FMO DATABASE

FMODB ID: 85MJY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-789253.947091
FMO2-HF: Nuclear repulsion	749215.658087
FMO2-HF: Total energy	-40038.289003
FMO2-MP2: Total energy	-40157.579163

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.
-7.232	-6.707	8.911	-3.8	-5.635	0.004

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 : 0.053 / q_NPA : 0.021

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	5	ARG	1	0.978	0.987	3.806	-1.132	0.983	-0.021	-0.974	-1.120	0.003
4	A	6	TRP	0	0.077	0.036	2.115	-1.570	-4.085	8.275	-2.221	-3.539	0.005
5	A	7	PHE	0	0.001	0.002	6.128	-0.184	-0.184	0.000	0.000	0.000	0.000
6	A	8	HIS	1	0.809	0.890	7.593	-1.261	-1.261	0.000	0.000	0.000	0.000
7	A	9	PRO	0	0.018	0.007	10.396	-0.090	-0.090	0.000	0.000	0.000	0.000
8	A	10	ASN	0	-0.010	-0.018	12.698	-0.041	-0.041	0.000	0.000	0.000	0.000
9	A	11	ILE	0	0.005	0.025	14.629	-0.056	-0.056	0.000	0.000	0.000	0.000
10	A	12	THR	0	-0.022	-0.046	17.458	0.032	0.032	0.000	0.000	0.000	0.000
11	A	13	GLY	0	0.014	-0.008	18.747	0.034	0.034	0.000	0.000	0.000	0.000
12	A	14	VAL	0	0.109	0.052	20.125	0.007	0.007	0.000	0.000	0.000	0.000
13	A	15	GLU	-1	-0.809	-0.864	19.498	0.423	0.423	0.000	0.000	0.000	0.000
14	A	16	ALA	0	-0.023	-0.019	16.186	0.004	0.004	0.000	0.000	0.000	0.000
15	A	17	GLU	-1	-0.812	-0.900	17.645	0.324	0.324	0.000	0.000	0.000	0.000
16	A	18	ASN	0	0.008	-0.010	20.195	-0.045	-0.045	0.000	0.000	0.000	0.000
17	A	19	LEU	0	-0.053	-0.006	15.325	-0.017	-0.017	0.000	0.000	0.000	0.000
18	A	20	LEU	0	-0.017	-0.011	14.055	-0.033	-0.033	0.000	0.000	0.000	0.000
19	A	21	LEU	0	-0.013	-0.011	17.639	-0.039	-0.039	0.000	0.000	0.000	0.000
20	A	22	THR	0	-0.065	-0.034	20.558	-0.029	-0.029	0.000	0.000	0.000	0.000
21	A	23	ARG	1	0.900	0.949	17.387	-0.274	-0.274	0.000	0.000	0.000	0.000
22	A	24	GLY	0	-0.009	0.015	16.528	-0.008	-0.008	0.000	0.000	0.000	0.000
23	A	25	VAL	0	-0.008	-0.010	16.829	-0.027	-0.027	0.000	0.000	0.000	0.000
24	A	26	ASP	-1	-0.779	-0.888	17.680	0.182	0.182	0.000	0.000	0.000	0.000
25	A	27	GLY	0	0.054	0.030	16.364	-0.043	-0.043	0.000	0.000	0.000	0.000
26	A	28	SER	0	-0.034	-0.006	13.350	0.012	0.012	0.000	0.000	0.000	0.000
27	A	29	PHE	0	0.029	0.009	7.853	0.023	0.023	0.000	0.000	0.000	0.000
28	A	30	LEU	0	-0.034	-0.006	9.477	0.080	0.080	0.000	0.000	0.000	0.000
29	A	31	ALA	0	0.034	0.029	8.012	-0.088	-0.088	0.000	0.000	0.000	0.000
30	A	32	ARG	1	0.858	0.917	10.060	-0.623	-0.623	0.000	0.000	0.000	0.000
31	A	33	PRO	0	0.047	0.031	12.303	-0.019	-0.019	0.000	0.000	0.000	0.000
32	A	34	SER	0	-0.036	-0.002	14.291	-0.084	-0.084	0.000	0.000	0.000	0.000
33	A	35	LYS	1	0.889	0.925	17.450	-0.612	-0.612	0.000	0.000	0.000	0.000
34	A	36	SER	0	0.014	0.015	20.559	-0.020	-0.020	0.000	0.000	0.000	0.000
35	A	37	ASN	0	-0.034	-0.011	20.482	-0.036	-0.036	0.000	0.000	0.000	0.000
36	A	38	PRO	0	0.041	0.065	19.210	0.054	0.054	0.000	0.000	0.000	0.000
37	A	39	GLY	0	0.045	0.012	17.854	-0.046	-0.046	0.000	0.000	0.000	0.000
38	A	40	ASP	-1	-0.757	-0.866	15.971	0.544	0.544	0.000	0.000	0.000	0.000
39	A	41	PHE	0	-0.047	-0.043	10.916	0.133	0.133	0.000	0.000	0.000	0.000
40	A	42	THR	0	-0.060	-0.035	13.499	-0.132	-0.132	0.000	0.000	0.000	0.000
41	A	43	LEU	0	0.033	0.010	9.546	0.191	0.191	0.000	0.000	0.000	0.000
42	A	44	SER	0	-0.023	-0.016	13.229	-0.117	-0.117	0.000	0.000	0.000	0.000
43	A	45	VAL	0	0.026	-0.004	13.850	0.080	0.080	0.000	0.000	0.000	0.000
44	A	46	ARG	1	0.830	0.913	15.833	-0.226	-0.226	0.000	0.000	0.000	0.000
45	A	47	ARG	1	0.756	0.844	18.224	-0.178	-0.178	0.000	0.000	0.000	0.000
46	A	48	ASN	0	0.040	0.012	20.811	-0.010	-0.010	0.000	0.000	0.000	0.000
47	A	49	GLY	0	-0.015	0.000	23.225	-0.004	-0.004	0.000	0.000	0.000	0.000
48	A	50	ALA	0	0.001	0.013	23.418	0.004	0.004	0.000	0.000	0.000	0.000
49	A	51	VAL	0	-0.017	-0.019	18.395	0.018	0.018	0.000	0.000	0.000	0.000
50	A	52	THR	0	0.002	0.018	19.472	-0.012	-0.012	0.000	0.000	0.000	0.000
51	A	53	HIS	0	-0.043	-0.014	17.790	0.125	0.125	0.000	0.000	0.000	0.000
52	A	54	ILE	0	0.006	0.003	15.128	-0.047	-0.047	0.000	0.000	0.000	0.000
53	A	55	LYS	1	0.913	0.950	16.096	-0.252	-0.252	0.000	0.000	0.000	0.000
54	A	56	ILE	0	-0.019	-0.014	11.020	0.008	0.008	0.000	0.000	0.000	0.000
55	A	57	GLN	0	-0.026	-0.018	15.123	0.006	0.006	0.000	0.000	0.000	0.000
56	A	58	ASN	0	-0.048	-0.057	14.101	0.033	0.033	0.000	0.000	0.000	0.000
57	A	59	THR	0	0.029	0.012	15.771	-0.006	-0.006	0.000	0.000	0.000	0.000
58	A	60	GLY	0	-0.025	0.001	16.505	-0.033	-0.033	0.000	0.000	0.000	0.000
59	A	61	ASP	-1	-0.937	-0.958	17.071	0.227	0.227	0.000	0.000	0.000	0.000
60	A	62	TYR	0	-0.057	-0.037	14.268	-0.050	-0.050	0.000	0.000	0.000	0.000
61	A	63	TYR	0	-0.034	-0.017	10.507	0.201	0.201	0.000	0.000	0.000	0.000
62	A	64	ASP	-1	-0.737	-0.864	13.469	0.214	0.214	0.000	0.000	0.000	0.000
63	A	65	LEU	0	-0.048	-0.020	13.783	0.085	0.085	0.000	0.000	0.000	0.000
64	A	66	TYR	0	-0.087	-0.053	17.198	-0.045	-0.045	0.000	0.000	0.000	0.000
65	A	67	GLY	0	0.017	0.014	19.798	-0.031	-0.031	0.000	0.000	0.000	0.000
66	A	68	GLY	0	-0.054	-0.028	18.725	0.025	0.025	0.000	0.000	0.000	0.000
67	A	69	GLU	-1	-0.884	-0.954	15.256	-0.021	-0.021	0.000	0.000	0.000	0.000
68	A	70	LYS	1	0.802	0.910	15.568	-0.110	-0.110	0.000	0.000	0.000	0.000
69	A	71	PHE	0	-0.004	-0.009	10.565	-0.044	-0.044	0.000	0.000	0.000	0.000
70	A	72	ALA	0	0.084	0.052	11.218	0.105	0.105	0.000	0.000	0.000	0.000
71	A	73	THR	0	-0.076	-0.076	6.429	0.333	0.333	0.000	0.000	0.000	0.000
72	A	74	LEU	0	0.042	0.010	6.026	0.011	0.011	0.000	0.000	0.000	0.000
73	A	75	ALA	0	-0.054	-0.043	2.543	-0.429	0.457	0.657	-0.576	-0.967	-0.004
74	A	76	GLU	-1	-0.765	-0.844	4.152	-0.927	-0.888	0.000	-0.029	-0.009	0.000
75	A	77	LEU	0	0.007	0.026	7.098	-0.040	-0.040	0.000	0.000	0.000	0.000
76	A	78	VAL	0	-0.029	-0.035	5.402	-0.118	-0.118	0.000	0.000	0.000	0.000
77	A	79	GLN	0	-0.051	-0.032	5.412	-0.700	-0.700	0.000	0.000	0.000	0.000
78	A	80	TYR	0	0.028	0.009	7.099	-0.032	-0.032	0.000	0.000	0.000	0.000
79	A	81	TYR	0	0.018	-0.010	10.252	-0.058	-0.058	0.000	0.000	0.000	0.000
80	A	82	MET	0	-0.100	-0.030	8.041	0.062	0.062	0.000	0.000	0.000	0.000
81	A	83	GLU	-1	-0.899	-0.938	10.542	-0.771	-0.771	0.000	0.000	0.000	0.000
82	A	84	HIS	1	0.805	0.908	12.772	0.217	0.217	0.000	0.000	0.000	0.000
83	A	85	HIS	0	-0.034	-0.028	15.492	0.060	0.060	0.000	0.000	0.000	0.000
84	A	86	GLY	0	0.070	0.026	16.871	-0.016	-0.016	0.000	0.000	0.000	0.000
85	A	87	GLN	0	-0.024	-0.006	17.395	-0.022	-0.022	0.000	0.000	0.000	0.000
86	A	88	LEU	0	-0.020	0.008	14.419	0.013	0.013	0.000	0.000	0.000	0.000
87	A	89	LYS	1	0.944	0.979	18.987	-0.067	-0.067	0.000	0.000	0.000	0.000
88	A	90	GLU	-1	-0.794	-0.885	22.345	0.215	0.215	0.000	0.000	0.000	0.000
89	A	91	LYS	1	0.930	0.955	24.434	-0.144	-0.144	0.000	0.000	0.000	0.000
90	A	92	ASN	0	-0.008	-0.024	27.716	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	93	GLY	0	0.022	0.021	26.829	-0.013	-0.013	0.000	0.000	0.000	0.000
92	A	94	ASP	-1	-0.830	-0.893	24.502	0.098	0.098	0.000	0.000	0.000	0.000
93	A	95	VAL	0	-0.008	0.002	20.021	0.017	0.017	0.000	0.000	0.000	0.000
94	A	96	ILE	0	-0.014	-0.015	16.916	0.009	0.009	0.000	0.000	0.000	0.000
95	A	97	GLU	-1	-0.814	-0.890	16.627	0.042	0.042	0.000	0.000	0.000	0.000
96	A	98	LEU	0	-0.015	-0.006	10.674	0.047	0.047	0.000	0.000	0.000	0.000
97	A	99	LYS	1	0.870	0.937	12.153	-0.107	-0.107	0.000	0.000	0.000	0.000
98	A	100	TYR	0	-0.019	-0.029	10.936	-0.082	-0.082	0.000	0.000	0.000	0.000
99	A	101	PRO	0	0.021	0.020	6.429	0.135	0.135	0.000	0.000	0.000	0.000
100	A	102	LEU	0	0.008	0.018	8.547	-0.217	-0.217	0.000	0.000	0.000	0.000
101	A	103	ASN	0	-0.024	-0.022	6.878	0.167	0.167	0.000	0.000	0.000	0.000
102	A	104	LYS	1	0.985	1.004	9.064	-0.392	-0.392	0.000	0.000	0.000	0.000

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