FMO DATABASE

FMODB ID: 898NY

Calculation Name: 2A4D-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2A4D

Chain ID: A

ChEMBL ID:

UniProt ID: Q13404

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	139
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1291813.34644
FMO2-HF: Nuclear repulsion	1235615.960705
FMO2-HF: Total energy	-56197.385735
FMO2-MP2: Total energy	-56357.919033

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:82:GLY)

Summations of interaction energy for fragment #1(A:82:GLY)

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.
2.988	4.049	-0.004	-0.47	-0.586	0.001

Interaction energy analysis for fragmet #1(A:82:GLY)

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 : 0.004

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	84	LYS	1	0.925	0.963	3.873	2.379	3.440	-0.004	-0.470	-0.586	0.001
4	A	85	VAL	0	0.063	0.026	5.847	0.210	0.210	0.000	0.000	0.000	0.000
5	A	86	PRO	0	0.017	0.008	9.044	0.012	0.012	0.000	0.000	0.000	0.000
6	A	87	ARG	1	0.783	0.903	7.276	1.204	1.204	0.000	0.000	0.000	0.000
7	A	88	ASN	0	0.026	-0.003	7.053	-0.174	-0.174	0.000	0.000	0.000	0.000
8	A	89	PHE	0	0.036	0.017	10.267	0.112	0.112	0.000	0.000	0.000	0.000
9	A	90	ARG	1	0.809	0.901	13.597	0.328	0.328	0.000	0.000	0.000	0.000
10	A	91	LEU	0	-0.039	-0.029	10.721	0.039	0.039	0.000	0.000	0.000	0.000
11	A	92	LEU	0	0.017	0.007	13.352	0.041	0.041	0.000	0.000	0.000	0.000
12	A	93	GLU	-1	-0.912	-0.956	16.050	-0.175	-0.175	0.000	0.000	0.000	0.000
13	A	94	GLU	-1	-0.740	-0.851	17.583	-0.273	-0.273	0.000	0.000	0.000	0.000
14	A	95	LEU	0	0.007	0.024	16.629	0.014	0.014	0.000	0.000	0.000	0.000
15	A	96	GLU	-1	-0.835	-0.904	19.377	-0.072	-0.072	0.000	0.000	0.000	0.000
16	A	97	GLU	-1	-0.841	-0.910	22.068	-0.133	-0.133	0.000	0.000	0.000	0.000
17	A	98	GLY	0	-0.016	-0.001	22.535	0.011	0.011	0.000	0.000	0.000	0.000
18	A	99	GLN	0	-0.038	-0.014	21.221	0.015	0.015	0.000	0.000	0.000	0.000
19	A	100	LYS	1	0.813	0.892	25.131	0.097	0.097	0.000	0.000	0.000	0.000
20	A	101	GLY	0	-0.003	0.011	28.208	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	102	VAL	0	0.025	0.005	26.811	-0.001	-0.001	0.000	0.000	0.000	0.000
22	A	103	GLY	0	-0.016	-0.011	29.992	0.000	0.000	0.000	0.000	0.000	0.000
23	A	104	ASP	-1	-0.860	-0.914	31.735	-0.075	-0.075	0.000	0.000	0.000	0.000
24	A	105	GLY	0	0.015	0.014	32.497	0.005	0.005	0.000	0.000	0.000	0.000
25	A	106	THR	0	-0.107	-0.074	33.312	0.000	0.000	0.000	0.000	0.000	0.000
26	A	107	VAL	0	-0.010	-0.015	28.408	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	108	SER	0	-0.020	-0.007	26.927	0.005	0.005	0.000	0.000	0.000	0.000
28	A	109	TRP	0	-0.039	-0.046	20.579	0.005	0.005	0.000	0.000	0.000	0.000
29	A	110	GLY	0	0.058	0.034	20.785	0.009	0.009	0.000	0.000	0.000	0.000
30	A	111	LEU	0	0.039	0.021	14.843	-0.015	-0.015	0.000	0.000	0.000	0.000
31	A	112	GLU	-1	-0.900	-0.940	18.003	-0.146	-0.146	0.000	0.000	0.000	0.000
32	A	113	ASP	-1	-0.810	-0.901	16.531	-0.117	-0.117	0.000	0.000	0.000	0.000
33	A	114	ASP	-1	-0.904	-0.957	16.463	-0.144	-0.144	0.000	0.000	0.000	0.000
34	A	115	GLU	-1	-0.925	-0.945	15.671	-0.033	-0.033	0.000	0.000	0.000	0.000
35	A	116	ASP	-1	-0.801	-0.869	11.477	-0.413	-0.413	0.000	0.000	0.000	0.000
36	A	117	MET	0	-0.003	-0.016	9.664	-0.071	-0.071	0.000	0.000	0.000	0.000
37	A	118	THR	0	-0.137	-0.073	7.002	-0.176	-0.176	0.000	0.000	0.000	0.000
38	A	119	LEU	0	0.007	0.002	8.340	-0.230	-0.230	0.000	0.000	0.000	0.000
39	A	120	THR	0	-0.021	-0.021	9.397	-0.067	-0.067	0.000	0.000	0.000	0.000
40	A	121	ARG	1	0.775	0.865	11.685	0.256	0.256	0.000	0.000	0.000	0.000
41	A	122	TRP	0	-0.026	-0.008	14.056	0.048	0.048	0.000	0.000	0.000	0.000
42	A	123	THR	0	0.025	0.012	18.324	0.008	0.008	0.000	0.000	0.000	0.000
43	A	124	GLY	0	-0.005	-0.005	22.068	-0.008	-0.008	0.000	0.000	0.000	0.000
44	A	125	MET	0	-0.010	-0.011	24.313	0.010	0.010	0.000	0.000	0.000	0.000
45	A	126	ILE	0	-0.008	-0.013	28.109	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	127	ILE	0	0.030	0.019	31.064	0.004	0.004	0.000	0.000	0.000	0.000
47	A	128	GLY	0	0.055	0.018	34.572	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	129	PRO	0	-0.049	-0.032	35.878	0.004	0.004	0.000	0.000	0.000	0.000
49	A	130	PRO	0	0.034	0.018	38.843	0.002	0.002	0.000	0.000	0.000	0.000
50	A	131	ARG	1	0.804	0.880	42.560	0.042	0.042	0.000	0.000	0.000	0.000
51	A	132	THR	0	-0.051	-0.019	40.465	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	133	ILE	0	-0.043	-0.027	40.774	0.002	0.002	0.000	0.000	0.000	0.000
53	A	134	TYR	0	0.009	-0.022	36.736	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	135	GLU	-1	-0.829	-0.881	39.112	-0.047	-0.047	0.000	0.000	0.000	0.000
55	A	136	ASN	0	-0.040	-0.032	41.140	0.001	0.001	0.000	0.000	0.000	0.000
56	A	137	ARG	1	0.806	0.916	37.093	0.057	0.057	0.000	0.000	0.000	0.000
57	A	138	ILE	0	0.014	-0.003	32.204	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	139	TYR	0	-0.037	-0.014	31.299	0.002	0.002	0.000	0.000	0.000	0.000
59	A	140	SER	0	0.049	0.020	27.754	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	141	LEU	0	-0.050	-0.033	24.804	0.003	0.003	0.000	0.000	0.000	0.000
61	A	142	LYS	1	0.891	0.941	20.395	0.140	0.140	0.000	0.000	0.000	0.000
62	A	143	ILE	0	-0.014	-0.010	17.890	0.005	0.005	0.000	0.000	0.000	0.000
63	A	144	GLU	-1	-0.902	-0.953	14.641	-0.271	-0.271	0.000	0.000	0.000	0.000
64	A	145	CYS	0	0.010	0.020	12.894	0.014	0.014	0.000	0.000	0.000	0.000
65	A	146	GLY	0	0.079	0.043	10.410	-0.114	-0.114	0.000	0.000	0.000	0.000
66	A	147	PRO	0	-0.001	-0.027	5.879	-0.037	-0.037	0.000	0.000	0.000	0.000
67	A	148	LYS	1	0.906	0.947	7.627	0.396	0.396	0.000	0.000	0.000	0.000
68	A	149	TYR	0	-0.022	0.005	10.531	0.095	0.095	0.000	0.000	0.000	0.000
69	A	150	PRO	0	0.022	0.003	11.204	-0.125	-0.125	0.000	0.000	0.000	0.000
70	A	151	GLU	-1	-0.838	-0.928	13.358	-0.300	-0.300	0.000	0.000	0.000	0.000
71	A	152	ALA	0	-0.067	-0.026	14.024	0.048	0.048	0.000	0.000	0.000	0.000
72	A	153	PRO	0	0.005	0.003	15.472	-0.027	-0.027	0.000	0.000	0.000	0.000
73	A	154	PRO	0	-0.014	0.002	15.668	-0.028	-0.028	0.000	0.000	0.000	0.000
74	A	155	PHE	0	-0.015	-0.003	16.387	0.041	0.041	0.000	0.000	0.000	0.000
75	A	156	VAL	0	0.028	0.002	18.351	-0.004	-0.004	0.000	0.000	0.000	0.000
76	A	157	ARG	1	0.827	0.915	21.569	0.138	0.138	0.000	0.000	0.000	0.000
77	A	158	PHE	0	0.061	0.018	24.276	-0.003	-0.003	0.000	0.000	0.000	0.000
78	A	159	VAL	0	-0.040	-0.012	25.400	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	160	THR	0	0.047	0.021	27.972	0.005	0.005	0.000	0.000	0.000	0.000
80	A	161	LYS	1	0.890	0.948	31.603	0.061	0.061	0.000	0.000	0.000	0.000
81	A	162	ILE	0	-0.002	0.002	31.760	0.003	0.003	0.000	0.000	0.000	0.000
82	A	163	ASN	0	-0.057	-0.011	34.797	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	164	MET	0	0.023	0.015	31.859	0.001	0.001	0.000	0.000	0.000	0.000
84	A	165	ASN	0	-0.027	-0.017	34.167	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	166	GLY	0	0.034	0.001	31.482	-0.003	-0.003	0.000	0.000	0.000	0.000
86	A	167	VAL	0	-0.022	-0.002	29.104	-0.010	-0.010	0.000	0.000	0.000	0.000
87	A	168	ASN	0	0.018	0.034	29.576	0.012	0.012	0.000	0.000	0.000	0.000
88	A	169	SER	0	0.041	0.009	31.285	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	170	SER	0	-0.037	-0.026	32.328	0.002	0.002	0.000	0.000	0.000	0.000
90	A	171	ASN	0	-0.005	-0.027	28.174	-0.004	-0.004	0.000	0.000	0.000	0.000
91	A	172	GLY	0	0.083	0.041	27.778	-0.006	-0.006	0.000	0.000	0.000	0.000
92	A	173	VAL	0	-0.019	-0.006	24.164	-0.008	-0.008	0.000	0.000	0.000	0.000
93	A	174	VAL	0	0.001	0.008	24.955	0.011	0.011	0.000	0.000	0.000	0.000
94	A	175	ASP	-1	-0.812	-0.878	25.028	-0.128	-0.128	0.000	0.000	0.000	0.000
95	A	176	PRO	0	0.038	-0.005	22.683	0.004	0.004	0.000	0.000	0.000	0.000
96	A	177	ARG	1	0.830	0.875	25.090	0.110	0.110	0.000	0.000	0.000	0.000
97	A	178	ALA	0	-0.021	0.007	28.198	0.007	0.007	0.000	0.000	0.000	0.000
98	A	179	ILE	0	0.017	0.023	26.920	0.006	0.006	0.000	0.000	0.000	0.000
99	A	180	SER	0	-0.029	-0.036	27.524	-0.010	-0.010	0.000	0.000	0.000	0.000
100	A	181	VAL	0	0.003	-0.006	24.928	-0.003	-0.003	0.000	0.000	0.000	0.000
101	A	182	LEU	0	-0.013	-0.005	21.713	-0.016	-0.016	0.000	0.000	0.000	0.000
102	A	183	ALA	0	-0.003	0.000	23.551	-0.009	-0.009	0.000	0.000	0.000	0.000
103	A	184	LYS	1	0.888	0.943	25.827	0.123	0.123	0.000	0.000	0.000	0.000
104	A	185	TRP	0	0.026	0.004	17.746	0.020	0.020	0.000	0.000	0.000	0.000
105	A	186	GLN	0	-0.050	-0.022	21.892	0.016	0.016	0.000	0.000	0.000	0.000
106	A	187	ASN	0	-0.025	-0.004	17.707	0.018	0.018	0.000	0.000	0.000	0.000
107	A	188	SER	0	0.027	0.014	19.189	-0.013	-0.013	0.000	0.000	0.000	0.000
108	A	189	TYR	0	-0.068	-0.025	21.505	0.015	0.015	0.000	0.000	0.000	0.000
109	A	190	SER	0	0.054	0.019	19.647	-0.019	-0.019	0.000	0.000	0.000	0.000
110	A	191	ILE	0	0.029	0.009	16.861	0.018	0.018	0.000	0.000	0.000	0.000
111	A	192	LYS	1	0.801	0.892	20.903	0.168	0.168	0.000	0.000	0.000	0.000
112	A	193	VAL	0	0.018	0.011	23.871	0.012	0.012	0.000	0.000	0.000	0.000
113	A	194	VAL	0	-0.007	0.001	21.585	0.012	0.012	0.000	0.000	0.000	0.000
114	A	195	LEU	0	0.006	0.011	24.171	0.012	0.012	0.000	0.000	0.000	0.000
115	A	196	GLN	0	0.019	0.006	26.865	0.005	0.005	0.000	0.000	0.000	0.000
116	A	197	GLU	-1	-0.773	-0.835	28.093	-0.095	-0.095	0.000	0.000	0.000	0.000
117	A	198	LEU	0	-0.012	-0.005	26.324	0.008	0.008	0.000	0.000	0.000	0.000
118	A	199	ARG	1	0.911	0.954	30.238	0.084	0.084	0.000	0.000	0.000	0.000
119	A	200	ARG	1	0.836	0.885	32.725	0.097	0.097	0.000	0.000	0.000	0.000
120	A	201	LEU	0	-0.003	-0.005	31.117	0.006	0.006	0.000	0.000	0.000	0.000
121	A	202	MET	0	-0.011	0.024	31.969	0.006	0.006	0.000	0.000	0.000	0.000
122	A	203	MET	0	-0.009	-0.001	36.259	0.006	0.006	0.000	0.000	0.000	0.000
123	A	204	SER	0	-0.043	-0.019	37.674	0.004	0.004	0.000	0.000	0.000	0.000
124	A	205	LYS	1	0.953	0.946	39.684	0.050	0.050	0.000	0.000	0.000	0.000
125	A	206	GLU	-1	-0.857	-0.913	37.738	-0.070	-0.070	0.000	0.000	0.000	0.000
126	A	207	ASN	0	0.030	0.005	36.982	0.000	0.000	0.000	0.000	0.000	0.000
127	A	208	MET	0	-0.002	0.015	39.659	0.002	0.002	0.000	0.000	0.000	0.000
128	A	209	LYS	1	0.937	0.947	41.663	0.047	0.047	0.000	0.000	0.000	0.000
129	A	210	LEU	0	0.022	0.045	38.615	0.003	0.003	0.000	0.000	0.000	0.000
130	A	211	PRO	0	0.025	0.015	41.693	-0.001	-0.001	0.000	0.000	0.000	0.000
131	A	212	GLN	0	0.043	0.019	37.676	-0.005	-0.005	0.000	0.000	0.000	0.000
132	A	213	PRO	0	-0.016	0.007	36.912	0.003	0.003	0.000	0.000	0.000	0.000
133	A	214	PRO	0	0.042	0.001	40.109	0.000	0.000	0.000	0.000	0.000	0.000
134	A	215	GLU	-1	-0.778	-0.879	38.722	-0.058	-0.058	0.000	0.000	0.000	0.000
135	A	216	GLY	0	0.000	0.006	36.250	0.002	0.002	0.000	0.000	0.000	0.000
136	A	217	GLN	0	-0.029	-0.008	35.457	-0.003	-0.003	0.000	0.000	0.000	0.000
137	A	218	CYS	0	-0.005	-0.007	30.539	-0.005	-0.005	0.000	0.000	0.000	0.000
138	A	219	TYR	0	-0.096	-0.026	28.370	0.004	0.004	0.000	0.000	0.000	0.000
139	A	220	SER	0	0.038	0.024	25.064	-0.009	-0.009	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:82:GLY)