FMO DATABASE

FMODB ID: 1NL3Z

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	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. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-860275.550486
FMO2-HF: Nuclear repulsion	817500.174421
FMO2-HF: Total energy	-42775.376065
FMO2-MP2: Total energy	-42901.173224

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.
-23.638	-21.891	31.285	-14.285	-18.744	-0.062

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 : 0.000 / q_NPA : 0.031

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	0.015	-0.017	2.628	-2.538	3.814	3.222	-2.838	-6.736	-0.017
4	A	4	ILE	0	0.024	0.017	4.112	-0.053	0.032	0.001	-0.023	-0.062	0.000
5	A	5	LEU	0	0.011	0.000	7.521	0.066	0.066	0.000	0.000	0.000	0.000
6	A	6	ASN	0	0.036	0.006	10.158	0.069	0.069	0.000	0.000	0.000	0.000
7	A	7	SER	0	0.002	-0.001	13.430	0.026	0.026	0.000	0.000	0.000	0.000
8	A	8	ALA	0	0.036	0.027	13.439	-0.077	-0.077	0.000	0.000	0.000	0.000
9	A	9	ILE	0	-0.034	-0.011	11.915	-0.013	-0.013	0.000	0.000	0.000	0.000
10	A	10	LEU	0	0.073	0.028	11.092	-0.150	-0.150	0.000	0.000	0.000	0.000
11	A	11	PRO	0	-0.041	-0.016	9.348	0.131	0.131	0.000	0.000	0.000	0.000
12	A	12	LEU	0	0.018	0.014	10.210	-0.215	-0.215	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.914	0.971	9.789	0.962	0.962	0.000	0.000	0.000	0.000
14	A	14	PRO	0	0.007	0.016	11.730	0.034	0.034	0.000	0.000	0.000	0.000
15	A	15	GLY	0	-0.001	-0.020	14.590	-0.019	-0.019	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.856	-0.899	11.603	-0.791	-0.791	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.951	-0.957	15.585	-0.408	-0.408	0.000	0.000	0.000	0.000
18	A	18	TYR	0	-0.007	-0.041	10.009	-0.121	-0.121	0.000	0.000	0.000	0.000
19	A	19	THR	0	-0.038	-0.017	13.521	0.119	0.119	0.000	0.000	0.000	0.000
20	A	20	VAL	0	0.005	-0.007	11.618	-0.120	-0.120	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.901	0.965	12.346	0.680	0.680	0.000	0.000	0.000	0.000
22	A	22	ALA	0	0.041	0.010	12.802	-0.145	-0.145	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.947	0.984	14.311	0.383	0.383	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.884	-0.934	15.909	-0.229	-0.229	0.000	0.000	0.000	0.000
25	A	25	ILE	0	-0.076	-0.033	13.718	0.010	0.010	0.000	0.000	0.000	0.000
26	A	26	THR	0	0.015	-0.005	17.966	0.030	0.030	0.000	0.000	0.000	0.000
27	A	27	ILE	0	0.062	0.015	17.758	0.003	0.003	0.000	0.000	0.000	0.000
28	A	28	GLN	0	-0.051	-0.026	17.609	0.041	0.041	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.828	-0.920	16.155	-0.060	-0.060	0.000	0.000	0.000	0.000
30	A	30	ALA	0	0.021	0.010	13.568	0.025	0.025	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.944	0.973	13.003	-0.224	-0.224	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.925	-0.950	13.828	0.300	0.300	0.000	0.000	0.000	0.000
33	A	33	LEU	0	-0.021	-0.009	8.809	0.082	0.082	0.000	0.000	0.000	0.000
34	A	34	VAL	0	-0.034	-0.021	8.796	0.236	0.236	0.000	0.000	0.000	0.000
35	A	35	THR	0	-0.063	-0.034	9.693	0.209	0.209	0.000	0.000	0.000	0.000
36	A	36	LYS	1	0.879	0.934	11.313	-0.403	-0.403	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.869	-0.911	4.588	0.682	0.754	-0.001	-0.009	-0.062	0.000
38	A	38	GLN	0	-0.012	0.003	2.601	-2.686	-1.682	1.912	-0.769	-2.146	-0.010
39	A	39	PHE	0	0.029	0.012	3.420	0.709	1.839	0.654	-0.665	-1.119	-0.005
40	A	40	THR	0	-0.035	-0.044	2.345	-6.946	-9.922	10.302	-3.473	-3.853	0.015
41	A	41	SER	0	-0.025	-0.013	4.657	-2.082	-1.961	0.007	-0.038	-0.090	0.001
42	A	42	ALA	0	0.014	0.000	7.847	-0.051	-0.051	0.000	0.000	0.000	0.000
43	A	43	ILE	0	-0.031	0.013	9.307	-0.159	-0.159	0.000	0.000	0.000	0.000
44	A	44	GLY	0	0.015	-0.019	12.376	0.049	0.049	0.000	0.000	0.000	0.000
45	A	45	HIS	0	-0.013	-0.026	15.395	-0.043	-0.043	0.000	0.000	0.000	0.000
46	A	46	GLN	0	-0.012	-0.015	17.743	0.011	0.011	0.000	0.000	0.000	0.000
47	A	47	ALA	0	0.060	0.040	19.567	0.023	0.023	0.000	0.000	0.000	0.000
48	A	48	THR	0	0.001	-0.005	15.544	0.001	0.001	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.008	0.006	15.288	0.014	0.014	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.846	-0.917	16.268	0.165	0.165	0.000	0.000	0.000	0.000
51	A	51	LEU	0	-0.015	-0.001	19.177	0.019	0.019	0.000	0.000	0.000	0.000
52	A	52	LEU	0	0.000	-0.013	12.818	0.004	0.004	0.000	0.000	0.000	0.000
53	A	53	SER	0	0.008	-0.007	15.625	0.071	0.071	0.000	0.000	0.000	0.000
54	A	54	SER	0	-0.057	-0.013	16.569	0.019	0.019	0.000	0.000	0.000	0.000
55	A	55	ILE	0	0.005	-0.004	17.152	0.010	0.010	0.000	0.000	0.000	0.000
56	A	56	LEU	0	-0.021	-0.012	12.484	-0.006	-0.006	0.000	0.000	0.000	0.000
57	A	57	GLY	0	-0.050	-0.013	15.890	0.043	0.043	0.000	0.000	0.000	0.000
58	A	58	VAL	0	-0.022	-0.009	11.648	0.043	0.043	0.000	0.000	0.000	0.000
59	A	59	ASN	0	-0.008	-0.008	13.304	-0.093	-0.093	0.000	0.000	0.000	0.000
60	A	60	VAL	0	0.018	0.012	11.077	0.204	0.204	0.000	0.000	0.000	0.000
61	A	61	PRO	0	0.011	0.001	10.651	-0.133	-0.133	0.000	0.000	0.000	0.000
62	A	62	MET	0	-0.019	0.012	12.732	-0.019	-0.019	0.000	0.000	0.000	0.000
63	A	63	ASN	0	-0.044	-0.030	8.908	-0.053	-0.053	0.000	0.000	0.000	0.000
64	A	64	ARG	1	0.909	0.963	11.604	0.072	0.072	0.000	0.000	0.000	0.000
65	A	65	VAL	0	0.001	0.012	9.163	-0.028	-0.028	0.000	0.000	0.000	0.000
66	A	66	GLN	0	-0.034	-0.021	11.181	-0.070	-0.070	0.000	0.000	0.000	0.000
67	A	67	ILE	0	0.013	0.018	5.770	0.077	0.077	0.000	0.000	0.000	0.000
68	A	68	LYS	1	0.877	0.921	7.488	1.063	1.063	0.000	0.000	0.000	0.000
69	A	69	VAL	0	0.018	0.025	5.220	-0.360	-0.360	0.000	0.000	0.000	0.000
70	A	70	THR	0	-0.036	-0.032	5.532	1.081	1.081	0.000	0.000	0.000	0.000
71	A	71	HIS	1	0.842	0.894	5.948	0.166	0.166	0.000	0.000	0.000	0.000
72	A	72	GLY	0	-0.002	-0.004	5.225	0.309	0.309	0.000	0.000	0.000	0.000
73	A	73	ASP	-1	-0.796	-0.868	1.768	-15.990	-20.414	15.175	-6.460	-4.290	-0.046
74	A	74	ARG	1	0.809	0.886	3.422	3.716	4.155	0.014	0.006	-0.459	0.000
75	A	75	ILE	0	-0.023	-0.007	5.158	-0.821	-0.877	-0.001	-0.016	0.073	0.000
76	A	76	LEU	0	0.034	0.030	7.541	0.289	0.289	0.000	0.000	0.000	0.000
77	A	77	ALA	0	-0.024	-0.023	9.678	0.067	0.067	0.000	0.000	0.000	0.000
78	A	78	PHE	0	0.007	0.005	12.150	0.067	0.067	0.000	0.000	0.000	0.000
79	A	79	MET	0	-0.055	-0.020	15.086	-0.047	-0.047	0.000	0.000	0.000	0.000
80	A	80	LEU	0	-0.008	-0.001	17.992	0.029	0.029	0.000	0.000	0.000	0.000
81	A	81	LYS	1	0.873	0.916	21.197	0.111	0.111	0.000	0.000	0.000	0.000
82	A	82	GLN	0	-0.012	0.000	24.310	0.008	0.008	0.000	0.000	0.000	0.000
83	A	83	ARG	1	0.943	0.975	24.491	0.183	0.183	0.000	0.000	0.000	0.000
84	A	84	LEU	0	0.003	0.005	23.364	0.013	0.013	0.000	0.000	0.000	0.000
85	A	85	PRO	0	0.015	-0.004	26.812	-0.010	-0.010	0.000	0.000	0.000	0.000
86	A	86	GLU	-1	-0.888	-0.956	27.622	-0.129	-0.129	0.000	0.000	0.000	0.000
87	A	87	GLY	0	-0.037	-0.012	26.305	0.010	0.010	0.000	0.000	0.000	0.000
88	A	88	VAL	0	-0.028	-0.005	26.714	0.012	0.012	0.000	0.000	0.000	0.000
89	A	89	VAL	0	-0.044	-0.023	22.232	-0.009	-0.009	0.000	0.000	0.000	0.000
90	A	90	VAL	0	0.017	0.012	23.522	0.010	0.010	0.000	0.000	0.000	0.000
91	A	91	LYS	1	0.915	0.947	23.566	0.015	0.015	0.000	0.000	0.000	0.000
92	A	92	THR	0	0.042	0.036	25.748	0.011	0.011	0.000	0.000	0.000	0.000
93	A	93	THR	0	0.037	0.011	22.212	-0.010	-0.010	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.837	-0.925	24.437	0.039	0.039	0.000	0.000	0.000	0.000
95	A	95	GLU	-1	-0.964	-0.997	27.280	-0.043	-0.043	0.000	0.000	0.000	0.000
96	A	96	LEU	0	-0.030	-0.016	20.493	-0.013	-0.013	0.000	0.000	0.000	0.000
97	A	97	GLU	-1	-0.846	-0.943	23.342	0.013	0.013	0.000	0.000	0.000	0.000
98	A	98	LYS	1	0.871	0.946	25.762	0.004	0.004	0.000	0.000	0.000	0.000
99	A	99	ILE	0	-0.072	-0.017	25.100	-0.007	-0.007	0.000	0.000	0.000	0.000
100	A	100	GLY	0	0.057	0.038	24.996	-0.009	-0.009	0.000	0.000	0.000	0.000
101	A	101	TYR	0	-0.073	-0.060	19.050	-0.014	-0.014	0.000	0.000	0.000	0.000
102	A	102	GLU	-1	-0.770	-0.851	19.702	-0.191	-0.191	0.000	0.000	0.000	0.000
103	A	103	LEU	0	-0.019	-0.011	14.873	-0.013	-0.013	0.000	0.000	0.000	0.000
104	A	104	TRP	0	-0.009	-0.009	14.705	-0.026	-0.026	0.000	0.000	0.000	0.000
105	A	105	LEU	0	-0.020	-0.002	9.100	-0.043	-0.043	0.000	0.000	0.000	0.000
106	A	106	PHE	0	-0.031	-0.026	10.400	0.101	0.101	0.000	0.000	0.000	0.000
107	A	107	GLU	-1	-0.895	-0.958	8.000	-1.236	-1.236	0.000	0.000	0.000	0.000
108	A	108	ILE	0	0.005	0.004	6.831	0.523	0.523	0.000	0.000	0.000	0.000
109	A	109	GLN	0	0.043	0.021	7.926	-0.194	-0.194	0.000	0.000	0.000	0.000

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