FMO DATABASE

FMODB ID: LN7R9

Calculation Name: 3MLF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3MLF

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-09-22

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	95
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-699619.704633
FMO2-HF: Nuclear repulsion	660495.365694
FMO2-HF: Total energy	-39124.338939
FMO2-MP2: Total energy	-39238.451774

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:-9:THR)

Summations of interaction energy for fragment #1(A:-9:THR)

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.
-1.995	3.041	2.906	-2.931	-5.011	0.005

Interaction energy analysis for fragmet #1(A:-9:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.019 / q_NPA : -0.009

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	-7	ASN	0	-0.076	-0.028	3.803	-1.254	0.768	-0.017	-0.873	-1.132	0.000
4	A	-6	LEU	0	-0.026	-0.004	2.668	-0.537	0.642	0.518	-0.567	-1.130	-0.002
5	A	-5	TYR	0	-0.024	-0.012	1.943	-0.354	1.056	2.384	-1.339	-2.456	0.007
6	A	-4	PHE	0	-0.006	-0.003	5.150	-0.531	-0.585	-0.001	-0.004	0.060	0.000
7	A	-3	GLN	0	0.012	0.011	7.420	-0.097	-0.097	0.000	0.000	0.000	0.000
8	A	-2	SER	0	-0.003	-0.022	8.953	0.321	0.321	0.000	0.000	0.000	0.000
9	A	-1	ASN	0	-0.017	-0.007	12.198	-0.004	-0.004	0.000	0.000	0.000	0.000
10	A	0	ALA	0	-0.036	-0.005	14.747	0.053	0.053	0.000	0.000	0.000	0.000
11	A	1	MET	0	0.058	0.042	15.018	-0.034	-0.034	0.000	0.000	0.000	0.000
12	A	2	LYS	1	0.880	0.944	13.336	0.371	0.371	0.000	0.000	0.000	0.000
13	A	3	THR	0	0.048	0.056	16.685	0.016	0.016	0.000	0.000	0.000	0.000
14	A	4	LEU	0	0.064	0.009	17.384	-0.005	-0.005	0.000	0.000	0.000	0.000
15	A	5	LYS	1	0.946	0.980	17.828	0.044	0.044	0.000	0.000	0.000	0.000
16	A	6	GLU	-1	-0.828	-0.920	17.064	-0.178	-0.178	0.000	0.000	0.000	0.000
17	A	7	LEU	0	0.029	0.034	12.016	-0.009	-0.009	0.000	0.000	0.000	0.000
18	A	8	ARG	1	0.744	0.838	13.969	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	9	THR	0	-0.089	-0.061	16.185	0.029	0.029	0.000	0.000	0.000	0.000
20	A	10	ASP	-1	-0.882	-0.935	13.092	-0.251	-0.251	0.000	0.000	0.000	0.000
21	A	11	TYR	0	-0.025	-0.010	8.379	-0.074	-0.074	0.000	0.000	0.000	0.000
22	A	12	GLY	0	-0.028	-0.003	13.637	0.058	0.058	0.000	0.000	0.000	0.000
23	A	13	LEU	0	0.022	0.034	14.345	0.020	0.020	0.000	0.000	0.000	0.000
24	A	14	THR	0	-0.015	-0.004	18.248	-0.034	-0.034	0.000	0.000	0.000	0.000
25	A	15	GLN	0	-0.063	-0.062	20.671	0.014	0.014	0.000	0.000	0.000	0.000
26	A	16	LYS	1	0.893	0.945	22.561	-0.102	-0.102	0.000	0.000	0.000	0.000
27	A	17	GLU	-1	-0.816	-0.896	19.378	0.150	0.150	0.000	0.000	0.000	0.000
28	A	18	LEU	0	0.052	0.035	15.797	0.018	0.018	0.000	0.000	0.000	0.000
29	A	19	GLY	0	-0.002	-0.001	18.969	0.011	0.011	0.000	0.000	0.000	0.000
30	A	20	ASP	-1	-0.848	-0.932	21.421	0.140	0.140	0.000	0.000	0.000	0.000
31	A	21	LEU	0	-0.048	-0.011	13.764	0.010	0.010	0.000	0.000	0.000	0.000
32	A	22	PHE	0	-0.034	-0.032	14.146	0.017	0.017	0.000	0.000	0.000	0.000
33	A	23	LYS	1	0.883	0.943	19.091	-0.206	-0.206	0.000	0.000	0.000	0.000
34	A	24	VAL	0	-0.014	0.002	21.969	-0.016	-0.016	0.000	0.000	0.000	0.000
35	A	25	SER	0	0.047	0.028	24.582	0.002	0.002	0.000	0.000	0.000	0.000
36	A	26	SER	0	0.130	0.034	25.205	0.002	0.002	0.000	0.000	0.000	0.000
37	A	27	ARG	1	0.892	0.964	26.283	-0.029	-0.029	0.000	0.000	0.000	0.000
38	A	28	THR	0	0.006	-0.010	24.488	-0.009	-0.009	0.000	0.000	0.000	0.000
39	A	29	ILE	0	0.032	0.024	20.419	-0.007	-0.007	0.000	0.000	0.000	0.000
40	A	30	GLN	0	-0.007	-0.008	23.822	-0.016	-0.016	0.000	0.000	0.000	0.000
41	A	31	ASN	0	-0.022	-0.033	26.500	-0.010	-0.010	0.000	0.000	0.000	0.000
42	A	32	MET	0	0.010	0.029	23.110	-0.007	-0.007	0.000	0.000	0.000	0.000
43	A	33	GLU	-1	-0.770	-0.870	21.216	-0.008	-0.008	0.000	0.000	0.000	0.000
44	A	34	LYS	1	0.856	0.951	23.935	0.003	0.003	0.000	0.000	0.000	0.000
45	A	35	ASP	-1	-0.837	-0.919	27.457	-0.042	-0.042	0.000	0.000	0.000	0.000
46	A	36	SER	0	-0.002	-0.009	22.981	0.003	0.003	0.000	0.000	0.000	0.000
47	A	37	THR	0	-0.065	-0.028	25.117	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	38	ASN	0	-0.015	-0.016	27.436	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	39	ILE	0	-0.002	-0.007	20.509	0.012	0.012	0.000	0.000	0.000	0.000
50	A	40	LYS	1	0.930	0.970	24.296	-0.031	-0.031	0.000	0.000	0.000	0.000
51	A	41	ASP	-1	-0.802	-0.911	20.552	0.009	0.009	0.000	0.000	0.000	0.000
52	A	42	SER	0	-0.007	0.017	19.726	0.008	0.008	0.000	0.000	0.000	0.000
53	A	43	LEU	0	-0.049	-0.026	19.056	0.024	0.024	0.000	0.000	0.000	0.000
54	A	44	LEU	0	0.087	0.029	16.853	0.018	0.018	0.000	0.000	0.000	0.000
55	A	45	SER	0	0.044	0.005	15.530	-0.005	-0.005	0.000	0.000	0.000	0.000
56	A	46	LYS	1	0.841	0.934	14.022	-0.122	-0.122	0.000	0.000	0.000	0.000
57	A	47	TYR	0	0.009	0.002	13.178	0.071	0.071	0.000	0.000	0.000	0.000
58	A	48	MET	0	-0.025	0.000	11.660	0.007	0.007	0.000	0.000	0.000	0.000
59	A	49	SER	0	-0.039	-0.010	9.660	0.069	0.069	0.000	0.000	0.000	0.000
60	A	50	ALA	0	-0.009	-0.007	8.433	0.265	0.265	0.000	0.000	0.000	0.000
61	A	51	PHE	0	-0.030	-0.038	8.360	0.153	0.153	0.000	0.000	0.000	0.000
62	A	52	ASN	0	-0.023	0.015	3.156	0.393	0.872	0.022	-0.148	-0.353	0.000
63	A	53	VAL	0	-0.015	0.008	6.785	-0.450	-0.450	0.000	0.000	0.000	0.000
64	A	54	LYS	1	0.944	0.954	9.762	0.663	0.663	0.000	0.000	0.000	0.000
65	A	55	TYR	0	0.033	0.004	12.423	0.003	0.003	0.000	0.000	0.000	0.000
66	A	56	ASP	-1	-0.905	-0.958	16.007	-0.225	-0.225	0.000	0.000	0.000	0.000
67	A	57	ASP	-1	-0.894	-0.939	11.742	-0.630	-0.630	0.000	0.000	0.000	0.000
68	A	58	ILE	0	-0.068	-0.045	14.124	0.006	0.006	0.000	0.000	0.000	0.000
69	A	59	PHE	0	-0.022	-0.013	16.705	0.015	0.015	0.000	0.000	0.000	0.000
70	A	60	LEU	0	-0.004	-0.021	20.098	0.018	0.018	0.000	0.000	0.000	0.000
71	A	61	GLY	0	0.082	0.042	22.659	-0.004	-0.004	0.000	0.000	0.000	0.000
72	A	62	ASN	0	0.010	0.016	26.279	0.005	0.005	0.000	0.000	0.000	0.000
73	A	63	GLU	-1	-0.884	-0.960	28.125	-0.035	-0.035	0.000	0.000	0.000	0.000
74	A	64	TYR	0	-0.038	-0.020	29.467	-0.004	-0.004	0.000	0.000	0.000	0.000
75	A	65	GLU	-1	-0.835	-0.923	27.754	-0.076	-0.076	0.000	0.000	0.000	0.000
76	A	66	ASN	0	0.000	-0.010	24.050	-0.018	-0.018	0.000	0.000	0.000	0.000
77	A	67	PHE	0	-0.036	-0.005	25.905	-0.009	-0.009	0.000	0.000	0.000	0.000
78	A	68	VAL	0	0.035	0.011	28.158	-0.005	-0.005	0.000	0.000	0.000	0.000
79	A	69	PHE	0	0.042	0.038	19.787	-0.008	-0.008	0.000	0.000	0.000	0.000
80	A	70	THR	0	-0.065	-0.041	22.507	-0.009	-0.009	0.000	0.000	0.000	0.000
81	A	71	ASN	0	-0.078	-0.045	24.432	-0.003	-0.003	0.000	0.000	0.000	0.000
82	A	72	ASP	-1	-0.857	-0.936	26.663	-0.108	-0.108	0.000	0.000	0.000	0.000
83	A	73	LYS	1	0.812	0.898	18.501	0.224	0.224	0.000	0.000	0.000	0.000
84	A	74	LYS	1	0.933	0.974	24.211	0.071	0.071	0.000	0.000	0.000	0.000
85	A	75	LYS	1	0.943	0.966	26.106	0.088	0.088	0.000	0.000	0.000	0.000
86	A	76	SER	0	0.041	0.015	24.989	0.001	0.001	0.000	0.000	0.000	0.000
87	A	77	ILE	0	-0.023	0.006	21.502	0.002	0.002	0.000	0.000	0.000	0.000
88	A	78	ILE	0	-0.047	-0.029	25.314	0.007	0.007	0.000	0.000	0.000	0.000
89	A	79	LEU	0	-0.010	0.005	28.901	0.007	0.007	0.000	0.000	0.000	0.000
90	A	80	ALA	0	0.058	0.020	26.188	0.003	0.003	0.000	0.000	0.000	0.000
91	A	81	PHE	0	-0.033	-0.010	27.209	0.003	0.003	0.000	0.000	0.000	0.000
92	A	82	LYS	1	0.957	0.960	28.759	0.075	0.075	0.000	0.000	0.000	0.000
93	A	83	GLU	-1	-0.906	-0.953	31.131	-0.094	-0.094	0.000	0.000	0.000	0.000
94	A	84	LYS	1	0.871	0.958	24.528	0.150	0.150	0.000	0.000	0.000	0.000
95	A	85	GLN	0	-0.090	-0.033	30.277	0.012	0.012	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-9:THR)