FMO DATABASE

FMODB ID: 17MKZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-927533.315399
FMO2-HF: Nuclear repulsion	881878.359107
FMO2-HF: Total energy	-45654.956292
FMO2-MP2: Total energy	-45785.990424

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.
-5.996	-0.24	8.497	-4.443	-9.809	-0.011

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 : 0.014 / q_NPA : 0.019

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	0.831	0.902	3.128	2.285	5.846	0.143	-1.539	-2.165	-0.001
4	A	3	ILE	0	-0.005	-0.002	4.619	0.463	0.559	-0.001	-0.014	-0.081	0.000
5	A	4	GLN	0	0.010	-0.004	7.973	-0.044	-0.044	0.000	0.000	0.000	0.000
6	A	5	ALA	0	0.006	0.023	10.993	0.065	0.065	0.000	0.000	0.000	0.000
7	A	6	TYR	0	0.020	0.004	14.279	-0.043	-0.043	0.000	0.000	0.000	0.000
8	A	7	PHE	0	0.006	-0.027	17.368	0.031	0.031	0.000	0.000	0.000	0.000
9	A	8	ASN	0	-0.062	-0.023	19.349	0.013	0.013	0.000	0.000	0.000	0.000
10	A	9	GLU	-1	-0.894	-0.925	18.520	-0.169	-0.169	0.000	0.000	0.000	0.000
11	A	10	THR	0	-0.074	-0.048	17.845	0.037	0.037	0.000	0.000	0.000	0.000
12	A	11	ALA	0	-0.007	-0.001	12.422	-0.057	-0.057	0.000	0.000	0.000	0.000
13	A	12	ASP	-1	-0.784	-0.843	13.369	-0.021	-0.021	0.000	0.000	0.000	0.000
14	A	13	LEU	0	-0.032	-0.020	9.555	-0.068	-0.068	0.000	0.000	0.000	0.000
15	A	14	PRO	0	0.025	0.025	8.214	0.043	0.043	0.000	0.000	0.000	0.000
16	A	15	CYS	0	-0.034	0.018	7.962	-0.031	-0.031	0.000	0.000	0.000	0.000
17	A	16	GLN	0	-0.031	-0.032	5.609	0.505	0.505	0.000	0.000	0.000	0.000
18	A	17	PHE	0	0.018	0.013	10.386	0.093	0.093	0.000	0.000	0.000	0.000
19	A	18	ALA	0	0.019	0.004	13.457	-0.068	-0.068	0.000	0.000	0.000	0.000
20	A	19	ASN	0	0.030	0.022	15.647	-0.020	-0.020	0.000	0.000	0.000	0.000
21	A	20	SER	0	0.007	0.009	17.661	-0.019	-0.019	0.000	0.000	0.000	0.000
22	A	21	GLN	0	-0.033	-0.027	16.268	-0.043	-0.043	0.000	0.000	0.000	0.000
23	A	22	ASN	0	-0.045	-0.013	21.292	-0.023	-0.023	0.000	0.000	0.000	0.000
24	A	23	GLN	0	-0.041	-0.016	21.997	-0.011	-0.011	0.000	0.000	0.000	0.000
25	A	24	SER	0	0.004	-0.021	23.712	-0.009	-0.009	0.000	0.000	0.000	0.000
26	A	25	LEU	0	0.076	0.012	21.353	0.011	0.011	0.000	0.000	0.000	0.000
27	A	26	SER	0	0.002	0.008	24.194	0.004	0.004	0.000	0.000	0.000	0.000
28	A	27	GLU	-1	-0.883	-0.913	25.530	0.163	0.163	0.000	0.000	0.000	0.000
29	A	28	LEU	0	-0.045	-0.025	19.928	0.018	0.018	0.000	0.000	0.000	0.000
30	A	29	VAL	0	-0.018	-0.006	20.122	-0.022	-0.022	0.000	0.000	0.000	0.000
31	A	30	VAL	0	-0.031	0.000	15.904	0.041	0.041	0.000	0.000	0.000	0.000
32	A	31	PHE	0	0.004	0.004	15.170	-0.041	-0.041	0.000	0.000	0.000	0.000
33	A	32	TRP	0	0.067	0.025	9.815	0.107	0.107	0.000	0.000	0.000	0.000
34	A	33	GLN	0	-0.015	-0.009	11.065	-0.056	-0.056	0.000	0.000	0.000	0.000
35	A	34	ASP	-1	-0.701	-0.832	10.303	0.294	0.294	0.000	0.000	0.000	0.000
36	A	35	GLN	0	0.018	0.005	7.907	-0.085	-0.085	0.000	0.000	0.000	0.000
37	A	36	GLU	-1	-0.920	-0.937	9.900	-0.016	-0.016	0.000	0.000	0.000	0.000
38	A	37	ASN	0	-0.066	-0.036	12.170	0.031	0.031	0.000	0.000	0.000	0.000
39	A	38	LEU	0	-0.021	0.001	13.695	-0.013	-0.013	0.000	0.000	0.000	0.000
40	A	39	VAL	0	0.004	0.006	14.775	0.047	0.047	0.000	0.000	0.000	0.000
41	A	40	LEU	0	-0.050	-0.019	13.722	-0.036	-0.036	0.000	0.000	0.000	0.000
42	A	41	ASN	0	-0.055	-0.067	16.758	-0.018	-0.018	0.000	0.000	0.000	0.000
43	A	42	GLU	-1	-0.777	-0.888	17.570	0.222	0.222	0.000	0.000	0.000	0.000
44	A	43	VAL	0	-0.004	0.015	20.047	-0.031	-0.031	0.000	0.000	0.000	0.000
45	A	44	TYR	0	0.011	-0.004	22.012	0.021	0.021	0.000	0.000	0.000	0.000
46	A	45	LEU	0	-0.039	-0.014	24.117	-0.018	-0.018	0.000	0.000	0.000	0.000
47	A	46	GLY	0	0.029	0.013	24.537	-0.014	-0.014	0.000	0.000	0.000	0.000
48	A	47	LYS	1	0.887	0.941	26.006	-0.109	-0.109	0.000	0.000	0.000	0.000
49	A	48	GLU	-1	-0.829	-0.912	22.370	0.120	0.120	0.000	0.000	0.000	0.000
50	A	49	LYS	1	0.712	0.847	23.726	-0.164	-0.164	0.000	0.000	0.000	0.000
51	A	50	PHE	0	0.064	0.007	23.426	0.012	0.012	0.000	0.000	0.000	0.000
52	A	51	ASP	-1	-0.901	-0.934	25.174	0.110	0.110	0.000	0.000	0.000	0.000
53	A	52	SER	0	0.023	0.001	21.139	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	53	VAL	0	-0.053	-0.010	20.400	0.010	0.010	0.000	0.000	0.000	0.000
55	A	54	HIS	0	0.073	0.053	19.609	-0.019	-0.019	0.000	0.000	0.000	0.000
56	A	55	SER	0	0.051	0.007	21.403	-0.003	-0.003	0.000	0.000	0.000	0.000
57	A	56	LYS	1	0.784	0.886	15.915	-0.052	-0.052	0.000	0.000	0.000	0.000
58	A	57	TYR	0	-0.046	-0.078	14.708	-0.018	-0.018	0.000	0.000	0.000	0.000
59	A	58	MET	0	-0.027	0.009	20.471	0.000	0.000	0.000	0.000	0.000	0.000
60	A	59	GLY	0	-0.007	0.000	23.859	-0.013	-0.013	0.000	0.000	0.000	0.000
61	A	60	ARG	1	0.745	0.853	18.191	0.015	0.015	0.000	0.000	0.000	0.000
62	A	61	THR	0	-0.025	0.000	17.387	-0.007	-0.007	0.000	0.000	0.000	0.000
63	A	62	SER	0	0.018	0.004	18.876	-0.012	-0.012	0.000	0.000	0.000	0.000
64	A	63	PHE	0	0.031	0.018	15.770	0.007	0.007	0.000	0.000	0.000	0.000
65	A	64	ASP	-1	-0.766	-0.848	18.498	0.042	0.042	0.000	0.000	0.000	0.000
66	A	65	SER	0	-0.015	-0.020	18.961	0.019	0.019	0.000	0.000	0.000	0.000
67	A	66	ASP	-1	-0.951	-0.956	20.407	0.077	0.077	0.000	0.000	0.000	0.000
68	A	67	SER	0	-0.080	-0.081	17.034	0.004	0.004	0.000	0.000	0.000	0.000
69	A	68	TRP	0	-0.037	-0.024	15.348	0.058	0.058	0.000	0.000	0.000	0.000
70	A	69	THR	0	-0.012	-0.017	13.806	0.060	0.060	0.000	0.000	0.000	0.000
71	A	70	LEU	0	-0.038	0.002	13.729	-0.028	-0.028	0.000	0.000	0.000	0.000
72	A	71	ARG	1	0.853	0.889	14.492	0.048	0.048	0.000	0.000	0.000	0.000
73	A	72	LEU	0	-0.045	-0.025	14.044	0.019	0.019	0.000	0.000	0.000	0.000
74	A	73	HIS	0	-0.009	-0.035	16.636	-0.056	-0.056	0.000	0.000	0.000	0.000
75	A	74	ASN	0	0.000	-0.009	19.603	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	75	LEU	0	0.030	0.017	14.699	0.005	0.005	0.000	0.000	0.000	0.000
77	A	76	GLN	0	0.032	0.013	17.499	-0.009	-0.009	0.000	0.000	0.000	0.000
78	A	77	ILE	0	0.023	0.011	16.606	-0.012	-0.012	0.000	0.000	0.000	0.000
79	A	78	LYS	1	0.865	0.907	15.838	0.073	0.073	0.000	0.000	0.000	0.000
80	A	79	ASP	-1	-0.736	-0.819	14.388	-0.054	-0.054	0.000	0.000	0.000	0.000
81	A	80	LYS	1	0.922	0.994	11.225	0.429	0.429	0.000	0.000	0.000	0.000
82	A	81	GLY	0	0.029	0.014	8.743	0.025	0.025	0.000	0.000	0.000	0.000
83	A	82	LEU	0	-0.043	-0.030	2.565	-0.439	-1.951	5.280	-0.958	-2.810	0.000
84	A	83	TYR	0	-0.034	-0.048	6.243	-0.278	-0.278	0.000	0.000	0.000	0.000
85	A	84	GLN	0	0.037	0.020	6.258	0.841	0.841	0.000	0.000	0.000	0.000
86	A	86	ILE	0	-0.022	-0.027	10.179	0.117	0.117	0.000	0.000	0.000	0.000
87	A	87	ILE	0	0.039	0.021	12.654	-0.085	-0.085	0.000	0.000	0.000	0.000
88	A	88	HIS	0	-0.018	-0.017	15.793	0.016	0.016	0.000	0.000	0.000	0.000
89	A	89	HIS	0	0.039	0.029	18.779	-0.016	-0.016	0.000	0.000	0.000	0.000
90	A	90	LYS	1	0.864	0.936	22.009	-0.166	-0.166	0.000	0.000	0.000	0.000
91	A	91	LYS	1	0.969	0.992	24.698	-0.211	-0.211	0.000	0.000	0.000	0.000
92	A	92	PRO	0	0.037	-0.001	27.449	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	93	THR	0	-0.032	-0.005	28.540	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	94	GLY	0	0.047	0.008	26.361	-0.007	-0.007	0.000	0.000	0.000	0.000
95	A	95	MET	0	-0.017	-0.004	21.234	0.000	0.000	0.000	0.000	0.000	0.000
96	A	96	ILE	0	0.007	0.010	20.094	-0.004	-0.004	0.000	0.000	0.000	0.000
97	A	97	ARG	1	0.897	0.958	12.524	-0.584	-0.584	0.000	0.000	0.000	0.000
98	A	98	ILE	0	-0.034	-0.026	16.837	0.004	0.004	0.000	0.000	0.000	0.000
99	A	99	HIS	0	-0.006	-0.012	10.695	-0.020	-0.020	0.000	0.000	0.000	0.000
100	A	100	GLN	0	0.010	-0.006	8.390	-0.144	-0.144	0.000	0.000	0.000	0.000
101	A	101	MET	0	-0.020	0.019	4.186	-0.217	-0.026	0.000	-0.035	-0.156	0.000
102	A	102	ASN	0	0.009	0.001	2.391	-2.364	-1.885	2.098	-0.760	-1.817	0.001
103	A	103	SER	0	0.030	0.013	3.669	-0.143	1.306	0.703	-0.670	-1.482	-0.008
104	A	104	GLU	-1	-0.836	-0.902	2.909	-5.831	-4.359	0.274	-0.454	-1.291	-0.003
105	A	105	LEU	0	0.014	0.022	4.493	-0.672	-0.652	0.000	-0.013	-0.007	0.000
106	A	106	SER	0	-0.024	-0.025	8.069	0.054	0.054	0.000	0.000	0.000	0.000
107	A	107	VAL	0	-0.004	-0.003	10.161	0.031	0.031	0.000	0.000	0.000	0.000
108	A	108	LEU	0	-0.041	-0.010	13.526	0.008	0.008	0.000	0.000	0.000	0.000
109	A	109	ALA	0	0.052	0.020	16.348	0.028	0.028	0.000	0.000	0.000	0.000

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