FMO DATABASE

FMODB ID: K9J43

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1076247.097132
FMO2-HF: Nuclear repulsion	1026236.241721
FMO2-HF: Total energy	-50010.855411
FMO2-MP2: Total energy	-50157.969682

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.
-2.66	-3.776	8.215	-3	-4.097	-0.018

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 : 0.019 / q_NPA : -0.008

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	3	PHE	0	-0.016	-0.010	3.583	-0.186	0.905	-0.002	-0.463	-0.625	0.001
4	A	4	ARG	1	0.867	0.934	4.304	0.104	0.209	-0.001	-0.039	-0.064	0.000
5	A	5	VAL	0	-0.006	0.004	6.878	0.238	0.238	0.000	0.000	0.000	0.000
6	A	6	ILE	0	-0.079	-0.046	10.255	0.020	0.020	0.000	0.000	0.000	0.000
7	A	7	GLY	0	0.081	0.048	13.695	0.031	0.031	0.000	0.000	0.000	0.000
8	A	8	PRO	0	-0.009	-0.010	17.265	-0.018	-0.018	0.000	0.000	0.000	0.000
9	A	9	GLY	0	-0.027	-0.003	19.387	0.005	0.005	0.000	0.000	0.000	0.000
10	A	10	HIS	0	-0.061	-0.035	20.155	0.008	0.008	0.000	0.000	0.000	0.000
11	A	11	PRO	0	-0.017	-0.015	23.605	-0.005	-0.005	0.000	0.000	0.000	0.000
12	A	12	ILE	0	0.000	0.019	24.267	0.002	0.002	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.929	0.951	27.079	0.108	0.108	0.000	0.000	0.000	0.000
14	A	14	ALA	0	0.015	0.016	30.857	-0.003	-0.003	0.000	0.000	0.000	0.000
15	A	15	LEU	0	0.004	0.004	33.217	0.001	0.001	0.000	0.000	0.000	0.000
16	A	16	VAL	0	-0.061	-0.041	36.107	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	17	GLY	0	-0.041	-0.020	37.370	0.003	0.003	0.000	0.000	0.000	0.000
18	A	18	ASP	-1	-0.845	-0.905	34.732	-0.069	-0.069	0.000	0.000	0.000	0.000
19	A	19	GLU	-1	-0.940	-0.981	32.262	-0.065	-0.065	0.000	0.000	0.000	0.000
20	A	20	ALA	0	-0.011	0.002	28.687	-0.004	-0.004	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.802	-0.904	26.205	-0.107	-0.107	0.000	0.000	0.000	0.000
22	A	22	LEU	0	-0.023	-0.008	22.330	-0.010	-0.010	0.000	0.000	0.000	0.000
23	A	23	PRO	0	0.009	0.006	20.767	-0.005	-0.005	0.000	0.000	0.000	0.000
24	A	24	CYS	0	-0.050	-0.011	15.296	-0.012	-0.012	0.000	0.000	0.000	0.000
25	A	25	ARG	1	0.924	0.966	13.133	0.543	0.543	0.000	0.000	0.000	0.000
26	A	26	ILE	0	0.018	0.033	9.536	-0.067	-0.067	0.000	0.000	0.000	0.000
27	A	27	SER	0	-0.007	-0.011	9.504	0.223	0.223	0.000	0.000	0.000	0.000
28	A	28	PRO	0	0.018	-0.005	7.412	-0.338	-0.338	0.000	0.000	0.000	0.000
29	A	29	GLY	0	0.019	0.036	10.262	-0.034	-0.034	0.000	0.000	0.000	0.000
30	A	30	LYS	1	0.857	0.910	8.708	0.128	0.128	0.000	0.000	0.000	0.000
31	A	31	ASN	0	0.052	0.035	13.684	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	32	ALA	0	0.054	0.018	13.684	0.015	0.015	0.000	0.000	0.000	0.000
33	A	33	THR	0	-0.021	-0.024	14.965	0.022	0.022	0.000	0.000	0.000	0.000
34	A	34	GLY	0	0.009	0.016	16.979	0.011	0.011	0.000	0.000	0.000	0.000
35	A	35	MET	0	-0.093	-0.018	10.316	0.013	0.013	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.795	-0.868	14.104	0.052	0.052	0.000	0.000	0.000	0.000
37	A	37	VAL	0	-0.019	-0.020	13.957	-0.026	-0.026	0.000	0.000	0.000	0.000
38	A	38	GLY	0	0.022	0.006	15.853	0.028	0.028	0.000	0.000	0.000	0.000
39	A	39	TRP	0	0.022	0.011	16.955	-0.038	-0.038	0.000	0.000	0.000	0.000
40	A	40	TYR	0	-0.066	-0.043	14.896	0.036	0.036	0.000	0.000	0.000	0.000
41	A	41	ARG	1	0.810	0.897	20.905	0.074	0.074	0.000	0.000	0.000	0.000
42	A	42	SER	0	-0.021	0.000	19.792	0.002	0.002	0.000	0.000	0.000	0.000
43	A	43	PRO	0	0.005	-0.002	21.606	0.003	0.003	0.000	0.000	0.000	0.000
44	A	44	PHE	0	-0.009	0.000	20.965	0.009	0.009	0.000	0.000	0.000	0.000
45	A	45	SER	0	0.013	-0.016	20.158	0.004	0.004	0.000	0.000	0.000	0.000
46	A	46	ARG	1	0.796	0.861	22.797	0.039	0.039	0.000	0.000	0.000	0.000
47	A	47	VAL	0	0.063	0.038	21.211	-0.013	-0.013	0.000	0.000	0.000	0.000
48	A	48	VAL	0	-0.024	-0.001	22.853	0.007	0.007	0.000	0.000	0.000	0.000
49	A	49	HIS	0	0.008	0.001	22.437	0.007	0.007	0.000	0.000	0.000	0.000
50	A	50	LEU	0	-0.007	0.003	18.291	-0.011	-0.011	0.000	0.000	0.000	0.000
51	A	51	TYR	0	-0.041	-0.022	18.482	0.006	0.006	0.000	0.000	0.000	0.000
52	A	52	ARG	1	0.836	0.874	18.532	-0.039	-0.039	0.000	0.000	0.000	0.000
53	A	53	ASN	0	-0.041	-0.022	19.598	0.003	0.003	0.000	0.000	0.000	0.000
54	A	54	GLY	0	0.046	0.037	21.349	0.002	0.002	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.820	0.904	23.208	0.000	0.000	0.000	0.000	0.000	0.000
56	A	56	ASP	-1	-0.707	-0.843	23.380	-0.060	-0.060	0.000	0.000	0.000	0.000
57	A	57	GLN	0	-0.051	-0.036	22.731	0.008	0.008	0.000	0.000	0.000	0.000
58	A	58	ASP	-1	-0.807	-0.907	25.303	-0.018	-0.018	0.000	0.000	0.000	0.000
59	A	59	ALA	0	-0.020	-0.011	27.993	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.802	-0.868	22.605	0.023	0.023	0.000	0.000	0.000	0.000
61	A	61	GLN	0	-0.015	0.003	25.487	0.002	0.002	0.000	0.000	0.000	0.000
62	A	62	ALA	0	0.001	-0.007	26.579	0.007	0.007	0.000	0.000	0.000	0.000
63	A	63	PRO	0	0.010	-0.021	28.699	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.755	-0.834	29.561	-0.038	-0.038	0.000	0.000	0.000	0.000
65	A	65	TYR	0	0.003	-0.027	28.088	-0.005	-0.005	0.000	0.000	0.000	0.000
66	A	66	ARG	1	0.786	0.898	29.439	0.015	0.015	0.000	0.000	0.000	0.000
67	A	67	GLY	0	-0.023	-0.001	31.750	0.001	0.001	0.000	0.000	0.000	0.000
68	A	68	ARG	1	0.745	0.861	31.508	0.058	0.058	0.000	0.000	0.000	0.000
69	A	69	THR	0	-0.009	-0.024	26.759	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.831	-0.891	27.384	-0.060	-0.060	0.000	0.000	0.000	0.000
71	A	71	LEU	0	-0.034	-0.001	19.393	-0.010	-0.010	0.000	0.000	0.000	0.000
72	A	72	LEU	0	0.023	0.020	23.896	0.009	0.009	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.792	0.855	21.036	0.058	0.058	0.000	0.000	0.000	0.000
74	A	74	GLU	-1	-0.919	-0.938	22.719	-0.099	-0.099	0.000	0.000	0.000	0.000
75	A	75	SER	0	0.031	-0.001	20.575	0.005	0.005	0.000	0.000	0.000	0.000
76	A	76	ILE	0	-0.007	0.004	17.582	-0.031	-0.031	0.000	0.000	0.000	0.000
77	A	77	GLY	0	0.010	0.000	17.482	-0.012	-0.012	0.000	0.000	0.000	0.000
78	A	78	GLU	-1	-0.841	-0.903	17.873	-0.210	-0.210	0.000	0.000	0.000	0.000
79	A	79	GLY	0	-0.015	0.003	14.352	-0.057	-0.057	0.000	0.000	0.000	0.000
80	A	80	LYS	1	0.777	0.861	14.796	0.175	0.175	0.000	0.000	0.000	0.000
81	A	81	VAL	0	0.006	-0.001	17.194	0.030	0.030	0.000	0.000	0.000	0.000
82	A	82	ALA	0	0.016	0.006	19.655	-0.021	-0.021	0.000	0.000	0.000	0.000
83	A	83	LEU	0	-0.036	0.003	22.044	0.016	0.016	0.000	0.000	0.000	0.000
84	A	84	ARG	1	0.834	0.907	23.582	0.078	0.078	0.000	0.000	0.000	0.000
85	A	85	ILE	0	-0.043	-0.030	25.697	0.006	0.006	0.000	0.000	0.000	0.000
86	A	86	GLN	0	0.033	0.003	29.257	0.003	0.003	0.000	0.000	0.000	0.000
87	A	87	ASN	0	-0.032	-0.023	32.946	0.003	0.003	0.000	0.000	0.000	0.000
88	A	88	VAL	0	-0.006	0.014	31.603	0.002	0.002	0.000	0.000	0.000	0.000
89	A	89	ARG	1	0.909	0.945	33.487	0.053	0.053	0.000	0.000	0.000	0.000
90	A	90	PHE	0	0.081	0.028	33.787	-0.003	-0.003	0.000	0.000	0.000	0.000
91	A	91	SER	0	-0.024	-0.002	32.645	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	92	ASP	-1	-0.778	-0.847	29.705	-0.067	-0.067	0.000	0.000	0.000	0.000
93	A	93	GLU	-1	-0.795	-0.873	28.875	-0.088	-0.088	0.000	0.000	0.000	0.000
94	A	94	GLY	0	0.016	0.029	27.526	0.004	0.004	0.000	0.000	0.000	0.000
95	A	95	GLY	0	-0.004	-0.019	23.382	-0.008	-0.008	0.000	0.000	0.000	0.000
96	A	96	TYR	0	-0.040	-0.039	21.265	0.019	0.019	0.000	0.000	0.000	0.000
97	A	97	THR	0	0.012	0.010	15.314	-0.017	-0.017	0.000	0.000	0.000	0.000
98	A	99	PHE	0	0.014	-0.007	12.214	-0.054	-0.054	0.000	0.000	0.000	0.000
99	A	100	PHE	0	0.022	-0.006	10.275	0.033	0.033	0.000	0.000	0.000	0.000
100	A	101	ARG	1	0.835	0.889	9.631	-0.215	-0.215	0.000	0.000	0.000	0.000
101	A	102	ASP	-1	-0.816	-0.890	8.188	0.259	0.259	0.000	0.000	0.000	0.000
102	A	103	HIS	0	-0.005	-0.026	9.371	0.212	0.212	0.000	0.000	0.000	0.000
103	A	104	SER	0	-0.012	-0.003	10.319	-0.055	-0.055	0.000	0.000	0.000	0.000
104	A	105	TYR	0	-0.034	-0.012	2.054	-1.564	-3.876	8.218	-2.498	-3.408	-0.019
105	A	106	GLN	0	0.021	-0.007	6.607	-0.177	-0.177	0.000	0.000	0.000	0.000
106	A	107	GLU	-1	-0.816	-0.881	5.259	-1.360	-1.360	0.000	0.000	0.000	0.000
107	A	108	GLU	-1	-0.849	-0.940	7.622	-0.071	-0.071	0.000	0.000	0.000	0.000
108	A	109	ALA	0	-0.026	-0.010	11.125	-0.084	-0.084	0.000	0.000	0.000	0.000
109	A	110	ALA	0	0.012	0.018	13.910	0.049	0.049	0.000	0.000	0.000	0.000
110	A	111	VAL	0	-0.027	-0.022	17.385	-0.021	-0.021	0.000	0.000	0.000	0.000
111	A	112	GLU	-1	-0.861	-0.929	20.316	-0.108	-0.108	0.000	0.000	0.000	0.000
112	A	113	LEU	0	-0.009	0.012	24.071	-0.007	-0.007	0.000	0.000	0.000	0.000
113	A	114	LYS	1	0.838	0.899	27.274	0.114	0.114	0.000	0.000	0.000	0.000
114	A	115	VAL	0	-0.007	-0.013	30.672	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	116	GLU	-1	-0.937	-0.954	33.992	-0.064	-0.064	0.000	0.000	0.000	0.000
116	A	117	ASP	-1	-0.822	-0.923	37.578	-0.047	-0.047	0.000	0.000	0.000	0.000
117	A	118	PRO	0	0.024	0.012	40.333	0.002	0.002	0.000	0.000	0.000	0.000
118	A	119	PHE	0	-0.012	-0.014	43.229	0.003	0.003	0.000	0.000	0.000	0.000
119	A	120	TYR	0	-0.005	0.000	43.785	0.003	0.003	0.000	0.000	0.000	0.000
120	A	121	TRP	0	-0.036	-0.010	45.404	0.003	0.003	0.000	0.000	0.000	0.000
121	A	122	ILE	0	-0.018	-0.010	46.868	0.003	0.003	0.000	0.000	0.000	0.000
122	A	123	ASN	0	-0.055	-0.031	49.468	0.002	0.002	0.000	0.000	0.000	0.000
123	A	124	PRO	0	0.084	0.043	51.376	0.000	0.000	0.000	0.000	0.000	0.000
124	A	125	GLY	0	-0.019	-0.016	52.563	0.001	0.001	0.000	0.000	0.000	0.000
125	A	126	ARG	1	0.883	0.963	50.376	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)