FMO DATABASE

FMODB ID: VKQ91

Calculation Name: 2P4V-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2P4V

Chain ID: A

ChEMBL ID:

UniProt ID: P30128

Base Structure: X-ray

Registration Date: 2023-09-27

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	156
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1437308.109947
FMO2-HF: Nuclear repulsion	1373439.142001
FMO2-HF: Total energy	-63868.967947
FMO2-MP2: Total energy	-64056.648192

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:1:MET)

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

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.
-8.478	-6.351	0.155	-0.722	-1.56	-0.003

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.033 / q_NPA : 0.024

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	3	THR	0	0.000	-0.026	3.844	-0.846	0.168	0.039	-0.084	-0.968	0.002
4	A	4	PRO	0	0.004	0.001	5.829	0.021	0.021	0.000	0.000	0.000	0.000
5	A	5	LEU	0	-0.055	-0.011	9.381	-0.034	-0.034	0.000	0.000	0.000	0.000
6	A	6	VAL	0	0.007	-0.002	11.361	-0.080	-0.080	0.000	0.000	0.000	0.000
7	A	7	THR	0	0.054	0.032	14.145	0.030	0.030	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.870	0.926	17.422	-0.022	-0.022	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.804	-0.912	20.648	-0.069	-0.069	0.000	0.000	0.000	0.000
10	A	10	GLY	0	0.014	-0.005	17.782	0.019	0.019	0.000	0.000	0.000	0.000
11	A	11	TYR	0	-0.003	-0.007	17.622	0.033	0.033	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.901	-0.955	19.646	0.078	0.078	0.000	0.000	0.000	0.000
13	A	13	LYN	0	-0.021	-0.001	18.920	0.013	0.013	0.000	0.000	0.000	0.000
14	A	14	LEU	0	0.048	0.041	14.358	0.024	0.024	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.831	0.880	18.589	-0.323	-0.323	0.000	0.000	0.000	0.000
16	A	16	GLN	0	-0.012	0.004	21.769	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.793	-0.866	17.827	0.278	0.278	0.000	0.000	0.000	0.000
18	A	18	LEU	0	0.033	0.019	19.120	-0.006	-0.006	0.000	0.000	0.000	0.000
19	A	19	ASN	0	-0.076	-0.052	21.560	-0.015	-0.015	0.000	0.000	0.000	0.000
20	A	20	TYR	0	0.027	0.014	23.776	-0.005	-0.005	0.000	0.000	0.000	0.000
21	A	21	LEU	0	-0.006	-0.010	19.208	-0.005	-0.005	0.000	0.000	0.000	0.000
22	A	22	TRP	0	-0.042	-0.028	23.786	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.847	0.923	25.720	-0.236	-0.236	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.881	-0.933	27.706	0.106	0.106	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.809	-0.888	24.525	0.138	0.138	0.000	0.000	0.000	0.000
26	A	26	ARG	1	0.807	0.870	24.606	-0.304	-0.304	0.000	0.000	0.000	0.000
27	A	27	PRO	0	-0.041	-0.008	27.288	-0.006	-0.006	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.879	-0.929	29.652	0.096	0.096	0.000	0.000	0.000	0.000
29	A	29	VAL	0	-0.012	-0.015	25.739	-0.005	-0.005	0.000	0.000	0.000	0.000
30	A	30	THR	0	-0.077	-0.066	29.082	0.003	0.003	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.997	1.006	30.717	-0.146	-0.146	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.879	0.944	31.687	-0.094	-0.094	0.000	0.000	0.000	0.000
33	A	33	VAL	0	-0.054	-0.038	29.125	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	34	THR	0	-0.035	-0.016	32.500	0.000	0.000	0.000	0.000	0.000	0.000
35	A	35	TRP	0	0.051	0.020	35.676	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	36	ALA	0	-0.029	-0.012	34.298	-0.005	-0.005	0.000	0.000	0.000	0.000
37	A	37	ALA	0	-0.036	-0.012	35.862	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	38	SER	0	-0.020	-0.016	37.444	-0.004	-0.004	0.000	0.000	0.000	0.000
39	A	39	LEU	0	-0.030	-0.010	39.030	-0.005	-0.005	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.037	0.031	39.782	-0.007	-0.007	0.000	0.000	0.000	0.000
41	A	41	ASH	0	-0.109	-0.084	38.919	0.010	0.010	0.000	0.000	0.000	0.000
42	A	42	ARG	1	0.924	0.949	34.107	-0.119	-0.119	0.000	0.000	0.000	0.000
43	A	43	SER	0	0.014	-0.001	33.518	0.003	0.003	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.837	-0.881	34.081	0.060	0.060	0.000	0.000	0.000	0.000
45	A	45	ASN	0	0.037	0.038	35.084	-0.007	-0.007	0.000	0.000	0.000	0.000
46	A	46	ALA	0	0.095	0.030	31.746	0.009	0.009	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.782	-0.880	30.684	0.094	0.094	0.000	0.000	0.000	0.000
48	A	48	TYR	0	0.022	0.016	31.078	0.022	0.022	0.000	0.000	0.000	0.000
49	A	49	GLN	0	-0.052	-0.027	28.539	0.016	0.016	0.000	0.000	0.000	0.000
50	A	50	TYR	0	0.012	0.011	24.508	0.023	0.023	0.000	0.000	0.000	0.000
51	A	51	ASN	0	0.002	-0.025	25.814	0.018	0.018	0.000	0.000	0.000	0.000
52	A	52	LYS	1	0.930	0.973	26.122	-0.179	-0.179	0.000	0.000	0.000	0.000
53	A	53	LYS	1	0.801	0.891	19.209	-0.121	-0.121	0.000	0.000	0.000	0.000
54	A	54	ARG	1	0.928	0.966	21.735	-0.095	-0.095	0.000	0.000	0.000	0.000
55	A	55	LEU	0	0.048	0.028	22.162	0.019	0.019	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.945	0.961	20.425	-0.237	-0.237	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.874	-0.941	17.508	0.260	0.260	0.000	0.000	0.000	0.000
58	A	58	ILE	0	0.014	0.023	17.678	0.057	0.057	0.000	0.000	0.000	0.000
59	A	59	ASP	-1	-0.754	-0.858	19.315	0.410	0.410	0.000	0.000	0.000	0.000
60	A	60	ARG	1	0.849	0.925	14.941	-0.501	-0.501	0.000	0.000	0.000	0.000
61	A	61	ARG	1	0.748	0.819	12.907	-0.230	-0.230	0.000	0.000	0.000	0.000
62	A	62	VAL	0	0.065	0.041	15.584	0.054	0.054	0.000	0.000	0.000	0.000
63	A	63	ARG	1	0.934	0.981	14.245	-0.946	-0.946	0.000	0.000	0.000	0.000
64	A	64	TYR	0	-0.121	-0.087	7.860	0.331	0.331	0.000	0.000	0.000	0.000
65	A	65	LEU	0	0.060	0.021	13.382	0.114	0.114	0.000	0.000	0.000	0.000
66	A	66	THR	0	-0.023	-0.013	15.328	-0.011	-0.011	0.000	0.000	0.000	0.000
67	A	67	LYS	1	0.959	0.992	10.021	-2.367	-2.367	0.000	0.000	0.000	0.000
68	A	68	CYS	0	-0.053	-0.023	10.478	0.191	0.191	0.000	0.000	0.000	0.000
69	A	69	MET	0	0.034	0.051	13.639	-0.142	-0.142	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.919	-0.958	16.972	0.796	0.796	0.000	0.000	0.000	0.000
71	A	71	ASN	0	-0.076	-0.049	12.614	0.040	0.040	0.000	0.000	0.000	0.000
72	A	72	LEU	0	-0.049	-0.001	11.388	0.044	0.044	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.932	0.963	12.903	-0.262	-0.262	0.000	0.000	0.000	0.000
74	A	74	ILE	0	0.027	0.009	14.273	-0.082	-0.082	0.000	0.000	0.000	0.000
75	A	75	VAL	0	-0.072	-0.042	14.306	0.005	0.005	0.000	0.000	0.000	0.000
76	A	76	ASP	-1	-0.834	-0.904	17.459	-0.014	-0.014	0.000	0.000	0.000	0.000
77	A	77	TYR	0	-0.057	-0.017	20.262	0.011	0.011	0.000	0.000	0.000	0.000
78	A	78	SER	0	0.017	0.013	21.980	-0.020	-0.020	0.000	0.000	0.000	0.000
79	A	79	PRO	0	0.070	0.016	24.602	-0.007	-0.007	0.000	0.000	0.000	0.000
80	A	80	GLN	0	-0.046	-0.002	26.820	-0.011	-0.011	0.000	0.000	0.000	0.000
81	A	81	GLN	0	-0.030	-0.025	23.239	0.006	0.006	0.000	0.000	0.000	0.000
82	A	82	GLU	-1	-0.799	-0.905	23.356	-0.233	-0.233	0.000	0.000	0.000	0.000
83	A	83	GLY	0	-0.016	0.002	25.118	0.003	0.003	0.000	0.000	0.000	0.000
84	A	84	LYS	1	0.742	0.841	20.030	0.323	0.323	0.000	0.000	0.000	0.000
85	A	85	VAL	0	0.052	0.034	16.579	0.020	0.020	0.000	0.000	0.000	0.000
86	A	86	PHE	0	-0.081	-0.037	15.268	-0.011	-0.011	0.000	0.000	0.000	0.000
87	A	87	PHE	0	-0.016	-0.020	11.701	-0.079	-0.079	0.000	0.000	0.000	0.000
88	A	88	GLY	0	0.068	0.041	15.888	0.053	0.053	0.000	0.000	0.000	0.000
89	A	89	ALA	0	0.020	0.017	17.548	0.051	0.051	0.000	0.000	0.000	0.000
90	A	90	TRP	0	-0.044	-0.028	18.760	-0.074	-0.074	0.000	0.000	0.000	0.000
91	A	91	VAL	0	0.012	0.008	18.715	0.019	0.019	0.000	0.000	0.000	0.000
92	A	92	GLU	-1	-0.920	-0.952	21.141	-0.308	-0.308	0.000	0.000	0.000	0.000
93	A	93	ILE	0	-0.075	-0.038	20.092	-0.016	-0.016	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.858	-0.934	23.315	-0.294	-0.294	0.000	0.000	0.000	0.000
95	A	95	ASN	0	-0.018	-0.023	24.870	-0.012	-0.012	0.000	0.000	0.000	0.000
96	A	96	ASP	-1	-0.871	-0.933	26.629	-0.318	-0.318	0.000	0.000	0.000	0.000
97	A	97	ASP	-1	-0.979	-0.978	29.651	-0.291	-0.291	0.000	0.000	0.000	0.000
98	A	98	GLY	0	-0.006	0.008	29.922	0.017	0.017	0.000	0.000	0.000	0.000
99	A	99	VAL	0	-0.086	-0.052	24.663	0.000	0.000	0.000	0.000	0.000	0.000
100	A	100	THR	0	0.028	0.019	25.762	-0.023	-0.023	0.000	0.000	0.000	0.000
101	A	101	HIS	0	-0.036	-0.027	20.598	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	102	ARG	1	1.016	1.023	22.042	0.264	0.264	0.000	0.000	0.000	0.000
103	A	103	PHE	0	0.012	-0.023	16.342	-0.049	-0.049	0.000	0.000	0.000	0.000
104	A	104	ARG	1	0.843	0.931	17.928	0.265	0.265	0.000	0.000	0.000	0.000
105	A	105	ILE	0	-0.057	-0.015	11.848	-0.065	-0.065	0.000	0.000	0.000	0.000
106	A	106	VAL	0	-0.008	0.000	13.246	0.098	0.098	0.000	0.000	0.000	0.000
107	A	107	GLY	0	0.006	-0.002	9.874	-0.214	-0.214	0.000	0.000	0.000	0.000
108	A	108	TYR	0	0.003	-0.022	5.735	-0.017	-0.017	0.000	0.000	0.000	0.000
109	A	109	ASP	-1	-0.863	-0.909	9.458	1.406	1.406	0.000	0.000	0.000	0.000
110	A	110	GLU	-1	-0.820	-0.904	10.703	0.285	0.285	0.000	0.000	0.000	0.000
111	A	111	ILE	0	-0.005	0.056	11.696	-0.056	-0.056	0.000	0.000	0.000	0.000
112	A	112	PHE	0	0.026	-0.017	14.510	0.009	0.009	0.000	0.000	0.000	0.000
113	A	113	GLY	0	-0.007	0.003	17.066	-0.026	-0.026	0.000	0.000	0.000	0.000
114	A	114	ARG	1	0.873	0.947	19.687	0.057	0.057	0.000	0.000	0.000	0.000
115	A	115	LYS	1	0.919	0.966	19.889	0.069	0.069	0.000	0.000	0.000	0.000
116	A	116	ASP	-1	-0.717	-0.868	16.701	-0.294	-0.294	0.000	0.000	0.000	0.000
117	A	117	TYR	0	-0.080	-0.059	15.947	0.011	0.011	0.000	0.000	0.000	0.000
118	A	118	ILE	0	0.035	0.023	12.213	-0.089	-0.089	0.000	0.000	0.000	0.000
119	A	119	SER	0	0.029	0.027	8.145	0.092	0.092	0.000	0.000	0.000	0.000
120	A	120	ILE	0	0.049	0.011	7.204	-0.175	-0.175	0.000	0.000	0.000	0.000
121	A	121	ASP	-1	-0.887	-0.889	3.273	-7.340	-6.306	0.117	-0.636	-0.516	-0.005
122	A	122	SER	0	-0.045	-0.043	5.146	-0.615	-0.536	-0.001	-0.002	-0.076	0.000
123	A	123	PRO	0	0.073	0.015	7.876	0.179	0.179	0.000	0.000	0.000	0.000
124	A	124	MET	0	0.061	0.045	10.150	0.079	0.079	0.000	0.000	0.000	0.000
125	A	125	ALA	0	0.014	0.012	9.684	0.136	0.136	0.000	0.000	0.000	0.000
126	A	126	ARG	1	0.827	0.899	5.350	2.952	2.952	0.000	0.000	0.000	0.000
127	A	127	ALA	0	-0.004	0.012	10.695	0.143	0.143	0.000	0.000	0.000	0.000
128	A	128	LEU	0	0.045	0.013	14.220	0.096	0.096	0.000	0.000	0.000	0.000
129	A	129	LEU	0	-0.039	0.011	11.072	0.081	0.081	0.000	0.000	0.000	0.000
130	A	130	LYS	1	0.890	0.919	14.277	0.614	0.614	0.000	0.000	0.000	0.000
131	A	131	LYS	1	0.872	0.944	16.941	0.715	0.715	0.000	0.000	0.000	0.000
132	A	132	GLU	-1	-0.773	-0.881	20.324	-0.335	-0.335	0.000	0.000	0.000	0.000
133	A	133	VAL	0	0.010	-0.014	23.597	-0.022	-0.022	0.000	0.000	0.000	0.000
134	A	134	GLY	0	0.050	0.050	25.778	0.009	0.009	0.000	0.000	0.000	0.000
135	A	135	ASP	-1	-0.920	-0.951	21.888	-0.469	-0.469	0.000	0.000	0.000	0.000
136	A	136	LEU	0	0.004	0.005	23.615	-0.011	-0.011	0.000	0.000	0.000	0.000
137	A	137	ALA	0	-0.048	-0.019	18.030	-0.031	-0.031	0.000	0.000	0.000	0.000
138	A	138	VAL	0	0.012	0.006	17.370	0.017	0.017	0.000	0.000	0.000	0.000
139	A	139	VAL	0	-0.047	-0.037	14.763	-0.117	-0.117	0.000	0.000	0.000	0.000
140	A	140	ASN	0	-0.041	-0.012	14.130	0.001	0.001	0.000	0.000	0.000	0.000
141	A	141	THR	0	-0.029	-0.029	13.628	-0.168	-0.168	0.000	0.000	0.000	0.000
142	A	142	PRO	0	0.010	-0.003	13.501	0.085	0.085	0.000	0.000	0.000	0.000
143	A	143	ALA	0	-0.002	0.008	16.611	0.040	0.040	0.000	0.000	0.000	0.000
144	A	144	GLY	0	-0.016	-0.002	17.732	0.053	0.053	0.000	0.000	0.000	0.000
145	A	145	GLU	-1	-0.911	-0.939	17.899	-0.575	-0.575	0.000	0.000	0.000	0.000
146	A	146	ALA	0	-0.013	-0.019	18.716	0.035	0.035	0.000	0.000	0.000	0.000
147	A	147	SER	0	0.011	0.006	19.952	-0.041	-0.041	0.000	0.000	0.000	0.000
148	A	148	TRP	0	-0.018	-0.026	18.832	-0.021	-0.021	0.000	0.000	0.000	0.000
149	A	149	TYR	0	0.038	0.026	22.202	-0.008	-0.008	0.000	0.000	0.000	0.000
150	A	150	VAL	0	-0.074	-0.035	20.768	-0.009	-0.009	0.000	0.000	0.000	0.000
151	A	151	ASN	0	-0.036	-0.018	23.281	0.033	0.033	0.000	0.000	0.000	0.000
152	A	152	ALA	0	0.047	0.026	25.438	0.016	0.016	0.000	0.000	0.000	0.000
153	A	153	ILE	0	-0.059	-0.038	21.689	-0.028	-0.028	0.000	0.000	0.000	0.000
154	A	154	GLU	-1	-0.907	-0.939	23.833	-0.207	-0.207	0.000	0.000	0.000	0.000
155	A	155	TYR	0	-0.047	-0.045	19.957	-0.027	-0.027	0.000	0.000	0.000	0.000
156	A	156	VAL	0	-0.037	-0.020	24.277	0.020	0.020	0.000	0.000	0.000	0.000

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