FMO DATABASE

FMODB ID: 49JRN

Calculation Name: 5N9J-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5N9J

Chain ID: B

ChEMBL ID:

UniProt ID: P87310

Base Structure: X-ray

Registration Date: 2023-06-21

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	133
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-852672.974312
FMO2-HF: Nuclear repulsion	800264.842933
FMO2-HF: Total energy	-52408.131379
FMO2-MP2: Total energy	-52563.469304

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(B:8:THR)

Summations of interaction energy for fragment #1(B:8:THR)

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.
-14.655	-13.783	15.095	-7.353	-8.614	-0.066

Interaction energy analysis for fragmet #1(B:8:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.012 / q_NPA : -0.024

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	B	10	GLU	-1	-0.835	-0.916	1.813	-18.119	-19.531	11.086	-5.252	-4.423	-0.060
4	B	11	MET	0	0.006	0.000	2.812	1.050	2.124	3.852	-1.769	-3.156	-0.006
5	B	12	LYS	1	0.824	0.909	2.835	1.228	2.363	0.158	-0.329	-0.964	0.000
6	B	13	SER	0	-0.004	0.001	5.120	0.816	0.891	-0.001	-0.003	-0.071	0.000
7	B	14	LEU	0	-0.022	-0.010	7.351	0.450	0.450	0.000	0.000	0.000	0.000
8	B	15	ALA	0	0.000	-0.008	7.358	0.316	0.316	0.000	0.000	0.000	0.000
9	B	16	SER	0	0.007	0.013	8.835	0.179	0.179	0.000	0.000	0.000	0.000
10	B	17	ARG	1	0.850	0.925	10.802	0.768	0.768	0.000	0.000	0.000	0.000
11	B	18	LEU	0	-0.016	-0.022	11.995	0.111	0.111	0.000	0.000	0.000	0.000
12	B	19	GLU	-1	-0.941	-0.965	12.063	-0.305	-0.305	0.000	0.000	0.000	0.000
13	B	20	ASP	-1	-0.841	-0.909	14.853	-0.506	-0.506	0.000	0.000	0.000	0.000
14	B	21	THR	0	-0.031	-0.047	16.752	0.045	0.045	0.000	0.000	0.000	0.000
15	B	22	THR	0	-0.058	-0.030	17.552	0.048	0.048	0.000	0.000	0.000	0.000
16	B	23	GLN	0	-0.065	-0.024	19.081	0.041	0.041	0.000	0.000	0.000	0.000
17	B	24	ALA	0	0.037	0.016	20.876	0.026	0.026	0.000	0.000	0.000	0.000
18	B	25	PHE	0	-0.043	-0.037	21.566	0.022	0.022	0.000	0.000	0.000	0.000
19	B	26	TYR	0	-0.046	-0.009	23.584	0.026	0.026	0.000	0.000	0.000	0.000
20	B	27	ASP	-1	-0.812	-0.911	24.540	-0.162	-0.162	0.000	0.000	0.000	0.000
21	B	28	LEU	0	-0.016	0.001	26.824	0.014	0.014	0.000	0.000	0.000	0.000
22	B	29	ALA	0	-0.026	-0.018	28.320	0.013	0.013	0.000	0.000	0.000	0.000
23	B	30	LEU	0	-0.013	-0.001	29.166	0.012	0.012	0.000	0.000	0.000	0.000
24	B	31	ILE	0	-0.005	-0.014	29.717	0.009	0.009	0.000	0.000	0.000	0.000
25	B	32	VAL	0	-0.051	-0.025	32.819	0.007	0.007	0.000	0.000	0.000	0.000
26	B	33	TYR	0	-0.073	-0.024	34.073	0.010	0.010	0.000	0.000	0.000	0.000
27	B	34	ASN	0	-0.091	-0.050	34.517	0.005	0.005	0.000	0.000	0.000	0.000
28	B	35	LEU	0	0.022	0.024	36.884	-0.001	-0.001	0.000	0.000	0.000	0.000
29	B	36	GLU	-1	-0.901	-0.938	38.695	-0.058	-0.058	0.000	0.000	0.000	0.000
30	B	37	ASP	-1	-0.951	-0.973	41.238	-0.068	-0.068	0.000	0.000	0.000	0.000
31	B	38	THR	0	-0.058	-0.041	41.300	-0.003	-0.003	0.000	0.000	0.000	0.000
32	B	39	THR	0	-0.058	-0.029	37.222	-0.005	-0.005	0.000	0.000	0.000	0.000
33	B	40	PRO	0	0.007	0.000	36.037	0.000	0.000	0.000	0.000	0.000	0.000
34	B	41	SER	0	0.013	-0.019	37.011	-0.004	-0.004	0.000	0.000	0.000	0.000
35	B	42	ASP	-1	-0.901	-0.948	36.157	-0.124	-0.124	0.000	0.000	0.000	0.000
36	B	43	ALA	0	0.033	0.016	32.721	-0.011	-0.011	0.000	0.000	0.000	0.000
37	B	44	ILE	0	0.023	0.024	31.671	-0.011	-0.011	0.000	0.000	0.000	0.000
38	B	45	PRO	0	-0.042	-0.028	31.934	-0.011	-0.011	0.000	0.000	0.000	0.000
39	B	46	GLU	-1	-0.916	-0.949	28.602	-0.207	-0.207	0.000	0.000	0.000	0.000
40	B	47	SER	0	0.007	0.013	27.420	-0.018	-0.018	0.000	0.000	0.000	0.000
41	B	48	LEU	0	0.020	0.006	26.921	-0.018	-0.018	0.000	0.000	0.000	0.000
42	B	49	ASP	-1	-0.879	-0.935	27.427	-0.269	-0.269	0.000	0.000	0.000	0.000
43	B	50	THR	0	-0.062	-0.054	23.457	-0.029	-0.029	0.000	0.000	0.000	0.000
44	B	51	LEU	0	0.035	0.036	22.889	-0.039	-0.039	0.000	0.000	0.000	0.000
45	B	52	ILE	0	-0.035	-0.027	22.775	-0.033	-0.033	0.000	0.000	0.000	0.000
46	B	53	ARG	1	0.857	0.918	22.479	0.276	0.276	0.000	0.000	0.000	0.000
47	B	54	ASP	-1	-0.792	-0.879	18.522	-0.538	-0.538	0.000	0.000	0.000	0.000
48	B	55	LEU	0	-0.006	-0.001	18.403	-0.073	-0.073	0.000	0.000	0.000	0.000
49	B	56	LYS	1	0.862	0.942	20.056	0.331	0.331	0.000	0.000	0.000	0.000
50	B	57	SER	0	-0.035	-0.027	15.841	-0.052	-0.052	0.000	0.000	0.000	0.000
51	B	58	LEU	0	0.060	0.034	14.408	-0.126	-0.126	0.000	0.000	0.000	0.000
52	B	59	PRO	0	-0.009	-0.014	13.955	-0.116	-0.116	0.000	0.000	0.000	0.000
53	B	60	ASP	-1	-0.821	-0.894	14.617	-0.783	-0.783	0.000	0.000	0.000	0.000
54	B	61	ILE	0	-0.029	-0.008	9.132	-0.138	-0.138	0.000	0.000	0.000	0.000
55	B	62	SER	0	0.020	0.010	9.716	-0.338	-0.338	0.000	0.000	0.000	0.000
56	B	63	ARG	1	0.792	0.858	10.579	0.639	0.639	0.000	0.000	0.000	0.000
57	B	64	LYS	1	0.891	0.962	7.618	1.507	1.507	0.000	0.000	0.000	0.000
58	B	65	VAL	0	-0.010	0.014	5.410	-0.457	-0.457	0.000	0.000	0.000	0.000
59	B	66	ASN	0	-0.049	-0.025	7.031	0.067	0.067	0.000	0.000	0.000	0.000
60	B	67	ASN	0	0.018	0.009	6.023	-0.218	-0.218	0.000	0.000	0.000	0.000
61	B	68	LEU	0	-0.003	0.000	9.247	0.005	0.005	0.000	0.000	0.000	0.000
62	B	69	ILE	0	-0.003	-0.007	10.673	0.103	0.103	0.000	0.000	0.000	0.000
63	B	70	PRO	0	-0.006	0.001	14.228	-0.025	-0.025	0.000	0.000	0.000	0.000
64	B	71	GLN	0	0.018	0.006	17.456	-0.025	-0.025	0.000	0.000	0.000	0.000
65	B	72	ASP	-1	-0.780	-0.890	20.420	0.045	0.045	0.000	0.000	0.000	0.000
66	B	73	VAL	0	-0.053	-0.016	14.124	0.020	0.020	0.000	0.000	0.000	0.000
67	B	74	LEU	0	0.008	0.006	17.629	-0.007	-0.007	0.000	0.000	0.000	0.000
68	B	75	GLU	-1	-0.881	-0.939	18.574	-0.033	-0.033	0.000	0.000	0.000	0.000
69	B	76	TYR	0	-0.112	-0.093	19.105	0.009	0.009	0.000	0.000	0.000	0.000
70	B	77	ILE	0	-0.005	-0.002	15.077	0.005	0.005	0.000	0.000	0.000	0.000
71	B	78	GLU	-1	-0.913	-0.941	19.056	-0.121	-0.121	0.000	0.000	0.000	0.000
72	B	79	GLN	0	-0.088	-0.049	22.324	0.009	0.009	0.000	0.000	0.000	0.000
73	B	80	GLY	0	-0.025	-0.005	21.247	0.011	0.011	0.000	0.000	0.000	0.000
74	B	81	ARG	1	0.834	0.936	21.195	-0.088	-0.088	0.000	0.000	0.000	0.000
75	B	82	ASN	0	0.011	-0.015	16.085	-0.002	-0.002	0.000	0.000	0.000	0.000
76	B	83	PRO	0	0.079	0.032	13.731	0.013	0.013	0.000	0.000	0.000	0.000
77	B	84	ASP	-1	-0.824	-0.904	13.457	0.443	0.443	0.000	0.000	0.000	0.000
78	B	85	VAL	0	-0.076	-0.043	15.600	0.019	0.019	0.000	0.000	0.000	0.000
79	B	86	TYR	0	-0.012	-0.020	16.727	0.009	0.009	0.000	0.000	0.000	0.000
80	B	87	ALA	0	0.032	0.017	14.145	0.005	0.005	0.000	0.000	0.000	0.000
81	B	88	ARG	1	0.878	0.948	16.177	-0.258	-0.258	0.000	0.000	0.000	0.000
82	B	89	GLN	0	0.021	0.025	19.041	-0.015	-0.015	0.000	0.000	0.000	0.000
83	B	90	PHE	0	0.038	0.020	18.670	-0.009	-0.009	0.000	0.000	0.000	0.000
84	B	91	SER	0	-0.034	-0.033	17.737	-0.006	-0.006	0.000	0.000	0.000	0.000
85	B	92	GLU	-1	-0.810	-0.898	19.785	0.220	0.220	0.000	0.000	0.000	0.000
86	B	93	LEU	0	-0.042	-0.007	23.199	-0.015	-0.015	0.000	0.000	0.000	0.000
87	B	94	VAL	0	0.023	0.009	20.445	-0.016	-0.016	0.000	0.000	0.000	0.000
88	B	95	GLN	0	-0.036	-0.019	23.565	0.009	0.009	0.000	0.000	0.000	0.000
89	B	96	LYS	1	0.863	0.916	25.536	-0.212	-0.212	0.000	0.000	0.000	0.000
90	B	97	ASP	-1	-0.844	-0.944	27.464	0.129	0.129	0.000	0.000	0.000	0.000
91	B	98	ASN	0	-0.051	-0.003	26.162	-0.018	-0.018	0.000	0.000	0.000	0.000
92	B	99	GLN	0	0.036	0.012	28.546	0.000	0.000	0.000	0.000	0.000	0.000
93	B	100	TYR	0	-0.020	0.000	31.361	-0.017	-0.017	0.000	0.000	0.000	0.000
94	B	101	VAL	0	0.000	-0.008	31.186	-0.012	-0.012	0.000	0.000	0.000	0.000
95	B	102	ASN	0	0.020	0.003	32.004	-0.014	-0.014	0.000	0.000	0.000	0.000
96	B	103	GLY	0	0.018	0.013	33.946	-0.006	-0.006	0.000	0.000	0.000	0.000
97	B	104	LYS	1	0.882	0.941	35.809	-0.101	-0.101	0.000	0.000	0.000	0.000
98	B	105	LEU	0	0.008	0.011	34.135	-0.007	-0.007	0.000	0.000	0.000	0.000
99	B	106	TYR	0	0.035	0.011	35.395	-0.003	-0.003	0.000	0.000	0.000	0.000
100	B	107	ALA	0	-0.022	0.003	39.983	-0.005	-0.005	0.000	0.000	0.000	0.000
101	B	108	ILE	0	-0.005	-0.005	40.671	-0.005	-0.005	0.000	0.000	0.000	0.000
102	B	109	GLU	-1	-0.834	-0.899	40.926	0.084	0.084	0.000	0.000	0.000	0.000
103	B	110	GLY	0	0.024	0.006	43.346	-0.003	-0.003	0.000	0.000	0.000	0.000
104	B	111	PHE	0	-0.030	-0.013	45.762	-0.004	-0.004	0.000	0.000	0.000	0.000
105	B	112	GLN	0	-0.006	-0.008	45.802	-0.002	-0.002	0.000	0.000	0.000	0.000
106	B	113	LYS	1	0.831	0.908	43.815	-0.087	-0.087	0.000	0.000	0.000	0.000
107	B	114	ALA	0	0.057	0.032	49.459	-0.003	-0.003	0.000	0.000	0.000	0.000
108	B	115	PHE	0	-0.016	-0.008	51.356	-0.003	-0.003	0.000	0.000	0.000	0.000
109	B	116	ALA	0	0.011	0.000	51.675	-0.003	-0.003	0.000	0.000	0.000	0.000
110	B	117	GLU	-1	-0.962	-0.990	52.082	0.059	0.059	0.000	0.000	0.000	0.000
111	B	118	GLU	-1	-0.895	-0.937	55.469	0.044	0.044	0.000	0.000	0.000	0.000
112	B	119	ILE	0	-0.034	-0.021	54.998	-0.003	-0.003	0.000	0.000	0.000	0.000
113	B	120	LYS	1	0.795	0.878	54.495	-0.053	-0.053	0.000	0.000	0.000	0.000
114	B	121	GLN	0	-0.111	-0.058	59.202	-0.003	-0.003	0.000	0.000	0.000	0.000
115	B	122	ALA	0	-0.014	0.001	61.493	-0.002	-0.002	0.000	0.000	0.000	0.000
116	B	123	TYR	0	-0.048	-0.018	61.220	-0.002	-0.002	0.000	0.000	0.000	0.000
117	B	124	PRO	0	0.039	0.033	61.586	0.001	0.001	0.000	0.000	0.000	0.000
118	B	125	GLU	-1	-0.921	-0.974	61.970	0.034	0.034	0.000	0.000	0.000	0.000
119	B	126	VAL	0	-0.019	-0.013	59.113	0.000	0.000	0.000	0.000	0.000	0.000
120	B	127	SER	0	0.003	-0.007	57.123	0.002	0.002	0.000	0.000	0.000	0.000
121	B	128	SER	0	-0.036	-0.019	56.182	0.001	0.001	0.000	0.000	0.000	0.000
122	B	129	VAL	0	-0.009	-0.003	55.187	0.001	0.001	0.000	0.000	0.000	0.000
123	B	130	VAL	0	0.050	0.021	53.096	0.001	0.001	0.000	0.000	0.000	0.000
124	B	131	ASP	-1	-0.779	-0.868	51.596	0.055	0.055	0.000	0.000	0.000	0.000
125	B	132	LYS	1	0.923	0.963	50.925	-0.038	-0.038	0.000	0.000	0.000	0.000
126	B	133	ILE	0	0.038	0.023	48.798	0.002	0.002	0.000	0.000	0.000	0.000
127	B	134	LEU	0	-0.019	-0.013	47.130	0.002	0.002	0.000	0.000	0.000	0.000
128	B	135	ASN	0	-0.121	-0.074	45.962	0.008	0.008	0.000	0.000	0.000	0.000
129	B	136	GLU	-1	-0.931	-0.952	45.284	0.054	0.054	0.000	0.000	0.000	0.000
130	B	137	GLY	0	0.041	0.040	42.786	0.001	0.001	0.000	0.000	0.000	0.000
131	B	138	LYS	1	0.800	0.890	40.316	-0.069	-0.069	0.000	0.000	0.000	0.000
132	B	139	VAL	0	0.025	0.020	35.576	-0.003	-0.003	0.000	0.000	0.000	0.000
133	B	140	GLU	-1	-1.016	-1.004	38.970	0.064	0.064	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:8:THR)