FMO DATABASE

FMODB ID: 49K3N

Calculation Name: 4IDL-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4IDL

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-26

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	122
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-975199.890659
FMO2-HF: Nuclear repulsion	927779.992515
FMO2-HF: Total energy	-47419.898144
FMO2-MP2: Total energy	-47557.449812

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:1:LYS)

Summations of interaction energy for fragment #1(A:1:LYS)

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.
-1.049	13.112	4.103	-7.478	-10.788	-0.075

Interaction energy analysis for fragmet #1(A:1:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.911 / q_NPA : 0.955

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

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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	3	GLN	0	0.011	0.006	2.574	-29.405	-24.652	0.801	-2.236	-3.318	-0.025
4	A	4	LEU	0	0.013	-0.003	5.198	3.962	4.034	-0.001	-0.004	-0.067	0.000
5	A	5	GLN	0	-0.008	0.009	7.798	1.579	1.579	0.000	0.000	0.000	0.000
6	A	6	GLN	0	0.018	0.003	11.350	-1.515	-1.515	0.000	0.000	0.000	0.000
7	A	7	SER	0	0.001	0.010	14.057	0.893	0.893	0.000	0.000	0.000	0.000
8	A	8	GLY	0	0.053	0.019	17.875	-0.241	-0.241	0.000	0.000	0.000	0.000
9	A	9	GLY	0	0.005	-0.012	21.098	0.217	0.217	0.000	0.000	0.000	0.000
10	A	10	GLY	0	0.001	-0.002	22.231	0.383	0.383	0.000	0.000	0.000	0.000
11	A	11	ALA	0	-0.016	-0.007	25.931	-0.218	-0.218	0.000	0.000	0.000	0.000
12	A	12	VAL	0	-0.003	0.007	29.034	0.253	0.253	0.000	0.000	0.000	0.000
13	A	13	GLN	0	0.034	0.023	31.370	0.070	0.070	0.000	0.000	0.000	0.000
14	A	14	THR	0	-0.007	-0.044	33.472	-0.194	-0.194	0.000	0.000	0.000	0.000
15	A	15	GLY	0	-0.013	-0.002	33.510	0.263	0.263	0.000	0.000	0.000	0.000
16	A	16	GLY	0	-0.029	0.001	32.540	0.032	0.032	0.000	0.000	0.000	0.000
17	A	17	SER	0	-0.020	-0.074	28.912	-0.059	-0.059	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.051	-0.022	24.598	0.060	0.060	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.964	0.995	21.738	13.451	13.451	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.039	-0.001	17.949	-0.228	-0.228	0.000	0.000	0.000	0.000
21	A	21	THR	0	0.021	0.002	16.547	0.269	0.269	0.000	0.000	0.000	0.000
22	A	22	CYS	0	-0.056	-0.027	11.056	-1.074	-1.074	0.000	0.000	0.000	0.000
23	A	23	LEU	0	0.024	0.020	12.529	0.263	0.263	0.000	0.000	0.000	0.000
24	A	24	ALA	0	0.029	0.009	8.399	-2.486	-2.486	0.000	0.000	0.000	0.000
25	A	25	SER	0	0.005	0.001	7.643	2.454	2.454	0.000	0.000	0.000	0.000
26	A	26	GLY	0	0.024	0.006	4.597	-5.573	-5.528	-0.001	-0.042	-0.002	0.000
27	A	27	ASN	0	0.004	-0.007	3.598	4.159	5.075	0.015	-0.397	-0.535	0.001
28	A	28	THR	0	0.024	0.003	5.145	-2.342	-2.269	-0.001	-0.003	-0.069	0.000
29	A	29	ALA	0	0.050	0.034	8.341	0.553	0.553	0.000	0.000	0.000	0.000
30	A	30	SER	0	-0.084	-0.039	5.935	-1.028	-1.028	0.000	0.000	0.000	0.000
31	A	31	ILE	0	-0.028	-0.006	7.251	-1.325	-1.325	0.000	0.000	0.000	0.000
32	A	32	ARG	1	0.882	0.948	9.087	28.573	28.573	0.000	0.000	0.000	0.000
33	A	33	ALA	0	0.018	0.005	10.579	2.677	2.677	0.000	0.000	0.000	0.000
34	A	34	MET	0	-0.038	-0.001	9.752	-2.871	-2.871	0.000	0.000	0.000	0.000
35	A	35	GLY	0	0.074	0.036	11.700	2.332	2.332	0.000	0.000	0.000	0.000
36	A	36	TRP	0	-0.042	-0.016	13.000	-1.654	-1.654	0.000	0.000	0.000	0.000
37	A	37	TYR	0	0.053	0.021	12.223	1.549	1.549	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.829	0.911	15.482	13.697	13.697	0.000	0.000	0.000	0.000
39	A	39	ARG	1	0.928	0.986	17.717	16.264	16.264	0.000	0.000	0.000	0.000
40	A	40	ALA	0	0.065	0.034	19.430	0.237	0.237	0.000	0.000	0.000	0.000
41	A	41	PRO	0	-0.007	-0.018	23.071	-0.287	-0.287	0.000	0.000	0.000	0.000
42	A	42	GLY	0	-0.001	-0.001	24.594	0.292	0.292	0.000	0.000	0.000	0.000
43	A	43	LYS	1	0.962	1.004	23.142	12.322	12.322	0.000	0.000	0.000	0.000
44	A	44	GLN	0	0.009	-0.006	19.196	-0.203	-0.203	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.843	0.931	10.268	25.686	25.686	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.845	-0.915	17.281	-14.084	-14.084	0.000	0.000	0.000	0.000
47	A	47	TRP	0	0.015	-0.019	15.436	-0.136	-0.136	0.000	0.000	0.000	0.000
48	A	48	VAL	0	-0.048	-0.015	17.301	1.098	1.098	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.045	0.012	17.513	1.054	1.054	0.000	0.000	0.000	0.000
50	A	50	SER	0	0.011	0.029	15.196	-1.742	-1.742	0.000	0.000	0.000	0.000
51	A	51	LEU	0	0.032	0.034	15.409	1.217	1.217	0.000	0.000	0.000	0.000
52	A	52	THR	0	0.038	0.019	15.192	-1.516	-1.516	0.000	0.000	0.000	0.000
53	A	53	THR	0	-0.026	-0.043	13.422	0.338	0.338	0.000	0.000	0.000	0.000
54	A	54	THR	0	-0.031	-0.018	16.288	0.308	0.308	0.000	0.000	0.000	0.000
55	A	55	GLY	0	0.019	0.019	19.240	0.790	0.790	0.000	0.000	0.000	0.000
56	A	56	THR	0	-0.034	-0.008	20.050	0.742	0.742	0.000	0.000	0.000	0.000
57	A	57	ALA	0	-0.017	-0.012	19.503	-0.959	-0.959	0.000	0.000	0.000	0.000
58	A	58	ASP	-1	-0.883	-0.926	19.815	-14.160	-14.160	0.000	0.000	0.000	0.000
59	A	59	TYR	0	0.014	-0.017	20.310	-0.899	-0.899	0.000	0.000	0.000	0.000
60	A	60	GLY	0	0.047	0.027	21.924	0.262	0.262	0.000	0.000	0.000	0.000
61	A	61	ASP	-1	-0.844	-0.928	23.088	-11.659	-11.659	0.000	0.000	0.000	0.000
62	A	62	PHE	0	-0.080	-0.052	21.384	0.683	0.683	0.000	0.000	0.000	0.000
63	A	63	VAL	0	-0.016	0.008	23.162	0.300	0.300	0.000	0.000	0.000	0.000
64	A	64	LYS	1	0.904	0.950	26.411	10.782	10.782	0.000	0.000	0.000	0.000
65	A	65	GLY	0	0.039	0.012	28.451	0.325	0.325	0.000	0.000	0.000	0.000
66	A	66	ARG	1	0.728	0.850	27.557	11.405	11.405	0.000	0.000	0.000	0.000
67	A	67	PHE	0	-0.021	-0.017	22.844	-0.175	-0.175	0.000	0.000	0.000	0.000
68	A	68	THR	0	0.029	0.019	24.140	0.185	0.185	0.000	0.000	0.000	0.000
69	A	69	ILE	0	-0.048	-0.016	16.067	-0.308	-0.308	0.000	0.000	0.000	0.000
70	A	70	SER	0	-0.014	-0.014	19.607	0.472	0.472	0.000	0.000	0.000	0.000
71	A	71	ARG	1	0.867	0.921	13.244	20.638	20.638	0.000	0.000	0.000	0.000
72	A	72	ASP	-1	-0.827	-0.897	17.122	-14.303	-14.303	0.000	0.000	0.000	0.000
73	A	73	ASN	0	0.016	-0.018	16.591	-0.994	-0.994	0.000	0.000	0.000	0.000
74	A	74	ALA	0	0.002	0.013	16.561	-0.501	-0.501	0.000	0.000	0.000	0.000
75	A	75	ASN	0	-0.060	-0.029	17.025	0.117	0.117	0.000	0.000	0.000	0.000
76	A	76	ASN	0	-0.047	-0.020	12.041	-1.600	-1.600	0.000	0.000	0.000	0.000
77	A	77	ALA	0	0.027	0.018	12.767	-1.783	-1.783	0.000	0.000	0.000	0.000
78	A	78	ALA	0	0.007	-0.004	13.727	0.425	0.425	0.000	0.000	0.000	0.000
79	A	79	THR	0	-0.042	-0.032	15.381	0.082	0.082	0.000	0.000	0.000	0.000
80	A	80	LEU	0	-0.001	-0.002	18.379	-0.045	-0.045	0.000	0.000	0.000	0.000
81	A	81	GLN	0	-0.004	-0.001	20.335	-0.186	-0.186	0.000	0.000	0.000	0.000
82	A	82	MET	0	-0.036	-0.016	22.130	-0.029	-0.029	0.000	0.000	0.000	0.000
83	A	83	ASP	-1	-0.722	-0.818	25.704	-10.703	-10.703	0.000	0.000	0.000	0.000
84	A	84	SER	0	-0.013	-0.012	29.493	0.003	0.003	0.000	0.000	0.000	0.000
85	A	85	LEU	0	0.003	0.019	26.078	-0.053	-0.053	0.000	0.000	0.000	0.000
86	A	86	LYS	1	0.967	0.977	29.621	10.795	10.795	0.000	0.000	0.000	0.000
87	A	87	PRO	0	0.066	0.029	29.582	-0.409	-0.409	0.000	0.000	0.000	0.000
88	A	88	GLU	-1	-0.966	-0.983	28.489	-10.954	-10.954	0.000	0.000	0.000	0.000
89	A	89	ASP	-1	-0.782	-0.856	25.702	-12.193	-12.193	0.000	0.000	0.000	0.000
90	A	90	THR	0	-0.013	0.012	24.565	-0.601	-0.601	0.000	0.000	0.000	0.000
91	A	91	ALA	0	-0.005	-0.014	20.962	-0.067	-0.067	0.000	0.000	0.000	0.000
92	A	92	VAL	0	-0.060	-0.008	16.681	0.074	0.074	0.000	0.000	0.000	0.000
93	A	93	TYR	0	0.047	-0.014	17.263	-0.587	-0.587	0.000	0.000	0.000	0.000
94	A	94	TYR	0	-0.015	-0.013	11.712	0.172	0.172	0.000	0.000	0.000	0.000
95	A	96	ASN	0	0.011	-0.008	8.159	-0.392	-0.392	0.000	0.000	0.000	0.000
96	A	97	ALA	0	0.008	0.005	6.241	3.250	3.250	0.000	0.000	0.000	0.000
97	A	98	ASP	-1	-0.782	-0.870	5.667	-43.368	-43.368	0.000	0.000	0.000	0.000
98	A	99	GLY	0	0.017	-0.029	6.632	4.171	4.171	0.000	0.000	0.000	0.000
99	A	100	ARG	1	0.922	0.969	7.497	21.043	21.043	0.000	0.000	0.000	0.000
100	A	101	ARG	1	0.958	0.980	3.056	41.043	42.311	0.195	-0.306	-1.158	0.000
101	A	102	PHE	0	0.053	0.030	6.750	0.114	0.114	0.000	0.000	0.000	0.000
102	A	103	ASP	-1	-0.941	-0.975	7.335	-26.587	-26.587	0.000	0.000	0.000	0.000
103	A	104	GLY	0	0.036	0.020	8.328	0.641	0.641	0.000	0.000	0.000	0.000
104	A	105	ALA	0	-0.005	0.002	11.284	1.533	1.533	0.000	0.000	0.000	0.000
105	A	106	ARG	1	0.926	0.981	11.822	23.935	23.935	0.000	0.000	0.000	0.000
106	A	107	TRP	0	0.015	0.005	9.862	-2.651	-2.651	0.000	0.000	0.000	0.000
107	A	108	ARG	1	0.891	0.920	7.970	29.184	29.184	0.000	0.000	0.000	0.000
108	A	109	GLU	-1	-0.915	-0.950	8.117	-29.192	-29.192	0.000	0.000	0.000	0.000
109	A	110	TYR	0	-0.114	-0.073	2.595	-9.002	-6.838	0.400	-0.915	-1.649	-0.009
110	A	111	GLU	-1	-0.752	-0.889	3.654	-32.013	-31.645	0.001	-0.137	-0.232	-0.001
111	A	112	SER	0	-0.152	-0.077	2.246	-38.601	-34.337	2.686	-3.374	-3.575	-0.040
112	A	113	TRP	0	0.043	0.004	3.674	12.699	12.937	0.008	-0.064	-0.183	-0.001
113	A	114	GLY	0	0.009	0.013	6.711	-1.684	-1.684	0.000	0.000	0.000	0.000
114	A	115	GLN	0	-0.012	-0.023	9.494	-1.408	-1.408	0.000	0.000	0.000	0.000
115	A	116	GLY	0	-0.037	-0.010	12.148	1.368	1.368	0.000	0.000	0.000	0.000
116	A	117	THR	0	-0.045	-0.002	14.775	0.281	0.281	0.000	0.000	0.000	0.000
117	A	118	GLN	0	-0.007	-0.011	18.012	0.544	0.544	0.000	0.000	0.000	0.000
118	A	119	VAL	0	0.028	0.026	21.392	0.217	0.217	0.000	0.000	0.000	0.000
119	A	120	THR	0	-0.018	-0.015	23.893	0.067	0.067	0.000	0.000	0.000	0.000
120	A	121	ILE	0	0.001	0.016	27.055	0.152	0.152	0.000	0.000	0.000	0.000
121	A	122	SER	0	0.001	0.003	30.162	0.141	0.141	0.000	0.000	0.000	0.000
122	A	123	SER	0	0.032	0.021	33.621	0.058	0.058	0.000	0.000	0.000	0.000

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