FMO DATABASE

FMODB ID: MN9ZZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-702594.194383
FMO2-HF: Nuclear repulsion	663468.638274
FMO2-HF: Total energy	-39125.556109
FMO2-MP2: Total energy	-39239.620599

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.
1.465	6.803	1.074	-2.388	-4.023	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 : 0.021 / q_NPA : -0.013

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	-0.074	-0.033	3.751	1.205	3.089	0.002	-0.766	-1.120	0.001
4	A	-6	LEU	0	-0.065	-0.015	2.865	-0.229	1.534	0.390	-0.821	-1.332	0.001
5	A	-5	TYR	0	-0.012	-0.022	2.317	0.091	1.812	0.683	-0.795	-1.609	0.003
6	A	-4	PHE	0	0.007	0.005	4.664	-0.747	-0.777	-0.001	-0.006	0.038	0.000
7	A	-3	GLN	0	0.022	0.005	6.485	0.167	0.167	0.000	0.000	0.000	0.000
8	A	-2	SER	0	-0.032	-0.006	8.077	0.325	0.325	0.000	0.000	0.000	0.000
9	A	-1	ASN	0	-0.037	-0.022	11.659	0.028	0.028	0.000	0.000	0.000	0.000
10	A	0	ALA	0	0.000	-0.005	13.938	0.078	0.078	0.000	0.000	0.000	0.000
11	A	1	MET	0	0.004	0.023	15.335	-0.024	-0.024	0.000	0.000	0.000	0.000
12	A	2	LYS	1	0.782	0.877	13.578	0.369	0.369	0.000	0.000	0.000	0.000
13	A	3	THR	0	0.013	0.003	16.518	0.041	0.041	0.000	0.000	0.000	0.000
14	A	4	LEU	0	0.035	0.009	17.464	-0.005	-0.005	0.000	0.000	0.000	0.000
15	A	5	LYS	1	0.908	0.963	18.049	0.041	0.041	0.000	0.000	0.000	0.000
16	A	6	GLU	-1	-0.785	-0.864	16.504	-0.229	-0.229	0.000	0.000	0.000	0.000
17	A	7	LEU	0	0.038	0.032	12.026	-0.003	-0.003	0.000	0.000	0.000	0.000
18	A	8	ARG	1	0.756	0.842	13.621	-0.007	-0.007	0.000	0.000	0.000	0.000
19	A	9	THR	0	-0.060	-0.030	15.785	0.024	0.024	0.000	0.000	0.000	0.000
20	A	10	ASP	-1	-0.820	-0.906	12.597	-0.311	-0.311	0.000	0.000	0.000	0.000
21	A	11	TYR	0	0.003	0.002	7.812	-0.131	-0.131	0.000	0.000	0.000	0.000
22	A	12	GLY	0	-0.016	-0.003	13.131	0.072	0.072	0.000	0.000	0.000	0.000
23	A	13	LEU	0	0.011	0.027	14.508	0.017	0.017	0.000	0.000	0.000	0.000
24	A	14	THR	0	-0.022	-0.051	17.892	-0.034	-0.034	0.000	0.000	0.000	0.000
25	A	15	GLN	0	-0.062	-0.080	20.641	0.019	0.019	0.000	0.000	0.000	0.000
26	A	16	LYS	1	0.817	0.885	22.683	-0.136	-0.136	0.000	0.000	0.000	0.000
27	A	17	GLU	-1	-0.772	-0.838	19.055	0.167	0.167	0.000	0.000	0.000	0.000
28	A	18	LEU	0	0.034	0.022	15.706	0.027	0.027	0.000	0.000	0.000	0.000
29	A	19	GLY	0	0.007	0.003	18.885	0.016	0.016	0.000	0.000	0.000	0.000
30	A	20	ASP	-1	-0.845	-0.903	21.651	0.177	0.177	0.000	0.000	0.000	0.000
31	A	21	LEU	0	-0.017	0.000	14.014	0.009	0.009	0.000	0.000	0.000	0.000
32	A	22	PHE	0	-0.003	-0.013	14.414	0.028	0.028	0.000	0.000	0.000	0.000
33	A	23	LYS	1	0.931	0.977	19.313	-0.305	-0.305	0.000	0.000	0.000	0.000
34	A	24	VAL	0	-0.022	-0.001	22.214	-0.017	-0.017	0.000	0.000	0.000	0.000
35	A	25	SER	0	0.044	0.030	24.770	0.000	0.000	0.000	0.000	0.000	0.000
36	A	26	SER	0	0.104	0.028	25.047	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	27	ARG	1	0.883	0.943	26.135	-0.047	-0.047	0.000	0.000	0.000	0.000
38	A	28	THR	0	-0.001	-0.006	24.755	-0.011	-0.011	0.000	0.000	0.000	0.000
39	A	29	ILE	0	0.031	0.025	20.504	-0.009	-0.009	0.000	0.000	0.000	0.000
40	A	30	GLN	0	-0.005	0.006	23.735	-0.021	-0.021	0.000	0.000	0.000	0.000
41	A	31	ASN	0	0.001	0.001	26.507	-0.014	-0.014	0.000	0.000	0.000	0.000
42	A	32	MET	0	0.028	0.028	23.136	-0.007	-0.007	0.000	0.000	0.000	0.000
43	A	33	GLU	-1	-0.738	-0.830	20.920	0.008	0.008	0.000	0.000	0.000	0.000
44	A	34	LYS	1	0.734	0.860	24.089	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	35	ASP	-1	-0.803	-0.908	27.661	-0.017	-0.017	0.000	0.000	0.000	0.000
46	A	36	SER	0	-0.025	-0.010	22.927	0.005	0.005	0.000	0.000	0.000	0.000
47	A	37	THR	0	-0.046	-0.038	24.997	0.002	0.002	0.000	0.000	0.000	0.000
48	A	38	ASN	0	-0.056	-0.031	27.565	0.003	0.003	0.000	0.000	0.000	0.000
49	A	39	ILE	0	-0.021	-0.008	20.704	0.014	0.014	0.000	0.000	0.000	0.000
50	A	40	LYS	1	0.955	0.980	24.687	-0.075	-0.075	0.000	0.000	0.000	0.000
51	A	41	ASP	-1	-0.751	-0.873	20.125	0.120	0.120	0.000	0.000	0.000	0.000
52	A	42	SER	0	-0.017	-0.009	20.023	0.017	0.017	0.000	0.000	0.000	0.000
53	A	43	LEU	0	-0.070	-0.041	19.635	0.027	0.027	0.000	0.000	0.000	0.000
54	A	44	LEU	0	0.041	0.028	17.095	0.022	0.022	0.000	0.000	0.000	0.000
55	A	45	SER	0	0.069	-0.001	15.874	0.013	0.013	0.000	0.000	0.000	0.000
56	A	46	LYS	1	0.778	0.907	14.364	-0.165	-0.165	0.000	0.000	0.000	0.000
57	A	47	TYR	0	0.007	-0.007	13.477	0.081	0.081	0.000	0.000	0.000	0.000
58	A	48	MET	0	-0.021	0.003	12.050	0.003	0.003	0.000	0.000	0.000	0.000
59	A	49	SER	0	-0.016	-0.011	9.984	0.037	0.037	0.000	0.000	0.000	0.000
60	A	50	ALA	0	-0.053	-0.017	8.984	0.313	0.313	0.000	0.000	0.000	0.000
61	A	51	PHE	0	-0.003	-0.015	8.339	0.164	0.164	0.000	0.000	0.000	0.000
62	A	52	ASN	0	-0.038	0.003	4.821	0.544	0.544	0.000	0.000	0.000	0.000
63	A	53	VAL	0	-0.019	0.004	7.036	-0.487	-0.487	0.000	0.000	0.000	0.000
64	A	54	LYS	1	0.846	0.888	10.170	0.524	0.524	0.000	0.000	0.000	0.000
65	A	55	TYR	0	0.054	0.006	12.719	-0.014	-0.014	0.000	0.000	0.000	0.000
66	A	56	ASP	-1	-0.863	-0.924	15.889	-0.219	-0.219	0.000	0.000	0.000	0.000
67	A	57	ASP	-1	-0.816	-0.886	12.008	-0.456	-0.456	0.000	0.000	0.000	0.000
68	A	58	ILE	0	-0.046	-0.033	14.370	-0.014	-0.014	0.000	0.000	0.000	0.000
69	A	59	PHE	0	-0.021	-0.017	16.983	0.012	0.012	0.000	0.000	0.000	0.000
70	A	60	LEU	0	-0.002	-0.030	20.227	0.022	0.022	0.000	0.000	0.000	0.000
71	A	61	GLY	0	0.059	0.040	22.992	-0.006	-0.006	0.000	0.000	0.000	0.000
72	A	62	ASN	0	-0.002	-0.014	26.526	0.006	0.006	0.000	0.000	0.000	0.000
73	A	63	GLU	-1	-0.782	-0.871	28.183	-0.030	-0.030	0.000	0.000	0.000	0.000
74	A	64	TYR	0	-0.015	-0.001	29.343	-0.008	-0.008	0.000	0.000	0.000	0.000
75	A	65	GLU	-1	-0.787	-0.887	27.615	-0.061	-0.061	0.000	0.000	0.000	0.000
76	A	66	ASN	0	-0.009	-0.022	23.562	-0.022	-0.022	0.000	0.000	0.000	0.000
77	A	67	PHE	0	-0.036	0.001	25.702	-0.014	-0.014	0.000	0.000	0.000	0.000
78	A	68	VAL	0	0.018	0.008	28.028	-0.009	-0.009	0.000	0.000	0.000	0.000
79	A	69	PHE	0	0.045	0.029	20.044	-0.011	-0.011	0.000	0.000	0.000	0.000
80	A	70	THR	0	-0.030	-0.037	22.163	-0.016	-0.016	0.000	0.000	0.000	0.000
81	A	71	ASN	0	-0.052	-0.024	24.477	-0.010	-0.010	0.000	0.000	0.000	0.000
82	A	72	ASP	-1	-0.777	-0.887	27.085	-0.125	-0.125	0.000	0.000	0.000	0.000
83	A	73	LYS	1	0.803	0.913	18.858	0.233	0.233	0.000	0.000	0.000	0.000
84	A	74	LYS	1	0.936	0.970	24.087	0.099	0.099	0.000	0.000	0.000	0.000
85	A	75	LYS	1	0.830	0.897	25.882	0.108	0.108	0.000	0.000	0.000	0.000
86	A	76	SER	0	0.002	-0.007	24.597	0.001	0.001	0.000	0.000	0.000	0.000
87	A	77	ILE	0	-0.004	0.004	20.993	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	78	ILE	0	-0.019	-0.017	25.132	0.007	0.007	0.000	0.000	0.000	0.000
89	A	79	LEU	0	-0.007	0.007	28.706	0.010	0.010	0.000	0.000	0.000	0.000
90	A	80	ALA	0	0.068	0.029	25.521	0.003	0.003	0.000	0.000	0.000	0.000
91	A	81	PHE	0	-0.030	-0.001	26.607	-0.008	-0.008	0.000	0.000	0.000	0.000
92	A	82	LYS	1	0.913	0.938	27.994	0.129	0.129	0.000	0.000	0.000	0.000
93	A	83	GLU	-1	-0.923	-0.961	30.506	-0.144	-0.144	0.000	0.000	0.000	0.000
94	A	84	LYS	1	0.849	0.927	24.926	0.231	0.231	0.000	0.000	0.000	0.000
95	A	85	GLN	0	-0.060	-0.009	29.912	0.011	0.011	0.000	0.000	0.000	0.000

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