FMO DATABASE

FMODB ID: YZKV2

Calculation Name: 3A01-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3A01

Chain ID: A

ChEMBL ID:

UniProt ID: Q06453

Base Structure: X-ray

Registration Date: 2023-09-20

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	78
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-500477.431616
FMO2-HF: Nuclear repulsion	468147.086978
FMO2-HF: Total energy	-32330.344637
FMO2-MP2: Total energy	-32426.751053

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:170:ALA)

Summations of interaction energy for fragment #1(A:170:ALA)

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.
-7.811	-5.258	0.165	-1.224	-1.494	0.005

Interaction energy analysis for fragmet #1(A:170:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.028 / q_NPA : 0.008

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	172	ARG	1	0.915	0.949	2.949	-6.678	-4.176	0.166	-1.220	-1.448	0.005
4	A	173	ILE	0	0.078	0.063	5.173	-0.536	-0.485	-0.001	-0.004	-0.046	0.000
5	A	174	GLY	0	0.013	0.005	8.557	0.140	0.140	0.000	0.000	0.000	0.000
6	A	175	HIS	0	0.045	0.018	11.757	-0.024	-0.024	0.000	0.000	0.000	0.000
7	A	176	PRO	0	0.065	0.046	15.452	-0.049	-0.049	0.000	0.000	0.000	0.000
8	A	177	TYR	0	0.002	-0.036	17.933	-0.003	-0.003	0.000	0.000	0.000	0.000
9	A	178	GLN	0	0.029	0.006	20.821	0.002	0.002	0.000	0.000	0.000	0.000
10	A	179	ASN	0	0.052	0.038	20.661	-0.023	-0.023	0.000	0.000	0.000	0.000
11	A	180	ARG	1	0.797	0.920	17.074	-0.175	-0.175	0.000	0.000	0.000	0.000
12	A	181	THR	0	0.057	0.029	23.570	-0.010	-0.010	0.000	0.000	0.000	0.000
13	A	182	PRO	0	0.001	-0.003	26.482	-0.002	-0.002	0.000	0.000	0.000	0.000
14	A	183	PRO	0	-0.022	-0.018	25.964	-0.001	-0.001	0.000	0.000	0.000	0.000
15	A	184	LYS	1	1.019	1.008	28.341	-0.078	-0.078	0.000	0.000	0.000	0.000
16	A	185	ARG	1	0.948	0.977	26.722	-0.044	-0.044	0.000	0.000	0.000	0.000
17	A	186	LYS	1	0.988	0.994	31.633	-0.053	-0.053	0.000	0.000	0.000	0.000
18	A	187	LYS	1	1.020	0.978	33.335	-0.019	-0.019	0.000	0.000	0.000	0.000
19	A	188	PRO	0	-0.022	0.025	33.125	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	189	ARG	1	1.011	1.004	29.362	0.020	0.020	0.000	0.000	0.000	0.000
21	A	190	THR	0	0.018	0.010	31.398	-0.001	-0.001	0.000	0.000	0.000	0.000
22	A	191	SER	0	-0.019	-0.022	31.915	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	192	PHE	0	-0.031	-0.004	27.653	0.002	0.002	0.000	0.000	0.000	0.000
24	A	193	THR	0	0.074	0.043	32.592	-0.005	-0.005	0.000	0.000	0.000	0.000
25	A	194	ARG	1	1.037	1.003	33.381	0.042	0.042	0.000	0.000	0.000	0.000
26	A	195	ILE	0	0.069	0.053	33.300	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	196	GLN	0	0.036	-0.002	32.002	-0.003	-0.003	0.000	0.000	0.000	0.000
28	A	197	VAL	0	-0.033	-0.024	28.159	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	198	ALA	0	0.027	0.002	28.856	-0.005	-0.005	0.000	0.000	0.000	0.000
30	A	199	GLU	-1	-0.910	-0.952	29.979	-0.052	-0.052	0.000	0.000	0.000	0.000
31	A	200	LEU	0	-0.063	-0.028	26.014	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	201	GLU	-1	-0.829	-0.919	24.042	-0.110	-0.110	0.000	0.000	0.000	0.000
33	A	202	LYS	1	0.991	1.010	25.347	0.052	0.052	0.000	0.000	0.000	0.000
34	A	203	ARG	1	0.817	0.891	24.713	0.034	0.034	0.000	0.000	0.000	0.000
35	A	204	PHE	0	-0.004	-0.009	17.332	-0.007	-0.007	0.000	0.000	0.000	0.000
36	A	205	HIS	0	-0.011	-0.013	21.264	-0.013	-0.013	0.000	0.000	0.000	0.000
37	A	206	LYS	1	0.966	0.984	22.467	0.058	0.058	0.000	0.000	0.000	0.000
38	A	207	GLN	0	0.014	0.026	21.133	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	208	LYS	1	0.925	0.978	16.513	0.181	0.181	0.000	0.000	0.000	0.000
40	A	209	TYR	0	0.001	-0.014	11.713	-0.011	-0.011	0.000	0.000	0.000	0.000
41	A	210	LEU	0	-0.002	0.012	18.589	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	211	ALA	0	0.049	0.034	21.498	0.014	0.014	0.000	0.000	0.000	0.000
43	A	212	SER	0	-0.016	-0.029	23.139	-0.007	-0.007	0.000	0.000	0.000	0.000
44	A	213	ALA	0	0.101	0.056	25.448	-0.005	-0.005	0.000	0.000	0.000	0.000
45	A	214	GLU	-1	-0.775	-0.888	24.455	-0.024	-0.024	0.000	0.000	0.000	0.000
46	A	215	ARG	1	0.845	0.922	22.705	-0.043	-0.043	0.000	0.000	0.000	0.000
47	A	216	ALA	0	0.028	0.015	26.833	-0.004	-0.004	0.000	0.000	0.000	0.000
48	A	217	ALA	0	-0.045	-0.021	30.178	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	218	LEU	0	0.003	0.003	26.749	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	219	ALA	0	0.013	-0.003	29.717	-0.003	-0.003	0.000	0.000	0.000	0.000
51	A	220	ARG	1	0.968	0.975	31.290	-0.009	-0.009	0.000	0.000	0.000	0.000
52	A	221	GLY	0	0.001	0.013	33.819	0.000	0.000	0.000	0.000	0.000	0.000
53	A	222	LEU	0	-0.020	-0.006	30.365	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	223	LYS	1	0.961	0.988	34.400	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	224	MET	0	-0.047	0.004	28.374	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	225	THR	0	0.021	-0.006	30.863	0.004	0.004	0.000	0.000	0.000	0.000
57	A	226	ASP	-1	-0.772	-0.905	28.315	0.025	0.025	0.000	0.000	0.000	0.000
58	A	227	ALA	0	-0.027	-0.013	26.293	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	228	GLN	0	0.049	0.030	25.666	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	229	VAL	0	0.089	0.062	24.988	-0.006	-0.006	0.000	0.000	0.000	0.000
61	A	230	LYS	1	0.975	0.983	20.402	-0.093	-0.093	0.000	0.000	0.000	0.000
62	A	231	THR	0	-0.045	-0.019	21.240	0.002	0.002	0.000	0.000	0.000	0.000
63	A	232	TRP	0	0.010	0.012	21.356	-0.008	-0.008	0.000	0.000	0.000	0.000
64	A	233	PHE	0	0.013	0.001	19.951	-0.013	-0.013	0.000	0.000	0.000	0.000
65	A	234	GLN	0	-0.034	-0.006	13.659	-0.006	-0.006	0.000	0.000	0.000	0.000
66	A	235	ASN	0	0.006	-0.019	16.876	-0.016	-0.016	0.000	0.000	0.000	0.000
67	A	236	ARG	1	0.851	0.938	18.513	0.118	0.118	0.000	0.000	0.000	0.000
68	A	237	ARG	1	0.896	0.919	13.898	0.016	0.016	0.000	0.000	0.000	0.000
69	A	238	THR	0	-0.030	-0.001	13.762	-0.042	-0.042	0.000	0.000	0.000	0.000
70	A	239	LYS	1	0.935	0.975	14.637	0.091	0.091	0.000	0.000	0.000	0.000
71	A	240	TRP	0	0.000	-0.010	13.445	-0.014	-0.014	0.000	0.000	0.000	0.000
72	A	241	ARG	1	0.949	0.996	9.173	0.269	0.269	0.000	0.000	0.000	0.000
73	A	242	ARG	1	0.920	0.957	12.563	0.181	0.181	0.000	0.000	0.000	0.000
74	A	243	GLN	0	0.045	0.017	14.117	0.032	0.032	0.000	0.000	0.000	0.000
75	A	244	THR	0	-0.031	-0.047	12.405	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	245	ALA	0	0.022	0.018	10.296	-0.008	-0.008	0.000	0.000	0.000	0.000
77	A	246	GLU	-1	-1.024	-0.985	12.295	-0.329	-0.329	0.000	0.000	0.000	0.000
78	A	247	GLU	-1	-0.958	-0.976	13.812	-0.527	-0.527	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:170:ALA)