FMO DATABASE

FMODB ID: 946Q2

Calculation Name: 3E6M-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3E6M

Chain ID: A

ChEMBL ID:

UniProt ID: Q5LLB9

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:

Apendix: None

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	149
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1203807.316886
FMO2-HF: Nuclear repulsion	1147534.601177
FMO2-HF: Total energy	-56272.715709
FMO2-MP2: Total energy	-56439.494016

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:8:PRO)

Summations of interaction energy for fragment #1(A:8:PRO)

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.
-2.273	-0.865	-0.014	-0.632	-0.761	0.003

Interaction energy analysis for fragmet #1(A:8:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.024 / 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	10	PRO	0	0.061	0.049	3.832	-2.427	-1.019	-0.014	-0.632	-0.761	0.003
4	A	11	SER	0	-0.005	0.000	6.532	0.485	0.485	0.000	0.000	0.000	0.000
5	A	12	PHE	0	-0.023	0.011	8.667	-0.079	-0.079	0.000	0.000	0.000	0.000
6	A	13	PRO	0	-0.029	-0.018	11.412	0.004	0.004	0.000	0.000	0.000	0.000
7	A	14	TYR	0	0.002	-0.027	9.875	-0.072	-0.072	0.000	0.000	0.000	0.000
8	A	15	GLY	0	0.039	0.013	10.264	0.081	0.081	0.000	0.000	0.000	0.000
9	A	16	SER	0	-0.056	-0.049	11.347	0.100	0.100	0.000	0.000	0.000	0.000
10	A	17	PRO	0	0.017	-0.018	13.418	0.024	0.024	0.000	0.000	0.000	0.000
11	A	18	GLY	0	0.002	0.001	14.276	0.054	0.054	0.000	0.000	0.000	0.000
12	A	19	GLU	-1	-0.803	-0.867	9.223	-1.058	-1.058	0.000	0.000	0.000	0.000
13	A	20	LEU	0	0.019	0.014	12.252	0.074	0.074	0.000	0.000	0.000	0.000
14	A	21	ASN	0	-0.018	-0.015	15.305	0.064	0.064	0.000	0.000	0.000	0.000
15	A	22	SER	0	0.022	0.015	12.612	0.075	0.075	0.000	0.000	0.000	0.000
16	A	23	PHE	0	-0.026	-0.003	14.041	0.059	0.059	0.000	0.000	0.000	0.000
17	A	24	LEU	0	0.074	0.025	15.293	-0.013	-0.013	0.000	0.000	0.000	0.000
18	A	25	PRO	0	0.010	-0.002	17.262	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	26	TYR	0	-0.001	0.006	18.491	-0.010	-0.010	0.000	0.000	0.000	0.000
20	A	27	LEU	0	-0.021	-0.008	18.188	0.000	0.000	0.000	0.000	0.000	0.000
21	A	28	LEU	0	0.017	0.003	21.626	0.002	0.002	0.000	0.000	0.000	0.000
22	A	29	THR	0	0.003	0.014	23.524	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	30	ARG	1	0.930	0.974	23.646	0.093	0.093	0.000	0.000	0.000	0.000
24	A	31	ILE	0	0.066	0.030	24.169	0.001	0.001	0.000	0.000	0.000	0.000
25	A	32	THR	0	-0.011	-0.006	27.759	0.007	0.007	0.000	0.000	0.000	0.000
26	A	33	HIS	0	-0.043	-0.028	29.292	0.001	0.001	0.000	0.000	0.000	0.000
27	A	34	ILE	0	0.009	0.013	28.632	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	35	TRP	0	0.031	0.028	31.851	0.001	0.001	0.000	0.000	0.000	0.000
29	A	36	SER	0	-0.042	-0.038	33.659	0.001	0.001	0.000	0.000	0.000	0.000
30	A	37	SER	0	-0.076	-0.045	34.403	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	38	GLU	-1	-0.906	-0.956	34.877	-0.016	-0.016	0.000	0.000	0.000	0.000
32	A	39	LEU	0	0.032	0.027	38.110	0.002	0.002	0.000	0.000	0.000	0.000
33	A	40	ASN	0	0.006	0.011	38.924	0.004	0.004	0.000	0.000	0.000	0.000
34	A	41	GLN	0	-0.035	-0.025	40.210	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	42	ALA	0	0.039	0.041	42.685	0.000	0.000	0.000	0.000	0.000	0.000
36	A	43	LEU	0	-0.027	-0.023	42.724	0.002	0.002	0.000	0.000	0.000	0.000
37	A	44	ALA	0	-0.043	-0.023	45.361	0.001	0.001	0.000	0.000	0.000	0.000
38	A	45	SER	0	-0.013	-0.003	47.210	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	46	GLU	-1	-0.881	-0.930	48.811	0.003	0.003	0.000	0.000	0.000	0.000
40	A	47	LYS	1	0.904	0.955	48.980	0.005	0.005	0.000	0.000	0.000	0.000
41	A	48	LEU	0	-0.007	0.012	47.469	0.001	0.001	0.000	0.000	0.000	0.000
42	A	49	PRO	0	-0.009	-0.022	45.636	0.001	0.001	0.000	0.000	0.000	0.000
43	A	50	THR	0	0.119	0.025	39.054	0.003	0.003	0.000	0.000	0.000	0.000
44	A	51	PRO	0	-0.032	-0.013	42.251	0.003	0.003	0.000	0.000	0.000	0.000
45	A	52	LYS	1	0.837	0.882	43.809	0.003	0.003	0.000	0.000	0.000	0.000
46	A	53	LEU	0	-0.014	0.020	41.571	0.002	0.002	0.000	0.000	0.000	0.000
47	A	54	ARG	1	0.900	0.936	36.297	0.002	0.002	0.000	0.000	0.000	0.000
48	A	55	LEU	0	0.004	-0.011	41.794	0.003	0.003	0.000	0.000	0.000	0.000
49	A	56	LEU	0	0.017	0.017	44.298	0.002	0.002	0.000	0.000	0.000	0.000
50	A	57	SER	0	0.046	0.020	41.542	0.002	0.002	0.000	0.000	0.000	0.000
51	A	58	SER	0	-0.031	-0.011	40.995	0.004	0.004	0.000	0.000	0.000	0.000
52	A	59	LEU	0	-0.004	-0.006	42.475	0.003	0.003	0.000	0.000	0.000	0.000
53	A	60	SER	0	-0.053	-0.026	45.234	0.001	0.001	0.000	0.000	0.000	0.000
54	A	61	ALA	0	-0.061	-0.013	41.289	0.001	0.001	0.000	0.000	0.000	0.000
55	A	62	TYR	0	-0.001	-0.020	37.152	0.003	0.003	0.000	0.000	0.000	0.000
56	A	63	GLY	0	-0.005	0.012	44.009	0.001	0.001	0.000	0.000	0.000	0.000
57	A	64	GLU	-1	-0.813	-0.855	47.761	0.020	0.020	0.000	0.000	0.000	0.000
58	A	65	LEU	0	-0.027	0.003	42.935	0.001	0.001	0.000	0.000	0.000	0.000
59	A	66	THR	0	0.003	-0.028	45.019	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	67	VAL	0	0.039	0.003	45.303	0.000	0.000	0.000	0.000	0.000	0.000
61	A	68	GLY	0	0.016	0.005	43.052	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	69	GLN	0	0.069	0.053	40.918	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	70	LEU	0	0.015	0.010	40.583	0.001	0.001	0.000	0.000	0.000	0.000
64	A	71	ALA	0	-0.042	-0.009	40.783	0.000	0.000	0.000	0.000	0.000	0.000
65	A	72	THR	0	-0.018	-0.001	35.776	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	73	LEU	0	0.006	0.011	36.392	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	74	GLY	0	0.028	0.023	36.873	0.000	0.000	0.000	0.000	0.000	0.000
68	A	75	VAL	0	-0.039	-0.013	33.129	-0.005	-0.005	0.000	0.000	0.000	0.000
69	A	76	MET	0	-0.068	-0.038	36.149	-0.005	-0.005	0.000	0.000	0.000	0.000
70	A	77	GLU	-1	-0.709	-0.795	38.949	-0.006	-0.006	0.000	0.000	0.000	0.000
71	A	78	GLN	0	0.075	0.021	40.343	0.001	0.001	0.000	0.000	0.000	0.000
72	A	79	SER	0	-0.023	-0.033	43.038	0.001	0.001	0.000	0.000	0.000	0.000
73	A	80	THR	0	-0.003	-0.045	43.001	0.000	0.000	0.000	0.000	0.000	0.000
74	A	81	THR	0	0.001	0.004	42.511	0.001	0.001	0.000	0.000	0.000	0.000
75	A	82	SER	0	0.006	-0.004	45.034	0.001	0.001	0.000	0.000	0.000	0.000
76	A	83	ARG	1	0.887	0.952	45.441	0.009	0.009	0.000	0.000	0.000	0.000
77	A	84	THR	0	-0.037	-0.032	46.253	0.000	0.000	0.000	0.000	0.000	0.000
78	A	85	VAL	0	-0.026	-0.022	47.534	0.001	0.001	0.000	0.000	0.000	0.000
79	A	86	ASP	-1	-0.784	-0.881	50.108	0.005	0.005	0.000	0.000	0.000	0.000
80	A	87	GLN	0	0.005	0.029	50.175	0.000	0.000	0.000	0.000	0.000	0.000
81	A	88	LEU	0	0.045	0.025	48.308	0.001	0.001	0.000	0.000	0.000	0.000
82	A	89	VAL	0	-0.047	-0.008	52.921	0.001	0.001	0.000	0.000	0.000	0.000
83	A	90	ASP	-1	-0.862	-0.918	55.526	0.003	0.003	0.000	0.000	0.000	0.000
84	A	91	GLU	-1	-0.904	-0.936	53.299	0.000	0.000	0.000	0.000	0.000	0.000
85	A	92	GLY	0	-0.047	-0.032	57.290	0.000	0.000	0.000	0.000	0.000	0.000
86	A	93	LEU	0	-0.055	-0.040	52.276	0.001	0.001	0.000	0.000	0.000	0.000
87	A	94	ALA	0	0.007	-0.003	51.602	0.002	0.002	0.000	0.000	0.000	0.000
88	A	95	ALA	0	0.003	0.004	53.711	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	96	ARG	1	0.794	0.876	51.747	-0.007	-0.007	0.000	0.000	0.000	0.000
90	A	97	SER	0	-0.035	-0.050	53.700	0.000	0.000	0.000	0.000	0.000	0.000
91	A	98	ILE	0	-0.064	-0.026	54.407	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	99	SER	0	-0.007	-0.015	53.683	0.000	0.000	0.000	0.000	0.000	0.000
93	A	100	ASP	-1	-0.965	-0.998	56.149	0.020	0.020	0.000	0.000	0.000	0.000
94	A	101	ALA	0	0.011	-0.001	57.559	0.000	0.000	0.000	0.000	0.000	0.000
95	A	102	ASP	-1	-0.879	-0.886	52.398	0.030	0.030	0.000	0.000	0.000	0.000
96	A	103	GLN	0	-0.009	-0.006	48.632	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	104	ARG	1	0.996	0.987	53.506	-0.015	-0.015	0.000	0.000	0.000	0.000
98	A	105	LYS	1	0.868	0.936	48.121	-0.026	-0.026	0.000	0.000	0.000	0.000
99	A	106	ARG	1	0.956	0.969	51.063	-0.007	-0.007	0.000	0.000	0.000	0.000
100	A	107	THR	0	-0.020	-0.027	49.134	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	108	VAL	0	-0.035	-0.025	49.260	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	109	VAL	0	0.070	0.038	50.164	0.002	0.002	0.000	0.000	0.000	0.000
103	A	110	LEU	0	0.028	0.015	49.222	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	111	THR	0	0.009	0.015	52.142	0.001	0.001	0.000	0.000	0.000	0.000
105	A	112	ARG	1	0.975	0.958	54.663	-0.017	-0.017	0.000	0.000	0.000	0.000
106	A	113	LYS	1	0.909	0.953	56.276	-0.008	-0.008	0.000	0.000	0.000	0.000
107	A	114	GLY	0	0.074	0.040	52.821	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	115	LYS	1	0.954	0.975	51.372	-0.024	-0.024	0.000	0.000	0.000	0.000
109	A	116	LYS	1	0.877	0.940	51.602	-0.010	-0.010	0.000	0.000	0.000	0.000
110	A	117	LYS	1	0.852	0.924	50.980	-0.006	-0.006	0.000	0.000	0.000	0.000
111	A	118	LEU	0	0.035	0.010	45.876	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	119	ALA	0	-0.014	-0.019	48.421	0.000	0.000	0.000	0.000	0.000	0.000
113	A	120	GLU	-1	-0.798	-0.873	50.197	0.009	0.009	0.000	0.000	0.000	0.000
114	A	121	ILE	0	0.017	0.018	45.331	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	122	SER	0	-0.054	-0.035	45.129	0.001	0.001	0.000	0.000	0.000	0.000
116	A	123	PRO	0	-0.021	-0.006	44.549	0.001	0.001	0.000	0.000	0.000	0.000
117	A	124	LEU	0	0.030	0.025	43.595	0.000	0.000	0.000	0.000	0.000	0.000
118	A	125	ILE	0	-0.023	-0.019	39.823	0.000	0.000	0.000	0.000	0.000	0.000
119	A	126	ASN	0	-0.024	-0.026	39.867	0.003	0.003	0.000	0.000	0.000	0.000
120	A	127	ASP	-1	-0.865	-0.923	39.496	0.019	0.019	0.000	0.000	0.000	0.000
121	A	128	PHE	0	-0.011	-0.010	37.895	-0.002	-0.002	0.000	0.000	0.000	0.000
122	A	129	HIS	0	-0.033	-0.016	32.899	-0.004	-0.004	0.000	0.000	0.000	0.000
123	A	130	ALA	0	-0.007	-0.008	34.805	0.003	0.003	0.000	0.000	0.000	0.000
124	A	131	GLU	-1	-0.926	-0.952	35.400	0.010	0.010	0.000	0.000	0.000	0.000
125	A	132	LEU	0	-0.090	-0.048	30.348	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	133	VAL	0	-0.056	-0.027	30.496	0.001	0.001	0.000	0.000	0.000	0.000
127	A	134	GLY	0	0.050	0.037	30.683	0.003	0.003	0.000	0.000	0.000	0.000
128	A	135	ASN	0	-0.080	-0.056	31.293	0.006	0.006	0.000	0.000	0.000	0.000
129	A	136	VAL	0	-0.059	-0.015	26.476	0.007	0.007	0.000	0.000	0.000	0.000
130	A	137	ASP	-1	-0.841	-0.931	27.178	0.121	0.121	0.000	0.000	0.000	0.000
131	A	138	PRO	0	0.083	0.028	28.921	0.005	0.005	0.000	0.000	0.000	0.000
132	A	139	ASP	-1	-0.832	-0.918	29.544	0.117	0.117	0.000	0.000	0.000	0.000
133	A	140	LYS	1	0.813	0.903	23.026	-0.130	-0.130	0.000	0.000	0.000	0.000
134	A	141	LEU	0	-0.032	-0.010	25.738	0.007	0.007	0.000	0.000	0.000	0.000
135	A	142	GLN	0	-0.014	-0.016	28.144	-0.012	-0.012	0.000	0.000	0.000	0.000
136	A	143	THR	0	0.025	0.005	23.138	0.010	0.010	0.000	0.000	0.000	0.000
137	A	144	CYS	0	-0.053	-0.028	23.959	0.004	0.004	0.000	0.000	0.000	0.000
138	A	145	ILE	0	-0.032	-0.014	24.982	-0.003	-0.003	0.000	0.000	0.000	0.000
139	A	146	GLU	-1	-0.850	-0.895	27.021	0.140	0.140	0.000	0.000	0.000	0.000
140	A	147	VAL	0	0.006	0.008	20.807	0.003	0.003	0.000	0.000	0.000	0.000
141	A	148	LEU	0	-0.023	-0.021	23.230	-0.005	-0.005	0.000	0.000	0.000	0.000
142	A	149	GLY	0	0.019	0.018	25.281	-0.012	-0.012	0.000	0.000	0.000	0.000
143	A	150	GLU	-1	-0.972	-0.986	23.455	0.209	0.209	0.000	0.000	0.000	0.000
144	A	151	ILE	0	-0.055	-0.048	20.356	-0.006	-0.006	0.000	0.000	0.000	0.000
145	A	152	LEU	0	-0.025	-0.009	24.125	-0.010	-0.010	0.000	0.000	0.000	0.000
146	A	153	LYS	1	0.989	0.991	27.454	-0.116	-0.116	0.000	0.000	0.000	0.000
147	A	154	GLY	0	-0.016	0.010	25.094	-0.005	-0.005	0.000	0.000	0.000	0.000
148	A	155	LYS	1	0.879	0.939	22.373	-0.067	-0.067	0.000	0.000	0.000	0.000
149	A	156	THR	0	-0.058	-0.016	26.330	-0.017	-0.017	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:8:PRO)