FMO DATABASE

FMODB ID: 176NZ

Calculation Name: 3LF9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LF9

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-22

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	120
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-893703.742298
FMO2-HF: Nuclear repulsion	846381.381106
FMO2-HF: Total energy	-47322.361192
FMO2-MP2: Total energy	-47461.252978

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:MET)

Summations of interaction energy for fragment #1(A: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.
-6.22	-1.62	5.621	-2.609	-7.614	-0.007

Interaction energy analysis for fragmet #1(A: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 : 0.018

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	ASN	0	-0.015	-0.020	3.566	-2.567	-0.913	-0.006	-0.687	-0.962	0.002
4	A	4	GLU	-1	-0.832	-0.909	3.145	-1.188	0.031	0.502	-0.399	-1.321	0.000
5	A	5	ILE	0	0.012	0.015	2.261	-1.656	-0.891	2.971	-0.889	-2.846	-0.005
6	A	6	LYS	1	0.871	0.920	4.270	0.300	0.506	0.000	-0.039	-0.168	0.000
7	A	7	LYS	1	0.850	0.929	7.363	0.484	0.484	0.000	0.000	0.000	0.000
8	A	8	ASP	-1	-0.834	-0.921	5.836	-1.425	-1.425	0.000	0.000	0.000	0.000
9	A	9	ALA	0	0.025	0.012	7.694	0.183	0.183	0.000	0.000	0.000	0.000
10	A	10	GLN	0	-0.014	-0.023	9.598	0.122	0.122	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.845	-0.920	10.848	-0.359	-0.359	0.000	0.000	0.000	0.000
12	A	12	ARG	1	0.800	0.892	8.228	1.328	1.328	0.000	0.000	0.000	0.000
13	A	13	MET	0	-0.037	-0.003	12.940	0.092	0.092	0.000	0.000	0.000	0.000
14	A	14	ASP	-1	-0.839	-0.905	15.381	-0.213	-0.213	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.839	0.904	13.295	0.456	0.456	0.000	0.000	0.000	0.000
16	A	16	SER	0	-0.044	-0.023	16.465	0.027	0.027	0.000	0.000	0.000	0.000
17	A	17	VAL	0	-0.001	0.000	18.935	0.033	0.033	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.806	-0.888	20.878	-0.132	-0.132	0.000	0.000	0.000	0.000
19	A	19	ALA	0	0.018	0.025	21.331	0.021	0.021	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.002	0.012	23.127	0.018	0.018	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.828	0.897	24.997	0.167	0.167	0.000	0.000	0.000	0.000
22	A	22	ASN	0	-0.029	-0.024	25.229	0.021	0.021	0.000	0.000	0.000	0.000
23	A	23	ASN	0	-0.017	0.006	25.415	0.021	0.021	0.000	0.000	0.000	0.000
24	A	24	LEU	0	0.069	0.031	28.855	0.012	0.012	0.000	0.000	0.000	0.000
25	A	25	SER	0	-0.110	-0.057	30.928	0.012	0.012	0.000	0.000	0.000	0.000
26	A	26	LYS	1	0.872	0.931	28.804	0.158	0.158	0.000	0.000	0.000	0.000
27	A	27	VAL	0	-0.014	0.018	33.347	0.007	0.007	0.000	0.000	0.000	0.000
28	A	28	ARG	1	0.783	0.845	35.876	0.079	0.079	0.000	0.000	0.000	0.000
29	A	29	THR	0	0.006	-0.014	39.230	0.000	0.000	0.000	0.000	0.000	0.000
30	A	30	GLY	0	0.012	0.017	42.504	0.002	0.002	0.000	0.000	0.000	0.000
31	A	31	GLY	0	0.013	0.013	44.304	0.003	0.003	0.000	0.000	0.000	0.000
32	A	32	GLY	0	0.032	0.012	46.357	0.003	0.003	0.000	0.000	0.000	0.000
33	A	33	GLY	0	0.031	0.014	46.868	-0.003	-0.003	0.000	0.000	0.000	0.000
34	A	34	THR	0	0.026	0.014	48.215	0.000	0.000	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.814	-0.905	46.906	-0.061	-0.061	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.792	-0.893	45.645	-0.074	-0.074	0.000	0.000	0.000	0.000
37	A	37	ARG	1	0.901	0.932	44.536	0.069	0.069	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.785	0.878	43.126	0.058	0.058	0.000	0.000	0.000	0.000
39	A	39	LYS	1	0.880	0.921	41.369	0.061	0.061	0.000	0.000	0.000	0.000
40	A	40	ASP	-1	-0.857	-0.911	40.490	-0.084	-0.084	0.000	0.000	0.000	0.000
41	A	41	LEU	0	-0.014	0.001	38.563	-0.006	-0.006	0.000	0.000	0.000	0.000
42	A	42	VAL	0	0.001	0.000	36.805	-0.007	-0.007	0.000	0.000	0.000	0.000
43	A	43	LYS	1	0.803	0.885	35.765	0.077	0.077	0.000	0.000	0.000	0.000
44	A	44	ILE	0	-0.005	0.008	33.572	-0.007	-0.007	0.000	0.000	0.000	0.000
45	A	45	VAL	0	0.048	0.020	31.965	-0.009	-0.009	0.000	0.000	0.000	0.000
46	A	46	ARG	1	0.794	0.864	30.872	0.092	0.092	0.000	0.000	0.000	0.000
47	A	47	GLY	0	-0.011	0.006	30.302	-0.009	-0.009	0.000	0.000	0.000	0.000
48	A	48	GLU	-1	-0.879	-0.958	27.862	-0.171	-0.171	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.006	0.001	26.229	-0.018	-0.018	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.843	-0.912	25.424	-0.223	-0.223	0.000	0.000	0.000	0.000
51	A	51	GLY	0	0.021	0.015	24.297	-0.020	-0.020	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.004	-0.006	21.833	-0.029	-0.029	0.000	0.000	0.000	0.000
53	A	53	ARG	1	0.773	0.847	20.573	0.142	0.142	0.000	0.000	0.000	0.000
54	A	54	VAL	0	-0.016	-0.006	20.308	-0.030	-0.030	0.000	0.000	0.000	0.000
55	A	55	ALA	0	-0.005	0.004	17.949	-0.042	-0.042	0.000	0.000	0.000	0.000
56	A	56	VAL	0	0.033	0.011	16.145	-0.067	-0.067	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.935	0.964	15.509	0.198	0.198	0.000	0.000	0.000	0.000
58	A	58	ASN	0	-0.069	-0.022	13.674	0.027	0.027	0.000	0.000	0.000	0.000
59	A	59	ILE	0	-0.019	0.000	10.723	-0.096	-0.096	0.000	0.000	0.000	0.000
60	A	60	ALA	0	0.020	0.011	10.946	-0.154	-0.154	0.000	0.000	0.000	0.000
61	A	61	ARG	1	0.929	0.963	11.900	0.403	0.403	0.000	0.000	0.000	0.000
62	A	62	ASP	-1	-0.827	-0.909	9.164	-0.987	-0.987	0.000	0.000	0.000	0.000
63	A	63	ALA	0	0.060	0.025	7.192	-0.231	-0.231	0.000	0.000	0.000	0.000
64	A	64	ALA	0	0.005	-0.007	7.630	-0.154	-0.154	0.000	0.000	0.000	0.000
65	A	65	ASN	0	-0.037	-0.020	9.649	0.172	0.172	0.000	0.000	0.000	0.000
66	A	66	ASP	-1	-0.899	-0.948	4.513	-3.026	-2.841	-0.001	-0.008	-0.177	0.000
67	A	67	LEU	0	-0.061	-0.038	5.159	-0.122	-0.122	0.000	0.000	0.000	0.000
68	A	68	ALA	0	-0.001	-0.004	6.623	0.375	0.375	0.000	0.000	0.000	0.000
69	A	69	ALA	0	-0.025	-0.002	6.293	0.249	0.249	0.000	0.000	0.000	0.000
70	A	70	LEU	0	0.010	-0.004	2.386	-0.860	-0.289	2.155	-0.587	-2.140	-0.004
71	A	71	GLY	0	0.032	0.027	5.961	0.369	0.369	0.000	0.000	0.000	0.000
72	A	72	LYS	1	0.798	0.887	7.980	0.627	0.627	0.000	0.000	0.000	0.000
73	A	73	ASP	-1	-0.907	-0.953	6.865	0.903	0.903	0.000	0.000	0.000	0.000
74	A	74	LYS	1	0.806	0.879	9.065	-0.345	-0.345	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.819	-0.886	8.175	0.588	0.588	0.000	0.000	0.000	0.000
76	A	76	VAL	0	-0.064	-0.015	4.848	0.434	0.434	0.000	0.000	0.000	0.000
77	A	77	ASN	0	-0.030	-0.013	7.914	-0.543	-0.543	0.000	0.000	0.000	0.000
78	A	78	TRP	0	0.080	0.015	9.892	0.042	0.042	0.000	0.000	0.000	0.000
79	A	79	PHE	0	0.008	0.016	12.136	-0.090	-0.090	0.000	0.000	0.000	0.000
80	A	80	ASP	-1	-0.812	-0.904	8.289	1.253	1.253	0.000	0.000	0.000	0.000
81	A	81	ILE	0	-0.005	-0.002	7.057	-0.108	-0.108	0.000	0.000	0.000	0.000
82	A	82	SER	0	-0.037	-0.031	9.287	-0.252	-0.252	0.000	0.000	0.000	0.000
83	A	83	GLN	0	-0.018	-0.001	12.047	-0.105	-0.105	0.000	0.000	0.000	0.000
84	A	84	ALA	0	-0.007	-0.011	8.372	-0.112	-0.112	0.000	0.000	0.000	0.000
85	A	85	LEU	0	0.006	0.004	10.486	-0.187	-0.187	0.000	0.000	0.000	0.000
86	A	86	TRP	0	0.009	0.014	12.118	-0.044	-0.044	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.853	-0.931	12.018	0.030	0.030	0.000	0.000	0.000	0.000
88	A	88	ILE	0	0.001	0.015	9.011	-0.030	-0.030	0.000	0.000	0.000	0.000
89	A	89	GLN	0	-0.002	0.002	12.852	0.030	0.030	0.000	0.000	0.000	0.000
90	A	90	LYS	1	0.938	0.970	16.372	0.044	0.044	0.000	0.000	0.000	0.000
91	A	91	LEU	0	-0.030	-0.007	12.112	0.014	0.014	0.000	0.000	0.000	0.000
92	A	92	THR	0	-0.024	-0.031	15.726	-0.015	-0.015	0.000	0.000	0.000	0.000
93	A	93	ASP	-1	-0.906	-0.943	17.541	-0.160	-0.160	0.000	0.000	0.000	0.000
94	A	94	VAL	0	-0.070	-0.036	19.446	0.020	0.020	0.000	0.000	0.000	0.000
95	A	95	ALA	0	0.025	0.012	18.126	0.015	0.015	0.000	0.000	0.000	0.000
96	A	96	VAL	0	-0.008	-0.023	20.230	0.011	0.011	0.000	0.000	0.000	0.000
97	A	97	LYS	1	0.922	0.966	22.687	0.112	0.112	0.000	0.000	0.000	0.000
98	A	98	LYS	1	0.899	0.955	23.263	0.128	0.128	0.000	0.000	0.000	0.000
99	A	99	ILE	0	0.000	-0.005	21.324	0.011	0.011	0.000	0.000	0.000	0.000
100	A	100	ASP	-1	-0.810	-0.894	25.435	-0.146	-0.146	0.000	0.000	0.000	0.000
101	A	101	GLU	-1	-0.865	-0.916	28.144	-0.093	-0.093	0.000	0.000	0.000	0.000
102	A	102	VAL	0	-0.061	-0.033	26.677	0.009	0.009	0.000	0.000	0.000	0.000
103	A	103	LEU	0	-0.009	0.005	29.508	0.006	0.006	0.000	0.000	0.000	0.000
104	A	104	ALA	0	0.000	0.003	31.188	0.007	0.007	0.000	0.000	0.000	0.000
105	A	105	ALA	0	-0.017	-0.011	33.035	0.007	0.007	0.000	0.000	0.000	0.000
106	A	106	LYS	1	0.853	0.914	32.754	0.106	0.106	0.000	0.000	0.000	0.000
107	A	107	GLU	-1	-0.761	-0.870	34.740	-0.097	-0.097	0.000	0.000	0.000	0.000
108	A	108	LYS	1	0.837	0.906	37.073	0.064	0.064	0.000	0.000	0.000	0.000
109	A	109	GLU	-1	-0.789	-0.847	36.579	-0.085	-0.085	0.000	0.000	0.000	0.000
110	A	110	LEU	0	-0.030	-0.005	36.573	0.004	0.004	0.000	0.000	0.000	0.000
111	A	111	MET	0	-0.042	-0.018	40.378	0.003	0.003	0.000	0.000	0.000	0.000
112	A	112	GLU	-1	-0.844	-0.888	42.885	-0.053	-0.053	0.000	0.000	0.000	0.000
113	A	113	VAL	0	-0.023	-0.005	44.920	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	114	LEU	0	0.018	0.003	44.414	0.002	0.002	0.000	0.000	0.000	0.000
115	A	115	GLU	-1	-0.898	-0.953	48.813	-0.037	-0.037	0.000	0.000	0.000	0.000
116	A	116	HIS	0	-0.008	-0.005	45.576	0.002	0.002	0.000	0.000	0.000	0.000
117	A	117	HIS	0	-0.028	0.006	45.008	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	118	HIS	0	0.010	0.009	49.807	0.003	0.003	0.000	0.000	0.000	0.000
119	A	119	HIS	0	-0.046	-0.035	51.371	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	120	HIS	0	0.006	0.012	51.219	-0.001	-0.001	0.000	0.000	0.000	0.000

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