FMO DATABASE

FMODB ID: 491QN

Calculation Name: 2P25-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2P25

Chain ID: A

ChEMBL ID:

UniProt ID: Q832L2

Base Structure: X-ray

Registration Date: 2023-09-20

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	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	126
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1083230.555577
FMO2-HF: Nuclear repulsion	1032390.03751
FMO2-HF: Total energy	-50840.518067
FMO2-MP2: Total energy	-50991.466931

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.
-13.069	-14.552	12.294	-4.92	-5.892	0.035

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 : 0.057 / q_NPA : 0.018

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	PHE	0	0.027	0.007	3.877	-2.580	-0.212	-0.020	-1.115	-1.234	-0.002
4	A	4	LYS	1	0.833	0.923	2.282	-12.517	-16.475	12.315	-3.803	-4.555	0.037
5	A	5	GLU	-1	-0.916	-0.956	5.369	1.583	1.690	-0.001	-0.002	-0.103	0.000
6	A	6	ILE	0	0.007	0.006	8.377	-0.027	-0.027	0.000	0.000	0.000	0.000
7	A	7	HIS	0	0.028	0.035	11.841	-0.089	-0.089	0.000	0.000	0.000	0.000
8	A	8	HIS	1	0.793	0.863	14.063	-0.586	-0.586	0.000	0.000	0.000	0.000
9	A	9	VAL	0	0.024	0.028	16.435	0.064	0.064	0.000	0.000	0.000	0.000
10	A	10	ALA	0	-0.012	-0.014	18.771	-0.031	-0.031	0.000	0.000	0.000	0.000
11	A	11	ILE	0	0.007	0.013	21.899	0.007	0.007	0.000	0.000	0.000	0.000
12	A	12	ASN	0	-0.048	-0.022	25.459	0.012	0.012	0.000	0.000	0.000	0.000
13	A	13	ALA	0	0.035	0.023	28.863	-0.002	-0.002	0.000	0.000	0.000	0.000
14	A	14	SER	0	-0.046	-0.060	32.080	-0.006	-0.006	0.000	0.000	0.000	0.000
15	A	15	ASN	0	0.003	-0.004	35.668	-0.007	-0.007	0.000	0.000	0.000	0.000
16	A	16	TYR	0	-0.023	-0.032	34.916	0.004	0.004	0.000	0.000	0.000	0.000
17	A	17	GLN	0	0.029	0.006	35.861	0.008	0.008	0.000	0.000	0.000	0.000
18	A	18	ALA	0	0.024	0.012	36.867	0.000	0.000	0.000	0.000	0.000	0.000
19	A	19	THR	0	0.006	-0.010	30.909	0.008	0.008	0.000	0.000	0.000	0.000
20	A	20	LYS	1	0.841	0.919	32.596	-0.146	-0.146	0.000	0.000	0.000	0.000
21	A	21	ASN	0	0.006	-0.009	34.134	0.002	0.002	0.000	0.000	0.000	0.000
22	A	22	PHE	0	0.067	0.035	29.701	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	23	TYR	0	-0.008	-0.063	26.785	0.007	0.007	0.000	0.000	0.000	0.000
24	A	24	VAL	0	-0.055	-0.018	29.380	0.009	0.009	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.985	-1.000	31.491	0.129	0.129	0.000	0.000	0.000	0.000
26	A	26	LYS	1	0.835	0.946	33.169	-0.128	-0.128	0.000	0.000	0.000	0.000
27	A	27	LEU	0	-0.034	-0.021	27.428	0.001	0.001	0.000	0.000	0.000	0.000
28	A	28	GLY	0	0.005	0.020	27.894	0.009	0.009	0.000	0.000	0.000	0.000
29	A	29	PHE	0	-0.072	-0.037	22.493	0.012	0.012	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.896	-0.946	26.384	0.161	0.161	0.000	0.000	0.000	0.000
31	A	31	VAL	0	-0.017	-0.031	26.960	0.020	0.020	0.000	0.000	0.000	0.000
32	A	32	LEU	0	-0.053	-0.006	22.290	-0.008	-0.008	0.000	0.000	0.000	0.000
33	A	33	ARG	1	0.759	0.850	21.808	-0.310	-0.310	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.714	-0.820	28.485	0.161	0.161	0.000	0.000	0.000	0.000
35	A	35	ASN	0	-0.076	-0.044	28.973	0.001	0.001	0.000	0.000	0.000	0.000
36	A	36	HIS	0	-0.002	-0.002	31.856	0.004	0.004	0.000	0.000	0.000	0.000
37	A	37	ARG	1	0.801	0.884	27.226	-0.220	-0.220	0.000	0.000	0.000	0.000
38	A	38	PRO	0	0.026	-0.002	33.890	0.002	0.002	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.968	-0.998	33.787	0.130	0.130	0.000	0.000	0.000	0.000
40	A	40	LYS	1	0.905	0.954	29.539	-0.182	-0.182	0.000	0.000	0.000	0.000
41	A	41	ASN	0	0.009	0.043	34.015	0.006	0.006	0.000	0.000	0.000	0.000
42	A	42	ASP	-1	-0.813	-0.885	31.019	0.201	0.201	0.000	0.000	0.000	0.000
43	A	43	ILE	0	-0.011	0.000	32.447	-0.007	-0.007	0.000	0.000	0.000	0.000
44	A	44	LYS	1	0.767	0.877	23.209	-0.299	-0.299	0.000	0.000	0.000	0.000
45	A	45	LEU	0	-0.007	-0.011	28.630	-0.013	-0.013	0.000	0.000	0.000	0.000
46	A	46	ASP	-1	-0.760	-0.852	23.822	0.314	0.314	0.000	0.000	0.000	0.000
47	A	47	LEU	0	0.015	0.009	24.681	-0.020	-0.020	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.808	0.879	18.056	-0.369	-0.369	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.036	0.037	21.483	-0.026	-0.026	0.000	0.000	0.000	0.000
50	A	50	GLY	0	0.029	0.021	19.713	0.022	0.022	0.000	0.000	0.000	0.000
51	A	51	SER	0	-0.002	-0.021	14.586	-0.011	-0.011	0.000	0.000	0.000	0.000
52	A	52	GLN	0	0.036	0.024	16.759	0.062	0.062	0.000	0.000	0.000	0.000
53	A	53	GLU	-1	-0.781	-0.887	18.098	0.345	0.345	0.000	0.000	0.000	0.000
54	A	54	LEU	0	-0.005	0.000	19.332	0.052	0.052	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.826	-0.883	21.865	0.359	0.359	0.000	0.000	0.000	0.000
56	A	56	ILE	0	0.034	0.006	23.509	0.007	0.007	0.000	0.000	0.000	0.000
57	A	57	PHE	0	-0.034	-0.008	24.106	-0.016	-0.016	0.000	0.000	0.000	0.000
58	A	58	ILE	0	-0.010	-0.006	29.047	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	59	SER	0	0.009	-0.030	32.680	-0.009	-0.009	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.846	-0.913	35.332	0.133	0.133	0.000	0.000	0.000	0.000
61	A	61	GLN	0	-0.069	-0.039	35.944	-0.004	-0.004	0.000	0.000	0.000	0.000
62	A	62	PHE	0	-0.060	-0.023	30.976	0.007	0.007	0.000	0.000	0.000	0.000
63	A	63	PRO	0	-0.012	-0.001	34.043	-0.006	-0.006	0.000	0.000	0.000	0.000
64	A	64	ALA	0	0.034	0.009	34.302	0.009	0.009	0.000	0.000	0.000	0.000
65	A	65	ARG	1	0.840	0.906	27.484	-0.228	-0.228	0.000	0.000	0.000	0.000
66	A	66	PRO	0	-0.016	-0.010	31.065	-0.008	-0.008	0.000	0.000	0.000	0.000
67	A	67	SER	0	-0.001	-0.024	31.994	0.009	0.009	0.000	0.000	0.000	0.000
68	A	68	TYR	0	-0.024	0.012	34.202	-0.008	-0.008	0.000	0.000	0.000	0.000
69	A	69	PRO	0	0.006	0.009	33.263	-0.008	-0.008	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.779	-0.872	29.501	0.217	0.217	0.000	0.000	0.000	0.000
71	A	71	ALA	0	-0.012	0.001	29.217	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	72	LEU	0	-0.027	-0.018	24.757	0.013	0.013	0.000	0.000	0.000	0.000
73	A	73	GLY	0	0.023	0.005	22.806	-0.006	-0.006	0.000	0.000	0.000	0.000
74	A	74	LEU	0	-0.021	-0.013	18.344	0.018	0.018	0.000	0.000	0.000	0.000
75	A	75	ARG	1	0.882	0.943	22.051	-0.274	-0.274	0.000	0.000	0.000	0.000
76	A	76	HIS	0	-0.044	-0.021	21.939	-0.012	-0.012	0.000	0.000	0.000	0.000
77	A	77	LEU	0	0.026	0.023	19.586	0.046	0.046	0.000	0.000	0.000	0.000
78	A	78	ALA	0	0.013	0.013	20.685	-0.034	-0.034	0.000	0.000	0.000	0.000
79	A	79	PHE	0	-0.007	-0.001	20.623	0.037	0.037	0.000	0.000	0.000	0.000
80	A	80	LYS	1	0.861	0.931	18.653	-0.185	-0.185	0.000	0.000	0.000	0.000
81	A	81	VAL	0	0.014	0.006	21.451	-0.005	-0.005	0.000	0.000	0.000	0.000
82	A	82	GLU	-1	-0.932	-0.979	22.095	0.111	0.111	0.000	0.000	0.000	0.000
83	A	83	HIS	0	0.026	0.010	25.503	-0.011	-0.011	0.000	0.000	0.000	0.000
84	A	84	ILE	0	-0.005	-0.005	28.607	0.005	0.005	0.000	0.000	0.000	0.000
85	A	85	GLU	-1	-0.803	-0.894	30.230	0.092	0.092	0.000	0.000	0.000	0.000
86	A	86	GLU	-1	-0.938	-0.967	30.848	0.090	0.090	0.000	0.000	0.000	0.000
87	A	87	VAL	0	0.008	0.005	28.212	0.002	0.002	0.000	0.000	0.000	0.000
88	A	88	ILE	0	-0.010	-0.006	31.603	0.003	0.003	0.000	0.000	0.000	0.000
89	A	89	ALA	0	-0.037	-0.013	34.164	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	90	PHE	0	0.007	0.008	31.692	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	91	LEU	0	0.015	0.005	30.867	0.000	0.000	0.000	0.000	0.000	0.000
92	A	92	ASN	0	0.026	0.013	35.048	0.001	0.001	0.000	0.000	0.000	0.000
93	A	93	GLU	-1	-0.957	-0.955	38.530	0.087	0.087	0.000	0.000	0.000	0.000
94	A	94	GLN	0	-0.054	-0.040	35.922	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	95	GLY	0	-0.046	-0.023	38.588	0.003	0.003	0.000	0.000	0.000	0.000
96	A	96	ILE	0	-0.083	-0.036	33.514	0.004	0.004	0.000	0.000	0.000	0.000
97	A	97	GLU	-1	-0.917	-0.959	36.659	0.106	0.106	0.000	0.000	0.000	0.000
98	A	98	THR	0	-0.029	-0.038	33.630	0.008	0.008	0.000	0.000	0.000	0.000
99	A	99	GLU	-1	-0.828	-0.893	33.363	0.144	0.144	0.000	0.000	0.000	0.000
100	A	100	PRO	0	-0.026	-0.017	35.790	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	101	LEU	0	-0.023	0.006	32.344	0.006	0.006	0.000	0.000	0.000	0.000
102	A	102	ARG	1	0.809	0.892	31.757	-0.150	-0.150	0.000	0.000	0.000	0.000
103	A	103	VAL	0	-0.005	-0.006	30.707	0.002	0.002	0.000	0.000	0.000	0.000
104	A	104	ASP	-1	-0.751	-0.849	24.672	0.183	0.183	0.000	0.000	0.000	0.000
105	A	105	ASP	-1	-0.917	-0.958	28.305	0.125	0.125	0.000	0.000	0.000	0.000
106	A	106	PHE	0	-0.054	-0.031	25.239	-0.010	-0.010	0.000	0.000	0.000	0.000
107	A	107	THR	0	-0.124	-0.084	22.415	-0.012	-0.012	0.000	0.000	0.000	0.000
108	A	108	GLY	0	0.002	0.003	25.698	-0.011	-0.011	0.000	0.000	0.000	0.000
109	A	109	LYS	1	0.902	0.956	21.500	-0.122	-0.122	0.000	0.000	0.000	0.000
110	A	110	LYS	1	0.806	0.881	27.576	-0.081	-0.081	0.000	0.000	0.000	0.000
111	A	111	MET	0	-0.034	-0.011	26.373	0.011	0.011	0.000	0.000	0.000	0.000
112	A	112	THR	0	-0.010	-0.025	29.162	-0.011	-0.011	0.000	0.000	0.000	0.000
113	A	113	PHE	0	-0.006	0.003	26.812	0.018	0.018	0.000	0.000	0.000	0.000
114	A	114	PHE	0	0.046	0.025	27.871	-0.014	-0.014	0.000	0.000	0.000	0.000
115	A	115	PHE	0	-0.004	-0.003	30.876	0.013	0.013	0.000	0.000	0.000	0.000
116	A	116	ASP	-1	-0.767	-0.852	30.033	0.206	0.206	0.000	0.000	0.000	0.000
117	A	117	PRO	0	-0.042	-0.035	32.336	-0.007	-0.007	0.000	0.000	0.000	0.000
118	A	118	ASP	-1	-0.789	-0.843	32.680	0.160	0.160	0.000	0.000	0.000	0.000
119	A	119	GLY	0	-0.016	0.000	33.540	0.001	0.001	0.000	0.000	0.000	0.000
120	A	120	LEU	0	-0.036	-0.027	25.364	0.006	0.006	0.000	0.000	0.000	0.000
121	A	121	PRO	0	-0.027	-0.018	28.015	-0.005	-0.005	0.000	0.000	0.000	0.000
122	A	122	LEU	0	-0.031	-0.010	25.490	0.027	0.027	0.000	0.000	0.000	0.000
123	A	123	GLU	-1	-0.826	-0.920	24.273	0.240	0.240	0.000	0.000	0.000	0.000
124	A	124	LEU	0	0.005	0.005	25.314	0.015	0.015	0.000	0.000	0.000	0.000
125	A	125	HIS	1	0.873	0.910	23.280	-0.214	-0.214	0.000	0.000	0.000	0.000
126	A	126	GLU	-1	-0.852	-0.902	22.959	0.119	0.119	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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