FMO DATABASE

FMODB ID: JLMY9

Calculation Name: 5V3S-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5V3S

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0U4

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:

Apendix: None

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	146
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1340266.033771
FMO2-HF: Nuclear repulsion	1282742.993411
FMO2-HF: Total energy	-57523.040361
FMO2-MP2: Total energy	-57691.512135

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:9:GLU)

Summations of interaction energy for fragment #1(A:9:GLU)

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.
-37.545	-32.992	0.435	-1.93	-3.059	0.008

Interaction energy analysis for fragmet #1(A:9:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.923 / q_NPA : -0.966

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	11	SER	0	-0.043	-0.046	2.971	-8.993	-6.471	0.097	-1.232	-1.387	0.006
4	A	12	LYS	1	0.834	0.908	2.646	-48.163	-46.569	0.336	-0.566	-1.365	0.002
5	A	13	ILE	0	0.016	0.015	3.922	-5.456	-5.019	0.002	-0.132	-0.307	0.000
6	A	14	ARG	1	0.916	0.953	6.355	-31.815	-31.815	0.000	0.000	0.000	0.000
7	A	15	ALA	0	0.010	0.017	8.285	-2.187	-2.187	0.000	0.000	0.000	0.000
8	A	16	TYR	0	-0.015	-0.054	7.436	-1.710	-1.710	0.000	0.000	0.000	0.000
9	A	17	ALA	0	-0.006	0.014	10.238	-1.352	-1.352	0.000	0.000	0.000	0.000
10	A	18	GLN	0	-0.048	-0.020	12.395	-1.089	-1.089	0.000	0.000	0.000	0.000
11	A	19	TRP	0	-0.022	-0.023	14.444	0.789	0.789	0.000	0.000	0.000	0.000
12	A	20	MET	0	-0.004	0.018	16.459	-0.522	-0.522	0.000	0.000	0.000	0.000
13	A	21	GLU	-1	-0.815	-0.916	17.584	16.564	16.564	0.000	0.000	0.000	0.000
14	A	22	ILE	0	0.003	0.000	21.185	-0.396	-0.396	0.000	0.000	0.000	0.000
15	A	23	THR	0	-0.014	-0.011	24.910	0.037	0.037	0.000	0.000	0.000	0.000
16	A	24	ILE	0	-0.034	-0.023	27.262	-0.288	-0.288	0.000	0.000	0.000	0.000
17	A	25	PHE	0	0.016	-0.005	30.682	0.072	0.072	0.000	0.000	0.000	0.000
18	A	26	VAL	0	-0.051	-0.019	33.565	-0.142	-0.142	0.000	0.000	0.000	0.000
19	A	27	VAL	0	0.041	0.021	36.968	-0.032	-0.032	0.000	0.000	0.000	0.000
20	A	28	ASN	0	-0.046	-0.031	40.667	-0.124	-0.124	0.000	0.000	0.000	0.000
21	A	29	SER	0	0.006	-0.039	41.421	-0.222	-0.222	0.000	0.000	0.000	0.000
22	A	30	ASN	0	-0.032	0.007	39.075	0.309	0.309	0.000	0.000	0.000	0.000
23	A	31	PHE	0	0.009	0.002	36.351	-0.160	-0.160	0.000	0.000	0.000	0.000
24	A	32	LYS	1	0.849	0.922	34.920	-7.976	-7.976	0.000	0.000	0.000	0.000
25	A	33	VAL	0	0.010	0.008	28.760	-0.103	-0.103	0.000	0.000	0.000	0.000
26	A	34	GLU	-1	-0.818	-0.903	31.987	8.750	8.750	0.000	0.000	0.000	0.000
27	A	35	GLY	0	0.015	0.000	31.410	0.085	0.085	0.000	0.000	0.000	0.000
28	A	36	ALA	0	-0.012	-0.008	25.962	0.098	0.098	0.000	0.000	0.000	0.000
29	A	37	TYR	0	-0.064	-0.032	25.539	0.060	0.060	0.000	0.000	0.000	0.000
30	A	38	LEU	0	0.006	-0.003	19.045	0.149	0.149	0.000	0.000	0.000	0.000
31	A	39	ARG	1	0.799	0.897	22.640	-10.760	-10.760	0.000	0.000	0.000	0.000
32	A	40	TRP	0	0.012	0.003	18.018	0.649	0.649	0.000	0.000	0.000	0.000
33	A	41	GLY	0	0.039	0.018	15.405	-0.221	-0.221	0.000	0.000	0.000	0.000
34	A	42	LYS	1	0.769	0.884	9.867	-24.016	-24.016	0.000	0.000	0.000	0.000
35	A	43	PHE	0	0.077	0.031	16.146	0.193	0.193	0.000	0.000	0.000	0.000
36	A	44	HIS	0	-0.055	-0.048	14.682	0.837	0.837	0.000	0.000	0.000	0.000
37	A	45	VAL	0	0.017	0.009	16.675	-0.905	-0.905	0.000	0.000	0.000	0.000
38	A	46	PRO	0	0.006	0.008	16.832	0.924	0.924	0.000	0.000	0.000	0.000
39	A	47	GLY	0	-0.010	-0.001	16.465	-0.144	-0.144	0.000	0.000	0.000	0.000
40	A	48	ASP	-1	-0.873	-0.933	12.793	23.300	23.300	0.000	0.000	0.000	0.000
41	A	49	LYS	1	0.892	0.940	10.449	-21.419	-21.419	0.000	0.000	0.000	0.000
42	A	50	ASP	-1	-0.810	-0.858	7.704	34.609	34.609	0.000	0.000	0.000	0.000
43	A	51	LYS	1	0.808	0.898	10.494	-21.534	-21.534	0.000	0.000	0.000	0.000
44	A	52	GLU	-1	-0.802	-0.870	13.770	17.136	17.136	0.000	0.000	0.000	0.000
45	A	53	ILE	0	-0.062	-0.023	15.342	-0.530	-0.530	0.000	0.000	0.000	0.000
46	A	54	SER	0	0.010	-0.004	19.171	-0.171	-0.171	0.000	0.000	0.000	0.000
47	A	55	PRO	0	0.068	0.013	21.624	-0.180	-0.180	0.000	0.000	0.000	0.000
48	A	56	SER	0	-0.025	-0.029	24.305	-0.397	-0.397	0.000	0.000	0.000	0.000
49	A	57	GLN	0	-0.011	0.027	21.285	-0.127	-0.127	0.000	0.000	0.000	0.000
50	A	58	ILE	0	0.003	0.021	22.244	0.034	0.034	0.000	0.000	0.000	0.000
51	A	59	ASN	0	-0.005	0.000	26.581	-0.430	-0.430	0.000	0.000	0.000	0.000
52	A	60	GLY	0	0.029	0.021	29.861	0.083	0.083	0.000	0.000	0.000	0.000
53	A	61	THR	0	-0.061	-0.039	28.912	-0.122	-0.122	0.000	0.000	0.000	0.000
54	A	62	ILE	0	-0.016	-0.013	31.441	-0.125	-0.125	0.000	0.000	0.000	0.000
55	A	63	ILE	0	-0.031	-0.004	31.340	0.232	0.232	0.000	0.000	0.000	0.000
56	A	64	LYS	1	0.810	0.881	33.988	-8.649	-8.649	0.000	0.000	0.000	0.000
57	A	65	ASP	-1	-0.786	-0.914	36.613	7.633	7.633	0.000	0.000	0.000	0.000
58	A	66	GLU	-1	-0.969	-0.978	38.388	7.615	7.615	0.000	0.000	0.000	0.000
59	A	67	ASP	-1	-0.854	-0.884	33.355	9.022	9.022	0.000	0.000	0.000	0.000
60	A	68	SER	0	-0.075	-0.067	30.446	0.063	0.063	0.000	0.000	0.000	0.000
61	A	69	TYR	0	0.021	0.019	25.842	0.208	0.208	0.000	0.000	0.000	0.000
62	A	70	THR	0	0.013	0.003	22.634	-0.323	-0.323	0.000	0.000	0.000	0.000
63	A	71	ILE	0	0.006	0.033	22.714	0.287	0.287	0.000	0.000	0.000	0.000
64	A	72	ALA	0	0.011	0.009	18.143	-0.079	-0.079	0.000	0.000	0.000	0.000
65	A	73	SER	0	0.019	-0.002	17.227	0.184	0.184	0.000	0.000	0.000	0.000
66	A	74	CYS	0	-0.053	-0.029	11.926	0.289	0.289	0.000	0.000	0.000	0.000
67	A	75	GLY	0	0.022	0.025	12.950	-0.664	-0.664	0.000	0.000	0.000	0.000
68	A	76	ARG	1	0.776	0.855	11.322	-17.746	-17.746	0.000	0.000	0.000	0.000
69	A	77	GLU	-1	-0.765	-0.890	6.428	24.602	24.602	0.000	0.000	0.000	0.000
70	A	78	ASN	0	-0.078	-0.042	6.793	1.345	1.345	0.000	0.000	0.000	0.000
71	A	79	ALA	0	-0.008	0.010	8.629	-1.364	-1.364	0.000	0.000	0.000	0.000
72	A	80	SER	0	-0.029	-0.002	12.406	-0.713	-0.713	0.000	0.000	0.000	0.000
73	A	81	SER	0	0.026	0.012	14.337	0.897	0.897	0.000	0.000	0.000	0.000
74	A	82	GLY	0	0.006	0.003	15.358	-0.629	-0.629	0.000	0.000	0.000	0.000
75	A	83	THR	0	-0.008	-0.001	16.322	0.194	0.194	0.000	0.000	0.000	0.000
76	A	84	GLU	-1	-0.750	-0.853	18.605	10.927	10.927	0.000	0.000	0.000	0.000
77	A	85	GLY	0	0.039	0.010	22.314	0.267	0.267	0.000	0.000	0.000	0.000
78	A	86	GLY	0	0.041	0.018	24.465	-0.287	-0.287	0.000	0.000	0.000	0.000
79	A	87	PHE	0	-0.020	-0.007	26.101	0.246	0.246	0.000	0.000	0.000	0.000
80	A	88	SER	0	-0.004	-0.002	29.437	-0.172	-0.172	0.000	0.000	0.000	0.000
81	A	89	LEU	0	-0.014	0.003	32.534	0.195	0.195	0.000	0.000	0.000	0.000
82	A	90	TYR	0	0.024	0.009	34.859	-0.267	-0.267	0.000	0.000	0.000	0.000
83	A	91	ASP	-1	-0.737	-0.806	38.194	7.257	7.257	0.000	0.000	0.000	0.000
84	A	92	GLY	0	0.023	0.013	40.943	-0.206	-0.206	0.000	0.000	0.000	0.000
85	A	93	ASP	-1	-0.908	-0.958	40.749	7.258	7.258	0.000	0.000	0.000	0.000
86	A	94	LYS	1	0.829	0.916	42.816	-6.675	-6.675	0.000	0.000	0.000	0.000
87	A	95	LEU	0	-0.005	0.004	37.028	0.143	0.143	0.000	0.000	0.000	0.000
88	A	96	VAL	0	-0.026	-0.007	38.228	-0.132	-0.132	0.000	0.000	0.000	0.000
89	A	97	PHE	0	-0.013	-0.028	31.838	-0.093	-0.093	0.000	0.000	0.000	0.000
90	A	98	GLU	-1	-0.769	-0.854	33.582	8.151	8.151	0.000	0.000	0.000	0.000
91	A	99	TYR	0	-0.071	-0.072	26.132	-0.017	-0.017	0.000	0.000	0.000	0.000
92	A	100	TYR	0	-0.064	-0.049	27.357	-0.017	-0.017	0.000	0.000	0.000	0.000
93	A	101	TRP	0	-0.002	-0.008	21.190	-0.367	-0.367	0.000	0.000	0.000	0.000
94	A	102	ASP	-1	-0.840	-0.927	23.411	12.222	12.222	0.000	0.000	0.000	0.000
95	A	103	CYS	0	-0.049	-0.007	20.138	-0.256	-0.256	0.000	0.000	0.000	0.000
96	A	104	PRO	0	0.088	0.062	19.138	0.951	0.951	0.000	0.000	0.000	0.000
97	A	105	TRP	0	-0.023	-0.016	12.984	0.852	0.852	0.000	0.000	0.000	0.000
98	A	106	SER	0	-0.079	-0.050	17.365	0.254	0.254	0.000	0.000	0.000	0.000
99	A	107	GLY	0	0.032	0.013	20.328	-0.543	-0.543	0.000	0.000	0.000	0.000
100	A	108	SER	0	-0.031	-0.002	22.814	0.286	0.286	0.000	0.000	0.000	0.000
101	A	109	ASN	0	0.005	-0.020	21.673	0.266	0.266	0.000	0.000	0.000	0.000
102	A	110	SER	0	0.006	0.017	24.589	-0.563	-0.563	0.000	0.000	0.000	0.000
103	A	111	ASP	-1	-0.760	-0.865	26.582	10.710	10.710	0.000	0.000	0.000	0.000
104	A	112	GLU	-1	-0.855	-0.908	28.968	8.295	8.295	0.000	0.000	0.000	0.000
105	A	113	LEU	0	-0.055	-0.036	31.666	0.247	0.247	0.000	0.000	0.000	0.000
106	A	114	THR	0	0.003	0.013	34.057	-0.322	-0.322	0.000	0.000	0.000	0.000
107	A	115	VAL	0	-0.010	-0.017	37.082	-0.025	-0.025	0.000	0.000	0.000	0.000
108	A	116	LYS	1	0.805	0.878	38.942	-7.919	-7.919	0.000	0.000	0.000	0.000
109	A	117	ASP	-1	-0.765	-0.856	41.485	6.500	6.500	0.000	0.000	0.000	0.000
110	A	118	LYS	1	0.909	0.938	41.745	-7.153	-7.153	0.000	0.000	0.000	0.000
111	A	119	GLU	-1	-0.924	-0.942	44.915	6.076	6.076	0.000	0.000	0.000	0.000
112	A	120	ASN	0	-0.003	-0.030	46.536	-0.141	-0.141	0.000	0.000	0.000	0.000
113	A	121	TYR	0	-0.034	-0.045	41.846	0.023	0.023	0.000	0.000	0.000	0.000
114	A	122	THR	0	-0.035	-0.011	41.946	-0.130	-0.130	0.000	0.000	0.000	0.000
115	A	123	VAL	0	0.008	0.004	36.476	0.118	0.118	0.000	0.000	0.000	0.000
116	A	124	ILE	0	-0.037	-0.016	36.509	-0.061	-0.061	0.000	0.000	0.000	0.000
117	A	125	LYS	1	0.854	0.933	29.547	-9.865	-9.865	0.000	0.000	0.000	0.000
118	A	126	LYS	1	0.846	0.913	31.574	-9.017	-9.017	0.000	0.000	0.000	0.000
119	A	127	GLY	0	0.092	0.051	27.906	0.275	0.275	0.000	0.000	0.000	0.000
120	A	128	GLY	0	0.041	0.018	26.229	-0.314	-0.314	0.000	0.000	0.000	0.000
121	A	129	GLY	0	-0.010	-0.007	27.267	-0.194	-0.194	0.000	0.000	0.000	0.000
122	A	130	SER	0	-0.026	-0.042	27.250	0.127	0.127	0.000	0.000	0.000	0.000
123	A	131	PRO	0	-0.033	0.009	24.060	-0.223	-0.223	0.000	0.000	0.000	0.000
124	A	132	SER	0	-0.001	-0.009	23.860	0.088	0.088	0.000	0.000	0.000	0.000
125	A	133	GLY	0	-0.011	-0.006	19.830	0.200	0.200	0.000	0.000	0.000	0.000
126	A	134	ALA	0	0.010	0.017	17.113	-0.111	-0.111	0.000	0.000	0.000	0.000
127	A	135	MET	0	-0.036	0.013	18.986	-0.609	-0.609	0.000	0.000	0.000	0.000
128	A	136	GLY	0	-0.009	0.001	19.854	-0.495	-0.495	0.000	0.000	0.000	0.000
129	A	137	ASN	0	-0.011	-0.022	20.845	0.289	0.289	0.000	0.000	0.000	0.000
130	A	138	ILE	0	-0.021	-0.014	23.306	-0.435	-0.435	0.000	0.000	0.000	0.000
131	A	139	PHE	0	-0.020	-0.012	26.290	0.112	0.112	0.000	0.000	0.000	0.000
132	A	140	ILE	0	-0.003	-0.004	29.271	-0.257	-0.257	0.000	0.000	0.000	0.000
133	A	141	THR	0	-0.027	0.005	32.217	-0.015	-0.015	0.000	0.000	0.000	0.000
134	A	142	VAL	0	0.013	-0.007	35.405	-0.110	-0.110	0.000	0.000	0.000	0.000
135	A	143	VAL	0	0.020	0.008	38.027	0.006	0.006	0.000	0.000	0.000	0.000
136	A	144	LYS	1	0.847	0.909	41.650	-7.009	-7.009	0.000	0.000	0.000	0.000
137	A	145	LYS	1	0.771	0.893	44.202	-6.668	-6.668	0.000	0.000	0.000	0.000
138	A	146	SER	0	0.051	0.031	47.384	-0.027	-0.027	0.000	0.000	0.000	0.000
139	A	147	LEU	0	0.006	0.009	49.966	-0.048	-0.048	0.000	0.000	0.000	0.000
140	A	148	GLU	-1	-0.888	-0.953	53.072	5.907	5.907	0.000	0.000	0.000	0.000
141	A	149	HIS	0	-0.060	-0.029	48.845	-0.057	-0.057	0.000	0.000	0.000	0.000
142	A	150	HIS	0	0.005	-0.017	46.921	-0.058	-0.058	0.000	0.000	0.000	0.000
143	A	151	HIS	0	-0.061	-0.023	52.040	-0.071	-0.071	0.000	0.000	0.000	0.000
144	A	152	HIS	0	0.004	-0.001	50.445	-0.086	-0.086	0.000	0.000	0.000	0.000
145	A	153	HIS	0	-0.023	-0.011	52.280	0.032	0.032	0.000	0.000	0.000	0.000
146	A	154	HIS	0	-0.021	0.011	55.207	-0.081	-0.081	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:9:GLU)