FMO DATABASE

FMODB ID: YZ7Q2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-897673.1303
FMO2-HF: Nuclear repulsion	852189.278845
FMO2-HF: Total energy	-45483.851455
FMO2-MP2: Total energy	-45612.508808

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.
-9.987	-2.732	15.125	-8.126	-14.254	-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 : -0.017 / 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	C	4	LEU	0	-0.013	-0.011	3.734	-1.054	1.591	-0.014	-1.320	-1.310	0.005
4	C	5	VAL	0	-0.014	-0.007	5.301	0.069	0.093	-0.001	-0.002	-0.021	0.000
5	C	6	GLU	-1	-0.813	-0.915	8.507	-0.482	-0.482	0.000	0.000	0.000	0.000
6	C	7	SER	0	-0.025	-0.033	11.564	0.016	0.016	0.000	0.000	0.000	0.000
7	C	8	GLY	0	0.043	0.001	14.998	0.018	0.018	0.000	0.000	0.000	0.000
8	C	9	GLY	0	-0.002	0.026	18.462	0.020	0.020	0.000	0.000	0.000	0.000
9	C	10	GLY	0	0.018	0.009	20.342	0.004	0.004	0.000	0.000	0.000	0.000
10	C	11	THR	0	-0.016	-0.017	24.063	-0.002	-0.002	0.000	0.000	0.000	0.000
11	C	12	VAL	0	0.010	0.026	27.637	0.006	0.006	0.000	0.000	0.000	0.000
12	C	13	PRO	0	0.080	0.019	29.735	-0.002	-0.002	0.000	0.000	0.000	0.000
13	C	14	ALA	0	0.025	-0.004	32.085	-0.001	-0.001	0.000	0.000	0.000	0.000
14	C	15	GLY	0	-0.027	-0.018	32.514	0.005	0.005	0.000	0.000	0.000	0.000
15	C	16	GLY	0	-0.030	-0.002	30.725	0.004	0.004	0.000	0.000	0.000	0.000
16	C	17	SER	0	-0.021	-0.060	26.587	0.001	0.001	0.000	0.000	0.000	0.000
17	C	18	LEU	0	-0.049	-0.017	22.523	-0.005	-0.005	0.000	0.000	0.000	0.000
18	C	19	ARG	1	0.964	0.996	18.574	0.133	0.133	0.000	0.000	0.000	0.000
19	C	20	LEU	0	-0.012	0.016	16.162	-0.017	-0.017	0.000	0.000	0.000	0.000
20	C	21	SER	0	-0.011	-0.016	13.665	0.049	0.049	0.000	0.000	0.000	0.000
21	C	22	CYS	0	-0.045	-0.007	9.311	-0.027	-0.027	0.000	0.000	0.000	0.000
22	C	23	ALA	0	0.015	0.010	7.342	0.120	0.120	0.000	0.000	0.000	0.000
23	C	24	ALA	0	0.010	0.016	3.264	-0.754	-0.341	0.070	-0.125	-0.357	0.001
24	C	25	SER	0	-0.005	-0.012	3.176	-0.842	0.344	0.289	-0.453	-1.023	-0.004
25	C	26	GLY	0	0.065	0.021	2.194	-2.670	-2.960	7.280	-3.901	-3.090	-0.031
26	C	27	ASN	0	0.029	0.006	2.278	-0.144	-0.227	2.703	-0.525	-2.095	-0.001
27	C	28	THR	0	0.012	0.003	3.490	-0.403	-0.403	-0.002	0.201	-0.199	0.000
28	C	29	LEU	0	0.035	0.044	6.415	-0.342	-0.342	0.000	0.000	0.000	0.000
29	C	30	CYS	0	-0.066	0.005	3.708	0.342	1.230	0.133	-0.213	-0.808	0.000
30	C	31	THR	0	0.013	0.004	5.765	-0.083	-0.083	0.000	0.000	0.000	0.000
31	C	32	TYR	0	-0.034	-0.038	2.567	-2.252	-0.426	0.870	-0.805	-1.892	-0.008
32	C	33	ASP	-1	-0.730	-0.828	7.444	0.058	0.058	0.000	0.000	0.000	0.000
33	C	34	MET	0	-0.040	-0.026	6.917	-0.100	-0.100	0.000	0.000	0.000	0.000
34	C	35	SER	0	0.019	0.004	11.579	0.045	0.045	0.000	0.000	0.000	0.000
35	C	36	TRP	0	0.011	0.003	13.812	-0.045	-0.045	0.000	0.000	0.000	0.000
36	C	37	TYR	0	-0.033	-0.017	15.185	0.032	0.032	0.000	0.000	0.000	0.000
37	C	38	ARG	1	0.874	0.934	17.966	0.118	0.118	0.000	0.000	0.000	0.000
38	C	39	ARG	1	0.908	0.953	19.552	0.286	0.286	0.000	0.000	0.000	0.000
39	C	40	ALA	0	0.060	0.040	22.580	-0.008	-0.008	0.000	0.000	0.000	0.000
40	C	41	PRO	0	0.027	0.008	25.996	-0.003	-0.003	0.000	0.000	0.000	0.000
41	C	42	GLY	0	0.007	-0.004	27.933	0.010	0.010	0.000	0.000	0.000	0.000
42	C	43	LYS	1	0.921	0.974	26.908	0.123	0.123	0.000	0.000	0.000	0.000
43	C	44	GLY	0	0.042	0.022	24.961	-0.010	-0.010	0.000	0.000	0.000	0.000
44	C	45	ARG	1	0.821	0.919	15.585	0.355	0.355	0.000	0.000	0.000	0.000
45	C	46	ASP	-1	-0.862	-0.925	21.244	-0.149	-0.149	0.000	0.000	0.000	0.000
46	C	47	PHE	0	0.005	0.000	17.854	-0.017	-0.017	0.000	0.000	0.000	0.000
47	C	48	VAL	0	-0.032	-0.015	19.643	0.012	0.012	0.000	0.000	0.000	0.000
48	C	49	SER	0	0.017	-0.016	19.117	0.020	0.020	0.000	0.000	0.000	0.000
49	C	50	GLY	0	0.003	0.002	16.417	-0.030	-0.030	0.000	0.000	0.000	0.000
50	C	51	ILE	0	-0.036	-0.008	14.491	0.014	0.014	0.000	0.000	0.000	0.000
51	C	52	ASP	-1	-0.785	-0.879	14.068	0.022	0.022	0.000	0.000	0.000	0.000
52	C	53	ASN	0	-0.044	-0.043	12.342	0.025	0.025	0.000	0.000	0.000	0.000
53	C	54	ASP	-1	-0.877	-0.915	14.178	0.134	0.134	0.000	0.000	0.000	0.000
54	C	55	GLY	0	-0.039	-0.012	17.030	-0.005	-0.005	0.000	0.000	0.000	0.000
55	C	56	THR	0	-0.030	-0.014	18.774	-0.011	-0.011	0.000	0.000	0.000	0.000
56	C	57	THR	0	-0.018	-0.015	18.962	-0.012	-0.012	0.000	0.000	0.000	0.000
57	C	58	THR	0	-0.033	-0.016	20.371	0.007	0.007	0.000	0.000	0.000	0.000
58	C	59	TYR	0	0.025	0.012	21.211	-0.018	-0.018	0.000	0.000	0.000	0.000
59	C	60	VAL	0	0.011	0.020	23.772	0.007	0.007	0.000	0.000	0.000	0.000
60	C	61	ASP	-1	-0.834	-0.935	25.662	-0.060	-0.060	0.000	0.000	0.000	0.000
61	C	62	SER	0	-0.068	-0.031	27.881	0.001	0.001	0.000	0.000	0.000	0.000
62	C	63	VAL	0	-0.021	-0.020	23.820	-0.001	-0.001	0.000	0.000	0.000	0.000
63	C	64	ALA	0	0.045	0.032	27.192	0.001	0.001	0.000	0.000	0.000	0.000
64	C	65	GLY	0	-0.009	0.000	28.218	0.002	0.002	0.000	0.000	0.000	0.000
65	C	66	ARG	1	0.718	0.838	28.209	0.097	0.097	0.000	0.000	0.000	0.000
66	C	67	PHE	0	-0.004	-0.015	22.386	-0.008	-0.008	0.000	0.000	0.000	0.000
67	C	68	THR	0	0.026	0.022	22.638	0.012	0.012	0.000	0.000	0.000	0.000
68	C	69	ILE	0	-0.062	-0.025	15.677	-0.014	-0.014	0.000	0.000	0.000	0.000
69	C	70	SER	0	-0.007	-0.004	17.771	0.019	0.019	0.000	0.000	0.000	0.000
70	C	71	GLN	0	0.029	0.013	13.335	-0.008	-0.008	0.000	0.000	0.000	0.000
71	C	72	GLY	0	-0.012	-0.016	13.490	0.000	0.000	0.000	0.000	0.000	0.000
72	C	73	ASN	0	-0.001	-0.011	11.829	0.000	0.000	0.000	0.000	0.000	0.000
73	C	74	ALA	0	-0.005	0.009	10.850	0.037	0.037	0.000	0.000	0.000	0.000
74	C	75	LYS	1	0.931	0.979	8.753	-0.681	-0.681	0.000	0.000	0.000	0.000
75	C	76	ASN	0	-0.012	-0.016	5.077	-0.091	-0.091	0.000	0.000	0.000	0.000
76	C	77	THR	0	-0.011	-0.023	7.150	-0.137	-0.137	0.000	0.000	0.000	0.000
77	C	78	ALA	0	0.029	0.020	9.934	0.049	0.049	0.000	0.000	0.000	0.000
78	C	79	TYR	0	-0.049	-0.031	13.058	-0.036	-0.036	0.000	0.000	0.000	0.000
79	C	80	LEU	0	0.019	0.005	16.185	0.018	0.018	0.000	0.000	0.000	0.000
80	C	81	GLN	0	-0.044	-0.034	18.575	-0.020	-0.020	0.000	0.000	0.000	0.000
81	C	82	MET	0	-0.036	-0.015	21.392	0.004	0.004	0.000	0.000	0.000	0.000
82	C	83	ASP	-1	-0.736	-0.836	24.197	-0.086	-0.086	0.000	0.000	0.000	0.000
83	C	84	SER	0	-0.013	-0.011	27.908	0.002	0.002	0.000	0.000	0.000	0.000
84	C	85	LEU	0	-0.034	-0.003	25.315	0.000	0.000	0.000	0.000	0.000	0.000
85	C	86	LYS	1	0.996	1.002	29.486	0.089	0.089	0.000	0.000	0.000	0.000
86	C	87	PRO	0	0.061	0.021	30.095	-0.008	-0.008	0.000	0.000	0.000	0.000
87	C	88	ASP	-1	-0.929	-0.972	30.400	-0.108	-0.108	0.000	0.000	0.000	0.000
88	C	89	ASP	-1	-0.753	-0.827	26.039	-0.119	-0.119	0.000	0.000	0.000	0.000
89	C	90	THR	0	-0.019	0.002	25.330	-0.016	-0.016	0.000	0.000	0.000	0.000
90	C	91	ALA	0	-0.043	-0.025	23.007	0.004	0.004	0.000	0.000	0.000	0.000
91	C	92	MET	0	-0.029	0.020	18.582	-0.004	-0.004	0.000	0.000	0.000	0.000
92	C	93	TYR	0	0.015	-0.027	17.546	0.011	0.011	0.000	0.000	0.000	0.000
93	C	94	TYR	0	-0.012	-0.016	13.989	-0.013	-0.013	0.000	0.000	0.000	0.000
94	C	96	LYS	1	0.908	0.950	9.883	0.332	0.332	0.000	0.000	0.000	0.000
95	C	97	PRO	0	0.036	0.000	5.797	0.083	0.083	0.000	0.000	0.000	0.000
96	C	98	SER	0	-0.044	-0.012	8.127	-0.063	-0.063	0.000	0.000	0.000	0.000
97	C	99	LEU	0	-0.058	-0.032	5.887	0.030	0.030	0.000	0.000	0.000	0.000
98	C	100	ARG	1	0.753	0.853	8.202	-0.091	-0.091	0.000	0.000	0.000	0.000
99	C	101	TYR	0	0.039	0.007	10.159	-0.011	-0.011	0.000	0.000	0.000	0.000
100	C	102	GLY	0	-0.021	0.003	9.609	0.058	0.058	0.000	0.000	0.000	0.000
101	C	103	LEU	0	0.024	-0.003	8.219	0.001	0.001	0.000	0.000	0.000	0.000
102	C	104	PRO	0	0.014	-0.009	8.586	0.059	0.059	0.000	0.000	0.000	0.000
103	C	105	GLY	0	0.032	0.015	6.782	0.106	0.106	0.000	0.000	0.000	0.000
104	C	107	PRO	0	-0.007	0.004	2.380	-1.572	-0.918	2.153	-0.664	-2.143	0.000
105	C	108	ILE	0	0.048	0.029	5.108	-0.262	-0.139	-0.001	-0.003	-0.118	0.000
106	C	109	ILE	0	-0.008	-0.001	2.317	-0.483	-0.614	1.645	-0.316	-1.198	0.002
107	C	110	PRO	0	0.002	0.006	6.262	0.252	0.252	0.000	0.000	0.000	0.000
108	C	111	TRP	0	-0.019	-0.029	8.738	-0.087	-0.087	0.000	0.000	0.000	0.000
109	C	112	GLY	0	0.095	0.058	10.422	-0.082	-0.082	0.000	0.000	0.000	0.000
110	C	113	GLN	0	-0.034	-0.047	11.013	0.117	0.117	0.000	0.000	0.000	0.000
111	C	114	GLY	0	-0.031	0.009	13.056	0.073	0.073	0.000	0.000	0.000	0.000
112	C	115	THR	0	-0.026	-0.006	14.804	-0.001	-0.001	0.000	0.000	0.000	0.000
113	C	116	GLN	0	0.027	-0.015	17.375	0.032	0.032	0.000	0.000	0.000	0.000
114	C	117	VAL	0	0.003	0.016	20.796	0.004	0.004	0.000	0.000	0.000	0.000
115	C	118	THR	0	-0.042	-0.024	23.361	0.004	0.004	0.000	0.000	0.000	0.000
116	C	119	VAL	0	0.005	0.014	27.123	0.004	0.004	0.000	0.000	0.000	0.000
117	C	120	SER	0	-0.072	-0.018	29.698	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)