FMO DATABASE

FMODB ID: YNV42

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1436883.394779
FMO2-HF: Nuclear repulsion	1373016.658626
FMO2-HF: Total energy	-63866.736152
FMO2-MP2: Total energy	-64054.694088

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.
-10.063	-7.753	2.351	-1.703	-2.956	-0.022

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 : -0.013 / q_NPA : -0.006

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	-0.058	-0.062	3.844	-0.726	0.142	0.046	0.012	-0.925	0.002
4	A	4	PRO	0	0.016	0.003	5.824	0.136	0.136	0.000	0.000	0.000	0.000
5	A	5	LEU	0	-0.037	-0.004	9.383	-0.025	-0.025	0.000	0.000	0.000	0.000
6	A	6	VAL	0	0.012	0.002	11.350	-0.046	-0.046	0.000	0.000	0.000	0.000
7	A	7	THR	0	0.023	0.019	14.135	0.001	0.001	0.000	0.000	0.000	0.000
8	A	8	ARG	1	1.004	1.003	17.409	-0.058	-0.058	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.828	-0.929	20.638	0.000	0.000	0.000	0.000	0.000	0.000
10	A	10	GLY	0	-0.009	-0.012	17.782	0.013	0.013	0.000	0.000	0.000	0.000
11	A	11	TYR	0	0.025	0.006	18.101	0.032	0.032	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.927	-0.969	19.574	0.115	0.115	0.000	0.000	0.000	0.000
13	A	13	LYN	0	0.005	0.014	19.453	0.001	0.001	0.000	0.000	0.000	0.000
14	A	14	LEU	0	0.047	0.037	14.770	0.011	0.011	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.926	0.944	18.888	-0.243	-0.243	0.000	0.000	0.000	0.000
16	A	16	GLN	0	-0.029	-0.010	22.027	-0.007	-0.007	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.830	-0.900	17.614	0.289	0.289	0.000	0.000	0.000	0.000
18	A	18	LEU	0	0.025	0.014	19.129	-0.008	-0.008	0.000	0.000	0.000	0.000
19	A	19	ASN	0	-0.051	-0.023	21.714	0.002	0.002	0.000	0.000	0.000	0.000
20	A	20	TYR	0	0.057	0.028	24.347	-0.007	-0.007	0.000	0.000	0.000	0.000
21	A	21	LEU	0	0.000	-0.015	19.533	-0.007	-0.007	0.000	0.000	0.000	0.000
22	A	22	TRP	0	-0.010	-0.012	23.899	-0.010	-0.010	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.852	0.922	25.782	-0.193	-0.193	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.903	-0.944	27.828	0.096	0.096	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.924	-0.955	25.223	0.124	0.124	0.000	0.000	0.000	0.000
26	A	26	ARG	1	0.837	0.902	23.997	-0.229	-0.229	0.000	0.000	0.000	0.000
27	A	27	PRO	0	-0.052	-0.010	27.305	-0.008	-0.008	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.856	-0.918	29.658	0.091	0.091	0.000	0.000	0.000	0.000
29	A	29	VAL	0	-0.014	-0.010	25.749	-0.005	-0.005	0.000	0.000	0.000	0.000
30	A	30	THR	0	-0.085	-0.080	29.072	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.972	0.987	30.654	-0.116	-0.116	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.910	0.968	31.692	-0.081	-0.081	0.000	0.000	0.000	0.000
33	A	33	VAL	0	-0.062	-0.039	29.096	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	34	THR	0	-0.026	-0.004	32.394	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	35	TRP	0	0.039	0.013	35.564	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	36	ALA	0	-0.021	-0.016	34.199	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	37	ALA	0	-0.038	-0.013	35.753	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	38	SER	0	-0.054	-0.022	37.276	-0.004	-0.004	0.000	0.000	0.000	0.000
39	A	39	LEU	0	-0.015	-0.004	38.905	-0.004	-0.004	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.026	0.024	39.631	-0.005	-0.005	0.000	0.000	0.000	0.000
41	A	41	ASH	0	-0.121	-0.083	38.727	0.007	0.007	0.000	0.000	0.000	0.000
42	A	42	ARG	1	0.944	0.951	34.005	-0.084	-0.084	0.000	0.000	0.000	0.000
43	A	43	SER	0	0.026	0.005	33.293	0.002	0.002	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.833	-0.876	33.887	0.045	0.045	0.000	0.000	0.000	0.000
45	A	45	ASN	0	0.047	0.054	34.692	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	46	ALA	0	0.092	0.026	31.615	0.006	0.006	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.823	-0.915	30.587	0.079	0.079	0.000	0.000	0.000	0.000
48	A	48	TYR	0	0.039	0.014	30.992	0.016	0.016	0.000	0.000	0.000	0.000
49	A	49	GLN	0	-0.043	-0.025	28.372	0.007	0.007	0.000	0.000	0.000	0.000
50	A	50	TYR	0	-0.003	0.000	24.401	0.015	0.015	0.000	0.000	0.000	0.000
51	A	51	ASN	0	0.036	0.001	25.737	0.017	0.017	0.000	0.000	0.000	0.000
52	A	52	LYS	1	0.926	0.972	25.752	-0.128	-0.128	0.000	0.000	0.000	0.000
53	A	53	LYS	1	0.872	0.949	19.094	-0.099	-0.099	0.000	0.000	0.000	0.000
54	A	54	ARG	1	1.029	1.022	21.240	-0.096	-0.096	0.000	0.000	0.000	0.000
55	A	55	LEU	0	0.050	0.010	22.129	0.017	0.017	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.945	0.965	20.218	-0.162	-0.162	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.950	-1.003	17.590	0.214	0.214	0.000	0.000	0.000	0.000
58	A	58	ILE	0	-0.002	0.041	17.637	0.047	0.047	0.000	0.000	0.000	0.000
59	A	59	ASP	-1	-0.795	-0.899	19.305	0.311	0.311	0.000	0.000	0.000	0.000
60	A	60	ARG	1	0.880	0.932	14.522	-0.356	-0.356	0.000	0.000	0.000	0.000
61	A	61	ARG	1	0.809	0.867	13.239	-0.309	-0.309	0.000	0.000	0.000	0.000
62	A	62	VAL	0	0.042	0.033	15.600	0.048	0.048	0.000	0.000	0.000	0.000
63	A	63	ARG	1	0.923	0.972	12.845	-0.682	-0.682	0.000	0.000	0.000	0.000
64	A	64	TYR	0	-0.100	-0.062	7.875	0.250	0.250	0.000	0.000	0.000	0.000
65	A	65	LEU	0	0.060	0.027	13.371	0.092	0.092	0.000	0.000	0.000	0.000
66	A	66	THR	0	0.013	0.014	15.445	0.002	0.002	0.000	0.000	0.000	0.000
67	A	67	LYS	1	0.949	0.983	10.436	-1.485	-1.485	0.000	0.000	0.000	0.000
68	A	68	CYS	0	-0.049	-0.027	10.497	0.138	0.138	0.000	0.000	0.000	0.000
69	A	69	MET	0	-0.026	0.008	13.516	-0.085	-0.085	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.967	-0.974	16.940	0.572	0.572	0.000	0.000	0.000	0.000
71	A	71	ASN	0	-0.039	-0.023	12.372	-0.134	-0.134	0.000	0.000	0.000	0.000
72	A	72	LEU	0	-0.052	-0.004	11.422	0.037	0.037	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.910	0.962	12.942	-0.232	-0.232	0.000	0.000	0.000	0.000
74	A	74	ILE	0	0.003	0.004	14.271	-0.055	-0.055	0.000	0.000	0.000	0.000
75	A	75	VAL	0	-0.061	-0.039	14.366	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	76	ASP	-1	-0.923	-0.968	17.454	0.011	0.011	0.000	0.000	0.000	0.000
77	A	77	TYR	0	-0.054	-0.018	20.308	0.002	0.002	0.000	0.000	0.000	0.000
78	A	78	SER	0	0.019	0.013	21.970	-0.011	-0.011	0.000	0.000	0.000	0.000
79	A	79	PRO	0	0.048	0.000	24.589	-0.006	-0.006	0.000	0.000	0.000	0.000
80	A	80	GLN	0	-0.024	0.007	26.766	-0.006	-0.006	0.000	0.000	0.000	0.000
81	A	81	GLN	0	-0.039	-0.022	23.180	0.003	0.003	0.000	0.000	0.000	0.000
82	A	82	GLU	-1	-0.845	-0.916	23.343	-0.144	-0.144	0.000	0.000	0.000	0.000
83	A	83	GLY	0	-0.004	0.002	25.102	0.000	0.000	0.000	0.000	0.000	0.000
84	A	84	LYS	1	0.897	0.935	19.727	0.244	0.244	0.000	0.000	0.000	0.000
85	A	85	VAL	0	0.052	0.034	16.632	0.014	0.014	0.000	0.000	0.000	0.000
86	A	86	PHE	0	-0.107	-0.049	15.290	-0.009	-0.009	0.000	0.000	0.000	0.000
87	A	87	PHE	0	-0.024	-0.027	11.459	-0.059	-0.059	0.000	0.000	0.000	0.000
88	A	88	GLY	0	0.024	0.015	15.897	0.039	0.039	0.000	0.000	0.000	0.000
89	A	89	ALA	0	0.013	0.013	17.562	0.034	0.034	0.000	0.000	0.000	0.000
90	A	90	TRP	0	-0.038	-0.007	18.766	-0.044	-0.044	0.000	0.000	0.000	0.000
91	A	91	VAL	0	0.036	0.020	18.820	0.007	0.007	0.000	0.000	0.000	0.000
92	A	92	GLU	-1	-0.929	-0.945	21.144	-0.194	-0.194	0.000	0.000	0.000	0.000
93	A	93	ILE	0	-0.075	-0.037	20.162	-0.013	-0.013	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.901	-0.971	23.314	-0.192	-0.192	0.000	0.000	0.000	0.000
95	A	95	ASN	0	-0.034	-0.012	24.837	-0.007	-0.007	0.000	0.000	0.000	0.000
96	A	96	ASP	-1	-0.845	-0.931	26.623	-0.195	-0.195	0.000	0.000	0.000	0.000
97	A	97	ASP	-1	-0.988	-0.980	29.611	-0.183	-0.183	0.000	0.000	0.000	0.000
98	A	98	GLY	0	-0.018	0.000	29.981	0.011	0.011	0.000	0.000	0.000	0.000
99	A	99	VAL	0	-0.084	-0.058	24.665	0.002	0.002	0.000	0.000	0.000	0.000
100	A	100	THR	0	0.028	0.024	25.811	-0.012	-0.012	0.000	0.000	0.000	0.000
101	A	101	HIS	0	-0.036	-0.052	21.741	0.012	0.012	0.000	0.000	0.000	0.000
102	A	102	ARG	1	0.990	1.020	22.036	0.147	0.147	0.000	0.000	0.000	0.000
103	A	103	PHE	0	0.032	-0.018	16.756	-0.025	-0.025	0.000	0.000	0.000	0.000
104	A	104	ARG	1	0.932	1.005	17.733	0.137	0.137	0.000	0.000	0.000	0.000
105	A	105	ILE	0	-0.058	-0.021	11.964	-0.033	-0.033	0.000	0.000	0.000	0.000
106	A	106	VAL	0	-0.008	-0.001	13.242	0.058	0.058	0.000	0.000	0.000	0.000
107	A	107	GLY	0	0.024	0.004	9.876	-0.140	-0.140	0.000	0.000	0.000	0.000
108	A	108	TYR	0	-0.013	-0.032	5.544	0.052	0.052	0.000	0.000	0.000	0.000
109	A	109	ASP	-1	-0.898	-0.949	9.489	1.197	1.197	0.000	0.000	0.000	0.000
110	A	110	GLU	-1	-0.838	-0.926	11.062	0.293	0.293	0.000	0.000	0.000	0.000
111	A	111	ILE	0	-0.017	0.054	12.154	-0.063	-0.063	0.000	0.000	0.000	0.000
112	A	112	PHE	0	0.040	-0.019	15.154	0.014	0.014	0.000	0.000	0.000	0.000
113	A	113	GLY	0	-0.014	-0.003	17.801	-0.023	-0.023	0.000	0.000	0.000	0.000
114	A	114	ARG	1	0.868	0.945	20.486	-0.033	-0.033	0.000	0.000	0.000	0.000
115	A	115	LYS	1	0.863	0.940	19.866	-0.014	-0.014	0.000	0.000	0.000	0.000
116	A	116	ASP	-1	-0.757	-0.905	16.775	-0.144	-0.144	0.000	0.000	0.000	0.000
117	A	117	TYR	0	-0.077	-0.040	16.008	0.019	0.019	0.000	0.000	0.000	0.000
118	A	118	ILE	0	0.043	0.028	12.060	-0.051	-0.051	0.000	0.000	0.000	0.000
119	A	119	SER	0	0.021	0.019	8.152	0.006	0.006	0.000	0.000	0.000	0.000
120	A	120	ILE	0	0.083	0.032	7.066	-0.139	-0.139	0.000	0.000	0.000	0.000
121	A	121	ASP	-1	-0.937	-0.920	2.496	-9.719	-8.357	2.306	-1.713	-1.955	-0.024
122	A	122	SER	0	-0.021	-0.022	5.136	-0.360	-0.280	-0.001	-0.002	-0.076	0.000
123	A	123	PRO	0	0.083	0.019	7.867	0.075	0.075	0.000	0.000	0.000	0.000
124	A	124	MET	0	0.066	0.041	10.143	0.033	0.033	0.000	0.000	0.000	0.000
125	A	125	ALA	0	0.019	0.018	9.592	0.091	0.091	0.000	0.000	0.000	0.000
126	A	126	ARG	1	0.859	0.927	5.888	2.090	2.090	0.000	0.000	0.000	0.000
127	A	127	ALA	0	-0.015	0.005	10.704	0.102	0.102	0.000	0.000	0.000	0.000
128	A	128	LEU	0	0.036	0.003	14.227	0.063	0.063	0.000	0.000	0.000	0.000
129	A	129	LEU	0	-0.025	0.015	10.823	0.054	0.054	0.000	0.000	0.000	0.000
130	A	130	LYS	1	0.874	0.910	14.291	0.453	0.453	0.000	0.000	0.000	0.000
131	A	131	LYS	1	0.897	0.949	16.734	0.520	0.520	0.000	0.000	0.000	0.000
132	A	132	GLU	-1	-0.883	-0.944	20.338	-0.212	-0.212	0.000	0.000	0.000	0.000
133	A	133	VAL	0	0.003	-0.018	23.608	-0.016	-0.016	0.000	0.000	0.000	0.000
134	A	134	GLY	0	0.054	0.046	25.780	0.008	0.008	0.000	0.000	0.000	0.000
135	A	135	ASP	-1	-0.927	-0.958	22.309	-0.294	-0.294	0.000	0.000	0.000	0.000
136	A	136	LEU	0	-0.028	-0.002	23.620	-0.009	-0.009	0.000	0.000	0.000	0.000
137	A	137	ALA	0	-0.057	-0.026	18.001	-0.026	-0.026	0.000	0.000	0.000	0.000
138	A	138	VAL	0	0.008	0.009	17.129	0.015	0.015	0.000	0.000	0.000	0.000
139	A	139	VAL	0	-0.049	-0.037	14.762	-0.085	-0.085	0.000	0.000	0.000	0.000
140	A	140	ASN	0	-0.035	-0.016	13.910	-0.014	-0.014	0.000	0.000	0.000	0.000
141	A	141	THR	0	-0.037	-0.020	13.655	-0.112	-0.112	0.000	0.000	0.000	0.000
142	A	142	PRO	0	0.004	-0.007	13.633	0.057	0.057	0.000	0.000	0.000	0.000
143	A	143	ALA	0	-0.002	0.009	16.655	0.026	0.026	0.000	0.000	0.000	0.000
144	A	144	GLY	0	-0.017	-0.014	17.755	0.035	0.035	0.000	0.000	0.000	0.000
145	A	145	GLU	-1	-0.897	-0.933	17.978	-0.395	-0.395	0.000	0.000	0.000	0.000
146	A	146	ALA	0	0.005	-0.019	19.102	0.027	0.027	0.000	0.000	0.000	0.000
147	A	147	SER	0	-0.013	-0.003	19.947	-0.026	-0.026	0.000	0.000	0.000	0.000
148	A	148	TRP	0	-0.002	-0.013	19.631	-0.005	-0.005	0.000	0.000	0.000	0.000
149	A	149	TYR	0	0.033	0.021	22.200	-0.008	-0.008	0.000	0.000	0.000	0.000
150	A	150	VAL	0	-0.076	-0.029	20.777	-0.005	-0.005	0.000	0.000	0.000	0.000
151	A	151	ASN	0	0.011	0.000	23.286	0.025	0.025	0.000	0.000	0.000	0.000
152	A	152	ALA	0	0.046	0.020	25.304	0.010	0.010	0.000	0.000	0.000	0.000
153	A	153	ILE	0	-0.049	-0.021	21.695	-0.018	-0.018	0.000	0.000	0.000	0.000
154	A	154	GLU	-1	-0.900	-0.937	23.883	-0.133	-0.133	0.000	0.000	0.000	0.000
155	A	155	TYR	0	0.004	-0.022	19.368	-0.010	-0.010	0.000	0.000	0.000	0.000
156	A	156	VAL	0	-0.019	-0.011	24.288	0.014	0.014	0.000	0.000	0.000	0.000

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