FMO DATABASE

FMODB ID: 89V6Y

Calculation Name: 2J6B-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2J6B

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-09-23

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	OptAll
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. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-860511.893335
FMO2-HF: Nuclear repulsion	817736.047734
FMO2-HF: Total energy	-42775.845601
FMO2-MP2: Total energy	-42901.680069

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.
-23.951	-23.526	33.246	-13.859	-19.812	-0.051

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 : 0.043

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	3	TYR	0	0.025	-0.012	2.606	-2.092	3.896	3.498	-2.649	-6.837	-0.015
4	A	4	ILE	0	0.022	0.014	3.956	0.109	0.220	0.002	-0.021	-0.093	0.000
5	A	5	LEU	0	0.004	-0.004	7.467	0.052	0.052	0.000	0.000	0.000	0.000
6	A	6	ASN	0	0.017	-0.003	10.198	0.055	0.055	0.000	0.000	0.000	0.000
7	A	7	SER	0	0.009	-0.003	13.389	0.012	0.012	0.000	0.000	0.000	0.000
8	A	8	ALA	0	0.034	0.022	13.360	-0.077	-0.077	0.000	0.000	0.000	0.000
9	A	9	ILE	0	-0.043	-0.009	11.732	-0.040	-0.040	0.000	0.000	0.000	0.000
10	A	10	LEU	0	0.085	0.031	10.824	-0.146	-0.146	0.000	0.000	0.000	0.000
11	A	11	PRO	0	-0.005	0.011	9.150	0.097	0.097	0.000	0.000	0.000	0.000
12	A	12	LEU	0	0.019	-0.006	9.925	-0.158	-0.158	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.906	0.951	10.000	0.945	0.945	0.000	0.000	0.000	0.000
14	A	14	PRO	0	0.021	0.018	11.657	0.056	0.056	0.000	0.000	0.000	0.000
15	A	15	GLY	0	-0.006	-0.021	14.812	-0.012	-0.012	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.793	-0.841	11.837	-0.844	-0.844	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.930	-0.947	15.675	-0.424	-0.424	0.000	0.000	0.000	0.000
18	A	18	TYR	0	-0.052	-0.057	10.032	-0.135	-0.135	0.000	0.000	0.000	0.000
19	A	19	THR	0	-0.026	-0.012	13.729	0.109	0.109	0.000	0.000	0.000	0.000
20	A	20	VAL	0	0.004	-0.002	11.298	-0.110	-0.110	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.872	0.945	12.244	0.717	0.717	0.000	0.000	0.000	0.000
22	A	22	ALA	0	0.049	0.003	12.787	-0.148	-0.148	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.859	0.950	15.109	0.297	0.297	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.849	-0.920	16.162	-0.192	-0.192	0.000	0.000	0.000	0.000
25	A	25	ILE	0	-0.082	-0.040	13.639	0.005	0.005	0.000	0.000	0.000	0.000
26	A	26	THR	0	0.015	-0.027	18.008	0.035	0.035	0.000	0.000	0.000	0.000
27	A	27	ILE	0	0.067	0.018	17.862	0.007	0.007	0.000	0.000	0.000	0.000
28	A	28	GLN	0	-0.031	-0.011	17.659	0.049	0.049	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.783	-0.871	15.994	-0.050	-0.050	0.000	0.000	0.000	0.000
30	A	30	ALA	0	0.022	0.011	13.607	0.037	0.037	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.871	0.930	12.819	-0.325	-0.325	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.878	-0.925	13.486	0.355	0.355	0.000	0.000	0.000	0.000
33	A	33	LEU	0	-0.017	-0.004	8.538	0.086	0.086	0.000	0.000	0.000	0.000
34	A	34	VAL	0	-0.025	-0.013	8.607	0.235	0.235	0.000	0.000	0.000	0.000
35	A	35	THR	0	-0.067	-0.053	9.734	0.136	0.136	0.000	0.000	0.000	0.000
36	A	36	LYS	1	0.829	0.914	11.078	-0.413	-0.413	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.835	-0.892	5.478	0.224	0.224	0.000	0.000	0.000	0.000
38	A	38	GLN	0	-0.023	-0.006	2.651	-1.958	-0.962	1.238	-0.434	-1.800	-0.003
39	A	39	PHE	0	0.009	0.004	3.175	0.841	1.771	1.398	-0.845	-1.483	-0.007
40	A	40	THR	0	-0.034	-0.055	2.244	-6.022	-11.824	14.759	-4.262	-4.695	0.015
41	A	41	SER	0	-0.025	-0.026	4.461	-2.348	-2.323	0.012	0.065	-0.103	0.002
42	A	42	ALA	0	0.017	0.007	7.686	-0.022	-0.022	0.000	0.000	0.000	0.000
43	A	43	ILE	0	-0.028	0.015	9.140	-0.197	-0.197	0.000	0.000	0.000	0.000
44	A	44	GLY	0	0.030	-0.003	12.244	0.054	0.054	0.000	0.000	0.000	0.000
45	A	45	HIS	0	-0.005	-0.001	15.102	-0.046	-0.046	0.000	0.000	0.000	0.000
46	A	46	GLN	0	-0.015	-0.022	17.534	0.008	0.008	0.000	0.000	0.000	0.000
47	A	47	ALA	0	0.089	0.055	19.115	0.029	0.029	0.000	0.000	0.000	0.000
48	A	48	THR	0	-0.009	-0.010	15.492	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.006	0.009	15.033	0.020	0.020	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.843	-0.906	16.019	0.216	0.216	0.000	0.000	0.000	0.000
51	A	51	LEU	0	-0.012	-0.004	19.255	0.021	0.021	0.000	0.000	0.000	0.000
52	A	52	LEU	0	-0.007	-0.009	12.666	0.000	0.000	0.000	0.000	0.000	0.000
53	A	53	SER	0	0.005	-0.015	15.378	0.075	0.075	0.000	0.000	0.000	0.000
54	A	54	SER	0	-0.054	-0.015	16.291	0.011	0.011	0.000	0.000	0.000	0.000
55	A	55	ILE	0	0.006	-0.004	17.527	0.015	0.015	0.000	0.000	0.000	0.000
56	A	56	LEU	0	0.005	0.006	12.444	-0.013	-0.013	0.000	0.000	0.000	0.000
57	A	57	GLY	0	0.026	0.033	15.719	0.054	0.054	0.000	0.000	0.000	0.000
58	A	58	VAL	0	-0.041	-0.029	11.585	0.024	0.024	0.000	0.000	0.000	0.000
59	A	59	ASN	0	-0.002	-0.003	12.924	-0.101	-0.101	0.000	0.000	0.000	0.000
60	A	60	VAL	0	0.025	0.011	10.631	0.241	0.241	0.000	0.000	0.000	0.000
61	A	61	PRO	0	0.024	0.012	10.651	-0.146	-0.146	0.000	0.000	0.000	0.000
62	A	62	MET	0	-0.025	0.007	12.516	0.006	0.006	0.000	0.000	0.000	0.000
63	A	63	ASN	0	-0.053	-0.031	8.747	-0.094	-0.094	0.000	0.000	0.000	0.000
64	A	64	ARG	1	0.858	0.920	11.665	0.028	0.028	0.000	0.000	0.000	0.000
65	A	65	VAL	0	0.011	0.014	9.358	-0.027	-0.027	0.000	0.000	0.000	0.000
66	A	66	GLN	0	-0.042	-0.024	11.307	-0.109	-0.109	0.000	0.000	0.000	0.000
67	A	67	ILE	0	0.019	0.021	5.744	0.108	0.108	0.000	0.000	0.000	0.000
68	A	68	LYS	1	0.804	0.897	6.987	1.282	1.282	0.000	0.000	0.000	0.000
69	A	69	VAL	0	0.016	0.021	4.941	-0.658	-0.658	0.000	0.000	0.000	0.000
70	A	70	THR	0	-0.065	-0.051	5.610	1.094	1.094	0.000	0.000	0.000	0.000
71	A	71	HIS	1	0.824	0.880	6.122	0.294	0.294	0.000	0.000	0.000	0.000
72	A	72	GLY	0	0.016	0.007	5.084	0.466	0.466	0.000	0.000	0.000	0.000
73	A	73	ASP	-1	-0.799	-0.875	1.830	-17.777	-20.045	12.327	-5.683	-4.375	-0.044
74	A	74	ARG	1	0.784	0.855	3.390	3.453	3.936	0.013	-0.013	-0.483	0.001
75	A	75	ILE	0	-0.030	-0.014	5.146	-0.802	-0.840	-0.001	-0.017	0.057	0.000
76	A	76	LEU	0	0.036	0.031	7.580	0.278	0.278	0.000	0.000	0.000	0.000
77	A	77	ALA	0	-0.006	-0.009	9.722	0.091	0.091	0.000	0.000	0.000	0.000
78	A	78	PHE	0	0.018	0.013	12.119	0.061	0.061	0.000	0.000	0.000	0.000
79	A	79	MET	0	-0.054	-0.031	14.908	-0.067	-0.067	0.000	0.000	0.000	0.000
80	A	80	LEU	0	-0.001	0.005	17.877	0.027	0.027	0.000	0.000	0.000	0.000
81	A	81	LYS	1	0.828	0.896	21.193	0.096	0.096	0.000	0.000	0.000	0.000
82	A	82	GLN	0	0.002	0.003	24.243	0.009	0.009	0.000	0.000	0.000	0.000
83	A	83	ARG	1	0.940	0.977	24.386	0.173	0.173	0.000	0.000	0.000	0.000
84	A	84	LEU	0	0.017	0.013	23.363	0.014	0.014	0.000	0.000	0.000	0.000
85	A	85	PRO	0	0.007	-0.010	26.399	-0.013	-0.013	0.000	0.000	0.000	0.000
86	A	86	GLU	-1	-0.904	-0.954	27.107	-0.128	-0.128	0.000	0.000	0.000	0.000
87	A	87	GLY	0	-0.024	-0.010	26.390	0.011	0.011	0.000	0.000	0.000	0.000
88	A	88	VAL	0	-0.031	-0.011	26.674	0.013	0.013	0.000	0.000	0.000	0.000
89	A	89	VAL	0	-0.049	-0.032	22.033	-0.010	-0.010	0.000	0.000	0.000	0.000
90	A	90	VAL	0	0.005	0.000	23.173	0.011	0.011	0.000	0.000	0.000	0.000
91	A	91	LYS	1	0.882	0.944	23.683	0.001	0.001	0.000	0.000	0.000	0.000
92	A	92	THR	0	0.021	0.026	25.908	0.011	0.011	0.000	0.000	0.000	0.000
93	A	93	THR	0	-0.003	-0.018	22.290	-0.008	-0.008	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.774	-0.894	24.278	0.059	0.059	0.000	0.000	0.000	0.000
95	A	95	GLU	-1	-0.923	-0.974	26.691	-0.015	-0.015	0.000	0.000	0.000	0.000
96	A	96	LEU	0	-0.013	-0.003	20.124	-0.014	-0.014	0.000	0.000	0.000	0.000
97	A	97	GLU	-1	-0.826	-0.905	23.531	0.035	0.035	0.000	0.000	0.000	0.000
98	A	98	LYS	1	0.857	0.937	25.745	-0.020	-0.020	0.000	0.000	0.000	0.000
99	A	99	ILE	0	-0.043	-0.011	25.322	-0.006	-0.006	0.000	0.000	0.000	0.000
100	A	100	GLY	0	0.055	0.046	25.125	-0.012	-0.012	0.000	0.000	0.000	0.000
101	A	101	TYR	0	-0.103	-0.094	19.194	-0.013	-0.013	0.000	0.000	0.000	0.000
102	A	102	GLU	-1	-0.793	-0.851	19.438	-0.184	-0.184	0.000	0.000	0.000	0.000
103	A	103	LEU	0	-0.011	-0.013	14.891	0.003	0.003	0.000	0.000	0.000	0.000
104	A	104	TRP	0	-0.010	-0.015	14.960	-0.028	-0.028	0.000	0.000	0.000	0.000
105	A	105	LEU	0	-0.017	0.006	9.260	-0.011	-0.011	0.000	0.000	0.000	0.000
106	A	106	PHE	0	-0.027	-0.028	10.495	0.092	0.092	0.000	0.000	0.000	0.000
107	A	107	GLU	-1	-0.868	-0.933	7.886	-1.246	-1.246	0.000	0.000	0.000	0.000
108	A	108	ILE	0	0.003	0.004	6.822	0.548	0.548	0.000	0.000	0.000	0.000
109	A	109	GLN	0	0.047	0.033	8.092	-0.180	-0.180	0.000	0.000	0.000	0.000

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