FMO DATABASE

FMODB ID: 766QK

Calculation Name: 5SV2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5SV2

Chain ID: A

ChEMBL ID:

UniProt ID: P9WF91

Base Structure: X-ray

Registration Date: 2023-09-21

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	135
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1234262.49356
FMO2-HF: Nuclear repulsion	1180713.920966
FMO2-HF: Total energy	-53548.572593
FMO2-MP2: Total energy	-53707.054718

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:2:THR)

Summations of interaction energy for fragment #1(A:2: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.
-5.241	-1.869	2.164	-2.491	-3.045	0.004

Interaction energy analysis for fragmet #1(A:2:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / q_NPA : 0.004

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	4	ARG	1	0.818	0.900	3.679	-3.643	-0.728	-0.015	-1.615	-1.285	0.009
4	A	5	TYR	0	-0.011	-0.035	5.334	0.542	0.542	0.000	0.000	0.000	0.000
5	A	6	LEU	0	-0.010	0.001	8.841	-0.027	-0.027	0.000	0.000	0.000	0.000
6	A	7	LEU	0	-0.020	-0.005	12.436	0.052	0.052	0.000	0.000	0.000	0.000
7	A	8	ALA	0	0.022	0.012	14.091	0.032	0.032	0.000	0.000	0.000	0.000
8	A	9	LYS	1	0.862	0.906	17.566	0.097	0.097	0.000	0.000	0.000	0.000
9	A	10	SER	0	-0.038	-0.002	20.427	-0.003	-0.003	0.000	0.000	0.000	0.000
10	A	11	ALA	0	0.056	0.034	16.065	0.012	0.012	0.000	0.000	0.000	0.000
11	A	12	ALA	0	0.029	0.011	17.792	0.004	0.004	0.000	0.000	0.000	0.000
12	A	13	TYR	0	-0.065	-0.050	18.609	0.012	0.012	0.000	0.000	0.000	0.000
13	A	14	ARG	1	0.878	0.932	20.268	0.104	0.104	0.000	0.000	0.000	0.000
14	A	15	ALA	0	0.034	0.022	18.120	0.005	0.005	0.000	0.000	0.000	0.000
15	A	16	HIS	0	-0.007	0.005	19.171	-0.003	-0.003	0.000	0.000	0.000	0.000
16	A	17	LEU	0	-0.030	-0.014	21.505	0.012	0.012	0.000	0.000	0.000	0.000
17	A	18	PRO	0	0.038	0.012	20.340	-0.010	-0.010	0.000	0.000	0.000	0.000
18	A	19	ALA	0	0.032	0.016	19.002	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	20	VAL	0	0.003	0.000	16.724	-0.008	-0.008	0.000	0.000	0.000	0.000
20	A	21	ARG	1	0.888	0.937	15.549	0.059	0.059	0.000	0.000	0.000	0.000
21	A	22	HIS	0	-0.027	-0.007	15.216	-0.019	-0.019	0.000	0.000	0.000	0.000
22	A	23	ARG	1	0.827	0.907	7.320	0.329	0.329	0.000	0.000	0.000	0.000
23	A	24	LEU	0	-0.007	-0.026	10.922	-0.054	-0.054	0.000	0.000	0.000	0.000
24	A	25	GLU	-1	-0.802	-0.887	11.649	-0.164	-0.164	0.000	0.000	0.000	0.000
25	A	26	PRO	0	0.016	0.012	9.519	-0.025	-0.025	0.000	0.000	0.000	0.000
26	A	27	LEU	0	-0.016	-0.012	5.719	-0.037	-0.037	0.000	0.000	0.000	0.000
27	A	28	MET	0	-0.041	-0.008	7.680	-0.195	-0.195	0.000	0.000	0.000	0.000
28	A	29	GLU	-1	-0.855	-0.907	10.106	-0.048	-0.048	0.000	0.000	0.000	0.000
29	A	30	ARG	1	0.796	0.890	5.144	-0.144	-0.144	0.000	0.000	0.000	0.000
30	A	31	GLY	0	0.042	0.037	6.004	-0.306	-0.306	0.000	0.000	0.000	0.000
31	A	32	LEU	0	-0.055	-0.036	2.161	-1.348	-0.891	2.179	-0.876	-1.760	-0.005
32	A	33	LEU	0	-0.011	0.005	5.764	0.149	0.149	0.000	0.000	0.000	0.000
33	A	34	ALA	0	0.038	0.014	9.352	0.031	0.031	0.000	0.000	0.000	0.000
34	A	35	ARG	1	0.832	0.913	11.434	0.306	0.306	0.000	0.000	0.000	0.000
35	A	36	CYS	0	0.035	0.029	15.213	0.013	0.013	0.000	0.000	0.000	0.000
36	A	37	GLY	0	0.075	0.028	18.022	0.005	0.005	0.000	0.000	0.000	0.000
37	A	38	ILE	0	0.038	0.011	21.305	0.003	0.003	0.000	0.000	0.000	0.000
38	A	39	THR	0	0.024	0.010	17.203	-0.005	-0.005	0.000	0.000	0.000	0.000
39	A	40	ASP	-1	-0.793	-0.881	19.135	-0.194	-0.194	0.000	0.000	0.000	0.000
40	A	41	LEU	0	-0.020	-0.002	21.456	0.010	0.010	0.000	0.000	0.000	0.000
41	A	42	GLU	-1	-0.808	-0.897	20.849	-0.120	-0.120	0.000	0.000	0.000	0.000
42	A	43	PHE	0	0.005	-0.005	20.678	0.003	0.003	0.000	0.000	0.000	0.000
43	A	44	GLY	0	0.032	0.029	23.277	0.006	0.006	0.000	0.000	0.000	0.000
44	A	45	VAL	0	-0.030	-0.020	26.250	0.008	0.008	0.000	0.000	0.000	0.000
45	A	46	SER	0	-0.082	-0.037	25.350	0.005	0.005	0.000	0.000	0.000	0.000
46	A	47	ALA	0	-0.037	-0.009	27.876	0.003	0.003	0.000	0.000	0.000	0.000
47	A	48	ARG	1	0.954	0.965	27.680	0.074	0.074	0.000	0.000	0.000	0.000
48	A	49	SER	0	0.004	-0.004	32.252	0.005	0.005	0.000	0.000	0.000	0.000
49	A	50	ARG	1	1.010	1.002	32.280	0.044	0.044	0.000	0.000	0.000	0.000
50	A	51	GLU	-1	-0.774	-0.868	31.869	-0.059	-0.059	0.000	0.000	0.000	0.000
51	A	52	ASP	-1	-0.820	-0.906	28.690	-0.078	-0.078	0.000	0.000	0.000	0.000
52	A	53	HIS	0	0.032	0.019	27.732	-0.009	-0.009	0.000	0.000	0.000	0.000
53	A	54	ARG	1	0.774	0.862	26.929	0.051	0.051	0.000	0.000	0.000	0.000
54	A	55	THR	0	0.004	0.006	25.601	-0.006	-0.006	0.000	0.000	0.000	0.000
55	A	56	LEU	0	0.012	0.009	23.533	-0.011	-0.011	0.000	0.000	0.000	0.000
56	A	57	GLY	0	-0.014	-0.005	22.120	-0.016	-0.016	0.000	0.000	0.000	0.000
57	A	58	THR	0	-0.041	-0.048	21.599	-0.012	-0.012	0.000	0.000	0.000	0.000
58	A	59	TYR	0	0.055	0.037	17.017	-0.013	-0.013	0.000	0.000	0.000	0.000
59	A	60	ARG	1	0.853	0.910	17.406	0.189	0.189	0.000	0.000	0.000	0.000
60	A	61	ARG	1	0.827	0.909	16.631	0.086	0.086	0.000	0.000	0.000	0.000
61	A	62	ASP	-1	-0.904	-0.940	16.726	-0.158	-0.158	0.000	0.000	0.000	0.000
62	A	63	ALA	0	-0.032	-0.012	14.127	-0.021	-0.021	0.000	0.000	0.000	0.000
63	A	64	LEU	0	-0.068	-0.037	11.954	-0.063	-0.063	0.000	0.000	0.000	0.000
64	A	65	GLU	-1	-0.822	-0.896	9.928	-0.452	-0.452	0.000	0.000	0.000	0.000
65	A	66	TYR	0	-0.059	-0.036	11.931	0.020	0.020	0.000	0.000	0.000	0.000
66	A	67	VAL	0	0.028	0.018	12.229	-0.016	-0.016	0.000	0.000	0.000	0.000
67	A	68	ASN	0	0.017	-0.003	15.103	0.016	0.016	0.000	0.000	0.000	0.000
68	A	69	THR	0	-0.002	0.000	18.301	-0.006	-0.006	0.000	0.000	0.000	0.000
69	A	70	PRO	0	-0.019	0.008	19.659	0.003	0.003	0.000	0.000	0.000	0.000
70	A	71	ASP	-1	-0.870	-0.946	22.616	-0.024	-0.024	0.000	0.000	0.000	0.000
71	A	72	THR	0	0.040	0.007	22.606	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	73	VAL	0	-0.031	-0.012	21.742	0.001	0.001	0.000	0.000	0.000	0.000
73	A	74	TRP	0	-0.013	-0.006	24.389	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	75	VAL	0	0.033	0.016	27.962	0.000	0.000	0.000	0.000	0.000	0.000
75	A	76	ARG	1	0.807	0.872	20.869	0.003	0.003	0.000	0.000	0.000	0.000
76	A	77	ALA	0	0.002	-0.011	25.180	0.000	0.000	0.000	0.000	0.000	0.000
77	A	78	TRP	0	-0.039	-0.022	25.975	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	79	GLU	-1	-0.845	-0.919	26.156	-0.006	-0.006	0.000	0.000	0.000	0.000
79	A	80	ILE	0	-0.023	-0.013	21.989	0.000	0.000	0.000	0.000	0.000	0.000
80	A	81	GLN	0	-0.026	-0.021	26.181	-0.003	-0.003	0.000	0.000	0.000	0.000
81	A	82	GLU	-1	-0.904	-0.945	29.057	-0.013	-0.013	0.000	0.000	0.000	0.000
82	A	83	ALA	0	0.014	0.006	27.415	0.001	0.001	0.000	0.000	0.000	0.000
83	A	84	LEU	0	-0.075	-0.040	25.618	0.000	0.000	0.000	0.000	0.000	0.000
84	A	85	THR	0	-0.042	-0.038	29.458	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	86	ASP	-1	-0.893	-0.931	33.183	-0.014	-0.014	0.000	0.000	0.000	0.000
86	A	87	LYS	1	0.880	0.930	28.342	0.019	0.019	0.000	0.000	0.000	0.000
87	A	88	GLY	0	0.007	0.013	33.331	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	89	PHE	0	0.010	-0.013	28.371	-0.002	-0.002	0.000	0.000	0.000	0.000
89	A	90	HIS	0	0.044	0.042	29.953	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	91	ARG	1	0.917	0.958	31.413	0.022	0.022	0.000	0.000	0.000	0.000
91	A	92	SER	0	-0.024	-0.013	29.393	0.001	0.001	0.000	0.000	0.000	0.000
92	A	93	VAL	0	-0.047	-0.005	25.077	-0.004	-0.004	0.000	0.000	0.000	0.000
93	A	94	LYS	1	0.782	0.879	25.140	0.070	0.070	0.000	0.000	0.000	0.000
94	A	95	ILE	0	0.093	0.033	26.259	-0.004	-0.004	0.000	0.000	0.000	0.000
95	A	96	PRO	0	0.012	-0.019	24.920	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	97	ASP	-1	-0.769	-0.875	21.991	-0.094	-0.094	0.000	0.000	0.000	0.000
97	A	98	LEU	0	0.037	0.025	21.431	-0.003	-0.003	0.000	0.000	0.000	0.000
98	A	99	ILE	0	-0.006	0.002	22.235	0.002	0.002	0.000	0.000	0.000	0.000
99	A	100	ILE	0	-0.027	-0.013	17.542	-0.004	-0.004	0.000	0.000	0.000	0.000
100	A	101	ALA	0	0.000	0.006	17.545	-0.009	-0.009	0.000	0.000	0.000	0.000
101	A	102	ALA	0	0.065	0.043	17.615	0.009	0.009	0.000	0.000	0.000	0.000
102	A	103	VAL	0	-0.028	-0.023	16.345	0.009	0.009	0.000	0.000	0.000	0.000
103	A	104	ALA	0	-0.003	-0.008	13.444	0.001	0.001	0.000	0.000	0.000	0.000
104	A	105	GLU	-1	-0.808	-0.872	13.543	0.033	0.033	0.000	0.000	0.000	0.000
105	A	106	HIS	0	-0.036	-0.018	15.107	0.043	0.043	0.000	0.000	0.000	0.000
106	A	107	HIS	0	-0.092	-0.052	12.239	0.026	0.026	0.000	0.000	0.000	0.000
107	A	108	GLY	0	-0.003	0.022	10.958	0.055	0.055	0.000	0.000	0.000	0.000
108	A	109	ILE	0	-0.063	-0.023	8.142	0.134	0.134	0.000	0.000	0.000	0.000
109	A	110	PRO	0	-0.017	-0.013	7.261	-0.026	-0.026	0.000	0.000	0.000	0.000
110	A	111	VAL	0	-0.003	0.009	10.182	-0.098	-0.098	0.000	0.000	0.000	0.000
111	A	112	MET	0	-0.033	0.008	9.519	0.011	0.011	0.000	0.000	0.000	0.000
112	A	113	HIS	0	-0.001	-0.005	12.986	-0.003	-0.003	0.000	0.000	0.000	0.000
113	A	114	TYR	0	-0.054	-0.038	16.637	0.002	0.002	0.000	0.000	0.000	0.000
114	A	115	ASP	-1	-0.825	-0.925	19.561	-0.062	-0.062	0.000	0.000	0.000	0.000
115	A	116	GLN	0	0.060	0.034	20.683	-0.003	-0.003	0.000	0.000	0.000	0.000
116	A	117	ASP	-1	-0.804	-0.901	22.420	-0.048	-0.048	0.000	0.000	0.000	0.000
117	A	118	PHE	0	-0.002	-0.010	17.654	0.001	0.001	0.000	0.000	0.000	0.000
118	A	119	GLU	-1	-0.827	-0.903	17.382	-0.063	-0.063	0.000	0.000	0.000	0.000
119	A	120	ARG	1	0.801	0.895	19.977	0.050	0.050	0.000	0.000	0.000	0.000
120	A	121	ILE	0	0.023	0.013	19.989	0.005	0.005	0.000	0.000	0.000	0.000
121	A	122	ALA	0	0.042	0.036	17.204	0.007	0.007	0.000	0.000	0.000	0.000
122	A	123	ALA	0	-0.067	-0.025	19.040	0.009	0.009	0.000	0.000	0.000	0.000
123	A	124	ILE	0	-0.047	-0.015	21.823	0.005	0.005	0.000	0.000	0.000	0.000
124	A	125	THR	0	0.007	-0.022	18.659	0.005	0.005	0.000	0.000	0.000	0.000
125	A	126	ARG	1	0.823	0.909	18.155	0.014	0.014	0.000	0.000	0.000	0.000
126	A	127	GLN	0	0.000	0.029	14.774	0.016	0.016	0.000	0.000	0.000	0.000
127	A	128	PRO	0	0.012	0.001	10.113	-0.020	-0.020	0.000	0.000	0.000	0.000
128	A	129	VAL	0	-0.013	-0.019	12.259	-0.026	-0.026	0.000	0.000	0.000	0.000
129	A	130	GLU	-1	-0.780	-0.857	8.707	-0.247	-0.247	0.000	0.000	0.000	0.000
130	A	131	TRP	0	-0.045	-0.023	12.663	-0.026	-0.026	0.000	0.000	0.000	0.000
131	A	132	VAL	0	-0.002	-0.008	13.358	-0.007	-0.007	0.000	0.000	0.000	0.000
132	A	133	VAL	0	-0.005	-0.013	14.195	0.001	0.001	0.000	0.000	0.000	0.000
133	A	134	ALA	0	0.036	0.018	16.614	0.002	0.002	0.000	0.000	0.000	0.000
134	A	135	PRO	0	0.020	0.017	18.236	0.002	0.002	0.000	0.000	0.000	0.000
135	A	136	GLY	0	-0.047	-0.023	21.070	0.007	0.007	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:THR)