FMO DATABASE

FMODB ID: V5Q81

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1473413.454521
FMO2-HF: Nuclear repulsion	1402294.984947
FMO2-HF: Total energy	-71118.469575
FMO2-MP2: Total energy	-71323.09387

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.
-0.778	1.696	0.126	-0.8	-1.799	0.001

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 : 0.002 / q_NPA : -0.019

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	S	11	LEU	0	0.018	0.001	3.412	-1.812	0.373	0.126	-0.779	-1.532	0.001
4	S	12	THR	0	0.033	-0.020	4.059	0.449	0.597	0.001	-0.011	-0.138	0.000
5	S	13	SER	0	-0.122	-0.047	6.455	0.170	0.170	0.000	0.000	0.000	0.000
6	S	14	ILE	0	-0.031	0.009	4.276	0.013	0.154	-0.001	-0.010	-0.129	0.000
7	S	15	GLN	0	0.034	0.006	7.437	-0.029	-0.029	0.000	0.000	0.000	0.000
8	S	16	TRP	0	0.012	0.029	8.188	0.010	0.010	0.000	0.000	0.000	0.000
9	S	17	ARG	1	0.960	0.960	10.447	0.305	0.305	0.000	0.000	0.000	0.000
10	S	18	MET	0	-0.064	-0.001	13.271	-0.011	-0.011	0.000	0.000	0.000	0.000
11	S	19	PRO	0	0.072	0.024	15.290	0.006	0.006	0.000	0.000	0.000	0.000
12	S	20	GLU	-1	-0.918	-0.958	18.310	-0.175	-0.175	0.000	0.000	0.000	0.000
13	S	21	TRP	0	0.041	-0.008	17.357	0.012	0.012	0.000	0.000	0.000	0.000
14	S	22	VAL	0	-0.016	-0.010	19.000	0.009	0.009	0.000	0.000	0.000	0.000
15	S	23	GLN	0	0.024	0.017	21.239	0.011	0.011	0.000	0.000	0.000	0.000
16	S	24	SER	0	-0.050	-0.015	22.188	0.013	0.013	0.000	0.000	0.000	0.000
17	S	25	MET	0	-0.075	-0.027	23.369	0.010	0.010	0.000	0.000	0.000	0.000
18	S	26	GLY	0	0.028	0.008	24.804	0.012	0.012	0.000	0.000	0.000	0.000
19	S	27	GLY	0	-0.050	-0.025	25.549	-0.001	-0.001	0.000	0.000	0.000	0.000
20	S	28	LEU	0	0.020	-0.009	20.461	-0.011	-0.011	0.000	0.000	0.000	0.000
21	S	29	ARG	1	0.867	0.933	24.152	0.151	0.151	0.000	0.000	0.000	0.000
22	S	30	THR	0	0.083	0.041	23.711	-0.016	-0.016	0.000	0.000	0.000	0.000
23	S	31	GLU	-1	-0.818	-0.926	23.160	-0.237	-0.237	0.000	0.000	0.000	0.000
24	S	32	ASN	0	0.040	0.042	20.710	-0.003	-0.003	0.000	0.000	0.000	0.000
25	S	33	VAL	0	0.006	0.013	19.246	-0.027	-0.027	0.000	0.000	0.000	0.000
26	S	34	LEU	0	-0.028	-0.011	18.358	-0.045	-0.045	0.000	0.000	0.000	0.000
27	S	35	GLU	-1	-0.856	-0.943	17.969	-0.298	-0.298	0.000	0.000	0.000	0.000
28	S	36	TYR	0	-0.039	0.000	14.950	-0.050	-0.050	0.000	0.000	0.000	0.000
29	S	37	PHE	0	-0.016	-0.028	12.900	-0.064	-0.064	0.000	0.000	0.000	0.000
30	S	38	SER	0	-0.050	-0.025	13.115	-0.070	-0.070	0.000	0.000	0.000	0.000
31	S	39	GLN	0	-0.037	-0.034	13.249	0.000	0.000	0.000	0.000	0.000	0.000
32	S	40	SER	0	-0.033	-0.009	9.982	-0.084	-0.084	0.000	0.000	0.000	0.000
33	S	41	PRO	0	-0.021	-0.022	4.934	-0.037	-0.037	0.000	0.000	0.000	0.000
34	S	42	PHE	0	-0.048	-0.016	6.342	-0.136	-0.136	0.000	0.000	0.000	0.000
35	S	43	TYR	0	0.003	0.024	8.751	0.034	0.034	0.000	0.000	0.000	0.000
36	S	44	SER	0	-0.054	-0.028	10.351	-0.115	-0.115	0.000	0.000	0.000	0.000
37	S	45	HIS	0	0.123	0.033	12.083	0.083	0.083	0.000	0.000	0.000	0.000
38	S	46	LYS	1	0.902	0.952	13.818	0.472	0.472	0.000	0.000	0.000	0.000
39	S	47	SER	0	-0.019	0.003	15.935	0.044	0.044	0.000	0.000	0.000	0.000
40	S	48	ASN	0	0.051	0.019	17.320	-0.007	-0.007	0.000	0.000	0.000	0.000
41	S	49	ASN	0	0.023	-0.007	19.384	0.030	0.030	0.000	0.000	0.000	0.000
42	S	50	GLU	-1	-0.885	-0.930	17.616	-0.363	-0.363	0.000	0.000	0.000	0.000
43	S	51	MET	0	-0.041	-0.008	19.919	0.020	0.020	0.000	0.000	0.000	0.000
44	S	52	LEU	0	0.024	0.006	22.557	0.019	0.019	0.000	0.000	0.000	0.000
45	S	53	LYS	1	0.902	0.950	19.779	0.308	0.308	0.000	0.000	0.000	0.000
46	S	54	MET	0	-0.077	-0.031	19.754	0.017	0.017	0.000	0.000	0.000	0.000
47	S	55	GLN	0	-0.033	0.004	24.721	0.015	0.015	0.000	0.000	0.000	0.000
48	S	56	SER	0	-0.073	-0.028	27.725	0.014	0.014	0.000	0.000	0.000	0.000
49	S	57	GLN	0	0.013	0.013	28.048	-0.015	-0.015	0.000	0.000	0.000	0.000
50	S	58	PHE	0	-0.036	-0.025	29.275	0.009	0.009	0.000	0.000	0.000	0.000
51	S	59	ASN	0	0.015	-0.007	30.963	0.003	0.003	0.000	0.000	0.000	0.000
52	S	60	ALA	0	-0.018	0.004	31.399	-0.007	-0.007	0.000	0.000	0.000	0.000
53	S	61	LEU	0	0.029	0.010	28.458	-0.001	-0.001	0.000	0.000	0.000	0.000
54	S	62	ASP	-1	-0.879	-0.942	32.277	-0.118	-0.118	0.000	0.000	0.000	0.000
55	S	63	LEU	0	0.017	-0.002	27.953	-0.005	-0.005	0.000	0.000	0.000	0.000
56	S	64	GLY	0	-0.022	-0.008	29.894	-0.005	-0.005	0.000	0.000	0.000	0.000
57	S	65	ASP	-1	-0.883	-0.940	31.028	-0.144	-0.144	0.000	0.000	0.000	0.000
58	S	66	LEU	0	0.084	0.045	24.215	-0.005	-0.005	0.000	0.000	0.000	0.000
59	S	67	ASN	0	-0.009	-0.004	27.344	-0.009	-0.009	0.000	0.000	0.000	0.000
60	S	68	SER	0	-0.054	-0.040	28.385	-0.002	-0.002	0.000	0.000	0.000	0.000
61	S	69	GLN	0	0.020	-0.004	26.871	-0.007	-0.007	0.000	0.000	0.000	0.000
62	S	70	LEU	0	-0.007	-0.003	23.657	-0.005	-0.005	0.000	0.000	0.000	0.000
63	S	71	LYS	1	0.875	0.939	26.511	0.141	0.141	0.000	0.000	0.000	0.000
64	S	72	ARG	1	0.945	0.991	28.740	0.127	0.127	0.000	0.000	0.000	0.000
65	S	73	LEU	0	-0.023	0.016	24.345	0.003	0.003	0.000	0.000	0.000	0.000
66	S	74	THR	0	0.009	-0.005	25.983	0.003	0.003	0.000	0.000	0.000	0.000
67	S	75	GLY	0	-0.023	-0.016	22.025	-0.002	-0.002	0.000	0.000	0.000	0.000
68	S	76	ILE	0	-0.067	-0.031	15.671	-0.001	-0.001	0.000	0.000	0.000	0.000
69	S	77	GLN	0	0.047	0.034	19.097	0.008	0.008	0.000	0.000	0.000	0.000
70	S	78	PHE	0	-0.018	-0.017	13.007	-0.023	-0.023	0.000	0.000	0.000	0.000
71	S	79	VAL	0	0.038	0.029	18.401	0.019	0.019	0.000	0.000	0.000	0.000
72	S	80	ILE	0	0.055	0.013	20.135	-0.023	-0.023	0.000	0.000	0.000	0.000
73	S	81	ILE	0	-0.093	-0.043	20.584	0.016	0.016	0.000	0.000	0.000	0.000
74	S	82	HIS	0	-0.004	-0.019	23.021	0.030	0.030	0.000	0.000	0.000	0.000
75	S	83	GLU	-1	-0.803	-0.906	23.494	-0.192	-0.192	0.000	0.000	0.000	0.000
76	S	84	ARG	1	0.908	0.963	25.254	0.131	0.131	0.000	0.000	0.000	0.000
77	S	85	PRO	0	0.026	0.013	26.123	-0.005	-0.005	0.000	0.000	0.000	0.000
78	S	86	PRO	0	-0.072	-0.023	27.328	-0.003	-0.003	0.000	0.000	0.000	0.000
79	S	87	PHE	0	0.047	0.011	24.546	0.000	0.000	0.000	0.000	0.000	0.000
80	S	88	LEU	0	-0.017	-0.006	21.595	-0.012	-0.012	0.000	0.000	0.000	0.000
81	S	89	TRP	0	0.016	-0.026	20.588	0.007	0.007	0.000	0.000	0.000	0.000
82	S	90	VAL	0	-0.034	-0.003	19.316	-0.017	-0.017	0.000	0.000	0.000	0.000
83	S	91	ILE	0	0.023	0.033	16.402	0.011	0.011	0.000	0.000	0.000	0.000
84	S	92	GLN	0	0.031	0.007	16.723	-0.002	-0.002	0.000	0.000	0.000	0.000
85	S	93	LYS	1	0.948	0.992	11.022	0.827	0.827	0.000	0.000	0.000	0.000
86	S	94	GLN	0	-0.037	-0.017	16.122	0.013	0.013	0.000	0.000	0.000	0.000
87	S	95	ASN	0	-0.016	-0.004	18.924	0.003	0.003	0.000	0.000	0.000	0.000
88	S	96	ARG	1	0.873	0.961	20.724	0.195	0.195	0.000	0.000	0.000	0.000
89	S	97	LEU	0	0.020	0.008	24.480	-0.007	-0.007	0.000	0.000	0.000	0.000
90	S	98	ASN	0	0.049	0.009	26.148	0.000	0.000	0.000	0.000	0.000	0.000
91	S	99	GLU	-1	-0.853	-0.940	28.568	-0.123	-0.123	0.000	0.000	0.000	0.000
92	S	100	ASN	0	-0.058	-0.032	30.585	0.000	0.000	0.000	0.000	0.000	0.000
93	S	101	GLU	-1	-0.957	-0.957	28.624	-0.104	-0.104	0.000	0.000	0.000	0.000
94	S	102	VAL	0	-0.025	-0.033	22.738	-0.011	-0.011	0.000	0.000	0.000	0.000
95	S	103	LYS	1	0.973	0.988	21.980	0.141	0.141	0.000	0.000	0.000	0.000
96	S	104	PRO	0	-0.001	-0.020	19.779	-0.028	-0.028	0.000	0.000	0.000	0.000
97	S	105	LEU	0	-0.020	0.004	15.482	0.011	0.011	0.000	0.000	0.000	0.000
98	S	106	THR	0	-0.055	-0.028	11.208	-0.057	-0.057	0.000	0.000	0.000	0.000
99	S	107	VAL	0	-0.020	-0.011	14.448	0.040	0.040	0.000	0.000	0.000	0.000
100	S	108	TYR	0	0.038	0.018	9.421	-0.009	-0.009	0.000	0.000	0.000	0.000
101	S	109	PHE	0	-0.030	-0.005	13.938	0.062	0.062	0.000	0.000	0.000	0.000
102	S	110	VAL	0	0.072	0.034	14.945	-0.042	-0.042	0.000	0.000	0.000	0.000
103	S	111	CYS	0	0.003	-0.017	17.529	0.042	0.042	0.000	0.000	0.000	0.000
104	S	112	ASN	0	-0.005	0.014	18.840	-0.010	-0.010	0.000	0.000	0.000	0.000
105	S	113	GLU	-1	-0.874	-0.929	19.350	-0.181	-0.181	0.000	0.000	0.000	0.000
106	S	114	ASN	0	-0.070	-0.054	15.404	-0.025	-0.025	0.000	0.000	0.000	0.000
107	S	115	ILE	0	0.003	0.014	10.062	0.021	0.021	0.000	0.000	0.000	0.000
108	S	116	TYR	0	-0.032	-0.036	11.309	-0.019	-0.019	0.000	0.000	0.000	0.000
109	S	117	MET	0	0.031	0.029	8.987	-0.077	-0.077	0.000	0.000	0.000	0.000
110	S	118	ALA	0	-0.053	-0.010	10.929	0.032	0.032	0.000	0.000	0.000	0.000
111	S	119	PRO	0	0.023	0.022	12.095	-0.003	-0.003	0.000	0.000	0.000	0.000
112	S	120	ASN	0	0.024	0.009	13.920	0.011	0.011	0.000	0.000	0.000	0.000
113	S	121	ALA	0	0.069	0.014	16.503	0.026	0.026	0.000	0.000	0.000	0.000
114	S	122	TYR	0	0.006	0.002	17.693	0.019	0.019	0.000	0.000	0.000	0.000
115	S	123	THR	0	0.092	0.039	13.031	0.046	0.046	0.000	0.000	0.000	0.000
116	S	124	LEU	0	-0.001	0.066	16.456	0.036	0.036	0.000	0.000	0.000	0.000
117	S	125	LEU	0	0.013	-0.003	17.663	0.025	0.025	0.000	0.000	0.000	0.000
118	S	126	ALA	0	0.014	0.023	18.391	0.018	0.018	0.000	0.000	0.000	0.000
119	S	127	THR	0	-0.018	-0.075	14.529	0.016	0.016	0.000	0.000	0.000	0.000
120	S	128	ARG	1	0.946	0.984	17.894	0.014	0.014	0.000	0.000	0.000	0.000
121	S	129	MET	0	0.028	0.016	20.997	0.006	0.006	0.000	0.000	0.000	0.000
122	S	130	LEU	0	0.005	0.012	16.843	0.008	0.008	0.000	0.000	0.000	0.000
123	S	131	ASN	0	-0.004	-0.020	17.909	-0.003	-0.003	0.000	0.000	0.000	0.000
124	S	132	ALA	0	0.029	0.022	21.274	0.004	0.004	0.000	0.000	0.000	0.000
125	S	133	THR	0	0.014	-0.001	23.614	-0.002	-0.002	0.000	0.000	0.000	0.000
126	S	134	TYR	0	-0.004	0.007	21.516	-0.006	-0.006	0.000	0.000	0.000	0.000
127	S	135	CYS	0	-0.080	-0.049	23.776	-0.002	-0.002	0.000	0.000	0.000	0.000
128	S	136	PHE	0	0.013	0.008	26.211	-0.003	-0.003	0.000	0.000	0.000	0.000
129	S	137	GLN	0	0.061	0.035	25.122	0.002	0.002	0.000	0.000	0.000	0.000
130	S	138	LYS	1	0.944	1.005	25.533	-0.143	-0.143	0.000	0.000	0.000	0.000
131	S	139	ALA	0	-0.015	-0.014	28.125	-0.004	-0.004	0.000	0.000	0.000	0.000
132	S	140	LEU	0	0.033	0.012	31.281	-0.005	-0.005	0.000	0.000	0.000	0.000
133	S	141	THR	0	-0.019	-0.034	30.088	-0.001	-0.001	0.000	0.000	0.000	0.000
134	S	142	LYS	1	0.869	0.929	31.264	-0.105	-0.105	0.000	0.000	0.000	0.000
135	S	143	ILE	0	-0.024	-0.011	33.577	-0.004	-0.004	0.000	0.000	0.000	0.000
136	S	144	GLU	-1	-0.884	-0.952	33.925	0.104	0.104	0.000	0.000	0.000	0.000
137	S	145	LYS	1	0.935	0.961	36.493	-0.103	-0.103	0.000	0.000	0.000	0.000
138	S	146	PHE	0	-0.059	-0.014	38.466	-0.003	-0.003	0.000	0.000	0.000	0.000
139	S	147	PRO	0	-0.039	0.014	40.551	-0.003	-0.003	0.000	0.000	0.000	0.000
140	S	148	GLN	0	0.057	0.011	43.526	0.001	0.001	0.000	0.000	0.000	0.000
141	S	149	TYR	0	-0.007	-0.009	46.686	-0.002	-0.002	0.000	0.000	0.000	0.000
142	S	150	ASN	0	0.049	0.045	49.047	0.000	0.000	0.000	0.000	0.000	0.000
143	S	151	PRO	0	0.005	-0.003	52.656	-0.001	-0.001	0.000	0.000	0.000	0.000
144	S	152	GLN	0	-0.066	-0.039	54.682	-0.001	-0.001	0.000	0.000	0.000	0.000
145	S	153	GLU	-1	-0.961	-0.992	54.571	0.039	0.039	0.000	0.000	0.000	0.000
146	S	154	GLY	0	0.006	0.016	53.120	-0.001	-0.001	0.000	0.000	0.000	0.000
147	S	155	TYR	0	-0.045	-0.032	46.594	0.002	0.002	0.000	0.000	0.000	0.000
148	S	156	THR	0	0.002	0.005	48.751	-0.003	-0.003	0.000	0.000	0.000	0.000
149	S	157	TYR	0	-0.012	-0.014	42.668	0.003	0.003	0.000	0.000	0.000	0.000
150	S	158	PRO	0	-0.009	0.008	45.113	-0.003	-0.003	0.000	0.000	0.000	0.000
151	S	192	SER	0	0.050	0.011	62.172	0.001	0.001	0.000	0.000	0.000	0.000
152	S	193	PRO	0	-0.037	-0.034	63.649	0.000	0.000	0.000	0.000	0.000	0.000
153	S	194	GLU	-1	-0.845	-0.931	65.570	0.018	0.018	0.000	0.000	0.000	0.000
154	S	195	ASP	-1	-0.816	-0.899	62.977	0.024	0.024	0.000	0.000	0.000	0.000
155	S	196	PHE	0	-0.055	-0.028	61.953	0.000	0.000	0.000	0.000	0.000	0.000
156	S	197	SER	0	0.020	0.002	63.676	-0.001	-0.001	0.000	0.000	0.000	0.000
157	S	198	VAL	0	0.026	0.021	65.004	-0.001	-0.001	0.000	0.000	0.000	0.000
158	S	199	VAL	0	-0.019	-0.008	60.099	-0.001	-0.001	0.000	0.000	0.000	0.000
159	S	200	ARG	1	0.872	0.945	62.732	-0.018	-0.018	0.000	0.000	0.000	0.000
160	S	201	ALA	0	0.040	0.026	65.360	-0.001	-0.001	0.000	0.000	0.000	0.000
161	S	202	PHE	0	-0.007	0.004	62.587	-0.001	-0.001	0.000	0.000	0.000	0.000
162	S	203	MET	0	-0.009	-0.023	57.708	0.000	0.000	0.000	0.000	0.000	0.000
163	S	204	GLN	0	0.008	0.005	63.339	-0.001	-0.001	0.000	0.000	0.000	0.000
164	S	205	SER	0	-0.003	0.014	66.595	-0.001	-0.001	0.000	0.000	0.000	0.000
165	S	206	LEU	0	-0.028	-0.018	59.849	-0.001	-0.001	0.000	0.000	0.000	0.000
166	S	207	HIS	0	-0.008	-0.017	64.124	-0.001	-0.001	0.000	0.000	0.000	0.000
167	S	208	SER	0	-0.022	-0.002	65.093	-0.001	-0.001	0.000	0.000	0.000	0.000
168	S	209	SER	0	-0.017	-0.010	65.594	0.000	0.000	0.000	0.000	0.000	0.000
169	S	210	LYS	1	0.857	0.920	60.016	-0.014	-0.014	0.000	0.000	0.000	0.000
170	S	211	GLU	-1	-0.987	-0.984	64.755	0.008	0.008	0.000	0.000	0.000	0.000
171	S	212	ALA	0	-0.021	0.008	67.427	-0.001	-0.001	0.000	0.000	0.000	0.000

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