FMO DATABASE

FMODB ID: V5Z21

Calculation Name: 1KXV-C-Xray372

Preferred Name: Pancreatic alpha-amylase

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1KXV

Chain ID: C

ChEMBL ID: CHEMBL5730

UniProt ID: P00690

Base Structure: X-ray

Registration Date: 2023-06-26

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	117
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-899367.185105
FMO2-HF: Nuclear repulsion	853883.011003
FMO2-HF: Total energy	-45484.174102
FMO2-MP2: Total energy	-45612.790965

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(C:2:VAL)

Summations of interaction energy for fragment #1(C:2:VAL)

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.
-10.914	-1.956	11.45	-6.762	-13.641	-0.036

Interaction energy analysis for fragmet #1(C:2:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.024 / q_NPA : -0.012

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	C	4	LEU	0	-0.013	-0.006	3.506	-0.794	1.588	0.021	-1.168	-1.234	0.003
4	C	5	VAL	0	-0.012	-0.005	5.311	0.026	0.040	-0.001	-0.002	-0.011	0.000
5	C	6	GLU	-1	-0.777	-0.901	8.567	-0.471	-0.471	0.000	0.000	0.000	0.000
6	C	7	SER	0	-0.017	-0.022	11.787	0.013	0.013	0.000	0.000	0.000	0.000
7	C	8	GLY	0	0.058	0.020	15.257	0.015	0.015	0.000	0.000	0.000	0.000
8	C	9	GLY	0	0.003	0.010	18.579	0.018	0.018	0.000	0.000	0.000	0.000
9	C	10	GLY	0	-0.018	-0.009	20.380	0.004	0.004	0.000	0.000	0.000	0.000
10	C	11	THR	0	-0.033	-0.020	24.075	-0.003	-0.003	0.000	0.000	0.000	0.000
11	C	12	VAL	0	0.006	0.015	27.710	0.005	0.005	0.000	0.000	0.000	0.000
12	C	13	PRO	0	0.044	0.020	29.909	-0.001	-0.001	0.000	0.000	0.000	0.000
13	C	14	ALA	0	0.029	0.000	32.259	-0.001	-0.001	0.000	0.000	0.000	0.000
14	C	15	GLY	0	-0.023	-0.010	33.036	0.005	0.005	0.000	0.000	0.000	0.000
15	C	16	GLY	0	-0.018	0.002	31.381	0.004	0.004	0.000	0.000	0.000	0.000
16	C	17	SER	0	-0.026	-0.061	27.208	0.000	0.000	0.000	0.000	0.000	0.000
17	C	18	LEU	0	-0.045	-0.018	22.871	-0.004	-0.004	0.000	0.000	0.000	0.000
18	C	19	ARG	1	0.931	0.975	17.584	0.127	0.127	0.000	0.000	0.000	0.000
19	C	20	LEU	0	0.002	0.024	16.479	-0.013	-0.013	0.000	0.000	0.000	0.000
20	C	21	SER	0	-0.020	-0.022	14.379	0.048	0.048	0.000	0.000	0.000	0.000
21	C	22	CYS	0	-0.051	-0.012	9.587	-0.038	-0.038	0.000	0.000	0.000	0.000
22	C	23	ALA	0	0.011	0.009	7.306	0.127	0.127	0.000	0.000	0.000	0.000
23	C	24	ALA	0	0.026	0.020	3.345	-0.682	-0.332	0.036	-0.107	-0.279	0.000
24	C	25	SER	0	-0.023	-0.011	3.090	-0.573	0.430	0.353	-0.319	-1.037	-0.002
25	C	26	GLY	0	0.055	0.010	2.299	-3.423	-2.305	4.740	-3.138	-2.720	-0.027
26	C	27	ASN	0	0.013	-0.001	2.388	-0.889	-0.801	2.330	-0.328	-2.089	-0.003
27	C	28	THR	0	0.027	0.011	3.496	-0.486	-0.484	-0.001	0.200	-0.200	0.000
28	C	29	LEU	0	0.040	0.041	6.713	-0.328	-0.328	0.000	0.000	0.000	0.000
29	C	30	CYS	0	-0.079	-0.019	3.422	0.326	1.477	0.259	-0.306	-1.104	-0.001
30	C	31	THR	0	0.031	0.021	5.624	-0.073	-0.073	0.000	0.000	0.000	0.000
31	C	32	TYR	0	-0.062	-0.049	2.594	-2.123	-0.359	0.718	-0.735	-1.747	-0.007
32	C	33	ASP	-1	-0.739	-0.835	7.516	0.046	0.046	0.000	0.000	0.000	0.000
33	C	34	MET	0	-0.009	-0.011	7.196	-0.108	-0.108	0.000	0.000	0.000	0.000
34	C	35	SER	0	0.001	-0.010	11.753	0.048	0.048	0.000	0.000	0.000	0.000
35	C	36	TRP	0	-0.001	0.001	13.720	-0.052	-0.052	0.000	0.000	0.000	0.000
36	C	37	TYR	0	-0.016	-0.011	15.071	0.032	0.032	0.000	0.000	0.000	0.000
37	C	38	ARG	1	0.826	0.915	18.288	0.121	0.121	0.000	0.000	0.000	0.000
38	C	39	ARG	1	0.936	0.973	19.963	0.288	0.288	0.000	0.000	0.000	0.000
39	C	40	ALA	0	0.062	0.045	22.970	-0.007	-0.007	0.000	0.000	0.000	0.000
40	C	41	PRO	0	0.018	-0.002	26.368	-0.005	-0.005	0.000	0.000	0.000	0.000
41	C	42	GLY	0	0.020	0.008	28.533	0.011	0.011	0.000	0.000	0.000	0.000
42	C	43	LYS	1	0.844	0.925	26.878	0.139	0.139	0.000	0.000	0.000	0.000
43	C	44	GLY	0	0.067	0.048	25.090	-0.009	-0.009	0.000	0.000	0.000	0.000
44	C	45	ARG	1	0.821	0.916	15.546	0.367	0.367	0.000	0.000	0.000	0.000
45	C	46	ASP	-1	-0.842	-0.918	20.719	-0.165	-0.165	0.000	0.000	0.000	0.000
46	C	47	PHE	0	-0.006	-0.010	18.155	-0.014	-0.014	0.000	0.000	0.000	0.000
47	C	48	VAL	0	-0.019	0.000	19.979	0.011	0.011	0.000	0.000	0.000	0.000
48	C	49	SER	0	0.010	-0.020	19.371	0.021	0.021	0.000	0.000	0.000	0.000
49	C	50	GLY	0	0.005	0.005	16.503	-0.031	-0.031	0.000	0.000	0.000	0.000
50	C	51	ILE	0	-0.026	-0.006	14.636	0.015	0.015	0.000	0.000	0.000	0.000
51	C	52	ASP	-1	-0.777	-0.859	14.009	0.017	0.017	0.000	0.000	0.000	0.000
52	C	53	ASN	0	-0.046	-0.058	12.286	0.037	0.037	0.000	0.000	0.000	0.000
53	C	54	ASP	-1	-0.854	-0.892	13.928	0.145	0.145	0.000	0.000	0.000	0.000
54	C	55	GLY	0	-0.018	0.002	17.191	-0.003	-0.003	0.000	0.000	0.000	0.000
55	C	56	THR	0	-0.029	-0.032	18.677	-0.012	-0.012	0.000	0.000	0.000	0.000
56	C	57	THR	0	-0.042	-0.016	19.190	-0.013	-0.013	0.000	0.000	0.000	0.000
57	C	58	THR	0	-0.043	-0.027	20.454	0.007	0.007	0.000	0.000	0.000	0.000
58	C	59	TYR	0	0.028	0.012	21.258	-0.016	-0.016	0.000	0.000	0.000	0.000
59	C	60	VAL	0	0.023	0.030	23.807	0.005	0.005	0.000	0.000	0.000	0.000
60	C	61	ASP	-1	-0.824	-0.930	26.091	-0.064	-0.064	0.000	0.000	0.000	0.000
61	C	62	SER	0	-0.056	-0.022	28.106	0.002	0.002	0.000	0.000	0.000	0.000
62	C	63	VAL	0	-0.019	-0.018	24.141	-0.002	-0.002	0.000	0.000	0.000	0.000
63	C	64	ALA	0	0.046	0.034	27.502	0.002	0.002	0.000	0.000	0.000	0.000
64	C	65	GLY	0	-0.015	-0.007	28.544	0.002	0.002	0.000	0.000	0.000	0.000
65	C	66	ARG	1	0.740	0.854	28.554	0.093	0.093	0.000	0.000	0.000	0.000
66	C	67	PHE	0	0.013	-0.002	22.781	-0.007	-0.007	0.000	0.000	0.000	0.000
67	C	68	THR	0	-0.032	-0.023	22.724	0.013	0.013	0.000	0.000	0.000	0.000
68	C	69	ILE	0	-0.048	-0.011	15.704	-0.013	-0.013	0.000	0.000	0.000	0.000
69	C	70	SER	0	-0.006	-0.001	17.813	0.019	0.019	0.000	0.000	0.000	0.000
70	C	71	GLN	0	0.040	0.011	13.230	-0.003	-0.003	0.000	0.000	0.000	0.000
71	C	72	GLY	0	0.000	-0.004	13.463	-0.004	-0.004	0.000	0.000	0.000	0.000
72	C	73	ASN	0	-0.014	-0.008	11.967	-0.008	-0.008	0.000	0.000	0.000	0.000
73	C	74	ALA	0	-0.010	-0.003	10.650	0.039	0.039	0.000	0.000	0.000	0.000
74	C	75	LYS	1	0.940	0.985	8.802	-0.704	-0.704	0.000	0.000	0.000	0.000
75	C	76	ASN	0	-0.013	-0.011	5.313	-0.097	-0.097	0.000	0.000	0.000	0.000
76	C	77	THR	0	-0.037	-0.030	7.258	-0.145	-0.145	0.000	0.000	0.000	0.000
77	C	78	ALA	0	0.038	0.018	9.949	0.045	0.045	0.000	0.000	0.000	0.000
78	C	79	TYR	0	-0.038	-0.037	13.153	-0.034	-0.034	0.000	0.000	0.000	0.000
79	C	80	LEU	0	0.011	0.004	16.410	0.017	0.017	0.000	0.000	0.000	0.000
80	C	81	GLN	0	-0.030	-0.023	18.772	-0.018	-0.018	0.000	0.000	0.000	0.000
81	C	82	MET	0	-0.042	-0.015	21.780	-0.002	-0.002	0.000	0.000	0.000	0.000
82	C	83	ASP	-1	-0.732	-0.832	24.615	-0.079	-0.079	0.000	0.000	0.000	0.000
83	C	84	SER	0	-0.020	-0.011	28.319	0.002	0.002	0.000	0.000	0.000	0.000
84	C	85	LEU	0	-0.033	-0.001	25.502	-0.001	-0.001	0.000	0.000	0.000	0.000
85	C	86	LYS	1	0.896	0.946	29.680	0.093	0.093	0.000	0.000	0.000	0.000
86	C	87	PRO	0	0.051	0.020	30.322	-0.008	-0.008	0.000	0.000	0.000	0.000
87	C	88	ASP	-1	-0.857	-0.930	30.669	-0.104	-0.104	0.000	0.000	0.000	0.000
88	C	89	ASP	-1	-0.756	-0.850	26.357	-0.117	-0.117	0.000	0.000	0.000	0.000
89	C	90	THR	0	-0.013	0.006	25.656	-0.014	-0.014	0.000	0.000	0.000	0.000
90	C	91	ALA	0	-0.052	-0.033	23.238	0.003	0.003	0.000	0.000	0.000	0.000
91	C	92	MET	0	-0.025	0.014	18.899	-0.004	-0.004	0.000	0.000	0.000	0.000
92	C	93	TYR	0	0.030	-0.019	17.875	0.009	0.009	0.000	0.000	0.000	0.000
93	C	94	TYR	0	-0.024	-0.013	14.413	-0.012	-0.012	0.000	0.000	0.000	0.000
94	C	96	LYS	1	0.875	0.934	9.752	0.413	0.413	0.000	0.000	0.000	0.000
95	C	97	PRO	0	0.058	0.019	5.838	0.075	0.075	0.000	0.000	0.000	0.000
96	C	98	SER	0	-0.067	-0.030	8.350	-0.067	-0.067	0.000	0.000	0.000	0.000
97	C	99	LEU	0	-0.050	-0.031	5.807	0.040	0.040	0.000	0.000	0.000	0.000
98	C	100	ARG	1	0.765	0.862	8.337	-0.076	-0.076	0.000	0.000	0.000	0.000
99	C	101	TYR	0	0.024	-0.001	10.102	0.002	0.002	0.000	0.000	0.000	0.000
100	C	102	GLY	0	-0.012	0.004	9.273	0.071	0.071	0.000	0.000	0.000	0.000
101	C	103	LEU	0	0.022	0.001	7.989	0.002	0.002	0.000	0.000	0.000	0.000
102	C	104	PRO	0	0.025	-0.007	8.159	0.066	0.066	0.000	0.000	0.000	0.000
103	C	105	GLY	0	0.020	0.017	6.085	0.115	0.115	0.000	0.000	0.000	0.000
104	C	107	PRO	0	0.034	0.031	2.429	-1.654	-0.801	1.795	-0.591	-2.057	0.000
105	C	108	ILE	0	0.042	0.015	5.060	-0.250	-0.141	-0.001	-0.002	-0.104	0.000
106	C	109	ILE	0	-0.006	0.012	2.394	-0.630	-0.506	1.201	-0.266	-1.059	0.001
107	C	110	PRO	0	0.017	0.007	6.271	0.286	0.286	0.000	0.000	0.000	0.000
108	C	111	TRP	0	-0.033	-0.037	8.746	-0.040	-0.040	0.000	0.000	0.000	0.000
109	C	112	GLY	0	0.084	0.052	10.697	-0.079	-0.079	0.000	0.000	0.000	0.000
110	C	113	GLN	0	-0.033	-0.037	11.188	0.096	0.096	0.000	0.000	0.000	0.000
111	C	114	GLY	0	-0.010	0.008	13.582	0.070	0.070	0.000	0.000	0.000	0.000
112	C	115	THR	0	-0.034	-0.024	15.235	0.004	0.004	0.000	0.000	0.000	0.000
113	C	116	GLN	0	0.033	0.006	17.611	0.034	0.034	0.000	0.000	0.000	0.000
114	C	117	VAL	0	0.014	0.022	21.045	0.003	0.003	0.000	0.000	0.000	0.000
115	C	118	THR	0	-0.032	-0.027	23.667	0.004	0.004	0.000	0.000	0.000	0.000
116	C	119	VAL	0	0.016	0.021	27.427	0.004	0.004	0.000	0.000	0.000	0.000
117	C	120	SER	0	-0.048	-0.024	30.167	0.007	0.007	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:2:VAL)