FMO DATABASE

FMODB ID: LZ2R9

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1203622.356976
FMO2-HF: Nuclear repulsion	1147350.984676
FMO2-HF: Total energy	-56271.372301
FMO2-MP2: Total energy	-56438.235975

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.
-2.055	-0.529	-0.013	-0.714	-0.799	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 : 0.010 / q_NPA : -0.019

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	0.053	0.052	3.832	-1.762	-0.236	-0.013	-0.714	-0.799	0.003
4	A	11	SER	0	-0.005	-0.004	6.358	0.567	0.567	0.000	0.000	0.000	0.000
5	A	12	PHE	0	-0.033	0.011	8.586	-0.064	-0.064	0.000	0.000	0.000	0.000
6	A	13	PRO	0	-0.003	-0.010	11.061	0.047	0.047	0.000	0.000	0.000	0.000
7	A	14	TYR	0	-0.010	-0.026	9.767	-0.086	-0.086	0.000	0.000	0.000	0.000
8	A	15	GLY	0	0.047	0.023	10.028	0.134	0.134	0.000	0.000	0.000	0.000
9	A	16	SER	0	-0.023	-0.006	11.223	0.124	0.124	0.000	0.000	0.000	0.000
10	A	17	PRO	0	0.038	-0.007	13.166	0.005	0.005	0.000	0.000	0.000	0.000
11	A	18	GLY	0	-0.001	0.000	14.253	0.068	0.068	0.000	0.000	0.000	0.000
12	A	19	GLU	-1	-0.861	-0.936	8.237	-1.876	-1.876	0.000	0.000	0.000	0.000
13	A	20	LEU	0	0.022	0.013	12.109	0.065	0.065	0.000	0.000	0.000	0.000
14	A	21	ASN	0	-0.010	-0.014	15.071	0.106	0.106	0.000	0.000	0.000	0.000
15	A	22	SER	0	0.003	0.007	12.188	0.098	0.098	0.000	0.000	0.000	0.000
16	A	23	PHE	0	-0.021	0.007	14.002	0.039	0.039	0.000	0.000	0.000	0.000
17	A	24	LEU	0	0.066	0.021	15.234	0.024	0.024	0.000	0.000	0.000	0.000
18	A	25	PRO	0	-0.002	-0.010	17.192	0.015	0.015	0.000	0.000	0.000	0.000
19	A	26	TYR	0	0.016	0.009	18.405	0.016	0.016	0.000	0.000	0.000	0.000
20	A	27	LEU	0	-0.001	-0.002	18.176	0.017	0.017	0.000	0.000	0.000	0.000
21	A	28	LEU	0	0.014	0.004	21.378	0.017	0.017	0.000	0.000	0.000	0.000
22	A	29	THR	0	-0.038	0.003	23.420	0.013	0.013	0.000	0.000	0.000	0.000
23	A	30	ARG	1	0.978	0.989	23.589	0.224	0.224	0.000	0.000	0.000	0.000
24	A	31	ILE	0	0.063	0.029	23.901	0.008	0.008	0.000	0.000	0.000	0.000
25	A	32	THR	0	-0.017	-0.001	27.414	0.016	0.016	0.000	0.000	0.000	0.000
26	A	33	HIS	0	-0.042	-0.032	29.201	0.010	0.010	0.000	0.000	0.000	0.000
27	A	34	ILE	0	0.026	0.009	28.368	0.004	0.004	0.000	0.000	0.000	0.000
28	A	35	TRP	0	0.026	0.027	31.525	0.006	0.006	0.000	0.000	0.000	0.000
29	A	36	SER	0	-0.062	-0.053	33.458	0.005	0.005	0.000	0.000	0.000	0.000
30	A	37	SER	0	-0.064	-0.022	34.529	0.005	0.005	0.000	0.000	0.000	0.000
31	A	38	GLU	-1	-0.925	-0.960	35.041	-0.086	-0.086	0.000	0.000	0.000	0.000
32	A	39	LEU	0	0.038	0.031	37.784	0.006	0.006	0.000	0.000	0.000	0.000
33	A	40	ASN	0	0.039	0.022	38.694	0.008	0.008	0.000	0.000	0.000	0.000
34	A	41	GLN	0	-0.037	-0.025	40.784	0.001	0.001	0.000	0.000	0.000	0.000
35	A	42	ALA	0	0.046	0.045	42.351	0.001	0.001	0.000	0.000	0.000	0.000
36	A	43	LEU	0	-0.022	-0.023	42.512	0.004	0.004	0.000	0.000	0.000	0.000
37	A	44	ALA	0	-0.057	-0.027	45.113	0.003	0.003	0.000	0.000	0.000	0.000
38	A	45	SER	0	-0.016	0.000	47.008	0.001	0.001	0.000	0.000	0.000	0.000
39	A	46	GLU	-1	-0.921	-0.963	48.063	-0.033	-0.033	0.000	0.000	0.000	0.000
40	A	47	LYS	1	0.907	0.966	48.866	0.036	0.036	0.000	0.000	0.000	0.000
41	A	48	LEU	0	-0.006	0.002	46.940	0.003	0.003	0.000	0.000	0.000	0.000
42	A	49	PRO	0	-0.033	-0.032	45.588	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	50	THR	0	0.083	0.017	39.232	0.004	0.004	0.000	0.000	0.000	0.000
44	A	51	PRO	0	-0.045	-0.017	42.447	0.002	0.002	0.000	0.000	0.000	0.000
45	A	52	LYS	1	0.965	0.967	43.809	0.035	0.035	0.000	0.000	0.000	0.000
46	A	53	LEU	0	0.002	0.029	41.072	0.003	0.003	0.000	0.000	0.000	0.000
47	A	54	ARG	1	0.921	0.952	36.200	0.056	0.056	0.000	0.000	0.000	0.000
48	A	55	LEU	0	0.024	0.004	41.797	0.003	0.003	0.000	0.000	0.000	0.000
49	A	56	LEU	0	0.011	0.017	44.353	0.003	0.003	0.000	0.000	0.000	0.000
50	A	57	SER	0	0.024	0.013	40.690	0.004	0.004	0.000	0.000	0.000	0.000
51	A	58	SER	0	-0.001	-0.007	41.278	0.002	0.002	0.000	0.000	0.000	0.000
52	A	59	LEU	0	-0.017	-0.015	42.541	0.003	0.003	0.000	0.000	0.000	0.000
53	A	60	SER	0	-0.047	-0.018	45.207	0.002	0.002	0.000	0.000	0.000	0.000
54	A	61	ALA	0	-0.061	-0.011	41.309	0.002	0.002	0.000	0.000	0.000	0.000
55	A	62	TYR	0	-0.007	-0.023	37.322	0.004	0.004	0.000	0.000	0.000	0.000
56	A	63	GLY	0	-0.004	0.011	44.081	0.002	0.002	0.000	0.000	0.000	0.000
57	A	64	GLU	-1	-0.869	-0.925	47.832	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	65	LEU	0	-0.005	0.010	43.189	0.001	0.001	0.000	0.000	0.000	0.000
59	A	66	THR	0	0.004	-0.016	44.895	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	67	VAL	0	0.058	0.010	45.351	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	68	GLY	0	0.000	-0.020	43.075	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	69	GLN	0	0.032	0.021	40.973	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	70	LEU	0	0.031	0.018	40.633	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	71	ALA	0	-0.040	-0.009	40.795	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	72	THR	0	-0.014	0.009	35.699	-0.003	-0.003	0.000	0.000	0.000	0.000
66	A	73	LEU	0	0.005	0.008	36.440	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	74	GLY	0	0.024	0.021	36.929	-0.003	-0.003	0.000	0.000	0.000	0.000
68	A	75	VAL	0	-0.055	-0.024	33.352	-0.005	-0.005	0.000	0.000	0.000	0.000
69	A	76	MET	0	-0.075	-0.042	36.191	-0.006	-0.006	0.000	0.000	0.000	0.000
70	A	77	GLU	-1	-0.845	-0.911	38.864	-0.042	-0.042	0.000	0.000	0.000	0.000
71	A	78	GLN	0	0.062	0.021	40.368	0.001	0.001	0.000	0.000	0.000	0.000
72	A	79	SER	0	0.012	0.008	43.064	0.001	0.001	0.000	0.000	0.000	0.000
73	A	80	THR	0	0.039	0.003	42.823	0.001	0.001	0.000	0.000	0.000	0.000
74	A	81	THR	0	0.018	0.010	42.526	0.001	0.001	0.000	0.000	0.000	0.000
75	A	82	SER	0	0.005	-0.004	45.069	0.002	0.002	0.000	0.000	0.000	0.000
76	A	83	ARG	1	0.924	0.977	45.249	0.038	0.038	0.000	0.000	0.000	0.000
77	A	84	THR	0	-0.023	-0.024	46.517	0.000	0.000	0.000	0.000	0.000	0.000
78	A	85	VAL	0	-0.031	-0.020	47.680	0.001	0.001	0.000	0.000	0.000	0.000
79	A	86	ASP	-1	-0.880	-0.951	50.150	-0.018	-0.018	0.000	0.000	0.000	0.000
80	A	87	GLN	0	-0.016	0.008	50.451	0.000	0.000	0.000	0.000	0.000	0.000
81	A	88	LEU	0	0.034	0.016	48.546	0.001	0.001	0.000	0.000	0.000	0.000
82	A	89	VAL	0	-0.038	-0.003	52.956	0.002	0.002	0.000	0.000	0.000	0.000
83	A	90	ASP	-1	-0.877	-0.930	55.575	-0.016	-0.016	0.000	0.000	0.000	0.000
84	A	91	GLU	-1	-1.010	-1.009	53.462	-0.027	-0.027	0.000	0.000	0.000	0.000
85	A	92	GLY	0	-0.066	-0.038	57.290	0.000	0.000	0.000	0.000	0.000	0.000
86	A	93	LEU	0	-0.075	-0.055	52.240	0.001	0.001	0.000	0.000	0.000	0.000
87	A	94	ALA	0	0.003	-0.006	51.643	0.001	0.001	0.000	0.000	0.000	0.000
88	A	95	ALA	0	0.009	0.009	53.769	0.000	0.000	0.000	0.000	0.000	0.000
89	A	96	ARG	1	0.873	0.929	52.122	0.013	0.013	0.000	0.000	0.000	0.000
90	A	97	SER	0	0.028	0.013	53.694	0.000	0.000	0.000	0.000	0.000	0.000
91	A	98	ILE	0	-0.104	-0.045	54.465	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	99	SER	0	0.032	-0.002	53.737	0.000	0.000	0.000	0.000	0.000	0.000
93	A	100	ASP	-1	-0.975	-0.998	56.197	0.003	0.003	0.000	0.000	0.000	0.000
94	A	101	ALA	0	0.016	0.004	57.393	0.001	0.001	0.000	0.000	0.000	0.000
95	A	102	ASP	-1	-0.875	-0.880	52.429	0.010	0.010	0.000	0.000	0.000	0.000
96	A	103	GLN	0	-0.024	-0.029	48.421	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	104	ARG	1	0.995	0.991	53.559	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	105	LYS	1	0.886	0.949	48.458	-0.005	-0.005	0.000	0.000	0.000	0.000
99	A	106	ARG	1	0.979	0.988	51.129	0.013	0.013	0.000	0.000	0.000	0.000
100	A	107	THR	0	-0.050	-0.026	49.609	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	108	VAL	0	-0.037	-0.019	48.913	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	109	VAL	0	0.082	0.041	50.223	0.001	0.001	0.000	0.000	0.000	0.000
103	A	110	LEU	0	0.038	0.017	49.287	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	111	THR	0	0.006	0.010	52.208	0.001	0.001	0.000	0.000	0.000	0.000
105	A	112	ARG	1	0.968	0.954	54.601	0.004	0.004	0.000	0.000	0.000	0.000
106	A	113	LYS	1	0.958	0.984	56.060	0.013	0.013	0.000	0.000	0.000	0.000
107	A	114	GLY	0	0.076	0.042	52.750	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	115	LYS	1	0.966	0.978	51.149	0.006	0.006	0.000	0.000	0.000	0.000
109	A	116	LYS	1	0.936	0.984	51.268	0.014	0.014	0.000	0.000	0.000	0.000
110	A	117	LYS	1	0.985	1.004	50.620	0.026	0.026	0.000	0.000	0.000	0.000
111	A	118	LEU	0	0.020	0.001	45.743	-0.002	-0.002	0.000	0.000	0.000	0.000
112	A	119	ALA	0	-0.020	-0.022	48.009	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	120	GLU	-1	-0.892	-0.951	49.658	-0.022	-0.022	0.000	0.000	0.000	0.000
114	A	121	ILE	0	0.024	0.030	44.857	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	122	SER	0	-0.090	-0.053	44.642	-0.002	-0.002	0.000	0.000	0.000	0.000
116	A	123	PRO	0	-0.038	-0.015	44.007	-0.001	-0.001	0.000	0.000	0.000	0.000
117	A	124	LEU	0	0.049	0.032	43.330	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	125	ILE	0	-0.034	-0.020	39.377	-0.003	-0.003	0.000	0.000	0.000	0.000
119	A	126	ASN	0	0.024	-0.003	39.356	-0.003	-0.003	0.000	0.000	0.000	0.000
120	A	127	ASP	-1	-0.882	-0.930	38.965	-0.035	-0.035	0.000	0.000	0.000	0.000
121	A	128	PHE	0	-0.011	-0.010	37.421	-0.004	-0.004	0.000	0.000	0.000	0.000
122	A	129	HIS	0	-0.039	-0.021	32.349	-0.009	-0.009	0.000	0.000	0.000	0.000
123	A	130	ALA	0	0.006	-0.005	34.285	-0.003	-0.003	0.000	0.000	0.000	0.000
124	A	131	GLU	-1	-0.935	-0.956	34.906	-0.062	-0.062	0.000	0.000	0.000	0.000
125	A	132	LEU	0	-0.096	-0.046	29.759	-0.007	-0.007	0.000	0.000	0.000	0.000
126	A	133	VAL	0	-0.053	-0.029	29.959	-0.006	-0.006	0.000	0.000	0.000	0.000
127	A	134	GLY	0	0.052	0.039	30.178	-0.003	-0.003	0.000	0.000	0.000	0.000
128	A	135	ASN	0	-0.068	-0.053	30.785	0.010	0.010	0.000	0.000	0.000	0.000
129	A	136	VAL	0	-0.069	-0.016	25.880	0.001	0.001	0.000	0.000	0.000	0.000
130	A	137	ASP	-1	-0.846	-0.939	26.650	0.010	0.010	0.000	0.000	0.000	0.000
131	A	138	PRO	0	0.061	0.022	28.288	0.000	0.000	0.000	0.000	0.000	0.000
132	A	139	ASP	-1	-0.823	-0.921	28.614	0.032	0.032	0.000	0.000	0.000	0.000
133	A	140	LYS	1	0.827	0.920	21.641	0.035	0.035	0.000	0.000	0.000	0.000
134	A	141	LEU	0	-0.041	-0.017	25.055	-0.004	-0.004	0.000	0.000	0.000	0.000
135	A	142	GLN	0	0.011	-0.010	27.483	-0.010	-0.010	0.000	0.000	0.000	0.000
136	A	143	THR	0	0.019	0.005	22.321	0.008	0.008	0.000	0.000	0.000	0.000
137	A	144	CYS	0	-0.076	-0.038	23.263	0.000	0.000	0.000	0.000	0.000	0.000
138	A	145	ILE	0	-0.016	-0.008	24.286	-0.004	-0.004	0.000	0.000	0.000	0.000
139	A	146	GLU	-1	-0.856	-0.897	26.399	0.056	0.056	0.000	0.000	0.000	0.000
140	A	147	VAL	0	0.008	0.012	20.536	0.005	0.005	0.000	0.000	0.000	0.000
141	A	148	LEU	0	-0.017	-0.017	23.024	-0.001	-0.001	0.000	0.000	0.000	0.000
142	A	149	GLY	0	0.009	0.015	25.168	-0.005	-0.005	0.000	0.000	0.000	0.000
143	A	150	GLU	-1	-0.969	-0.985	23.135	0.114	0.114	0.000	0.000	0.000	0.000
144	A	151	ILE	0	-0.049	-0.043	20.370	0.000	0.000	0.000	0.000	0.000	0.000
145	A	152	LEU	0	-0.044	-0.026	24.200	-0.004	-0.004	0.000	0.000	0.000	0.000
146	A	153	LYS	1	0.973	0.986	27.521	-0.055	-0.055	0.000	0.000	0.000	0.000
147	A	154	GLY	0	-0.025	0.003	25.158	0.003	0.003	0.000	0.000	0.000	0.000
148	A	155	LYS	1	0.892	0.945	22.634	0.012	0.012	0.000	0.000	0.000	0.000
149	A	156	THR	0	-0.033	0.003	26.380	-0.011	-0.011	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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