FMO DATABASE

FMODB ID: N9Q3Q

Calculation Name: 4JE4-A-Xray372

Preferred Name: Fibronectin

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4JE4

Chain ID: A

ChEMBL ID: CHEMBL3810

UniProt ID: P02751

Base Structure: X-ray

Registration Date: 2023-09-19

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

Total energy (hartree)

FMO2-HF: Electronic energy	-790223.589356
FMO2-HF: Nuclear repulsion	750185.043423
FMO2-HF: Total energy	-40038.545933
FMO2-MP2: Total energy	-40157.837061

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:3:SER)

Summations of interaction energy for fragment #1(A:3:SER)

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.
-15.709	-17.172	12.868	-5.513	-5.892	0.012

Interaction energy analysis for fragmet #1(A:3:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.077 / q_NPA : 0.041

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	A	5	ARG	1	0.928	0.938	3.903	-1.854	0.488	-0.008	-1.250	-1.084	0.002
4	A	6	TRP	0	0.059	0.022	2.003	-9.279	-13.842	12.696	-3.947	-4.186	0.012
5	A	7	PHE	0	0.016	0.013	6.324	-0.285	-0.285	0.000	0.000	0.000	0.000
6	A	8	HIS	1	0.834	0.917	7.797	-1.499	-1.499	0.000	0.000	0.000	0.000
7	A	9	PRO	0	0.018	0.009	10.816	-0.090	-0.090	0.000	0.000	0.000	0.000
8	A	10	ASN	0	0.031	-0.008	13.239	-0.038	-0.038	0.000	0.000	0.000	0.000
9	A	11	ILE	0	-0.028	0.012	14.643	-0.044	-0.044	0.000	0.000	0.000	0.000
10	A	12	THR	0	-0.012	-0.040	17.428	0.034	0.034	0.000	0.000	0.000	0.000
11	A	13	GLY	0	0.010	-0.004	18.641	0.047	0.047	0.000	0.000	0.000	0.000
12	A	14	VAL	0	0.112	0.061	19.964	0.017	0.017	0.000	0.000	0.000	0.000
13	A	15	GLU	-1	-0.796	-0.862	19.293	0.471	0.471	0.000	0.000	0.000	0.000
14	A	16	ALA	0	-0.018	-0.012	16.249	0.018	0.018	0.000	0.000	0.000	0.000
15	A	17	GLU	-1	-0.814	-0.902	17.661	0.409	0.409	0.000	0.000	0.000	0.000
16	A	18	ASN	0	-0.001	-0.014	20.592	-0.036	-0.036	0.000	0.000	0.000	0.000
17	A	19	LEU	0	-0.042	-0.007	15.623	-0.015	-0.015	0.000	0.000	0.000	0.000
18	A	20	LEU	0	-0.026	-0.015	14.578	-0.011	-0.011	0.000	0.000	0.000	0.000
19	A	21	LEU	0	-0.014	-0.005	18.094	-0.031	-0.031	0.000	0.000	0.000	0.000
20	A	22	THR	0	-0.058	-0.034	21.018	-0.033	-0.033	0.000	0.000	0.000	0.000
21	A	23	ARG	1	0.888	0.943	17.573	-0.388	-0.388	0.000	0.000	0.000	0.000
22	A	24	GLY	0	0.003	0.012	16.753	0.043	0.043	0.000	0.000	0.000	0.000
23	A	25	VAL	0	0.015	0.001	17.135	-0.053	-0.053	0.000	0.000	0.000	0.000
24	A	26	ASP	-1	-0.759	-0.876	17.918	0.337	0.337	0.000	0.000	0.000	0.000
25	A	27	GLY	0	0.083	0.048	16.619	-0.048	-0.048	0.000	0.000	0.000	0.000
26	A	28	SER	0	-0.033	-0.012	13.607	0.051	0.051	0.000	0.000	0.000	0.000
27	A	29	PHE	0	0.014	0.005	7.976	-0.035	-0.035	0.000	0.000	0.000	0.000
28	A	30	LEU	0	-0.054	-0.014	9.829	0.190	0.190	0.000	0.000	0.000	0.000
29	A	31	ALA	0	0.047	0.035	7.914	-0.141	-0.141	0.000	0.000	0.000	0.000
30	A	32	ARG	1	0.866	0.927	9.907	-0.649	-0.649	0.000	0.000	0.000	0.000
31	A	33	PRO	0	0.035	0.025	12.321	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	34	SER	0	-0.009	0.009	14.518	-0.048	-0.048	0.000	0.000	0.000	0.000
33	A	35	LYS	1	0.832	0.895	17.616	-0.614	-0.614	0.000	0.000	0.000	0.000
34	A	36	SER	0	0.006	0.013	20.682	-0.025	-0.025	0.000	0.000	0.000	0.000
35	A	37	ASN	0	-0.022	-0.004	21.009	-0.033	-0.033	0.000	0.000	0.000	0.000
36	A	38	PRO	0	0.040	0.035	19.460	0.041	0.041	0.000	0.000	0.000	0.000
37	A	39	GLY	0	0.040	0.017	18.216	-0.044	-0.044	0.000	0.000	0.000	0.000
38	A	40	ASP	-1	-0.746	-0.841	16.212	0.493	0.493	0.000	0.000	0.000	0.000
39	A	41	PHE	0	-0.039	-0.030	11.141	0.113	0.113	0.000	0.000	0.000	0.000
40	A	42	THR	0	-0.063	-0.045	13.286	-0.143	-0.143	0.000	0.000	0.000	0.000
41	A	43	LEU	0	0.029	0.019	9.822	0.186	0.186	0.000	0.000	0.000	0.000
42	A	44	SER	0	-0.026	-0.018	13.146	-0.135	-0.135	0.000	0.000	0.000	0.000
43	A	45	VAL	0	0.022	-0.006	14.168	0.131	0.131	0.000	0.000	0.000	0.000
44	A	46	ARG	1	0.826	0.917	16.115	-0.390	-0.390	0.000	0.000	0.000	0.000
45	A	47	ARG	1	0.785	0.843	18.667	-0.253	-0.253	0.000	0.000	0.000	0.000
46	A	48	ASN	0	0.011	0.010	21.323	-0.020	-0.020	0.000	0.000	0.000	0.000
47	A	49	GLY	0	-0.012	-0.005	23.811	-0.015	-0.015	0.000	0.000	0.000	0.000
48	A	50	ALA	0	-0.006	0.009	24.060	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	51	VAL	0	-0.029	-0.032	18.867	0.033	0.033	0.000	0.000	0.000	0.000
50	A	52	THR	0	-0.017	-0.006	19.764	-0.029	-0.029	0.000	0.000	0.000	0.000
51	A	53	HIS	0	-0.041	-0.019	17.759	0.138	0.138	0.000	0.000	0.000	0.000
52	A	54	ILE	0	0.014	0.014	15.225	-0.053	-0.053	0.000	0.000	0.000	0.000
53	A	55	LYS	1	0.922	0.952	15.885	-0.256	-0.256	0.000	0.000	0.000	0.000
54	A	56	ILE	0	-0.028	-0.017	10.792	0.024	0.024	0.000	0.000	0.000	0.000
55	A	57	GLN	0	-0.017	-0.012	14.941	0.004	0.004	0.000	0.000	0.000	0.000
56	A	58	ASN	0	-0.039	-0.051	14.556	0.018	0.018	0.000	0.000	0.000	0.000
57	A	59	THR	0	0.024	0.015	16.176	-0.007	-0.007	0.000	0.000	0.000	0.000
58	A	60	GLY	0	-0.035	0.000	16.824	-0.029	-0.029	0.000	0.000	0.000	0.000
59	A	61	ASP	-1	-0.927	-0.957	16.696	0.119	0.119	0.000	0.000	0.000	0.000
60	A	62	TYR	0	-0.063	-0.035	14.651	-0.052	-0.052	0.000	0.000	0.000	0.000
61	A	63	TYR	0	-0.017	-0.007	11.076	0.193	0.193	0.000	0.000	0.000	0.000
62	A	64	ASP	-1	-0.757	-0.870	13.646	0.200	0.200	0.000	0.000	0.000	0.000
63	A	65	LEU	0	-0.040	-0.021	13.802	0.090	0.090	0.000	0.000	0.000	0.000
64	A	66	TYR	0	-0.095	-0.077	17.104	-0.038	-0.038	0.000	0.000	0.000	0.000
65	A	67	GLY	0	0.010	0.009	19.468	-0.035	-0.035	0.000	0.000	0.000	0.000
66	A	68	GLY	0	-0.036	-0.017	18.762	0.030	0.030	0.000	0.000	0.000	0.000
67	A	69	GLU	-1	-0.858	-0.935	15.786	-0.042	-0.042	0.000	0.000	0.000	0.000
68	A	70	LYS	1	0.775	0.884	15.395	-0.078	-0.078	0.000	0.000	0.000	0.000
69	A	71	PHE	0	-0.007	-0.004	10.522	-0.037	-0.037	0.000	0.000	0.000	0.000
70	A	72	ALA	0	0.091	0.048	10.811	0.095	0.095	0.000	0.000	0.000	0.000
71	A	73	THR	0	-0.078	-0.082	6.590	0.386	0.386	0.000	0.000	0.000	0.000
72	A	74	LEU	0	0.026	0.002	6.193	0.008	0.008	0.000	0.000	0.000	0.000
73	A	75	ALA	0	-0.049	-0.030	2.924	-0.032	0.674	0.181	-0.295	-0.591	-0.002
74	A	76	GLU	-1	-0.767	-0.848	4.334	-0.873	-0.821	-0.001	-0.021	-0.031	0.000
75	A	77	LEU	0	-0.002	0.029	7.618	0.052	0.052	0.000	0.000	0.000	0.000
76	A	78	VAL	0	-0.024	-0.029	5.697	-0.062	-0.062	0.000	0.000	0.000	0.000
77	A	79	GLN	0	-0.064	-0.038	5.419	-0.723	-0.723	0.000	0.000	0.000	0.000
78	A	80	TYR	0	0.026	0.007	7.067	-0.038	-0.038	0.000	0.000	0.000	0.000
79	A	81	TYR	0	0.029	-0.009	10.537	-0.066	-0.066	0.000	0.000	0.000	0.000
80	A	82	MET	0	-0.082	-0.023	8.198	0.173	0.173	0.000	0.000	0.000	0.000
81	A	83	GLU	-1	-0.891	-0.943	10.355	-0.596	-0.596	0.000	0.000	0.000	0.000
82	A	84	HIS	1	0.789	0.906	12.656	0.056	0.056	0.000	0.000	0.000	0.000
83	A	85	HIS	0	0.003	-0.013	15.464	0.040	0.040	0.000	0.000	0.000	0.000
84	A	86	GLY	0	0.045	0.023	16.799	-0.037	-0.037	0.000	0.000	0.000	0.000
85	A	87	GLN	0	-0.009	-0.001	17.675	-0.027	-0.027	0.000	0.000	0.000	0.000
86	A	88	LEU	0	-0.013	0.010	14.506	0.005	0.005	0.000	0.000	0.000	0.000
87	A	89	LYS	1	0.939	0.967	19.007	-0.141	-0.141	0.000	0.000	0.000	0.000
88	A	90	GLU	-1	-0.762	-0.841	22.365	0.306	0.306	0.000	0.000	0.000	0.000
89	A	91	LYS	1	0.929	0.952	24.578	-0.176	-0.176	0.000	0.000	0.000	0.000
90	A	92	ASN	0	-0.009	-0.019	27.884	-0.004	-0.004	0.000	0.000	0.000	0.000
91	A	93	GLY	0	0.008	0.011	27.083	-0.015	-0.015	0.000	0.000	0.000	0.000
92	A	94	ASP	-1	-0.815	-0.884	24.571	0.178	0.178	0.000	0.000	0.000	0.000
93	A	95	VAL	0	-0.016	-0.005	19.662	0.016	0.016	0.000	0.000	0.000	0.000
94	A	96	ILE	0	-0.028	-0.014	17.029	0.012	0.012	0.000	0.000	0.000	0.000
95	A	97	GLU	-1	-0.812	-0.893	16.915	0.244	0.244	0.000	0.000	0.000	0.000
96	A	98	LEU	0	-0.024	-0.012	11.204	0.071	0.071	0.000	0.000	0.000	0.000
97	A	99	LYS	1	0.811	0.907	12.527	-0.301	-0.301	0.000	0.000	0.000	0.000
98	A	100	TYR	0	-0.010	-0.018	11.082	-0.016	-0.016	0.000	0.000	0.000	0.000
99	A	101	PRO	0	0.037	0.023	6.546	0.072	0.072	0.000	0.000	0.000	0.000
100	A	102	LEU	0	0.023	0.026	8.766	-0.187	-0.187	0.000	0.000	0.000	0.000
101	A	103	ASN	0	-0.010	-0.012	7.572	0.010	0.010	0.000	0.000	0.000	0.000
102	A	104	LYS	1	0.928	0.965	9.450	-0.658	-0.658	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:SER)