FMO DATABASE

FMODB ID: QVV1Y

Calculation Name: 3SQF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3SQF

Chain ID: A

ChEMBL ID:

UniProt ID: P07570

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:

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	95
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-709764.522095
FMO2-HF: Nuclear repulsion	672264.380682
FMO2-HF: Total energy	-37500.141413
FMO2-MP2: Total energy	-37611.071517

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:LYS)

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

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.
-36.511	-33.31	14.285	-8.816	-8.67	-0.09

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.948 / q_NPA : 0.972

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	0.011	0.014	2.748	0.039	3.915	0.103	-1.977	-2.002	0.003
4	A	12	LEU	0	0.002	-0.005	1.768	-54.839	-56.203	14.125	-6.779	-5.982	-0.091
5	A	13	THR	0	0.046	0.031	3.447	11.125	11.272	0.024	0.064	-0.235	-0.001
6	A	14	LEU	0	-0.024	0.005	5.795	-3.483	-3.483	0.000	0.000	0.000	0.000
7	A	15	TRP	0	-0.003	-0.008	8.414	1.138	1.138	0.000	0.000	0.000	0.000
8	A	16	LEU	0	0.001	0.004	12.148	-0.599	-0.599	0.000	0.000	0.000	0.000
9	A	17	ASP	-1	-0.778	-0.890	14.737	-15.479	-15.479	0.000	0.000	0.000	0.000
10	A	18	ASP	-1	-0.836	-0.906	17.293	-15.505	-15.505	0.000	0.000	0.000	0.000
11	A	19	LYS	1	0.812	0.907	16.614	15.988	15.988	0.000	0.000	0.000	0.000
12	A	20	MET	0	-0.016	-0.002	10.463	-0.306	-0.306	0.000	0.000	0.000	0.000
13	A	21	PHE	0	0.024	0.018	11.049	1.220	1.220	0.000	0.000	0.000	0.000
14	A	22	THR	0	0.003	-0.026	6.599	-2.197	-2.197	0.000	0.000	0.000	0.000
15	A	23	GLY	0	0.029	0.022	7.174	4.656	4.656	0.000	0.000	0.000	0.000
16	A	24	LEU	0	-0.007	-0.007	6.360	-7.929	-7.929	0.000	0.000	0.000	0.000
17	A	25	ILE	0	-0.022	-0.013	3.204	2.039	2.581	0.033	-0.124	-0.451	-0.001
18	A	26	ASN	0	0.002	0.002	7.310	2.283	2.283	0.000	0.000	0.000	0.000
19	A	27	THR	0	0.051	0.017	9.836	1.775	1.775	0.000	0.000	0.000	0.000
20	A	28	GLY	0	0.020	0.025	12.401	1.758	1.758	0.000	0.000	0.000	0.000
21	A	29	ALA	0	-0.005	0.001	14.874	1.685	1.685	0.000	0.000	0.000	0.000
22	A	30	ASP	-1	-0.856	-0.936	15.615	-17.025	-17.025	0.000	0.000	0.000	0.000
23	A	31	VAL	0	-0.034	-0.005	17.269	-0.216	-0.216	0.000	0.000	0.000	0.000
24	A	32	THR	0	-0.007	-0.029	12.939	-1.292	-1.292	0.000	0.000	0.000	0.000
25	A	33	ILE	0	-0.064	-0.027	14.451	1.634	1.634	0.000	0.000	0.000	0.000
26	A	34	ILE	0	-0.004	-0.003	13.855	-1.744	-1.744	0.000	0.000	0.000	0.000
27	A	35	LYS	1	0.803	0.885	15.330	20.052	20.052	0.000	0.000	0.000	0.000
28	A	36	LEU	0	-0.019	-0.033	18.220	-0.122	-0.122	0.000	0.000	0.000	0.000
29	A	37	GLU	-1	-0.889	-0.933	19.664	-16.114	-16.114	0.000	0.000	0.000	0.000
30	A	38	ASP	-1	-0.769	-0.861	15.101	-20.292	-20.292	0.000	0.000	0.000	0.000
31	A	39	TRP	0	-0.047	-0.033	18.358	-0.809	-0.809	0.000	0.000	0.000	0.000
32	A	40	PRO	0	0.016	0.007	19.096	0.736	0.736	0.000	0.000	0.000	0.000
33	A	41	PRO	0	0.022	0.013	22.259	0.240	0.240	0.000	0.000	0.000	0.000
34	A	42	ASN	0	-0.035	-0.021	25.729	0.265	0.265	0.000	0.000	0.000	0.000
35	A	43	TRP	0	-0.023	-0.004	17.416	0.032	0.032	0.000	0.000	0.000	0.000
36	A	44	PRO	0	0.003	0.010	24.733	0.051	0.051	0.000	0.000	0.000	0.000
37	A	45	ILE	0	0.042	0.022	23.551	-0.508	-0.508	0.000	0.000	0.000	0.000
38	A	46	THR	0	-0.032	-0.019	26.283	0.546	0.546	0.000	0.000	0.000	0.000
39	A	47	ASP	-1	-0.792	-0.881	27.555	-11.183	-11.183	0.000	0.000	0.000	0.000
40	A	48	THR	0	-0.019	-0.002	25.517	0.187	0.187	0.000	0.000	0.000	0.000
41	A	49	LEU	0	0.036	0.017	28.989	-0.072	-0.072	0.000	0.000	0.000	0.000
42	A	50	THR	0	-0.026	-0.017	24.839	0.115	0.115	0.000	0.000	0.000	0.000
43	A	51	ASN	0	-0.005	-0.003	27.146	-0.161	-0.161	0.000	0.000	0.000	0.000
44	A	52	LEU	0	0.039	0.025	21.023	-0.207	-0.207	0.000	0.000	0.000	0.000
45	A	53	ARG	1	0.973	0.976	21.297	13.834	13.834	0.000	0.000	0.000	0.000
46	A	54	GLY	0	-0.033	-0.017	21.765	-0.596	-0.596	0.000	0.000	0.000	0.000
47	A	55	ILE	0	-0.012	0.005	20.537	0.039	0.039	0.000	0.000	0.000	0.000
48	A	56	GLY	0	0.030	0.021	25.064	0.224	0.224	0.000	0.000	0.000	0.000
49	A	57	GLN	0	0.043	-0.006	28.517	-0.140	-0.140	0.000	0.000	0.000	0.000
50	A	58	SER	0	0.007	0.012	30.685	-0.037	-0.037	0.000	0.000	0.000	0.000
51	A	59	ASN	0	-0.039	-0.018	24.202	0.353	0.353	0.000	0.000	0.000	0.000
52	A	60	ASN	0	-0.008	0.002	27.220	-0.426	-0.426	0.000	0.000	0.000	0.000
53	A	61	PRO	0	0.031	0.043	25.098	-0.264	-0.264	0.000	0.000	0.000	0.000
54	A	62	LYS	1	0.832	0.888	24.547	11.774	11.774	0.000	0.000	0.000	0.000
55	A	63	GLN	0	0.006	0.010	22.017	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	64	SER	0	0.057	0.030	20.875	0.635	0.635	0.000	0.000	0.000	0.000
57	A	65	SER	0	-0.035	-0.033	22.966	0.096	0.096	0.000	0.000	0.000	0.000
58	A	66	LYS	1	0.892	0.948	24.086	11.767	11.767	0.000	0.000	0.000	0.000
59	A	67	TYR	0	0.012	0.007	20.173	-0.140	-0.140	0.000	0.000	0.000	0.000
60	A	68	LEU	0	-0.012	0.009	17.405	0.423	0.423	0.000	0.000	0.000	0.000
61	A	69	THR	0	-0.001	-0.029	16.845	-0.422	-0.422	0.000	0.000	0.000	0.000
62	A	70	TRP	0	-0.034	0.002	10.083	-1.599	-1.599	0.000	0.000	0.000	0.000
63	A	71	ARG	1	0.900	0.948	12.102	20.711	20.711	0.000	0.000	0.000	0.000
64	A	72	ASP	-1	-0.739	-0.857	7.177	-33.654	-33.654	0.000	0.000	0.000	0.000
65	A	73	LYS	1	0.819	0.877	6.532	34.194	34.194	0.000	0.000	0.000	0.000
66	A	74	GLU	-1	-0.860	-0.901	8.617	-29.462	-29.462	0.000	0.000	0.000	0.000
67	A	75	ASN	0	-0.058	-0.025	11.580	2.033	2.033	0.000	0.000	0.000	0.000
68	A	76	ASN	0	-0.021	-0.015	9.879	4.078	4.078	0.000	0.000	0.000	0.000
69	A	77	SER	0	-0.043	-0.057	12.588	-0.318	-0.318	0.000	0.000	0.000	0.000
70	A	78	GLY	0	0.042	0.027	14.450	0.501	0.501	0.000	0.000	0.000	0.000
71	A	79	LEU	0	-0.025	-0.002	16.342	0.074	0.074	0.000	0.000	0.000	0.000
72	A	80	ILE	0	0.002	0.019	13.382	-0.104	-0.104	0.000	0.000	0.000	0.000
73	A	81	LYS	1	0.841	0.905	17.467	13.376	13.376	0.000	0.000	0.000	0.000
74	A	82	PRO	0	0.018	0.028	16.189	0.444	0.444	0.000	0.000	0.000	0.000
75	A	83	PHE	0	0.026	-0.011	18.307	1.085	1.085	0.000	0.000	0.000	0.000
76	A	84	VAL	0	0.001	0.005	18.720	-1.015	-1.015	0.000	0.000	0.000	0.000
77	A	85	ILE	0	-0.028	-0.009	19.915	0.876	0.876	0.000	0.000	0.000	0.000
78	A	86	PRO	0	0.055	0.034	21.405	-0.658	-0.658	0.000	0.000	0.000	0.000
79	A	87	ASN	0	-0.001	-0.027	22.886	-0.168	-0.168	0.000	0.000	0.000	0.000
80	A	88	LEU	0	-0.019	0.017	15.930	0.060	0.060	0.000	0.000	0.000	0.000
81	A	89	PRO	0	0.020	0.010	16.620	-0.246	-0.246	0.000	0.000	0.000	0.000
82	A	90	VAL	0	0.001	-0.015	11.941	-0.806	-0.806	0.000	0.000	0.000	0.000
83	A	91	ASN	0	-0.007	-0.014	11.287	2.155	2.155	0.000	0.000	0.000	0.000
84	A	92	LEU	0	-0.060	-0.027	10.966	-2.430	-2.430	0.000	0.000	0.000	0.000
85	A	93	TRP	0	-0.006	-0.008	6.583	3.811	3.811	0.000	0.000	0.000	0.000
86	A	94	GLY	0	0.071	0.035	10.457	-0.688	-0.688	0.000	0.000	0.000	0.000
87	A	95	ARG	1	0.809	0.870	12.626	17.105	17.105	0.000	0.000	0.000	0.000
88	A	96	ASP	-1	-0.788	-0.846	14.637	-20.903	-20.903	0.000	0.000	0.000	0.000
89	A	97	LEU	0	0.026	0.023	8.835	0.481	0.481	0.000	0.000	0.000	0.000
90	A	98	LEU	0	-0.024	-0.027	7.771	-0.900	-0.900	0.000	0.000	0.000	0.000
91	A	99	SER	0	-0.062	-0.039	10.848	-0.270	-0.270	0.000	0.000	0.000	0.000
92	A	100	GLN	0	-0.027	-0.026	13.222	1.239	1.239	0.000	0.000	0.000	0.000
93	A	101	MET	0	-0.045	-0.010	6.337	-1.441	-1.441	0.000	0.000	0.000	0.000
94	A	102	LYS	1	0.890	0.940	9.957	23.072	23.072	0.000	0.000	0.000	0.000
95	A	103	ILE	0	-0.016	0.001	5.891	-1.743	-1.743	0.000	0.000	0.000	0.000

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