FMO DATABASE

FMODB ID: 984J2

Calculation Name: 3I3U-D-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 3I3U

Chain ID: D

ChEMBL ID:
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UniProt ID: F9UPN6

Base Structure: X-ray

Registration Date: 2023-09-21

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	103
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-719503.348946
FMO2-HF: Nuclear repulsion	680553.266348
FMO2-HF: Total energy	-38950.082598
FMO2-MP2: Total energy	-39065.112146

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(D:2:ASN)

Summations of interaction energy for fragment #1(D:2:ASN)

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.
-37.3	-35.65	11.727	-6.068	-7.309	0.062

Interaction energy analysis for fragmet #1(D:2:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.065 / q_NPA : 0.024

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	D	4	LYS	1	0.978	0.975	3.884	3.028	4.336	-0.001	-0.568	-0.739	0.001
4	D	5	LYS	1	0.903	0.954	1.780	-40.215	-41.225	11.387	-5.091	-5.286	0.064
5	D	6	ILE	0	0.034	0.016	2.677	-0.293	0.928	0.342	-0.404	-1.159	-0.003
6	D	7	GLU	-1	-0.870	-0.907	5.293	-0.929	-0.798	-0.001	-0.005	-0.125	0.000
7	D	8	LEU	0	0.000	0.003	7.740	0.548	0.548	0.000	0.000	0.000	0.000
8	D	9	LEU	0	-0.023	-0.020	5.968	0.348	0.348	0.000	0.000	0.000	0.000
9	D	10	THR	0	-0.006	-0.013	8.955	0.151	0.151	0.000	0.000	0.000	0.000
10	D	11	THR	0	0.009	-0.005	11.113	0.227	0.227	0.000	0.000	0.000	0.000
11	D	12	TYR	0	-0.037	-0.009	12.420	0.132	0.132	0.000	0.000	0.000	0.000
12	D	13	LEU	0	-0.012	-0.023	11.766	0.083	0.083	0.000	0.000	0.000	0.000
13	D	14	SER	0	-0.059	-0.034	14.968	0.019	0.019	0.000	0.000	0.000	0.000
14	D	15	LEU	0	-0.001	0.012	17.135	0.022	0.022	0.000	0.000	0.000	0.000
15	D	16	TYR	0	-0.063	-0.043	17.610	0.088	0.088	0.000	0.000	0.000	0.000
16	D	17	ILE	0	0.001	0.013	20.593	-0.050	-0.050	0.000	0.000	0.000	0.000
17	D	18	ASP	-1	-0.896	-0.955	22.862	0.075	0.075	0.000	0.000	0.000	0.000
18	D	19	HIS	0	0.040	0.003	24.008	-0.019	-0.019	0.000	0.000	0.000	0.000
19	D	20	HIS	0	0.020	0.021	26.921	0.003	0.003	0.000	0.000	0.000	0.000
20	D	21	THR	0	-0.001	-0.012	25.808	-0.005	-0.005	0.000	0.000	0.000	0.000
21	D	22	VAL	0	0.007	0.010	27.882	-0.010	-0.010	0.000	0.000	0.000	0.000
22	D	23	LEU	0	-0.027	-0.027	30.504	0.000	0.000	0.000	0.000	0.000	0.000
23	D	24	ALA	0	0.004	-0.003	32.009	0.000	0.000	0.000	0.000	0.000	0.000
24	D	25	ASP	-1	-0.784	-0.869	32.746	-0.086	-0.086	0.000	0.000	0.000	0.000
25	D	26	MET	0	-0.020	0.006	33.810	0.004	0.004	0.000	0.000	0.000	0.000
26	D	27	GLN	0	-0.021	0.004	36.950	0.009	0.009	0.000	0.000	0.000	0.000
27	D	28	ASN	0	-0.074	-0.054	39.164	0.003	0.003	0.000	0.000	0.000	0.000
28	D	29	ALA	0	-0.013	0.003	39.217	-0.004	-0.004	0.000	0.000	0.000	0.000
29	D	30	THR	0	-0.058	-0.039	36.255	-0.011	-0.011	0.000	0.000	0.000	0.000
30	D	31	GLY	0	0.019	0.008	37.199	0.011	0.011	0.000	0.000	0.000	0.000
31	D	32	LYS	1	0.780	0.890	32.133	0.099	0.099	0.000	0.000	0.000	0.000
32	D	33	TYR	0	0.039	0.010	28.133	-0.001	-0.001	0.000	0.000	0.000	0.000
33	D	34	VAL	0	-0.017	-0.003	32.821	0.010	0.010	0.000	0.000	0.000	0.000
34	D	35	VAL	0	0.005	0.003	31.792	0.001	0.001	0.000	0.000	0.000	0.000
35	D	36	LEU	0	-0.013	-0.002	32.082	0.003	0.003	0.000	0.000	0.000	0.000
36	D	37	ASP	-1	-0.755	-0.848	32.175	0.096	0.096	0.000	0.000	0.000	0.000
37	D	38	VAL	0	0.012	0.015	29.809	-0.004	-0.004	0.000	0.000	0.000	0.000
38	D	39	ARG	1	0.827	0.902	32.285	-0.110	-0.110	0.000	0.000	0.000	0.000
39	D	40	ASN	0	0.012	-0.017	33.449	-0.020	-0.020	0.000	0.000	0.000	0.000
40	D	41	ALA	0	-0.015	0.010	36.442	-0.001	-0.001	0.000	0.000	0.000	0.000
41	D	42	PRO	0	0.006	-0.012	38.110	-0.009	-0.009	0.000	0.000	0.000	0.000
42	D	43	ALA	0	0.032	0.026	41.079	0.005	0.005	0.000	0.000	0.000	0.000
43	D	44	GLN	0	0.015	0.005	40.344	0.007	0.007	0.000	0.000	0.000	0.000
44	D	45	VAL	0	-0.017	-0.008	42.794	-0.005	-0.005	0.000	0.000	0.000	0.000
45	D	46	LYS	1	0.856	0.921	44.517	-0.059	-0.059	0.000	0.000	0.000	0.000
46	D	47	LYS	1	0.871	0.935	37.879	-0.056	-0.056	0.000	0.000	0.000	0.000
47	D	48	ASP	-1	-0.799	-0.881	40.875	0.043	0.043	0.000	0.000	0.000	0.000
48	D	49	GLN	0	0.018	0.018	36.670	0.002	0.002	0.000	0.000	0.000	0.000
49	D	50	ILE	0	0.098	0.064	31.380	0.008	0.008	0.000	0.000	0.000	0.000
50	D	51	LYS	1	0.801	0.883	35.935	-0.045	-0.045	0.000	0.000	0.000	0.000
51	D	52	GLY	0	0.038	0.007	37.112	-0.003	-0.003	0.000	0.000	0.000	0.000
52	D	53	ALA	0	-0.022	0.002	35.233	-0.007	-0.007	0.000	0.000	0.000	0.000
53	D	54	ILE	0	0.044	0.020	36.726	0.009	0.009	0.000	0.000	0.000	0.000
54	D	55	ALA	0	-0.034	-0.020	36.956	0.005	0.005	0.000	0.000	0.000	0.000
55	D	56	MET	0	0.011	0.018	35.440	-0.006	-0.006	0.000	0.000	0.000	0.000
56	D	57	PRO	0	0.019	0.021	35.050	0.002	0.002	0.000	0.000	0.000	0.000
57	D	58	ALA	0	0.017	0.003	31.421	-0.009	-0.009	0.000	0.000	0.000	0.000
58	D	59	LYS	1	0.803	0.893	33.365	-0.071	-0.071	0.000	0.000	0.000	0.000
59	D	60	ASP	-1	-0.832	-0.908	35.969	0.043	0.043	0.000	0.000	0.000	0.000
60	D	61	LEU	0	-0.009	-0.002	31.754	-0.008	-0.008	0.000	0.000	0.000	0.000
61	D	62	ALA	0	0.011	0.002	34.819	-0.011	-0.011	0.000	0.000	0.000	0.000
62	D	63	THR	0	-0.031	-0.017	36.179	-0.009	-0.009	0.000	0.000	0.000	0.000
63	D	64	ARG	1	0.737	0.816	38.924	-0.012	-0.012	0.000	0.000	0.000	0.000
64	D	65	ILE	0	0.020	0.027	35.071	-0.004	-0.004	0.000	0.000	0.000	0.000
65	D	66	GLY	0	0.001	-0.001	37.790	-0.008	-0.008	0.000	0.000	0.000	0.000
66	D	67	GLU	-1	-0.834	-0.882	40.206	-0.011	-0.011	0.000	0.000	0.000	0.000
67	D	68	LEU	0	-0.085	-0.025	34.336	0.002	0.002	0.000	0.000	0.000	0.000
68	D	69	ASP	-1	-0.782	-0.891	37.516	-0.103	-0.103	0.000	0.000	0.000	0.000
69	D	70	PRO	0	-0.004	-0.019	34.764	-0.003	-0.003	0.000	0.000	0.000	0.000
70	D	71	ALA	0	-0.052	-0.009	34.373	-0.014	-0.014	0.000	0.000	0.000	0.000
71	D	72	LYS	1	0.812	0.895	34.669	0.079	0.079	0.000	0.000	0.000	0.000
72	D	73	THR	0	0.010	0.003	28.299	0.003	0.003	0.000	0.000	0.000	0.000
73	D	74	TYR	0	-0.009	-0.011	29.954	0.021	0.021	0.000	0.000	0.000	0.000
74	D	75	VAL	0	0.005	-0.004	27.205	-0.008	-0.008	0.000	0.000	0.000	0.000
75	D	76	VAL	0	-0.001	0.016	26.607	0.016	0.016	0.000	0.000	0.000	0.000
76	D	77	TYR	0	-0.051	-0.052	27.485	0.013	0.013	0.000	0.000	0.000	0.000
77	D	78	ASP	-1	-0.799	-0.932	28.039	0.156	0.156	0.000	0.000	0.000	0.000
78	D	79	TRP	0	-0.025	-0.021	29.550	-0.008	-0.008	0.000	0.000	0.000	0.000
79	D	80	THR	0	0.029	0.015	24.251	0.029	0.029	0.000	0.000	0.000	0.000
80	D	81	GLY	0	0.007	0.010	23.250	0.014	0.014	0.000	0.000	0.000	0.000
81	D	82	GLY	0	0.004	-0.010	20.988	0.042	0.042	0.000	0.000	0.000	0.000
82	D	83	THR	0	-0.044	-0.015	21.640	-0.004	-0.004	0.000	0.000	0.000	0.000
83	D	84	THR	0	0.063	0.013	23.841	-0.028	-0.028	0.000	0.000	0.000	0.000
84	D	85	LEU	0	-0.015	0.022	25.416	-0.032	-0.032	0.000	0.000	0.000	0.000
85	D	86	GLY	0	0.067	0.028	26.539	-0.023	-0.023	0.000	0.000	0.000	0.000
86	D	87	LYS	1	0.836	0.908	19.582	-0.249	-0.249	0.000	0.000	0.000	0.000
87	D	88	THR	0	-0.021	-0.018	24.366	-0.031	-0.031	0.000	0.000	0.000	0.000
88	D	89	ALA	0	0.004	-0.009	27.244	-0.024	-0.024	0.000	0.000	0.000	0.000
89	D	90	LEU	0	0.011	0.011	22.213	-0.016	-0.016	0.000	0.000	0.000	0.000
90	D	91	LEU	0	0.006	0.008	23.707	-0.029	-0.029	0.000	0.000	0.000	0.000
91	D	92	VAL	0	-0.015	0.003	25.995	-0.025	-0.025	0.000	0.000	0.000	0.000
92	D	93	LEU	0	-0.008	-0.003	28.387	-0.014	-0.014	0.000	0.000	0.000	0.000
93	D	94	LEU	0	0.016	0.007	22.731	-0.016	-0.016	0.000	0.000	0.000	0.000
94	D	95	SER	0	-0.074	-0.051	26.903	-0.026	-0.026	0.000	0.000	0.000	0.000
95	D	96	ALA	0	-0.058	-0.026	28.579	-0.007	-0.007	0.000	0.000	0.000	0.000
96	D	97	GLY	0	-0.016	0.005	29.353	-0.002	-0.002	0.000	0.000	0.000	0.000
97	D	98	PHE	0	-0.034	-0.020	30.312	-0.009	-0.009	0.000	0.000	0.000	0.000
98	D	99	GLU	-1	-0.804	-0.853	26.361	-0.235	-0.235	0.000	0.000	0.000	0.000
99	D	100	ALA	0	-0.023	-0.027	26.198	0.026	0.026	0.000	0.000	0.000	0.000
100	D	101	TYR	0	-0.030	-0.039	21.848	-0.021	-0.021	0.000	0.000	0.000	0.000
101	D	102	GLU	-1	-0.819	-0.887	22.112	0.206	0.206	0.000	0.000	0.000	0.000
102	D	103	LEU	0	-0.020	-0.017	23.499	-0.013	-0.013	0.000	0.000	0.000	0.000
103	D	104	ALA	0	-0.032	-0.010	21.375	0.040	0.040	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:2:ASN)