FMO DATABASE

FMODB ID: YVQ12

Calculation Name: 3M5B-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3M5B

Chain ID: A

ChEMBL ID:

UniProt ID: Q9Y2Y4

Base Structure: X-ray

Registration Date: 2023-09-20

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	109
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-804109.01823
FMO2-HF: Nuclear repulsion	763042.782065
FMO2-HF: Total energy	-41066.236165
FMO2-MP2: Total energy	-41187.574778

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:5:PRO)

Summations of interaction energy for fragment #1(A:5:PRO)

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.
-5.652	0.034999999999998	0.74	-2.496	-3.929	-0.008

Interaction energy analysis for fragmet #1(A:5:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.010 / q_NPA : -0.014

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

Sort

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	ARG	1	0.954	0.973	3.357	0.092	2.035	0.036	-0.935	-1.044	0.001
4	A	8	LEU	0	-0.025	-0.013	5.299	0.470	0.511	-0.001	-0.004	-0.036	0.000
5	A	9	PRO	0	-0.034	-0.027	8.747	0.054	0.054	0.000	0.000	0.000	0.000
6	A	10	SER	0	0.021	0.011	11.457	0.102	0.102	0.000	0.000	0.000	0.000
7	A	11	PRO	0	-0.040	-0.019	14.204	0.002	0.002	0.000	0.000	0.000	0.000
8	A	12	TYR	0	0.052	0.024	17.314	0.041	0.041	0.000	0.000	0.000	0.000
9	A	13	GLY	0	0.030	0.021	17.435	0.021	0.021	0.000	0.000	0.000	0.000
10	A	14	SER	0	-0.038	-0.014	18.257	0.002	0.002	0.000	0.000	0.000	0.000
11	A	15	ASP	-1	-0.811	-0.882	21.756	-0.186	-0.186	0.000	0.000	0.000	0.000
12	A	16	ARG	1	0.975	0.969	23.865	0.152	0.152	0.000	0.000	0.000	0.000
13	A	17	LEU	0	-0.035	-0.023	26.128	0.002	0.002	0.000	0.000	0.000	0.000
14	A	18	VAL	0	0.041	0.020	20.790	0.005	0.005	0.000	0.000	0.000	0.000
15	A	19	GLN	0	-0.016	-0.024	20.927	0.012	0.012	0.000	0.000	0.000	0.000
16	A	20	LEU	0	-0.073	-0.033	22.591	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	21	ALA	0	0.012	0.002	24.150	0.006	0.006	0.000	0.000	0.000	0.000
18	A	22	ALA	0	0.015	0.011	19.334	0.006	0.006	0.000	0.000	0.000	0.000
19	A	23	ARG	1	0.885	0.944	21.207	0.237	0.237	0.000	0.000	0.000	0.000
20	A	24	LEU	0	-0.048	-0.014	23.081	0.011	0.011	0.000	0.000	0.000	0.000
21	A	25	ARG	1	0.866	0.968	16.475	0.325	0.325	0.000	0.000	0.000	0.000
22	A	26	PRO	0	0.045	-0.001	23.675	-0.009	-0.009	0.000	0.000	0.000	0.000
23	A	27	ALA	0	0.022	0.002	26.065	0.012	0.012	0.000	0.000	0.000	0.000
24	A	28	LEU	0	-0.016	-0.026	28.547	-0.008	-0.008	0.000	0.000	0.000	0.000
25	A	29	CYS	0	-0.088	-0.001	26.382	-0.003	-0.003	0.000	0.000	0.000	0.000
26	A	30	ASP	-1	-0.746	-0.839	28.999	-0.107	-0.107	0.000	0.000	0.000	0.000
27	A	31	THR	0	-0.032	-0.014	27.463	0.010	0.010	0.000	0.000	0.000	0.000
28	A	32	LEU	0	-0.024	-0.007	26.586	-0.010	-0.010	0.000	0.000	0.000	0.000
29	A	33	ILE	0	0.030	0.020	23.719	0.009	0.009	0.000	0.000	0.000	0.000
30	A	34	THR	0	0.041	0.018	24.779	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	35	VAL	0	0.022	0.009	20.483	0.004	0.004	0.000	0.000	0.000	0.000
32	A	36	GLY	0	-0.002	-0.004	23.209	0.005	0.005	0.000	0.000	0.000	0.000
33	A	37	SER	0	-0.013	-0.021	24.830	0.000	0.000	0.000	0.000	0.000	0.000
34	A	38	GLN	0	-0.030	-0.005	18.675	-0.017	-0.017	0.000	0.000	0.000	0.000
35	A	39	GLU	-1	-0.883	-0.953	23.554	-0.073	-0.073	0.000	0.000	0.000	0.000
36	A	40	PHE	0	-0.003	-0.002	18.048	-0.012	-0.012	0.000	0.000	0.000	0.000
37	A	41	PRO	0	-0.002	-0.003	23.093	0.004	0.004	0.000	0.000	0.000	0.000
38	A	42	ALA	0	0.019	0.006	23.297	-0.019	-0.019	0.000	0.000	0.000	0.000
39	A	43	HIS	0	-0.015	-0.001	24.932	0.004	0.004	0.000	0.000	0.000	0.000
40	A	44	SER	0	-0.018	-0.050	26.502	-0.010	-0.010	0.000	0.000	0.000	0.000
41	A	45	LEU	0	-0.022	-0.017	28.435	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	46	VAL	0	0.010	-0.002	22.567	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	47	LEU	0	0.001	0.003	22.665	-0.010	-0.010	0.000	0.000	0.000	0.000
44	A	48	ALA	0	0.027	0.005	24.958	0.000	0.000	0.000	0.000	0.000	0.000
45	A	49	GLY	0	-0.079	-0.017	26.197	0.005	0.005	0.000	0.000	0.000	0.000
46	A	50	VAL	0	-0.052	-0.025	20.246	-0.009	-0.009	0.000	0.000	0.000	0.000
47	A	51	SER	0	-0.007	-0.019	23.685	0.006	0.006	0.000	0.000	0.000	0.000
48	A	52	GLN	0	0.011	0.005	25.575	0.005	0.005	0.000	0.000	0.000	0.000
49	A	53	GLN	0	-0.028	-0.019	26.459	0.002	0.002	0.000	0.000	0.000	0.000
50	A	54	LEU	0	0.020	0.009	22.222	0.007	0.007	0.000	0.000	0.000	0.000
51	A	55	GLY	0	0.001	0.017	26.775	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	56	ARG	1	0.830	0.918	29.229	0.094	0.094	0.000	0.000	0.000	0.000
53	A	57	ARG	1	0.977	0.996	30.274	0.073	0.073	0.000	0.000	0.000	0.000
54	A	58	GLY	0	-0.014	-0.007	32.490	0.006	0.006	0.000	0.000	0.000	0.000
55	A	59	GLN	0	-0.034	-0.023	29.946	-0.005	-0.005	0.000	0.000	0.000	0.000
56	A	60	TRP	0	-0.034	-0.027	25.909	0.007	0.007	0.000	0.000	0.000	0.000
57	A	61	ALA	0	-0.004	0.008	28.024	-0.006	-0.006	0.000	0.000	0.000	0.000
58	A	62	LEU	0	0.014	0.011	22.341	0.002	0.002	0.000	0.000	0.000	0.000
59	A	63	GLY	0	0.012	-0.014	25.231	0.003	0.003	0.000	0.000	0.000	0.000
60	A	64	GLU	-1	-0.982	-0.986	24.141	-0.048	-0.048	0.000	0.000	0.000	0.000
61	A	65	GLY	0	0.003	0.008	22.899	0.004	0.004	0.000	0.000	0.000	0.000
62	A	66	ILE	0	-0.004	0.006	18.347	0.004	0.004	0.000	0.000	0.000	0.000
63	A	67	SER	0	-0.019	-0.012	15.625	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	68	PRO	0	0.064	0.010	17.591	-0.021	-0.021	0.000	0.000	0.000	0.000
65	A	69	SER	0	0.024	0.016	11.652	-0.031	-0.031	0.000	0.000	0.000	0.000
66	A	70	THR	0	-0.009	0.007	13.117	-0.037	-0.037	0.000	0.000	0.000	0.000
67	A	71	PHE	0	0.023	0.003	14.163	-0.047	-0.047	0.000	0.000	0.000	0.000
68	A	72	ALA	0	0.016	0.016	14.226	-0.025	-0.025	0.000	0.000	0.000	0.000
69	A	73	GLN	0	-0.025	-0.026	8.748	-0.019	-0.019	0.000	0.000	0.000	0.000
70	A	74	LEU	0	-0.013	0.001	12.290	-0.059	-0.059	0.000	0.000	0.000	0.000
71	A	75	LEU	0	-0.010	-0.005	14.942	-0.015	-0.015	0.000	0.000	0.000	0.000
72	A	76	ASN	0	0.046	0.008	12.830	0.058	0.058	0.000	0.000	0.000	0.000
73	A	77	PHE	0	0.017	0.021	11.790	-0.008	-0.008	0.000	0.000	0.000	0.000
74	A	78	VAL	0	-0.038	-0.012	14.062	0.005	0.005	0.000	0.000	0.000	0.000
75	A	79	TYR	0	-0.030	-0.035	17.208	0.032	0.032	0.000	0.000	0.000	0.000
76	A	80	GLY	0	-0.032	-0.010	16.620	0.009	0.009	0.000	0.000	0.000	0.000
77	A	81	GLU	-1	-0.886	-0.929	12.171	-0.538	-0.538	0.000	0.000	0.000	0.000
78	A	82	SER	0	-0.045	-0.038	8.860	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	83	VAL	0	0.020	0.017	7.257	0.025	0.025	0.000	0.000	0.000	0.000
80	A	84	GLU	-1	-0.920	-0.970	2.481	-4.687	-3.657	0.393	-0.439	-0.984	-0.001
81	A	85	LEU	0	-0.040	-0.004	3.308	0.139	0.675	0.033	-0.146	-0.423	-0.001
82	A	86	GLN	0	0.060	0.014	3.144	-0.418	1.641	0.280	-0.960	-1.378	-0.007
83	A	87	PRO	0	0.033	-0.004	4.245	-0.593	-0.515	-0.001	-0.012	-0.064	0.000
84	A	88	GLY	0	-0.060	-0.029	6.537	-0.293	-0.293	0.000	0.000	0.000	0.000
85	A	89	GLU	-1	-0.829	-0.903	6.570	-0.129	-0.129	0.000	0.000	0.000	0.000
86	A	90	LEU	0	0.011	0.020	8.488	-0.106	-0.106	0.000	0.000	0.000	0.000
87	A	91	ARG	1	0.881	0.944	10.151	-0.224	-0.224	0.000	0.000	0.000	0.000
88	A	92	PRO	0	0.067	0.035	12.475	-0.028	-0.028	0.000	0.000	0.000	0.000
89	A	93	LEU	0	0.035	0.013	10.174	-0.023	-0.023	0.000	0.000	0.000	0.000
90	A	94	GLN	0	-0.009	-0.004	13.875	0.000	0.000	0.000	0.000	0.000	0.000
91	A	95	GLU	-1	-0.931	-0.980	15.784	0.040	0.040	0.000	0.000	0.000	0.000
92	A	96	ALA	0	0.016	0.013	16.813	0.001	0.001	0.000	0.000	0.000	0.000
93	A	97	ALA	0	-0.013	-0.019	16.608	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	98	ARG	1	0.928	0.978	18.621	0.053	0.053	0.000	0.000	0.000	0.000
95	A	99	ALA	0	-0.035	-0.002	21.506	0.004	0.004	0.000	0.000	0.000	0.000
96	A	100	LEU	0	0.004	0.008	20.340	0.003	0.003	0.000	0.000	0.000	0.000
97	A	101	GLY	0	0.051	0.037	23.374	-0.006	-0.006	0.000	0.000	0.000	0.000
98	A	102	VAL	0	-0.025	-0.005	18.107	-0.009	-0.009	0.000	0.000	0.000	0.000
99	A	103	GLN	0	0.027	0.002	19.272	-0.022	-0.022	0.000	0.000	0.000	0.000
100	A	104	SER	0	-0.003	-0.023	18.116	-0.007	-0.007	0.000	0.000	0.000	0.000
101	A	105	LEU	0	0.015	0.009	12.517	-0.031	-0.031	0.000	0.000	0.000	0.000
102	A	106	GLU	-1	-0.837	-0.934	14.933	-0.129	-0.129	0.000	0.000	0.000	0.000
103	A	107	GLU	-1	-0.795	-0.885	16.620	-0.187	-0.187	0.000	0.000	0.000	0.000
104	A	108	ALA	0	-0.030	-0.012	12.504	-0.006	-0.006	0.000	0.000	0.000	0.000
105	A	109	CYS	0	-0.037	-0.020	11.796	-0.064	-0.064	0.000	0.000	0.000	0.000
106	A	110	TRP	0	-0.037	-0.020	12.583	0.043	0.043	0.000	0.000	0.000	0.000
107	A	111	ARG	1	0.825	0.887	14.194	0.321	0.321	0.000	0.000	0.000	0.000
108	A	112	ALA	0	-0.038	-0.005	8.803	0.017	0.017	0.000	0.000	0.000	0.000
109	A	113	ARG	1	0.913	0.983	9.958	0.106	0.106	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:PRO)