FMO DATABASE

FMODB ID: 6YN7Z

Calculation Name: 2P84-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2P84

Chain ID: A

ChEMBL ID:

UniProt ID: Q4ZC86

Base Structure: X-ray

Registration Date: 2023-09-21

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	OptAll
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	133
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1219807.109731
FMO2-HF: Nuclear repulsion	1164093.005554
FMO2-HF: Total energy	-55714.104177
FMO2-MP2: Total energy	-55876.720001

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:3:LEU)

Summations of interaction energy for fragment #1(A:3:LEU)

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.
-19.394	-11.363	9.305	-5.828	-11.509	-0.054

Interaction energy analysis for fragmet #1(A:3:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.054 / q_NPA : -0.033

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	5	PRO	0	0.012	0.008	3.849	-1.534	-0.056	-0.017	-0.590	-0.871	0.001
4	A	6	LYS	1	0.886	0.947	6.091	-0.347	-0.347	0.000	0.000	0.000	0.000
5	A	7	PHE	0	0.039	0.004	5.737	0.255	0.255	0.000	0.000	0.000	0.000
6	A	8	ARG	1	0.751	0.824	10.437	0.361	0.361	0.000	0.000	0.000	0.000
7	A	9	GLU	-1	-0.761	-0.841	14.022	-0.552	-0.552	0.000	0.000	0.000	0.000
8	A	10	PHE	0	0.018	-0.004	16.304	0.037	0.037	0.000	0.000	0.000	0.000
9	A	11	ASP	-1	-0.706	-0.836	20.110	-0.315	-0.315	0.000	0.000	0.000	0.000
10	A	12	ARG	1	0.865	0.923	22.818	0.215	0.215	0.000	0.000	0.000	0.000
11	A	13	GLU	-1	-0.768	-0.853	26.381	-0.172	-0.172	0.000	0.000	0.000	0.000
12	A	14	ARG	1	0.752	0.842	19.241	0.426	0.426	0.000	0.000	0.000	0.000
13	A	15	HIS	0	-0.007	-0.010	26.150	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	16	ARG	1	0.726	0.832	27.554	0.191	0.191	0.000	0.000	0.000	0.000
15	A	17	THR	0	-0.040	-0.004	29.150	0.018	0.018	0.000	0.000	0.000	0.000
16	A	18	ASP	-1	-0.906	-0.956	29.628	-0.161	-0.161	0.000	0.000	0.000	0.000
17	A	19	TYR	0	-0.085	-0.042	28.166	-0.003	-0.003	0.000	0.000	0.000	0.000
18	A	20	GLN	0	-0.088	-0.056	25.694	-0.014	-0.014	0.000	0.000	0.000	0.000
19	A	21	LYS	1	0.975	0.977	21.867	0.303	0.303	0.000	0.000	0.000	0.000
20	A	22	GLY	0	0.085	0.057	23.052	-0.021	-0.021	0.000	0.000	0.000	0.000
21	A	23	MET	0	-0.042	0.007	18.377	-0.046	-0.046	0.000	0.000	0.000	0.000
22	A	24	SER	0	-0.044	-0.040	17.047	-0.014	-0.014	0.000	0.000	0.000	0.000
23	A	25	TYR	0	0.000	-0.028	14.246	-0.020	-0.020	0.000	0.000	0.000	0.000
24	A	26	ALA	0	-0.009	0.005	9.770	0.017	0.017	0.000	0.000	0.000	0.000
25	A	27	GLU	-1	-0.942	-0.952	9.828	-0.915	-0.915	0.000	0.000	0.000	0.000
26	A	28	GLN	0	-0.071	-0.053	2.404	-1.182	-0.464	3.213	-1.302	-2.630	-0.010
27	A	29	GLN	0	-0.037	-0.019	6.122	0.344	0.344	0.000	0.000	0.000	0.000
28	A	30	ASP	-1	-0.820	-0.909	2.608	-11.165	-7.939	1.666	-2.029	-2.863	-0.029
29	A	31	PHE	0	-0.060	-0.036	4.920	0.597	0.647	-0.001	-0.007	-0.042	0.000
30	A	32	ASP	-1	-0.915	-0.969	6.082	-0.422	-0.422	0.000	0.000	0.000	0.000
31	A	33	MET	0	-0.092	-0.042	8.464	0.158	0.158	0.000	0.000	0.000	0.000
32	A	34	GLY	0	-0.015	-0.002	5.289	0.102	0.102	0.000	0.000	0.000	0.000
33	A	35	PHE	0	-0.006	0.000	2.477	-4.031	-1.522	4.445	-1.880	-5.074	-0.016
34	A	36	THR	0	-0.018	-0.001	4.497	0.308	0.358	-0.001	-0.020	-0.029	0.000
35	A	37	ILE	0	0.000	-0.001	4.963	-0.434	-0.434	0.000	0.000	0.000	0.000
36	A	38	TRP	0	-0.035	-0.017	8.700	0.310	0.310	0.000	0.000	0.000	0.000
37	A	39	PHE	0	0.022	0.001	11.670	-0.062	-0.062	0.000	0.000	0.000	0.000
38	A	40	ASP	-1	-0.896	-0.917	15.179	-0.414	-0.414	0.000	0.000	0.000	0.000
39	A	41	HIS	0	-0.088	-0.052	18.539	-0.042	-0.042	0.000	0.000	0.000	0.000
40	A	42	ILE	0	-0.009	0.008	20.027	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	43	GLU	-1	-0.859	-0.921	21.857	-0.266	-0.266	0.000	0.000	0.000	0.000
42	A	44	ASP	-1	-0.918	-0.971	23.955	-0.228	-0.228	0.000	0.000	0.000	0.000
43	A	45	LEU	0	-0.038	-0.039	24.614	-0.013	-0.013	0.000	0.000	0.000	0.000
44	A	46	ASP	-1	-0.936	-0.960	25.935	-0.198	-0.198	0.000	0.000	0.000	0.000
45	A	47	LEU	0	-0.044	-0.002	21.855	0.002	0.002	0.000	0.000	0.000	0.000
46	A	48	ILE	0	-0.061	-0.026	21.987	-0.027	-0.027	0.000	0.000	0.000	0.000
47	A	49	GLU	-1	-0.787	-0.858	22.839	-0.175	-0.175	0.000	0.000	0.000	0.000
48	A	50	LYS	1	0.774	0.839	24.450	0.177	0.177	0.000	0.000	0.000	0.000
49	A	51	ASP	-1	-0.901	-0.925	22.564	-0.273	-0.273	0.000	0.000	0.000	0.000
50	A	52	GLY	0	-0.027	-0.006	21.382	-0.010	-0.010	0.000	0.000	0.000	0.000
51	A	53	THR	0	-0.077	-0.055	18.378	-0.048	-0.048	0.000	0.000	0.000	0.000
52	A	54	ILE	0	0.006	-0.012	17.767	0.021	0.021	0.000	0.000	0.000	0.000
53	A	55	ASN	0	-0.062	-0.019	17.819	-0.047	-0.047	0.000	0.000	0.000	0.000
54	A	56	ARG	1	0.878	0.913	14.847	0.643	0.643	0.000	0.000	0.000	0.000
55	A	57	ILE	0	0.038	0.025	17.456	-0.027	-0.027	0.000	0.000	0.000	0.000
56	A	58	VAL	0	-0.037	-0.024	11.798	-0.019	-0.019	0.000	0.000	0.000	0.000
57	A	59	MET	0	-0.032	0.036	14.141	0.083	0.083	0.000	0.000	0.000	0.000
58	A	60	MET	0	-0.008	-0.008	9.631	-0.190	-0.190	0.000	0.000	0.000	0.000
59	A	61	SER	0	-0.056	-0.055	10.469	0.176	0.176	0.000	0.000	0.000	0.000
60	A	62	THR	0	-0.010	-0.039	11.599	0.035	0.035	0.000	0.000	0.000	0.000
61	A	63	GLY	0	-0.047	-0.016	11.683	0.100	0.100	0.000	0.000	0.000	0.000
62	A	64	LEU	0	-0.017	0.002	12.459	0.068	0.068	0.000	0.000	0.000	0.000
63	A	65	LYS	1	0.803	0.892	14.879	-0.016	-0.016	0.000	0.000	0.000	0.000
64	A	66	ASP	-1	-0.668	-0.814	18.531	-0.036	-0.036	0.000	0.000	0.000	0.000
65	A	67	LYS	1	0.828	0.889	22.082	0.031	0.031	0.000	0.000	0.000	0.000
66	A	68	ASN	0	-0.140	-0.062	23.823	0.010	0.010	0.000	0.000	0.000	0.000
67	A	69	VAL	0	-0.049	-0.026	18.637	-0.007	-0.007	0.000	0.000	0.000	0.000
68	A	70	LYS	1	0.923	0.969	18.822	0.123	0.123	0.000	0.000	0.000	0.000
69	A	71	GLU	-1	-0.822	-0.872	12.034	-0.129	-0.129	0.000	0.000	0.000	0.000
70	A	72	ILE	0	0.028	0.027	16.459	-0.033	-0.033	0.000	0.000	0.000	0.000
71	A	73	TYR	0	-0.012	-0.007	12.288	-0.042	-0.042	0.000	0.000	0.000	0.000
72	A	74	GLU	-1	-0.805	-0.905	14.875	-0.335	-0.335	0.000	0.000	0.000	0.000
73	A	75	SER	0	0.019	0.004	17.271	-0.047	-0.047	0.000	0.000	0.000	0.000
74	A	76	ASP	-1	-0.771	-0.868	19.620	-0.211	-0.211	0.000	0.000	0.000	0.000
75	A	77	ILE	0	-0.005	0.013	21.844	0.014	0.014	0.000	0.000	0.000	0.000
76	A	78	VAL	0	-0.035	-0.029	23.039	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	79	ARG	1	0.898	0.950	26.108	0.040	0.040	0.000	0.000	0.000	0.000
78	A	80	ASN	0	0.012	-0.010	28.005	0.001	0.001	0.000	0.000	0.000	0.000
79	A	81	LEU	0	-0.035	-0.028	30.023	-0.004	-0.004	0.000	0.000	0.000	0.000
80	A	82	TYR	0	-0.077	-0.026	32.561	0.002	0.002	0.000	0.000	0.000	0.000
81	A	83	GLY	0	-0.049	-0.020	33.911	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	84	GLU	-1	-0.840	-0.883	32.248	0.003	0.003	0.000	0.000	0.000	0.000
83	A	85	LEU	0	-0.012	-0.024	30.252	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	86	TYR	0	-0.060	-0.041	26.827	0.004	0.004	0.000	0.000	0.000	0.000
85	A	87	VAL	0	0.006	0.003	23.557	-0.010	-0.010	0.000	0.000	0.000	0.000
86	A	88	VAL	0	-0.033	-0.011	18.884	0.017	0.017	0.000	0.000	0.000	0.000
87	A	89	GLU	-1	-0.852	-0.898	20.032	-0.152	-0.152	0.000	0.000	0.000	0.000
88	A	90	TRP	0	-0.018	-0.015	13.432	0.031	0.031	0.000	0.000	0.000	0.000
89	A	91	LEU	0	0.017	0.009	18.130	-0.015	-0.015	0.000	0.000	0.000	0.000
90	A	92	ASP	-1	-0.934	-0.970	19.547	0.001	0.001	0.000	0.000	0.000	0.000
91	A	93	GLY	0	-0.056	-0.024	15.907	0.029	0.029	0.000	0.000	0.000	0.000
92	A	94	SER	0	-0.069	-0.044	15.958	0.067	0.067	0.000	0.000	0.000	0.000
93	A	95	PHE	0	0.031	0.020	12.570	-0.026	-0.026	0.000	0.000	0.000	0.000
94	A	96	VAL	0	-0.034	-0.012	17.872	0.042	0.042	0.000	0.000	0.000	0.000
95	A	97	LEU	0	-0.026	-0.014	21.685	-0.023	-0.023	0.000	0.000	0.000	0.000
96	A	98	THR	0	0.018	-0.018	24.507	0.017	0.017	0.000	0.000	0.000	0.000
97	A	99	GLU	-1	-0.815	-0.905	26.784	-0.017	-0.017	0.000	0.000	0.000	0.000
98	A	100	PHE	0	0.047	0.012	29.636	-0.006	-0.006	0.000	0.000	0.000	0.000
99	A	101	TYR	0	-0.049	-0.017	32.129	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	102	ASN	0	-0.076	-0.039	35.478	0.004	0.004	0.000	0.000	0.000	0.000
101	A	103	GLY	0	-0.049	-0.008	35.071	0.004	0.004	0.000	0.000	0.000	0.000
102	A	104	GLY	0	0.004	-0.013	31.655	-0.007	-0.007	0.000	0.000	0.000	0.000
103	A	105	TYR	0	-0.124	-0.050	30.737	0.001	0.001	0.000	0.000	0.000	0.000
104	A	106	ASP	-1	-0.842	-0.924	25.186	-0.033	-0.033	0.000	0.000	0.000	0.000
105	A	107	HIS	0	-0.086	-0.045	26.562	0.022	0.022	0.000	0.000	0.000	0.000
106	A	108	TYR	0	-0.019	-0.021	21.511	-0.003	-0.003	0.000	0.000	0.000	0.000
107	A	109	ILE	0	-0.015	0.008	18.256	0.002	0.002	0.000	0.000	0.000	0.000
108	A	110	ILE	0	-0.023	-0.019	21.294	0.030	0.030	0.000	0.000	0.000	0.000
109	A	111	ASP	-1	-0.912	-0.976	18.901	0.229	0.229	0.000	0.000	0.000	0.000
110	A	112	SER	0	-0.056	-0.038	21.280	-0.002	-0.002	0.000	0.000	0.000	0.000
111	A	113	SER	0	0.020	-0.016	20.262	-0.010	-0.010	0.000	0.000	0.000	0.000
112	A	114	THR	0	-0.049	-0.046	22.071	-0.018	-0.018	0.000	0.000	0.000	0.000
113	A	115	GLU	-1	-0.884	-0.891	24.154	0.075	0.075	0.000	0.000	0.000	0.000
114	A	116	TYR	0	0.018	-0.003	24.193	-0.012	-0.012	0.000	0.000	0.000	0.000
115	A	117	GLU	-1	-0.833	-0.898	25.372	-0.033	-0.033	0.000	0.000	0.000	0.000
116	A	118	VAL	0	0.017	0.005	20.909	-0.002	-0.002	0.000	0.000	0.000	0.000
117	A	119	LEU	0	-0.053	-0.024	24.371	-0.006	-0.006	0.000	0.000	0.000	0.000
118	A	120	GLY	0	0.030	0.016	25.489	-0.003	-0.003	0.000	0.000	0.000	0.000
119	A	121	ASN	0	-0.045	-0.027	22.079	-0.004	-0.004	0.000	0.000	0.000	0.000
120	A	122	ILE	0	0.065	0.029	23.407	0.005	0.005	0.000	0.000	0.000	0.000
121	A	123	TYR	0	-0.035	-0.011	20.501	0.010	0.010	0.000	0.000	0.000	0.000
122	A	124	GLU	-1	-0.875	-0.946	22.979	-0.258	-0.258	0.000	0.000	0.000	0.000
123	A	125	ASN	0	-0.089	-0.042	26.511	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	126	PRO	0	0.005	0.006	28.746	0.008	0.008	0.000	0.000	0.000	0.000
125	A	127	GLU	-1	-0.791	-0.900	30.198	-0.112	-0.112	0.000	0.000	0.000	0.000
126	A	128	LEU	0	-0.078	-0.036	28.902	0.009	0.009	0.000	0.000	0.000	0.000
127	A	129	LEU	0	-0.039	-0.021	28.311	0.003	0.003	0.000	0.000	0.000	0.000
128	A	130	GLU	-1	-0.921	-0.956	32.378	-0.078	-0.078	0.000	0.000	0.000	0.000
129	A	131	ASP	-1	-0.870	-0.942	36.181	-0.047	-0.047	0.000	0.000	0.000	0.000
130	A	132	ASP	-1	-0.973	-0.982	38.256	-0.040	-0.040	0.000	0.000	0.000	0.000
131	A	133	ASN	0	-0.133	-0.066	36.885	0.004	0.004	0.000	0.000	0.000	0.000
132	A	134	HIS	0	0.002	0.000	35.470	-0.004	-0.004	0.000	0.000	0.000	0.000
133	A	135	ALA	0	-0.025	0.001	36.322	0.003	0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:LEU)