FMO DATABASE

FMODB ID: 6Y2GZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-824111.555226
FMO2-HF: Nuclear repulsion	776204.435554
FMO2-HF: Total energy	-47907.119672
FMO2-MP2: Total energy	-48041.694223

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.
-11.151	-7.403	7.164	-5.093	-5.819	-0.03

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 : 0.020 / q_NPA : 0.021

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	0.030	0.024	3.266	-2.056	1.106	-0.003	-1.798	-1.361	0.005
4	A	43	SER	0	-0.001	-0.019	4.929	1.362	1.338	-0.001	-0.010	0.035	0.000
5	A	44	HIS	0	0.002	-0.004	7.682	-0.160	-0.160	0.000	0.000	0.000	0.000
6	A	45	MET	0	-0.047	-0.008	10.647	-0.158	-0.158	0.000	0.000	0.000	0.000
7	A	46	PHE	0	0.051	0.006	12.432	-0.078	-0.078	0.000	0.000	0.000	0.000
8	A	47	ASP	-1	-0.772	-0.855	13.523	0.501	0.501	0.000	0.000	0.000	0.000
9	A	48	GLY	0	0.012	0.009	15.758	-0.027	-0.027	0.000	0.000	0.000	0.000
10	A	49	ILE	0	-0.002	0.008	18.082	-0.011	-0.011	0.000	0.000	0.000	0.000
11	A	50	SER	0	-0.012	0.000	20.238	-0.013	-0.013	0.000	0.000	0.000	0.000
12	A	51	LEU	0	-0.002	-0.002	18.385	-0.009	-0.009	0.000	0.000	0.000	0.000
13	A	52	THR	0	0.024	-0.001	23.099	-0.001	-0.001	0.000	0.000	0.000	0.000
14	A	53	GLU	-1	-0.731	-0.876	22.638	-0.080	-0.080	0.000	0.000	0.000	0.000
15	A	54	HIS	0	0.066	0.033	23.576	-0.015	-0.015	0.000	0.000	0.000	0.000
16	A	55	GLN	0	0.005	0.009	21.738	-0.010	-0.010	0.000	0.000	0.000	0.000
17	A	56	ARG	1	0.892	0.954	18.937	-0.008	-0.008	0.000	0.000	0.000	0.000
18	A	57	GLN	0	0.003	0.000	18.784	0.002	0.002	0.000	0.000	0.000	0.000
19	A	58	GLN	0	0.015	-0.001	19.166	-0.042	-0.042	0.000	0.000	0.000	0.000
20	A	59	MET	0	-0.017	-0.014	15.720	-0.045	-0.045	0.000	0.000	0.000	0.000
21	A	60	ARG	1	0.769	0.873	14.734	0.085	0.085	0.000	0.000	0.000	0.000
22	A	61	ASP	-1	-0.826	-0.904	14.754	-0.362	-0.362	0.000	0.000	0.000	0.000
23	A	62	LEU	0	-0.027	-0.015	14.191	-0.084	-0.084	0.000	0.000	0.000	0.000
24	A	63	MET	0	-0.025	-0.021	7.639	-0.178	-0.178	0.000	0.000	0.000	0.000
25	A	64	GLN	0	-0.042	-0.011	10.187	-0.192	-0.192	0.000	0.000	0.000	0.000
26	A	65	GLN	0	-0.021	-0.029	11.829	-0.065	-0.065	0.000	0.000	0.000	0.000
27	A	66	ALA	0	0.013	-0.003	8.597	-0.126	-0.126	0.000	0.000	0.000	0.000
28	A	67	ARG	1	0.807	0.881	6.248	0.267	0.267	0.000	0.000	0.000	0.000
29	A	68	HIS	0	-0.022	0.016	8.225	-0.021	-0.021	0.000	0.000	0.000	0.000
30	A	69	GLU	-1	-0.879	-0.925	10.308	-0.864	-0.864	0.000	0.000	0.000	0.000
31	A	70	GLN	0	-0.056	-0.030	2.005	-7.822	-8.420	6.287	-2.651	-3.037	-0.037
32	A	71	PRO	0	0.006	0.003	6.592	0.150	0.150	0.000	0.000	0.000	0.000
33	A	72	PRO	0	0.005	0.004	5.588	-0.479	-0.479	0.000	0.000	0.000	0.000
34	A	73	VAL	0	0.003	-0.010	5.837	0.126	0.126	0.000	0.000	0.000	0.000
35	A	74	ASN	0	0.029	0.020	7.420	-0.056	-0.056	0.000	0.000	0.000	0.000
36	A	75	VAL	0	0.042	0.006	10.121	0.074	0.074	0.000	0.000	0.000	0.000
37	A	76	SER	0	0.013	0.010	12.870	0.020	0.020	0.000	0.000	0.000	0.000
38	A	77	GLH	0	0.007	-0.015	11.732	-0.018	-0.018	0.000	0.000	0.000	0.000
39	A	78	LEU	0	0.005	0.012	9.706	0.030	0.030	0.000	0.000	0.000	0.000
40	A	79	GLU	-1	-0.831	-0.904	13.884	0.052	0.052	0.000	0.000	0.000	0.000
41	A	80	THR	0	-0.050	-0.041	17.177	-0.012	-0.012	0.000	0.000	0.000	0.000
42	A	81	MET	0	-0.003	0.004	15.130	-0.015	-0.015	0.000	0.000	0.000	0.000
43	A	82	HIS	0	0.010	0.009	17.339	0.015	0.015	0.000	0.000	0.000	0.000
44	A	83	ARG	1	0.829	0.898	18.905	-0.068	-0.068	0.000	0.000	0.000	0.000
45	A	84	LEU	0	-0.026	-0.001	20.020	-0.011	-0.011	0.000	0.000	0.000	0.000
46	A	85	VAL	0	-0.037	-0.030	18.698	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	86	THR	0	-0.074	-0.050	21.924	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	87	ALA	0	-0.008	0.011	24.520	-0.010	-0.010	0.000	0.000	0.000	0.000
49	A	88	GLU	-1	-0.925	-0.968	27.080	0.070	0.070	0.000	0.000	0.000	0.000
50	A	89	ASN	0	-0.096	-0.048	29.922	-0.005	-0.005	0.000	0.000	0.000	0.000
51	A	90	PHE	0	0.015	0.021	22.492	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	91	ASP	-1	-0.748	-0.869	26.031	0.041	0.041	0.000	0.000	0.000	0.000
53	A	92	GLU	-1	-0.819	-0.892	23.334	0.099	0.099	0.000	0.000	0.000	0.000
54	A	93	ASN	0	-0.087	-0.050	23.173	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	94	ALA	0	0.024	0.008	23.051	-0.007	-0.007	0.000	0.000	0.000	0.000
56	A	95	VAL	0	-0.012	-0.008	19.144	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	96	ARG	1	0.823	0.896	18.734	-0.056	-0.056	0.000	0.000	0.000	0.000
58	A	97	ALA	0	0.058	0.033	18.408	-0.006	-0.006	0.000	0.000	0.000	0.000
59	A	98	GLN	0	-0.037	-0.022	15.981	-0.042	-0.042	0.000	0.000	0.000	0.000
60	A	99	ALA	0	0.026	0.005	14.373	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	100	GLU	-1	-0.899	-0.957	13.616	-0.017	-0.017	0.000	0.000	0.000	0.000
62	A	101	LYS	1	0.889	0.948	14.301	0.080	0.080	0.000	0.000	0.000	0.000
63	A	102	MET	0	-0.015	-0.012	10.641	-0.077	-0.077	0.000	0.000	0.000	0.000
64	A	103	ALA	0	0.002	0.001	9.423	-0.061	-0.061	0.000	0.000	0.000	0.000
65	A	104	ASN	0	-0.034	-0.029	10.044	-0.172	-0.172	0.000	0.000	0.000	0.000
66	A	105	GLU	-1	-0.786	-0.845	7.675	-0.422	-0.422	0.000	0.000	0.000	0.000
67	A	106	GLN	0	0.017	0.020	3.353	-0.713	-0.340	0.002	-0.092	-0.284	0.000
68	A	107	ILE	0	-0.005	-0.001	6.179	-0.555	-0.555	0.000	0.000	0.000	0.000
69	A	108	ALA	0	0.014	0.013	8.652	-0.130	-0.130	0.000	0.000	0.000	0.000
70	A	109	ARG	1	0.860	0.911	2.235	0.546	1.173	0.881	-0.490	-1.019	0.002
71	A	110	GLN	0	0.010	-0.002	4.891	-0.278	-0.278	0.000	0.000	0.000	0.000
72	A	111	VAL	0	-0.002	0.003	6.271	0.363	0.363	0.000	0.000	0.000	0.000
73	A	112	GLU	-1	-0.789	-0.869	8.101	-0.845	-0.845	0.000	0.000	0.000	0.000
74	A	113	MET	0	-0.029	-0.018	4.563	-0.087	0.020	-0.001	-0.032	-0.074	0.000
75	A	114	ALA	0	-0.022	-0.011	7.700	0.437	0.437	0.000	0.000	0.000	0.000
76	A	115	LYS	1	0.828	0.905	10.587	0.983	0.983	0.000	0.000	0.000	0.000
77	A	116	VAL	0	0.057	0.026	9.930	0.144	0.144	0.000	0.000	0.000	0.000
78	A	117	ARG	1	0.898	0.945	4.498	-0.600	-0.499	-0.001	-0.020	-0.079	0.000
79	A	118	ASN	0	0.012	0.011	12.546	0.098	0.098	0.000	0.000	0.000	0.000
80	A	119	GLN	0	-0.008	-0.007	15.397	0.019	0.019	0.000	0.000	0.000	0.000
81	A	120	MET	0	-0.024	-0.016	12.207	0.004	0.004	0.000	0.000	0.000	0.000
82	A	121	TYR	0	-0.015	-0.014	16.355	0.050	0.050	0.000	0.000	0.000	0.000
83	A	122	ARG	1	0.876	0.929	18.005	0.269	0.269	0.000	0.000	0.000	0.000
84	A	123	LEU	0	-0.023	0.018	18.712	0.005	0.005	0.000	0.000	0.000	0.000
85	A	124	LEU	0	-0.054	-0.009	18.798	0.021	0.021	0.000	0.000	0.000	0.000
86	A	125	THR	0	0.005	-0.023	22.928	-0.005	-0.005	0.000	0.000	0.000	0.000
87	A	126	PRO	0	0.038	0.011	25.206	0.008	0.008	0.000	0.000	0.000	0.000
88	A	127	GLU	-1	-0.787	-0.876	26.450	0.002	0.002	0.000	0.000	0.000	0.000
89	A	128	GLN	0	-0.013	0.001	22.747	0.003	0.003	0.000	0.000	0.000	0.000
90	A	129	GLN	0	0.000	0.000	21.574	0.023	0.023	0.000	0.000	0.000	0.000
91	A	130	ALA	0	0.005	0.019	22.109	0.019	0.019	0.000	0.000	0.000	0.000
92	A	131	VAL	0	0.005	-0.003	22.272	0.019	0.019	0.000	0.000	0.000	0.000
93	A	132	LEU	0	-0.039	-0.017	16.180	0.022	0.022	0.000	0.000	0.000	0.000
94	A	133	ASN	0	-0.040	-0.043	18.907	0.045	0.045	0.000	0.000	0.000	0.000
95	A	134	GLU	-1	-0.792	-0.861	20.618	0.161	0.161	0.000	0.000	0.000	0.000
96	A	135	LYS	1	0.832	0.912	18.578	-0.166	-0.166	0.000	0.000	0.000	0.000
97	A	136	HIS	0	-0.006	-0.006	13.345	0.066	0.066	0.000	0.000	0.000	0.000
98	A	137	GLN	0	-0.045	-0.034	17.729	0.038	0.038	0.000	0.000	0.000	0.000
99	A	138	GLN	0	-0.019	-0.025	20.794	0.029	0.029	0.000	0.000	0.000	0.000
100	A	139	ARG	1	0.849	0.913	13.353	-0.457	-0.457	0.000	0.000	0.000	0.000
101	A	140	MET	0	-0.069	-0.041	13.727	0.045	0.045	0.000	0.000	0.000	0.000
102	A	141	GLU	-1	-0.810	-0.884	18.174	0.190	0.190	0.000	0.000	0.000	0.000
103	A	142	GLN	0	-0.034	-0.019	18.535	0.022	0.022	0.000	0.000	0.000	0.000
104	A	143	LEU	0	-0.078	-0.027	14.887	0.022	0.022	0.000	0.000	0.000	0.000
105	A	144	ARG	1	0.815	0.895	19.443	-0.231	-0.231	0.000	0.000	0.000	0.000
106	A	145	ASP	-1	-0.773	-0.847	23.153	0.185	0.185	0.000	0.000	0.000	0.000
107	A	146	VAL	0	-0.003	-0.013	24.349	0.018	0.018	0.000	0.000	0.000	0.000
108	A	147	THR	0	-0.050	-0.050	25.959	0.005	0.005	0.000	0.000	0.000	0.000
109	A	148	GLN	0	-0.053	-0.039	22.611	0.023	0.023	0.000	0.000	0.000	0.000
110	A	149	TRP	0	-0.084	-0.032	17.274	0.043	0.043	0.000	0.000	0.000	0.000
111	A	150	GLN	0	-0.051	-0.013	24.323	-0.012	-0.012	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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