FMO DATABASE

FMODB ID: QYZ2Y

Calculation Name: 1PKO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1PKO

Chain ID: A

ChEMBL ID:

UniProt ID: Q63345

Base Structure: X-ray

Registration Date: 2023-09-19

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	125
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1076795.169768
FMO2-HF: Nuclear repulsion	1026784.839611
FMO2-HF: Total energy	-50010.330157
FMO2-MP2: Total energy	-50157.523707

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:1:GLY)

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

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.
-1.8	-2.589	7.266	-2.625	-3.852	-0.017

Interaction energy analysis for fragmet #1(A:1:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / q_NPA : -0.006

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	3	PHE	0	-0.012	-0.015	3.699	-0.361	0.716	0.004	-0.459	-0.622	0.001
4	A	4	ARG	1	0.993	1.008	4.695	0.439	0.541	-0.001	-0.015	-0.086	0.000
5	A	5	VAL	0	-0.002	0.002	6.607	0.158	0.158	0.000	0.000	0.000	0.000
6	A	6	ILE	0	-0.087	-0.043	10.270	0.027	0.027	0.000	0.000	0.000	0.000
7	A	7	GLY	0	0.077	0.046	13.053	0.028	0.028	0.000	0.000	0.000	0.000
8	A	8	PRO	0	-0.022	-0.016	16.713	-0.016	-0.016	0.000	0.000	0.000	0.000
9	A	9	GLY	0	-0.032	-0.012	18.742	0.003	0.003	0.000	0.000	0.000	0.000
10	A	10	HIS	0	-0.042	-0.018	19.483	0.007	0.007	0.000	0.000	0.000	0.000
11	A	11	PRO	0	-0.025	-0.024	23.165	-0.005	-0.005	0.000	0.000	0.000	0.000
12	A	12	ILE	0	-0.002	0.019	23.957	0.001	0.001	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.930	0.958	26.909	0.101	0.101	0.000	0.000	0.000	0.000
14	A	14	ALA	0	0.023	0.017	30.678	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	15	LEU	0	0.028	0.023	33.041	0.002	0.002	0.000	0.000	0.000	0.000
16	A	16	VAL	0	-0.062	-0.039	36.182	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	17	GLY	0	-0.054	-0.026	37.156	0.003	0.003	0.000	0.000	0.000	0.000
18	A	18	ASP	-1	-0.871	-0.924	34.950	-0.066	-0.066	0.000	0.000	0.000	0.000
19	A	19	GLU	-1	-0.935	-0.980	32.143	-0.069	-0.069	0.000	0.000	0.000	0.000
20	A	20	ALA	0	-0.018	-0.015	28.939	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.824	-0.908	26.143	-0.108	-0.108	0.000	0.000	0.000	0.000
22	A	22	LEU	0	-0.023	-0.008	22.335	-0.008	-0.008	0.000	0.000	0.000	0.000
23	A	23	PRO	0	-0.003	0.001	20.096	-0.004	-0.004	0.000	0.000	0.000	0.000
24	A	24	CYS	0	-0.036	-0.001	15.178	-0.015	-0.015	0.000	0.000	0.000	0.000
25	A	25	ARG	1	0.969	0.990	13.313	0.461	0.461	0.000	0.000	0.000	0.000
26	A	26	ILE	0	0.003	0.025	9.857	-0.067	-0.067	0.000	0.000	0.000	0.000
27	A	27	SER	0	-0.066	-0.026	9.159	0.191	0.191	0.000	0.000	0.000	0.000
28	A	28	PRO	0	0.041	-0.011	7.100	-0.316	-0.316	0.000	0.000	0.000	0.000
29	A	29	GLY	0	0.007	0.027	10.198	-0.025	-0.025	0.000	0.000	0.000	0.000
30	A	30	LYS	1	0.887	0.930	8.826	0.277	0.277	0.000	0.000	0.000	0.000
31	A	31	ASN	0	0.047	0.035	13.861	-0.008	-0.008	0.000	0.000	0.000	0.000
32	A	32	ALA	0	0.054	0.016	13.993	0.003	0.003	0.000	0.000	0.000	0.000
33	A	33	THR	0	-0.021	-0.028	15.175	0.021	0.021	0.000	0.000	0.000	0.000
34	A	34	GLY	0	0.004	0.012	16.961	0.014	0.014	0.000	0.000	0.000	0.000
35	A	35	MET	0	-0.093	-0.012	10.376	0.003	0.003	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.802	-0.872	14.084	0.008	0.008	0.000	0.000	0.000	0.000
37	A	37	VAL	0	-0.024	-0.025	14.166	-0.033	-0.033	0.000	0.000	0.000	0.000
38	A	38	GLY	0	0.032	0.012	15.897	0.031	0.031	0.000	0.000	0.000	0.000
39	A	39	TRP	0	0.013	0.008	17.086	-0.035	-0.035	0.000	0.000	0.000	0.000
40	A	40	TYR	0	-0.058	-0.059	14.961	0.036	0.036	0.000	0.000	0.000	0.000
41	A	41	ARG	1	0.832	0.919	20.919	0.078	0.078	0.000	0.000	0.000	0.000
42	A	42	SER	0	-0.057	0.037	19.733	0.008	0.008	0.000	0.000	0.000	0.000
43	A	43	PRO	0	0.071	0.009	21.905	0.001	0.001	0.000	0.000	0.000	0.000
44	A	44	PHE	0	-0.001	-0.009	20.918	0.008	0.008	0.000	0.000	0.000	0.000
45	A	45	SER	0	0.096	-0.010	19.952	0.006	0.006	0.000	0.000	0.000	0.000
46	A	46	ARG	1	0.656	0.825	22.276	0.044	0.044	0.000	0.000	0.000	0.000
47	A	47	VAL	0	0.057	0.039	21.462	-0.012	-0.012	0.000	0.000	0.000	0.000
48	A	48	VAL	0	-0.033	-0.002	22.820	0.008	0.008	0.000	0.000	0.000	0.000
49	A	49	HIS	0	0.011	0.000	22.495	0.007	0.007	0.000	0.000	0.000	0.000
50	A	50	LEU	0	-0.002	0.010	18.335	-0.013	-0.013	0.000	0.000	0.000	0.000
51	A	51	TYR	0	-0.046	-0.017	18.500	0.012	0.012	0.000	0.000	0.000	0.000
52	A	52	ARG	1	0.851	0.873	18.527	-0.007	-0.007	0.000	0.000	0.000	0.000
53	A	53	ASN	0	-0.035	-0.021	19.558	0.006	0.006	0.000	0.000	0.000	0.000
54	A	54	GLY	0	0.022	0.015	21.005	0.003	0.003	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.876	0.939	22.907	0.020	0.020	0.000	0.000	0.000	0.000
56	A	56	ASP	-1	-0.724	-0.841	23.541	-0.075	-0.075	0.000	0.000	0.000	0.000
57	A	57	GLN	0	-0.043	-0.033	22.890	0.010	0.010	0.000	0.000	0.000	0.000
58	A	58	ASP	-1	-0.823	-0.919	25.494	-0.036	-0.036	0.000	0.000	0.000	0.000
59	A	59	ALA	0	-0.052	-0.029	28.591	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.809	-0.873	22.776	-0.004	-0.004	0.000	0.000	0.000	0.000
61	A	61	GLN	0	-0.028	0.002	25.088	0.001	0.001	0.000	0.000	0.000	0.000
62	A	62	ALA	0	-0.026	-0.031	26.584	0.007	0.007	0.000	0.000	0.000	0.000
63	A	63	PRO	0	0.001	-0.026	28.749	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.790	-0.857	29.560	-0.045	-0.045	0.000	0.000	0.000	0.000
65	A	65	TYR	0	0.019	-0.041	28.078	-0.005	-0.005	0.000	0.000	0.000	0.000
66	A	66	ARG	1	0.850	0.941	29.886	0.027	0.027	0.000	0.000	0.000	0.000
67	A	67	GLY	0	-0.029	-0.007	32.013	0.001	0.001	0.000	0.000	0.000	0.000
68	A	68	ARG	1	0.729	0.847	31.547	0.062	0.062	0.000	0.000	0.000	0.000
69	A	69	THR	0	-0.014	-0.021	26.784	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.827	-0.885	27.583	-0.066	-0.066	0.000	0.000	0.000	0.000
71	A	71	LEU	0	-0.012	0.003	19.863	-0.009	-0.009	0.000	0.000	0.000	0.000
72	A	72	LEU	0	0.019	0.009	24.240	0.008	0.008	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.788	0.852	21.488	0.070	0.070	0.000	0.000	0.000	0.000
74	A	74	GLU	-1	-0.916	-0.934	23.165	-0.100	-0.100	0.000	0.000	0.000	0.000
75	A	75	SER	0	0.037	0.001	21.035	0.006	0.006	0.000	0.000	0.000	0.000
76	A	76	ILE	0	-0.001	0.007	17.907	-0.029	-0.029	0.000	0.000	0.000	0.000
77	A	77	GLY	0	0.001	0.003	17.782	-0.019	-0.019	0.000	0.000	0.000	0.000
78	A	78	GLU	-1	-0.858	-0.917	17.904	-0.197	-0.197	0.000	0.000	0.000	0.000
79	A	79	GLY	0	-0.033	-0.015	14.641	-0.047	-0.047	0.000	0.000	0.000	0.000
80	A	80	LYS	1	0.788	0.881	15.101	0.170	0.170	0.000	0.000	0.000	0.000
81	A	81	VAL	0	0.023	0.013	17.282	0.027	0.027	0.000	0.000	0.000	0.000
82	A	82	ALA	0	0.015	0.001	19.728	-0.018	-0.018	0.000	0.000	0.000	0.000
83	A	83	LEU	0	-0.022	0.012	22.195	0.014	0.014	0.000	0.000	0.000	0.000
84	A	84	ARG	1	0.829	0.900	23.649	0.081	0.081	0.000	0.000	0.000	0.000
85	A	85	ILE	0	-0.050	-0.023	26.003	0.006	0.006	0.000	0.000	0.000	0.000
86	A	86	GLN	0	0.026	0.003	29.345	0.003	0.003	0.000	0.000	0.000	0.000
87	A	87	ASN	0	-0.026	-0.023	33.049	0.002	0.002	0.000	0.000	0.000	0.000
88	A	88	VAL	0	0.009	0.020	31.389	0.001	0.001	0.000	0.000	0.000	0.000
89	A	89	ARG	1	0.939	0.965	33.746	0.056	0.056	0.000	0.000	0.000	0.000
90	A	90	PHE	0	0.105	0.034	33.794	-0.003	-0.003	0.000	0.000	0.000	0.000
91	A	91	SER	0	-0.019	0.000	32.935	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	92	ASP	-1	-0.781	-0.842	29.879	-0.070	-0.070	0.000	0.000	0.000	0.000
93	A	93	GLU	-1	-0.821	-0.885	28.765	-0.085	-0.085	0.000	0.000	0.000	0.000
94	A	94	GLY	0	0.011	0.017	27.336	0.004	0.004	0.000	0.000	0.000	0.000
95	A	95	GLY	0	-0.001	-0.011	23.239	-0.008	-0.008	0.000	0.000	0.000	0.000
96	A	96	TYR	0	-0.031	-0.036	21.271	0.015	0.015	0.000	0.000	0.000	0.000
97	A	97	THR	0	0.029	0.024	15.402	-0.009	-0.009	0.000	0.000	0.000	0.000
98	A	99	PHE	0	0.020	0.004	12.140	-0.051	-0.051	0.000	0.000	0.000	0.000
99	A	100	PHE	0	0.023	-0.011	10.464	0.036	0.036	0.000	0.000	0.000	0.000
100	A	101	ARG	1	0.828	0.888	9.675	-0.146	-0.146	0.000	0.000	0.000	0.000
101	A	102	ASP	-1	-0.813	-0.894	8.609	0.088	0.088	0.000	0.000	0.000	0.000
102	A	103	HIS	0	-0.019	-0.034	9.414	0.163	0.163	0.000	0.000	0.000	0.000
103	A	104	SER	0	-0.001	0.000	9.793	-0.046	-0.046	0.000	0.000	0.000	0.000
104	A	105	TYR	0	-0.036	-0.014	1.897	-0.880	-2.848	7.263	-2.151	-3.144	-0.018
105	A	106	GLN	0	0.053	0.010	6.614	-0.107	-0.107	0.000	0.000	0.000	0.000
106	A	107	GLU	-1	-0.900	-0.938	5.238	-1.257	-1.257	0.000	0.000	0.000	0.000
107	A	108	GLU	-1	-0.869	-0.941	7.776	-0.088	-0.088	0.000	0.000	0.000	0.000
108	A	109	ALA	0	-0.032	-0.004	11.179	-0.058	-0.058	0.000	0.000	0.000	0.000
109	A	110	ALA	0	0.014	0.012	13.868	0.043	0.043	0.000	0.000	0.000	0.000
110	A	111	VAL	0	-0.029	-0.028	17.402	-0.013	-0.013	0.000	0.000	0.000	0.000
111	A	112	GLU	-1	-0.851	-0.921	20.318	-0.103	-0.103	0.000	0.000	0.000	0.000
112	A	113	LEU	0	-0.024	0.002	23.903	-0.004	-0.004	0.000	0.000	0.000	0.000
113	A	114	LYS	1	0.815	0.891	27.191	0.107	0.107	0.000	0.000	0.000	0.000
114	A	115	VAL	0	-0.005	-0.023	30.449	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	116	GLU	-1	-0.935	-0.951	33.713	-0.060	-0.060	0.000	0.000	0.000	0.000
116	A	117	ASP	-1	-0.839	-0.930	37.216	-0.047	-0.047	0.000	0.000	0.000	0.000
117	A	118	PRO	0	0.027	0.012	39.908	0.002	0.002	0.000	0.000	0.000	0.000
118	A	119	PHE	0	-0.045	-0.036	42.687	0.003	0.003	0.000	0.000	0.000	0.000
119	A	120	TYR	0	0.021	0.007	43.584	0.003	0.003	0.000	0.000	0.000	0.000
120	A	121	TRP	0	-0.027	-0.004	45.230	0.003	0.003	0.000	0.000	0.000	0.000
121	A	122	ILE	0	-0.025	-0.003	46.919	0.003	0.003	0.000	0.000	0.000	0.000
122	A	123	ASN	0	-0.060	-0.032	49.211	0.001	0.001	0.000	0.000	0.000	0.000
123	A	124	PRO	0	0.084	0.047	50.797	0.000	0.000	0.000	0.000	0.000	0.000
124	A	125	GLY	0	-0.022	-0.030	52.167	0.001	0.001	0.000	0.000	0.000	0.000
125	A	126	ARG	1	0.912	0.981	50.734	0.026	0.026	0.000	0.000	0.000	0.000

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