FMO DATABASE

FMODB ID: YY522

Calculation Name: 4DX9-k-Xray372

Preferred Name: Fibronectin receptor beta

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4DX9

Chain ID: k

ChEMBL ID: CHEMBL1905

UniProt ID: P05556

Base Structure: X-ray

Registration Date: 2023-06-20

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	123
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1020731.709499
FMO2-HF: Nuclear repulsion	971945.039269
FMO2-HF: Total energy	-48786.670231
FMO2-MP2: Total energy	-48926.657543

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(k:60:CYS)

Summations of interaction energy for fragment #1(k:60:CYS)

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.
-23.854	-24.705	17.497	-6.487	-10.158	-0.006

Interaction energy analysis for fragmet #1(k:60:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.012 / q_NPA : 0.011

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	k	62	GLU	-1	-0.818	-0.903	3.879	-0.046	2.127	-0.020	-1.032	-1.121	0.002
4	k	63	PHE	0	-0.011	-0.001	6.300	-0.125	-0.125	0.000	0.000	0.000	0.000
5	k	64	ARG	1	0.835	0.905	10.030	0.760	0.760	0.000	0.000	0.000	0.000
6	k	65	ILE	0	-0.009	-0.003	13.052	-0.003	-0.003	0.000	0.000	0.000	0.000
7	k	66	LYS	1	0.835	0.918	16.023	0.307	0.307	0.000	0.000	0.000	0.000
8	k	67	TYR	0	-0.024	-0.024	18.547	0.016	0.016	0.000	0.000	0.000	0.000
9	k	68	VAL	0	-0.007	-0.008	19.951	-0.006	-0.006	0.000	0.000	0.000	0.000
10	k	69	GLY	0	0.059	0.022	21.671	0.005	0.005	0.000	0.000	0.000	0.000
11	k	70	ALA	0	-0.040	-0.022	21.385	0.012	0.012	0.000	0.000	0.000	0.000
12	k	71	ILE	0	-0.020	0.001	23.114	-0.017	-0.017	0.000	0.000	0.000	0.000
13	k	72	GLU	-1	-0.790	-0.845	24.660	0.240	0.240	0.000	0.000	0.000	0.000
14	k	84	GLY	0	0.024	0.014	24.847	0.013	0.013	0.000	0.000	0.000	0.000
15	k	85	PRO	0	-0.016	-0.023	21.913	0.009	0.009	0.000	0.000	0.000	0.000
16	k	86	LEU	0	0.054	0.018	23.336	-0.012	-0.012	0.000	0.000	0.000	0.000
17	k	87	ASP	-1	-0.823	-0.900	26.544	0.095	0.095	0.000	0.000	0.000	0.000
18	k	88	LEU	0	0.009	-0.001	20.515	0.001	0.001	0.000	0.000	0.000	0.000
19	k	89	ILE	0	0.002	0.003	22.885	-0.004	-0.004	0.000	0.000	0.000	0.000
20	k	90	ASN	0	-0.039	-0.039	25.552	-0.011	-0.011	0.000	0.000	0.000	0.000
21	k	91	TYR	0	-0.008	0.001	26.421	-0.009	-0.009	0.000	0.000	0.000	0.000
22	k	92	ILE	0	-0.004	0.001	22.643	0.002	0.002	0.000	0.000	0.000	0.000
23	k	93	ASP	-1	-0.876	-0.916	26.932	-0.031	-0.031	0.000	0.000	0.000	0.000
24	k	94	VAL	0	0.043	0.009	29.835	-0.003	-0.003	0.000	0.000	0.000	0.000
25	k	95	ALA	0	-0.017	-0.008	28.575	0.000	0.000	0.000	0.000	0.000	0.000
26	k	96	GLN	0	-0.056	-0.039	26.929	0.000	0.000	0.000	0.000	0.000	0.000
27	k	97	GLN	0	-0.076	-0.046	30.872	-0.003	-0.003	0.000	0.000	0.000	0.000
28	k	98	ASP	-1	-0.885	-0.924	34.159	0.026	0.026	0.000	0.000	0.000	0.000
29	k	99	GLY	0	-0.045	-0.011	33.822	0.002	0.002	0.000	0.000	0.000	0.000
30	k	100	LYS	1	0.793	0.885	30.471	-0.039	-0.039	0.000	0.000	0.000	0.000
31	k	101	LEU	0	-0.024	-0.004	25.342	0.005	0.005	0.000	0.000	0.000	0.000
32	k	102	PRO	0	0.002	0.015	26.828	-0.003	-0.003	0.000	0.000	0.000	0.000
33	k	103	PHE	0	0.046	0.014	27.723	-0.004	-0.004	0.000	0.000	0.000	0.000
34	k	104	VAL	0	-0.044	-0.021	27.466	-0.017	-0.017	0.000	0.000	0.000	0.000
35	k	105	PRO	0	-0.027	-0.004	23.123	0.015	0.015	0.000	0.000	0.000	0.000
36	k	106	PRO	0	0.030	0.005	24.578	-0.010	-0.010	0.000	0.000	0.000	0.000
37	k	107	GLU	-1	-0.815	-0.897	24.110	-0.248	-0.248	0.000	0.000	0.000	0.000
38	k	108	GLU	-1	-0.951	-0.967	21.790	-0.098	-0.098	0.000	0.000	0.000	0.000
39	k	109	GLU	-1	-0.841	-0.916	17.665	-0.427	-0.427	0.000	0.000	0.000	0.000
40	k	110	PHE	0	-0.036	-0.032	14.979	0.027	0.027	0.000	0.000	0.000	0.000
41	k	111	ILE	0	-0.022	-0.007	9.198	-0.095	-0.095	0.000	0.000	0.000	0.000
42	k	112	MET	0	-0.028	-0.009	8.926	0.212	0.212	0.000	0.000	0.000	0.000
43	k	113	GLY	0	0.051	0.017	5.980	-0.623	-0.623	0.000	0.000	0.000	0.000
44	k	114	VAL	0	-0.032	-0.006	4.330	0.900	1.195	-0.001	-0.087	-0.207	0.000
45	k	115	SER	0	0.037	-0.015	2.315	-3.362	-2.815	8.668	-5.207	-4.007	-0.028
46	k	116	LYS	1	0.900	0.918	2.029	-22.720	-27.424	8.554	0.111	-3.961	0.023
47	k	117	TYR	0	0.002	0.001	4.811	-1.133	-1.004	-0.001	-0.021	-0.107	0.000
48	k	118	GLY	0	0.023	0.008	6.940	-0.672	-0.672	0.000	0.000	0.000	0.000
49	k	119	ILE	0	-0.016	0.014	6.832	0.733	0.733	0.000	0.000	0.000	0.000
50	k	120	LYS	1	0.845	0.926	7.848	0.172	0.172	0.000	0.000	0.000	0.000
51	k	121	VAL	0	-0.009	-0.015	9.757	-0.227	-0.227	0.000	0.000	0.000	0.000
52	k	122	SER	0	0.016	0.013	11.724	0.086	0.086	0.000	0.000	0.000	0.000
53	k	123	THR	0	0.004	0.014	13.805	-0.090	-0.090	0.000	0.000	0.000	0.000
54	k	124	SER	0	-0.030	-0.057	14.937	-0.057	-0.057	0.000	0.000	0.000	0.000
55	k	125	ASP	-1	-0.910	-0.920	15.776	-0.338	-0.338	0.000	0.000	0.000	0.000
56	k	126	GLN	0	-0.008	-0.007	16.695	0.047	0.047	0.000	0.000	0.000	0.000
57	k	127	TYR	0	-0.038	-0.014	14.821	-0.014	-0.014	0.000	0.000	0.000	0.000
58	k	128	ASP	-1	-0.767	-0.888	16.406	0.133	0.133	0.000	0.000	0.000	0.000
59	k	129	VAL	0	-0.127	-0.088	12.572	0.039	0.039	0.000	0.000	0.000	0.000
60	k	130	LEU	0	0.028	0.033	15.080	0.064	0.064	0.000	0.000	0.000	0.000
61	k	131	HIS	1	0.869	0.945	14.762	-0.165	-0.165	0.000	0.000	0.000	0.000
62	k	132	ARG	1	0.966	0.984	12.249	-0.645	-0.645	0.000	0.000	0.000	0.000
63	k	133	HIS	0	0.007	0.018	11.882	-0.055	-0.055	0.000	0.000	0.000	0.000
64	k	134	ALA	0	0.048	0.025	11.024	0.258	0.258	0.000	0.000	0.000	0.000
65	k	135	LEU	0	0.031	0.006	7.164	-0.204	-0.204	0.000	0.000	0.000	0.000
66	k	136	TYR	0	-0.001	-0.002	11.350	-0.112	-0.112	0.000	0.000	0.000	0.000
67	k	137	LEU	0	0.001	0.014	14.686	-0.098	-0.098	0.000	0.000	0.000	0.000
68	k	138	ILE	0	-0.056	-0.017	10.942	-0.109	-0.109	0.000	0.000	0.000	0.000
69	k	139	ILE	0	-0.021	0.000	15.104	0.018	0.018	0.000	0.000	0.000	0.000
70	k	140	ARG	1	0.843	0.905	16.294	-0.226	-0.226	0.000	0.000	0.000	0.000
71	k	141	MET	0	-0.007	0.015	11.153	-0.027	-0.027	0.000	0.000	0.000	0.000
72	k	142	VAL	0	-0.030	-0.013	15.533	-0.009	-0.009	0.000	0.000	0.000	0.000
73	k	143	CYS	0	-0.046	-0.020	15.353	-0.006	-0.006	0.000	0.000	0.000	0.000
74	k	144	TYR	0	0.029	0.014	18.429	0.012	0.012	0.000	0.000	0.000	0.000
75	k	145	ASP	-1	-0.862	-0.947	21.615	-0.222	-0.222	0.000	0.000	0.000	0.000
76	k	146	ASP	-1	-0.860	-0.959	23.716	-0.145	-0.145	0.000	0.000	0.000	0.000
77	k	147	GLY	0	0.010	0.025	25.956	0.018	0.018	0.000	0.000	0.000	0.000
78	k	148	LEU	0	-0.079	-0.029	28.168	0.013	0.013	0.000	0.000	0.000	0.000
79	k	149	GLY	0	-0.014	-0.023	30.409	-0.001	-0.001	0.000	0.000	0.000	0.000
80	k	150	ALA	0	-0.049	-0.019	29.075	0.008	0.008	0.000	0.000	0.000	0.000
81	k	151	GLY	0	0.020	0.011	26.469	-0.006	-0.006	0.000	0.000	0.000	0.000
82	k	152	LYS	1	0.849	0.944	22.928	0.201	0.201	0.000	0.000	0.000	0.000
83	k	153	SER	0	-0.006	0.000	19.261	-0.008	-0.008	0.000	0.000	0.000	0.000
84	k	154	LEU	0	0.013	0.015	20.139	-0.021	-0.021	0.000	0.000	0.000	0.000
85	k	155	LEU	0	-0.028	-0.030	13.422	-0.015	-0.015	0.000	0.000	0.000	0.000
86	k	156	ALA	0	0.015	0.018	17.655	0.012	0.012	0.000	0.000	0.000	0.000
87	k	157	LEU	0	-0.021	-0.018	12.474	0.007	0.007	0.000	0.000	0.000	0.000
88	k	158	LYS	1	0.945	0.991	16.507	-0.263	-0.263	0.000	0.000	0.000	0.000
89	k	159	THR	0	-0.049	-0.040	15.958	0.072	0.072	0.000	0.000	0.000	0.000
90	k	160	THR	0	0.010	-0.011	18.420	-0.058	-0.058	0.000	0.000	0.000	0.000
91	k	161	ASP	-1	-0.764	-0.863	20.131	0.382	0.382	0.000	0.000	0.000	0.000
92	k	162	ALA	0	-0.075	-0.034	22.557	0.008	0.008	0.000	0.000	0.000	0.000
93	k	163	SER	0	-0.139	-0.081	24.484	-0.011	-0.011	0.000	0.000	0.000	0.000
94	k	164	ASN	0	-0.077	-0.058	26.745	-0.031	-0.031	0.000	0.000	0.000	0.000
95	k	165	GLU	-1	-0.941	-0.971	26.741	0.284	0.284	0.000	0.000	0.000	0.000
96	k	166	GLU	-1	-0.831	-0.901	26.238	0.191	0.191	0.000	0.000	0.000	0.000
97	k	167	TYR	0	-0.085	-0.072	22.851	0.045	0.045	0.000	0.000	0.000	0.000
98	k	168	SER	0	0.016	-0.010	21.343	-0.012	-0.012	0.000	0.000	0.000	0.000
99	k	169	LEU	0	-0.054	-0.019	20.046	0.038	0.038	0.000	0.000	0.000	0.000
100	k	170	TRP	0	-0.017	-0.015	17.236	-0.042	-0.042	0.000	0.000	0.000	0.000
101	k	171	VAL	0	0.021	0.005	18.519	-0.005	-0.005	0.000	0.000	0.000	0.000
102	k	172	TYR	0	0.026	0.004	15.198	-0.005	-0.005	0.000	0.000	0.000	0.000
103	k	173	GLN	0	0.068	0.033	18.429	-0.008	-0.008	0.000	0.000	0.000	0.000
104	k	174	CYS	0	-0.013	0.009	15.453	-0.051	-0.051	0.000	0.000	0.000	0.000
105	k	175	ASN	0	-0.007	-0.010	18.145	0.015	0.015	0.000	0.000	0.000	0.000
106	k	176	SER	0	0.025	-0.006	18.995	0.010	0.010	0.000	0.000	0.000	0.000
107	k	177	LEU	0	0.080	0.046	18.067	-0.054	-0.054	0.000	0.000	0.000	0.000
108	k	178	GLU	-1	-0.819	-0.912	16.462	-0.461	-0.461	0.000	0.000	0.000	0.000
109	k	179	GLN	0	-0.031	-0.010	13.865	-0.028	-0.028	0.000	0.000	0.000	0.000
110	k	180	ALA	0	0.071	0.030	12.708	-0.114	-0.114	0.000	0.000	0.000	0.000
111	k	181	GLN	0	-0.044	-0.039	13.014	0.074	0.074	0.000	0.000	0.000	0.000
112	k	182	ALA	0	-0.027	-0.016	10.145	0.003	0.003	0.000	0.000	0.000	0.000
113	k	183	ILE	0	0.004	0.005	8.382	-0.223	-0.223	0.000	0.000	0.000	0.000
114	k	184	CYS	0	-0.002	-0.009	8.166	0.155	0.155	0.000	0.000	0.000	0.000
115	k	185	LYS	1	0.928	0.965	8.702	0.590	0.590	0.000	0.000	0.000	0.000
116	k	186	VAL	0	-0.007	-0.003	2.518	-0.654	-0.059	0.299	-0.249	-0.646	-0.003
117	k	187	LEU	0	0.022	0.010	5.195	1.305	1.395	-0.001	-0.001	-0.088	0.000
118	k	188	SER	0	-0.060	-0.026	7.742	0.307	0.307	0.000	0.000	0.000	0.000
119	k	189	THR	0	-0.038	-0.008	5.184	0.030	0.054	-0.001	-0.001	-0.021	0.000
120	k	190	ALA	0	-0.064	-0.040	5.274	1.649	1.649	0.000	0.000	0.000	0.000
121	k	191	PHE	0	0.021	0.005	7.122	-0.147	-0.147	0.000	0.000	0.000	0.000
122	k	192	ASP	-1	-0.928	-0.949	10.705	0.954	0.954	0.000	0.000	0.000	0.000
123	k	193	SER	0	-0.074	-0.028	8.108	0.254	0.254	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(k:60:CYS)