FMO DATABASE

FMODB ID: 767MK

Calculation Name: 3ITF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ITF

Chain ID: A

ChEMBL ID:

UniProt ID: P0AE85

Base Structure: X-ray

Registration Date: 2023-09-23

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	111
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-820386.451
FMO2-HF: Nuclear repulsion	772480.156981
FMO2-HF: Total energy	-47906.294019
FMO2-MP2: Total energy	-48040.956639

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:40:SER)

Summations of interaction energy for fragment #1(A:40: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.
-15.211	-13.778	11.779	-7.011	-6.2	-0.052

Interaction energy analysis for fragmet #1(A:40:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.031 / q_NPA : -0.019

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	42	GLN	0	0.014	0.019	2.876	-2.856	0.602	0.010	-1.823	-1.645	-0.001
4	A	43	SER	0	0.002	-0.008	4.824	1.783	1.783	-0.001	-0.008	0.010	0.000
5	A	44	HIS	0	0.016	0.000	7.630	-0.200	-0.200	0.000	0.000	0.000	0.000
6	A	45	MET	0	-0.060	-0.019	10.598	-0.179	-0.179	0.000	0.000	0.000	0.000
7	A	46	PHE	0	0.022	-0.007	12.391	-0.113	-0.113	0.000	0.000	0.000	0.000
8	A	47	ASP	-1	-0.834	-0.905	13.033	0.707	0.707	0.000	0.000	0.000	0.000
9	A	48	GLY	0	-0.051	-0.037	15.443	-0.025	-0.025	0.000	0.000	0.000	0.000
10	A	49	ILE	0	-0.004	0.012	18.143	-0.034	-0.034	0.000	0.000	0.000	0.000
11	A	50	SER	0	-0.032	-0.013	20.180	-0.018	-0.018	0.000	0.000	0.000	0.000
12	A	51	LEU	0	-0.008	-0.001	18.113	-0.006	-0.006	0.000	0.000	0.000	0.000
13	A	52	THR	0	0.039	0.013	22.754	-0.016	-0.016	0.000	0.000	0.000	0.000
14	A	53	GLU	-1	-0.866	-0.947	23.638	-0.009	-0.009	0.000	0.000	0.000	0.000
15	A	54	HIS	0	0.057	0.020	23.677	-0.014	-0.014	0.000	0.000	0.000	0.000
16	A	55	GLN	0	-0.011	-0.009	21.573	-0.010	-0.010	0.000	0.000	0.000	0.000
17	A	56	ARG	1	0.962	0.980	17.759	-0.115	-0.115	0.000	0.000	0.000	0.000
18	A	57	GLN	0	0.026	0.026	18.740	0.002	0.002	0.000	0.000	0.000	0.000
19	A	58	GLN	0	0.026	0.012	19.146	-0.040	-0.040	0.000	0.000	0.000	0.000
20	A	59	MET	0	-0.015	-0.012	15.737	-0.033	-0.033	0.000	0.000	0.000	0.000
21	A	60	ARG	1	0.845	0.925	14.607	0.062	0.062	0.000	0.000	0.000	0.000
22	A	61	ASP	-1	-0.840	-0.921	14.536	-0.291	-0.291	0.000	0.000	0.000	0.000
23	A	62	LEU	0	-0.033	-0.024	14.391	-0.073	-0.073	0.000	0.000	0.000	0.000
24	A	63	MET	0	-0.027	-0.018	7.604	-0.089	-0.089	0.000	0.000	0.000	0.000
25	A	64	GLN	0	-0.045	-0.014	10.147	-0.213	-0.213	0.000	0.000	0.000	0.000
26	A	65	GLN	0	-0.003	-0.004	11.932	-0.138	-0.138	0.000	0.000	0.000	0.000
27	A	66	ALA	0	0.024	0.003	8.614	-0.108	-0.108	0.000	0.000	0.000	0.000
28	A	67	ARG	1	0.834	0.907	6.321	0.484	0.484	0.000	0.000	0.000	0.000
29	A	68	HIS	0	-0.030	0.005	8.111	-0.258	-0.258	0.000	0.000	0.000	0.000
30	A	69	GLU	-1	-0.882	-0.944	9.950	-0.763	-0.763	0.000	0.000	0.000	0.000
31	A	70	GLN	0	-0.069	-0.019	1.859	-9.480	-12.578	11.260	-4.676	-3.486	-0.053
32	A	71	PRO	0	-0.012	-0.006	6.496	-0.101	-0.101	0.000	0.000	0.000	0.000
33	A	72	PRO	0	0.019	0.004	5.722	-0.967	-0.967	0.000	0.000	0.000	0.000
34	A	73	VAL	0	0.001	-0.011	5.245	-0.044	-0.044	0.000	0.000	0.000	0.000
35	A	74	ASN	0	0.008	0.015	6.962	0.434	0.434	0.000	0.000	0.000	0.000
36	A	75	VAL	0	0.057	0.009	9.831	0.137	0.137	0.000	0.000	0.000	0.000
37	A	76	SER	0	0.019	0.023	12.160	0.126	0.126	0.000	0.000	0.000	0.000
38	A	77	GLH	0	-0.058	-0.081	10.965	0.125	0.125	0.000	0.000	0.000	0.000
39	A	78	LEU	0	-0.011	0.005	9.635	0.088	0.088	0.000	0.000	0.000	0.000
40	A	79	GLU	-1	-0.932	-0.966	13.290	-0.297	-0.297	0.000	0.000	0.000	0.000
41	A	80	THR	0	-0.074	-0.036	16.543	0.060	0.060	0.000	0.000	0.000	0.000
42	A	81	MET	0	0.001	-0.002	15.088	0.045	0.045	0.000	0.000	0.000	0.000
43	A	82	HIS	0	-0.002	0.006	17.035	0.041	0.041	0.000	0.000	0.000	0.000
44	A	83	ARG	1	0.959	0.971	18.647	0.246	0.246	0.000	0.000	0.000	0.000
45	A	84	LEU	0	-0.017	0.001	19.551	0.015	0.015	0.000	0.000	0.000	0.000
46	A	85	VAL	0	-0.041	-0.025	18.887	0.019	0.019	0.000	0.000	0.000	0.000
47	A	86	THR	0	-0.089	-0.052	21.949	0.011	0.011	0.000	0.000	0.000	0.000
48	A	87	ALA	0	-0.018	0.011	24.524	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	88	GLU	-1	-0.928	-0.970	26.734	-0.020	-0.020	0.000	0.000	0.000	0.000
50	A	89	ASN	0	-0.049	-0.019	29.785	0.014	0.014	0.000	0.000	0.000	0.000
51	A	90	PHE	0	-0.002	0.007	22.766	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	91	ASP	-1	-0.797	-0.904	25.860	-0.023	-0.023	0.000	0.000	0.000	0.000
53	A	92	GLU	-1	-0.856	-0.934	24.004	0.070	0.070	0.000	0.000	0.000	0.000
54	A	93	ASN	0	-0.031	-0.019	23.563	0.014	0.014	0.000	0.000	0.000	0.000
55	A	94	ALA	0	0.005	0.017	23.368	-0.006	-0.006	0.000	0.000	0.000	0.000
56	A	95	VAL	0	-0.011	-0.012	19.137	-0.018	-0.018	0.000	0.000	0.000	0.000
57	A	96	ARG	1	0.875	0.927	18.874	-0.073	-0.073	0.000	0.000	0.000	0.000
58	A	97	ALA	0	0.055	0.040	18.966	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	98	GLN	0	-0.028	-0.025	15.555	-0.083	-0.083	0.000	0.000	0.000	0.000
60	A	99	ALA	0	0.027	-0.002	14.564	-0.042	-0.042	0.000	0.000	0.000	0.000
61	A	100	GLU	-1	-0.927	-0.968	14.173	0.023	0.023	0.000	0.000	0.000	0.000
62	A	101	LYS	1	0.916	0.965	14.608	0.305	0.305	0.000	0.000	0.000	0.000
63	A	102	MET	0	-0.022	-0.013	10.542	-0.042	-0.042	0.000	0.000	0.000	0.000
64	A	103	ALA	0	-0.007	0.002	9.936	-0.042	-0.042	0.000	0.000	0.000	0.000
65	A	104	ASN	0	0.023	0.003	11.118	0.085	0.085	0.000	0.000	0.000	0.000
66	A	105	GLU	-1	-0.793	-0.860	8.090	-1.003	-1.003	0.000	0.000	0.000	0.000
67	A	106	GLN	0	-0.018	-0.010	4.663	-0.136	-0.056	-0.001	-0.004	-0.075	0.000
68	A	107	ILE	0	0.007	0.006	7.279	0.229	0.229	0.000	0.000	0.000	0.000
69	A	108	ALA	0	0.012	0.011	9.118	0.047	0.047	0.000	0.000	0.000	0.000
70	A	109	ARG	1	0.936	0.975	2.440	-0.116	0.810	0.512	-0.491	-0.948	0.002
71	A	110	GLN	0	-0.010	-0.013	5.328	0.190	0.190	0.000	0.000	0.000	0.000
72	A	111	VAL	0	-0.019	-0.006	7.166	0.040	0.040	0.000	0.000	0.000	0.000
73	A	112	GLU	-1	-0.879	-0.934	8.119	-0.444	-0.444	0.000	0.000	0.000	0.000
74	A	113	MET	0	-0.039	-0.036	4.963	-0.320	-0.320	0.000	0.000	0.000	0.000
75	A	114	ALA	0	-0.020	-0.006	8.298	0.224	0.224	0.000	0.000	0.000	0.000
76	A	115	LYS	1	0.939	0.980	10.947	0.234	0.234	0.000	0.000	0.000	0.000
77	A	116	VAL	0	0.054	0.025	9.463	0.059	0.059	0.000	0.000	0.000	0.000
78	A	117	ARG	1	0.939	0.968	4.837	-2.115	-2.048	-0.001	-0.009	-0.056	0.000
79	A	118	ASN	0	0.002	0.008	12.669	-0.034	-0.034	0.000	0.000	0.000	0.000
80	A	119	GLN	0	0.012	0.012	15.678	-0.023	-0.023	0.000	0.000	0.000	0.000
81	A	120	MET	0	-0.030	-0.020	12.185	-0.013	-0.013	0.000	0.000	0.000	0.000
82	A	121	TYR	0	0.022	0.007	16.518	0.011	0.011	0.000	0.000	0.000	0.000
83	A	122	ARG	1	0.874	0.929	18.155	-0.056	-0.056	0.000	0.000	0.000	0.000
84	A	123	LEU	0	-0.002	0.023	19.089	-0.016	-0.016	0.000	0.000	0.000	0.000
85	A	124	LEU	0	-0.090	-0.024	18.773	-0.002	-0.002	0.000	0.000	0.000	0.000
86	A	125	THR	0	0.037	0.015	22.798	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	126	PRO	0	0.066	0.027	25.046	0.020	0.020	0.000	0.000	0.000	0.000
88	A	127	GLU	-1	-0.861	-0.940	26.303	0.131	0.131	0.000	0.000	0.000	0.000
89	A	128	GLN	0	-0.006	-0.003	22.574	0.012	0.012	0.000	0.000	0.000	0.000
90	A	129	GLN	0	-0.041	-0.026	21.533	0.033	0.033	0.000	0.000	0.000	0.000
91	A	130	ALA	0	0.013	0.009	22.080	0.034	0.034	0.000	0.000	0.000	0.000
92	A	131	VAL	0	0.007	0.007	22.028	0.021	0.021	0.000	0.000	0.000	0.000
93	A	132	LEU	0	-0.036	-0.015	16.288	0.026	0.026	0.000	0.000	0.000	0.000
94	A	133	ASN	0	-0.024	-0.031	18.900	0.091	0.091	0.000	0.000	0.000	0.000
95	A	134	GLU	-1	-0.886	-0.928	20.643	0.325	0.325	0.000	0.000	0.000	0.000
96	A	135	LYS	1	0.932	0.963	18.717	-0.332	-0.332	0.000	0.000	0.000	0.000
97	A	136	HIS	0	-0.045	-0.020	13.391	0.078	0.078	0.000	0.000	0.000	0.000
98	A	137	GLN	0	-0.026	-0.011	17.670	0.046	0.046	0.000	0.000	0.000	0.000
99	A	138	GLN	0	0.035	0.009	20.735	0.019	0.019	0.000	0.000	0.000	0.000
100	A	139	ARG	1	0.946	0.984	13.643	-0.765	-0.765	0.000	0.000	0.000	0.000
101	A	140	MET	0	-0.105	-0.064	13.917	0.042	0.042	0.000	0.000	0.000	0.000
102	A	141	GLU	-1	-0.894	-0.944	18.305	0.327	0.327	0.000	0.000	0.000	0.000
103	A	142	GLN	0	0.022	0.018	18.154	0.004	0.004	0.000	0.000	0.000	0.000
104	A	143	LEU	0	-0.074	-0.029	14.905	0.001	0.001	0.000	0.000	0.000	0.000
105	A	144	ARG	1	0.892	0.946	19.441	-0.439	-0.439	0.000	0.000	0.000	0.000
106	A	145	ASP	-1	-0.752	-0.844	23.011	0.263	0.263	0.000	0.000	0.000	0.000
107	A	146	VAL	0	-0.008	-0.013	24.591	0.013	0.013	0.000	0.000	0.000	0.000
108	A	147	THR	0	-0.046	-0.033	26.366	-0.003	-0.003	0.000	0.000	0.000	0.000
109	A	148	GLN	0	-0.069	-0.043	22.831	0.016	0.016	0.000	0.000	0.000	0.000
110	A	149	TRP	0	-0.099	-0.048	17.675	0.034	0.034	0.000	0.000	0.000	0.000
111	A	150	GLN	0	-0.043	-0.010	24.468	-0.010	-0.010	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:40:SER)