FMO DATABASE

FMODB ID: 17N2Z

Calculation Name: 5N9J-S-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5N9J

Chain ID: S

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	171
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1471970.030366
FMO2-HF: Nuclear repulsion	1400849.904476
FMO2-HF: Total energy	-71120.12589
FMO2-MP2: Total energy	-71324.532169

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(S:9:VAL)

Summations of interaction energy for fragment #1(S:9:VAL)

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.
-1.132	1.347	0.1	-0.902	-1.678	0

Interaction energy analysis for fragmet #1(S:9:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.013 / q_NPA : -0.025

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].
3	S	11	LEU	0	0.016	0.002	3.261	-1.950	0.248	0.102	-0.880	-1.420
4	S	12	THR	0	0.024	-0.023	4.276	0.400	0.542	-0.001	-0.011	-0.131
5	S	13	SER	0	-0.131	-0.076	6.701	0.141	0.141	0.000	0.000	0.000
6	S	14	ILE	0	-0.033	0.006	4.157	-0.001	0.138	-0.001	-0.011	-0.127
7	S	15	GLN	0	-0.006	-0.006	7.370	0.001	0.001	0.000	0.000	0.000
8	S	16	TRP	0	0.010	0.005	7.948	0.021	0.021	0.000	0.000	0.000
9	S	17	ARG	1	0.976	0.981	10.495	0.287	0.287	0.000	0.000	0.000
10	S	18	MET	0	-0.041	-0.006	13.257	-0.018	-0.018	0.000	0.000	0.000
11	S	19	PRO	0	0.063	0.022	15.277	0.006	0.006	0.000	0.000	0.000
12	S	20	GLU	-1	-0.916	-0.957	18.158	-0.184	-0.184	0.000	0.000	0.000
13	S	21	TRP	0	0.055	0.000	17.234	0.016	0.016	0.000	0.000	0.000
14	S	22	VAL	0	-0.012	-0.010	18.878	0.010	0.010	0.000	0.000	0.000
15	S	23	GLN	0	0.004	0.013	21.254	0.016	0.016	0.000	0.000	0.000
16	S	24	SER	0	-0.020	-0.001	22.429	0.010	0.010	0.000	0.000	0.000
17	S	25	MET	0	-0.092	-0.032	23.342	0.009	0.009	0.000	0.000	0.000
18	S	26	GLY	0	0.032	0.008	24.804	0.012	0.012	0.000	0.000	0.000
19	S	27	GLY	0	-0.043	-0.020	25.576	-0.001	-0.001	0.000	0.000	0.000
20	S	28	LEU	0	0.014	0.001	20.594	-0.010	-0.010	0.000	0.000	0.000
21	S	29	ARG	1	0.861	0.916	24.173	0.141	0.141	0.000	0.000	0.000
22	S	30	THR	0	0.077	0.039	23.820	-0.015	-0.015	0.000	0.000	0.000
23	S	31	GLU	-1	-0.811	-0.915	23.334	-0.215	-0.215	0.000	0.000	0.000
24	S	32	ASN	0	0.020	0.020	21.090	-0.009	-0.009	0.000	0.000	0.000
25	S	33	VAL	0	0.006	0.011	19.241	-0.026	-0.026	0.000	0.000	0.000
26	S	34	LEU	0	-0.018	-0.009	18.476	-0.041	-0.041	0.000	0.000	0.000
27	S	35	GLU	-1	-0.822	-0.910	18.082	-0.304	-0.304	0.000	0.000	0.000
28	S	36	TYR	0	-0.071	-0.036	15.068	-0.047	-0.047	0.000	0.000	0.000
29	S	37	PHE	0	-0.030	-0.031	12.823	-0.061	-0.061	0.000	0.000	0.000
30	S	38	SER	0	-0.024	-0.009	13.226	-0.067	-0.067	0.000	0.000	0.000
31	S	39	GLN	0	-0.006	-0.013	13.290	-0.012	-0.012	0.000	0.000	0.000
32	S	40	SER	0	-0.038	0.004	9.885	-0.106	-0.106	0.000	0.000	0.000
33	S	41	PRO	0	-0.010	-0.022	5.020	-0.034	-0.034	0.000	0.000	0.000
34	S	42	PHE	0	-0.038	-0.013	6.697	-0.126	-0.126	0.000	0.000	0.000
35	S	43	TYR	0	-0.022	-0.036	9.123	0.029	0.029	0.000	0.000	0.000
36	S	44	SER	0	-0.057	-0.022	10.448	-0.112	-0.112	0.000	0.000	0.000
37	S	45	HIS	0	0.131	0.037	12.022	0.069	0.069	0.000	0.000	0.000
38	S	46	LYS	1	0.900	0.951	14.091	0.436	0.436	0.000	0.000	0.000
39	S	47	SER	0	-0.024	0.006	15.800	0.044	0.044	0.000	0.000	0.000
40	S	48	ASN	0	0.045	0.007	17.266	0.001	0.001	0.000	0.000	0.000
41	S	49	ASN	0	0.039	0.006	19.538	0.014	0.014	0.000	0.000	0.000
42	S	50	GLU	-1	-0.809	-0.870	17.492	-0.348	-0.348	0.000	0.000	0.000
43	S	51	MET	0	-0.036	-0.009	19.915	0.019	0.019	0.000	0.000	0.000
44	S	52	LEU	0	0.011	-0.002	22.523	0.017	0.017	0.000	0.000	0.000
45	S	53	LYS	1	0.831	0.914	18.764	0.317	0.317	0.000	0.000	0.000
46	S	54	MET	0	-0.078	-0.036	19.664	0.015	0.015	0.000	0.000	0.000
47	S	55	GLN	0	-0.061	-0.011	24.772	0.019	0.019	0.000	0.000	0.000
48	S	56	SER	0	-0.042	-0.007	27.806	0.012	0.012	0.000	0.000	0.000
49	S	57	GLN	0	0.012	0.006	28.104	-0.013	-0.013	0.000	0.000	0.000
50	S	58	PHE	0	-0.026	-0.019	29.312	0.009	0.009	0.000	0.000	0.000
51	S	59	ASN	0	-0.002	-0.015	30.998	0.005	0.005	0.000	0.000	0.000
52	S	60	ALA	0	-0.013	0.006	31.466	-0.007	-0.007	0.000	0.000	0.000
53	S	61	LEU	0	0.024	0.009	28.510	0.000	0.000	0.000	0.000	0.000
54	S	62	ASP	-1	-0.878	-0.941	32.136	-0.110	-0.110	0.000	0.000	0.000
55	S	63	LEU	0	0.043	0.020	28.390	-0.004	-0.004	0.000	0.000	0.000
56	S	64	GLY	0	-0.008	0.006	30.271	-0.005	-0.005	0.000	0.000	0.000
57	S	65	ASP	-1	-0.881	-0.952	31.505	-0.133	-0.133	0.000	0.000	0.000
58	S	66	LEU	0	0.040	0.032	24.591	-0.005	-0.005	0.000	0.000	0.000
59	S	67	ASN	0	-0.016	-0.022	27.773	-0.008	-0.008	0.000	0.000	0.000
60	S	68	SER	0	-0.057	-0.035	28.812	-0.001	-0.001	0.000	0.000	0.000
61	S	69	GLN	0	-0.020	-0.021	28.089	-0.003	-0.003	0.000	0.000	0.000
62	S	70	LEU	0	0.005	-0.001	23.655	-0.006	-0.006	0.000	0.000	0.000
63	S	71	LYS	1	0.929	0.965	26.684	0.113	0.113	0.000	0.000	0.000
64	S	72	ARG	1	0.920	0.980	28.980	0.118	0.118	0.000	0.000	0.000
65	S	73	LEU	0	-0.036	0.009	24.493	0.004	0.004	0.000	0.000	0.000
66	S	74	THR	0	0.012	0.006	25.934	0.003	0.003	0.000	0.000	0.000
67	S	75	GLY	0	-0.006	-0.010	21.979	-0.003	-0.003	0.000	0.000	0.000
68	S	76	ILE	0	-0.051	-0.021	15.543	0.001	0.001	0.000	0.000	0.000
69	S	77	GLN	0	0.026	0.014	19.025	0.008	0.008	0.000	0.000	0.000
70	S	78	PHE	0	-0.030	-0.016	13.114	-0.024	-0.024	0.000	0.000	0.000
71	S	79	VAL	0	0.045	0.027	18.841	0.017	0.017	0.000	0.000	0.000
72	S	80	ILE	0	0.050	0.010	20.503	-0.021	-0.021	0.000	0.000	0.000
73	S	81	ILE	0	-0.105	-0.044	21.343	0.014	0.014	0.000	0.000	0.000
74	S	82	HIS	0	0.007	-0.009	23.283	0.027	0.027	0.000	0.000	0.000
75	S	83	GLU	-1	-0.808	-0.912	23.738	-0.177	-0.177	0.000	0.000	0.000
76	S	84	ARG	1	0.911	0.957	25.413	0.116	0.116	0.000	0.000	0.000
77	S	85	PRO	0	0.026	0.018	26.242	-0.005	-0.005	0.000	0.000	0.000
78	S	86	PRO	0	-0.063	-0.021	27.413	-0.004	-0.004	0.000	0.000	0.000
79	S	87	PHE	0	0.033	0.010	24.575	0.000	0.000	0.000	0.000	0.000
80	S	88	LEU	0	-0.017	-0.007	21.772	-0.011	-0.011	0.000	0.000	0.000
81	S	89	TRP	0	0.011	-0.020	20.782	0.006	0.006	0.000	0.000	0.000
82	S	90	VAL	0	-0.025	-0.010	19.512	-0.014	-0.014	0.000	0.000	0.000
83	S	91	ILE	0	0.029	0.037	16.399	0.011	0.011	0.000	0.000	0.000
84	S	92	GLN	0	0.014	0.006	17.056	0.002	0.002	0.000	0.000	0.000
85	S	93	LYS	1	0.918	0.981	10.552	0.837	0.837	0.000	0.000	0.000
86	S	94	GLN	0	-0.046	-0.028	16.591	0.015	0.015	0.000	0.000	0.000
87	S	95	ASN	0	0.016	0.006	19.005	-0.006	-0.006	0.000	0.000	0.000
88	S	96	ARG	1	0.842	0.950	20.874	0.176	0.176	0.000	0.000	0.000
89	S	97	LEU	0	0.014	0.011	24.570	-0.007	-0.007	0.000	0.000	0.000
90	S	98	ASN	0	0.020	0.000	26.088	0.003	0.003	0.000	0.000	0.000
91	S	99	GLU	-1	-0.764	-0.904	28.674	-0.120	-0.120	0.000	0.000	0.000
92	S	100	ASN	0	-0.115	-0.064	30.735	0.002	0.002	0.000	0.000	0.000
93	S	101	GLU	-1	-0.959	-0.967	28.602	-0.091	-0.091	0.000	0.000	0.000
94	S	102	VAL	0	-0.014	-0.023	23.150	-0.009	-0.009	0.000	0.000	0.000
95	S	103	LYS	1	0.971	0.990	22.401	0.114	0.114	0.000	0.000	0.000
96	S	104	PRO	0	0.004	-0.020	20.255	-0.025	-0.025	0.000	0.000	0.000
97	S	105	LEU	0	-0.008	0.015	15.799	0.014	0.014	0.000	0.000	0.000
98	S	106	THR	0	-0.060	-0.032	11.558	-0.047	-0.047	0.000	0.000	0.000
99	S	107	VAL	0	-0.033	-0.016	14.848	0.033	0.033	0.000	0.000	0.000
100	S	108	TYR	0	0.043	0.015	9.378	-0.026	-0.026	0.000	0.000	0.000
101	S	109	PHE	0	-0.009	-0.007	14.128	0.055	0.055	0.000	0.000	0.000
102	S	110	VAL	0	0.063	0.032	15.070	-0.040	-0.040	0.000	0.000	0.000
103	S	111	CYS	0	-0.011	-0.015	17.633	0.040	0.040	0.000	0.000	0.000
104	S	112	ASN	0	-0.007	0.007	18.791	-0.009	-0.009	0.000	0.000	0.000
105	S	113	GLU	-1	-0.876	-0.928	19.435	-0.171	-0.171	0.000	0.000	0.000
106	S	114	ASN	0	-0.033	-0.013	15.119	-0.027	-0.027	0.000	0.000	0.000
107	S	115	ILE	0	0.001	0.017	10.331	0.011	0.011	0.000	0.000	0.000
108	S	116	TYR	0	-0.049	-0.043	11.326	-0.020	-0.020	0.000	0.000	0.000
109	S	117	MET	0	0.041	0.036	9.164	-0.072	-0.072	0.000	0.000	0.000
110	S	118	ALA	0	-0.048	-0.011	11.090	0.029	0.029	0.000	0.000	0.000
111	S	119	PRO	0	0.024	0.025	12.236	0.000	0.000	0.000	0.000	0.000
112	S	120	ASN	0	0.036	0.020	14.110	0.014	0.014	0.000	0.000	0.000
113	S	121	ALA	0	0.073	0.017	16.736	0.026	0.026	0.000	0.000	0.000
114	S	122	TYR	0	0.000	0.001	17.781	0.019	0.019	0.000	0.000	0.000
115	S	123	THR	0	0.064	0.018	13.090	0.047	0.047	0.000	0.000	0.000
116	S	124	LEU	0	0.006	0.031	16.566	0.032	0.032	0.000	0.000	0.000
117	S	125	LEU	0	0.020	0.000	17.694	0.023	0.023	0.000	0.000	0.000
118	S	126	ALA	0	0.021	0.024	18.428	0.016	0.016	0.000	0.000	0.000
119	S	127	THR	0	-0.017	-0.029	14.522	0.017	0.017	0.000	0.000	0.000
120	S	128	ARG	1	0.942	0.976	17.906	-0.014	-0.014	0.000	0.000	0.000
121	S	129	MET	0	0.032	0.016	21.012	0.004	0.004	0.000	0.000	0.000
122	S	130	LEU	0	0.010	0.021	16.883	0.005	0.005	0.000	0.000	0.000
123	S	131	ASN	0	-0.015	-0.023	17.722	-0.010	-0.010	0.000	0.000	0.000
124	S	132	ALA	0	0.034	0.026	21.285	0.002	0.002	0.000	0.000	0.000
125	S	133	THR	0	0.007	-0.014	23.648	-0.003	-0.003	0.000	0.000	0.000
126	S	134	TYR	0	-0.008	0.007	21.663	-0.005	-0.005	0.000	0.000	0.000
127	S	135	CYS	0	-0.066	-0.043	23.780	-0.003	-0.003	0.000	0.000	0.000
128	S	136	PHE	0	0.022	0.010	26.218	-0.004	-0.004	0.000	0.000	0.000
129	S	137	GLN	0	0.040	0.027	24.899	0.001	0.001	0.000	0.000	0.000
130	S	138	LYS	1	0.952	0.996	24.989	-0.148	-0.148	0.000	0.000	0.000
131	S	139	ALA	0	-0.003	-0.007	28.126	-0.005	-0.005	0.000	0.000	0.000
132	S	140	LEU	0	0.035	0.013	31.286	-0.005	-0.005	0.000	0.000	0.000
133	S	141	THR	0	-0.014	-0.029	30.045	-0.001	-0.001	0.000	0.000	0.000
134	S	142	LYS	1	0.896	0.943	31.777	-0.101	-0.101	0.000	0.000	0.000
135	S	143	ILE	0	-0.016	-0.007	33.577	-0.004	-0.004	0.000	0.000	0.000
136	S	144	GLU	-1	-0.811	-0.889	34.763	0.100	0.100	0.000	0.000	0.000
137	S	145	LYS	1	0.805	0.875	35.447	-0.105	-0.105	0.000	0.000	0.000
138	S	146	PHE	0	-0.067	-0.010	38.462	-0.003	-0.003	0.000	0.000	0.000
139	S	147	PRO	0	-0.037	0.001	40.550	-0.003	-0.003	0.000	0.000	0.000
140	S	148	GLN	0	0.041	0.013	43.526	0.001	0.001	0.000	0.000	0.000
141	S	149	TYR	0	-0.015	-0.012	46.684	-0.002	-0.002	0.000	0.000	0.000
142	S	150	ASN	0	0.021	0.012	49.044	0.000	0.000	0.000	0.000	0.000
143	S	151	PRO	0	0.007	-0.001	52.653	-0.001	-0.001	0.000	0.000	0.000
144	S	152	GLN	0	-0.057	-0.034	54.679	0.000	0.000	0.000	0.000	0.000
145	S	153	GLU	-1	-0.941	-0.964	54.570	0.039	0.039	0.000	0.000	0.000
146	S	154	GLY	0	0.000	0.013	53.120	-0.001	-0.001	0.000	0.000	0.000
147	S	155	TYR	0	-0.033	-0.027	46.302	0.001	0.001	0.000	0.000	0.000
148	S	156	THR	0	0.022	0.012	48.814	-0.002	-0.002	0.000	0.000	0.000
149	S	157	TYR	0	-0.009	-0.007	42.875	0.004	0.004	0.000	0.000	0.000
150	S	158	PRO	0	-0.008	0.005	45.103	-0.003	-0.003	0.000	0.000	0.000
151	S	192	SER	0	0.052	0.012	62.147	0.000	0.000	0.000	0.000	0.000
152	S	193	PRO	0	-0.030	-0.034	63.657	0.000	0.000	0.000	0.000	0.000
153	S	194	GLU	-1	-0.869	-0.934	65.577	0.018	0.018	0.000	0.000	0.000
154	S	195	ASP	-1	-0.836	-0.905	63.072	0.023	0.023	0.000	0.000	0.000
155	S	196	PHE	0	-0.027	-0.021	61.601	0.000	0.000	0.000	0.000	0.000
156	S	197	SER	0	0.018	0.002	63.686	-0.001	-0.001	0.000	0.000	0.000
157	S	198	VAL	0	0.023	0.018	65.187	-0.001	-0.001	0.000	0.000	0.000
158	S	199	VAL	0	-0.015	-0.005	60.161	-0.001	-0.001	0.000	0.000	0.000
159	S	200	ARG	1	0.881	0.948	62.810	-0.018	-0.018	0.000	0.000	0.000
160	S	201	ALA	0	0.038	0.022	65.415	-0.001	-0.001	0.000	0.000	0.000
161	S	202	PHE	0	-0.005	0.009	62.221	-0.001	-0.001	0.000	0.000	0.000
162	S	203	MET	0	-0.004	-0.024	57.887	0.000	0.000	0.000	0.000	0.000
163	S	204	GLN	0	0.007	0.007	63.381	-0.001	-0.001	0.000	0.000	0.000
164	S	205	SER	0	-0.003	0.011	66.670	-0.001	-0.001	0.000	0.000	0.000
165	S	206	LEU	0	-0.035	-0.019	59.738	-0.001	-0.001	0.000	0.000	0.000
166	S	207	HIS	0	-0.016	-0.025	64.335	-0.001	-0.001	0.000	0.000	0.000
167	S	208	SER	0	-0.009	0.011	65.147	-0.001	-0.001	0.000	0.000	0.000
168	S	209	SER	0	-0.017	-0.008	65.718	0.000	0.000	0.000	0.000	0.000
169	S	210	LYS	1	0.868	0.915	59.662	-0.014	-0.014	0.000	0.000	0.000
170	S	211	GLU	-1	-0.989	-0.983	64.789	0.008	0.008	0.000	0.000	0.000
171	S	212	ALA	0	-0.031	0.003	67.485	-0.001	-0.001	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(S:9:VAL)