FMO DATABASE

FMODB ID: R5ZZ8

Calculation Name: 2P19-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2P19

Chain ID: A

ChEMBL ID:

UniProt ID: Q8NTZ4

Base Structure: X-ray

Registration Date: 2023-06-20

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	148
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1272424.359683
FMO2-HF: Nuclear repulsion	1216580.021303
FMO2-HF: Total energy	-55844.33838
FMO2-MP2: Total energy	-56009.603065

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:2:LYS)

Summations of interaction energy for fragment #1(A:2:LYS)

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.
-63.861	-59.438	2.501	-3.19	-3.736	-0.017

Interaction energy analysis for fragmet #1(A:2:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.986 / q_NPA : 0.974

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	4	ALA	0	0.026	0.018	3.126	0.817	2.698	0.000	-0.822	-1.060	0.001
4	A	5	ASN	0	-0.045	-0.012	2.623	-0.112	2.398	2.502	-2.348	-2.664	-0.018
5	A	6	LEU	0	0.049	0.028	4.391	-0.488	-0.456	-0.001	-0.020	-0.012	0.000
6	A	7	ASP	-1	-0.859	-0.918	6.624	-35.017	-35.017	0.000	0.000	0.000	0.000
7	A	8	PRO	0	-0.009	-0.001	8.542	2.168	2.168	0.000	0.000	0.000	0.000
8	A	9	LYS	1	0.872	0.929	10.203	25.135	25.135	0.000	0.000	0.000	0.000
9	A	10	THR	0	0.028	0.004	14.861	0.679	0.679	0.000	0.000	0.000	0.000
10	A	11	ARG	1	0.992	1.019	18.321	12.376	12.376	0.000	0.000	0.000	0.000
11	A	12	VAL	0	0.029	0.006	21.760	0.127	0.127	0.000	0.000	0.000	0.000
12	A	13	LEU	0	-0.091	-0.042	25.070	0.168	0.168	0.000	0.000	0.000	0.000
13	A	14	GLU	-1	-0.801	-0.893	27.788	-8.829	-8.829	0.000	0.000	0.000	0.000
14	A	15	HIS	0	-0.035	-0.030	28.991	-0.190	-0.190	0.000	0.000	0.000	0.000
15	A	16	ARG	1	0.888	0.939	31.376	8.651	8.651	0.000	0.000	0.000	0.000
16	A	17	LEU	0	0.052	0.043	35.024	-0.109	-0.109	0.000	0.000	0.000	0.000
17	A	18	LEU	0	-0.079	-0.039	36.551	0.155	0.155	0.000	0.000	0.000	0.000
18	A	19	ALA	0	0.029	0.024	39.865	-0.041	-0.041	0.000	0.000	0.000	0.000
19	A	20	ALA	0	-0.015	0.001	40.546	-0.072	-0.072	0.000	0.000	0.000	0.000
20	A	21	SER	0	0.051	0.017	41.050	0.214	0.214	0.000	0.000	0.000	0.000
21	A	22	SER	0	0.042	-0.003	42.853	-0.070	-0.070	0.000	0.000	0.000	0.000
22	A	23	ALA	0	0.020	0.020	41.081	-0.030	-0.030	0.000	0.000	0.000	0.000
23	A	24	ILE	0	-0.006	0.002	36.175	-0.101	-0.101	0.000	0.000	0.000	0.000
24	A	25	ALA	0	0.024	0.008	39.148	-0.143	-0.143	0.000	0.000	0.000	0.000
25	A	26	GLU	-1	-0.951	-0.968	41.533	-7.132	-7.132	0.000	0.000	0.000	0.000
26	A	27	LYS	1	0.854	0.924	35.261	8.472	8.472	0.000	0.000	0.000	0.000
27	A	28	LEU	0	-0.022	-0.020	34.668	-0.194	-0.194	0.000	0.000	0.000	0.000
28	A	29	GLY	0	-0.017	0.011	38.027	-0.067	-0.067	0.000	0.000	0.000	0.000
29	A	30	VAL	0	-0.081	-0.035	40.015	0.041	0.041	0.000	0.000	0.000	0.000
30	A	31	SER	0	-0.001	-0.014	42.771	0.164	0.164	0.000	0.000	0.000	0.000
31	A	32	ALA	0	-0.050	-0.045	44.531	-0.131	-0.131	0.000	0.000	0.000	0.000
32	A	33	GLY	0	-0.039	-0.022	44.675	0.132	0.132	0.000	0.000	0.000	0.000
33	A	34	ASP	-1	-0.812	-0.887	42.211	-7.180	-7.180	0.000	0.000	0.000	0.000
34	A	35	GLU	-1	-0.926	-0.971	39.396	-7.917	-7.917	0.000	0.000	0.000	0.000
35	A	36	VAL	0	-0.001	0.009	36.436	-0.160	-0.160	0.000	0.000	0.000	0.000
36	A	37	LEU	0	-0.018	-0.004	30.688	0.051	0.051	0.000	0.000	0.000	0.000
37	A	38	LEU	0	-0.025	0.006	31.493	-0.178	-0.178	0.000	0.000	0.000	0.000
38	A	39	ILE	0	-0.004	-0.014	26.333	-0.148	-0.148	0.000	0.000	0.000	0.000
39	A	40	ARG	1	0.889	0.933	27.444	9.810	9.810	0.000	0.000	0.000	0.000
40	A	41	ARG	1	0.907	0.944	21.326	13.074	13.074	0.000	0.000	0.000	0.000
41	A	42	LEU	0	0.026	0.028	21.263	0.218	0.218	0.000	0.000	0.000	0.000
42	A	43	ARG	1	0.854	0.921	15.241	16.766	16.766	0.000	0.000	0.000	0.000
43	A	44	SER	0	0.042	0.012	16.376	0.835	0.835	0.000	0.000	0.000	0.000
44	A	45	THR	0	0.013	-0.001	10.805	-0.952	-0.952	0.000	0.000	0.000	0.000
45	A	46	GLY	0	-0.013	-0.009	11.720	0.266	0.266	0.000	0.000	0.000	0.000
46	A	47	ASP	-1	-0.932	-0.970	12.375	-18.295	-18.295	0.000	0.000	0.000	0.000
47	A	48	ILE	0	0.001	0.004	14.514	1.077	1.077	0.000	0.000	0.000	0.000
48	A	49	PRO	0	0.004	0.017	16.686	-0.791	-0.791	0.000	0.000	0.000	0.000
49	A	50	VAL	0	-0.025	-0.023	15.535	0.113	0.113	0.000	0.000	0.000	0.000
50	A	51	ALA	0	0.006	-0.014	18.893	0.508	0.508	0.000	0.000	0.000	0.000
51	A	52	ILE	0	0.007	0.022	21.479	-0.242	-0.242	0.000	0.000	0.000	0.000
52	A	53	LEU	0	-0.069	-0.040	19.919	0.077	0.077	0.000	0.000	0.000	0.000
53	A	54	GLU	-1	-0.803	-0.897	24.536	-9.474	-9.474	0.000	0.000	0.000	0.000
54	A	55	ASN	0	-0.053	-0.043	25.332	-0.397	-0.397	0.000	0.000	0.000	0.000
55	A	56	TYR	0	-0.015	-0.008	28.960	0.255	0.255	0.000	0.000	0.000	0.000
56	A	57	LEU	0	-0.001	-0.006	28.830	-0.193	-0.193	0.000	0.000	0.000	0.000
57	A	58	PRO	0	0.052	0.025	32.712	0.238	0.238	0.000	0.000	0.000	0.000
58	A	59	PRO	0	0.054	0.017	35.477	-0.184	-0.184	0.000	0.000	0.000	0.000
59	A	60	ALA	0	-0.043	-0.013	36.055	-0.060	-0.060	0.000	0.000	0.000	0.000
60	A	61	PHE	0	-0.021	-0.020	31.213	-0.179	-0.179	0.000	0.000	0.000	0.000
61	A	62	ASN	0	-0.065	-0.033	32.064	-0.416	-0.416	0.000	0.000	0.000	0.000
62	A	63	ASP	-1	-0.755	-0.864	32.678	-9.764	-9.764	0.000	0.000	0.000	0.000
63	A	64	VAL	0	-0.057	-0.012	26.774	-0.293	-0.293	0.000	0.000	0.000	0.000
64	A	65	SER	0	0.009	-0.015	28.164	0.065	0.065	0.000	0.000	0.000	0.000
65	A	66	LEU	0	0.019	-0.012	26.838	-0.394	-0.394	0.000	0.000	0.000	0.000
66	A	67	ASP	-1	-0.765	-0.862	25.198	-12.890	-12.890	0.000	0.000	0.000	0.000
67	A	68	GLU	-1	-0.753	-0.845	23.512	-12.101	-12.101	0.000	0.000	0.000	0.000
68	A	69	LEU	0	-0.073	-0.033	22.107	-0.597	-0.597	0.000	0.000	0.000	0.000
69	A	70	GLU	-1	-0.986	-0.983	20.903	-13.275	-13.275	0.000	0.000	0.000	0.000
70	A	71	LYS	1	0.763	0.867	18.903	12.203	12.203	0.000	0.000	0.000	0.000
71	A	72	GLY	0	-0.008	0.006	17.558	-1.043	-1.043	0.000	0.000	0.000	0.000
72	A	73	GLY	0	-0.034	-0.014	18.626	0.416	0.416	0.000	0.000	0.000	0.000
73	A	74	LEU	0	0.022	0.000	19.867	0.280	0.280	0.000	0.000	0.000	0.000
74	A	75	TYR	0	-0.003	-0.052	21.181	0.274	0.274	0.000	0.000	0.000	0.000
75	A	76	ASP	-1	-0.834	-0.880	18.302	-16.604	-16.604	0.000	0.000	0.000	0.000
76	A	77	ALA	0	0.060	0.042	21.273	0.319	0.319	0.000	0.000	0.000	0.000
77	A	78	LEU	0	-0.014	-0.009	24.612	0.420	0.420	0.000	0.000	0.000	0.000
78	A	79	ARG	1	0.891	0.923	18.860	15.608	15.608	0.000	0.000	0.000	0.000
79	A	80	SER	0	-0.051	-0.016	24.272	0.167	0.167	0.000	0.000	0.000	0.000
80	A	81	ARG	1	0.715	0.814	26.406	11.022	11.022	0.000	0.000	0.000	0.000
81	A	82	GLY	0	-0.025	-0.003	28.367	0.376	0.376	0.000	0.000	0.000	0.000
82	A	83	VAL	0	-0.025	0.001	28.618	0.236	0.236	0.000	0.000	0.000	0.000
83	A	84	VAL	0	-0.029	-0.029	25.053	-0.585	-0.585	0.000	0.000	0.000	0.000
84	A	85	LEU	0	-0.055	-0.023	24.208	0.355	0.355	0.000	0.000	0.000	0.000
85	A	86	LYS	1	0.868	0.946	27.259	9.825	9.825	0.000	0.000	0.000	0.000
86	A	87	ILE	0	-0.008	-0.010	29.314	-0.067	-0.067	0.000	0.000	0.000	0.000
87	A	88	ALA	0	0.019	0.012	26.633	-0.049	-0.049	0.000	0.000	0.000	0.000
88	A	89	ASN	0	-0.030	0.006	28.651	-0.063	-0.063	0.000	0.000	0.000	0.000
89	A	90	GLN	0	0.027	0.001	23.792	-0.282	-0.282	0.000	0.000	0.000	0.000
90	A	91	LYS	1	0.964	0.990	29.190	8.632	8.632	0.000	0.000	0.000	0.000
91	A	92	ILE	0	0.018	0.010	25.333	-0.104	-0.104	0.000	0.000	0.000	0.000
92	A	93	GLY	0	-0.028	-0.012	28.732	0.334	0.334	0.000	0.000	0.000	0.000
93	A	94	ALA	0	0.011	0.007	28.561	-0.394	-0.394	0.000	0.000	0.000	0.000
94	A	95	ARG	1	0.748	0.836	30.289	9.797	9.797	0.000	0.000	0.000	0.000
95	A	96	ARG	1	0.902	0.942	30.765	8.017	8.017	0.000	0.000	0.000	0.000
96	A	97	ALA	0	0.002	0.015	29.423	0.056	0.056	0.000	0.000	0.000	0.000
97	A	98	VAL	0	0.008	-0.012	31.379	0.312	0.312	0.000	0.000	0.000	0.000
98	A	99	GLY	0	0.011	0.003	33.108	-0.188	-0.188	0.000	0.000	0.000	0.000
99	A	100	GLU	-1	-0.841	-0.922	31.664	-9.099	-9.099	0.000	0.000	0.000	0.000
100	A	101	GLU	-1	-0.787	-0.834	29.055	-9.960	-9.960	0.000	0.000	0.000	0.000
101	A	102	SER	0	-0.023	-0.008	27.737	-0.430	-0.430	0.000	0.000	0.000	0.000
102	A	103	THR	0	0.016	-0.002	27.741	-0.379	-0.379	0.000	0.000	0.000	0.000
103	A	104	LEU	0	-0.074	-0.043	26.126	-0.421	-0.421	0.000	0.000	0.000	0.000
104	A	105	LEU	0	-0.051	-0.042	22.268	-0.602	-0.602	0.000	0.000	0.000	0.000
105	A	106	ASP	-1	-0.924	-0.949	22.993	-12.377	-12.377	0.000	0.000	0.000	0.000
106	A	107	ILE	0	-0.044	-0.019	24.114	-0.181	-0.181	0.000	0.000	0.000	0.000
107	A	108	GLU	-1	-0.919	-0.960	26.481	-9.235	-9.235	0.000	0.000	0.000	0.000
108	A	109	ASP	-1	-0.859	-0.943	30.046	-8.685	-8.685	0.000	0.000	0.000	0.000
109	A	110	GLY	0	-0.031	-0.007	32.840	0.145	0.145	0.000	0.000	0.000	0.000
110	A	111	GLY	0	0.033	0.019	29.623	0.124	0.124	0.000	0.000	0.000	0.000
111	A	112	PRO	0	-0.055	-0.025	27.207	0.061	0.061	0.000	0.000	0.000	0.000
112	A	113	LEU	0	0.030	0.014	25.702	-0.369	-0.369	0.000	0.000	0.000	0.000
113	A	114	LEU	0	-0.018	0.004	22.144	0.355	0.355	0.000	0.000	0.000	0.000
114	A	115	THR	0	0.010	-0.017	25.694	-0.122	-0.122	0.000	0.000	0.000	0.000
115	A	116	VAL	0	-0.037	-0.025	24.579	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	117	GLU	-1	-0.855	-0.885	27.459	-9.117	-9.117	0.000	0.000	0.000	0.000
117	A	118	ARG	1	0.817	0.876	24.125	11.984	11.984	0.000	0.000	0.000	0.000
118	A	119	VAL	0	0.021	0.017	29.362	0.120	0.120	0.000	0.000	0.000	0.000
119	A	120	ALA	0	-0.005	0.001	27.914	-0.125	-0.125	0.000	0.000	0.000	0.000
120	A	121	LEU	0	0.009	0.008	29.936	0.231	0.231	0.000	0.000	0.000	0.000
121	A	122	ASP	-1	-0.661	-0.806	30.791	-9.502	-9.502	0.000	0.000	0.000	0.000
122	A	123	ASN	0	-0.036	-0.047	32.384	-0.030	-0.030	0.000	0.000	0.000	0.000
123	A	124	SER	0	-0.062	-0.045	34.083	0.191	0.191	0.000	0.000	0.000	0.000
124	A	125	GLY	0	-0.044	-0.016	35.925	0.252	0.252	0.000	0.000	0.000	0.000
125	A	126	GLN	0	-0.037	-0.026	35.897	0.381	0.381	0.000	0.000	0.000	0.000
126	A	127	VAL	0	-0.003	-0.007	33.718	-0.357	-0.357	0.000	0.000	0.000	0.000
127	A	128	ILE	0	-0.038	-0.013	29.071	0.031	0.031	0.000	0.000	0.000	0.000
128	A	129	GLU	-1	-0.757	-0.857	26.734	-11.621	-11.621	0.000	0.000	0.000	0.000
129	A	130	LEU	0	-0.029	0.002	30.546	0.101	0.101	0.000	0.000	0.000	0.000
130	A	131	GLY	0	-0.012	-0.011	27.545	-0.214	-0.214	0.000	0.000	0.000	0.000
131	A	132	SER	0	-0.046	-0.051	28.394	0.251	0.251	0.000	0.000	0.000	0.000
132	A	133	HIS	0	-0.004	0.009	24.214	-0.087	-0.087	0.000	0.000	0.000	0.000
133	A	134	CYS	0	-0.039	-0.013	25.503	0.306	0.306	0.000	0.000	0.000	0.000
134	A	135	TYR	0	0.031	-0.006	19.735	-0.179	-0.179	0.000	0.000	0.000	0.000
135	A	136	ARG	1	0.864	0.922	20.008	13.523	13.523	0.000	0.000	0.000	0.000
136	A	137	PRO	0	-0.021	-0.009	20.501	-0.543	-0.543	0.000	0.000	0.000	0.000
137	A	138	ASP	-1	-0.845	-0.899	19.833	-13.264	-13.264	0.000	0.000	0.000	0.000
138	A	139	MET	0	-0.026	-0.006	14.123	-0.685	-0.685	0.000	0.000	0.000	0.000
139	A	140	TYR	0	-0.027	-0.015	15.795	-1.168	-1.168	0.000	0.000	0.000	0.000
140	A	141	ASN	0	-0.029	-0.018	17.770	1.117	1.117	0.000	0.000	0.000	0.000
141	A	142	PHE	0	-0.004	-0.006	18.713	-0.569	-0.569	0.000	0.000	0.000	0.000
142	A	143	GLU	-1	-0.917	-0.937	16.033	-15.536	-15.536	0.000	0.000	0.000	0.000
143	A	144	THR	0	-0.025	-0.023	20.447	0.076	0.076	0.000	0.000	0.000	0.000
144	A	145	THR	0	-0.019	-0.015	22.052	0.017	0.017	0.000	0.000	0.000	0.000
145	A	146	LEU	0	-0.017	0.001	24.410	0.070	0.070	0.000	0.000	0.000	0.000
146	A	147	VAL	0	0.013	0.003	26.772	0.061	0.061	0.000	0.000	0.000	0.000
147	A	148	ALA	0	-0.009	0.003	29.399	0.178	0.178	0.000	0.000	0.000	0.000
148	A	149	ARG	1	0.998	0.995	32.817	8.306	8.306	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:LYS)