FMO DATABASE

FMODB ID: G6GQ1

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	OptH
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	-788554.819122
FMO2-HF: Nuclear repulsion	748516.946827
FMO2-HF: Total energy	-40037.872295
FMO2-MP2: Total energy	-40157.128997

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.
-8.056	-9.143	11.16	-4.387	-5.687	0.005

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 : 0.052 / q_NPA : 0.024

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	0.963	0.976	3.806	-1.873	0.301	-0.020	-1.026	-1.128	0.003
4	A	6	TRP	0	0.089	0.042	2.016	-1.650	-5.831	10.592	-2.777	-3.634	0.006
5	A	7	PHE	0	0.001	0.002	6.032	-0.229	-0.229	0.000	0.000	0.000	0.000
6	A	8	HIS	1	0.810	0.877	7.594	-1.311	-1.311	0.000	0.000	0.000	0.000
7	A	9	PRO	0	0.008	0.002	10.428	-0.098	-0.098	0.000	0.000	0.000	0.000
8	A	10	ASN	0	-0.017	-0.020	12.690	-0.070	-0.070	0.000	0.000	0.000	0.000
9	A	11	ILE	0	0.000	0.024	14.659	-0.049	-0.049	0.000	0.000	0.000	0.000
10	A	12	THR	0	-0.025	-0.028	17.456	0.019	0.019	0.000	0.000	0.000	0.000
11	A	13	GLY	0	0.001	-0.020	18.752	0.035	0.035	0.000	0.000	0.000	0.000
12	A	14	VAL	0	0.092	0.045	20.134	0.008	0.008	0.000	0.000	0.000	0.000
13	A	15	GLU	-1	-0.837	-0.907	19.345	0.442	0.442	0.000	0.000	0.000	0.000
14	A	16	ALA	0	-0.023	-0.019	16.219	0.008	0.008	0.000	0.000	0.000	0.000
15	A	17	GLU	-1	-0.825	-0.910	17.645	0.323	0.323	0.000	0.000	0.000	0.000
16	A	18	ASN	0	0.062	0.027	20.195	-0.032	-0.032	0.000	0.000	0.000	0.000
17	A	19	LEU	0	-0.061	0.009	15.091	-0.021	-0.021	0.000	0.000	0.000	0.000
18	A	20	LEU	0	-0.016	-0.016	14.038	-0.032	-0.032	0.000	0.000	0.000	0.000
19	A	21	LEU	0	-0.016	-0.015	17.654	-0.040	-0.040	0.000	0.000	0.000	0.000
20	A	22	THR	0	-0.077	-0.058	20.582	-0.028	-0.028	0.000	0.000	0.000	0.000
21	A	23	ARG	1	0.897	0.946	17.383	-0.309	-0.309	0.000	0.000	0.000	0.000
22	A	24	GLY	0	-0.011	0.016	16.541	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	25	VAL	0	-0.003	-0.006	16.754	-0.029	-0.029	0.000	0.000	0.000	0.000
24	A	26	ASP	-1	-0.809	-0.920	17.692	0.186	0.186	0.000	0.000	0.000	0.000
25	A	27	GLY	0	0.033	0.014	16.374	-0.042	-0.042	0.000	0.000	0.000	0.000
26	A	28	SER	0	-0.032	-0.007	13.363	0.012	0.012	0.000	0.000	0.000	0.000
27	A	29	PHE	0	0.024	0.009	7.858	0.023	0.023	0.000	0.000	0.000	0.000
28	A	30	LEU	0	-0.042	-0.009	9.474	0.106	0.106	0.000	0.000	0.000	0.000
29	A	31	ALA	0	0.029	0.028	8.025	-0.095	-0.095	0.000	0.000	0.000	0.000
30	A	32	ARG	1	0.866	0.924	10.074	-0.597	-0.597	0.000	0.000	0.000	0.000
31	A	33	PRO	0	0.042	0.026	12.309	-0.027	-0.027	0.000	0.000	0.000	0.000
32	A	34	SER	0	-0.038	0.010	14.294	-0.077	-0.077	0.000	0.000	0.000	0.000
33	A	35	LYS	1	0.932	0.946	17.457	-0.566	-0.566	0.000	0.000	0.000	0.000
34	A	36	SER	0	0.032	0.017	20.563	-0.019	-0.019	0.000	0.000	0.000	0.000
35	A	37	ASN	0	-0.062	-0.031	20.252	-0.033	-0.033	0.000	0.000	0.000	0.000
36	A	38	PRO	0	0.042	0.064	19.216	0.050	0.050	0.000	0.000	0.000	0.000
37	A	39	GLY	0	0.040	0.007	17.854	-0.044	-0.044	0.000	0.000	0.000	0.000
38	A	40	ASP	-1	-0.790	-0.908	15.970	0.508	0.508	0.000	0.000	0.000	0.000
39	A	41	PHE	0	-0.050	-0.049	11.212	0.134	0.134	0.000	0.000	0.000	0.000
40	A	42	THR	0	-0.070	-0.040	13.513	-0.136	-0.136	0.000	0.000	0.000	0.000
41	A	43	LEU	0	0.026	0.009	9.621	0.193	0.193	0.000	0.000	0.000	0.000
42	A	44	SER	0	-0.027	-0.013	13.229	-0.113	-0.113	0.000	0.000	0.000	0.000
43	A	45	VAL	0	0.027	0.001	13.898	0.085	0.085	0.000	0.000	0.000	0.000
44	A	46	ARG	1	0.895	0.961	15.833	-0.242	-0.242	0.000	0.000	0.000	0.000
45	A	47	ARG	1	0.854	0.901	18.236	-0.186	-0.186	0.000	0.000	0.000	0.000
46	A	48	ASN	0	0.034	0.023	20.823	-0.008	-0.008	0.000	0.000	0.000	0.000
47	A	49	GLY	0	-0.039	-0.011	23.213	-0.004	-0.004	0.000	0.000	0.000	0.000
48	A	50	ALA	0	0.015	0.021	23.438	0.004	0.004	0.000	0.000	0.000	0.000
49	A	51	VAL	0	-0.011	-0.013	18.436	0.019	0.019	0.000	0.000	0.000	0.000
50	A	52	THR	0	0.024	0.029	19.418	-0.015	-0.015	0.000	0.000	0.000	0.000
51	A	53	HIS	0	-0.044	-0.023	17.790	0.117	0.117	0.000	0.000	0.000	0.000
52	A	54	ILE	0	0.014	0.007	15.492	-0.047	-0.047	0.000	0.000	0.000	0.000
53	A	55	LYS	1	0.918	0.958	16.116	-0.242	-0.242	0.000	0.000	0.000	0.000
54	A	56	ILE	0	-0.004	-0.004	11.067	0.006	0.006	0.000	0.000	0.000	0.000
55	A	57	GLN	0	-0.034	-0.021	15.141	0.010	0.010	0.000	0.000	0.000	0.000
56	A	58	ASN	0	-0.022	-0.031	14.138	0.021	0.021	0.000	0.000	0.000	0.000
57	A	59	THR	0	0.009	0.004	15.779	-0.009	-0.009	0.000	0.000	0.000	0.000
58	A	60	GLY	0	-0.024	0.001	16.505	-0.028	-0.028	0.000	0.000	0.000	0.000
59	A	61	ASP	-1	-0.917	-0.948	17.070	0.200	0.200	0.000	0.000	0.000	0.000
60	A	62	TYR	0	-0.065	-0.043	14.266	-0.044	-0.044	0.000	0.000	0.000	0.000
61	A	63	TYR	0	-0.050	-0.022	10.463	0.162	0.162	0.000	0.000	0.000	0.000
62	A	64	ASP	-1	-0.761	-0.899	13.484	0.203	0.203	0.000	0.000	0.000	0.000
63	A	65	LEU	0	-0.050	-0.022	13.802	0.087	0.087	0.000	0.000	0.000	0.000
64	A	66	TYR	0	-0.059	-0.015	17.187	-0.034	-0.034	0.000	0.000	0.000	0.000
65	A	67	GLY	0	0.013	0.012	19.809	-0.027	-0.027	0.000	0.000	0.000	0.000
66	A	68	GLY	0	-0.052	-0.027	18.716	0.022	0.022	0.000	0.000	0.000	0.000
67	A	69	GLU	-1	-0.930	-0.973	15.216	-0.063	-0.063	0.000	0.000	0.000	0.000
68	A	70	LYS	1	0.904	0.970	15.553	-0.064	-0.064	0.000	0.000	0.000	0.000
69	A	71	PHE	0	0.023	0.006	10.572	-0.038	-0.038	0.000	0.000	0.000	0.000
70	A	72	ALA	0	0.094	0.059	11.113	0.104	0.104	0.000	0.000	0.000	0.000
71	A	73	THR	0	-0.026	-0.020	6.433	0.250	0.250	0.000	0.000	0.000	0.000
72	A	74	LEU	0	0.054	0.012	5.894	0.005	0.005	0.000	0.000	0.000	0.000
73	A	75	ALA	0	-0.060	-0.043	2.580	-0.445	0.458	0.589	-0.557	-0.936	-0.004
74	A	76	GLU	-1	-0.849	-0.918	4.142	-1.151	-1.134	-0.001	-0.027	0.011	0.000
75	A	77	LEU	0	0.016	0.030	7.092	0.005	0.005	0.000	0.000	0.000	0.000
76	A	78	VAL	0	-0.034	-0.038	5.361	-0.082	-0.082	0.000	0.000	0.000	0.000
77	A	79	GLN	0	-0.019	-0.007	5.440	-0.390	-0.390	0.000	0.000	0.000	0.000
78	A	80	TYR	0	0.037	0.028	7.095	-0.010	-0.010	0.000	0.000	0.000	0.000
79	A	81	TYR	0	-0.003	-0.021	10.250	-0.045	-0.045	0.000	0.000	0.000	0.000
80	A	82	MET	0	-0.100	-0.031	8.021	0.068	0.068	0.000	0.000	0.000	0.000
81	A	83	GLU	-1	-0.931	-0.964	10.398	-0.861	-0.861	0.000	0.000	0.000	0.000
82	A	84	HIS	1	0.829	0.926	12.770	0.224	0.224	0.000	0.000	0.000	0.000
83	A	85	HIS	0	-0.042	-0.038	15.488	0.053	0.053	0.000	0.000	0.000	0.000
84	A	86	GLY	0	0.062	0.023	16.867	-0.015	-0.015	0.000	0.000	0.000	0.000
85	A	87	GLN	0	-0.037	-0.028	17.392	-0.029	-0.029	0.000	0.000	0.000	0.000
86	A	88	LEU	0	-0.027	0.003	14.484	0.013	0.013	0.000	0.000	0.000	0.000
87	A	89	LYS	1	0.960	0.983	18.979	-0.058	-0.058	0.000	0.000	0.000	0.000
88	A	90	GLU	-1	-0.839	-0.909	22.337	0.201	0.201	0.000	0.000	0.000	0.000
89	A	91	LYS	1	0.916	0.951	24.425	-0.142	-0.142	0.000	0.000	0.000	0.000
90	A	92	ASN	0	-0.003	-0.022	27.812	-0.005	-0.005	0.000	0.000	0.000	0.000
91	A	93	GLY	0	0.014	0.020	26.822	-0.012	-0.012	0.000	0.000	0.000	0.000
92	A	94	ASP	-1	-0.890	-0.923	24.698	0.093	0.093	0.000	0.000	0.000	0.000
93	A	95	VAL	0	-0.003	-0.005	19.971	0.017	0.017	0.000	0.000	0.000	0.000
94	A	96	ILE	0	-0.024	-0.022	16.994	0.012	0.012	0.000	0.000	0.000	0.000
95	A	97	GLU	-1	-0.897	-0.939	16.603	0.046	0.046	0.000	0.000	0.000	0.000
96	A	98	LEU	0	-0.018	-0.008	10.550	0.051	0.051	0.000	0.000	0.000	0.000
97	A	99	LYS	1	0.966	0.991	12.159	-0.087	-0.087	0.000	0.000	0.000	0.000
98	A	100	TYR	0	-0.022	-0.029	10.939	-0.081	-0.081	0.000	0.000	0.000	0.000
99	A	101	PRO	0	0.019	0.023	6.473	0.144	0.144	0.000	0.000	0.000	0.000
100	A	102	LEU	0	0.027	0.030	8.559	-0.207	-0.207	0.000	0.000	0.000	0.000
101	A	103	ASN	0	-0.018	-0.014	6.828	0.356	0.356	0.000	0.000	0.000	0.000
102	A	104	LYS	1	0.969	0.991	9.072	-0.487	-0.487	0.000	0.000	0.000	0.000

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