FMO DATABASE

FMODB ID: ZYM7N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1203642.845
FMO2-HF: Nuclear repulsion	1151486.756601
FMO2-HF: Total energy	-52156.088399
FMO2-MP2: Total energy	-52312.301763

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.
-7.299	-3.211	12.952	-4.929	-12.106	-0.024

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 : 0.046 / q_NPA : 0.013

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	0.049	0.005	3.568	-1.360	0.999	0.008	-0.914	-1.453	0.002
4	A	7	ASN	0	-0.023	-0.020	4.513	0.097	0.229	-0.001	-0.007	-0.123	0.000
5	A	8	LYS	1	0.919	0.977	5.288	-0.398	-0.398	0.000	0.000	0.000	0.000
6	A	9	LEU	0	-0.040	-0.003	2.215	0.271	-0.820	3.065	-0.440	-1.534	-0.003
7	A	10	GLU	-1	-0.873	-0.922	6.429	-0.288	-0.288	0.000	0.000	0.000	0.000
8	A	11	LEU	0	-0.103	-0.058	5.407	-0.050	-0.050	0.000	0.000	0.000	0.000
9	A	12	GLU	-1	-0.831	-0.912	9.508	-0.259	-0.259	0.000	0.000	0.000	0.000
10	A	13	GLU	-1	-0.930	-0.988	12.074	-0.507	-0.507	0.000	0.000	0.000	0.000
11	A	14	ARG	1	0.827	0.916	14.256	0.358	0.358	0.000	0.000	0.000	0.000
12	A	15	VAL	0	-0.002	-0.006	16.578	-0.030	-0.030	0.000	0.000	0.000	0.000
13	A	16	VAL	0	-0.010	0.004	17.101	0.025	0.025	0.000	0.000	0.000	0.000
14	A	17	ALA	0	-0.037	-0.038	19.945	0.030	0.030	0.000	0.000	0.000	0.000
15	A	18	VAL	0	0.039	0.042	21.931	-0.013	-0.013	0.000	0.000	0.000	0.000
16	A	19	ASN	0	-0.087	-0.054	24.698	0.018	0.018	0.000	0.000	0.000	0.000
17	A	20	ARG	1	0.917	0.947	27.130	0.116	0.116	0.000	0.000	0.000	0.000
18	A	21	VAL	0	0.113	0.084	30.507	0.000	0.000	0.000	0.000	0.000	0.000
19	A	22	ALA	0	-0.008	0.022	34.008	0.002	0.002	0.000	0.000	0.000	0.000
20	A	23	LYS	1	0.933	0.926	30.815	0.111	0.111	0.000	0.000	0.000	0.000
21	A	24	VAL	0	0.055	0.050	27.805	-0.009	-0.009	0.000	0.000	0.000	0.000
22	A	25	VAL	0	-0.022	-0.007	28.243	0.004	0.004	0.000	0.000	0.000	0.000
23	A	26	LYS	1	0.954	0.961	24.694	0.180	0.180	0.000	0.000	0.000	0.000
24	A	27	GLY	0	0.059	0.014	25.918	-0.011	-0.011	0.000	0.000	0.000	0.000
25	A	28	GLY	0	-0.027	-0.006	27.959	0.009	0.009	0.000	0.000	0.000	0.000
26	A	29	ARG	1	0.989	0.980	30.790	0.097	0.097	0.000	0.000	0.000	0.000
27	A	30	ARG	1	0.962	0.973	33.158	0.088	0.088	0.000	0.000	0.000	0.000
28	A	31	LEU	0	0.084	0.067	33.521	0.000	0.000	0.000	0.000	0.000	0.000
29	A	32	ARG	1	0.985	0.984	25.557	0.125	0.125	0.000	0.000	0.000	0.000
30	A	33	PHE	0	-0.050	-0.022	26.515	0.001	0.001	0.000	0.000	0.000	0.000
31	A	34	SER	0	-0.047	-0.036	22.683	0.001	0.001	0.000	0.000	0.000	0.000
32	A	35	ALA	0	-0.022	-0.001	20.244	0.015	0.015	0.000	0.000	0.000	0.000
33	A	36	LEU	0	-0.022	-0.001	16.233	-0.006	-0.006	0.000	0.000	0.000	0.000
34	A	37	VAL	0	0.007	-0.007	13.846	0.039	0.039	0.000	0.000	0.000	0.000
35	A	38	VAL	0	0.005	0.001	11.566	-0.037	-0.037	0.000	0.000	0.000	0.000
36	A	39	VAL	0	0.010	0.001	8.222	0.068	0.068	0.000	0.000	0.000	0.000
37	A	40	GLY	0	0.049	-0.006	7.625	-0.133	-0.133	0.000	0.000	0.000	0.000
38	A	41	ASP	-1	-0.757	-0.891	6.187	-0.535	-0.535	0.000	0.000	0.000	0.000
39	A	42	LYS	1	0.827	0.930	8.712	0.432	0.432	0.000	0.000	0.000	0.000
40	A	43	ASN	0	-0.006	-0.004	8.365	0.078	0.078	0.000	0.000	0.000	0.000
41	A	44	GLY	0	0.057	0.051	7.034	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	45	HIS	1	0.798	0.903	1.966	0.200	-0.371	4.735	-1.206	-2.957	-0.003
43	A	46	VAL	0	0.030	0.033	5.154	0.096	0.149	-0.001	-0.003	-0.048	0.000
44	A	47	GLY	0	0.013	0.006	5.590	-0.367	-0.367	0.000	0.000	0.000	0.000
45	A	48	PHE	0	-0.066	-0.036	7.621	0.216	0.216	0.000	0.000	0.000	0.000
46	A	49	GLY	0	0.075	0.039	11.326	-0.066	-0.066	0.000	0.000	0.000	0.000
47	A	50	THR	0	-0.086	-0.045	13.670	0.077	0.077	0.000	0.000	0.000	0.000
48	A	51	GLY	0	0.078	0.058	16.981	-0.013	-0.013	0.000	0.000	0.000	0.000
49	A	52	LYS	1	0.924	0.937	19.409	0.193	0.193	0.000	0.000	0.000	0.000
50	A	53	ALA	0	-0.026	-0.008	23.106	0.002	0.002	0.000	0.000	0.000	0.000
51	A	54	GLN	0	0.065	0.027	25.539	0.003	0.003	0.000	0.000	0.000	0.000
52	A	55	GLU	-1	-0.889	-0.938	27.562	-0.106	-0.106	0.000	0.000	0.000	0.000
53	A	56	VAL	0	-0.008	-0.009	24.941	-0.011	-0.011	0.000	0.000	0.000	0.000
54	A	57	PRO	0	0.043	0.006	23.616	-0.017	-0.017	0.000	0.000	0.000	0.000
55	A	58	GLU	-1	-0.793	-0.883	22.045	-0.195	-0.195	0.000	0.000	0.000	0.000
56	A	59	ALA	0	-0.069	-0.021	21.153	-0.019	-0.019	0.000	0.000	0.000	0.000
57	A	60	ILE	0	0.017	-0.006	18.723	-0.025	-0.025	0.000	0.000	0.000	0.000
58	A	61	ARG	1	0.934	0.941	17.717	0.153	0.153	0.000	0.000	0.000	0.000
59	A	62	LYS	1	0.945	0.981	16.442	0.155	0.155	0.000	0.000	0.000	0.000
60	A	63	ALA	0	-0.019	-0.006	15.626	-0.031	-0.031	0.000	0.000	0.000	0.000
61	A	64	ILE	0	0.014	0.008	12.553	-0.078	-0.078	0.000	0.000	0.000	0.000
62	A	65	GLU	-1	-0.981	-0.989	11.745	-0.454	-0.454	0.000	0.000	0.000	0.000
63	A	66	ASP	-1	-0.887	-0.946	10.735	-0.632	-0.632	0.000	0.000	0.000	0.000
64	A	67	ALA	0	0.046	0.021	10.085	-0.120	-0.120	0.000	0.000	0.000	0.000
65	A	68	LYS	1	0.921	0.970	7.169	0.396	0.396	0.000	0.000	0.000	0.000
66	A	69	LYS	1	0.850	0.929	5.989	0.098	0.098	0.000	0.000	0.000	0.000
67	A	70	ASN	0	-0.062	-0.025	6.303	-0.028	-0.028	0.000	0.000	0.000	0.000
68	A	71	LEU	0	-0.002	-0.005	2.395	-1.280	0.200	1.138	-0.627	-1.991	-0.001
69	A	72	ILE	0	-0.047	-0.019	3.108	-1.969	-0.851	0.333	-0.478	-0.972	-0.004
70	A	73	GLU	-1	-0.857	-0.965	2.064	-2.396	-1.826	3.642	-1.323	-2.889	-0.015
71	A	74	VAL	0	-0.080	-0.023	3.655	0.003	0.041	0.033	0.069	-0.139	0.000
72	A	75	PRO	0	0.017	0.003	7.371	0.034	0.034	0.000	0.000	0.000	0.000
73	A	76	ILE	0	0.018	0.008	9.690	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	77	VAL	0	-0.020	-0.016	12.559	0.024	0.024	0.000	0.000	0.000	0.000
75	A	78	GLY	0	-0.008	-0.005	15.920	0.004	0.004	0.000	0.000	0.000	0.000
76	A	79	THR	0	0.030	0.011	16.640	-0.011	-0.011	0.000	0.000	0.000	0.000
77	A	80	THR	0	0.018	0.004	17.193	-0.017	-0.017	0.000	0.000	0.000	0.000
78	A	81	ILE	0	0.018	0.011	13.625	-0.017	-0.017	0.000	0.000	0.000	0.000
79	A	82	PRO	0	0.007	-0.001	13.820	0.024	0.024	0.000	0.000	0.000	0.000
80	A	83	HIS	0	-0.004	-0.020	16.048	0.017	0.017	0.000	0.000	0.000	0.000
81	A	84	GLU	-1	-0.854	-0.926	17.715	-0.130	-0.130	0.000	0.000	0.000	0.000
82	A	85	VAL	0	-0.016	0.025	15.094	0.006	0.006	0.000	0.000	0.000	0.000
83	A	86	ILE	0	0.010	-0.012	18.409	0.002	0.002	0.000	0.000	0.000	0.000
84	A	87	GLY	0	0.022	0.036	17.186	-0.005	-0.005	0.000	0.000	0.000	0.000
85	A	88	HIS	1	0.883	0.909	17.865	0.167	0.167	0.000	0.000	0.000	0.000
86	A	89	PHE	0	-0.005	-0.007	16.406	-0.011	-0.011	0.000	0.000	0.000	0.000
87	A	90	GLY	0	-0.029	-0.001	19.578	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	91	ALA	0	0.015	0.007	22.814	0.008	0.008	0.000	0.000	0.000	0.000
89	A	92	GLY	0	-0.037	-0.009	21.759	0.007	0.007	0.000	0.000	0.000	0.000
90	A	93	GLU	-1	-0.797	-0.909	21.483	-0.134	-0.134	0.000	0.000	0.000	0.000
91	A	94	ILE	0	-0.057	-0.015	18.432	0.008	0.008	0.000	0.000	0.000	0.000
92	A	95	ILE	0	0.009	0.018	20.188	-0.007	-0.007	0.000	0.000	0.000	0.000
93	A	96	LEU	0	0.004	0.004	15.715	-0.004	-0.004	0.000	0.000	0.000	0.000
94	A	97	LYS	1	0.915	0.939	19.730	0.116	0.116	0.000	0.000	0.000	0.000
95	A	98	PRO	0	0.014	0.009	19.164	-0.007	-0.007	0.000	0.000	0.000	0.000
96	A	99	ALA	0	-0.040	-0.007	20.822	0.010	0.010	0.000	0.000	0.000	0.000
97	A	100	SER	0	-0.011	0.001	22.271	-0.003	-0.003	0.000	0.000	0.000	0.000
98	A	101	GLU	-1	-0.935	-0.976	22.958	-0.108	-0.108	0.000	0.000	0.000	0.000
99	A	102	GLY	0	0.082	0.055	24.286	0.009	0.009	0.000	0.000	0.000	0.000
100	A	103	THR	0	-0.130	-0.061	24.210	0.003	0.003	0.000	0.000	0.000	0.000
101	A	104	GLY	0	0.041	0.019	23.327	0.002	0.002	0.000	0.000	0.000	0.000
102	A	105	VAL	0	-0.035	-0.008	18.818	-0.005	-0.005	0.000	0.000	0.000	0.000
103	A	106	ILE	0	-0.001	0.007	21.479	0.003	0.003	0.000	0.000	0.000	0.000
104	A	107	ALA	0	0.057	0.035	20.730	-0.005	-0.005	0.000	0.000	0.000	0.000
105	A	108	GLY	0	-0.015	0.004	22.672	0.007	0.007	0.000	0.000	0.000	0.000
106	A	109	GLY	0	0.030	0.000	21.456	-0.016	-0.016	0.000	0.000	0.000	0.000
107	A	110	PRO	0	-0.045	-0.046	19.536	-0.015	-0.015	0.000	0.000	0.000	0.000
108	A	111	ALA	0	0.062	0.041	17.430	-0.032	-0.032	0.000	0.000	0.000	0.000
109	A	112	ARG	1	0.967	0.989	16.765	0.169	0.169	0.000	0.000	0.000	0.000
110	A	113	ALA	0	-0.010	-0.006	16.651	-0.010	-0.010	0.000	0.000	0.000	0.000
111	A	114	VAL	0	-0.005	0.003	11.657	-0.032	-0.032	0.000	0.000	0.000	0.000
112	A	115	LEU	0	0.012	-0.010	12.457	-0.037	-0.037	0.000	0.000	0.000	0.000
113	A	116	GLU	-1	-0.801	-0.896	13.761	-0.254	-0.254	0.000	0.000	0.000	0.000
114	A	117	LEU	0	-0.072	-0.021	11.088	-0.004	-0.004	0.000	0.000	0.000	0.000
115	A	118	ALA	0	-0.008	0.002	9.153	-0.055	-0.055	0.000	0.000	0.000	0.000
116	A	119	GLY	0	0.032	0.011	9.938	-0.004	-0.004	0.000	0.000	0.000	0.000
117	A	120	ILE	0	-0.092	-0.021	12.384	0.033	0.033	0.000	0.000	0.000	0.000
118	A	121	SER	0	-0.042	-0.038	14.929	0.000	0.000	0.000	0.000	0.000	0.000
119	A	122	ASP	-1	-0.761	-0.862	18.579	-0.130	-0.130	0.000	0.000	0.000	0.000
120	A	123	ILE	0	-0.051	-0.032	16.719	-0.011	-0.011	0.000	0.000	0.000	0.000
121	A	124	LEU	0	0.032	0.026	20.513	0.005	0.005	0.000	0.000	0.000	0.000
122	A	125	SER	0	-0.051	-0.056	20.553	-0.009	-0.009	0.000	0.000	0.000	0.000
123	A	126	LYS	1	0.925	0.967	22.382	0.119	0.119	0.000	0.000	0.000	0.000
124	A	127	SER	0	-0.048	-0.039	23.962	-0.010	-0.010	0.000	0.000	0.000	0.000
125	A	128	ILE	0	0.000	-0.016	24.799	0.013	0.013	0.000	0.000	0.000	0.000
126	A	129	GLY	0	0.068	0.045	25.781	0.007	0.007	0.000	0.000	0.000	0.000
127	A	130	SER	0	-0.072	-0.047	24.804	-0.001	-0.001	0.000	0.000	0.000	0.000
128	A	131	ASN	0	0.077	0.043	24.340	-0.018	-0.018	0.000	0.000	0.000	0.000
129	A	132	THR	0	-0.028	-0.007	24.794	-0.007	-0.007	0.000	0.000	0.000	0.000
130	A	133	PRO	0	0.036	-0.007	21.348	-0.009	-0.009	0.000	0.000	0.000	0.000
131	A	134	ILE	0	0.043	0.023	19.023	-0.016	-0.016	0.000	0.000	0.000	0.000
132	A	135	ASN	0	-0.047	-0.031	18.909	-0.025	-0.025	0.000	0.000	0.000	0.000
133	A	136	MET	0	0.036	0.030	19.514	-0.008	-0.008	0.000	0.000	0.000	0.000
134	A	137	VAL	0	0.006	0.007	14.482	-0.011	-0.011	0.000	0.000	0.000	0.000
135	A	138	ARG	1	0.946	0.984	14.637	0.229	0.229	0.000	0.000	0.000	0.000
136	A	139	ALA	0	0.011	0.019	15.314	-0.014	-0.014	0.000	0.000	0.000	0.000
137	A	140	THR	0	0.007	-0.013	13.961	0.010	0.010	0.000	0.000	0.000	0.000
138	A	141	PHE	0	-0.010	-0.016	7.733	0.018	0.018	0.000	0.000	0.000	0.000
139	A	142	ASP	-1	-0.896	-0.943	11.514	-0.306	-0.306	0.000	0.000	0.000	0.000
140	A	143	GLY	0	0.047	0.017	13.437	0.016	0.016	0.000	0.000	0.000	0.000
141	A	144	LEU	0	-0.013	-0.006	9.895	0.015	0.015	0.000	0.000	0.000	0.000
142	A	145	LYS	1	0.941	0.960	7.956	0.551	0.551	0.000	0.000	0.000	0.000
143	A	146	GLN	0	-0.083	-0.027	9.824	0.060	0.060	0.000	0.000	0.000	0.000
144	A	147	LEU	0	-0.038	-0.006	11.301	0.046	0.046	0.000	0.000	0.000	0.000
145	A	148	LYS	1	0.903	0.962	11.135	0.149	0.149	0.000	0.000	0.000	0.000

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