FMO DATABASE

FMODB ID: ZYJJN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1271234.196102
FMO2-HF: Nuclear repulsion	1215390.460594
FMO2-HF: Total energy	-55843.735508
FMO2-MP2: Total energy	-56009.038289

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.
-61.24	-58.762	5.358	-3.896	-3.94	-0.011

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 : 0.989 / q_NPA : 0.968

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	0.008	0.011	3.184	0.595	2.463	-0.001	-0.831	-1.036	0.001
4	A	5	ASN	0	-0.030	0.003	2.386	5.459	6.044	5.360	-3.050	-2.895	-0.012
5	A	6	LEU	0	0.029	0.015	4.401	-0.331	-0.306	-0.001	-0.015	-0.009	0.000
6	A	7	ASP	-1	-0.916	-0.954	6.269	-37.373	-37.373	0.000	0.000	0.000	0.000
7	A	8	PRO	0	-0.002	0.002	8.598	2.454	2.454	0.000	0.000	0.000	0.000
8	A	9	LYS	1	0.929	0.971	10.970	23.840	23.840	0.000	0.000	0.000	0.000
9	A	10	THR	0	0.013	-0.004	14.919	0.728	0.728	0.000	0.000	0.000	0.000
10	A	11	ARG	1	0.996	1.021	18.375	12.359	12.359	0.000	0.000	0.000	0.000
11	A	12	VAL	0	0.033	0.009	21.820	0.121	0.121	0.000	0.000	0.000	0.000
12	A	13	LEU	0	-0.094	-0.046	25.125	0.182	0.182	0.000	0.000	0.000	0.000
13	A	14	GLU	-1	-0.825	-0.925	27.842	-8.846	-8.846	0.000	0.000	0.000	0.000
14	A	15	HIS	0	-0.044	-0.043	29.009	-0.204	-0.204	0.000	0.000	0.000	0.000
15	A	16	ARG	1	0.916	0.972	31.434	8.619	8.619	0.000	0.000	0.000	0.000
16	A	17	LEU	0	0.050	0.036	35.077	-0.116	-0.116	0.000	0.000	0.000	0.000
17	A	18	LEU	0	-0.077	-0.034	36.482	0.158	0.158	0.000	0.000	0.000	0.000
18	A	19	ALA	0	0.033	0.025	39.899	-0.044	-0.044	0.000	0.000	0.000	0.000
19	A	20	ALA	0	-0.018	-0.001	40.545	-0.071	-0.071	0.000	0.000	0.000	0.000
20	A	21	SER	0	0.052	0.020	40.956	0.219	0.219	0.000	0.000	0.000	0.000
21	A	22	SER	0	0.047	0.000	42.864	-0.067	-0.067	0.000	0.000	0.000	0.000
22	A	23	ALA	0	0.013	0.016	41.036	-0.035	-0.035	0.000	0.000	0.000	0.000
23	A	24	ILE	0	-0.012	-0.002	36.370	-0.101	-0.101	0.000	0.000	0.000	0.000
24	A	25	ALA	0	0.029	0.011	39.152	-0.148	-0.148	0.000	0.000	0.000	0.000
25	A	26	GLU	-1	-0.952	-0.968	41.534	-7.133	-7.133	0.000	0.000	0.000	0.000
26	A	27	LYS	1	0.897	0.941	36.023	8.315	8.315	0.000	0.000	0.000	0.000
27	A	28	LEU	0	-0.012	-0.017	34.586	-0.192	-0.192	0.000	0.000	0.000	0.000
28	A	29	GLY	0	-0.011	0.015	38.026	-0.070	-0.070	0.000	0.000	0.000	0.000
29	A	30	VAL	0	-0.073	-0.029	39.962	0.041	0.041	0.000	0.000	0.000	0.000
30	A	31	SER	0	0.012	0.011	42.711	0.167	0.167	0.000	0.000	0.000	0.000
31	A	32	ALA	0	-0.031	-0.036	44.544	-0.136	-0.136	0.000	0.000	0.000	0.000
32	A	33	GLY	0	-0.043	-0.024	44.694	0.132	0.132	0.000	0.000	0.000	0.000
33	A	34	ASP	-1	-0.828	-0.918	42.079	-7.231	-7.231	0.000	0.000	0.000	0.000
34	A	35	GLU	-1	-0.950	-0.979	39.301	-7.914	-7.914	0.000	0.000	0.000	0.000
35	A	36	VAL	0	-0.004	0.010	36.433	-0.166	-0.166	0.000	0.000	0.000	0.000
36	A	37	LEU	0	-0.014	-0.001	30.635	0.058	0.058	0.000	0.000	0.000	0.000
37	A	38	LEU	0	-0.025	0.002	31.649	-0.170	-0.170	0.000	0.000	0.000	0.000
38	A	39	ILE	0	-0.002	-0.013	26.302	-0.148	-0.148	0.000	0.000	0.000	0.000
39	A	40	ARG	1	0.927	0.959	27.474	9.921	9.921	0.000	0.000	0.000	0.000
40	A	41	ARG	1	0.906	0.951	21.059	13.274	13.274	0.000	0.000	0.000	0.000
41	A	42	LEU	0	0.029	0.028	21.242	0.210	0.210	0.000	0.000	0.000	0.000
42	A	43	ARG	1	0.864	0.926	15.319	16.633	16.633	0.000	0.000	0.000	0.000
43	A	44	SER	0	0.029	0.002	16.402	0.877	0.877	0.000	0.000	0.000	0.000
44	A	45	THR	0	0.005	-0.001	10.875	-1.189	-1.189	0.000	0.000	0.000	0.000
45	A	46	GLY	0	-0.015	-0.015	11.791	0.314	0.314	0.000	0.000	0.000	0.000
46	A	47	ASP	-1	-0.922	-0.964	12.388	-17.802	-17.802	0.000	0.000	0.000	0.000
47	A	48	ILE	0	-0.010	0.002	14.080	1.057	1.057	0.000	0.000	0.000	0.000
48	A	49	PRO	0	0.008	0.018	16.690	-0.816	-0.816	0.000	0.000	0.000	0.000
49	A	50	VAL	0	-0.029	-0.020	15.622	0.063	0.063	0.000	0.000	0.000	0.000
50	A	51	ALA	0	0.013	-0.013	18.901	0.494	0.494	0.000	0.000	0.000	0.000
51	A	52	ILE	0	0.009	0.019	21.485	-0.243	-0.243	0.000	0.000	0.000	0.000
52	A	53	LEU	0	-0.078	-0.042	19.979	0.047	0.047	0.000	0.000	0.000	0.000
53	A	54	GLU	-1	-0.875	-0.939	24.556	-9.503	-9.503	0.000	0.000	0.000	0.000
54	A	55	ASN	0	-0.046	-0.048	25.598	-0.421	-0.421	0.000	0.000	0.000	0.000
55	A	56	TYR	0	0.013	0.013	28.977	0.255	0.255	0.000	0.000	0.000	0.000
56	A	57	LEU	0	-0.004	-0.011	28.686	-0.202	-0.202	0.000	0.000	0.000	0.000
57	A	58	PRO	0	0.051	0.027	32.637	0.247	0.247	0.000	0.000	0.000	0.000
58	A	59	PRO	0	0.052	0.016	35.342	-0.192	-0.192	0.000	0.000	0.000	0.000
59	A	60	ALA	0	-0.037	-0.012	35.844	-0.062	-0.062	0.000	0.000	0.000	0.000
60	A	61	PHE	0	-0.014	-0.017	31.043	-0.192	-0.192	0.000	0.000	0.000	0.000
61	A	62	ASN	0	-0.053	-0.032	31.970	-0.422	-0.422	0.000	0.000	0.000	0.000
62	A	63	ASP	-1	-0.788	-0.902	32.770	-9.663	-9.663	0.000	0.000	0.000	0.000
63	A	64	VAL	0	-0.068	-0.021	26.712	-0.308	-0.308	0.000	0.000	0.000	0.000
64	A	65	SER	0	0.025	0.018	28.138	0.067	0.067	0.000	0.000	0.000	0.000
65	A	66	LEU	0	0.016	-0.016	26.906	-0.394	-0.394	0.000	0.000	0.000	0.000
66	A	67	ASP	-1	-0.771	-0.863	25.341	-13.019	-13.019	0.000	0.000	0.000	0.000
67	A	68	GLU	-1	-0.811	-0.898	23.578	-12.226	-12.226	0.000	0.000	0.000	0.000
68	A	69	LEU	0	-0.087	-0.045	22.150	-0.622	-0.622	0.000	0.000	0.000	0.000
69	A	70	GLU	-1	-0.972	-0.977	21.091	-13.299	-13.299	0.000	0.000	0.000	0.000
70	A	71	LYS	1	0.789	0.880	19.047	12.414	12.414	0.000	0.000	0.000	0.000
71	A	72	GLY	0	0.010	0.017	17.559	-1.079	-1.079	0.000	0.000	0.000	0.000
72	A	73	GLY	0	-0.050	-0.016	18.535	0.456	0.456	0.000	0.000	0.000	0.000
73	A	74	LEU	0	0.026	0.004	19.799	0.260	0.260	0.000	0.000	0.000	0.000
74	A	75	TYR	0	-0.016	-0.063	20.930	0.252	0.252	0.000	0.000	0.000	0.000
75	A	76	ASP	-1	-0.834	-0.884	17.799	-17.104	-17.104	0.000	0.000	0.000	0.000
76	A	77	ALA	0	0.048	0.031	21.106	0.337	0.337	0.000	0.000	0.000	0.000
77	A	78	LEU	0	-0.008	-0.006	24.497	0.430	0.430	0.000	0.000	0.000	0.000
78	A	79	ARG	1	0.921	0.937	18.899	15.704	15.704	0.000	0.000	0.000	0.000
79	A	80	SER	0	-0.047	-0.008	24.185	0.190	0.190	0.000	0.000	0.000	0.000
80	A	81	ARG	1	0.755	0.871	26.238	11.140	11.140	0.000	0.000	0.000	0.000
81	A	82	GLY	0	-0.023	-0.003	28.140	0.382	0.382	0.000	0.000	0.000	0.000
82	A	83	VAL	0	-0.020	0.008	28.210	0.239	0.239	0.000	0.000	0.000	0.000
83	A	84	VAL	0	-0.040	-0.037	24.519	-0.601	-0.601	0.000	0.000	0.000	0.000
84	A	85	LEU	0	-0.040	-0.019	24.046	0.356	0.356	0.000	0.000	0.000	0.000
85	A	86	LYS	1	0.889	0.962	26.847	10.160	10.160	0.000	0.000	0.000	0.000
86	A	87	ILE	0	-0.010	-0.010	29.162	-0.076	-0.076	0.000	0.000	0.000	0.000
87	A	88	ALA	0	0.017	0.009	26.588	-0.058	-0.058	0.000	0.000	0.000	0.000
88	A	89	ASN	0	-0.028	0.007	28.620	-0.085	-0.085	0.000	0.000	0.000	0.000
89	A	90	GLN	0	0.033	0.000	23.832	-0.331	-0.331	0.000	0.000	0.000	0.000
90	A	91	LYS	1	0.959	0.985	29.190	8.697	8.697	0.000	0.000	0.000	0.000
91	A	92	ILE	0	0.017	0.011	25.333	-0.105	-0.105	0.000	0.000	0.000	0.000
92	A	93	GLY	0	0.002	0.000	28.752	0.328	0.328	0.000	0.000	0.000	0.000
93	A	94	ALA	0	-0.019	-0.006	28.582	-0.405	-0.405	0.000	0.000	0.000	0.000
94	A	95	ARG	1	0.779	0.863	30.310	9.824	9.824	0.000	0.000	0.000	0.000
95	A	96	ARG	1	0.915	0.955	30.784	7.950	7.950	0.000	0.000	0.000	0.000
96	A	97	ALA	0	0.002	0.011	29.448	0.049	0.049	0.000	0.000	0.000	0.000
97	A	98	VAL	0	0.010	-0.008	31.393	0.308	0.308	0.000	0.000	0.000	0.000
98	A	99	GLY	0	0.008	0.000	33.116	-0.192	-0.192	0.000	0.000	0.000	0.000
99	A	100	GLU	-1	-0.855	-0.940	31.641	-8.997	-8.997	0.000	0.000	0.000	0.000
100	A	101	GLU	-1	-0.796	-0.854	29.059	-9.973	-9.973	0.000	0.000	0.000	0.000
101	A	102	SER	0	-0.007	-0.003	27.744	-0.405	-0.405	0.000	0.000	0.000	0.000
102	A	103	THR	0	0.031	0.017	27.749	-0.361	-0.361	0.000	0.000	0.000	0.000
103	A	104	LEU	0	-0.074	-0.041	26.128	-0.408	-0.408	0.000	0.000	0.000	0.000
104	A	105	LEU	0	-0.055	-0.044	22.325	-0.592	-0.592	0.000	0.000	0.000	0.000
105	A	106	ASP	-1	-0.937	-0.957	23.000	-12.198	-12.198	0.000	0.000	0.000	0.000
106	A	107	ILE	0	-0.046	-0.018	24.169	-0.167	-0.167	0.000	0.000	0.000	0.000
107	A	108	GLU	-1	-0.914	-0.960	26.494	-9.125	-9.125	0.000	0.000	0.000	0.000
108	A	109	ASP	-1	-0.896	-0.960	30.061	-8.557	-8.557	0.000	0.000	0.000	0.000
109	A	110	GLY	0	-0.035	-0.007	32.854	0.137	0.137	0.000	0.000	0.000	0.000
110	A	111	GLY	0	0.031	0.011	29.642	0.112	0.112	0.000	0.000	0.000	0.000
111	A	112	PRO	0	-0.055	-0.023	27.158	0.062	0.062	0.000	0.000	0.000	0.000
112	A	113	LEU	0	0.016	0.008	25.940	-0.379	-0.379	0.000	0.000	0.000	0.000
113	A	114	LEU	0	-0.012	0.006	22.412	0.349	0.349	0.000	0.000	0.000	0.000
114	A	115	THR	0	-0.042	-0.034	25.710	-0.060	-0.060	0.000	0.000	0.000	0.000
115	A	116	VAL	0	0.003	-0.013	24.538	-0.023	-0.023	0.000	0.000	0.000	0.000
116	A	117	GLU	-1	-0.889	-0.901	27.473	-9.424	-9.424	0.000	0.000	0.000	0.000
117	A	118	ARG	1	0.853	0.910	23.831	12.185	12.185	0.000	0.000	0.000	0.000
118	A	119	VAL	0	0.015	0.018	29.346	0.129	0.129	0.000	0.000	0.000	0.000
119	A	120	ALA	0	-0.008	-0.001	27.876	-0.132	-0.132	0.000	0.000	0.000	0.000
120	A	121	LEU	0	0.003	0.007	29.919	0.232	0.232	0.000	0.000	0.000	0.000
121	A	122	ASP	-1	-0.694	-0.836	30.583	-9.662	-9.662	0.000	0.000	0.000	0.000
122	A	123	ASN	0	-0.042	-0.054	32.011	0.085	0.085	0.000	0.000	0.000	0.000
123	A	124	SER	0	-0.080	-0.040	33.662	0.205	0.205	0.000	0.000	0.000	0.000
124	A	125	GLY	0	-0.029	-0.013	35.585	0.255	0.255	0.000	0.000	0.000	0.000
125	A	126	GLN	0	-0.024	-0.011	35.764	0.408	0.408	0.000	0.000	0.000	0.000
126	A	127	VAL	0	0.004	-0.001	33.655	-0.363	-0.363	0.000	0.000	0.000	0.000
127	A	128	ILE	0	-0.040	-0.018	28.976	0.020	0.020	0.000	0.000	0.000	0.000
128	A	129	GLU	-1	-0.793	-0.888	26.859	-11.589	-11.589	0.000	0.000	0.000	0.000
129	A	130	LEU	0	-0.038	-0.006	30.547	0.119	0.119	0.000	0.000	0.000	0.000
130	A	131	GLY	0	0.003	-0.001	27.541	-0.212	-0.212	0.000	0.000	0.000	0.000
131	A	132	SER	0	-0.051	-0.039	28.412	0.247	0.247	0.000	0.000	0.000	0.000
132	A	133	HIS	0	0.010	0.007	24.186	-0.059	-0.059	0.000	0.000	0.000	0.000
133	A	134	CYS	0	-0.039	-0.017	25.547	0.230	0.230	0.000	0.000	0.000	0.000
134	A	135	TYR	0	0.021	-0.006	19.804	-0.206	-0.206	0.000	0.000	0.000	0.000
135	A	136	ARG	1	0.899	0.941	20.227	13.628	13.628	0.000	0.000	0.000	0.000
136	A	137	PRO	0	-0.030	-0.012	20.520	-0.550	-0.550	0.000	0.000	0.000	0.000
137	A	138	ASP	-1	-0.840	-0.905	19.837	-13.240	-13.240	0.000	0.000	0.000	0.000
138	A	139	MET	0	-0.026	-0.004	14.131	-0.578	-0.578	0.000	0.000	0.000	0.000
139	A	140	TYR	0	-0.016	-0.008	15.815	-1.145	-1.145	0.000	0.000	0.000	0.000
140	A	141	ASN	0	-0.045	-0.028	17.800	1.084	1.084	0.000	0.000	0.000	0.000
141	A	142	PHE	0	0.000	-0.005	18.737	-0.559	-0.559	0.000	0.000	0.000	0.000
142	A	143	GLU	-1	-0.918	-0.941	16.203	-15.711	-15.711	0.000	0.000	0.000	0.000
143	A	144	THR	0	-0.045	-0.032	20.475	-0.010	-0.010	0.000	0.000	0.000	0.000
144	A	145	THR	0	0.006	-0.001	22.144	-0.042	-0.042	0.000	0.000	0.000	0.000
145	A	146	LEU	0	-0.016	0.003	24.423	0.068	0.068	0.000	0.000	0.000	0.000
146	A	147	VAL	0	0.014	0.003	26.803	0.065	0.065	0.000	0.000	0.000	0.000
147	A	148	ALA	0	-0.011	0.002	29.459	0.180	0.180	0.000	0.000	0.000	0.000
148	A	149	ARG	1	0.991	0.991	32.872	8.412	8.412	0.000	0.000	0.000	0.000

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