FMO DATABASE

FMODB ID: 6Y95Z

Calculation Name: 4DX9-A-Xray372

Preferred Name: Fibronectin receptor beta

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4DX9

Chain ID: A

ChEMBL ID: CHEMBL1905

UniProt ID: P05556

Base Structure: X-ray

Registration Date: 2023-09-24

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	115
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-911363.03394
FMO2-HF: Nuclear repulsion	865585.814979
FMO2-HF: Total energy	-45777.218961
FMO2-MP2: Total energy	-45908.239423

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:60:CYS)

Summations of interaction energy for fragment #1(A: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.
-10.993	-6.17	6.692	-5.345	-6.171	-0.018

Interaction energy analysis for fragmet #1(A: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 : -0.015

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	62	GLU	-1	-0.837	-0.914	3.458	0.798	2.980	0.007	-0.893	-1.296	0.004
4	A	63	PHE	0	0.004	0.009	5.768	-0.070	-0.070	0.000	0.000	0.000	0.000
5	A	64	ARG	1	0.816	0.883	9.567	0.600	0.600	0.000	0.000	0.000	0.000
6	A	65	ILE	0	-0.029	-0.014	12.764	-0.017	-0.017	0.000	0.000	0.000	0.000
7	A	66	LYS	1	0.869	0.937	15.259	0.197	0.197	0.000	0.000	0.000	0.000
8	A	67	TYR	0	0.022	0.003	17.719	0.017	0.017	0.000	0.000	0.000	0.000
9	A	68	VAL	0	-0.009	-0.003	19.310	-0.024	-0.024	0.000	0.000	0.000	0.000
10	A	69	GLY	0	0.022	0.000	21.256	-0.003	-0.003	0.000	0.000	0.000	0.000
11	A	70	ALA	0	-0.027	-0.010	21.168	0.016	0.016	0.000	0.000	0.000	0.000
12	A	71	ILE	0	-0.012	-0.007	22.919	-0.024	-0.024	0.000	0.000	0.000	0.000
13	A	72	GLU	-1	-0.954	-0.960	25.111	0.242	0.242	0.000	0.000	0.000	0.000
14	A	83	GLU	-1	-0.892	-0.938	28.016	0.100	0.100	0.000	0.000	0.000	0.000
15	A	84	GLY	0	-0.025	-0.013	25.586	0.006	0.006	0.000	0.000	0.000	0.000
16	A	85	PRO	0	-0.006	-0.031	21.953	0.013	0.013	0.000	0.000	0.000	0.000
17	A	86	LEU	0	0.025	0.006	23.895	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	87	ASP	-1	-0.810	-0.900	27.358	0.051	0.051	0.000	0.000	0.000	0.000
19	A	88	LEU	0	-0.035	-0.022	21.180	0.009	0.009	0.000	0.000	0.000	0.000
20	A	89	ILE	0	-0.014	0.007	24.307	0.002	0.002	0.000	0.000	0.000	0.000
21	A	90	ASN	0	0.022	0.012	26.138	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	91	TYR	0	-0.021	-0.010	26.204	0.000	0.000	0.000	0.000	0.000	0.000
23	A	92	ILE	0	0.006	0.003	22.266	0.008	0.008	0.000	0.000	0.000	0.000
24	A	93	ASP	-1	-0.820	-0.895	26.815	-0.012	-0.012	0.000	0.000	0.000	0.000
25	A	94	VAL	0	-0.029	-0.019	29.791	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	95	ALA	0	0.006	0.004	28.328	0.000	0.000	0.000	0.000	0.000	0.000
27	A	96	GLN	0	-0.033	-0.025	26.092	-0.005	-0.005	0.000	0.000	0.000	0.000
28	A	97	GLN	0	-0.045	-0.023	30.597	-0.004	-0.004	0.000	0.000	0.000	0.000
29	A	98	ASP	-1	-0.876	-0.915	33.358	0.055	0.055	0.000	0.000	0.000	0.000
30	A	99	GLY	0	-0.040	-0.013	32.783	0.002	0.002	0.000	0.000	0.000	0.000
31	A	100	LYS	1	0.770	0.871	30.314	-0.070	-0.070	0.000	0.000	0.000	0.000
32	A	101	LEU	0	-0.004	0.008	24.788	0.014	0.014	0.000	0.000	0.000	0.000
33	A	102	PRO	0	-0.001	0.012	26.086	-0.011	-0.011	0.000	0.000	0.000	0.000
34	A	103	PHE	0	0.044	0.009	26.841	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	104	VAL	0	-0.035	-0.021	26.568	-0.014	-0.014	0.000	0.000	0.000	0.000
36	A	105	PRO	0	-0.010	0.018	22.442	0.015	0.015	0.000	0.000	0.000	0.000
37	A	106	PRO	0	0.023	0.000	23.935	-0.014	-0.014	0.000	0.000	0.000	0.000
38	A	107	GLU	-1	-0.869	-0.936	23.254	-0.144	-0.144	0.000	0.000	0.000	0.000
39	A	108	GLU	-1	-0.946	-0.965	20.422	0.021	0.021	0.000	0.000	0.000	0.000
40	A	109	GLU	-1	-0.810	-0.892	16.633	-0.299	-0.299	0.000	0.000	0.000	0.000
41	A	110	PHE	0	-0.045	-0.020	13.977	0.029	0.029	0.000	0.000	0.000	0.000
42	A	111	ILE	0	0.013	0.003	7.621	-0.093	-0.093	0.000	0.000	0.000	0.000
43	A	112	MET	0	0.004	0.021	8.973	0.282	0.282	0.000	0.000	0.000	0.000
44	A	113	GLY	0	0.054	0.017	5.275	-0.644	-0.644	0.000	0.000	0.000	0.000
45	A	114	VAL	0	-0.029	-0.012	4.049	0.561	0.897	0.000	-0.103	-0.234	0.000
46	A	115	SER	0	-0.028	-0.034	2.144	-5.507	-3.379	6.568	-5.040	-3.655	-0.022
47	A	116	LYS	1	0.953	0.951	2.998	-4.005	-4.311	0.111	0.782	-0.588	0.000
48	A	117	TYR	0	-0.009	0.002	4.366	-1.174	-1.033	-0.001	-0.022	-0.118	0.000
49	A	118	GLY	0	0.034	0.028	6.537	-0.731	-0.731	0.000	0.000	0.000	0.000
50	A	119	ILE	0	-0.030	0.008	6.155	1.005	1.005	0.000	0.000	0.000	0.000
51	A	120	LYS	1	0.819	0.885	4.250	-2.238	-1.970	0.008	-0.060	-0.216	0.000
52	A	131	HIS	0	0.002	0.006	13.607	0.050	0.050	0.000	0.000	0.000	0.000
53	A	132	ARG	1	0.897	0.934	10.209	-1.085	-1.085	0.000	0.000	0.000	0.000
54	A	133	HIS	0	-0.015	0.016	11.184	-0.131	-0.131	0.000	0.000	0.000	0.000
55	A	134	ALA	0	0.046	0.016	10.981	0.257	0.257	0.000	0.000	0.000	0.000
56	A	135	LEU	0	0.023	0.000	8.467	-0.126	-0.126	0.000	0.000	0.000	0.000
57	A	136	TYR	0	-0.016	-0.004	11.692	-0.121	-0.121	0.000	0.000	0.000	0.000
58	A	137	LEU	0	-0.010	0.002	15.198	-0.078	-0.078	0.000	0.000	0.000	0.000
59	A	138	ILE	0	-0.056	-0.009	12.084	-0.063	-0.063	0.000	0.000	0.000	0.000
60	A	139	ILE	0	0.014	0.005	15.565	-0.024	-0.024	0.000	0.000	0.000	0.000
61	A	140	ARG	1	0.816	0.898	17.633	-0.149	-0.149	0.000	0.000	0.000	0.000
62	A	141	MET	0	0.013	0.009	12.923	0.046	0.046	0.000	0.000	0.000	0.000
63	A	142	VAL	0	-0.030	-0.014	16.702	-0.027	-0.027	0.000	0.000	0.000	0.000
64	A	143	CYS	0	-0.053	-0.020	17.294	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	144	TYR	0	-0.004	-0.027	19.614	-0.007	-0.007	0.000	0.000	0.000	0.000
66	A	145	ASP	-1	-0.846	-0.924	23.125	-0.194	-0.194	0.000	0.000	0.000	0.000
67	A	146	ASP	-1	-0.808	-0.903	24.984	-0.088	-0.088	0.000	0.000	0.000	0.000
68	A	147	GLY	0	0.015	0.008	26.819	0.009	0.009	0.000	0.000	0.000	0.000
69	A	148	LEU	0	-0.128	-0.058	29.694	0.004	0.004	0.000	0.000	0.000	0.000
70	A	149	GLY	0	0.022	0.008	27.864	0.001	0.001	0.000	0.000	0.000	0.000
71	A	150	ALA	0	0.007	0.021	27.322	-0.016	-0.016	0.000	0.000	0.000	0.000
72	A	151	GLY	0	-0.065	-0.026	27.100	0.007	0.007	0.000	0.000	0.000	0.000
73	A	152	LYS	1	0.861	0.917	23.089	0.123	0.123	0.000	0.000	0.000	0.000
74	A	153	SER	0	0.026	-0.003	20.173	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	154	LEU	0	0.007	0.025	20.504	-0.009	-0.009	0.000	0.000	0.000	0.000
76	A	155	LEU	0	-0.042	-0.038	13.569	-0.036	-0.036	0.000	0.000	0.000	0.000
77	A	156	ALA	0	0.042	0.026	17.949	0.032	0.032	0.000	0.000	0.000	0.000
78	A	157	LEU	0	-0.018	-0.017	13.262	0.000	0.000	0.000	0.000	0.000	0.000
79	A	158	LYS	1	0.953	0.990	17.114	-0.213	-0.213	0.000	0.000	0.000	0.000
80	A	159	THR	0	-0.007	-0.006	15.912	0.040	0.040	0.000	0.000	0.000	0.000
81	A	160	THR	0	-0.007	-0.023	18.645	-0.052	-0.052	0.000	0.000	0.000	0.000
82	A	161	ASP	-1	-0.827	-0.900	20.061	0.478	0.478	0.000	0.000	0.000	0.000
83	A	162	ALA	0	-0.029	-0.010	22.423	-0.026	-0.026	0.000	0.000	0.000	0.000
84	A	163	SER	0	-0.059	-0.044	25.365	-0.036	-0.036	0.000	0.000	0.000	0.000
85	A	164	ASN	0	-0.105	-0.071	27.427	-0.020	-0.020	0.000	0.000	0.000	0.000
86	A	165	GLU	-1	-0.923	-0.957	27.727	0.177	0.177	0.000	0.000	0.000	0.000
87	A	166	GLU	-1	-0.865	-0.915	26.943	0.220	0.220	0.000	0.000	0.000	0.000
88	A	167	TYR	0	-0.040	-0.024	22.804	0.038	0.038	0.000	0.000	0.000	0.000
89	A	168	SER	0	0.039	0.030	21.149	0.003	0.003	0.000	0.000	0.000	0.000
90	A	169	LEU	0	-0.037	-0.023	20.888	0.010	0.010	0.000	0.000	0.000	0.000
91	A	170	TRP	0	-0.001	-0.010	17.211	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	171	VAL	0	0.035	0.008	18.845	-0.021	-0.021	0.000	0.000	0.000	0.000
93	A	172	TYR	0	-0.005	-0.011	14.376	0.031	0.031	0.000	0.000	0.000	0.000
94	A	173	GLN	0	0.027	0.006	18.407	-0.020	-0.020	0.000	0.000	0.000	0.000
95	A	174	CYS	0	-0.057	-0.015	16.128	-0.036	-0.036	0.000	0.000	0.000	0.000
96	A	175	ASN	0	-0.006	-0.022	16.547	0.051	0.051	0.000	0.000	0.000	0.000
97	A	176	SER	0	0.040	0.014	18.838	0.003	0.003	0.000	0.000	0.000	0.000
98	A	177	LEU	0	0.103	0.054	18.707	-0.030	-0.030	0.000	0.000	0.000	0.000
99	A	178	GLU	-1	-0.928	-0.959	18.153	-0.462	-0.462	0.000	0.000	0.000	0.000
100	A	179	GLN	0	0.022	0.005	14.104	-0.036	-0.036	0.000	0.000	0.000	0.000
101	A	180	ALA	0	0.027	0.023	13.754	-0.069	-0.069	0.000	0.000	0.000	0.000
102	A	181	GLN	0	0.020	-0.013	14.413	-0.011	-0.011	0.000	0.000	0.000	0.000
103	A	182	ALA	0	-0.052	-0.026	11.723	-0.021	-0.021	0.000	0.000	0.000	0.000
104	A	183	ILE	0	0.002	0.008	9.401	-0.173	-0.173	0.000	0.000	0.000	0.000
105	A	184	CYS	0	-0.007	-0.008	9.588	0.066	0.066	0.000	0.000	0.000	0.000
106	A	185	LYS	1	0.917	0.955	10.415	0.659	0.659	0.000	0.000	0.000	0.000
107	A	186	VAL	0	0.002	0.014	4.347	-0.168	-0.094	-0.001	-0.009	-0.064	0.000
108	A	187	LEU	0	0.054	0.019	6.840	0.349	0.349	0.000	0.000	0.000	0.000
109	A	188	SER	0	-0.046	-0.015	9.068	0.179	0.179	0.000	0.000	0.000	0.000
110	A	189	THR	0	-0.043	-0.023	7.536	-0.189	-0.189	0.000	0.000	0.000	0.000
111	A	190	ALA	0	-0.036	-0.018	5.614	0.283	0.283	0.000	0.000	0.000	0.000
112	A	191	PHE	0	0.006	-0.002	7.060	0.253	0.253	0.000	0.000	0.000	0.000
113	A	192	ASP	-1	-0.871	-0.930	10.897	0.207	0.207	0.000	0.000	0.000	0.000
114	A	193	SER	0	-0.089	-0.040	7.952	0.109	0.109	0.000	0.000	0.000	0.000
115	A	194	VAL	0	-0.032	0.008	9.862	0.131	0.131	0.000	0.000	0.000	0.000

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