	8.651	-3.523	-3.523	0.000	0.000	0.000	0.000
27	A	129	ASP	-1	-0.773	-0.882	6.967	31.841	31.841	0.000	0.000	0.000	0.000
28	A	130	GLU	-1	-0.828	-0.922	5.301	40.288	40.288	0.000	0.000	0.000	0.000
29	A	131	ASN	0	-0.105	-0.066	8.849	-2.832	-2.832	0.000	0.000	0.000	0.000
30	A	132	PHE	0	-0.019	-0.027	11.394	-1.927	-1.927	0.000	0.000	0.000	0.000
31	A	133	HIS	1	0.865	0.954	11.471	-23.124	-23.124	0.000	0.000	0.000	0.000
32	A	134	PRO	0	0.018	0.019	11.266	1.872	1.872	0.000	0.000	0.000	0.000
33	A	135	LEU	0	0.017	0.014	6.763	-0.156	-0.156	0.000	0.000	0.000	0.000
34	A	136	ASN	0	0.011	0.011	10.977	-0.102	-0.102	0.000	0.000	0.000	0.000
35	A	137	GLU	-1	-0.799	-0.863	6.617	41.022	41.022	0.000	0.000	0.000	0.000
36	A	138	LEU	0	-0.005	0.000	10.402	-1.938	-1.938	0.000	0.000	0.000	0.000
37	A	139	ILE	0	-0.005	-0.008	9.443	2.192	2.192	0.000	0.000	0.000	0.000
38	A	140	PRO	0	-0.017	-0.013	10.855	-1.950	-1.950	0.000	0.000	0.000	0.000
39	A	141	LEU	0	-0.041	-0.016	13.467	-1.831	-1.831	0.000	0.000	0.000	0.000
40	A	142	VAL	0	0.039	0.030	14.360	1.533	1.533	0.000	0.000	0.000	0.000
41	A	143	TYR	0	-0.014	-0.009	16.835	-0.836	-0.836	0.000	0.000	0.000	0.000
42	A	144	ILE	0	0.041	0.030	19.625	0.648	0.648	0.000	0.000	0.000	0.000
43	A	145	GLN	0	-0.089	-0.062	22.239	0.201	0.201	0.000	0.000	0.000	0.000
44	A	146	ASP	-1	-0.735	-0.867	23.859	11.134	11.134	0.000	0.000	0.000	0.000
45	A	147	PRO	0	0.017	-0.007	26.852	0.198	0.198	0.000	0.000	0.000	0.000
46	A	148	LYS	1	0.851	0.949	28.888	-9.697	-9.697	0.000	0.000	0.000	0.000
47	A	149	GLY	0	0.013	0.022	25.959	-0.005	-0.005	0.000	0.000	0.000	0.000
48	A	150	ASN	0	-0.060	-0.033	26.445	0.218	0.218	0.000	0.000	0.000	0.000
49	A	151	ARG	1	0.887	0.939	19.308	-15.282	-15.282	0.000	0.000	0.000	0.000
50	A	152	ILE	0	-0.008	0.004	25.363	-0.262	-0.262	0.000	0.000	0.000	0.000
51	A	153	ALA	0	0.010	0.009	24.685	-0.335	-0.335	0.000	0.000	0.000	0.000
52	A	154	GLN	0	-0.015	-0.014	20.539	0.674	0.674	0.000	0.000	0.000	0.000
53	A	155	TRP	0	0.012	0.018	19.725	-0.411	-0.411	0.000	0.000	0.000	0.000
54	A	156	GLN	0	0.025	-0.008	18.086	0.883	0.883	0.000	0.000	0.000	0.000
55	A	157	SER	0	-0.045	-0.020	16.028	-0.243	-0.243	0.000	0.000	0.000	0.000
56	A	158	PHE	0	0.032	0.036	14.750	-0.851	-0.851	0.000	0.000	0.000	0.000
57	A	159	GLN	0	-0.005	-0.019	14.029	1.089	1.089	0.000	0.000	0.000	0.000
58	A	160	LEU	0	-0.067	-0.021	11.563	-1.099	-1.099	0.000	0.000	0.000	0.000
59	A	161	GLU	-1	-0.832	-0.910	15.270	14.889	14.889	0.000	0.000	0.000	0.000
60	A	162	GLY	0	0.002	-0.001	17.074	-0.397	-0.397	0.000	0.000	0.000	0.000
61	A	163	GLY	0	0.013	0.003	13.573	0.004	0.004	0.000	0.000	0.000	0.000
62	A	164	LEU	0	-0.031	-0.026	13.732	1.293	1.293	0.000	0.000	0.000	0.000
63	A	165	LYS	1	0.856	0.928	15.983	-16.039	-16.039	0.000	0.000	0.000	0.000
64	A	166	GLN	0	-0.016	-0.006	18.257	0.575	0.575	0.000	0.000	0.000	0.000
65	A	167	PHE	0	-0.011	0.005	17.621	-0.316	-0.316	0.000	0.000	0.000	0.000
66	A	168	SER	0	-0.027	-0.028	22.788	-0.190	-0.190	0.000	0.000	0.000	0.000
67	A	169	PHE	0	0.005	-0.011	26.022	0.051	0.051	0.000	0.000	0.000	0.000
68	A	170	PRO	0	0.011	-0.003	27.831	-0.021	-0.021	0.000	0.000	0.000	0.000
69	A	171	LEU	0	0.006	0.023	29.187	0.013	0.013	0.000	0.000	0.000	0.000
70	A	172	SER	0	-0.012	-0.013	32.430	-0.281	-0.281	0.000	0.000	0.000	0.000
71	A	173	SER	0	-0.019	-0.046	35.830	0.133	0.133	0.000	0.000	0.000	0.000
72	A	174	GLU	-1	-0.855	-0.895	38.642	7.763	7.763	0.000	0.000	0.000	0.000
73	A	175	PRO	0	-0.068	-0.016	33.173	0.071	0.071	0.000	0.000	0.000	0.000
74	A	176	PHE	0	0.030	-0.006	32.279	-0.165	-0.165	0.000	0.000	0.000	0.000
75	A	177	GLN	0	0.058	0.037	32.661	0.255	0.255	0.000	0.000	0.000	0.000
76	A	178	GLY	0	0.030	0.013	30.975	-0.062	-0.062	0.000	0.000	0.000	0.000
77	A	179	SER	0	-0.024	-0.023	25.530	0.046	0.046	0.000	0.000	0.000	0.000
78	A	180	TYR	0	-0.042	-0.036	24.859	-0.022	-0.022	0.000	0.000	0.000	0.000
79	A	181	LYS	1	0.848	0.908	18.960	-16.068	-16.068	0.000	0.000	0.000	0.000
80	A	182	VAL	0	-0.009	0.010	17.723	-0.287	-0.287	0.000	0.000	0.000	0.000
81	A	183	VAL	0	-0.049	-0.022	14.910	0.916	0.916	0.000	0.000	0.000	0.000
82	A	184	VAL	0	0.030	0.017	10.930	-0.908	-0.908	0.000	0.000	0.000	0.000
83	A	185	GLN	0	-0.023	-0.020	11.011	1.304	1.304	0.000	0.000	0.000	0.000
84	A	186	LYS	1	0.883	0.953	2.914	-79.123	-77.028	0.172	-1.112	-1.154	0.011
85	A	187	LYS	1	1.033	1.000	7.268	-28.501	-28.501	0.000	0.000	0.000	0.000
86	A	188	SER	0	-0.036	-0.019	3.719	-4.903	-4.503	0.004	-0.176	-0.228	0.001
87	A	189	GLY	0	0.031	0.021	5.921	0.087	0.087	0.000	0.000	0.000	0.000
88	A	190	GLY	0	-0.005	0.016	6.352	-2.039	-2.039	0.000	0.000	0.000	0.000
89	A	191	ARG	1	0.875	0.917	7.347	-24.784	-24.784	0.000	0.000	0.000	0.000
90	A	192	THR	0	-0.007	0.003	9.732	0.245	0.245	0.000	0.000	0.000	0.000
91	A	193	GLU	-1	-0.808	-0.903	11.528	16.952	16.952	0.000	0.000	0.000	0.000
92	A	194	HIS	0	0.012	0.004	15.281	0.903	0.903	0.000	0.000	0.000	0.000
93	A	195	PRO	0	0.015	0.005	17.520	-0.599	-0.599	0.000	0.000	0.000	0.000
94	A	196	PHE	0	-0.021	-0.008	21.187	0.001	0.001	0.000	0.000	0.000	0.000
95	A	197	THR	0	-0.024	-0.033	24.309	0.020	0.020	0.000	0.000	0.000	0.000
96	A	198	VAL	0	-0.008	0.002	27.924	-0.047	-0.047	0.000	0.000	0.000	0.000
97	A	199	GLU	-1	-0.885	-0.936	31.021	9.953	9.953	0.000	0.000	0.000	0.000
98	A	200	GLU	-1	-0.845	-0.928	34.373	8.436	8.436	0.000	0.000	0.000	0.000
99	A	201	PHE	0	-0.013	0.005	35.885	-0.184	-0.184	0.000	0.000	0.000	0.000
100	A	202	VAL	0	-0.003	0.004	40.346	-0.094	-0.094	0.000	0.000	0.000	0.000
101	A	203	LEU	0	-0.008	0.000	43.795	-0.126	-0.126	0.000	0.000	0.000	0.000
102	A	204	PRO	0	0.017	0.020	44.098	0.185	0.185	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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