FMO DATABASE

FMODB ID: 435VN

Calculation Name: 3IX0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3IX0

Chain ID: A

ChEMBL ID:

UniProt ID: P08118

Base Structure: X-ray

Registration Date: 2023-06-19

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	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	82
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-555192.077892
FMO2-HF: Nuclear repulsion	517340.75838
FMO2-HF: Total energy	-37851.319512
FMO2-MP2: Total energy	-37952.789883

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:1:SER)

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

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.
-14.178	-20.777	22.699	-9.321	-6.778	0.019

Interaction energy analysis for fragmet #1(A:1:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.022 / q_NPA : 0.035

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

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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	3	TYR	0	-0.006	0.013	3.794	0.568	3.235	-0.029	-1.440	-1.198	0.003
4	A	4	PHE	0	0.020	0.001	6.493	-0.298	-0.298	0.000	0.000	0.000	0.000
5	A	5	ILE	0	-0.030	-0.017	9.956	0.060	0.060	0.000	0.000	0.000	0.000
6	A	6	PRO	0	0.054	0.029	13.290	-0.013	-0.013	0.000	0.000	0.000	0.000
7	A	7	ASN	0	-0.041	-0.014	16.925	-0.054	-0.054	0.000	0.000	0.000	0.000
8	A	8	GLU	-1	-0.927	-0.962	18.962	-0.108	-0.108	0.000	0.000	0.000	0.000
9	A	9	GLY	0	-0.082	-0.028	21.827	0.013	0.013	0.000	0.000	0.000	0.000
10	A	17	LYS	1	0.931	0.955	23.378	0.177	0.177	0.000	0.000	0.000	0.000
11	A	18	CYS	0	-0.008	0.023	13.340	0.003	0.003	0.000	0.000	0.000	0.000
12	A	19	MET	0	-0.028	-0.018	20.231	0.009	0.009	0.000	0.000	0.000	0.000
13	A	20	ASP	-1	-0.749	-0.842	16.330	-0.459	-0.459	0.000	0.000	0.000	0.000
14	A	21	LEU	0	0.055	-0.002	13.665	0.046	0.046	0.000	0.000	0.000	0.000
15	A	22	LYS	1	0.829	0.933	17.518	0.509	0.509	0.000	0.000	0.000	0.000
16	A	23	GLY	0	0.021	0.018	20.025	0.031	0.031	0.000	0.000	0.000	0.000
17	A	24	ASN	0	-0.044	-0.016	19.743	0.058	0.058	0.000	0.000	0.000	0.000
18	A	25	LYS	1	0.959	0.968	21.152	0.173	0.173	0.000	0.000	0.000	0.000
19	A	26	HIS	1	0.812	0.885	18.360	0.414	0.414	0.000	0.000	0.000	0.000
20	A	27	PRO	0	-0.012	-0.003	21.142	0.015	0.015	0.000	0.000	0.000	0.000
21	A	28	ILE	0	0.092	0.035	20.112	-0.031	-0.031	0.000	0.000	0.000	0.000
22	A	29	ASN	0	-0.063	-0.033	18.347	0.012	0.012	0.000	0.000	0.000	0.000
23	A	30	SER	0	-0.055	-0.008	18.244	0.008	0.008	0.000	0.000	0.000	0.000
24	A	31	GLU	-1	-0.837	-0.880	12.577	-0.654	-0.654	0.000	0.000	0.000	0.000
25	A	32	TRP	0	-0.049	-0.040	13.867	0.084	0.084	0.000	0.000	0.000	0.000
26	A	33	GLN	0	0.084	0.047	12.047	-0.097	-0.097	0.000	0.000	0.000	0.000
27	A	34	THR	0	-0.050	-0.015	11.162	0.144	0.144	0.000	0.000	0.000	0.000
28	A	35	ASP	-1	-0.899	-0.969	13.718	-0.570	-0.570	0.000	0.000	0.000	0.000
29	A	36	ASN	0	-0.094	-0.071	10.406	0.217	0.217	0.000	0.000	0.000	0.000
30	A	37	CYS	0	-0.097	-0.023	9.411	-0.115	-0.115	0.000	0.000	0.000	0.000
31	A	38	GLU	-1	-0.892	-0.949	7.114	-2.051	-2.051	0.000	0.000	0.000	0.000
32	A	39	THR	0	-0.048	-0.052	7.166	0.435	0.435	0.000	0.000	0.000	0.000
33	A	40	CYS	0	-0.021	-0.003	8.255	-0.246	-0.246	0.000	0.000	0.000	0.000
34	A	41	THR	0	0.007	0.000	11.137	0.174	0.174	0.000	0.000	0.000	0.000
35	A	43	TYR	0	0.031	0.019	12.047	0.020	0.020	0.000	0.000	0.000	0.000
36	A	44	GLU	-1	-0.944	-0.994	17.474	-0.121	-0.121	0.000	0.000	0.000	0.000
37	A	45	THR	0	0.015	0.004	17.251	0.002	0.002	0.000	0.000	0.000	0.000
38	A	46	GLU	-1	-0.932	-0.965	13.444	-0.013	-0.013	0.000	0.000	0.000	0.000
39	A	47	ILE	0	-0.014	-0.028	13.019	-0.030	-0.030	0.000	0.000	0.000	0.000
40	A	48	SER	0	0.012	0.022	8.528	-0.092	-0.092	0.000	0.000	0.000	0.000
41	A	51	THR	0	0.006	0.010	1.755	2.740	1.147	5.183	-1.764	-1.826	-0.001
42	A	52	LEU	0	0.040	0.010	4.175	-0.299	-0.135	-0.001	-0.039	-0.123	0.000
43	A	53	VAL	0	-0.048	-0.021	5.920	0.585	0.585	0.000	0.000	0.000	0.000
44	A	54	SER	0	0.009	0.014	5.824	0.582	0.582	0.000	0.000	0.000	0.000
45	A	55	THR	0	-0.031	-0.037	7.362	-0.522	-0.522	0.000	0.000	0.000	0.000
46	A	56	PRO	0	-0.029	0.025	9.502	0.174	0.174	0.000	0.000	0.000	0.000
47	A	57	VAL	0	-0.003	-0.039	10.889	-0.125	-0.125	0.000	0.000	0.000	0.000
48	A	58	GLY	0	0.052	0.043	13.806	-0.061	-0.061	0.000	0.000	0.000	0.000
49	A	59	TYR	0	-0.045	-0.031	15.816	-0.010	-0.010	0.000	0.000	0.000	0.000
50	A	60	ASP	-1	-0.757	-0.877	19.828	0.083	0.083	0.000	0.000	0.000	0.000
51	A	61	LYS	1	0.941	0.961	15.968	-0.168	-0.168	0.000	0.000	0.000	0.000
52	A	62	ASP	-1	-0.898	-0.924	22.393	0.040	0.040	0.000	0.000	0.000	0.000
53	A	63	ASN	0	-0.070	-0.049	26.115	-0.020	-0.020	0.000	0.000	0.000	0.000
54	A	64	CYS	0	-0.036	0.002	22.172	-0.013	-0.013	0.000	0.000	0.000	0.000
55	A	65	GLN	0	-0.025	-0.027	20.711	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	66	ARG	1	0.900	0.964	13.328	-0.085	-0.085	0.000	0.000	0.000	0.000
57	A	67	ILE	0	-0.032	-0.022	17.761	-0.028	-0.028	0.000	0.000	0.000	0.000
58	A	68	PHE	0	0.010	-0.001	11.310	0.020	0.020	0.000	0.000	0.000	0.000
59	A	69	LYS	1	0.939	0.965	15.116	0.072	0.072	0.000	0.000	0.000	0.000
60	A	70	LYS	1	0.994	0.990	14.400	0.431	0.431	0.000	0.000	0.000	0.000
61	A	71	GLU	-1	-0.933	-0.964	14.863	-0.253	-0.253	0.000	0.000	0.000	0.000
62	A	72	ASP	-1	-0.874	-0.935	15.931	-0.163	-0.163	0.000	0.000	0.000	0.000
63	A	74	LYS	1	0.942	0.982	11.169	0.105	0.105	0.000	0.000	0.000	0.000
64	A	75	TYR	0	0.005	-0.004	10.034	-0.023	-0.023	0.000	0.000	0.000	0.000
65	A	76	ILE	0	-0.046	-0.013	14.330	0.029	0.029	0.000	0.000	0.000	0.000
66	A	77	VAL	0	0.036	0.003	16.696	-0.009	-0.009	0.000	0.000	0.000	0.000
67	A	78	VAL	0	-0.043	-0.001	19.227	0.007	0.007	0.000	0.000	0.000	0.000
68	A	79	GLU	-1	-0.848	-0.934	22.932	0.046	0.046	0.000	0.000	0.000	0.000
69	A	80	LYS	1	0.882	0.938	24.073	-0.030	-0.030	0.000	0.000	0.000	0.000
70	A	81	LYS	1	0.937	0.965	26.925	-0.038	-0.038	0.000	0.000	0.000	0.000
71	A	82	ASP	-1	-0.842	-0.934	28.779	0.001	0.001	0.000	0.000	0.000	0.000
72	A	83	PRO	0	0.030	0.020	24.941	0.006	0.006	0.000	0.000	0.000	0.000
73	A	84	LYS	1	0.911	0.950	25.210	0.020	0.020	0.000	0.000	0.000	0.000
74	A	85	LYS	1	0.881	0.961	27.353	-0.017	-0.017	0.000	0.000	0.000	0.000
75	A	86	THR	0	-0.011	-0.008	22.499	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	88	SER	0	-0.016	-0.006	21.472	0.009	0.009	0.000	0.000	0.000	0.000
77	A	89	VAL	0	-0.063	-0.037	15.488	-0.007	-0.007	0.000	0.000	0.000	0.000
78	A	90	SER	0	-0.033	-0.026	18.384	0.016	0.016	0.000	0.000	0.000	0.000
79	A	91	GLU	-1	-0.906	-0.954	12.272	0.723	0.723	0.000	0.000	0.000	0.000
80	A	92	TRP	0	0.009	-0.014	10.623	-0.128	-0.128	0.000	0.000	0.000	0.000
81	A	93	ILE	0	0.046	0.024	5.714	0.114	0.114	0.000	0.000	0.000	0.000
82	A	94	ILE	0	-0.018	-0.025	1.849	-16.199	-24.036	17.546	-6.078	-3.631	0.017

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