FMO DATABASE

FMODB ID: K9G73

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

Total energy (hartree)

FMO2-HF: Electronic energy	-852140.240498
FMO2-HF: Nuclear repulsion	799732.764738
FMO2-HF: Total energy	-52407.475761
FMO2-MP2: Total energy	-52563.012795

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.
-8.965	-4.701	12.296	-7.112	-9.449	-0.028

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 : 0.043 / q_NPA : -0.017

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	-0.875	-0.943	2.161	-13.226	-10.214	2.691	-2.463	-3.241	-0.030
4	B	11	MET	0	-0.010	-0.005	2.122	1.477	1.947	7.239	-3.685	-4.025	-0.002
5	B	12	LYS	1	0.854	0.920	2.039	1.229	1.925	2.367	-0.959	-2.104	0.004
6	B	13	SER	0	-0.021	-0.004	4.962	0.838	0.924	-0.001	-0.005	-0.079	0.000
7	B	14	LEU	0	-0.022	-0.005	6.931	0.461	0.461	0.000	0.000	0.000	0.000
8	B	15	ALA	0	0.019	-0.002	7.458	0.294	0.294	0.000	0.000	0.000	0.000
9	B	16	SER	0	-0.002	0.017	8.943	0.165	0.165	0.000	0.000	0.000	0.000
10	B	17	ARG	1	0.860	0.915	10.736	0.687	0.687	0.000	0.000	0.000	0.000
11	B	18	LEU	0	-0.017	-0.020	11.538	0.096	0.096	0.000	0.000	0.000	0.000
12	B	19	GLU	-1	-0.953	-0.974	12.203	-0.189	-0.189	0.000	0.000	0.000	0.000
13	B	20	ASP	-1	-0.831	-0.906	14.721	-0.439	-0.439	0.000	0.000	0.000	0.000
14	B	21	THR	0	-0.027	-0.030	16.602	0.036	0.036	0.000	0.000	0.000	0.000
15	B	22	THR	0	-0.074	-0.034	16.672	0.045	0.045	0.000	0.000	0.000	0.000
16	B	23	GLN	0	-0.069	-0.039	18.895	0.039	0.039	0.000	0.000	0.000	0.000
17	B	24	ALA	0	0.050	0.034	20.735	0.019	0.019	0.000	0.000	0.000	0.000
18	B	25	PHE	0	-0.048	-0.036	21.375	0.016	0.016	0.000	0.000	0.000	0.000
19	B	26	TYR	0	-0.046	-0.009	23.389	0.021	0.021	0.000	0.000	0.000	0.000
20	B	27	ASP	-1	-0.824	-0.914	24.572	-0.124	-0.124	0.000	0.000	0.000	0.000
21	B	28	LEU	0	-0.015	-0.001	26.696	0.011	0.011	0.000	0.000	0.000	0.000
22	B	29	ALA	0	-0.026	-0.024	28.203	0.010	0.010	0.000	0.000	0.000	0.000
23	B	30	LEU	0	-0.015	0.000	29.260	0.010	0.010	0.000	0.000	0.000	0.000
24	B	31	ILE	0	-0.014	-0.013	29.726	0.006	0.006	0.000	0.000	0.000	0.000
25	B	32	VAL	0	-0.047	-0.021	32.753	0.005	0.005	0.000	0.000	0.000	0.000
26	B	33	TYR	0	-0.085	-0.032	33.913	0.008	0.008	0.000	0.000	0.000	0.000
27	B	34	ASN	0	-0.060	-0.034	34.528	0.004	0.004	0.000	0.000	0.000	0.000
28	B	35	LEU	0	0.009	0.016	36.957	-0.004	-0.004	0.000	0.000	0.000	0.000
29	B	36	GLU	-1	-0.940	-0.983	39.065	-0.042	-0.042	0.000	0.000	0.000	0.000
30	B	37	ASP	-1	-0.928	-0.957	41.201	-0.054	-0.054	0.000	0.000	0.000	0.000
31	B	38	THR	0	-0.056	-0.024	41.298	-0.004	-0.004	0.000	0.000	0.000	0.000
32	B	39	THR	0	-0.046	-0.023	37.112	-0.005	-0.005	0.000	0.000	0.000	0.000
33	B	40	PRO	0	0.026	0.008	36.110	0.000	0.000	0.000	0.000	0.000	0.000
34	B	41	SER	0	0.059	0.025	36.924	-0.003	-0.003	0.000	0.000	0.000	0.000
35	B	42	ASP	-1	-0.944	-0.992	36.120	-0.107	-0.107	0.000	0.000	0.000	0.000
36	B	43	ALA	0	0.014	0.003	32.987	-0.009	-0.009	0.000	0.000	0.000	0.000
37	B	44	ILE	0	-0.002	0.012	31.822	-0.007	-0.007	0.000	0.000	0.000	0.000
38	B	45	PRO	0	-0.035	-0.033	31.776	-0.009	-0.009	0.000	0.000	0.000	0.000
39	B	46	GLU	-1	-0.894	-0.922	28.765	-0.172	-0.172	0.000	0.000	0.000	0.000
40	B	47	SER	0	0.006	0.016	27.117	-0.016	-0.016	0.000	0.000	0.000	0.000
41	B	48	LEU	0	0.033	0.014	26.829	-0.017	-0.017	0.000	0.000	0.000	0.000
42	B	49	ASP	-1	-0.914	-0.957	27.067	-0.204	-0.204	0.000	0.000	0.000	0.000
43	B	50	THR	0	-0.142	-0.094	23.381	-0.028	-0.028	0.000	0.000	0.000	0.000
44	B	51	LEU	0	0.058	0.035	22.599	-0.034	-0.034	0.000	0.000	0.000	0.000
45	B	52	ILE	0	-0.007	-0.007	22.424	-0.032	-0.032	0.000	0.000	0.000	0.000
46	B	53	ARG	1	0.937	0.961	21.773	0.253	0.253	0.000	0.000	0.000	0.000
47	B	54	ASP	-1	-0.789	-0.882	18.490	-0.457	-0.457	0.000	0.000	0.000	0.000
48	B	55	LEU	0	-0.004	0.001	18.054	-0.064	-0.064	0.000	0.000	0.000	0.000
49	B	56	LYS	1	0.858	0.939	19.637	0.288	0.288	0.000	0.000	0.000	0.000
50	B	57	SER	0	-0.059	-0.034	15.657	-0.048	-0.048	0.000	0.000	0.000	0.000
51	B	58	LEU	0	0.043	0.021	14.236	-0.113	-0.113	0.000	0.000	0.000	0.000
52	B	59	PRO	0	-0.013	-0.018	13.890	-0.099	-0.099	0.000	0.000	0.000	0.000
53	B	60	ASP	-1	-0.819	-0.887	14.356	-0.696	-0.696	0.000	0.000	0.000	0.000
54	B	61	ILE	0	0.003	-0.003	8.897	-0.132	-0.132	0.000	0.000	0.000	0.000
55	B	62	SER	0	0.015	0.008	9.554	-0.301	-0.301	0.000	0.000	0.000	0.000
56	B	63	ARG	1	0.780	0.866	10.611	0.592	0.592	0.000	0.000	0.000	0.000
57	B	64	LYS	1	0.895	0.956	7.614	1.457	1.457	0.000	0.000	0.000	0.000
58	B	65	VAL	0	-0.049	-0.001	5.395	-0.295	-0.295	0.000	0.000	0.000	0.000
59	B	66	ASN	0	0.015	0.009	6.801	-0.066	-0.066	0.000	0.000	0.000	0.000
60	B	67	ASN	0	-0.022	-0.013	5.698	-0.286	-0.286	0.000	0.000	0.000	0.000
61	B	68	LEU	0	0.015	0.003	8.986	0.020	0.020	0.000	0.000	0.000	0.000
62	B	69	ILE	0	-0.016	-0.006	10.889	0.109	0.109	0.000	0.000	0.000	0.000
63	B	70	PRO	0	-0.002	0.000	14.216	-0.027	-0.027	0.000	0.000	0.000	0.000
64	B	71	GLN	0	0.067	0.030	17.522	-0.020	-0.020	0.000	0.000	0.000	0.000
65	B	72	ASP	-1	-0.865	-0.945	20.389	0.067	0.067	0.000	0.000	0.000	0.000
66	B	73	VAL	0	-0.036	-0.015	14.638	0.020	0.020	0.000	0.000	0.000	0.000
67	B	74	LEU	0	0.016	0.014	17.629	-0.001	-0.001	0.000	0.000	0.000	0.000
68	B	75	GLU	-1	-0.886	-0.942	18.976	0.001	0.001	0.000	0.000	0.000	0.000
69	B	76	TYR	0	-0.124	-0.103	19.391	0.004	0.004	0.000	0.000	0.000	0.000
70	B	77	ILE	0	-0.038	-0.024	14.990	0.010	0.010	0.000	0.000	0.000	0.000
71	B	78	GLU	-1	-0.918	-0.937	19.111	-0.070	-0.070	0.000	0.000	0.000	0.000
72	B	79	GLN	0	-0.073	-0.048	22.277	-0.001	-0.001	0.000	0.000	0.000	0.000
73	B	80	GLY	0	-0.011	0.007	21.598	0.006	0.006	0.000	0.000	0.000	0.000
74	B	81	ARG	1	0.861	0.945	21.610	-0.116	-0.116	0.000	0.000	0.000	0.000
75	B	82	ASN	0	0.007	-0.012	16.473	0.009	0.009	0.000	0.000	0.000	0.000
76	B	83	PRO	0	0.092	0.042	14.069	0.004	0.004	0.000	0.000	0.000	0.000
77	B	84	ASP	-1	-0.830	-0.917	13.445	0.540	0.540	0.000	0.000	0.000	0.000
78	B	85	VAL	0	-0.099	-0.057	15.656	0.003	0.003	0.000	0.000	0.000	0.000
79	B	86	TYR	0	0.038	0.028	17.056	-0.001	-0.001	0.000	0.000	0.000	0.000
80	B	87	ALA	0	0.030	0.015	14.514	-0.001	-0.001	0.000	0.000	0.000	0.000
81	B	88	ARG	1	0.885	0.945	16.606	-0.305	-0.305	0.000	0.000	0.000	0.000
82	B	89	GLN	0	0.030	0.028	19.333	-0.016	-0.016	0.000	0.000	0.000	0.000
83	B	90	PHE	0	0.035	0.025	18.652	-0.019	-0.019	0.000	0.000	0.000	0.000
84	B	91	SER	0	-0.029	-0.014	17.738	-0.011	-0.011	0.000	0.000	0.000	0.000
85	B	92	GLU	-1	-0.894	-0.955	19.693	0.232	0.232	0.000	0.000	0.000	0.000
86	B	93	LEU	0	-0.047	-0.013	23.021	-0.020	-0.020	0.000	0.000	0.000	0.000
87	B	94	VAL	0	0.024	0.011	20.138	-0.020	-0.020	0.000	0.000	0.000	0.000
88	B	95	GLN	0	-0.024	-0.009	23.319	0.000	0.000	0.000	0.000	0.000	0.000
89	B	96	LYS	1	0.928	0.960	25.222	-0.191	-0.191	0.000	0.000	0.000	0.000
90	B	97	ASP	-1	-0.849	-0.946	26.984	0.123	0.123	0.000	0.000	0.000	0.000
91	B	98	ASN	0	-0.070	-0.011	25.334	-0.024	-0.024	0.000	0.000	0.000	0.000
92	B	99	GLN	0	0.022	-0.001	28.165	-0.001	-0.001	0.000	0.000	0.000	0.000
93	B	100	TYR	0	-0.009	0.004	31.159	-0.017	-0.017	0.000	0.000	0.000	0.000
94	B	101	VAL	0	0.030	0.004	30.769	-0.010	-0.010	0.000	0.000	0.000	0.000
95	B	102	ASN	0	0.019	0.016	31.606	-0.015	-0.015	0.000	0.000	0.000	0.000
96	B	103	GLY	0	0.034	0.011	33.500	-0.007	-0.007	0.000	0.000	0.000	0.000
97	B	104	LYS	1	0.892	0.949	36.026	-0.092	-0.092	0.000	0.000	0.000	0.000
98	B	105	LEU	0	0.001	0.003	33.943	-0.007	-0.007	0.000	0.000	0.000	0.000
99	B	106	TYR	0	0.017	0.004	35.656	-0.002	-0.002	0.000	0.000	0.000	0.000
100	B	107	ALA	0	-0.032	-0.007	39.669	-0.005	-0.005	0.000	0.000	0.000	0.000
101	B	108	ILE	0	-0.007	-0.011	40.944	-0.005	-0.005	0.000	0.000	0.000	0.000
102	B	109	GLU	-1	-0.826	-0.903	40.394	0.074	0.074	0.000	0.000	0.000	0.000
103	B	110	GLY	0	-0.017	-0.003	43.224	-0.003	-0.003	0.000	0.000	0.000	0.000
104	B	111	PHE	0	-0.024	-0.005	45.695	-0.004	-0.004	0.000	0.000	0.000	0.000
105	B	112	GLN	0	0.008	0.001	45.983	-0.002	-0.002	0.000	0.000	0.000	0.000
106	B	113	LYS	1	0.851	0.910	43.182	-0.077	-0.077	0.000	0.000	0.000	0.000
107	B	114	ALA	0	0.044	0.025	49.208	-0.002	-0.002	0.000	0.000	0.000	0.000
108	B	115	PHE	0	-0.018	-0.007	51.129	-0.003	-0.003	0.000	0.000	0.000	0.000
109	B	116	ALA	0	0.007	-0.002	51.496	-0.002	-0.002	0.000	0.000	0.000	0.000
110	B	117	GLU	-1	-0.955	-0.981	52.372	0.051	0.051	0.000	0.000	0.000	0.000
111	B	118	GLU	-1	-0.896	-0.939	55.363	0.040	0.040	0.000	0.000	0.000	0.000
112	B	119	ILE	0	-0.013	-0.011	54.744	-0.002	-0.002	0.000	0.000	0.000	0.000
113	B	120	LYS	1	0.794	0.893	54.199	-0.046	-0.046	0.000	0.000	0.000	0.000
114	B	121	GLN	0	-0.107	-0.067	58.981	-0.003	-0.003	0.000	0.000	0.000	0.000
115	B	122	ALA	0	-0.020	0.002	60.982	-0.001	-0.001	0.000	0.000	0.000	0.000
116	B	123	TYR	0	-0.071	-0.038	60.981	-0.002	-0.002	0.000	0.000	0.000	0.000
117	B	124	PRO	0	0.026	0.027	61.423	0.001	0.001	0.000	0.000	0.000	0.000
118	B	125	GLU	-1	-0.923	-0.973	62.071	0.029	0.029	0.000	0.000	0.000	0.000
119	B	126	VAL	0	-0.013	-0.012	59.110	-0.001	-0.001	0.000	0.000	0.000	0.000
120	B	127	SER	0	0.031	0.009	57.303	0.002	0.002	0.000	0.000	0.000	0.000
121	B	128	SER	0	-0.051	-0.022	56.280	0.001	0.001	0.000	0.000	0.000	0.000
122	B	129	VAL	0	0.005	-0.001	54.991	0.001	0.001	0.000	0.000	0.000	0.000
123	B	130	VAL	0	0.061	0.026	53.204	0.001	0.001	0.000	0.000	0.000	0.000
124	B	131	ASP	-1	-0.810	-0.885	51.533	0.047	0.047	0.000	0.000	0.000	0.000
125	B	132	LYS	1	0.903	0.933	50.489	-0.031	-0.031	0.000	0.000	0.000	0.000
126	B	133	ILE	0	0.002	0.011	48.780	0.000	0.000	0.000	0.000	0.000	0.000
127	B	134	LEU	0	0.007	0.007	46.808	0.002	0.002	0.000	0.000	0.000	0.000
128	B	135	ASN	0	-0.076	-0.054	45.537	0.006	0.006	0.000	0.000	0.000	0.000
129	B	136	GLU	-1	-0.969	-0.966	45.361	0.044	0.044	0.000	0.000	0.000	0.000
130	B	137	GLY	0	0.054	0.047	42.870	0.000	0.000	0.000	0.000	0.000	0.000
131	B	138	LYS	1	0.804	0.904	40.220	-0.058	-0.058	0.000	0.000	0.000	0.000
132	B	139	VAL	0	0.024	0.014	35.721	-0.003	-0.003	0.000	0.000	0.000	0.000
133	B	140	GLU	-1	-1.009	-1.000	39.117	0.047	0.047	0.000	0.000	0.000	0.000

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