FMO DATABASE

FMODB ID: 66MLZ

Calculation Name: 4DX9-s-Xray372

Preferred Name: Fibronectin receptor beta

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4DX9

Chain ID: s

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

Total energy (hartree)

FMO2-HF: Electronic energy	-899953.991796
FMO2-HF: Nuclear repulsion	854395.966139
FMO2-HF: Total energy	-45558.025658
FMO2-MP2: Total energy	-45688.577532

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(s:60:CYS)

Summations of interaction energy for fragment #1(s: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.
-7.141	-4.604	6.429	-3.129	-5.837	-0.025

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.022 / q_NPA : -0.010

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	s	62	GLU	-1	-0.882	-0.930	3.755	-0.452	2.057	-0.024	-1.133	-1.352	0.004
4	s	63	PHE	0	0.016	0.008	5.694	0.032	0.032	0.000	0.000	0.000	0.000
5	s	64	ARG	1	0.824	0.895	9.403	0.762	0.762	0.000	0.000	0.000	0.000
6	s	65	ILE	0	-0.016	-0.010	12.552	-0.010	-0.010	0.000	0.000	0.000	0.000
7	s	66	LYS	1	0.896	0.949	15.116	0.331	0.331	0.000	0.000	0.000	0.000
8	s	67	TYR	0	-0.028	-0.031	17.872	0.009	0.009	0.000	0.000	0.000	0.000
9	s	68	VAL	0	0.011	0.011	19.480	0.004	0.004	0.000	0.000	0.000	0.000
10	s	69	GLY	0	0.046	0.015	22.009	0.014	0.014	0.000	0.000	0.000	0.000
11	s	70	ALA	0	-0.039	-0.024	21.968	-0.001	-0.001	0.000	0.000	0.000	0.000
12	s	71	ILE	0	0.027	0.039	23.673	0.000	0.000	0.000	0.000	0.000	0.000
13	s	84	GLY	0	0.050	0.039	25.722	0.005	0.005	0.000	0.000	0.000	0.000
14	s	85	PRO	0	-0.039	-0.031	22.408	0.003	0.003	0.000	0.000	0.000	0.000
15	s	86	LEU	0	0.059	0.013	23.868	-0.011	-0.011	0.000	0.000	0.000	0.000
16	s	87	ASP	-1	-0.888	-0.947	27.043	-0.026	-0.026	0.000	0.000	0.000	0.000
17	s	88	LEU	0	-0.016	-0.012	21.085	0.006	0.006	0.000	0.000	0.000	0.000
18	s	89	ILE	0	-0.001	0.005	23.805	-0.003	-0.003	0.000	0.000	0.000	0.000
19	s	90	ASN	0	0.029	0.007	26.152	-0.006	-0.006	0.000	0.000	0.000	0.000
20	s	91	TYR	0	-0.032	-0.012	26.791	0.005	0.005	0.000	0.000	0.000	0.000
21	s	92	ILE	0	-0.023	-0.008	22.958	0.008	0.008	0.000	0.000	0.000	0.000
22	s	93	ASP	-1	-0.863	-0.934	27.323	-0.106	-0.106	0.000	0.000	0.000	0.000
23	s	94	VAL	0	-0.020	-0.008	30.323	0.002	0.002	0.000	0.000	0.000	0.000
24	s	95	ALA	0	0.021	0.011	29.266	0.003	0.003	0.000	0.000	0.000	0.000
25	s	96	GLN	0	-0.023	-0.025	27.291	0.001	0.001	0.000	0.000	0.000	0.000
26	s	97	GLN	0	-0.073	-0.024	31.383	-0.002	-0.002	0.000	0.000	0.000	0.000
27	s	98	ASP	-1	-0.927	-0.961	34.023	-0.010	-0.010	0.000	0.000	0.000	0.000
28	s	99	GLY	0	-0.034	-0.011	34.209	0.005	0.005	0.000	0.000	0.000	0.000
29	s	100	LYS	1	0.829	0.930	30.514	-0.006	-0.006	0.000	0.000	0.000	0.000
30	s	101	LEU	0	-0.009	0.001	25.403	0.002	0.002	0.000	0.000	0.000	0.000
31	s	102	PRO	0	0.019	0.017	26.963	-0.004	-0.004	0.000	0.000	0.000	0.000
32	s	103	PHE	0	0.032	-0.005	27.823	-0.010	-0.010	0.000	0.000	0.000	0.000
33	s	104	VAL	0	-0.041	-0.014	27.649	-0.018	-0.018	0.000	0.000	0.000	0.000
34	s	105	PRO	0	-0.016	0.004	23.180	0.018	0.018	0.000	0.000	0.000	0.000
35	s	106	PRO	0	0.044	0.015	23.891	-0.008	-0.008	0.000	0.000	0.000	0.000
36	s	107	GLU	-1	-0.848	-0.897	23.510	-0.262	-0.262	0.000	0.000	0.000	0.000
37	s	108	GLU	-1	-0.951	-0.991	20.376	-0.076	-0.076	0.000	0.000	0.000	0.000
38	s	109	GLU	-1	-0.856	-0.912	17.165	-0.476	-0.476	0.000	0.000	0.000	0.000
39	s	110	PHE	0	-0.031	-0.015	14.680	0.038	0.038	0.000	0.000	0.000	0.000
40	s	111	ILE	0	0.002	-0.009	8.576	-0.102	-0.102	0.000	0.000	0.000	0.000
41	s	112	MET	0	-0.046	-0.006	9.096	0.192	0.192	0.000	0.000	0.000	0.000
42	s	113	GLY	0	0.029	0.005	5.377	-0.653	-0.653	0.000	0.000	0.000	0.000
43	s	114	VAL	0	0.000	0.009	4.459	1.040	1.364	-0.001	-0.087	-0.236	0.000
44	s	115	SER	0	0.011	-0.015	2.354	-2.189	-1.166	6.437	-3.918	-3.543	-0.029
45	s	116	LYS	1	0.985	0.968	3.396	-3.854	-5.402	0.012	2.065	-0.528	0.000
46	s	117	TYR	0	0.001	0.015	5.608	-1.052	-1.052	0.000	0.000	0.000	0.000
47	s	118	GLY	0	0.041	0.036	8.072	-0.201	-0.201	0.000	0.000	0.000	0.000
48	s	119	ILE	0	-0.011	-0.006	6.841	0.545	0.545	0.000	0.000	0.000	0.000
49	s	120	LYS	1	0.881	0.930	5.783	-1.188	-1.188	0.000	0.000	0.000	0.000
50	s	130	LEU	0	0.026	0.009	15.839	0.029	0.029	0.000	0.000	0.000	0.000
51	s	131	HIS	1	0.874	0.929	14.792	-0.183	-0.183	0.000	0.000	0.000	0.000
52	s	132	ARG	1	0.966	0.990	11.885	-0.875	-0.875	0.000	0.000	0.000	0.000
53	s	133	HIS	0	0.031	0.030	12.260	-0.084	-0.084	0.000	0.000	0.000	0.000
54	s	134	ALA	0	0.056	0.025	11.503	0.223	0.223	0.000	0.000	0.000	0.000
55	s	135	LEU	0	0.045	-0.006	9.304	-0.111	-0.111	0.000	0.000	0.000	0.000
56	s	136	TYR	0	-0.044	-0.016	12.193	-0.100	-0.100	0.000	0.000	0.000	0.000
57	s	137	LEU	0	0.020	0.012	15.378	-0.055	-0.055	0.000	0.000	0.000	0.000
58	s	138	ILE	0	-0.058	-0.014	11.464	-0.062	-0.062	0.000	0.000	0.000	0.000
59	s	139	ILE	0	0.042	0.040	15.493	0.003	0.003	0.000	0.000	0.000	0.000
60	s	140	ARG	1	0.891	0.929	17.197	-0.029	-0.029	0.000	0.000	0.000	0.000
61	s	141	MET	0	-0.028	-0.006	11.489	-0.018	-0.018	0.000	0.000	0.000	0.000
62	s	142	VAL	0	-0.022	-0.011	16.147	-0.017	-0.017	0.000	0.000	0.000	0.000
63	s	143	CYS	0	-0.023	-0.018	16.780	-0.028	-0.028	0.000	0.000	0.000	0.000
64	s	144	TYR	0	0.019	0.007	18.858	-0.002	-0.002	0.000	0.000	0.000	0.000
65	s	145	ASP	-1	-0.888	-0.960	22.175	-0.290	-0.290	0.000	0.000	0.000	0.000
66	s	146	ASP	-1	-0.833	-0.920	24.504	-0.206	-0.206	0.000	0.000	0.000	0.000
67	s	147	GLY	0	0.073	0.044	26.559	0.020	0.020	0.000	0.000	0.000	0.000
68	s	148	LEU	0	-0.088	-0.035	29.681	0.012	0.012	0.000	0.000	0.000	0.000
69	s	149	GLY	0	-0.034	-0.025	31.640	0.002	0.002	0.000	0.000	0.000	0.000
70	s	150	ALA	0	-0.034	-0.009	28.252	-0.007	-0.007	0.000	0.000	0.000	0.000
71	s	151	GLY	0	0.105	0.068	25.275	-0.021	-0.021	0.000	0.000	0.000	0.000
72	s	152	LYS	1	0.669	0.829	22.710	0.298	0.298	0.000	0.000	0.000	0.000
73	s	153	SER	0	0.009	-0.004	19.641	0.004	0.004	0.000	0.000	0.000	0.000
74	s	154	LEU	0	0.022	0.010	20.224	-0.006	-0.006	0.000	0.000	0.000	0.000
75	s	155	LEU	0	-0.043	-0.025	13.649	-0.014	-0.014	0.000	0.000	0.000	0.000
76	s	156	ALA	0	0.033	0.028	17.659	0.036	0.036	0.000	0.000	0.000	0.000
77	s	157	LEU	0	-0.039	-0.037	12.896	-0.015	-0.015	0.000	0.000	0.000	0.000
78	s	158	LYN	0	0.023	0.022	17.228	0.020	0.020	0.000	0.000	0.000	0.000
79	s	159	THR	0	-0.011	-0.011	17.343	0.032	0.032	0.000	0.000	0.000	0.000
80	s	160	THR	0	-0.093	-0.072	20.009	0.006	0.006	0.000	0.000	0.000	0.000
81	s	161	ASP	-1	-0.837	-0.910	23.066	0.292	0.292	0.000	0.000	0.000	0.000
82	s	162	ALA	0	-0.050	-0.039	24.823	-0.022	-0.022	0.000	0.000	0.000	0.000
83	s	163	SER	0	-0.074	-0.047	27.575	0.001	0.001	0.000	0.000	0.000	0.000
84	s	164	ASN	0	-0.124	-0.079	26.315	-0.012	-0.012	0.000	0.000	0.000	0.000
85	s	165	GLU	-1	-0.900	-0.932	29.088	0.147	0.147	0.000	0.000	0.000	0.000
86	s	166	GLU	-1	-0.879	-0.924	24.455	0.204	0.204	0.000	0.000	0.000	0.000
87	s	167	TYR	-1	-0.888	-0.933	23.923	0.143	0.143	0.000	0.000	0.000	0.000
88	s	168	SER	0	-0.048	-0.013	21.978	-0.032	-0.032	0.000	0.000	0.000	0.000
89	s	169	LEU	0	-0.009	0.000	20.498	0.014	0.014	0.000	0.000	0.000	0.000
90	s	170	TRP	0	-0.053	-0.035	17.588	-0.007	-0.007	0.000	0.000	0.000	0.000
91	s	171	VAL	0	0.053	0.019	18.646	-0.024	-0.024	0.000	0.000	0.000	0.000
92	s	172	TYR	0	-0.029	-0.022	15.240	0.019	0.019	0.000	0.000	0.000	0.000
93	s	173	GLN	0	0.049	0.020	18.220	0.003	0.003	0.000	0.000	0.000	0.000
94	s	174	CYS	0	-0.041	0.006	15.350	-0.056	-0.056	0.000	0.000	0.000	0.000
95	s	175	ASN	0	0.063	0.020	18.206	0.014	0.014	0.000	0.000	0.000	0.000
96	s	176	SER	0	-0.010	-0.003	18.950	0.029	0.029	0.000	0.000	0.000	0.000
97	s	177	LEU	0	0.114	0.056	19.009	-0.033	-0.033	0.000	0.000	0.000	0.000
98	s	178	GLU	-1	-0.853	-0.939	17.251	-0.610	-0.610	0.000	0.000	0.000	0.000
99	s	179	GLN	0	-0.031	-0.020	13.861	-0.026	-0.026	0.000	0.000	0.000	0.000
100	s	180	ALA	0	0.052	0.015	13.301	-0.136	-0.136	0.000	0.000	0.000	0.000
101	s	181	GLN	0	0.003	-0.007	14.005	0.033	0.033	0.000	0.000	0.000	0.000
102	s	182	ALA	0	-0.043	-0.020	10.697	-0.040	-0.040	0.000	0.000	0.000	0.000
103	s	183	ILE	0	-0.003	-0.001	8.989	-0.298	-0.298	0.000	0.000	0.000	0.000
104	s	184	CYS	0	0.010	-0.003	9.061	0.057	0.057	0.000	0.000	0.000	0.000
105	s	185	LYS	1	0.935	0.970	9.593	0.831	0.831	0.000	0.000	0.000	0.000
106	s	186	VAL	0	-0.022	-0.009	3.420	-0.315	-0.086	0.005	-0.056	-0.178	0.000
107	s	187	LEU	0	0.030	0.001	5.731	0.447	0.447	0.000	0.000	0.000	0.000
108	s	188	SER	0	-0.059	-0.019	8.187	0.264	0.264	0.000	0.000	0.000	0.000
109	s	189	THR	0	-0.015	-0.005	6.079	0.034	0.034	0.000	0.000	0.000	0.000
110	s	190	ALA	0	-0.027	-0.006	5.717	0.444	0.444	0.000	0.000	0.000	0.000
111	s	191	PHE	0	0.027	0.020	6.988	0.264	0.264	0.000	0.000	0.000	0.000
112	s	192	ASP	-1	-0.878	-0.933	10.592	0.260	0.260	0.000	0.000	0.000	0.000
113	s	193	SER	0	-0.142	-0.085	8.819	0.157	0.157	0.000	0.000	0.000	0.000
114	s	194	VAL	0	-0.043	-0.021	10.856	0.020	0.020	0.000	0.000	0.000	0.000
115	s	195	LEU	0	-0.014	0.020	13.101	-0.068	-0.068	0.000	0.000	0.000	0.000

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