FMO DATABASE

FMODB ID: 537ZZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1015636.405649
FMO2-HF: Nuclear repulsion	966850.118234
FMO2-HF: Total energy	-48786.287415
FMO2-MP2: Total energy	-48926.203597

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.
-27.277	-29.923	17.29	-5.649	-8.996	0.002

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 : -0.017 / q_NPA : 0.000

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

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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	-0.866	-0.924	3.816	-1.496	0.761	-0.025	-0.994	-1.237	0.001
4	k	63	PHE	0	-0.002	0.000	5.795	0.132	0.132	0.000	0.000	0.000	0.000
5	k	64	ARG	1	0.862	0.926	9.497	0.910	0.910	0.000	0.000	0.000	0.000
6	k	65	ILE	0	-0.015	-0.008	12.629	0.031	0.031	0.000	0.000	0.000	0.000
7	k	66	LYS	1	0.884	0.945	15.178	0.361	0.361	0.000	0.000	0.000	0.000
8	k	67	TYR	0	-0.009	-0.019	17.903	0.020	0.020	0.000	0.000	0.000	0.000
9	k	68	VAL	0	-0.010	-0.002	19.485	-0.001	-0.001	0.000	0.000	0.000	0.000
10	k	69	GLY	0	0.053	0.019	22.005	0.007	0.007	0.000	0.000	0.000	0.000
11	k	70	ALA	0	-0.037	-0.026	21.957	0.007	0.007	0.000	0.000	0.000	0.000
12	k	71	ILE	0	-0.032	0.001	23.665	-0.013	-0.013	0.000	0.000	0.000	0.000
13	k	72	GLU	-1	-0.797	-0.853	25.200	0.231	0.231	0.000	0.000	0.000	0.000
14	k	84	GLY	0	0.052	0.025	25.874	0.012	0.012	0.000	0.000	0.000	0.000
15	k	85	PRO	0	-0.045	-0.036	22.640	0.005	0.005	0.000	0.000	0.000	0.000
16	k	86	LEU	0	0.076	0.023	24.107	-0.014	-0.014	0.000	0.000	0.000	0.000
17	k	87	ASP	-1	-0.867	-0.934	27.227	0.085	0.085	0.000	0.000	0.000	0.000
18	k	88	LEU	0	-0.027	-0.019	21.125	0.003	0.003	0.000	0.000	0.000	0.000
19	k	89	ILE	0	0.008	0.012	23.945	-0.006	-0.006	0.000	0.000	0.000	0.000
20	k	90	ASN	0	-0.019	-0.022	26.143	-0.015	-0.015	0.000	0.000	0.000	0.000
21	k	91	TYR	0	-0.021	-0.005	26.738	-0.008	-0.008	0.000	0.000	0.000	0.000
22	k	92	ILE	0	-0.023	-0.010	23.116	0.003	0.003	0.000	0.000	0.000	0.000
23	k	93	ASP	-1	-0.877	-0.940	27.316	-0.048	-0.048	0.000	0.000	0.000	0.000
24	k	94	VAL	0	0.011	0.008	30.314	-0.003	-0.003	0.000	0.000	0.000	0.000
25	k	95	ALA	0	-0.004	-0.009	29.256	-0.001	-0.001	0.000	0.000	0.000	0.000
26	k	96	GLN	0	-0.032	-0.028	27.288	0.000	0.000	0.000	0.000	0.000	0.000
27	k	97	GLN	0	-0.080	-0.025	31.291	-0.004	-0.004	0.000	0.000	0.000	0.000
28	k	98	ASP	-1	-0.894	-0.915	34.870	0.016	0.016	0.000	0.000	0.000	0.000
29	k	99	GLY	0	-0.021	-0.017	34.255	-0.002	-0.002	0.000	0.000	0.000	0.000
30	k	100	LYS	1	0.792	0.902	30.676	-0.027	-0.027	0.000	0.000	0.000	0.000
31	k	101	LEU	0	-0.009	-0.001	25.382	-0.001	-0.001	0.000	0.000	0.000	0.000
32	k	102	PRO	0	0.015	0.017	26.985	-0.002	-0.002	0.000	0.000	0.000	0.000
33	k	103	PHE	0	0.033	0.004	27.844	-0.008	-0.008	0.000	0.000	0.000	0.000
34	k	104	VAL	0	-0.033	-0.016	27.656	-0.018	-0.018	0.000	0.000	0.000	0.000
35	k	105	PRO	0	-0.026	-0.002	23.218	0.015	0.015	0.000	0.000	0.000	0.000
36	k	106	PRO	0	0.028	0.003	23.973	-0.012	-0.012	0.000	0.000	0.000	0.000
37	k	107	GLU	-1	-0.829	-0.907	23.486	-0.307	-0.307	0.000	0.000	0.000	0.000
38	k	108	GLU	-1	-0.961	-0.976	21.135	-0.155	-0.155	0.000	0.000	0.000	0.000
39	k	109	GLU	-1	-0.853	-0.915	16.998	-0.530	-0.530	0.000	0.000	0.000	0.000
40	k	110	PHE	0	-0.070	-0.051	14.481	0.031	0.031	0.000	0.000	0.000	0.000
41	k	111	ILE	0	-0.005	-0.002	8.586	-0.099	-0.099	0.000	0.000	0.000	0.000
42	k	112	MET	0	-0.024	-0.012	9.134	0.223	0.223	0.000	0.000	0.000	0.000
43	k	113	GLY	0	0.012	-0.001	5.395	-0.673	-0.673	0.000	0.000	0.000	0.000
44	k	114	VAL	0	-0.005	0.008	4.437	1.044	1.387	-0.001	-0.101	-0.242	0.000
45	k	115	SER	0	0.045	-0.003	2.364	-2.039	-1.493	7.895	-4.490	-3.952	-0.031
46	k	116	LYS	1	0.916	0.925	2.023	-25.774	-31.854	9.418	0.003	-3.341	0.032
47	k	117	TYR	0	0.001	-0.001	5.522	-1.144	-1.072	-0.001	-0.013	-0.058	0.000
48	k	118	GLY	0	0.036	0.016	6.918	-0.707	-0.707	0.000	0.000	0.000	0.000
49	k	119	ILE	0	-0.027	0.000	7.027	0.541	0.541	0.000	0.000	0.000	0.000
50	k	120	LYS	1	0.862	0.937	7.001	0.428	0.428	0.000	0.000	0.000	0.000
51	k	121	VAL	0	-0.008	-0.007	9.314	-0.302	-0.302	0.000	0.000	0.000	0.000
52	k	122	SER	0	0.017	0.010	11.236	0.109	0.109	0.000	0.000	0.000	0.000
53	k	123	THR	0	0.009	0.020	13.141	-0.101	-0.101	0.000	0.000	0.000	0.000
54	k	124	SER	0	-0.013	-0.040	13.854	-0.081	-0.081	0.000	0.000	0.000	0.000
55	k	125	ASP	-1	-0.925	-0.939	15.051	-0.412	-0.412	0.000	0.000	0.000	0.000
56	k	126	GLN	0	-0.013	-0.009	16.089	0.067	0.067	0.000	0.000	0.000	0.000
57	k	127	TYR	0	-0.039	-0.015	13.963	-0.027	-0.027	0.000	0.000	0.000	0.000
58	k	128	ASP	-1	-0.775	-0.900	15.620	0.073	0.073	0.000	0.000	0.000	0.000
59	k	129	VAL	0	-0.127	-0.089	12.158	0.040	0.040	0.000	0.000	0.000	0.000
60	k	130	LEU	0	0.037	0.047	14.443	0.069	0.069	0.000	0.000	0.000	0.000
61	k	131	HIS	1	0.873	0.944	14.670	-0.098	-0.098	0.000	0.000	0.000	0.000
62	k	132	ARG	1	0.977	0.988	12.016	-0.687	-0.687	0.000	0.000	0.000	0.000
63	k	133	HIS	0	0.009	0.019	12.174	-0.047	-0.047	0.000	0.000	0.000	0.000
64	k	134	ALA	0	0.047	0.024	11.511	0.270	0.270	0.000	0.000	0.000	0.000
65	k	135	LEU	0	0.038	0.006	7.866	-0.193	-0.193	0.000	0.000	0.000	0.000
66	k	136	TYR	0	0.014	0.004	12.091	-0.089	-0.089	0.000	0.000	0.000	0.000
67	k	137	LEU	0	-0.019	0.001	15.303	-0.093	-0.093	0.000	0.000	0.000	0.000
68	k	138	ILE	0	-0.032	-0.004	11.374	-0.110	-0.110	0.000	0.000	0.000	0.000
69	k	139	ILE	0	-0.021	0.000	15.492	0.010	0.010	0.000	0.000	0.000	0.000
70	k	140	ARG	1	0.894	0.936	17.198	-0.214	-0.214	0.000	0.000	0.000	0.000
71	k	141	MET	0	-0.006	0.019	11.327	-0.026	-0.026	0.000	0.000	0.000	0.000
72	k	142	VAL	0	-0.039	-0.026	16.156	-0.006	-0.006	0.000	0.000	0.000	0.000
73	k	143	CYS	0	-0.045	-0.014	15.926	-0.012	-0.012	0.000	0.000	0.000	0.000
74	k	144	TYR	0	0.015	0.005	18.908	0.014	0.014	0.000	0.000	0.000	0.000
75	k	145	ASP	-1	-0.888	-0.959	22.226	-0.239	-0.239	0.000	0.000	0.000	0.000
76	k	146	ASP	-1	-0.858	-0.946	24.498	-0.167	-0.167	0.000	0.000	0.000	0.000
77	k	147	GLY	0	0.047	0.039	26.550	0.020	0.020	0.000	0.000	0.000	0.000
78	k	148	LEU	0	-0.102	-0.050	28.134	0.013	0.013	0.000	0.000	0.000	0.000
79	k	149	GLY	0	-0.012	-0.021	30.930	-0.002	-0.002	0.000	0.000	0.000	0.000
80	k	150	ALA	0	-0.033	-0.013	29.563	0.008	0.008	0.000	0.000	0.000	0.000
81	k	151	GLY	0	0.014	-0.004	27.017	-0.006	-0.006	0.000	0.000	0.000	0.000
82	k	152	LYS	1	0.823	0.950	22.841	0.254	0.254	0.000	0.000	0.000	0.000
83	k	153	SER	0	0.009	-0.006	19.584	0.021	0.021	0.000	0.000	0.000	0.000
84	k	154	LEU	0	0.032	0.028	20.086	-0.027	-0.027	0.000	0.000	0.000	0.000
85	k	155	LEU	0	-0.024	-0.042	13.573	-0.017	-0.017	0.000	0.000	0.000	0.000
86	k	156	ALA	0	0.003	0.027	17.513	0.019	0.019	0.000	0.000	0.000	0.000
87	k	157	LEU	0	-0.014	-0.022	12.713	0.010	0.010	0.000	0.000	0.000	0.000
88	k	158	LYS	1	0.944	0.985	17.037	-0.253	-0.253	0.000	0.000	0.000	0.000
89	k	159	THR	0	-0.022	-0.021	16.154	0.076	0.076	0.000	0.000	0.000	0.000
90	k	160	THR	0	-0.016	-0.012	18.707	-0.062	-0.062	0.000	0.000	0.000	0.000
91	k	161	ASP	-1	-0.743	-0.862	20.332	0.378	0.378	0.000	0.000	0.000	0.000
92	k	162	ALA	0	-0.084	-0.039	22.907	0.007	0.007	0.000	0.000	0.000	0.000
93	k	163	SER	0	-0.133	-0.077	24.971	-0.011	-0.011	0.000	0.000	0.000	0.000
94	k	164	ASN	0	-0.070	-0.053	27.063	-0.031	-0.031	0.000	0.000	0.000	0.000
95	k	165	GLU	-1	-0.945	-0.973	27.405	0.284	0.284	0.000	0.000	0.000	0.000
96	k	166	GLU	-1	-0.859	-0.918	26.711	0.185	0.185	0.000	0.000	0.000	0.000
97	k	167	TYR	0	-0.109	-0.074	23.319	0.048	0.048	0.000	0.000	0.000	0.000
98	k	168	SER	0	0.038	0.008	21.674	-0.018	-0.018	0.000	0.000	0.000	0.000
99	k	169	LEU	0	-0.073	-0.040	20.466	0.033	0.033	0.000	0.000	0.000	0.000
100	k	170	TRP	0	-0.029	-0.025	17.558	-0.046	-0.046	0.000	0.000	0.000	0.000
101	k	171	VAL	0	0.018	0.005	18.637	-0.007	-0.007	0.000	0.000	0.000	0.000
102	k	172	TYR	0	0.024	0.009	15.718	-0.016	-0.016	0.000	0.000	0.000	0.000
103	k	173	GLN	0	0.069	0.028	18.245	0.001	0.001	0.000	0.000	0.000	0.000
104	k	174	CYS	0	-0.038	-0.004	15.430	-0.075	-0.075	0.000	0.000	0.000	0.000
105	k	175	ASN	0	0.021	-0.001	18.190	0.025	0.025	0.000	0.000	0.000	0.000
106	k	176	SER	0	0.013	-0.002	18.837	0.015	0.015	0.000	0.000	0.000	0.000
107	k	177	LEU	0	0.088	0.053	18.898	-0.024	-0.024	0.000	0.000	0.000	0.000
108	k	178	GLU	-1	-0.837	-0.928	17.069	-0.470	-0.470	0.000	0.000	0.000	0.000
109	k	179	GLN	0	-0.029	-0.021	14.128	0.017	0.017	0.000	0.000	0.000	0.000
110	k	180	ALA	0	0.069	0.029	13.204	-0.113	-0.113	0.000	0.000	0.000	0.000
111	k	181	GLN	0	-0.016	-0.018	14.023	0.101	0.101	0.000	0.000	0.000	0.000
112	k	182	ALA	0	-0.036	-0.016	10.527	0.038	0.038	0.000	0.000	0.000	0.000
113	k	183	ILE	0	0.009	0.008	8.992	-0.156	-0.156	0.000	0.000	0.000	0.000
114	k	184	CYS	0	0.003	-0.006	9.176	0.237	0.237	0.000	0.000	0.000	0.000
115	k	185	LYS	1	0.935	0.970	9.583	0.507	0.507	0.000	0.000	0.000	0.000
116	k	186	VAL	0	-0.031	-0.012	3.522	-0.106	0.110	0.004	-0.054	-0.166	0.000
117	k	187	LEU	0	0.021	0.000	6.020	1.068	1.068	0.000	0.000	0.000	0.000
118	k	188	SER	0	-0.038	-0.004	8.494	0.184	0.184	0.000	0.000	0.000	0.000
119	k	189	THR	0	-0.028	-0.009	6.212	0.268	0.268	0.000	0.000	0.000	0.000
120	k	190	ALA	0	-0.060	-0.027	5.734	0.562	0.562	0.000	0.000	0.000	0.000
121	k	191	PHE	0	0.005	-0.007	7.580	-0.023	-0.023	0.000	0.000	0.000	0.000
122	k	192	ASP	-1	-0.933	-0.948	11.250	0.860	0.860	0.000	0.000	0.000	0.000
123	k	193	SER	0	-0.090	-0.033	8.847	0.201	0.201	0.000	0.000	0.000	0.000

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