FMO DATABASE

FMODB ID: V59L1

Calculation Name: 1NCN-A-Xray372

Preferred Name: T-lymphocyte activation antigen CD86

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1NCN

Chain ID: A

ChEMBL ID: CHEMBL2364156

UniProt ID: P42081

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	109
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-927280.48443
FMO2-HF: Nuclear repulsion	881626.544383
FMO2-HF: Total energy	-45653.940046
FMO2-MP2: Total energy	-45785.072816

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:0:MET)

Summations of interaction energy for fragment #1(A:0:MET)

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.
-3.026	0.555	12.748	-4.517	-11.812	-0.03

Interaction energy analysis for fragmet #1(A:0:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.031 / q_NPA : -0.014

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	2	LYS	1	0.936	0.979	2.842	1.231	5.073	0.476	-1.437	-2.881	-0.006
4	A	3	ILE	0	0.002	0.003	4.482	0.322	0.446	-0.001	-0.021	-0.101	0.000
5	A	4	GLN	0	0.023	0.001	7.934	-0.164	-0.164	0.000	0.000	0.000	0.000
6	A	5	ALA	0	0.006	0.024	10.865	0.076	0.076	0.000	0.000	0.000	0.000
7	A	6	TYR	0	0.020	0.002	14.210	-0.062	-0.062	0.000	0.000	0.000	0.000
8	A	7	PHE	0	0.007	-0.026	17.276	0.026	0.026	0.000	0.000	0.000	0.000
9	A	8	ASN	0	-0.044	-0.015	19.298	0.012	0.012	0.000	0.000	0.000	0.000
10	A	9	GLU	-1	-0.902	-0.926	18.357	-0.031	-0.031	0.000	0.000	0.000	0.000
11	A	10	THR	0	-0.082	-0.049	17.947	0.012	0.012	0.000	0.000	0.000	0.000
12	A	11	ALA	0	-0.024	-0.008	12.597	-0.026	-0.026	0.000	0.000	0.000	0.000
13	A	12	ASP	-1	-0.809	-0.884	13.507	0.250	0.250	0.000	0.000	0.000	0.000
14	A	13	LEU	0	-0.041	-0.027	9.077	0.050	0.050	0.000	0.000	0.000	0.000
15	A	14	PRO	0	0.006	0.016	7.850	-0.043	-0.043	0.000	0.000	0.000	0.000
16	A	15	CYS	0	-0.014	0.023	7.359	0.089	0.089	0.000	0.000	0.000	0.000
17	A	16	GLN	0	-0.031	-0.034	5.194	0.234	0.234	0.000	0.000	0.000	0.000
18	A	17	PHE	0	0.019	0.020	10.384	0.088	0.088	0.000	0.000	0.000	0.000
19	A	18	ALA	0	0.017	0.003	13.458	-0.082	-0.082	0.000	0.000	0.000	0.000
20	A	19	ASN	0	0.047	0.021	15.706	-0.074	-0.074	0.000	0.000	0.000	0.000
21	A	20	SER	0	-0.005	0.004	17.688	-0.027	-0.027	0.000	0.000	0.000	0.000
22	A	21	GLN	0	-0.022	-0.022	16.537	-0.043	-0.043	0.000	0.000	0.000	0.000
23	A	22	ASN	0	-0.054	-0.022	21.300	-0.027	-0.027	0.000	0.000	0.000	0.000
24	A	23	GLN	0	0.018	0.027	22.023	-0.030	-0.030	0.000	0.000	0.000	0.000
25	A	24	SER	0	0.036	0.017	23.712	0.005	0.005	0.000	0.000	0.000	0.000
26	A	25	LEU	0	0.056	0.008	20.991	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	26	SER	0	0.005	0.005	23.961	-0.005	-0.005	0.000	0.000	0.000	0.000
28	A	27	GLU	-1	-0.977	-0.985	25.369	0.195	0.195	0.000	0.000	0.000	0.000
29	A	28	LEU	0	-0.048	-0.026	19.665	0.008	0.008	0.000	0.000	0.000	0.000
30	A	29	VAL	0	-0.028	-0.009	19.718	-0.023	-0.023	0.000	0.000	0.000	0.000
31	A	30	VAL	0	-0.020	-0.001	15.517	0.026	0.026	0.000	0.000	0.000	0.000
32	A	31	PHE	0	-0.009	0.004	14.868	-0.037	-0.037	0.000	0.000	0.000	0.000
33	A	32	TRP	0	0.073	0.022	9.443	0.064	0.064	0.000	0.000	0.000	0.000
34	A	33	GLN	0	-0.018	-0.018	10.609	-0.094	-0.094	0.000	0.000	0.000	0.000
35	A	34	ASP	-1	-0.734	-0.854	9.600	-0.061	-0.061	0.000	0.000	0.000	0.000
36	A	35	GLN	0	0.012	-0.001	7.482	-0.227	-0.227	0.000	0.000	0.000	0.000
37	A	36	GLU	-1	-1.001	-0.986	9.364	-0.271	-0.271	0.000	0.000	0.000	0.000
38	A	37	ASN	0	-0.060	-0.027	11.707	0.035	0.035	0.000	0.000	0.000	0.000
39	A	38	LEU	0	-0.036	-0.013	13.280	0.038	0.038	0.000	0.000	0.000	0.000
40	A	39	VAL	0	0.002	0.010	14.093	0.025	0.025	0.000	0.000	0.000	0.000
41	A	40	LEU	0	-0.063	-0.029	12.610	-0.017	-0.017	0.000	0.000	0.000	0.000
42	A	41	ASN	0	-0.048	-0.049	16.004	0.008	0.008	0.000	0.000	0.000	0.000
43	A	42	GLU	-1	-0.815	-0.924	16.912	0.145	0.145	0.000	0.000	0.000	0.000
44	A	43	VAL	0	0.007	0.024	19.396	-0.019	-0.019	0.000	0.000	0.000	0.000
45	A	44	TYR	0	0.003	-0.006	21.461	0.016	0.016	0.000	0.000	0.000	0.000
46	A	45	LEU	0	-0.041	-0.017	23.760	-0.015	-0.015	0.000	0.000	0.000	0.000
47	A	46	GLY	0	0.031	0.009	24.104	-0.009	-0.009	0.000	0.000	0.000	0.000
48	A	47	LYS	1	0.937	0.973	25.547	-0.108	-0.108	0.000	0.000	0.000	0.000
49	A	48	GLU	-1	-0.860	-0.942	22.079	0.166	0.166	0.000	0.000	0.000	0.000
50	A	49	LYS	1	0.812	0.915	23.150	-0.114	-0.114	0.000	0.000	0.000	0.000
51	A	50	PHE	0	0.038	-0.006	22.827	0.002	0.002	0.000	0.000	0.000	0.000
52	A	51	ASP	-1	-0.966	-0.974	24.447	0.061	0.061	0.000	0.000	0.000	0.000
53	A	52	SER	0	0.056	0.019	20.768	-0.013	-0.013	0.000	0.000	0.000	0.000
54	A	53	VAL	0	-0.045	-0.012	19.596	-0.005	-0.005	0.000	0.000	0.000	0.000
55	A	54	HIS	0	0.047	0.064	18.784	-0.005	-0.005	0.000	0.000	0.000	0.000
56	A	55	SER	0	0.066	0.009	20.634	0.005	0.005	0.000	0.000	0.000	0.000
57	A	56	LYS	1	0.928	0.944	16.460	0.133	0.133	0.000	0.000	0.000	0.000
58	A	57	TYR	0	-0.049	-0.056	13.941	0.003	0.003	0.000	0.000	0.000	0.000
59	A	58	MET	0	-0.013	0.013	19.611	0.020	0.020	0.000	0.000	0.000	0.000
60	A	59	GLY	0	-0.012	0.000	23.020	-0.010	-0.010	0.000	0.000	0.000	0.000
61	A	60	ARG	1	0.733	0.849	17.550	0.024	0.024	0.000	0.000	0.000	0.000
62	A	61	THR	0	-0.011	0.004	17.099	0.012	0.012	0.000	0.000	0.000	0.000
63	A	62	SER	0	0.005	0.002	18.593	-0.013	-0.013	0.000	0.000	0.000	0.000
64	A	63	PHE	0	0.035	0.014	15.574	0.031	0.031	0.000	0.000	0.000	0.000
65	A	64	ASP	-1	-0.747	-0.806	18.257	0.281	0.281	0.000	0.000	0.000	0.000
66	A	65	SER	0	-0.020	-0.023	18.751	0.040	0.040	0.000	0.000	0.000	0.000
67	A	66	ASP	-1	-0.957	-0.957	20.399	0.281	0.281	0.000	0.000	0.000	0.000
68	A	67	SER	0	-0.100	-0.118	17.004	0.042	0.042	0.000	0.000	0.000	0.000
69	A	68	TRP	0	-0.032	-0.021	15.238	0.088	0.088	0.000	0.000	0.000	0.000
70	A	69	THR	0	0.009	-0.014	13.493	0.156	0.156	0.000	0.000	0.000	0.000
71	A	70	LEU	0	-0.060	-0.003	13.492	-0.084	-0.084	0.000	0.000	0.000	0.000
72	A	71	ARG	1	0.900	0.943	14.143	-0.152	-0.152	0.000	0.000	0.000	0.000
73	A	72	LEU	0	-0.052	-0.026	13.830	-0.021	-0.021	0.000	0.000	0.000	0.000
74	A	73	HIS	0	0.010	-0.034	16.385	-0.022	-0.022	0.000	0.000	0.000	0.000
75	A	74	ASN	0	0.007	0.000	19.539	-0.020	-0.020	0.000	0.000	0.000	0.000
76	A	75	LEU	0	0.022	0.010	14.427	-0.015	-0.015	0.000	0.000	0.000	0.000
77	A	76	GLN	0	-0.008	-0.009	17.593	-0.028	-0.028	0.000	0.000	0.000	0.000
78	A	77	ILE	0	0.033	0.019	16.632	-0.013	-0.013	0.000	0.000	0.000	0.000
79	A	78	LYS	1	0.889	0.917	15.809	0.105	0.105	0.000	0.000	0.000	0.000
80	A	79	ASP	-1	-0.736	-0.827	14.377	-0.089	-0.089	0.000	0.000	0.000	0.000
81	A	80	LYS	1	0.916	1.008	11.142	0.529	0.529	0.000	0.000	0.000	0.000
82	A	81	GLY	0	0.010	0.005	8.764	-0.027	-0.027	0.000	0.000	0.000	0.000
83	A	82	LEU	0	-0.025	-0.016	2.289	0.547	-1.460	5.882	-0.799	-3.076	-0.007
84	A	83	TYR	0	-0.042	-0.067	5.562	-0.202	-0.202	0.000	0.000	0.000	0.000
85	A	84	GLN	0	0.040	0.015	5.393	0.365	0.365	0.000	0.000	0.000	0.000
86	A	86	ILE	0	-0.022	-0.030	9.960	0.059	0.059	0.000	0.000	0.000	0.000
87	A	87	ILE	0	0.039	0.025	12.459	-0.058	-0.058	0.000	0.000	0.000	0.000
88	A	88	HIS	0	-0.007	-0.016	15.666	0.006	0.006	0.000	0.000	0.000	0.000
89	A	89	HIS	0	0.064	0.033	18.769	0.003	0.003	0.000	0.000	0.000	0.000
90	A	90	LYS	1	0.892	0.945	22.046	-0.152	-0.152	0.000	0.000	0.000	0.000
91	A	91	LYS	1	0.943	0.981	24.694	-0.174	-0.174	0.000	0.000	0.000	0.000
92	A	92	PRO	0	0.018	-0.007	27.555	-0.006	-0.006	0.000	0.000	0.000	0.000
93	A	93	THR	0	-0.034	-0.008	28.542	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	94	GLY	0	0.051	0.008	26.494	-0.008	-0.008	0.000	0.000	0.000	0.000
95	A	95	MET	0	-0.031	-0.004	21.254	0.012	0.012	0.000	0.000	0.000	0.000
96	A	96	ILE	0	0.011	0.015	20.354	-0.015	-0.015	0.000	0.000	0.000	0.000
97	A	97	ARG	1	0.898	0.959	12.958	-0.273	-0.273	0.000	0.000	0.000	0.000
98	A	98	ILE	0	-0.023	-0.025	17.004	-0.002	-0.002	0.000	0.000	0.000	0.000
99	A	99	HIS	0	-0.012	-0.010	10.634	-0.073	-0.073	0.000	0.000	0.000	0.000
100	A	100	GLN	0	-0.002	-0.002	8.692	-0.142	-0.142	0.000	0.000	0.000	0.000
101	A	101	MET	0	-0.020	0.022	4.772	0.119	0.260	-0.001	-0.014	-0.126	0.000
102	A	102	ASN	0	0.030	0.013	2.113	-0.691	-2.238	4.943	-1.146	-2.250	-0.003
103	A	103	SER	0	-0.006	-0.006	3.566	0.586	2.351	0.973	-0.835	-1.904	-0.011
104	A	104	GLU	-1	-0.910	-0.969	2.949	-5.033	-3.807	0.472	-0.262	-1.436	-0.003
105	A	105	LEU	0	-0.001	0.016	4.606	-0.608	-0.571	0.004	-0.003	-0.038	0.000
106	A	106	SER	0	-0.019	-0.019	7.842	-0.157	-0.157	0.000	0.000	0.000	0.000
107	A	107	VAL	0	-0.009	-0.009	10.041	0.068	0.068	0.000	0.000	0.000	0.000
108	A	108	LEU	0	-0.039	-0.013	13.094	-0.034	-0.034	0.000	0.000	0.000	0.000
109	A	109	ALA	0	0.039	0.017	16.174	0.034	0.034	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:MET)