FMO DATABASE

FMODB ID: LJ139

Calculation Name: 2AP6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2AP6

Chain ID: A

ChEMBL ID:

UniProt ID: A9CGA4

Base Structure: X-ray

Registration Date: 2023-06-20

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	104
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-829454.363093
FMO2-HF: Nuclear repulsion	786990.443453
FMO2-HF: Total energy	-42463.91964
FMO2-MP2: Total energy	-42588.139277

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:1:MET)

Summations of interaction energy for fragment #1(A:1: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.
-26.766	-26.372	26.32	-6.611	-20.102	-0.036

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : 0.036

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	3	TYR	0	0.063	0.035	2.437	-4.878	-0.673	1.163	-2.112	-3.255	-0.006
4	A	4	GLU	-1	-0.770	-0.882	5.414	-0.265	-0.265	0.000	0.000	0.000	0.000
5	A	5	ILE	0	-0.022	-0.014	8.456	-0.071	-0.071	0.000	0.000	0.000	0.000
6	A	6	ARG	1	0.827	0.896	11.498	0.756	0.756	0.000	0.000	0.000	0.000
7	A	7	THR	0	0.074	0.035	14.517	-0.060	-0.060	0.000	0.000	0.000	0.000
8	A	8	TYR	0	-0.017	-0.001	17.394	0.012	0.012	0.000	0.000	0.000	0.000
9	A	9	ARG	1	0.963	0.998	21.072	0.237	0.237	0.000	0.000	0.000	0.000
10	A	10	LEU	0	-0.023	-0.023	23.269	0.011	0.011	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.994	1.015	26.643	0.198	0.198	0.000	0.000	0.000	0.000
12	A	12	ASN	0	-0.034	-0.041	30.149	-0.013	-0.013	0.000	0.000	0.000	0.000
13	A	13	GLY	0	0.012	-0.001	31.152	0.013	0.013	0.000	0.000	0.000	0.000
14	A	14	ALA	0	-0.010	-0.007	28.648	0.003	0.003	0.000	0.000	0.000	0.000
15	A	15	ILE	0	0.025	0.022	24.769	-0.006	-0.006	0.000	0.000	0.000	0.000
16	A	16	PRO	0	0.016	0.005	25.885	-0.017	-0.017	0.000	0.000	0.000	0.000
17	A	17	ALA	0	0.014	0.010	27.398	-0.006	-0.006	0.000	0.000	0.000	0.000
18	A	18	TYR	0	0.017	-0.015	18.942	0.004	0.004	0.000	0.000	0.000	0.000
19	A	19	LEU	0	0.006	-0.016	21.182	-0.021	-0.021	0.000	0.000	0.000	0.000
20	A	20	LYS	1	0.956	1.010	23.022	0.218	0.218	0.000	0.000	0.000	0.000
21	A	21	VAL	0	0.035	0.024	23.982	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	22	VAL	0	-0.024	-0.009	18.599	-0.010	-0.010	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.978	-0.973	20.288	-0.413	-0.413	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.873	-0.948	21.345	-0.293	-0.293	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.956	-0.998	22.917	-0.235	-0.235	0.000	0.000	0.000	0.000
26	A	26	GLY	0	-0.040	-0.014	19.681	0.007	0.007	0.000	0.000	0.000	0.000
27	A	27	ILE	0	0.016	-0.019	14.028	-0.051	-0.051	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.847	-0.927	14.963	-0.693	-0.693	0.000	0.000	0.000	0.000
29	A	29	ILE	0	-0.035	-0.005	15.557	-0.030	-0.030	0.000	0.000	0.000	0.000
30	A	30	GLN	0	0.008	-0.006	12.601	0.008	0.008	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.935	0.966	10.969	0.818	0.818	0.000	0.000	0.000	0.000
32	A	32	SER	0	-0.063	-0.017	10.731	-0.082	-0.082	0.000	0.000	0.000	0.000
33	A	33	HIS	1	0.785	0.874	12.232	0.423	0.423	0.000	0.000	0.000	0.000
34	A	34	LEU	0	-0.036	-0.030	8.696	0.109	0.109	0.000	0.000	0.000	0.000
35	A	35	GLY	0	-0.002	0.013	6.211	-0.136	-0.136	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.894	-0.942	2.479	-13.976	-12.099	2.994	-2.203	-2.669	-0.029
37	A	37	LEU	0	-0.045	-0.018	5.785	-0.142	-0.142	0.000	0.000	0.000	0.000
38	A	38	VAL	0	-0.039	-0.036	6.002	-0.056	-0.056	0.000	0.000	0.000	0.000
39	A	39	GLY	0	0.012	0.002	8.758	0.250	0.250	0.000	0.000	0.000	0.000
40	A	40	TYR	0	0.011	0.000	12.378	-0.031	-0.031	0.000	0.000	0.000	0.000
41	A	41	PHE	0	-0.004	-0.005	13.817	0.038	0.038	0.000	0.000	0.000	0.000
42	A	42	PHE	0	0.028	0.008	18.395	-0.007	-0.007	0.000	0.000	0.000	0.000
43	A	43	SER	0	-0.028	-0.010	21.904	0.007	0.007	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.918	-0.950	24.174	-0.256	-0.256	0.000	0.000	0.000	0.000
45	A	45	ILE	0	0.008	-0.002	25.937	0.024	0.024	0.000	0.000	0.000	0.000
46	A	46	GLY	0	-0.004	-0.002	25.680	-0.017	-0.017	0.000	0.000	0.000	0.000
47	A	47	PRO	0	-0.025	-0.011	23.819	0.023	0.023	0.000	0.000	0.000	0.000
48	A	48	ILE	0	0.065	0.030	25.808	-0.015	-0.015	0.000	0.000	0.000	0.000
49	A	49	ASN	0	-0.061	-0.025	27.109	0.004	0.004	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.903	-0.954	21.041	-0.424	-0.424	0.000	0.000	0.000	0.000
51	A	51	ILE	0	-0.003	0.006	18.360	-0.009	-0.009	0.000	0.000	0.000	0.000
52	A	52	VAL	0	0.019	0.008	14.950	-0.014	-0.014	0.000	0.000	0.000	0.000
53	A	53	HIS	0	0.009	0.027	13.126	-0.097	-0.097	0.000	0.000	0.000	0.000
54	A	54	ILE	0	-0.037	-0.023	7.714	0.008	0.008	0.000	0.000	0.000	0.000
55	A	55	TRP	0	0.017	-0.005	7.082	-0.053	-0.053	0.000	0.000	0.000	0.000
56	A	56	ALA	0	0.020	0.021	2.203	0.161	-0.298	3.151	-0.865	-1.827	0.003
57	A	57	PHE	0	-0.010	-0.016	2.760	-2.957	-0.789	0.503	-0.727	-1.944	-0.004
58	A	58	SER	0	0.074	0.028	2.628	0.319	-0.654	11.405	-5.600	-4.832	0.001
59	A	59	SER	0	-0.004	-0.015	3.462	3.288	-3.785	-0.170	8.061	-0.818	-0.003
60	A	60	LEU	0	0.025	-0.010	5.904	-0.358	-0.358	0.000	0.000	0.000	0.000
61	A	61	ASP	-1	-0.841	-0.908	8.650	0.273	0.273	0.000	0.000	0.000	0.000
62	A	62	ASP	-1	-0.852	-0.922	6.634	0.823	0.823	0.000	0.000	0.000	0.000
63	A	63	ARG	1	0.815	0.913	7.890	0.158	0.158	0.000	0.000	0.000	0.000
64	A	64	ALA	0	-0.044	-0.026	9.287	-0.197	-0.197	0.000	0.000	0.000	0.000
65	A	65	GLU	-1	-0.827	-0.911	12.132	0.260	0.260	0.000	0.000	0.000	0.000
66	A	66	ARG	1	0.822	0.900	6.522	0.249	0.249	0.000	0.000	0.000	0.000
67	A	67	ARG	1	0.928	0.954	11.335	0.404	0.404	0.000	0.000	0.000	0.000
68	A	68	ALA	0	0.000	0.019	13.518	-0.015	-0.015	0.000	0.000	0.000	0.000
69	A	69	ARG	1	0.891	0.926	11.418	-0.042	-0.042	0.000	0.000	0.000	0.000
70	A	70	LEU	0	-0.053	-0.012	13.520	-0.015	-0.015	0.000	0.000	0.000	0.000
71	A	71	MET	0	-0.057	-0.033	16.174	-0.015	-0.015	0.000	0.000	0.000	0.000
72	A	72	ALA	0	0.024	0.029	18.996	0.021	0.021	0.000	0.000	0.000	0.000
73	A	73	ASP	-1	-0.777	-0.856	18.851	-0.252	-0.252	0.000	0.000	0.000	0.000
74	A	74	PRO	0	0.074	0.027	20.881	-0.016	-0.016	0.000	0.000	0.000	0.000
75	A	75	ARG	1	0.907	0.944	18.737	0.287	0.287	0.000	0.000	0.000	0.000
76	A	76	TRP	0	0.017	0.002	17.259	-0.029	-0.029	0.000	0.000	0.000	0.000
77	A	77	LEU	0	-0.025	-0.016	21.128	-0.006	-0.006	0.000	0.000	0.000	0.000
78	A	78	SER	0	-0.028	-0.016	24.098	0.013	0.013	0.000	0.000	0.000	0.000
79	A	79	PHE	0	0.010	0.012	20.118	0.002	0.002	0.000	0.000	0.000	0.000
80	A	80	LEU	0	0.008	0.004	20.215	0.002	0.002	0.000	0.000	0.000	0.000
81	A	81	PRO	0	-0.046	-0.037	23.797	-0.004	-0.004	0.000	0.000	0.000	0.000
82	A	82	LYS	1	0.868	0.956	25.742	0.231	0.231	0.000	0.000	0.000	0.000
83	A	83	ILE	0	0.021	0.002	20.946	-0.005	-0.005	0.000	0.000	0.000	0.000
84	A	84	ARG	1	0.907	0.958	25.321	0.187	0.187	0.000	0.000	0.000	0.000
85	A	85	ASP	-1	-0.896	-0.935	26.224	-0.190	-0.190	0.000	0.000	0.000	0.000
86	A	86	LEU	0	-0.076	-0.025	26.263	0.005	0.005	0.000	0.000	0.000	0.000
87	A	87	ILE	0	-0.025	-0.009	21.649	-0.011	-0.011	0.000	0.000	0.000	0.000
88	A	88	GLU	-1	-0.908	-0.958	25.683	-0.200	-0.200	0.000	0.000	0.000	0.000
89	A	89	VAL	0	-0.016	-0.011	24.083	0.013	0.013	0.000	0.000	0.000	0.000
90	A	90	ALA	0	-0.030	-0.020	19.924	-0.026	-0.026	0.000	0.000	0.000	0.000
91	A	91	GLU	-1	-0.914	-0.938	18.015	-0.376	-0.376	0.000	0.000	0.000	0.000
92	A	92	ASN	0	-0.071	-0.048	13.229	-0.007	-0.007	0.000	0.000	0.000	0.000
93	A	93	LYS	1	0.978	1.001	12.581	0.715	0.715	0.000	0.000	0.000	0.000
94	A	94	ILE	0	0.006	0.012	7.709	-0.137	-0.137	0.000	0.000	0.000	0.000
95	A	95	MET	0	-0.038	-0.026	8.304	0.237	0.237	0.000	0.000	0.000	0.000
96	A	96	LYS	1	0.970	0.978	5.021	0.296	0.296	0.000	0.000	0.000	0.000
97	A	97	PRO	0	-0.006	0.032	3.118	-0.402	0.389	0.052	-0.207	-0.635	0.000
98	A	98	ALA	0	0.025	0.016	5.933	0.269	0.269	0.000	0.000	0.000	0.000
99	A	99	ARG	1	0.982	0.958	7.963	-0.403	-0.403	0.000	0.000	0.000	0.000
100	A	100	PHE	0	-0.009	-0.006	9.230	0.150	0.150	0.000	0.000	0.000	0.000
101	A	101	SER	0	-0.046	-0.007	7.104	-0.171	-0.171	0.000	0.000	0.000	0.000
102	A	102	PRO	0	0.027	0.007	8.537	0.235	0.235	0.000	0.000	0.000	0.000
103	A	103	LEU	0	0.001	0.020	5.477	0.140	0.140	0.000	0.000	0.000	0.000
104	A	104	MET	0	0.044	0.004	2.226	-10.461	-10.603	7.222	-2.958	-4.122	0.002

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