FMO DATABASE

FMODB ID: R9678

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1075702.57826
FMO2-HF: Nuclear repulsion	1025692.877536
FMO2-HF: Total energy	-50009.700724
FMO2-MP2: Total energy	-50156.896706

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.
-3.023	-1.371	3.663	-2.006	-3.308	-0.013

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 : 0.014 / q_NPA : 0.001

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	-0.013	-0.010	3.755	-0.568	0.510	0.004	-0.463	-0.619	0.002
4	A	4	ARG	1	0.988	1.014	4.689	0.370	0.466	-0.001	-0.014	-0.080	0.000
5	A	5	VAL	0	0.023	0.007	6.602	0.158	0.158	0.000	0.000	0.000	0.000
6	A	6	ILE	0	-0.089	-0.042	10.266	0.012	0.012	0.000	0.000	0.000	0.000
7	A	7	GLY	0	0.081	0.045	13.049	0.029	0.029	0.000	0.000	0.000	0.000
8	A	8	PRO	0	-0.027	-0.022	16.710	-0.016	-0.016	0.000	0.000	0.000	0.000
9	A	9	GLY	0	-0.028	-0.007	18.741	0.002	0.002	0.000	0.000	0.000	0.000
10	A	10	HIS	0	-0.030	-0.010	19.481	0.007	0.007	0.000	0.000	0.000	0.000
11	A	11	PRO	0	-0.040	-0.036	23.162	-0.003	-0.003	0.000	0.000	0.000	0.000
12	A	12	ILE	0	0.008	0.026	24.101	0.001	0.001	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.932	0.955	26.905	0.097	0.097	0.000	0.000	0.000	0.000
14	A	14	ALA	0	0.024	0.020	30.675	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	15	LEU	0	0.027	0.023	33.037	0.001	0.001	0.000	0.000	0.000	0.000
16	A	16	VAL	0	-0.055	-0.035	36.182	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	17	GLY	0	-0.060	-0.031	37.156	0.002	0.002	0.000	0.000	0.000	0.000
18	A	18	ASP	-1	-0.872	-0.921	34.790	-0.061	-0.061	0.000	0.000	0.000	0.000
19	A	19	GLU	-1	-0.952	-0.987	32.088	-0.062	-0.062	0.000	0.000	0.000	0.000
20	A	20	ALA	0	-0.017	-0.015	28.892	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.835	-0.913	26.137	-0.095	-0.095	0.000	0.000	0.000	0.000
22	A	22	LEU	0	-0.026	-0.009	22.245	-0.009	-0.009	0.000	0.000	0.000	0.000
23	A	23	PRO	0	-0.008	-0.002	20.092	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	24	CYS	0	-0.041	-0.009	15.138	-0.015	-0.015	0.000	0.000	0.000	0.000
25	A	25	ARG	1	0.971	0.996	13.678	0.414	0.414	0.000	0.000	0.000	0.000
26	A	26	ILE	0	-0.001	0.023	9.861	-0.067	-0.067	0.000	0.000	0.000	0.000
27	A	27	SER	0	-0.066	-0.026	9.154	0.175	0.175	0.000	0.000	0.000	0.000
28	A	28	PRO	0	0.032	-0.016	7.151	-0.297	-0.297	0.000	0.000	0.000	0.000
29	A	29	GLY	0	0.013	0.029	10.196	-0.019	-0.019	0.000	0.000	0.000	0.000
30	A	30	LYS	1	0.972	0.973	8.775	0.247	0.247	0.000	0.000	0.000	0.000
31	A	31	ASN	0	0.066	0.046	13.861	-0.014	-0.014	0.000	0.000	0.000	0.000
32	A	32	ALA	0	0.045	0.016	14.117	0.009	0.009	0.000	0.000	0.000	0.000
33	A	33	THR	0	-0.026	-0.032	15.247	0.019	0.019	0.000	0.000	0.000	0.000
34	A	34	GLY	0	0.005	0.007	17.034	0.010	0.010	0.000	0.000	0.000	0.000
35	A	35	MET	0	-0.073	-0.005	10.605	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.802	-0.883	14.149	0.015	0.015	0.000	0.000	0.000	0.000
37	A	37	VAL	0	-0.026	-0.022	14.211	-0.028	-0.028	0.000	0.000	0.000	0.000
38	A	38	GLY	0	0.033	0.006	15.922	0.027	0.027	0.000	0.000	0.000	0.000
39	A	39	TRP	0	0.016	0.017	17.101	-0.034	-0.034	0.000	0.000	0.000	0.000
40	A	40	TYR	0	-0.008	-0.011	14.798	0.029	0.029	0.000	0.000	0.000	0.000
41	A	41	ARG	1	0.821	0.912	20.914	0.073	0.073	0.000	0.000	0.000	0.000
42	A	42	SER	0	-0.035	0.044	19.470	0.007	0.007	0.000	0.000	0.000	0.000
43	A	43	PRO	0	0.055	0.011	21.963	0.001	0.001	0.000	0.000	0.000	0.000
44	A	44	PHE	0	-0.014	-0.022	21.170	0.008	0.008	0.000	0.000	0.000	0.000
45	A	45	SER	0	0.015	-0.033	20.205	0.007	0.007	0.000	0.000	0.000	0.000
46	A	46	ARG	1	0.765	0.888	22.256	0.040	0.040	0.000	0.000	0.000	0.000
47	A	47	VAL	0	0.064	0.044	21.493	-0.012	-0.012	0.000	0.000	0.000	0.000
48	A	48	VAL	0	-0.033	-0.004	22.823	0.007	0.007	0.000	0.000	0.000	0.000
49	A	49	HIS	0	0.016	0.010	22.418	0.005	0.005	0.000	0.000	0.000	0.000
50	A	50	LEU	0	0.003	0.012	18.341	-0.011	-0.011	0.000	0.000	0.000	0.000
51	A	51	TYR	0	-0.053	-0.015	18.543	0.011	0.011	0.000	0.000	0.000	0.000
52	A	52	ARG	1	0.858	0.901	18.262	-0.021	-0.021	0.000	0.000	0.000	0.000
53	A	53	ASN	0	-0.013	-0.006	19.618	0.008	0.008	0.000	0.000	0.000	0.000
54	A	54	GLY	0	0.017	0.012	21.070	0.001	0.001	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.878	0.953	22.974	0.004	0.004	0.000	0.000	0.000	0.000
56	A	56	ASP	-1	-0.742	-0.865	23.594	-0.057	-0.057	0.000	0.000	0.000	0.000
57	A	57	GLN	0	-0.053	-0.039	22.837	0.010	0.010	0.000	0.000	0.000	0.000
58	A	58	ASP	-1	-0.816	-0.911	25.535	-0.030	-0.030	0.000	0.000	0.000	0.000
59	A	59	ALA	0	-0.064	-0.039	28.626	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.858	-0.934	22.949	0.007	0.007	0.000	0.000	0.000	0.000
61	A	61	GLN	0	-0.032	-0.005	25.104	0.001	0.001	0.000	0.000	0.000	0.000
62	A	62	ALA	0	-0.062	-0.045	26.600	0.006	0.006	0.000	0.000	0.000	0.000
63	A	63	PRO	0	-0.017	-0.034	28.755	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.783	-0.875	29.787	-0.040	-0.040	0.000	0.000	0.000	0.000
65	A	65	TYR	0	0.026	-0.022	28.028	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	66	ARG	1	0.894	0.962	30.482	0.021	0.021	0.000	0.000	0.000	0.000
67	A	67	GLY	0	-0.028	-0.006	32.030	0.001	0.001	0.000	0.000	0.000	0.000
68	A	68	ARG	1	0.727	0.855	31.616	0.055	0.055	0.000	0.000	0.000	0.000
69	A	69	THR	0	-0.029	-0.030	26.818	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.844	-0.907	27.615	-0.055	-0.055	0.000	0.000	0.000	0.000
71	A	71	LEU	0	-0.002	0.006	19.926	-0.009	-0.009	0.000	0.000	0.000	0.000
72	A	72	LEU	0	0.010	-0.001	24.279	0.008	0.008	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.826	0.879	21.785	0.054	0.054	0.000	0.000	0.000	0.000
74	A	74	GLU	-1	-0.914	-0.929	23.227	-0.085	-0.085	0.000	0.000	0.000	0.000
75	A	75	SER	0	0.056	0.020	21.117	0.003	0.003	0.000	0.000	0.000	0.000
76	A	76	ILE	0	0.001	0.004	17.954	-0.026	-0.026	0.000	0.000	0.000	0.000
77	A	77	GLY	0	0.005	0.004	17.851	-0.014	-0.014	0.000	0.000	0.000	0.000
78	A	78	GLU	-1	-0.990	-1.000	17.868	-0.163	-0.163	0.000	0.000	0.000	0.000
79	A	79	GLY	0	-0.049	-0.022	14.642	-0.045	-0.045	0.000	0.000	0.000	0.000
80	A	80	LYS	1	0.905	0.947	15.096	0.170	0.170	0.000	0.000	0.000	0.000
81	A	81	VAL	0	0.039	0.022	17.483	0.025	0.025	0.000	0.000	0.000	0.000
82	A	82	ALA	0	0.012	-0.004	19.769	-0.018	-0.018	0.000	0.000	0.000	0.000
83	A	83	LEU	0	-0.021	0.013	22.235	0.013	0.013	0.000	0.000	0.000	0.000
84	A	84	ARG	1	0.830	0.911	23.672	0.070	0.070	0.000	0.000	0.000	0.000
85	A	85	ILE	0	-0.044	-0.019	26.108	0.006	0.006	0.000	0.000	0.000	0.000
86	A	86	GLN	0	0.070	0.025	29.359	0.002	0.002	0.000	0.000	0.000	0.000
87	A	87	ASN	0	-0.021	-0.016	33.065	0.001	0.001	0.000	0.000	0.000	0.000
88	A	88	VAL	0	0.012	0.023	31.441	0.001	0.001	0.000	0.000	0.000	0.000
89	A	89	ARG	1	0.950	0.968	33.740	0.050	0.050	0.000	0.000	0.000	0.000
90	A	90	PHE	0	0.100	0.028	33.784	-0.003	-0.003	0.000	0.000	0.000	0.000
91	A	91	SER	0	-0.016	-0.001	33.085	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	92	ASP	-1	-0.798	-0.867	29.828	-0.064	-0.064	0.000	0.000	0.000	0.000
93	A	93	GLU	-1	-0.843	-0.903	28.751	-0.079	-0.079	0.000	0.000	0.000	0.000
94	A	94	GLY	0	0.010	0.014	27.309	0.003	0.003	0.000	0.000	0.000	0.000
95	A	95	GLY	0	0.004	-0.008	23.209	-0.008	-0.008	0.000	0.000	0.000	0.000
96	A	96	TYR	0	-0.030	-0.030	21.224	0.015	0.015	0.000	0.000	0.000	0.000
97	A	97	THR	0	0.058	0.037	15.309	-0.009	-0.009	0.000	0.000	0.000	0.000
98	A	99	PHE	0	0.013	0.006	12.125	-0.052	-0.052	0.000	0.000	0.000	0.000
99	A	100	PHE	0	0.018	-0.017	10.409	0.036	0.036	0.000	0.000	0.000	0.000
100	A	101	ARG	1	0.828	0.887	9.709	-0.167	-0.167	0.000	0.000	0.000	0.000
101	A	102	ASP	-1	-0.869	-0.923	8.703	0.210	0.210	0.000	0.000	0.000	0.000
102	A	103	HIS	0	-0.045	-0.044	9.479	0.167	0.167	0.000	0.000	0.000	0.000
103	A	104	SER	0	-0.014	-0.007	9.689	-0.037	-0.037	0.000	0.000	0.000	0.000
104	A	105	TYR	0	-0.027	-0.018	2.088	-1.912	-1.434	3.660	-1.529	-2.609	-0.015
105	A	106	GLN	0	0.048	0.006	6.615	-0.103	-0.103	0.000	0.000	0.000	0.000
106	A	107	GLU	-1	-0.916	-0.943	5.019	-1.232	-1.232	0.000	0.000	0.000	0.000
107	A	108	GLU	-1	-0.946	-0.996	7.773	-0.094	-0.094	0.000	0.000	0.000	0.000
108	A	109	ALA	0	-0.029	-0.011	11.156	-0.060	-0.060	0.000	0.000	0.000	0.000
109	A	110	ALA	0	0.008	0.012	13.849	0.043	0.043	0.000	0.000	0.000	0.000
110	A	111	VAL	0	-0.031	-0.029	17.375	-0.012	-0.012	0.000	0.000	0.000	0.000
111	A	112	GLU	-1	-0.904	-0.960	20.314	-0.104	-0.104	0.000	0.000	0.000	0.000
112	A	113	LEU	0	-0.028	-0.001	23.899	-0.004	-0.004	0.000	0.000	0.000	0.000
113	A	114	LYS	1	0.877	0.936	27.187	0.098	0.098	0.000	0.000	0.000	0.000
114	A	115	VAL	0	0.007	-0.012	30.446	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	116	GLU	-1	-0.921	-0.946	33.709	-0.056	-0.056	0.000	0.000	0.000	0.000
116	A	117	ASP	-1	-0.851	-0.937	37.212	-0.043	-0.043	0.000	0.000	0.000	0.000
117	A	118	PRO	0	0.020	0.009	39.931	0.002	0.002	0.000	0.000	0.000	0.000
118	A	119	PHE	0	-0.047	-0.036	42.682	0.003	0.003	0.000	0.000	0.000	0.000
119	A	120	TYR	0	0.019	0.009	43.581	0.003	0.003	0.000	0.000	0.000	0.000
120	A	121	TRP	0	-0.015	0.001	45.213	0.002	0.002	0.000	0.000	0.000	0.000
121	A	122	ILE	0	-0.020	-0.004	46.840	0.002	0.002	0.000	0.000	0.000	0.000
122	A	123	ASN	0	-0.077	-0.048	48.792	0.001	0.001	0.000	0.000	0.000	0.000
123	A	124	PRO	0	0.071	0.039	50.780	0.000	0.000	0.000	0.000	0.000	0.000
124	A	125	GLY	0	-0.013	-0.022	52.147	0.001	0.001	0.000	0.000	0.000	0.000
125	A	126	ARG	1	0.922	0.993	50.577	0.024	0.024	0.000	0.000	0.000	0.000

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