FMO DATABASE

FMODB ID: YV132

Calculation Name: 2A1B-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2A1B

Chain ID: A

ChEMBL ID:

UniProt ID: P72761

Base Structure: X-ray

Registration Date: 2023-09-23

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	101
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-678096.641429
FMO2-HF: Nuclear repulsion	640569.223667
FMO2-HF: Total energy	-37527.417762
FMO2-MP2: Total energy	-37638.051264

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:2:SER)

Summations of interaction energy for fragment #1(A:2:SER)

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.
-36.123	-25.48	7.169	-7.769	-10.046	-0.048

Interaction energy analysis for fragmet #1(A:2:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.050 / q_NPA : 0.032

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	4	ALA	0	0.071	0.038	3.805	-4.500	-3.024	0.006	-0.670	-0.813	0.003
4	A	5	VAL	0	0.009	-0.002	6.032	-0.175	-0.175	0.000	0.000	0.000	0.000
5	A	6	GLY	0	0.015	0.001	7.481	0.012	0.012	0.000	0.000	0.000	0.000
6	A	7	MET	0	-0.006	-0.002	10.325	-0.023	-0.023	0.000	0.000	0.000	0.000
7	A	8	ILE	0	0.004	-0.002	13.713	0.019	0.019	0.000	0.000	0.000	0.000
8	A	9	GLU	-1	-0.815	-0.890	17.410	-0.332	-0.332	0.000	0.000	0.000	0.000
9	A	10	THR	0	-0.012	-0.019	19.815	0.039	0.039	0.000	0.000	0.000	0.000
10	A	11	ARG	1	0.944	0.980	23.440	0.150	0.150	0.000	0.000	0.000	0.000
11	A	12	GLY	0	0.024	0.015	26.782	0.018	0.018	0.000	0.000	0.000	0.000
12	A	13	PHE	0	-0.011	-0.020	23.732	-0.005	-0.005	0.000	0.000	0.000	0.000
13	A	14	PRO	0	0.043	-0.016	25.982	0.005	0.005	0.000	0.000	0.000	0.000
14	A	15	ALA	0	0.072	0.054	26.694	0.014	0.014	0.000	0.000	0.000	0.000
15	A	16	VAL	0	-0.006	0.012	20.892	0.008	0.008	0.000	0.000	0.000	0.000
16	A	17	VAL	0	-0.009	-0.006	21.715	0.006	0.006	0.000	0.000	0.000	0.000
17	A	18	GLU	-1	-0.849	-0.926	22.974	0.081	0.081	0.000	0.000	0.000	0.000
18	A	19	ALA	0	0.000	0.019	20.890	0.022	0.022	0.000	0.000	0.000	0.000
19	A	20	ALA	0	0.003	-0.023	18.706	0.026	0.026	0.000	0.000	0.000	0.000
20	A	21	ASP	-1	-0.882	-0.943	19.334	0.161	0.161	0.000	0.000	0.000	0.000
21	A	22	SER	0	-0.009	0.004	21.539	0.037	0.037	0.000	0.000	0.000	0.000
22	A	23	MET	0	-0.079	-0.043	14.867	0.034	0.034	0.000	0.000	0.000	0.000
23	A	24	VAL	0	-0.004	-0.015	16.205	0.075	0.075	0.000	0.000	0.000	0.000
24	A	25	LYS	1	0.843	0.937	17.587	-0.102	-0.102	0.000	0.000	0.000	0.000
25	A	26	ALA	0	-0.055	-0.032	19.638	0.028	0.028	0.000	0.000	0.000	0.000
26	A	27	ALA	0	-0.029	-0.007	15.756	0.045	0.045	0.000	0.000	0.000	0.000
27	A	28	ARG	1	0.928	0.972	14.433	-0.872	-0.872	0.000	0.000	0.000	0.000
28	A	29	VAL	0	-0.032	-0.008	11.980	0.214	0.214	0.000	0.000	0.000	0.000
29	A	30	THR	0	0.020	-0.002	10.646	-0.086	-0.086	0.000	0.000	0.000	0.000
30	A	31	LEU	0	-0.017	-0.014	11.450	-0.074	-0.074	0.000	0.000	0.000	0.000
31	A	32	VAL	0	-0.042	-0.018	8.742	0.052	0.052	0.000	0.000	0.000	0.000
32	A	33	GLY	0	0.046	0.025	12.073	-0.037	-0.037	0.000	0.000	0.000	0.000
33	A	34	TYR	0	-0.043	-0.031	14.870	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	35	GLU	-1	-0.872	-0.929	16.154	-0.529	-0.529	0.000	0.000	0.000	0.000
35	A	36	LYS	1	0.912	0.953	18.237	0.246	0.246	0.000	0.000	0.000	0.000
36	A	37	ILE	0	0.044	0.038	19.742	-0.016	-0.016	0.000	0.000	0.000	0.000
37	A	38	GLY	0	0.014	0.018	22.212	0.009	0.009	0.000	0.000	0.000	0.000
38	A	39	SER	0	-0.027	-0.047	25.937	0.000	0.000	0.000	0.000	0.000	0.000
39	A	40	GLY	0	-0.005	-0.004	28.032	0.003	0.003	0.000	0.000	0.000	0.000
40	A	41	ARG	1	0.822	0.933	22.473	0.301	0.301	0.000	0.000	0.000	0.000
41	A	42	VAL	0	-0.031	-0.021	21.376	-0.018	-0.018	0.000	0.000	0.000	0.000
42	A	43	THR	0	0.024	0.006	15.505	0.015	0.015	0.000	0.000	0.000	0.000
43	A	44	VAL	0	-0.009	0.012	16.286	-0.006	-0.006	0.000	0.000	0.000	0.000
44	A	45	ILE	0	-0.018	-0.005	10.297	-0.025	-0.025	0.000	0.000	0.000	0.000
45	A	46	VAL	0	0.034	0.021	11.500	0.070	0.070	0.000	0.000	0.000	0.000
46	A	47	ARG	1	0.765	0.880	2.717	2.171	2.683	0.242	-0.220	-0.534	0.000
47	A	48	GLY	0	0.092	0.036	7.685	0.009	0.009	0.000	0.000	0.000	0.000
48	A	49	ASP	-1	-0.926	-0.959	7.630	2.450	2.450	0.000	0.000	0.000	0.000
49	A	50	VAL	0	0.041	0.011	9.037	-0.297	-0.297	0.000	0.000	0.000	0.000
50	A	51	SER	0	0.010	-0.005	10.242	-0.191	-0.191	0.000	0.000	0.000	0.000
51	A	52	GLY	0	0.019	0.017	12.654	-0.134	-0.134	0.000	0.000	0.000	0.000
52	A	53	VAL	0	0.024	0.004	8.906	-0.164	-0.164	0.000	0.000	0.000	0.000
53	A	54	GLN	0	0.013	-0.002	12.267	-0.122	-0.122	0.000	0.000	0.000	0.000
54	A	55	ALA	0	0.007	0.016	15.015	-0.090	-0.090	0.000	0.000	0.000	0.000
55	A	56	SER	0	-0.001	0.028	14.656	-0.083	-0.083	0.000	0.000	0.000	0.000
56	A	57	VAL	0	0.045	0.020	13.786	-0.063	-0.063	0.000	0.000	0.000	0.000
57	A	58	SER	0	-0.075	-0.040	17.039	-0.046	-0.046	0.000	0.000	0.000	0.000
58	A	59	ALA	0	0.017	0.009	20.092	-0.030	-0.030	0.000	0.000	0.000	0.000
59	A	60	GLY	0	0.029	0.004	20.194	-0.023	-0.023	0.000	0.000	0.000	0.000
60	A	61	ILE	0	0.012	0.003	19.304	-0.024	-0.024	0.000	0.000	0.000	0.000
61	A	62	GLU	-1	-0.899	-0.940	22.682	0.074	0.074	0.000	0.000	0.000	0.000
62	A	63	ALA	0	-0.045	-0.007	24.872	-0.008	-0.008	0.000	0.000	0.000	0.000
63	A	64	ALA	0	0.018	0.007	23.845	-0.009	-0.009	0.000	0.000	0.000	0.000
64	A	65	ASN	0	0.004	-0.017	25.941	-0.018	-0.018	0.000	0.000	0.000	0.000
65	A	66	ARG	1	0.834	0.917	28.420	-0.063	-0.063	0.000	0.000	0.000	0.000
66	A	67	VAL	0	-0.003	0.019	27.879	0.002	0.002	0.000	0.000	0.000	0.000
67	A	68	ASN	0	-0.029	-0.001	31.052	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	69	GLY	0	-0.022	-0.031	32.744	-0.004	-0.004	0.000	0.000	0.000	0.000
69	A	70	GLY	0	-0.064	-0.045	28.655	-0.013	-0.013	0.000	0.000	0.000	0.000
70	A	71	GLU	-1	-0.911	-0.952	27.798	-0.090	-0.090	0.000	0.000	0.000	0.000
71	A	72	VAL	0	-0.026	-0.009	21.901	-0.023	-0.023	0.000	0.000	0.000	0.000
72	A	73	LEU	0	-0.015	-0.002	22.886	-0.006	-0.006	0.000	0.000	0.000	0.000
73	A	74	SER	0	-0.016	-0.029	19.042	-0.016	-0.016	0.000	0.000	0.000	0.000
74	A	75	THR	0	0.011	-0.019	16.929	0.036	0.036	0.000	0.000	0.000	0.000
75	A	76	HIS	0	-0.024	0.002	11.676	0.047	0.047	0.000	0.000	0.000	0.000
76	A	77	ILE	0	0.034	0.011	9.940	0.041	0.041	0.000	0.000	0.000	0.000
77	A	78	ILE	0	-0.030	0.030	5.840	0.002	0.002	0.000	0.000	0.000	0.000
78	A	79	ALA	0	0.028	0.000	7.089	0.113	0.113	0.000	0.000	0.000	0.000
79	A	80	ARG	1	0.935	1.012	3.118	-7.269	-5.536	0.142	-0.841	-1.034	0.006
80	A	81	PRO	0	-0.027	-0.022	2.708	-4.022	-2.308	0.321	-0.619	-1.416	0.001
81	A	82	HIS	0	0.043	0.011	2.255	-9.959	-9.609	4.966	-2.488	-2.829	-0.028
82	A	83	GLU	-1	-0.816	-0.907	2.933	-4.163	-3.574	0.084	-0.202	-0.471	-0.001
83	A	84	ASN	0	-0.022	-0.033	4.419	0.943	0.972	-0.001	-0.012	-0.016	0.000
84	A	85	LEU	0	0.022	0.017	5.910	0.467	0.467	0.000	0.000	0.000	0.000
85	A	86	GLU	-1	-0.822	-0.964	2.746	-12.895	-8.655	1.409	-2.717	-2.933	-0.029
86	A	87	TYR	0	-0.081	-0.039	6.796	0.630	0.630	0.000	0.000	0.000	0.000
87	A	88	VAL	0	-0.018	-0.014	10.007	0.337	0.337	0.000	0.000	0.000	0.000
88	A	89	LEU	0	0.003	0.005	9.685	0.236	0.236	0.000	0.000	0.000	0.000
89	A	90	PRO	0	-0.040	-0.003	10.639	-0.147	-0.147	0.000	0.000	0.000	0.000
90	A	91	ILE	0	-0.002	0.013	5.605	0.103	0.103	0.000	0.000	0.000	0.000
91	A	92	ARG	1	0.854	0.967	7.627	1.270	1.270	0.000	0.000	0.000	0.000
92	A	93	TYR	0	0.042	0.019	6.674	0.128	0.128	0.000	0.000	0.000	0.000
93	A	94	THR	0	0.021	0.015	11.185	-0.154	-0.154	0.000	0.000	0.000	0.000
94	A	95	GLU	-1	-0.898	-0.935	14.859	0.038	0.038	0.000	0.000	0.000	0.000
95	A	96	GLU	-1	-0.943	-0.991	14.215	0.001	0.001	0.000	0.000	0.000	0.000
96	A	97	VAL	0	-0.047	-0.020	16.960	0.010	0.010	0.000	0.000	0.000	0.000
97	A	98	GLU	-1	-0.812	-0.915	19.383	-0.213	-0.213	0.000	0.000	0.000	0.000
98	A	99	GLN	0	-0.010	0.021	21.533	-0.006	-0.006	0.000	0.000	0.000	0.000
99	A	100	PHE	0	-0.035	-0.009	22.885	0.002	0.002	0.000	0.000	0.000	0.000
100	A	101	ARG	1	0.826	0.940	20.527	0.229	0.229	0.000	0.000	0.000	0.000
101	A	102	THR	0	-0.058	-0.075	24.282	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:2:SER)