FMO DATABASE

FMODB ID: 2NQLR

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	OptHSide
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	-820671.302212
FMO2-HF: Nuclear repulsion	772764.36733
FMO2-HF: Total energy	-47906.934881
FMO2-MP2: Total energy	-48041.559235

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.
-13.634	-9.357	8.613	-6.522	-6.367	-0.028

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 : 0.012 / q_NPA : 0.016

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	0.003	0.014	2.895	-4.493	0.644	0.006	-2.875	-2.268	0.009
4	A	43	SER	0	-0.003	-0.017	4.834	1.428	1.420	-0.001	-0.008	0.017	0.000
5	A	44	HIS	0	0.014	0.003	7.646	-0.107	-0.107	0.000	0.000	0.000	0.000
6	A	45	MET	0	-0.048	-0.010	10.676	-0.155	-0.155	0.000	0.000	0.000	0.000
7	A	46	PHE	0	0.039	0.001	12.525	-0.079	-0.079	0.000	0.000	0.000	0.000
8	A	47	ASP	-1	-0.801	-0.885	13.052	0.508	0.508	0.000	0.000	0.000	0.000
9	A	48	GLY	0	-0.030	-0.031	15.455	-0.021	-0.021	0.000	0.000	0.000	0.000
10	A	49	ILE	0	-0.015	0.008	18.103	-0.020	-0.020	0.000	0.000	0.000	0.000
11	A	50	SER	0	-0.024	-0.009	20.192	-0.010	-0.010	0.000	0.000	0.000	0.000
12	A	51	LEU	0	-0.012	-0.002	18.076	-0.010	-0.010	0.000	0.000	0.000	0.000
13	A	52	THR	0	0.034	0.003	22.766	-0.002	-0.002	0.000	0.000	0.000	0.000
14	A	53	GLU	-1	-0.816	-0.916	23.268	-0.072	-0.072	0.000	0.000	0.000	0.000
15	A	54	HIS	0	0.056	0.024	23.687	-0.013	-0.013	0.000	0.000	0.000	0.000
16	A	55	GLN	0	0.011	0.012	21.575	-0.009	-0.009	0.000	0.000	0.000	0.000
17	A	56	ARG	1	0.935	0.971	18.316	-0.027	-0.027	0.000	0.000	0.000	0.000
18	A	57	GLN	0	0.018	0.009	18.760	0.002	0.002	0.000	0.000	0.000	0.000
19	A	58	GLN	0	0.011	0.001	19.161	-0.042	-0.042	0.000	0.000	0.000	0.000
20	A	59	MET	0	-0.020	-0.014	15.799	-0.044	-0.044	0.000	0.000	0.000	0.000
21	A	60	ARG	1	0.804	0.888	14.636	0.080	0.080	0.000	0.000	0.000	0.000
22	A	61	ASP	-1	-0.820	-0.899	14.547	-0.352	-0.352	0.000	0.000	0.000	0.000
23	A	62	LEU	0	-0.028	-0.018	14.401	-0.077	-0.077	0.000	0.000	0.000	0.000
24	A	63	MET	0	-0.023	-0.019	7.660	-0.173	-0.173	0.000	0.000	0.000	0.000
25	A	64	GLN	0	-0.044	-0.014	10.168	-0.201	-0.201	0.000	0.000	0.000	0.000
26	A	65	GLN	0	-0.028	-0.028	11.928	-0.061	-0.061	0.000	0.000	0.000	0.000
27	A	66	ALA	0	0.004	-0.005	8.770	-0.117	-0.117	0.000	0.000	0.000	0.000
28	A	67	ARG	1	0.853	0.909	6.260	0.432	0.432	0.000	0.000	0.000	0.000
29	A	68	HIS	0	-0.023	0.011	8.130	-0.120	-0.120	0.000	0.000	0.000	0.000
30	A	69	GLU	-1	-0.874	-0.929	10.119	-0.860	-0.860	0.000	0.000	0.000	0.000
31	A	70	GLN	0	-0.076	-0.024	1.917	-8.413	-10.169	8.164	-3.318	-3.090	-0.038
32	A	71	PRO	0	0.000	-0.001	6.520	0.133	0.133	0.000	0.000	0.000	0.000
33	A	72	PRO	0	0.009	0.003	5.602	-0.456	-0.456	0.000	0.000	0.000	0.000
34	A	73	VAL	0	0.010	-0.009	5.987	0.082	0.082	0.000	0.000	0.000	0.000
35	A	74	ASN	0	0.008	0.006	7.445	-0.062	-0.062	0.000	0.000	0.000	0.000
36	A	75	VAL	0	0.061	0.009	10.280	0.077	0.077	0.000	0.000	0.000	0.000
37	A	76	SER	0	0.020	0.020	12.861	0.017	0.017	0.000	0.000	0.000	0.000
38	A	77	GLH	0	0.004	-0.039	11.864	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	78	LEU	0	-0.008	0.005	10.023	0.029	0.029	0.000	0.000	0.000	0.000
40	A	79	GLU	-1	-0.845	-0.906	14.158	0.046	0.046	0.000	0.000	0.000	0.000
41	A	80	THR	0	-0.076	-0.042	17.421	-0.011	-0.011	0.000	0.000	0.000	0.000
42	A	81	MET	0	0.006	0.000	15.461	-0.008	-0.008	0.000	0.000	0.000	0.000
43	A	82	HIS	0	0.000	0.007	17.641	0.018	0.018	0.000	0.000	0.000	0.000
44	A	83	ARG	1	0.850	0.910	19.041	-0.050	-0.050	0.000	0.000	0.000	0.000
45	A	84	LEU	0	-0.021	0.000	20.209	-0.008	-0.008	0.000	0.000	0.000	0.000
46	A	85	VAL	0	-0.041	-0.026	18.885	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	86	THR	0	-0.083	-0.054	22.112	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	87	ALA	0	-0.023	0.011	24.685	-0.009	-0.009	0.000	0.000	0.000	0.000
49	A	88	GLU	-1	-0.923	-0.967	27.156	0.061	0.061	0.000	0.000	0.000	0.000
50	A	89	ASN	0	-0.063	-0.029	30.282	0.001	0.001	0.000	0.000	0.000	0.000
51	A	90	PHE	0	0.009	0.012	22.866	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	91	ASP	-1	-0.776	-0.899	26.337	0.027	0.027	0.000	0.000	0.000	0.000
53	A	92	GLU	-1	-0.830	-0.904	23.771	0.081	0.081	0.000	0.000	0.000	0.000
54	A	93	ASN	0	-0.052	-0.026	23.611	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	94	ALA	0	0.028	0.027	23.751	-0.009	-0.009	0.000	0.000	0.000	0.000
56	A	95	VAL	0	-0.016	-0.015	19.374	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	96	ARG	1	0.828	0.894	19.157	-0.050	-0.050	0.000	0.000	0.000	0.000
58	A	97	ALA	0	0.057	0.038	19.077	-0.011	-0.011	0.000	0.000	0.000	0.000
59	A	98	GLN	0	-0.026	-0.020	16.483	-0.034	-0.034	0.000	0.000	0.000	0.000
60	A	99	ALA	0	0.017	-0.004	14.848	-0.009	-0.009	0.000	0.000	0.000	0.000
61	A	100	GLU	-1	-0.913	-0.960	14.293	-0.051	-0.051	0.000	0.000	0.000	0.000
62	A	101	LYS	1	0.878	0.942	14.891	0.098	0.098	0.000	0.000	0.000	0.000
63	A	102	MET	0	-0.005	-0.006	11.250	-0.064	-0.064	0.000	0.000	0.000	0.000
64	A	103	ALA	0	-0.009	0.000	10.067	-0.078	-0.078	0.000	0.000	0.000	0.000
65	A	104	ASN	0	-0.032	-0.031	10.605	-0.153	-0.153	0.000	0.000	0.000	0.000
66	A	105	GLU	-1	-0.795	-0.848	8.220	-0.472	-0.472	0.000	0.000	0.000	0.000
67	A	106	GLN	0	0.015	0.014	4.048	-0.906	-0.785	-0.001	-0.007	-0.112	0.000
68	A	107	ILE	0	-0.006	-0.002	6.744	-0.454	-0.454	0.000	0.000	0.000	0.000
69	A	108	ALA	0	0.021	0.020	9.127	-0.091	-0.091	0.000	0.000	0.000	0.000
70	A	109	ARG	1	0.922	0.956	2.571	1.197	1.811	0.447	-0.282	-0.779	0.001
71	A	110	GLN	0	-0.006	-0.010	5.631	-0.162	-0.162	0.000	0.000	0.000	0.000
72	A	111	VAL	0	-0.010	0.001	6.963	0.303	0.303	0.000	0.000	0.000	0.000
73	A	112	GLU	-1	-0.770	-0.856	8.183	-0.795	-0.795	0.000	0.000	0.000	0.000
74	A	113	MET	0	-0.028	-0.028	4.640	-0.122	-0.029	-0.001	-0.022	-0.070	0.000
75	A	114	ALA	0	-0.021	-0.006	7.933	0.390	0.390	0.000	0.000	0.000	0.000
76	A	115	LYS	1	0.824	0.897	10.997	0.907	0.907	0.000	0.000	0.000	0.000
77	A	116	VAL	0	0.056	0.023	9.788	0.132	0.132	0.000	0.000	0.000	0.000
78	A	117	ARG	1	0.906	0.952	4.834	-0.591	-0.515	-0.001	-0.010	-0.065	0.000
79	A	118	ASN	0	0.009	0.008	12.835	0.078	0.078	0.000	0.000	0.000	0.000
80	A	119	GLN	0	0.012	0.010	15.524	0.010	0.010	0.000	0.000	0.000	0.000
81	A	120	MET	0	-0.022	-0.017	12.312	0.003	0.003	0.000	0.000	0.000	0.000
82	A	121	TYR	0	-0.014	-0.013	16.654	0.045	0.045	0.000	0.000	0.000	0.000
83	A	122	ARG	1	0.881	0.937	18.300	0.238	0.238	0.000	0.000	0.000	0.000
84	A	123	LEU	0	-0.013	0.019	18.974	0.006	0.006	0.000	0.000	0.000	0.000
85	A	124	LEU	0	-0.074	-0.016	18.929	0.018	0.018	0.000	0.000	0.000	0.000
86	A	125	THR	0	0.008	-0.022	22.942	-0.006	-0.006	0.000	0.000	0.000	0.000
87	A	126	PRO	0	0.047	0.017	25.181	0.008	0.008	0.000	0.000	0.000	0.000
88	A	127	GLU	-1	-0.794	-0.887	26.428	0.007	0.007	0.000	0.000	0.000	0.000
89	A	128	GLN	0	-0.011	-0.003	22.748	0.004	0.004	0.000	0.000	0.000	0.000
90	A	129	GLN	0	-0.014	-0.008	21.637	0.024	0.024	0.000	0.000	0.000	0.000
91	A	130	ALA	0	0.020	0.021	22.195	0.019	0.019	0.000	0.000	0.000	0.000
92	A	131	VAL	0	0.004	0.001	22.217	0.018	0.018	0.000	0.000	0.000	0.000
93	A	132	LEU	0	-0.036	-0.014	16.341	0.021	0.021	0.000	0.000	0.000	0.000
94	A	133	ASN	0	-0.038	-0.042	18.995	0.046	0.046	0.000	0.000	0.000	0.000
95	A	134	GLU	-1	-0.812	-0.872	20.740	0.163	0.163	0.000	0.000	0.000	0.000
96	A	135	LYS	1	0.917	0.959	18.717	-0.170	-0.170	0.000	0.000	0.000	0.000
97	A	136	HIS	0	-0.027	-0.016	13.302	0.061	0.061	0.000	0.000	0.000	0.000
98	A	137	GLN	0	-0.036	-0.026	17.740	0.039	0.039	0.000	0.000	0.000	0.000
99	A	138	GLN	0	-0.026	-0.027	20.790	0.025	0.025	0.000	0.000	0.000	0.000
100	A	139	ARG	1	0.876	0.943	13.446	-0.472	-0.472	0.000	0.000	0.000	0.000
101	A	140	MET	0	-0.081	-0.051	13.895	0.029	0.029	0.000	0.000	0.000	0.000
102	A	141	GLU	-1	-0.826	-0.906	18.305	0.190	0.190	0.000	0.000	0.000	0.000
103	A	142	GLN	0	-0.015	-0.002	18.441	0.025	0.025	0.000	0.000	0.000	0.000
104	A	143	LEU	0	-0.083	-0.031	14.847	0.009	0.009	0.000	0.000	0.000	0.000
105	A	144	ARG	1	0.844	0.920	19.418	-0.223	-0.223	0.000	0.000	0.000	0.000
106	A	145	ASP	-1	-0.763	-0.834	22.987	0.174	0.174	0.000	0.000	0.000	0.000
107	A	146	VAL	0	-0.004	-0.015	24.558	0.015	0.015	0.000	0.000	0.000	0.000
108	A	147	THR	0	-0.053	-0.045	26.322	0.004	0.004	0.000	0.000	0.000	0.000
109	A	148	GLN	0	-0.055	-0.043	22.591	0.023	0.023	0.000	0.000	0.000	0.000
110	A	149	TRP	0	-0.094	-0.048	17.412	0.038	0.038	0.000	0.000	0.000	0.000
111	A	150	GLN	0	-0.047	-0.008	24.410	-0.004	-0.004	0.000	0.000	0.000	0.000

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