FMO DATABASE

FMODB ID: YY3N2

Calculation Name: 4LBI-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4LBI

Chain ID: C

ChEMBL ID:

UniProt ID: Q45075

Base Structure: X-ray

Registration Date: 2023-06-20

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	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	94
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-653033.559445
FMO2-HF: Nuclear repulsion	616422.030549
FMO2-HF: Total energy	-36611.528897
FMO2-MP2: Total energy	-36718.519943

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(C:1:MET)

Summations of interaction energy for fragment #1(C:1:MET)

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.
-42.612	-40.3	20.723	-10.442	-12.593	0.02

Interaction energy analysis for fragmet #1(C:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.050 / q_NPA : 0.030

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	C	3	PHE	0	0.020	-0.004	2.351	0.628	4.508	1.368	-2.138	-3.109	-0.001
4	C	4	LEU	0	-0.027	-0.004	6.259	-0.352	-0.352	0.000	0.000	0.000	0.000
5	C	5	ILE	0	0.009	0.000	9.359	0.205	0.205	0.000	0.000	0.000	0.000
6	C	6	TYR	0	0.020	0.005	12.081	-0.064	-0.064	0.000	0.000	0.000	0.000
7	C	7	ARG	1	0.874	0.933	15.607	0.541	0.541	0.000	0.000	0.000	0.000
8	C	8	LYS	1	0.896	0.962	18.491	0.007	0.007	0.000	0.000	0.000	0.000
9	C	9	ASP	-1	-0.715	-0.847	22.228	-0.177	-0.177	0.000	0.000	0.000	0.000
10	C	10	ARG	1	0.878	0.931	25.105	0.105	0.105	0.000	0.000	0.000	0.000
11	C	11	PRO	0	0.011	-0.002	27.697	-0.013	-0.013	0.000	0.000	0.000	0.000
12	C	12	GLY	0	0.016	0.000	30.827	0.001	0.001	0.000	0.000	0.000	0.000
13	C	13	SER	0	-0.017	-0.009	28.830	-0.005	-0.005	0.000	0.000	0.000	0.000
14	C	14	LEU	0	0.031	0.026	29.864	-0.017	-0.017	0.000	0.000	0.000	0.000
15	C	15	GLN	0	-0.021	-0.026	30.835	-0.008	-0.008	0.000	0.000	0.000	0.000
16	C	16	VAL	0	0.031	0.024	27.809	-0.012	-0.012	0.000	0.000	0.000	0.000
17	C	17	ARG	1	0.784	0.845	22.306	0.221	0.221	0.000	0.000	0.000	0.000
18	C	18	ILE	0	-0.004	-0.012	27.875	-0.028	-0.028	0.000	0.000	0.000	0.000
19	C	19	ASP	-1	-0.863	-0.919	30.545	-0.182	-0.182	0.000	0.000	0.000	0.000
20	C	20	ASN	0	-0.076	-0.049	26.154	-0.024	-0.024	0.000	0.000	0.000	0.000
21	C	21	TYR	0	-0.023	-0.006	23.838	-0.059	-0.059	0.000	0.000	0.000	0.000
22	C	22	ALA	0	0.029	0.017	25.028	-0.039	-0.039	0.000	0.000	0.000	0.000
23	C	23	ALA	0	0.051	0.019	25.202	-0.035	-0.035	0.000	0.000	0.000	0.000
24	C	24	HIS	1	0.831	0.903	18.305	0.499	0.499	0.000	0.000	0.000	0.000
25	C	25	LEU	0	0.000	-0.013	20.520	-0.075	-0.075	0.000	0.000	0.000	0.000
26	C	26	ALA	0	-0.022	-0.006	21.156	-0.051	-0.051	0.000	0.000	0.000	0.000
27	C	27	TYR	0	-0.063	-0.060	15.361	-0.057	-0.057	0.000	0.000	0.000	0.000
28	C	28	LEU	0	0.000	-0.009	15.253	-0.089	-0.089	0.000	0.000	0.000	0.000
29	C	29	GLU	-1	-0.807	-0.869	16.458	-0.817	-0.817	0.000	0.000	0.000	0.000
30	C	30	PRO	0	-0.030	-0.018	16.748	-0.053	-0.053	0.000	0.000	0.000	0.000
31	C	31	LEU	0	-0.011	-0.001	12.166	-0.093	-0.093	0.000	0.000	0.000	0.000
32	C	32	LYS	1	0.835	0.907	12.725	0.521	0.521	0.000	0.000	0.000	0.000
33	C	33	ALA	0	-0.022	-0.021	12.470	-0.026	-0.026	0.000	0.000	0.000	0.000
34	C	34	LYS	1	0.836	0.928	5.241	5.918	5.918	0.000	0.000	0.000	0.000
35	C	35	ILE	0	-0.024	-0.011	8.789	-0.410	-0.410	0.000	0.000	0.000	0.000
36	C	36	GLN	0	0.018	0.018	7.415	0.634	0.634	0.000	0.000	0.000	0.000
37	C	37	VAL	0	0.001	-0.002	11.639	0.253	0.253	0.000	0.000	0.000	0.000
38	C	38	GLY	0	0.012	-0.002	13.876	-0.110	-0.110	0.000	0.000	0.000	0.000
39	C	39	GLY	0	-0.007	0.010	16.538	0.044	0.044	0.000	0.000	0.000	0.000
40	C	40	PRO	0	-0.002	0.004	19.621	0.002	0.002	0.000	0.000	0.000	0.000
41	C	41	THR	0	-0.004	-0.003	20.713	0.021	0.021	0.000	0.000	0.000	0.000
42	C	42	LEU	0	-0.002	-0.011	23.099	-0.011	-0.011	0.000	0.000	0.000	0.000
43	C	43	GLY	0	-0.017	-0.007	26.847	0.021	0.021	0.000	0.000	0.000	0.000
44	C	44	ALA	0	-0.037	-0.017	29.712	0.005	0.005	0.000	0.000	0.000	0.000
45	C	45	GLY	0	-0.003	0.006	32.934	-0.009	-0.009	0.000	0.000	0.000	0.000
46	C	46	THR	0	0.022	-0.011	32.642	0.005	0.005	0.000	0.000	0.000	0.000
47	C	47	GLY	0	-0.035	0.009	33.008	-0.007	-0.007	0.000	0.000	0.000	0.000
48	C	48	THR	0	0.006	-0.014	29.013	0.004	0.004	0.000	0.000	0.000	0.000
49	C	49	ASP	-1	-0.898	-0.946	29.942	-0.151	-0.151	0.000	0.000	0.000	0.000
50	C	50	ASP	-1	-0.817	-0.923	29.310	-0.231	-0.231	0.000	0.000	0.000	0.000
51	C	51	LYS	1	0.767	0.878	30.245	0.108	0.108	0.000	0.000	0.000	0.000
52	C	52	ASP	-1	-0.801	-0.893	30.512	-0.095	-0.095	0.000	0.000	0.000	0.000
53	C	53	MET	0	-0.044	0.004	26.135	-0.005	-0.005	0.000	0.000	0.000	0.000
54	C	54	THR	0	-0.011	-0.006	25.891	0.017	0.017	0.000	0.000	0.000	0.000
55	C	55	GLY	0	0.042	0.010	22.431	0.027	0.027	0.000	0.000	0.000	0.000
56	C	56	SER	0	-0.075	-0.032	18.557	-0.018	-0.018	0.000	0.000	0.000	0.000
57	C	57	PHE	0	0.007	0.014	13.523	0.028	0.028	0.000	0.000	0.000	0.000
58	C	58	LEU	0	0.010	-0.005	12.730	-0.045	-0.045	0.000	0.000	0.000	0.000
59	C	59	ILE	0	-0.005	0.010	8.696	0.132	0.132	0.000	0.000	0.000	0.000
60	C	60	MET	0	-0.033	-0.017	7.987	0.202	0.202	0.000	0.000	0.000	0.000
61	C	61	GLU	-1	-0.875	-0.936	3.051	-6.642	-5.999	0.037	-0.172	-0.507	0.000
62	C	62	ALA	0	-0.013	-0.002	3.173	2.082	2.839	0.005	-0.309	-0.454	0.000
63	C	63	GLU	-1	-0.857	-0.943	1.883	-19.556	-21.056	8.019	-3.744	-2.775	-0.042
64	C	64	SER	0	-0.052	-0.026	3.838	0.829	1.364	0.001	-0.115	-0.422	-0.001
65	C	65	TRP	0	0.047	-0.002	5.180	-0.147	0.049	-0.001	-0.009	-0.186	0.000
66	C	66	ASP	-1	-0.913	-0.946	6.773	-0.443	-0.443	0.000	0.000	0.000	0.000
67	C	67	GLU	-1	-0.862	-0.927	6.724	-4.278	-4.278	0.000	0.000	0.000	0.000
68	C	68	VAL	0	-0.001	-0.002	5.719	0.104	0.104	0.000	0.000	0.000	0.000
69	C	69	HIS	0	0.024	-0.005	8.536	0.058	0.058	0.000	0.000	0.000	0.000
70	C	70	SER	0	0.008	0.017	11.511	0.105	0.105	0.000	0.000	0.000	0.000
71	C	71	PHE	0	0.014	0.010	11.029	0.088	0.088	0.000	0.000	0.000	0.000
72	C	72	VAL	0	-0.001	0.014	12.086	0.099	0.099	0.000	0.000	0.000	0.000
73	C	73	GLU	-1	-0.911	-0.949	14.494	-0.181	-0.181	0.000	0.000	0.000	0.000
74	C	74	ASN	0	-0.096	-0.057	16.133	0.119	0.119	0.000	0.000	0.000	0.000
75	C	75	ASP	-1	-0.767	-0.835	17.244	-0.547	-0.547	0.000	0.000	0.000	0.000
76	C	76	PRO	0	-0.002	-0.010	19.053	0.070	0.070	0.000	0.000	0.000	0.000
77	C	77	PHE	0	-0.006	-0.017	20.924	0.040	0.040	0.000	0.000	0.000	0.000
78	C	78	THR	0	-0.034	-0.031	18.123	0.061	0.061	0.000	0.000	0.000	0.000
79	C	79	LYS	1	0.937	0.975	21.300	0.382	0.382	0.000	0.000	0.000	0.000
80	C	80	ALA	0	-0.009	0.015	23.974	0.026	0.026	0.000	0.000	0.000	0.000
81	C	81	GLY	0	-0.008	0.007	24.774	0.025	0.025	0.000	0.000	0.000	0.000
82	C	82	LEU	0	-0.032	0.001	23.422	0.030	0.030	0.000	0.000	0.000	0.000
83	C	83	PHE	0	-0.011	-0.023	19.821	0.009	0.009	0.000	0.000	0.000	0.000
84	C	84	ALA	0	-0.009	0.004	23.143	0.011	0.011	0.000	0.000	0.000	0.000
85	C	85	ALA	0	-0.033	-0.008	21.070	0.036	0.036	0.000	0.000	0.000	0.000
86	C	86	THR	0	0.039	0.005	15.184	-0.073	-0.073	0.000	0.000	0.000	0.000
87	C	87	ILE	0	-0.026	-0.005	13.591	0.062	0.062	0.000	0.000	0.000	0.000
88	C	88	VAL	0	-0.001	0.000	8.493	-0.143	-0.143	0.000	0.000	0.000	0.000
89	C	89	GLU	-1	-0.905	-0.946	8.950	1.853	1.853	0.000	0.000	0.000	0.000
90	C	90	ARG	1	0.881	0.953	2.471	-21.952	-24.338	11.296	-3.943	-4.968	0.064
91	C	91	TRP	0	-0.005	-0.007	4.507	-0.231	-0.109	-0.001	-0.005	-0.115	0.000
92	C	92	LYS	1	0.938	0.965	4.948	-1.639	-1.574	-0.001	-0.007	-0.057	0.000
93	C	93	HIS	0	0.031	0.016	7.221	0.124	0.124	0.000	0.000	0.000	0.000
94	C	94	GLY	0	-0.030	-0.012	10.148	0.226	0.226	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:1:MET)