FMO DATABASE

FMODB ID: V5KQ1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-893089.428145
FMO2-HF: Nuclear repulsion	845767.78229
FMO2-HF: Total energy	-47321.645855
FMO2-MP2: Total energy	-47460.506787

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.
-6.947	-2.14	5.973	-2.768	-8.01	-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 : 0.057 / q_NPA : 0.026

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	-0.020	-0.026	3.740	-3.009	-1.345	-0.006	-0.713	-0.946	0.002
4	A	4	GLU	-1	-0.882	-0.937	2.601	-1.585	-0.115	0.716	-0.507	-1.678	-0.001
5	A	5	ILE	0	0.012	0.010	2.273	-1.453	-0.837	3.244	-0.921	-2.939	-0.004
6	A	6	LYS	1	0.919	0.955	4.295	0.249	0.463	0.000	-0.040	-0.174	0.000
7	A	7	LYS	1	0.887	0.951	7.229	0.620	0.620	0.000	0.000	0.000	0.000
8	A	8	ASP	-1	-0.888	-0.950	5.821	-1.491	-1.491	0.000	0.000	0.000	0.000
9	A	9	ALA	0	0.031	0.011	7.610	0.240	0.240	0.000	0.000	0.000	0.000
10	A	10	GLN	0	0.040	0.015	9.628	0.121	0.121	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.871	-0.926	10.825	-0.466	-0.466	0.000	0.000	0.000	0.000
12	A	12	ARG	1	0.844	0.933	9.356	1.256	1.256	0.000	0.000	0.000	0.000
13	A	13	MET	0	-0.045	-0.012	12.930	0.103	0.103	0.000	0.000	0.000	0.000
14	A	14	ASP	-1	-0.868	-0.932	15.391	-0.251	-0.251	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.894	0.937	12.503	0.596	0.596	0.000	0.000	0.000	0.000
16	A	16	SER	0	-0.048	-0.023	16.590	0.033	0.033	0.000	0.000	0.000	0.000
17	A	17	VAL	0	-0.018	-0.007	18.957	0.037	0.037	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.904	-0.955	20.854	-0.159	-0.159	0.000	0.000	0.000	0.000
19	A	19	ALA	0	-0.022	-0.006	21.329	0.022	0.022	0.000	0.000	0.000	0.000
20	A	20	LEU	0	0.005	0.017	23.116	0.020	0.020	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.957	0.981	25.173	0.170	0.170	0.000	0.000	0.000	0.000
22	A	22	ASN	0	0.018	0.009	24.464	0.028	0.028	0.000	0.000	0.000	0.000
23	A	23	ASN	0	-0.067	-0.027	25.237	0.018	0.018	0.000	0.000	0.000	0.000
24	A	24	LEU	0	0.054	0.019	28.865	0.014	0.014	0.000	0.000	0.000	0.000
25	A	25	SER	0	-0.111	-0.058	30.918	0.014	0.014	0.000	0.000	0.000	0.000
26	A	26	LYS	1	0.927	0.967	28.984	0.172	0.172	0.000	0.000	0.000	0.000
27	A	27	VAL	0	-0.011	0.020	33.464	0.008	0.008	0.000	0.000	0.000	0.000
28	A	28	ARG	1	0.828	0.906	35.901	0.087	0.087	0.000	0.000	0.000	0.000
29	A	29	THR	0	0.023	-0.007	39.245	0.000	0.000	0.000	0.000	0.000	0.000
30	A	30	GLY	0	0.012	0.008	42.503	0.002	0.002	0.000	0.000	0.000	0.000
31	A	31	GLY	0	0.005	0.009	44.300	0.003	0.003	0.000	0.000	0.000	0.000
32	A	32	GLY	0	0.032	0.010	46.385	0.003	0.003	0.000	0.000	0.000	0.000
33	A	33	GLY	0	0.027	0.013	46.895	-0.003	-0.003	0.000	0.000	0.000	0.000
34	A	34	THR	0	0.033	0.022	48.257	0.000	0.000	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.817	-0.921	47.118	-0.066	-0.066	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.879	-0.943	46.005	-0.079	-0.079	0.000	0.000	0.000	0.000
37	A	37	ARG	1	0.962	0.962	45.275	0.073	0.073	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.796	0.889	43.180	0.063	0.063	0.000	0.000	0.000	0.000
39	A	39	LYS	1	0.948	0.971	41.442	0.065	0.065	0.000	0.000	0.000	0.000
40	A	40	ASP	-1	-0.862	-0.918	40.591	-0.090	-0.090	0.000	0.000	0.000	0.000
41	A	41	LEU	0	-0.017	-0.001	38.625	-0.006	-0.006	0.000	0.000	0.000	0.000
42	A	42	VAL	0	-0.002	-0.004	36.883	-0.007	-0.007	0.000	0.000	0.000	0.000
43	A	43	LYS	1	0.805	0.888	35.863	0.083	0.083	0.000	0.000	0.000	0.000
44	A	44	ILE	0	0.006	0.014	33.546	-0.008	-0.008	0.000	0.000	0.000	0.000
45	A	45	VAL	0	0.035	0.015	32.035	-0.010	-0.010	0.000	0.000	0.000	0.000
46	A	46	ARG	1	0.810	0.892	30.962	0.099	0.099	0.000	0.000	0.000	0.000
47	A	47	GLY	0	-0.009	0.009	30.427	-0.009	-0.009	0.000	0.000	0.000	0.000
48	A	48	GLU	-1	-0.888	-0.964	27.967	-0.187	-0.187	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.007	0.003	26.327	-0.020	-0.020	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.878	-0.927	25.538	-0.233	-0.233	0.000	0.000	0.000	0.000
51	A	51	GLY	0	0.022	0.014	24.440	-0.021	-0.021	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.005	-0.004	21.927	-0.031	-0.031	0.000	0.000	0.000	0.000
53	A	53	ARG	1	0.800	0.876	20.686	0.152	0.152	0.000	0.000	0.000	0.000
54	A	54	VAL	0	-0.021	-0.004	20.466	-0.032	-0.032	0.000	0.000	0.000	0.000
55	A	55	ALA	0	-0.012	0.000	17.977	-0.044	-0.044	0.000	0.000	0.000	0.000
56	A	56	VAL	0	0.048	0.017	16.289	-0.070	-0.070	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.966	0.971	15.662	0.212	0.212	0.000	0.000	0.000	0.000
58	A	58	ASN	0	-0.053	-0.019	14.507	-0.029	-0.029	0.000	0.000	0.000	0.000
59	A	59	ILE	0	-0.004	0.009	10.785	-0.094	-0.094	0.000	0.000	0.000	0.000
60	A	60	ALA	0	0.022	0.009	11.139	-0.157	-0.157	0.000	0.000	0.000	0.000
61	A	61	ARG	1	0.917	0.958	12.132	0.417	0.417	0.000	0.000	0.000	0.000
62	A	62	ASP	-1	-0.855	-0.928	9.148	-1.055	-1.055	0.000	0.000	0.000	0.000
63	A	63	ALA	0	0.037	0.018	7.432	-0.227	-0.227	0.000	0.000	0.000	0.000
64	A	64	ALA	0	0.003	-0.009	7.667	-0.150	-0.150	0.000	0.000	0.000	0.000
65	A	65	ASN	0	-0.024	-0.019	9.734	0.161	0.161	0.000	0.000	0.000	0.000
66	A	66	ASP	-1	-0.895	-0.942	4.582	-3.066	-2.887	-0.001	-0.007	-0.170	0.000
67	A	67	LEU	0	-0.067	-0.041	5.138	-0.245	-0.138	-0.001	-0.008	-0.098	0.000
68	A	68	ALA	0	0.007	-0.001	6.730	0.376	0.376	0.000	0.000	0.000	0.000
69	A	69	ALA	0	-0.031	-0.005	6.250	0.255	0.255	0.000	0.000	0.000	0.000
70	A	70	LEU	0	0.009	-0.007	2.344	-0.791	-0.234	2.021	-0.572	-2.005	-0.004
71	A	71	GLY	0	0.037	0.030	5.939	0.362	0.362	0.000	0.000	0.000	0.000
72	A	72	LYS	1	0.789	0.884	7.760	0.590	0.590	0.000	0.000	0.000	0.000
73	A	73	ASP	-1	-0.898	-0.948	6.772	0.850	0.850	0.000	0.000	0.000	0.000
74	A	74	LYS	1	0.848	0.916	9.142	-0.345	-0.345	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.867	-0.924	7.967	0.592	0.592	0.000	0.000	0.000	0.000
76	A	76	VAL	0	-0.065	-0.016	5.168	0.422	0.422	0.000	0.000	0.000	0.000
77	A	77	ASN	0	-0.017	0.002	7.955	-0.512	-0.512	0.000	0.000	0.000	0.000
78	A	78	TRP	0	0.074	0.015	9.872	0.047	0.047	0.000	0.000	0.000	0.000
79	A	79	PHE	0	0.004	-0.005	12.107	-0.079	-0.079	0.000	0.000	0.000	0.000
80	A	80	ASP	-1	-0.825	-0.917	8.280	1.384	1.384	0.000	0.000	0.000	0.000
81	A	81	ILE	0	-0.013	-0.006	7.062	-0.098	-0.098	0.000	0.000	0.000	0.000
82	A	82	SER	0	-0.032	-0.018	9.198	-0.257	-0.257	0.000	0.000	0.000	0.000
83	A	83	GLN	0	-0.046	-0.012	12.004	-0.107	-0.107	0.000	0.000	0.000	0.000
84	A	84	ALA	0	-0.005	-0.011	8.431	-0.115	-0.115	0.000	0.000	0.000	0.000
85	A	85	LEU	0	0.007	0.001	10.370	-0.204	-0.204	0.000	0.000	0.000	0.000
86	A	86	TRP	0	-0.007	0.010	12.172	-0.054	-0.054	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.918	-0.977	11.962	0.085	0.085	0.000	0.000	0.000	0.000
88	A	88	ILE	0	-0.014	0.006	9.021	-0.041	-0.041	0.000	0.000	0.000	0.000
89	A	89	GLN	0	0.001	-0.001	12.842	0.025	0.025	0.000	0.000	0.000	0.000
90	A	90	LYS	1	0.995	1.011	16.377	0.046	0.046	0.000	0.000	0.000	0.000
91	A	91	LEU	0	-0.029	-0.015	12.150	0.013	0.013	0.000	0.000	0.000	0.000
92	A	92	THR	0	-0.008	-0.020	15.788	-0.018	-0.018	0.000	0.000	0.000	0.000
93	A	93	ASP	-1	-0.915	-0.947	17.657	-0.168	-0.168	0.000	0.000	0.000	0.000
94	A	94	VAL	0	-0.078	-0.040	19.458	0.022	0.022	0.000	0.000	0.000	0.000
95	A	95	ALA	0	0.034	0.018	18.160	0.016	0.016	0.000	0.000	0.000	0.000
96	A	96	VAL	0	0.005	-0.021	20.284	0.012	0.012	0.000	0.000	0.000	0.000
97	A	97	LYS	1	0.965	1.004	22.785	0.114	0.114	0.000	0.000	0.000	0.000
98	A	98	LYS	1	0.905	0.973	23.150	0.147	0.147	0.000	0.000	0.000	0.000
99	A	99	ILE	0	0.001	-0.010	21.469	0.012	0.012	0.000	0.000	0.000	0.000
100	A	100	ASP	-1	-0.836	-0.919	25.494	-0.154	-0.154	0.000	0.000	0.000	0.000
101	A	101	GLU	-1	-0.934	-0.973	28.208	-0.100	-0.100	0.000	0.000	0.000	0.000
102	A	102	VAL	0	-0.070	-0.037	26.762	0.009	0.009	0.000	0.000	0.000	0.000
103	A	103	LEU	0	-0.011	0.004	29.557	0.006	0.006	0.000	0.000	0.000	0.000
104	A	104	ALA	0	0.014	0.010	31.249	0.008	0.008	0.000	0.000	0.000	0.000
105	A	105	ALA	0	-0.019	-0.012	33.097	0.008	0.008	0.000	0.000	0.000	0.000
106	A	106	LYS	1	0.842	0.917	32.769	0.119	0.119	0.000	0.000	0.000	0.000
107	A	107	GLU	-1	-0.775	-0.896	34.769	-0.104	-0.104	0.000	0.000	0.000	0.000
108	A	108	LYS	1	0.945	0.982	37.130	0.071	0.071	0.000	0.000	0.000	0.000
109	A	109	GLU	-1	-0.825	-0.881	37.206	-0.092	-0.092	0.000	0.000	0.000	0.000
110	A	110	LEU	0	-0.070	-0.043	36.541	0.004	0.004	0.000	0.000	0.000	0.000
111	A	111	MET	0	-0.050	-0.011	40.415	0.003	0.003	0.000	0.000	0.000	0.000
112	A	112	GLU	-1	-0.935	-0.955	42.922	-0.057	-0.057	0.000	0.000	0.000	0.000
113	A	113	VAL	0	-0.043	-0.017	44.953	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	114	LEU	0	0.031	0.001	44.412	0.002	0.002	0.000	0.000	0.000	0.000
115	A	115	GLU	-1	-0.910	-0.958	48.812	-0.041	-0.041	0.000	0.000	0.000	0.000
116	A	116	HIS	0	-0.011	-0.001	45.550	0.002	0.002	0.000	0.000	0.000	0.000
117	A	117	HIS	0	-0.034	0.001	44.968	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	118	HIS	0	0.012	0.008	49.799	0.004	0.004	0.000	0.000	0.000	0.000
119	A	119	HIS	0	-0.041	-0.036	51.388	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	120	HIS	0	-0.002	0.009	51.340	-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)