FMO DATABASE

FMODB ID: G6Y51

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

Total energy (hartree)

FMO2-HF: Electronic energy	-894973.088693
FMO2-HF: Nuclear repulsion	847650.575663
FMO2-HF: Total energy	-47322.513031
FMO2-MP2: Total energy	-47461.333651

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.
-6.183	-1.641	5.471	-2.502	-7.509	-0.006

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 : 0.056 / q_NPA : 0.020

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	-0.010	-0.027	3.643	-2.395	-0.852	-0.005	-0.653	-0.885	0.001
4	A	4	GLU	-1	-0.821	-0.889	3.172	-1.291	-0.044	0.488	-0.421	-1.314	0.001
5	A	5	ILE	0	0.015	0.016	2.304	-1.636	-0.988	3.073	-0.853	-2.869	-0.004
6	A	6	LYS	1	0.869	0.932	4.304	0.209	0.407	0.000	-0.037	-0.160	0.000
7	A	7	LYS	1	0.827	0.912	7.421	0.488	0.488	0.000	0.000	0.000	0.000
8	A	8	ASP	-1	-0.822	-0.907	5.665	-1.535	-1.535	0.000	0.000	0.000	0.000
9	A	9	ALA	0	0.030	0.006	7.506	0.206	0.206	0.000	0.000	0.000	0.000
10	A	10	GLN	0	-0.017	-0.025	9.619	0.135	0.135	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.820	-0.897	10.710	-0.358	-0.358	0.000	0.000	0.000	0.000
12	A	12	ARG	1	0.781	0.871	8.220	1.333	1.333	0.000	0.000	0.000	0.000
13	A	13	MET	0	-0.031	0.010	12.955	0.091	0.091	0.000	0.000	0.000	0.000
14	A	14	ASP	-1	-0.847	-0.911	15.386	-0.225	-0.225	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.830	0.890	13.625	0.432	0.432	0.000	0.000	0.000	0.000
16	A	16	SER	0	-0.029	-0.016	16.347	0.025	0.025	0.000	0.000	0.000	0.000
17	A	17	VAL	0	-0.004	-0.006	18.830	0.034	0.034	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.816	-0.889	20.692	-0.135	-0.135	0.000	0.000	0.000	0.000
19	A	19	ALA	0	0.017	0.011	21.112	0.021	0.021	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.016	0.004	22.871	0.018	0.018	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.811	0.882	24.582	0.170	0.170	0.000	0.000	0.000	0.000
22	A	22	ASN	0	-0.007	-0.008	25.314	0.021	0.021	0.000	0.000	0.000	0.000
23	A	23	ASN	0	-0.022	0.022	25.629	0.021	0.021	0.000	0.000	0.000	0.000
24	A	24	LEU	0	0.079	0.033	28.742	0.012	0.012	0.000	0.000	0.000	0.000
25	A	25	SER	0	-0.091	-0.050	30.687	0.013	0.013	0.000	0.000	0.000	0.000
26	A	26	LYS	1	0.854	0.914	28.925	0.158	0.158	0.000	0.000	0.000	0.000
27	A	27	VAL	0	-0.007	0.015	33.276	0.007	0.007	0.000	0.000	0.000	0.000
28	A	28	ARG	1	0.824	0.866	35.850	0.080	0.080	0.000	0.000	0.000	0.000
29	A	29	THR	0	-0.012	-0.028	39.227	0.000	0.000	0.000	0.000	0.000	0.000
30	A	30	GLY	0	-0.007	-0.007	42.395	0.003	0.003	0.000	0.000	0.000	0.000
31	A	31	GLY	0	0.012	0.013	44.272	0.002	0.002	0.000	0.000	0.000	0.000
32	A	32	GLY	0	0.023	0.035	46.298	0.003	0.003	0.000	0.000	0.000	0.000
33	A	33	GLY	0	0.011	0.016	46.206	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	34	THR	0	0.031	0.010	47.876	0.001	0.001	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.816	-0.906	46.851	-0.062	-0.062	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.779	-0.878	45.157	-0.076	-0.076	0.000	0.000	0.000	0.000
37	A	37	ARG	1	0.883	0.925	44.411	0.071	0.071	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.790	0.884	42.798	0.059	0.059	0.000	0.000	0.000	0.000
39	A	39	LYS	1	0.898	0.913	41.152	0.062	0.062	0.000	0.000	0.000	0.000
40	A	40	ASP	-1	-0.860	-0.908	40.368	-0.085	-0.085	0.000	0.000	0.000	0.000
41	A	41	LEU	0	-0.009	0.004	38.152	-0.006	-0.006	0.000	0.000	0.000	0.000
42	A	42	VAL	0	-0.009	-0.003	36.545	-0.007	-0.007	0.000	0.000	0.000	0.000
43	A	43	LYS	1	0.788	0.863	35.627	0.078	0.078	0.000	0.000	0.000	0.000
44	A	44	ILE	0	-0.018	0.010	33.140	-0.007	-0.007	0.000	0.000	0.000	0.000
45	A	45	VAL	0	0.039	0.018	31.777	-0.010	-0.010	0.000	0.000	0.000	0.000
46	A	46	ARG	1	0.814	0.868	30.616	0.094	0.094	0.000	0.000	0.000	0.000
47	A	47	GLY	0	0.002	0.016	29.931	-0.009	-0.009	0.000	0.000	0.000	0.000
48	A	48	GLU	-1	-0.877	-0.959	27.575	-0.171	-0.171	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.014	0.004	25.964	-0.018	-0.018	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.797	-0.869	25.190	-0.223	-0.223	0.000	0.000	0.000	0.000
51	A	51	GLY	0	0.022	0.011	24.089	-0.020	-0.020	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.018	0.006	21.556	-0.031	-0.031	0.000	0.000	0.000	0.000
53	A	53	ARG	1	0.768	0.846	20.425	0.143	0.143	0.000	0.000	0.000	0.000
54	A	54	VAL	0	-0.035	-0.021	20.293	-0.027	-0.027	0.000	0.000	0.000	0.000
55	A	55	ALA	0	0.009	0.011	17.757	-0.041	-0.041	0.000	0.000	0.000	0.000
56	A	56	VAL	0	0.006	0.003	16.048	-0.068	-0.068	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.902	0.925	15.484	0.206	0.206	0.000	0.000	0.000	0.000
58	A	58	ASN	0	-0.091	-0.032	13.589	0.040	0.040	0.000	0.000	0.000	0.000
59	A	59	ILE	0	-0.019	0.003	10.760	-0.098	-0.098	0.000	0.000	0.000	0.000
60	A	60	ALA	0	0.012	0.008	10.732	-0.163	-0.163	0.000	0.000	0.000	0.000
61	A	61	ARG	1	0.944	0.967	11.900	0.416	0.416	0.000	0.000	0.000	0.000
62	A	62	ASP	-1	-0.831	-0.906	9.108	-0.971	-0.971	0.000	0.000	0.000	0.000
63	A	63	ALA	0	0.081	0.032	6.941	-0.211	-0.211	0.000	0.000	0.000	0.000
64	A	64	ALA	0	-0.010	-0.012	7.786	-0.075	-0.075	0.000	0.000	0.000	0.000
65	A	65	ASN	0	-0.027	-0.017	9.990	0.196	0.196	0.000	0.000	0.000	0.000
66	A	66	ASP	-1	-0.902	-0.946	4.531	-3.061	-2.878	-0.001	-0.007	-0.174	0.000
67	A	67	LEU	0	-0.049	-0.039	5.126	0.072	0.072	0.000	0.000	0.000	0.000
68	A	68	ALA	0	-0.001	0.000	6.679	0.395	0.395	0.000	0.000	0.000	0.000
69	A	69	ALA	0	-0.023	-0.007	6.817	0.225	0.225	0.000	0.000	0.000	0.000
70	A	70	LEU	0	-0.009	-0.007	2.402	-0.976	-0.253	1.916	-0.531	-2.107	-0.004
71	A	71	GLY	0	0.022	0.015	6.141	0.344	0.344	0.000	0.000	0.000	0.000
72	A	72	LYS	1	0.818	0.904	8.076	0.603	0.603	0.000	0.000	0.000	0.000
73	A	73	ASP	-1	-0.889	-0.941	7.492	0.841	0.841	0.000	0.000	0.000	0.000
74	A	74	LYS	1	0.801	0.874	9.600	-0.373	-0.373	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.820	-0.882	8.724	0.586	0.586	0.000	0.000	0.000	0.000
76	A	76	VAL	0	-0.064	-0.022	5.193	0.462	0.462	0.000	0.000	0.000	0.000
77	A	77	ASN	0	-0.043	-0.022	8.098	-0.502	-0.502	0.000	0.000	0.000	0.000
78	A	78	TRP	0	0.071	0.016	9.918	0.044	0.044	0.000	0.000	0.000	0.000
79	A	79	PHE	0	0.015	0.021	12.208	-0.093	-0.093	0.000	0.000	0.000	0.000
80	A	80	ASP	-1	-0.822	-0.901	8.324	1.227	1.227	0.000	0.000	0.000	0.000
81	A	81	ILE	0	0.003	0.000	7.032	-0.110	-0.110	0.000	0.000	0.000	0.000
82	A	82	SER	0	-0.038	-0.032	9.186	-0.244	-0.244	0.000	0.000	0.000	0.000
83	A	83	GLN	0	-0.003	0.003	12.328	-0.104	-0.104	0.000	0.000	0.000	0.000
84	A	84	ALA	0	-0.012	-0.010	8.380	-0.096	-0.096	0.000	0.000	0.000	0.000
85	A	85	LEU	0	0.024	0.012	10.484	-0.183	-0.183	0.000	0.000	0.000	0.000
86	A	86	TRP	0	0.007	0.010	11.956	-0.046	-0.046	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.853	-0.924	11.806	0.048	0.048	0.000	0.000	0.000	0.000
88	A	88	ILE	0	0.017	0.020	8.874	-0.020	-0.020	0.000	0.000	0.000	0.000
89	A	89	GLN	0	-0.040	-0.002	12.809	0.026	0.026	0.000	0.000	0.000	0.000
90	A	90	LYS	1	0.925	0.956	15.859	0.037	0.037	0.000	0.000	0.000	0.000
91	A	91	LEU	0	-0.038	-0.016	11.971	0.018	0.018	0.000	0.000	0.000	0.000
92	A	92	THR	0	-0.013	-0.032	15.507	-0.012	-0.012	0.000	0.000	0.000	0.000
93	A	93	ASP	-1	-0.906	-0.947	17.418	-0.169	-0.169	0.000	0.000	0.000	0.000
94	A	94	VAL	0	-0.059	-0.027	19.515	0.020	0.020	0.000	0.000	0.000	0.000
95	A	95	ALA	0	0.024	0.009	18.042	0.014	0.014	0.000	0.000	0.000	0.000
96	A	96	VAL	0	-0.016	-0.016	20.120	0.009	0.009	0.000	0.000	0.000	0.000
97	A	97	LYS	1	0.936	0.964	22.475	0.113	0.113	0.000	0.000	0.000	0.000
98	A	98	LYS	1	0.869	0.931	23.082	0.127	0.127	0.000	0.000	0.000	0.000
99	A	99	ILE	0	0.009	0.000	21.223	0.010	0.010	0.000	0.000	0.000	0.000
100	A	100	ASP	-1	-0.820	-0.892	25.295	-0.146	-0.146	0.000	0.000	0.000	0.000
101	A	101	GLU	-1	-0.864	-0.919	28.113	-0.093	-0.093	0.000	0.000	0.000	0.000
102	A	102	VAL	0	-0.036	-0.014	26.527	0.009	0.009	0.000	0.000	0.000	0.000
103	A	103	LEU	0	-0.001	0.006	29.333	0.005	0.005	0.000	0.000	0.000	0.000
104	A	104	ALA	0	-0.003	-0.002	31.081	0.007	0.007	0.000	0.000	0.000	0.000
105	A	105	ALA	0	-0.018	-0.010	32.744	0.007	0.007	0.000	0.000	0.000	0.000
106	A	106	LYS	1	0.824	0.901	32.624	0.109	0.109	0.000	0.000	0.000	0.000
107	A	107	GLU	-1	-0.762	-0.868	34.622	-0.099	-0.099	0.000	0.000	0.000	0.000
108	A	108	LYS	1	0.819	0.898	37.011	0.065	0.065	0.000	0.000	0.000	0.000
109	A	109	GLU	-1	-0.794	-0.860	36.042	-0.088	-0.088	0.000	0.000	0.000	0.000
110	A	110	LEU	0	-0.036	0.003	36.506	0.004	0.004	0.000	0.000	0.000	0.000
111	A	111	MET	0	-0.017	-0.012	40.185	0.003	0.003	0.000	0.000	0.000	0.000
112	A	112	GLU	-1	-0.836	-0.887	42.613	-0.054	-0.054	0.000	0.000	0.000	0.000
113	A	113	VAL	0	-0.021	-0.007	44.599	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	114	LEU	0	0.016	0.015	43.973	0.002	0.002	0.000	0.000	0.000	0.000
115	A	115	GLU	-1	-0.900	-0.956	48.351	-0.037	-0.037	0.000	0.000	0.000	0.000
116	A	116	HIS	0	-0.013	-0.005	45.494	0.002	0.002	0.000	0.000	0.000	0.000
117	A	117	HIS	0	-0.018	0.010	44.544	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	118	HIS	0	0.010	0.004	49.400	0.003	0.003	0.000	0.000	0.000	0.000
119	A	119	HIS	0	-0.041	-0.028	50.818	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	120	HIS	0	0.015	0.014	51.122	-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)