FMO DATABASE

FMODB ID: 66Z1Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-778490.249571
FMO2-HF: Nuclear repulsion	734570.328861
FMO2-HF: Total energy	-43919.920711
FMO2-MP2: Total energy	-44050.187404

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.
-10.547	-6.051	1.78	-3.278	-2.997	-0.025

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 : -0.034 / q_NPA : -0.023

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	0.972	0.959	3.800	0.342	1.633	-0.021	-0.634	-0.636	0.002
4	A	5	GLY	0	-0.009	-0.005	6.794	0.069	0.069	0.000	0.000	0.000	0.000
5	A	6	GLU	-1	-0.905	-0.939	2.529	-9.962	-7.004	1.802	-2.609	-2.151	-0.027
6	A	7	LEU	0	-0.056	-0.015	5.449	0.277	0.277	0.000	0.000	0.000	0.000
7	A	8	ASP	-1	-0.854	-0.935	4.942	-0.145	-0.042	-0.001	-0.007	-0.095	0.000
8	A	9	LEU	0	0.027	-0.008	6.325	0.234	0.234	0.000	0.000	0.000	0.000
9	A	10	THR	0	-0.044	-0.016	7.916	0.092	0.092	0.000	0.000	0.000	0.000
10	A	11	GLY	0	0.086	0.044	10.529	0.025	0.025	0.000	0.000	0.000	0.000
11	A	12	ALA	0	-0.002	-0.010	13.080	0.021	0.021	0.000	0.000	0.000	0.000
12	A	13	LYS	1	0.947	0.964	12.659	0.327	0.327	0.000	0.000	0.000	0.000
13	A	14	GLN	0	-0.047	-0.005	13.733	0.053	0.053	0.000	0.000	0.000	0.000
14	A	15	ASN	0	-0.058	-0.023	16.208	0.008	0.008	0.000	0.000	0.000	0.000
15	A	16	THR	0	0.007	0.019	16.022	0.029	0.029	0.000	0.000	0.000	0.000
16	A	17	GLY	0	-0.005	0.005	18.528	-0.021	-0.021	0.000	0.000	0.000	0.000
17	A	18	VAL	0	0.004	0.002	19.404	0.015	0.015	0.000	0.000	0.000	0.000
18	A	19	TRP	0	-0.004	-0.014	22.458	-0.006	-0.006	0.000	0.000	0.000	0.000
19	A	20	LEU	0	0.008	0.010	24.450	0.001	0.001	0.000	0.000	0.000	0.000
20	A	21	VAL	0	-0.001	-0.021	26.328	0.001	0.001	0.000	0.000	0.000	0.000
21	A	22	LYS	1	0.938	0.985	29.096	0.044	0.044	0.000	0.000	0.000	0.000
22	A	23	VAL	0	0.023	0.002	30.201	0.004	0.004	0.000	0.000	0.000	0.000
23	A	24	PRO	0	-0.003	0.009	32.787	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	25	LYS	1	1.030	0.998	30.931	0.040	0.040	0.000	0.000	0.000	0.000
25	A	26	TYR	0	0.075	0.030	35.273	0.001	0.001	0.000	0.000	0.000	0.000
26	A	27	LEU	0	0.016	0.021	34.498	0.003	0.003	0.000	0.000	0.000	0.000
27	A	28	SER	0	0.002	0.001	30.870	0.002	0.002	0.000	0.000	0.000	0.000
28	A	29	GLN	0	-0.028	-0.025	32.150	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	30	GLN	0	-0.044	-0.028	34.444	0.001	0.001	0.000	0.000	0.000	0.000
30	A	31	TRP	0	-0.008	-0.019	29.154	0.002	0.002	0.000	0.000	0.000	0.000
31	A	32	ALA	0	-0.016	-0.001	30.683	0.004	0.004	0.000	0.000	0.000	0.000
32	A	33	LYS	1	0.877	0.953	31.727	0.000	0.000	0.000	0.000	0.000	0.000
33	A	34	ALA	0	-0.002	0.019	30.950	0.002	0.002	0.000	0.000	0.000	0.000
34	A	35	SER	0	0.032	0.016	32.114	0.002	0.002	0.000	0.000	0.000	0.000
35	A	36	GLY	0	0.024	0.005	32.120	0.001	0.001	0.000	0.000	0.000	0.000
36	A	37	ARG	1	0.934	0.953	28.930	-0.068	-0.068	0.000	0.000	0.000	0.000
37	A	38	GLY	0	0.030	0.032	27.889	0.004	0.004	0.000	0.000	0.000	0.000
38	A	39	GLU	-1	-0.978	-0.981	29.214	0.046	0.046	0.000	0.000	0.000	0.000
39	A	40	VAL	0	0.038	0.008	30.703	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	41	GLY	0	0.011	-0.011	33.035	-0.004	-0.004	0.000	0.000	0.000	0.000
41	A	42	LYS	1	0.893	0.953	33.368	-0.024	-0.024	0.000	0.000	0.000	0.000
42	A	43	LEU	0	0.024	0.026	30.346	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	44	ARG	1	0.946	0.969	33.811	-0.004	-0.004	0.000	0.000	0.000	0.000
44	A	45	ILE	0	0.023	0.007	31.921	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	46	ALA	0	-0.022	-0.009	36.514	0.003	0.003	0.000	0.000	0.000	0.000
46	A	47	LYS	1	0.951	0.974	34.718	0.003	0.003	0.000	0.000	0.000	0.000
47	A	48	THR	0	0.062	0.026	40.924	0.002	0.002	0.000	0.000	0.000	0.000
48	A	49	GLN	0	0.012	-0.001	43.527	0.000	0.000	0.000	0.000	0.000	0.000
49	A	50	GLY	0	-0.009	0.005	43.149	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	51	ARG	1	0.883	0.938	42.933	0.007	0.007	0.000	0.000	0.000	0.000
51	A	52	THR	0	-0.026	-0.014	36.794	0.003	0.003	0.000	0.000	0.000	0.000
52	A	53	GLU	-1	-0.868	-0.921	40.243	-0.008	-0.008	0.000	0.000	0.000	0.000
53	A	54	VAL	0	0.001	-0.006	34.006	0.002	0.002	0.000	0.000	0.000	0.000
54	A	55	SER	0	0.011	0.017	37.047	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	56	PHE	0	0.037	0.018	32.997	0.002	0.002	0.000	0.000	0.000	0.000
56	A	57	THR	0	-0.019	-0.003	36.426	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	58	LEU	0	-0.002	-0.002	36.013	0.002	0.002	0.000	0.000	0.000	0.000
58	A	59	ASN	0	0.037	0.016	35.195	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	60	GLU	-1	-0.895	-0.962	38.351	0.020	0.020	0.000	0.000	0.000	0.000
60	A	61	ASP	-1	-0.858	-0.918	37.976	0.028	0.028	0.000	0.000	0.000	0.000
61	A	62	LEU	0	-0.033	-0.023	34.192	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	63	ALA	0	-0.086	-0.033	38.854	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	64	ASN	0	-0.045	-0.032	41.925	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	65	ILE	0	0.000	0.026	38.611	0.000	0.000	0.000	0.000	0.000	0.000
65	A	66	HIS	0	-0.018	-0.023	42.284	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	67	ASP	-1	-0.904	-0.937	42.064	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	68	ILE	0	-0.016	-0.041	44.835	0.001	0.001	0.000	0.000	0.000	0.000
68	A	69	GLY	0	0.017	0.007	48.249	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	70	GLY	0	-0.019	0.000	48.838	0.000	0.000	0.000	0.000	0.000	0.000
70	A	71	LYS	1	0.878	0.960	46.197	-0.005	-0.005	0.000	0.000	0.000	0.000
71	A	72	PRO	0	0.043	0.018	50.336	0.000	0.000	0.000	0.000	0.000	0.000
72	A	73	ALA	0	0.043	0.015	53.674	0.001	0.001	0.000	0.000	0.000	0.000
73	A	74	SER	0	-0.011	0.020	53.337	0.000	0.000	0.000	0.000	0.000	0.000
74	A	75	VAL	0	-0.004	-0.028	49.449	0.001	0.001	0.000	0.000	0.000	0.000
75	A	76	SER	0	-0.062	-0.046	49.145	0.000	0.000	0.000	0.000	0.000	0.000
76	A	77	ALA	0	0.050	0.055	46.864	0.001	0.001	0.000	0.000	0.000	0.000
77	A	78	PRO	0	0.006	-0.010	41.994	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	79	ARG	1	0.943	0.973	43.558	0.000	0.000	0.000	0.000	0.000	0.000
79	A	80	GLU	-1	-0.919	-0.954	41.226	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	81	HIS	0	-0.033	-0.015	38.059	-0.003	-0.003	0.000	0.000	0.000	0.000
81	A	82	PRO	0	0.057	0.028	38.572	0.000	0.000	0.000	0.000	0.000	0.000
82	A	83	PHE	0	0.018	-0.020	31.838	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	84	VAL	0	-0.019	0.002	37.093	0.000	0.000	0.000	0.000	0.000	0.000
84	A	85	LEU	0	0.001	-0.014	34.058	-0.003	-0.003	0.000	0.000	0.000	0.000
85	A	86	GLN	0	-0.026	-0.018	33.462	-0.003	-0.003	0.000	0.000	0.000	0.000
86	A	87	SER	0	0.014	-0.002	33.265	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	88	VAL	0	0.022	-0.002	26.800	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	89	GLY	0	0.007	0.013	28.874	-0.006	-0.006	0.000	0.000	0.000	0.000
89	A	90	GLY	0	-0.014	0.007	30.171	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	91	GLN	0	-0.002	-0.030	26.529	0.004	0.004	0.000	0.000	0.000	0.000
91	A	92	THR	0	-0.004	0.023	21.301	0.006	0.006	0.000	0.000	0.000	0.000
92	A	93	LEU	0	-0.027	-0.012	22.314	-0.011	-0.011	0.000	0.000	0.000	0.000
93	A	94	THR	0	0.017	0.005	17.089	0.016	0.016	0.000	0.000	0.000	0.000
94	A	95	VAL	0	0.006	0.004	16.313	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	96	PHE	0	-0.014	-0.005	12.761	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	97	THR	0	-0.073	-0.031	11.615	0.007	0.007	0.000	0.000	0.000	0.000
97	A	98	GLU	-1	-0.865	-0.938	10.915	-0.387	-0.387	0.000	0.000	0.000	0.000
98	A	99	SER	0	-0.078	-0.033	8.971	0.091	0.091	0.000	0.000	0.000	0.000
99	A	100	SER	0	0.041	-0.010	11.393	-0.043	-0.043	0.000	0.000	0.000	0.000
100	A	101	SER	0	-0.091	-0.035	8.605	0.037	0.037	0.000	0.000	0.000	0.000
101	A	102	ASP	-1	-0.855	-0.930	8.883	-0.353	-0.353	0.000	0.000	0.000	0.000
102	A	103	LYS	1	0.888	0.966	3.851	-1.547	-1.403	0.000	-0.028	-0.115	0.000
103	A	104	LEU	0	0.054	0.026	6.483	0.172	0.172	0.000	0.000	0.000	0.000
104	A	105	SER	0	-0.043	-0.031	6.923	-0.149	-0.149	0.000	0.000	0.000	0.000
105	A	106	LEU	0	-0.009	-0.013	8.939	0.049	0.049	0.000	0.000	0.000	0.000
106	A	107	GLU	-1	-0.811	-0.900	11.479	0.049	0.049	0.000	0.000	0.000	0.000
107	A	108	GLY	0	-0.029	-0.022	13.739	0.035	0.035	0.000	0.000	0.000	0.000
108	A	109	ILE	0	-0.043	-0.014	16.827	-0.029	-0.029	0.000	0.000	0.000	0.000
109	A	110	VAL	0	-0.029	-0.021	20.038	0.021	0.021	0.000	0.000	0.000	0.000
110	A	111	VAL	0	-0.009	-0.003	23.321	-0.003	-0.003	0.000	0.000	0.000	0.000
111	A	112	GLN	0	-0.052	-0.021	25.899	0.005	0.005	0.000	0.000	0.000	0.000
112	A	113	ARG	1	0.962	0.997	27.824	0.072	0.072	0.000	0.000	0.000	0.000
113	A	114	ALA	0	0.025	0.010	30.113	0.004	0.004	0.000	0.000	0.000	0.000
114	A	115	GLU	-1	-0.910	-0.946	32.123	-0.038	-0.038	0.000	0.000	0.000	0.000
115	A	116	CYS	0	-0.045	-0.003	34.103	0.004	0.004	0.000	0.000	0.000	0.000
116	A	117	ARG	1	0.900	0.931	35.827	0.027	0.027	0.000	0.000	0.000	0.000
117	A	118	PRO	0	0.011	-0.007	39.440	0.002	0.002	0.000	0.000	0.000	0.000
118	A	119	ALA	0	-0.001	0.016	41.243	0.000	0.000	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:2:ALA)