FMO DATABASE

FMODB ID: 52G3Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-897788.986093
FMO2-HF: Nuclear repulsion	852305.796284
FMO2-HF: Total energy	-45483.189809
FMO2-MP2: Total energy	-45611.975536

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.
-9.135	-2.29	14.637	-7.841	-13.639	-0.045

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 : -0.051 / q_NPA : -0.036

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	-0.021	-0.009	3.685	-0.631	1.051	-0.015	-0.670	-0.998	0.001
4	C	5	VAL	0	-0.020	-0.007	5.263	0.224	0.250	-0.001	-0.002	-0.023	0.000
5	C	6	GLU	-1	-0.787	-0.916	8.591	-0.524	-0.524	0.000	0.000	0.000	0.000
6	C	7	SER	0	-0.034	-0.035	11.629	0.037	0.037	0.000	0.000	0.000	0.000
7	C	8	GLY	0	0.035	-0.003	15.108	-0.013	-0.013	0.000	0.000	0.000	0.000
8	C	9	GLY	0	-0.003	0.027	18.528	0.005	0.005	0.000	0.000	0.000	0.000
9	C	10	GLY	0	0.019	0.008	20.397	0.014	0.014	0.000	0.000	0.000	0.000
10	C	11	THR	0	-0.013	-0.018	24.116	-0.007	-0.007	0.000	0.000	0.000	0.000
11	C	12	VAL	0	0.018	0.034	27.679	0.008	0.008	0.000	0.000	0.000	0.000
12	C	13	PRO	0	0.070	0.014	29.817	-0.005	-0.005	0.000	0.000	0.000	0.000
13	C	14	ALA	0	0.028	0.002	32.180	-0.002	-0.002	0.000	0.000	0.000	0.000
14	C	15	GLY	0	-0.033	-0.018	32.610	0.005	0.005	0.000	0.000	0.000	0.000
15	C	16	GLY	0	-0.023	-0.010	30.933	0.002	0.002	0.000	0.000	0.000	0.000
16	C	17	SER	0	-0.026	-0.068	26.608	-0.003	-0.003	0.000	0.000	0.000	0.000
17	C	18	LEU	0	-0.048	-0.015	22.561	0.004	0.004	0.000	0.000	0.000	0.000
18	C	19	ARG	1	0.942	0.987	18.760	0.053	0.053	0.000	0.000	0.000	0.000
19	C	20	LEU	0	-0.018	0.013	16.336	0.002	0.002	0.000	0.000	0.000	0.000
20	C	21	SER	0	-0.002	-0.014	13.259	0.022	0.022	0.000	0.000	0.000	0.000
21	C	22	CYS	0	-0.043	-0.002	9.275	-0.043	-0.043	0.000	0.000	0.000	0.000
22	C	23	ALA	0	0.009	0.007	7.290	0.079	0.079	0.000	0.000	0.000	0.000
23	C	24	ALA	0	0.014	0.019	3.165	-0.590	-0.175	0.082	-0.115	-0.382	0.000
24	C	25	SER	0	-0.007	-0.015	3.260	-1.104	0.000	0.185	-0.407	-0.881	-0.003
25	C	26	GLY	0	0.070	0.025	2.180	-1.659	-1.818	7.206	-4.067	-2.980	-0.031
26	C	27	ASN	0	0.017	-0.003	2.482	-0.344	0.008	2.151	-0.478	-2.024	-0.002
27	C	28	THR	0	-0.002	0.002	3.584	-0.523	-0.469	-0.002	0.122	-0.175	0.000
28	C	29	LEU	0	0.059	0.047	6.490	-0.142	-0.142	0.000	0.000	0.000	0.000
29	C	30	CYS	0	-0.068	0.007	3.753	-0.822	0.022	0.123	-0.206	-0.760	-0.001
30	C	31	THR	0	0.001	-0.005	5.758	0.099	0.099	0.000	0.000	0.000	0.000
31	C	32	TYR	0	-0.034	-0.043	2.735	-2.708	-0.731	0.714	-0.839	-1.853	-0.009
32	C	33	ASP	-1	-0.711	-0.824	7.523	-0.240	-0.240	0.000	0.000	0.000	0.000
33	C	34	MET	0	-0.053	-0.039	7.162	-0.122	-0.122	0.000	0.000	0.000	0.000
34	C	35	SER	0	-0.006	-0.007	11.565	0.059	0.059	0.000	0.000	0.000	0.000
35	C	36	TRP	0	0.019	0.013	13.799	-0.051	-0.051	0.000	0.000	0.000	0.000
36	C	37	TYR	0	-0.034	-0.014	15.446	0.029	0.029	0.000	0.000	0.000	0.000
37	C	38	ARG	1	0.873	0.940	17.904	0.133	0.133	0.000	0.000	0.000	0.000
38	C	39	ARG	1	0.896	0.952	18.643	0.246	0.246	0.000	0.000	0.000	0.000
39	C	40	ALA	0	0.068	0.041	22.433	0.002	0.002	0.000	0.000	0.000	0.000
40	C	41	PRO	0	0.004	0.006	25.862	-0.006	-0.006	0.000	0.000	0.000	0.000
41	C	42	GLY	0	0.018	-0.006	27.755	0.007	0.007	0.000	0.000	0.000	0.000
42	C	43	LYS	1	0.936	0.980	26.731	0.111	0.111	0.000	0.000	0.000	0.000
43	C	44	GLY	0	0.036	0.021	24.744	-0.007	-0.007	0.000	0.000	0.000	0.000
44	C	45	ARG	1	0.830	0.919	15.325	0.356	0.356	0.000	0.000	0.000	0.000
45	C	46	ASP	-1	-0.855	-0.926	21.070	-0.184	-0.184	0.000	0.000	0.000	0.000
46	C	47	PHE	0	0.015	0.001	17.584	-0.010	-0.010	0.000	0.000	0.000	0.000
47	C	48	VAL	0	-0.017	-0.009	19.629	0.019	0.019	0.000	0.000	0.000	0.000
48	C	49	SER	0	0.013	-0.017	19.153	0.024	0.024	0.000	0.000	0.000	0.000
49	C	50	GLY	0	-0.006	-0.009	16.390	-0.033	-0.033	0.000	0.000	0.000	0.000
50	C	51	ILE	0	-0.028	-0.004	14.506	0.030	0.030	0.000	0.000	0.000	0.000
51	C	52	ASP	-1	-0.820	-0.902	14.133	-0.219	-0.219	0.000	0.000	0.000	0.000
52	C	53	ASN	0	-0.014	-0.045	11.879	-0.007	-0.007	0.000	0.000	0.000	0.000
53	C	54	ASP	-1	-0.934	-0.943	14.325	-0.106	-0.106	0.000	0.000	0.000	0.000
54	C	55	GLY	0	-0.051	-0.021	17.178	0.018	0.018	0.000	0.000	0.000	0.000
55	C	56	THR	0	-0.027	-0.011	18.910	0.016	0.016	0.000	0.000	0.000	0.000
56	C	57	THR	0	-0.021	-0.013	19.022	-0.020	-0.020	0.000	0.000	0.000	0.000
57	C	58	THR	0	-0.018	-0.010	20.332	0.005	0.005	0.000	0.000	0.000	0.000
58	C	59	TYR	0	0.027	0.013	21.190	-0.016	-0.016	0.000	0.000	0.000	0.000
59	C	60	VAL	0	0.001	0.013	23.741	0.005	0.005	0.000	0.000	0.000	0.000
60	C	61	ASP	-1	-0.818	-0.929	25.633	-0.095	-0.095	0.000	0.000	0.000	0.000
61	C	62	SER	0	-0.074	-0.034	27.845	0.004	0.004	0.000	0.000	0.000	0.000
62	C	63	VAL	0	-0.023	-0.012	23.879	0.005	0.005	0.000	0.000	0.000	0.000
63	C	64	ALA	0	0.051	0.032	27.314	0.002	0.002	0.000	0.000	0.000	0.000
64	C	65	GLY	0	-0.016	-0.004	28.294	0.006	0.006	0.000	0.000	0.000	0.000
65	C	66	ARG	1	0.727	0.864	28.453	0.098	0.098	0.000	0.000	0.000	0.000
66	C	67	PHE	0	-0.001	-0.011	22.362	-0.001	-0.001	0.000	0.000	0.000	0.000
67	C	68	THR	0	0.020	0.016	22.551	0.004	0.004	0.000	0.000	0.000	0.000
68	C	69	ILE	0	-0.074	-0.022	15.718	-0.004	-0.004	0.000	0.000	0.000	0.000
69	C	70	SER	0	-0.024	-0.011	17.729	0.016	0.016	0.000	0.000	0.000	0.000
70	C	71	GLN	0	0.056	0.027	13.903	-0.041	-0.041	0.000	0.000	0.000	0.000
71	C	72	GLY	0	-0.042	-0.028	13.550	0.020	0.020	0.000	0.000	0.000	0.000
72	C	73	ASN	0	-0.006	-0.017	12.069	-0.014	-0.014	0.000	0.000	0.000	0.000
73	C	74	ALA	0	0.034	0.036	10.997	0.038	0.038	0.000	0.000	0.000	0.000
74	C	75	LYS	1	0.932	1.022	8.889	0.026	0.026	0.000	0.000	0.000	0.000
75	C	76	ASN	0	-0.017	-0.019	5.769	-0.024	-0.024	0.000	0.000	0.000	0.000
76	C	77	THR	0	-0.013	-0.064	7.204	-0.078	-0.078	0.000	0.000	0.000	0.000
77	C	78	ALA	0	0.027	0.021	9.984	0.019	0.019	0.000	0.000	0.000	0.000
78	C	79	TYR	0	-0.053	-0.028	13.032	0.001	0.001	0.000	0.000	0.000	0.000
79	C	80	LEU	0	0.024	0.007	16.121	-0.003	-0.003	0.000	0.000	0.000	0.000
80	C	81	GLN	0	-0.025	-0.020	18.710	0.005	0.005	0.000	0.000	0.000	0.000
81	C	82	MET	0	-0.031	-0.013	21.615	-0.006	-0.006	0.000	0.000	0.000	0.000
82	C	83	ASP	-1	-0.738	-0.838	24.352	-0.058	-0.058	0.000	0.000	0.000	0.000
83	C	84	SER	0	-0.020	-0.016	28.078	-0.002	-0.002	0.000	0.000	0.000	0.000
84	C	85	LEU	0	-0.029	-0.001	25.484	-0.004	-0.004	0.000	0.000	0.000	0.000
85	C	86	LYS	1	0.984	0.979	29.581	0.086	0.086	0.000	0.000	0.000	0.000
86	C	87	PRO	0	0.049	0.010	30.120	-0.006	-0.006	0.000	0.000	0.000	0.000
87	C	88	ASP	-1	-0.937	-0.972	30.372	-0.103	-0.103	0.000	0.000	0.000	0.000
88	C	89	ASP	-1	-0.730	-0.831	26.071	-0.111	-0.111	0.000	0.000	0.000	0.000
89	C	90	THR	0	-0.033	-0.002	25.320	-0.010	-0.010	0.000	0.000	0.000	0.000
90	C	91	ALA	0	-0.039	-0.021	22.907	-0.003	-0.003	0.000	0.000	0.000	0.000
91	C	92	MET	0	-0.019	0.018	18.411	0.009	0.009	0.000	0.000	0.000	0.000
92	C	93	TYR	0	-0.001	-0.038	17.558	-0.010	-0.010	0.000	0.000	0.000	0.000
93	C	94	TYR	0	-0.027	-0.021	13.851	0.001	0.001	0.000	0.000	0.000	0.000
94	C	96	LYS	1	0.907	0.947	9.853	0.500	0.500	0.000	0.000	0.000	0.000
95	C	97	PRO	0	0.051	0.006	5.867	0.072	0.072	0.000	0.000	0.000	0.000
96	C	98	SER	0	-0.072	-0.020	7.961	-0.065	-0.065	0.000	0.000	0.000	0.000
97	C	99	LEU	0	-0.033	-0.022	5.842	0.017	0.017	0.000	0.000	0.000	0.000
98	C	100	ARG	1	0.850	0.929	8.160	0.303	0.303	0.000	0.000	0.000	0.000
99	C	101	TYR	0	0.024	-0.001	10.096	0.058	0.058	0.000	0.000	0.000	0.000
100	C	102	GLY	0	-0.019	0.001	9.571	-0.060	-0.060	0.000	0.000	0.000	0.000
101	C	103	LEU	0	0.023	-0.005	8.188	0.072	0.072	0.000	0.000	0.000	0.000
102	C	104	PRO	0	0.004	-0.013	8.609	-0.078	-0.078	0.000	0.000	0.000	0.000
103	C	105	GLY	0	0.039	0.019	6.848	0.090	0.090	0.000	0.000	0.000	0.000
104	C	107	PRO	0	-0.011	0.005	2.151	-0.632	-0.599	3.338	-0.947	-2.423	-0.001
105	C	108	ILE	0	0.052	0.034	4.922	-0.308	-0.180	-0.001	-0.005	-0.122	0.000
106	C	109	ILE	0	-0.019	-0.011	2.456	-0.730	-0.341	0.857	-0.227	-1.018	0.001
107	C	110	PRO	0	-0.004	0.008	5.911	0.300	0.300	0.000	0.000	0.000	0.000
108	C	111	TRP	0	0.003	-0.015	8.424	-0.060	-0.060	0.000	0.000	0.000	0.000
109	C	112	GLY	0	0.089	0.052	10.207	-0.042	-0.042	0.000	0.000	0.000	0.000
110	C	113	GLN	0	-0.023	-0.045	10.768	0.087	0.087	0.000	0.000	0.000	0.000
111	C	114	GLY	0	-0.038	0.009	12.928	0.045	0.045	0.000	0.000	0.000	0.000
112	C	115	THR	0	-0.021	-0.001	14.696	0.029	0.029	0.000	0.000	0.000	0.000
113	C	116	GLN	0	0.029	-0.013	17.335	0.005	0.005	0.000	0.000	0.000	0.000
114	C	117	VAL	0	0.017	0.025	20.852	0.011	0.011	0.000	0.000	0.000	0.000
115	C	118	THR	0	-0.036	-0.020	23.361	0.000	0.000	0.000	0.000	0.000	0.000
116	C	119	VAL	0	0.000	0.014	27.113	0.007	0.007	0.000	0.000	0.000	0.000
117	C	120	SER	0	-0.079	-0.025	29.721	0.004	0.004	0.000	0.000	0.000	0.000

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