FMO DATABASE

FMODB ID: R5Q78

Calculation Name: 1F3U-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1F3U

Chain ID: A

ChEMBL ID:

UniProt ID: P35269

Base Structure: X-ray

Registration Date: 2023-03-13

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	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	118
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-780682.022923
FMO2-HF: Nuclear repulsion	736761.195297
FMO2-HF: Total energy	-43920.827627
FMO2-MP2: Total energy	-44051.096494

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:2:ALA)

Summations of interaction energy for fragment #1(A:2: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.
-16.337	-15.672	11.611	-6.609	-5.668	-0.068

Interaction energy analysis for fragmet #1(A:2:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.063 / q_NPA : -0.040

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	4	ARG	1	0.946	0.965	3.874	-0.065	1.168	-0.013	-0.676	-0.544	0.002
4	A	5	GLY	0	0.008	-0.013	6.032	0.488	0.488	0.000	0.000	0.000	0.000
5	A	6	GLU	-1	-0.909	-0.924	1.957	-16.800	-17.699	11.624	-5.878	-4.848	-0.070
6	A	7	LEU	0	-0.008	0.001	4.942	0.483	0.510	-0.001	-0.003	-0.023	0.000
7	A	8	ASP	-1	-0.771	-0.854	4.758	-0.163	-0.058	-0.001	-0.009	-0.095	0.000
8	A	9	LEU	0	0.018	-0.004	5.966	0.274	0.274	0.000	0.000	0.000	0.000
9	A	10	THR	0	-0.030	-0.029	7.463	0.130	0.130	0.000	0.000	0.000	0.000
10	A	11	GLY	0	0.023	0.016	9.901	0.040	0.040	0.000	0.000	0.000	0.000
11	A	12	ALA	0	0.002	-0.002	12.515	0.024	0.024	0.000	0.000	0.000	0.000
12	A	13	LYS	1	0.947	0.957	11.677	0.397	0.397	0.000	0.000	0.000	0.000
13	A	14	GLN	0	-0.029	-0.007	12.482	0.055	0.055	0.000	0.000	0.000	0.000
14	A	15	ASN	0	-0.064	-0.031	15.786	0.013	0.013	0.000	0.000	0.000	0.000
15	A	16	THR	0	0.015	0.015	14.957	0.027	0.027	0.000	0.000	0.000	0.000
16	A	17	GLY	0	0.001	0.017	17.979	-0.019	-0.019	0.000	0.000	0.000	0.000
17	A	18	VAL	0	0.001	-0.003	19.058	0.016	0.016	0.000	0.000	0.000	0.000
18	A	19	TRP	0	-0.003	-0.017	22.069	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	20	LEU	0	0.018	0.017	24.172	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	21	VAL	0	-0.018	-0.019	26.086	0.003	0.003	0.000	0.000	0.000	0.000
21	A	22	LYS	1	0.876	0.941	28.860	0.055	0.055	0.000	0.000	0.000	0.000
22	A	23	VAL	0	0.026	0.003	30.224	0.005	0.005	0.000	0.000	0.000	0.000
23	A	24	PRO	0	-0.011	0.002	32.750	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	25	LYS	1	0.994	0.997	30.856	0.056	0.056	0.000	0.000	0.000	0.000
25	A	26	TYR	0	0.087	0.026	35.024	0.000	0.000	0.000	0.000	0.000	0.000
26	A	27	LEU	0	0.008	0.021	34.530	0.003	0.003	0.000	0.000	0.000	0.000
27	A	28	SER	0	-0.039	-0.030	30.669	0.001	0.001	0.000	0.000	0.000	0.000
28	A	29	GLN	0	-0.005	-0.021	32.029	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	30	GLN	0	-0.009	-0.007	34.429	0.001	0.001	0.000	0.000	0.000	0.000
30	A	31	TRP	0	-0.019	-0.033	29.242	0.002	0.002	0.000	0.000	0.000	0.000
31	A	32	ALA	0	-0.016	-0.006	30.674	0.004	0.004	0.000	0.000	0.000	0.000
32	A	33	LYS	1	0.791	0.894	31.701	0.012	0.012	0.000	0.000	0.000	0.000
33	A	34	ALA	0	-0.010	0.008	30.629	0.003	0.003	0.000	0.000	0.000	0.000
34	A	35	SER	0	0.014	0.007	32.058	0.002	0.002	0.000	0.000	0.000	0.000
35	A	36	GLY	0	0.031	0.015	31.978	0.001	0.001	0.000	0.000	0.000	0.000
36	A	37	ARG	1	0.868	0.920	28.374	-0.045	-0.045	0.000	0.000	0.000	0.000
37	A	38	GLY	0	0.023	0.021	27.425	0.002	0.002	0.000	0.000	0.000	0.000
38	A	39	GLU	-1	-0.905	-0.943	28.989	0.029	0.029	0.000	0.000	0.000	0.000
39	A	40	VAL	0	0.040	0.012	30.433	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	41	GLY	0	0.021	0.000	33.028	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	42	LYS	1	0.885	0.946	33.100	-0.011	-0.011	0.000	0.000	0.000	0.000
42	A	43	LEU	0	0.020	0.021	29.884	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	44	ARG	1	0.854	0.911	33.408	0.012	0.012	0.000	0.000	0.000	0.000
44	A	45	ILE	0	0.013	-0.002	31.722	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	46	ALA	0	-0.001	0.008	36.305	0.003	0.003	0.000	0.000	0.000	0.000
46	A	47	LYS	1	0.937	0.956	34.431	0.018	0.018	0.000	0.000	0.000	0.000
47	A	48	THR	0	0.053	0.023	40.854	0.002	0.002	0.000	0.000	0.000	0.000
48	A	49	GLN	0	0.028	0.008	43.410	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	50	GLY	0	0.002	0.008	43.424	0.000	0.000	0.000	0.000	0.000	0.000
50	A	51	ARG	1	0.833	0.904	42.732	0.016	0.016	0.000	0.000	0.000	0.000
51	A	52	THR	0	-0.040	-0.037	36.573	0.002	0.002	0.000	0.000	0.000	0.000
52	A	53	GLU	-1	-0.841	-0.876	39.510	-0.018	-0.018	0.000	0.000	0.000	0.000
53	A	54	VAL	0	0.019	0.001	33.695	0.002	0.002	0.000	0.000	0.000	0.000
54	A	55	SER	0	-0.049	-0.044	36.479	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	56	PHE	0	0.053	0.027	32.582	0.001	0.001	0.000	0.000	0.000	0.000
56	A	57	THR	0	-0.007	0.002	36.005	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	58	LEU	0	-0.009	0.002	35.823	0.002	0.002	0.000	0.000	0.000	0.000
58	A	59	ASN	0	0.050	0.017	35.068	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	60	GLU	-1	-0.904	-0.961	38.089	0.008	0.008	0.000	0.000	0.000	0.000
60	A	61	ASP	-1	-0.869	-0.920	37.758	0.014	0.014	0.000	0.000	0.000	0.000
61	A	62	LEU	0	0.028	0.006	34.228	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	63	ALA	0	-0.067	-0.012	38.736	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	64	ASN	0	-0.049	-0.039	41.827	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	65	ILE	0	0.019	0.028	38.328	0.000	0.000	0.000	0.000	0.000	0.000
65	A	66	HIS	0	0.000	0.011	41.720	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	67	ASP	-1	-0.825	-0.894	41.565	-0.011	-0.011	0.000	0.000	0.000	0.000
67	A	68	ILE	0	-0.007	-0.030	44.489	0.001	0.001	0.000	0.000	0.000	0.000
68	A	69	GLY	0	0.023	0.008	47.955	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	70	GLY	0	-0.052	-0.015	48.619	0.000	0.000	0.000	0.000	0.000	0.000
70	A	71	LYS	1	0.833	0.922	45.788	0.003	0.003	0.000	0.000	0.000	0.000
71	A	72	PRO	0	0.041	0.021	49.830	0.001	0.001	0.000	0.000	0.000	0.000
72	A	73	ALA	0	0.037	-0.002	53.157	0.001	0.001	0.000	0.000	0.000	0.000
73	A	74	SER	0	-0.015	-0.001	53.400	0.000	0.000	0.000	0.000	0.000	0.000
74	A	75	VAL	0	0.069	0.052	49.532	0.001	0.001	0.000	0.000	0.000	0.000
75	A	76	SER	0	-0.094	-0.056	49.360	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	77	ALA	0	0.060	0.035	46.647	0.001	0.001	0.000	0.000	0.000	0.000
77	A	78	PRO	0	0.022	0.000	41.522	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	79	ARG	1	0.900	0.953	43.216	0.008	0.008	0.000	0.000	0.000	0.000
79	A	80	GLU	-1	-0.781	-0.837	40.548	-0.011	-0.011	0.000	0.000	0.000	0.000
80	A	81	HIS	0	-0.006	0.003	37.861	-0.003	-0.003	0.000	0.000	0.000	0.000
81	A	82	PRO	0	0.032	0.019	38.213	0.000	0.000	0.000	0.000	0.000	0.000
82	A	83	PHE	0	0.016	-0.025	31.346	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	84	VAL	0	-0.029	-0.006	36.907	0.001	0.001	0.000	0.000	0.000	0.000
84	A	85	LEU	0	0.010	-0.003	33.251	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	86	GLN	0	0.013	0.004	32.619	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	87	SER	0	0.031	0.005	32.460	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	88	VAL	0	0.030	0.000	26.193	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	89	GLY	0	0.014	0.013	28.477	-0.008	-0.008	0.000	0.000	0.000	0.000
89	A	90	GLY	0	-0.016	0.007	30.075	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	91	GLN	0	-0.022	-0.017	25.702	0.002	0.002	0.000	0.000	0.000	0.000
91	A	92	THR	0	-0.004	-0.006	21.243	0.002	0.002	0.000	0.000	0.000	0.000
92	A	93	LEU	0	-0.017	-0.003	21.683	-0.009	-0.009	0.000	0.000	0.000	0.000
93	A	94	THR	0	0.018	0.006	16.656	0.017	0.017	0.000	0.000	0.000	0.000
94	A	95	VAL	0	-0.012	0.000	16.205	0.002	0.002	0.000	0.000	0.000	0.000
95	A	96	PHE	0	-0.019	-0.009	12.482	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	97	THR	0	-0.078	-0.060	11.176	0.023	0.023	0.000	0.000	0.000	0.000
97	A	98	GLU	-1	-0.869	-0.945	10.798	-0.448	-0.448	0.000	0.000	0.000	0.000
98	A	99	SER	0	-0.021	0.005	8.717	0.091	0.091	0.000	0.000	0.000	0.000
99	A	100	SER	0	-0.012	-0.023	11.088	-0.035	-0.035	0.000	0.000	0.000	0.000
100	A	101	SER	0	-0.054	-0.033	8.861	0.082	0.082	0.000	0.000	0.000	0.000
101	A	102	ASP	-1	-0.888	-0.937	8.500	-0.384	-0.384	0.000	0.000	0.000	0.000
102	A	103	LYS	1	0.799	0.897	3.905	-0.915	-0.716	0.002	-0.043	-0.158	0.000
103	A	104	LEU	0	0.046	0.028	6.378	0.242	0.242	0.000	0.000	0.000	0.000
104	A	105	SER	0	-0.056	-0.062	6.476	-0.109	-0.109	0.000	0.000	0.000	0.000
105	A	106	LEU	0	-0.012	-0.004	8.631	0.040	0.040	0.000	0.000	0.000	0.000
106	A	107	GLU	-1	-0.781	-0.848	11.017	-0.075	-0.075	0.000	0.000	0.000	0.000
107	A	108	GLY	0	-0.012	-0.016	13.266	0.041	0.041	0.000	0.000	0.000	0.000
108	A	109	ILE	0	-0.030	-0.007	16.451	-0.032	-0.032	0.000	0.000	0.000	0.000
109	A	110	VAL	0	-0.034	-0.021	19.766	0.023	0.023	0.000	0.000	0.000	0.000
110	A	111	VAL	0	-0.002	0.004	23.066	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	112	GLN	0	-0.070	-0.032	25.474	0.007	0.007	0.000	0.000	0.000	0.000
112	A	113	ARG	1	0.919	0.967	27.360	0.089	0.089	0.000	0.000	0.000	0.000
113	A	114	ALA	0	0.005	0.003	29.714	0.006	0.006	0.000	0.000	0.000	0.000
114	A	115	GLU	-1	-0.817	-0.888	31.787	-0.054	-0.054	0.000	0.000	0.000	0.000
115	A	116	CYS	0	-0.026	0.011	33.795	0.005	0.005	0.000	0.000	0.000	0.000
116	A	117	ARG	1	0.869	0.923	35.507	0.039	0.039	0.000	0.000	0.000	0.000
117	A	118	PRO	0	0.032	-0.003	39.081	0.002	0.002	0.000	0.000	0.000	0.000
118	A	119	ALA	0	-0.013	0.015	41.058	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:ALA)