FMO DATABASE

FMODB ID: R53Q8

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1204712.551069
FMO2-HF: Nuclear repulsion	1152555.272044
FMO2-HF: Total energy	-52157.279025
FMO2-MP2: Total energy	-52313.475923

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.
-10.763	-3.211	8.873	-4.724	-11.702	-0.036

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 : 0.018 / 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

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	0.056	0.013	3.623	-1.356	0.879	0.006	-0.885	-1.356	0.002
4	A	7	ASN	0	-0.015	-0.019	4.665	0.081	0.201	-0.001	-0.006	-0.114	0.000
5	A	8	LYS	1	0.915	0.976	5.221	-0.521	-0.521	0.000	0.000	0.000	0.000
6	A	9	LEU	0	-0.034	0.003	2.380	-0.180	-0.349	1.673	-0.270	-1.233	-0.002
7	A	10	GLU	-1	-0.889	-0.925	6.303	-0.225	-0.225	0.000	0.000	0.000	0.000
8	A	11	LEU	0	-0.073	-0.043	5.728	-0.064	-0.064	0.000	0.000	0.000	0.000
9	A	12	GLU	-1	-0.784	-0.863	9.562	-0.255	-0.255	0.000	0.000	0.000	0.000
10	A	13	GLU	-1	-0.855	-0.946	12.235	-0.469	-0.469	0.000	0.000	0.000	0.000
11	A	14	ARG	1	0.812	0.892	14.425	0.350	0.350	0.000	0.000	0.000	0.000
12	A	15	VAL	0	0.021	0.004	16.524	-0.028	-0.028	0.000	0.000	0.000	0.000
13	A	16	VAL	0	0.000	0.011	16.948	0.024	0.024	0.000	0.000	0.000	0.000
14	A	17	ALA	0	-0.041	-0.031	19.947	0.028	0.028	0.000	0.000	0.000	0.000
15	A	18	VAL	0	0.057	0.037	21.966	-0.010	-0.010	0.000	0.000	0.000	0.000
16	A	19	ASN	0	-0.080	-0.046	24.706	0.016	0.016	0.000	0.000	0.000	0.000
17	A	20	ARG	1	0.899	0.931	27.025	0.110	0.110	0.000	0.000	0.000	0.000
18	A	21	VAL	0	0.123	0.087	30.396	0.000	0.000	0.000	0.000	0.000	0.000
19	A	22	ALA	0	-0.007	0.025	33.958	0.001	0.001	0.000	0.000	0.000	0.000
20	A	23	LYS	1	0.951	0.935	31.296	0.098	0.098	0.000	0.000	0.000	0.000
21	A	24	VAL	0	0.045	0.042	27.491	-0.007	-0.007	0.000	0.000	0.000	0.000
22	A	25	VAL	0	-0.029	-0.017	28.303	0.004	0.004	0.000	0.000	0.000	0.000
23	A	26	LYS	1	0.898	0.942	23.498	0.191	0.191	0.000	0.000	0.000	0.000
24	A	27	GLY	0	0.056	0.016	25.933	-0.010	-0.010	0.000	0.000	0.000	0.000
25	A	28	GLY	0	-0.022	-0.006	27.929	0.008	0.008	0.000	0.000	0.000	0.000
26	A	29	ARG	1	0.989	0.985	30.772	0.089	0.089	0.000	0.000	0.000	0.000
27	A	30	ARG	1	0.950	0.960	33.141	0.078	0.078	0.000	0.000	0.000	0.000
28	A	31	LEU	0	0.078	0.061	33.431	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	32	ARG	1	0.996	0.990	25.705	0.108	0.108	0.000	0.000	0.000	0.000
30	A	33	PHE	0	-0.018	0.005	26.297	0.001	0.001	0.000	0.000	0.000	0.000
31	A	34	SER	0	-0.054	-0.044	22.622	0.002	0.002	0.000	0.000	0.000	0.000
32	A	35	ALA	0	-0.021	0.002	20.346	0.012	0.012	0.000	0.000	0.000	0.000
33	A	36	LEU	0	-0.008	0.003	16.282	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	37	VAL	0	0.008	-0.006	13.840	0.037	0.037	0.000	0.000	0.000	0.000
35	A	38	VAL	0	-0.008	-0.004	11.415	-0.034	-0.034	0.000	0.000	0.000	0.000
36	A	39	VAL	0	0.004	-0.003	8.425	0.072	0.072	0.000	0.000	0.000	0.000
37	A	40	GLY	0	0.056	0.002	7.770	-0.130	-0.130	0.000	0.000	0.000	0.000
38	A	41	ASP	-1	-0.743	-0.865	6.164	-0.591	-0.591	0.000	0.000	0.000	0.000
39	A	42	LYS	1	0.797	0.894	8.730	0.435	0.435	0.000	0.000	0.000	0.000
40	A	43	ASN	0	-0.013	-0.008	7.690	0.088	0.088	0.000	0.000	0.000	0.000
41	A	44	GLY	0	0.053	0.052	7.329	-0.018	-0.018	0.000	0.000	0.000	0.000
42	A	45	HIS	1	0.777	0.846	2.246	-0.849	0.652	1.257	-0.799	-1.959	-0.005
43	A	46	VAL	0	-0.005	0.018	4.635	0.176	0.240	-0.001	-0.005	-0.058	0.000
44	A	47	GLY	0	0.032	0.020	5.646	-0.319	-0.319	0.000	0.000	0.000	0.000
45	A	48	PHE	0	-0.063	-0.039	7.690	0.210	0.210	0.000	0.000	0.000	0.000
46	A	49	GLY	0	0.074	0.037	11.055	-0.063	-0.063	0.000	0.000	0.000	0.000
47	A	50	THR	0	-0.090	-0.053	13.517	0.071	0.071	0.000	0.000	0.000	0.000
48	A	51	GLY	0	0.058	0.051	16.940	-0.006	-0.006	0.000	0.000	0.000	0.000
49	A	52	LYS	1	0.930	0.933	19.401	0.181	0.181	0.000	0.000	0.000	0.000
50	A	53	ALA	0	-0.021	0.002	23.027	0.005	0.005	0.000	0.000	0.000	0.000
51	A	54	GLN	0	0.035	0.004	25.482	0.002	0.002	0.000	0.000	0.000	0.000
52	A	55	GLU	-1	-0.878	-0.922	27.517	-0.090	-0.090	0.000	0.000	0.000	0.000
53	A	56	VAL	0	-0.028	-0.019	25.035	-0.010	-0.010	0.000	0.000	0.000	0.000
54	A	57	PRO	0	0.063	0.020	23.869	-0.016	-0.016	0.000	0.000	0.000	0.000
55	A	58	GLU	-1	-0.770	-0.868	22.217	-0.161	-0.161	0.000	0.000	0.000	0.000
56	A	59	ALA	0	-0.055	-0.019	21.127	-0.016	-0.016	0.000	0.000	0.000	0.000
57	A	60	ILE	0	0.032	-0.001	19.008	-0.024	-0.024	0.000	0.000	0.000	0.000
58	A	61	ARG	1	0.947	0.960	17.730	0.120	0.120	0.000	0.000	0.000	0.000
59	A	62	LYS	1	0.871	0.926	16.522	0.125	0.125	0.000	0.000	0.000	0.000
60	A	63	ALA	0	-0.015	0.002	15.565	-0.027	-0.027	0.000	0.000	0.000	0.000
61	A	64	ILE	0	0.003	0.004	12.777	-0.073	-0.073	0.000	0.000	0.000	0.000
62	A	65	GLU	-1	-0.892	-0.936	11.720	-0.378	-0.378	0.000	0.000	0.000	0.000
63	A	66	ASP	-1	-0.827	-0.909	10.697	-0.579	-0.579	0.000	0.000	0.000	0.000
64	A	67	ALA	0	0.027	0.016	10.012	-0.112	-0.112	0.000	0.000	0.000	0.000
65	A	68	LYS	1	0.827	0.921	7.125	0.279	0.279	0.000	0.000	0.000	0.000
66	A	69	LYS	1	0.786	0.880	5.931	-0.050	-0.050	0.000	0.000	0.000	0.000
67	A	70	ASN	0	-0.085	-0.035	6.217	-0.053	-0.053	0.000	0.000	0.000	0.000
68	A	71	LEU	0	-0.011	-0.008	2.437	-1.373	-0.064	1.907	-0.747	-2.469	0.000
69	A	72	ILE	0	-0.033	-0.014	2.486	-3.075	-1.871	1.949	-1.222	-1.932	-0.018
70	A	73	GLU	-1	-0.831	-0.919	2.245	-3.074	-1.814	2.057	-0.866	-2.451	-0.013
71	A	74	VAL	0	-0.078	-0.035	3.556	0.168	0.196	0.026	0.076	-0.130	0.000
72	A	75	PRO	0	0.007	0.008	7.325	0.036	0.036	0.000	0.000	0.000	0.000
73	A	76	ILE	0	0.002	-0.008	10.153	0.010	0.010	0.000	0.000	0.000	0.000
74	A	77	VAL	0	-0.016	-0.010	12.976	0.023	0.023	0.000	0.000	0.000	0.000
75	A	78	GLY	0	-0.004	-0.003	16.396	0.009	0.009	0.000	0.000	0.000	0.000
76	A	79	THR	0	0.022	-0.002	17.086	-0.012	-0.012	0.000	0.000	0.000	0.000
77	A	80	THR	0	0.008	-0.020	17.344	-0.017	-0.017	0.000	0.000	0.000	0.000
78	A	81	ILE	0	0.028	0.014	13.610	-0.023	-0.023	0.000	0.000	0.000	0.000
79	A	82	PRO	0	-0.004	0.000	13.684	0.029	0.029	0.000	0.000	0.000	0.000
80	A	83	HIS	0	-0.001	-0.021	15.758	0.014	0.014	0.000	0.000	0.000	0.000
81	A	84	GLU	-1	-0.808	-0.885	17.554	-0.154	-0.154	0.000	0.000	0.000	0.000
82	A	85	VAL	0	-0.001	0.026	15.130	0.004	0.004	0.000	0.000	0.000	0.000
83	A	86	ILE	0	0.009	-0.008	18.311	0.006	0.006	0.000	0.000	0.000	0.000
84	A	87	GLY	0	0.030	0.038	17.141	-0.008	-0.008	0.000	0.000	0.000	0.000
85	A	88	HIS	1	0.888	0.895	17.803	0.199	0.199	0.000	0.000	0.000	0.000
86	A	89	PHE	0	-0.011	-0.006	15.418	-0.012	-0.012	0.000	0.000	0.000	0.000
87	A	90	GLY	0	-0.011	0.005	19.229	0.000	0.000	0.000	0.000	0.000	0.000
88	A	91	ALA	0	0.012	0.005	22.408	0.008	0.008	0.000	0.000	0.000	0.000
89	A	92	GLY	0	-0.036	-0.010	21.611	0.008	0.008	0.000	0.000	0.000	0.000
90	A	93	GLU	-1	-0.805	-0.892	21.398	-0.152	-0.152	0.000	0.000	0.000	0.000
91	A	94	ILE	0	-0.050	-0.016	18.581	0.010	0.010	0.000	0.000	0.000	0.000
92	A	95	ILE	0	0.005	0.014	20.065	-0.010	-0.010	0.000	0.000	0.000	0.000
93	A	96	LEU	0	0.003	0.007	15.593	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	97	LYS	1	0.853	0.892	19.534	0.135	0.135	0.000	0.000	0.000	0.000
95	A	98	PRO	0	0.033	0.017	19.402	-0.007	-0.007	0.000	0.000	0.000	0.000
96	A	99	ALA	0	-0.056	-0.015	20.803	0.012	0.012	0.000	0.000	0.000	0.000
97	A	100	SER	0	0.002	0.007	22.523	-0.005	-0.005	0.000	0.000	0.000	0.000
98	A	101	GLU	-1	-0.936	-0.974	23.261	-0.118	-0.118	0.000	0.000	0.000	0.000
99	A	102	GLY	0	0.084	0.051	24.501	0.011	0.011	0.000	0.000	0.000	0.000
100	A	103	THR	0	-0.139	-0.065	24.209	0.004	0.004	0.000	0.000	0.000	0.000
101	A	104	GLY	0	0.049	0.023	23.122	0.004	0.004	0.000	0.000	0.000	0.000
102	A	105	VAL	0	-0.021	-0.004	18.389	-0.007	-0.007	0.000	0.000	0.000	0.000
103	A	106	ILE	0	-0.012	0.004	21.151	0.006	0.006	0.000	0.000	0.000	0.000
104	A	107	ALA	0	0.049	0.020	20.578	-0.007	-0.007	0.000	0.000	0.000	0.000
105	A	108	GLY	0	-0.016	0.002	22.506	0.008	0.008	0.000	0.000	0.000	0.000
106	A	109	GLY	0	0.038	0.004	21.348	-0.017	-0.017	0.000	0.000	0.000	0.000
107	A	110	PRO	0	-0.055	-0.050	19.498	-0.014	-0.014	0.000	0.000	0.000	0.000
108	A	111	ALA	0	0.054	0.035	17.377	-0.031	-0.031	0.000	0.000	0.000	0.000
109	A	112	ARG	1	0.884	0.926	16.630	0.170	0.170	0.000	0.000	0.000	0.000
110	A	113	ALA	0	-0.022	-0.012	16.525	-0.011	-0.011	0.000	0.000	0.000	0.000
111	A	114	VAL	0	0.006	0.013	11.473	-0.029	-0.029	0.000	0.000	0.000	0.000
112	A	115	LEU	0	0.018	-0.007	12.220	-0.042	-0.042	0.000	0.000	0.000	0.000
113	A	116	GLU	-1	-0.732	-0.831	13.395	-0.254	-0.254	0.000	0.000	0.000	0.000
114	A	117	LEU	0	-0.064	-0.019	10.913	-0.004	-0.004	0.000	0.000	0.000	0.000
115	A	118	ALA	0	-0.006	-0.009	8.731	-0.057	-0.057	0.000	0.000	0.000	0.000
116	A	119	GLY	0	0.033	0.017	9.760	-0.019	-0.019	0.000	0.000	0.000	0.000
117	A	120	ILE	0	-0.086	-0.025	12.407	0.033	0.033	0.000	0.000	0.000	0.000
118	A	121	SER	0	-0.031	-0.029	14.836	0.006	0.006	0.000	0.000	0.000	0.000
119	A	122	ASP	-1	-0.759	-0.847	18.466	-0.144	-0.144	0.000	0.000	0.000	0.000
120	A	123	ILE	0	-0.046	-0.025	16.563	-0.015	-0.015	0.000	0.000	0.000	0.000
121	A	124	LEU	0	0.031	0.029	20.436	0.008	0.008	0.000	0.000	0.000	0.000
122	A	125	SER	0	-0.039	-0.033	20.342	-0.012	-0.012	0.000	0.000	0.000	0.000
123	A	126	LYS	1	0.953	0.970	22.270	0.133	0.133	0.000	0.000	0.000	0.000
124	A	127	SER	0	-0.059	-0.043	23.994	-0.009	-0.009	0.000	0.000	0.000	0.000
125	A	128	ILE	0	-0.013	-0.014	24.778	0.014	0.014	0.000	0.000	0.000	0.000
126	A	129	GLY	0	0.062	0.041	25.688	0.007	0.007	0.000	0.000	0.000	0.000
127	A	130	SER	0	-0.074	-0.040	24.725	-0.001	-0.001	0.000	0.000	0.000	0.000
128	A	131	ASN	0	0.089	0.047	24.323	-0.021	-0.021	0.000	0.000	0.000	0.000
129	A	132	THR	0	-0.028	-0.010	24.737	-0.007	-0.007	0.000	0.000	0.000	0.000
130	A	133	PRO	0	0.043	-0.004	21.355	-0.009	-0.009	0.000	0.000	0.000	0.000
131	A	134	ILE	0	0.016	0.007	18.919	-0.017	-0.017	0.000	0.000	0.000	0.000
132	A	135	ASN	0	-0.008	-0.011	18.759	-0.029	-0.029	0.000	0.000	0.000	0.000
133	A	136	MET	0	0.035	0.034	19.411	-0.011	-0.011	0.000	0.000	0.000	0.000
134	A	137	VAL	0	0.017	0.023	14.389	-0.013	-0.013	0.000	0.000	0.000	0.000
135	A	138	ARG	1	0.912	0.968	14.577	0.224	0.224	0.000	0.000	0.000	0.000
136	A	139	ALA	0	-0.008	0.007	15.103	-0.018	-0.018	0.000	0.000	0.000	0.000
137	A	140	THR	0	0.004	-0.026	14.259	0.005	0.005	0.000	0.000	0.000	0.000
138	A	141	PHE	0	0.026	0.009	7.445	0.024	0.024	0.000	0.000	0.000	0.000
139	A	142	ASP	-1	-0.881	-0.928	11.430	-0.362	-0.362	0.000	0.000	0.000	0.000
140	A	143	GLY	0	0.062	0.026	13.420	0.012	0.012	0.000	0.000	0.000	0.000
141	A	144	LEU	0	0.009	-0.003	9.806	0.014	0.014	0.000	0.000	0.000	0.000
142	A	145	LYS	1	0.869	0.920	8.373	0.453	0.453	0.000	0.000	0.000	0.000
143	A	146	GLN	0	-0.077	-0.028	9.812	0.056	0.056	0.000	0.000	0.000	0.000
144	A	147	LEU	0	-0.034	0.015	11.084	0.048	0.048	0.000	0.000	0.000	0.000
145	A	148	LYS	1	0.865	0.927	11.114	0.255	0.255	0.000	0.000	0.000	0.000

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