FMO DATABASE

FMODB ID: Q19KY

Calculation Name: 1PKP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1PKP

Chain ID: A

ChEMBL ID:

UniProt ID: P02357

Base Structure: X-ray

Registration Date: 2023-06-21

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	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	145
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1204780.222193
FMO2-HF: Nuclear repulsion	1152622.277924
FMO2-HF: Total energy	-52157.944269
FMO2-MP2: Total energy	-52314.130255

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:4:ILE)

Summations of interaction energy for fragment #1(A:4:ILE)

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.
-8.428	-3.2	7.734	-2.725	-10.236	-0.022

Interaction energy analysis for fragmet #1(A:4:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / q_NPA : 0.004

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	6	PRO	0	0.073	0.044	3.714	-1.869	0.033	0.006	-0.754	-1.154	0.003
4	A	7	ASN	0	-0.003	-0.011	4.803	0.052	0.169	-0.001	-0.005	-0.110	0.000
5	A	8	LYS	1	0.852	0.913	5.427	-0.617	-0.617	0.000	0.000	0.000	0.000
6	A	9	LEU	0	-0.001	0.016	2.741	-0.545	-0.156	0.637	-0.161	-0.864	-0.001
7	A	10	GLU	-1	-0.885	-0.931	6.599	-0.235	-0.235	0.000	0.000	0.000	0.000
8	A	11	LEU	0	-0.093	-0.045	5.593	-0.042	-0.042	0.000	0.000	0.000	0.000
9	A	12	GLU	-1	-0.752	-0.841	9.466	-0.274	-0.274	0.000	0.000	0.000	0.000
10	A	13	GLU	-1	-0.836	-0.937	11.984	-0.445	-0.445	0.000	0.000	0.000	0.000
11	A	14	ARG	1	0.794	0.878	14.349	0.375	0.375	0.000	0.000	0.000	0.000
12	A	15	VAL	0	0.005	0.004	16.747	-0.026	-0.026	0.000	0.000	0.000	0.000
13	A	16	VAL	0	0.019	0.020	16.978	0.017	0.017	0.000	0.000	0.000	0.000
14	A	17	ALA	0	-0.051	-0.035	19.955	0.026	0.026	0.000	0.000	0.000	0.000
15	A	18	VAL	0	0.046	0.031	21.923	-0.008	-0.008	0.000	0.000	0.000	0.000
16	A	19	ASN	0	-0.024	-0.014	24.499	0.011	0.011	0.000	0.000	0.000	0.000
17	A	20	ARG	1	0.892	0.925	27.241	0.102	0.102	0.000	0.000	0.000	0.000
18	A	21	VAL	0	0.042	0.032	30.675	0.003	0.003	0.000	0.000	0.000	0.000
19	A	22	ALA	0	0.040	0.036	33.892	0.003	0.003	0.000	0.000	0.000	0.000
20	A	23	LYS	1	0.960	0.966	31.515	0.091	0.091	0.000	0.000	0.000	0.000
21	A	24	VAL	0	-0.002	-0.002	27.402	-0.007	-0.007	0.000	0.000	0.000	0.000
22	A	25	VAL	0	-0.013	-0.012	28.633	0.006	0.006	0.000	0.000	0.000	0.000
23	A	26	LYS	1	0.891	0.939	23.385	0.196	0.196	0.000	0.000	0.000	0.000
24	A	27	GLY	0	0.065	0.030	25.930	-0.010	-0.010	0.000	0.000	0.000	0.000
25	A	28	GLY	0	-0.054	-0.022	28.312	0.008	0.008	0.000	0.000	0.000	0.000
26	A	29	ARG	1	1.010	0.998	30.687	0.083	0.083	0.000	0.000	0.000	0.000
27	A	30	ARG	1	0.964	0.970	33.086	0.069	0.069	0.000	0.000	0.000	0.000
28	A	31	LEU	0	0.068	0.048	33.740	-0.004	-0.004	0.000	0.000	0.000	0.000
29	A	32	ARG	1	0.993	0.989	26.209	0.084	0.084	0.000	0.000	0.000	0.000
30	A	33	PHE	0	0.011	0.026	26.274	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	34	SER	0	-0.059	-0.034	23.016	0.004	0.004	0.000	0.000	0.000	0.000
32	A	35	ALA	0	-0.013	-0.001	20.740	0.008	0.008	0.000	0.000	0.000	0.000
33	A	36	LEU	0	0.002	0.007	16.258	0.001	0.001	0.000	0.000	0.000	0.000
34	A	37	VAL	0	0.007	-0.006	13.823	0.033	0.033	0.000	0.000	0.000	0.000
35	A	38	VAL	0	-0.003	-0.004	11.474	-0.034	-0.034	0.000	0.000	0.000	0.000
36	A	39	VAL	0	0.009	-0.005	8.464	0.089	0.089	0.000	0.000	0.000	0.000
37	A	40	GLY	0	0.064	0.015	7.832	-0.154	-0.154	0.000	0.000	0.000	0.000
38	A	41	ASP	-1	-0.745	-0.861	6.744	-0.676	-0.676	0.000	0.000	0.000	0.000
39	A	42	LYS	1	0.792	0.896	8.914	0.518	0.518	0.000	0.000	0.000	0.000
40	A	43	ASN	0	-0.031	-0.022	7.725	0.120	0.120	0.000	0.000	0.000	0.000
41	A	44	GLY	0	0.068	0.048	7.377	-0.024	-0.024	0.000	0.000	0.000	0.000
42	A	45	HIS	1	0.749	0.836	2.319	-0.243	1.038	0.708	-0.526	-1.464	-0.002
43	A	46	VAL	0	0.008	0.013	5.010	0.264	0.264	0.000	0.000	0.000	0.000
44	A	47	GLY	0	0.053	0.030	5.486	-0.377	-0.377	0.000	0.000	0.000	0.000
45	A	48	PHE	0	-0.073	-0.035	7.504	0.243	0.243	0.000	0.000	0.000	0.000
46	A	49	GLY	0	0.095	0.044	10.969	-0.046	-0.046	0.000	0.000	0.000	0.000
47	A	50	THR	0	-0.119	-0.070	13.491	0.059	0.059	0.000	0.000	0.000	0.000
48	A	51	GLY	0	0.056	0.045	17.186	0.007	0.007	0.000	0.000	0.000	0.000
49	A	52	LYS	1	0.927	0.934	19.399	0.161	0.161	0.000	0.000	0.000	0.000
50	A	53	ALA	0	-0.013	0.002	23.125	0.010	0.010	0.000	0.000	0.000	0.000
51	A	54	GLN	0	0.030	0.010	25.886	0.002	0.002	0.000	0.000	0.000	0.000
52	A	55	GLU	-1	-0.918	-0.955	27.548	-0.071	-0.071	0.000	0.000	0.000	0.000
53	A	56	VAL	0	-0.006	-0.004	25.146	-0.008	-0.008	0.000	0.000	0.000	0.000
54	A	57	PRO	0	0.079	0.030	23.914	-0.015	-0.015	0.000	0.000	0.000	0.000
55	A	58	GLU	-1	-0.733	-0.836	22.419	-0.109	-0.109	0.000	0.000	0.000	0.000
56	A	59	ALA	0	-0.094	-0.040	21.526	-0.009	-0.009	0.000	0.000	0.000	0.000
57	A	60	ILE	0	0.030	0.000	19.202	-0.020	-0.020	0.000	0.000	0.000	0.000
58	A	61	ARG	1	0.937	0.962	17.924	0.077	0.077	0.000	0.000	0.000	0.000
59	A	62	LYS	1	0.856	0.909	16.830	0.090	0.090	0.000	0.000	0.000	0.000
60	A	63	ALA	0	-0.021	-0.003	15.632	-0.025	-0.025	0.000	0.000	0.000	0.000
61	A	64	ILE	0	0.015	0.011	13.128	-0.065	-0.065	0.000	0.000	0.000	0.000
62	A	65	GLU	-1	-0.850	-0.925	11.898	-0.255	-0.255	0.000	0.000	0.000	0.000
63	A	66	ASP	-1	-0.836	-0.889	11.470	-0.452	-0.452	0.000	0.000	0.000	0.000
64	A	67	ALA	0	-0.020	-0.010	10.145	-0.115	-0.115	0.000	0.000	0.000	0.000
65	A	68	LYS	1	0.866	0.926	7.401	0.230	0.230	0.000	0.000	0.000	0.000
66	A	69	LYS	1	0.794	0.890	6.215	-0.100	-0.100	0.000	0.000	0.000	0.000
67	A	70	ASN	0	-0.098	-0.045	5.864	-0.280	-0.280	0.000	0.000	0.000	0.000
68	A	71	LEU	0	-0.019	-0.013	2.349	-0.949	-0.226	2.285	-0.673	-2.336	-0.002
69	A	72	ILE	0	-0.052	-0.028	2.536	-2.262	-1.239	1.379	-0.802	-1.599	-0.009
70	A	73	GLU	-1	-0.858	-0.931	2.420	-1.571	-1.807	2.690	0.113	-2.568	-0.011
71	A	74	VAL	0	-0.050	-0.023	3.669	0.122	0.151	0.030	0.083	-0.141	0.000
72	A	75	PRO	0	0.001	0.013	7.463	0.044	0.044	0.000	0.000	0.000	0.000
73	A	76	ILE	0	-0.004	-0.016	10.264	0.014	0.014	0.000	0.000	0.000	0.000
74	A	77	VAL	0	-0.007	-0.007	13.000	0.021	0.021	0.000	0.000	0.000	0.000
75	A	78	GLY	0	0.019	0.011	16.552	0.013	0.013	0.000	0.000	0.000	0.000
76	A	79	THR	0	0.001	-0.023	17.125	-0.012	-0.012	0.000	0.000	0.000	0.000
77	A	80	THR	0	0.000	-0.005	17.404	-0.018	-0.018	0.000	0.000	0.000	0.000
78	A	81	ILE	0	0.006	0.001	13.863	-0.024	-0.024	0.000	0.000	0.000	0.000
79	A	82	PRO	0	0.012	0.000	13.668	0.030	0.030	0.000	0.000	0.000	0.000
80	A	83	HIS	0	0.004	-0.006	15.618	0.010	0.010	0.000	0.000	0.000	0.000
81	A	84	GLU	-1	-0.799	-0.882	17.950	-0.179	-0.179	0.000	0.000	0.000	0.000
82	A	85	VAL	0	-0.021	0.008	15.371	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	86	ILE	0	0.027	0.005	18.618	0.008	0.008	0.000	0.000	0.000	0.000
84	A	87	GLY	0	0.029	0.040	16.990	-0.006	-0.006	0.000	0.000	0.000	0.000
85	A	88	HIS	1	0.833	0.873	17.684	0.237	0.237	0.000	0.000	0.000	0.000
86	A	89	PHE	0	0.022	-0.005	14.902	-0.015	-0.015	0.000	0.000	0.000	0.000
87	A	90	GLY	0	0.012	0.014	19.244	0.005	0.005	0.000	0.000	0.000	0.000
88	A	91	ALA	0	0.015	0.008	22.680	0.005	0.005	0.000	0.000	0.000	0.000
89	A	92	GLY	0	-0.041	-0.009	21.536	0.008	0.008	0.000	0.000	0.000	0.000
90	A	93	GLU	-1	-0.821	-0.901	21.242	-0.181	-0.181	0.000	0.000	0.000	0.000
91	A	94	ILE	0	-0.043	-0.022	18.491	0.013	0.013	0.000	0.000	0.000	0.000
92	A	95	ILE	0	0.020	0.020	19.994	-0.015	-0.015	0.000	0.000	0.000	0.000
93	A	96	LEU	0	-0.012	-0.014	15.800	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	97	LYS	1	0.847	0.894	19.769	0.161	0.161	0.000	0.000	0.000	0.000
95	A	98	PRO	0	0.047	0.023	19.469	-0.007	-0.007	0.000	0.000	0.000	0.000
96	A	99	ALA	0	-0.061	-0.025	20.937	0.014	0.014	0.000	0.000	0.000	0.000
97	A	100	SER	0	0.023	0.017	22.647	-0.004	-0.004	0.000	0.000	0.000	0.000
98	A	101	GLU	-1	-0.939	-0.962	23.495	-0.140	-0.140	0.000	0.000	0.000	0.000
99	A	102	GLY	0	0.073	0.048	24.544	0.012	0.012	0.000	0.000	0.000	0.000
100	A	103	THR	0	-0.121	-0.072	24.301	0.009	0.009	0.000	0.000	0.000	0.000
101	A	104	GLY	0	0.019	0.004	22.988	0.003	0.003	0.000	0.000	0.000	0.000
102	A	105	VAL	0	-0.019	-0.013	18.612	-0.007	-0.007	0.000	0.000	0.000	0.000
103	A	106	ILE	0	0.000	0.014	21.257	0.005	0.005	0.000	0.000	0.000	0.000
104	A	107	ALA	0	0.037	0.026	20.410	-0.006	-0.006	0.000	0.000	0.000	0.000
105	A	108	GLY	0	-0.003	0.005	22.388	0.009	0.009	0.000	0.000	0.000	0.000
106	A	109	GLY	0	0.018	-0.002	21.428	-0.019	-0.019	0.000	0.000	0.000	0.000
107	A	110	PRO	0	-0.052	-0.040	19.483	-0.016	-0.016	0.000	0.000	0.000	0.000
108	A	111	ALA	0	0.058	0.035	17.205	-0.031	-0.031	0.000	0.000	0.000	0.000
109	A	112	ARG	1	0.898	0.932	16.695	0.186	0.186	0.000	0.000	0.000	0.000
110	A	113	ALA	0	-0.013	-0.008	16.931	-0.013	-0.013	0.000	0.000	0.000	0.000
111	A	114	VAL	0	-0.019	-0.011	11.467	-0.028	-0.028	0.000	0.000	0.000	0.000
112	A	115	LEU	0	0.008	0.004	12.249	-0.054	-0.054	0.000	0.000	0.000	0.000
113	A	116	GLU	-1	-0.730	-0.842	13.587	-0.280	-0.280	0.000	0.000	0.000	0.000
114	A	117	LEU	0	-0.063	-0.021	11.295	-0.003	-0.003	0.000	0.000	0.000	0.000
115	A	118	ALA	0	0.011	0.004	9.079	-0.065	-0.065	0.000	0.000	0.000	0.000
116	A	119	GLY	0	0.035	0.022	10.084	-0.019	-0.019	0.000	0.000	0.000	0.000
117	A	120	ILE	0	-0.086	-0.025	12.137	0.042	0.042	0.000	0.000	0.000	0.000
118	A	121	SER	0	-0.034	-0.031	14.819	0.010	0.010	0.000	0.000	0.000	0.000
119	A	122	ASP	-1	-0.770	-0.848	18.389	-0.164	-0.164	0.000	0.000	0.000	0.000
120	A	123	ILE	0	-0.031	-0.015	16.836	-0.018	-0.018	0.000	0.000	0.000	0.000
121	A	124	LEU	0	0.031	0.037	20.393	0.010	0.010	0.000	0.000	0.000	0.000
122	A	125	SER	0	-0.059	-0.055	20.729	-0.017	-0.017	0.000	0.000	0.000	0.000
123	A	126	LYS	1	0.918	0.960	22.686	0.156	0.156	0.000	0.000	0.000	0.000
124	A	127	SER	0	-0.030	-0.015	23.870	-0.009	-0.009	0.000	0.000	0.000	0.000
125	A	128	ILE	0	-0.004	-0.017	24.758	0.015	0.015	0.000	0.000	0.000	0.000
126	A	129	GLY	0	0.044	0.041	25.319	0.010	0.010	0.000	0.000	0.000	0.000
127	A	130	SER	0	-0.022	-0.014	24.867	0.000	0.000	0.000	0.000	0.000	0.000
128	A	131	ASN	0	0.060	0.024	24.053	-0.024	-0.024	0.000	0.000	0.000	0.000
129	A	132	THR	0	-0.009	-0.012	24.866	-0.005	-0.005	0.000	0.000	0.000	0.000
130	A	133	PRO	0	0.038	-0.005	21.393	-0.012	-0.012	0.000	0.000	0.000	0.000
131	A	134	ILE	0	-0.007	-0.002	19.264	-0.021	-0.021	0.000	0.000	0.000	0.000
132	A	135	ASN	0	0.008	0.005	18.642	-0.027	-0.027	0.000	0.000	0.000	0.000
133	A	136	MET	0	0.029	0.038	19.158	-0.011	-0.011	0.000	0.000	0.000	0.000
134	A	137	VAL	0	0.016	0.032	14.044	-0.015	-0.015	0.000	0.000	0.000	0.000
135	A	138	ARG	1	0.873	0.943	14.491	0.230	0.230	0.000	0.000	0.000	0.000
136	A	139	ALA	0	-0.006	0.006	14.810	-0.028	-0.028	0.000	0.000	0.000	0.000
137	A	140	THR	0	0.025	-0.014	14.170	0.006	0.006	0.000	0.000	0.000	0.000
138	A	141	PHE	0	0.031	0.012	7.319	0.019	0.019	0.000	0.000	0.000	0.000
139	A	142	ASP	-1	-0.850	-0.899	11.232	-0.408	-0.408	0.000	0.000	0.000	0.000
140	A	143	GLY	0	0.060	0.023	13.439	0.006	0.006	0.000	0.000	0.000	0.000
141	A	144	LEU	0	-0.007	-0.015	9.850	0.012	0.012	0.000	0.000	0.000	0.000
142	A	145	LYS	1	0.874	0.929	8.630	0.473	0.473	0.000	0.000	0.000	0.000
143	A	146	GLN	0	-0.073	-0.042	9.800	0.044	0.044	0.000	0.000	0.000	0.000
144	A	147	LEU	0	-0.021	0.023	11.191	0.044	0.044	0.000	0.000	0.000	0.000
145	A	148	LYS	1	0.848	0.918	10.836	0.374	0.374	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:ILE)