FMO DATABASE

FMODB ID: MV7ZZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1205607.452396
FMO2-HF: Nuclear repulsion	1149334.069679
FMO2-HF: Total energy	-56273.382718
FMO2-MP2: Total energy	-56440.096705

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.
-1.51	-0.0039999999999998	-0.016	-0.607	-0.883	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 : -0.003 / q_NPA : -0.025

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	0.045	0.026	3.858	-1.664	-0.158	-0.016	-0.607	-0.883	0.003
4	A	11	SER	0	-0.011	-0.007	6.569	0.461	0.461	0.000	0.000	0.000	0.000
5	A	12	PHE	0	-0.016	0.012	8.697	-0.102	-0.102	0.000	0.000	0.000	0.000
6	A	13	PRO	0	-0.039	-0.016	11.866	0.042	0.042	0.000	0.000	0.000	0.000
7	A	14	TYR	0	0.003	-0.020	9.901	-0.041	-0.041	0.000	0.000	0.000	0.000
8	A	15	GLY	0	0.030	0.018	10.063	0.072	0.072	0.000	0.000	0.000	0.000
9	A	16	SER	0	-0.051	-0.056	11.094	0.097	0.097	0.000	0.000	0.000	0.000
10	A	17	PRO	0	0.032	-0.008	13.305	0.025	0.025	0.000	0.000	0.000	0.000
11	A	18	GLY	0	0.001	0.010	13.985	0.050	0.050	0.000	0.000	0.000	0.000
12	A	19	GLU	-1	-0.768	-0.858	9.087	-0.982	-0.982	0.000	0.000	0.000	0.000
13	A	20	LEU	0	0.007	0.013	12.149	0.089	0.089	0.000	0.000	0.000	0.000
14	A	21	ASN	0	-0.022	-0.018	15.376	0.075	0.075	0.000	0.000	0.000	0.000
15	A	22	SER	0	0.031	0.015	13.035	0.046	0.046	0.000	0.000	0.000	0.000
16	A	23	PHE	0	-0.030	-0.007	14.278	0.062	0.062	0.000	0.000	0.000	0.000
17	A	24	LEU	0	0.075	0.028	15.534	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	25	PRO	0	0.013	0.004	17.439	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	26	TYR	0	0.003	0.012	18.798	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	27	LEU	0	-0.010	0.003	18.349	0.002	0.002	0.000	0.000	0.000	0.000
21	A	28	LEU	0	0.035	0.017	21.772	0.002	0.002	0.000	0.000	0.000	0.000
22	A	29	THR	0	-0.028	-0.014	23.418	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	30	ARG	1	0.916	0.963	23.426	0.099	0.099	0.000	0.000	0.000	0.000
24	A	31	ILE	0	0.051	0.026	24.630	0.000	0.000	0.000	0.000	0.000	0.000
25	A	32	THR	0	-0.022	-0.025	27.790	0.005	0.005	0.000	0.000	0.000	0.000
26	A	33	HIS	0	-0.032	-0.012	29.325	0.003	0.003	0.000	0.000	0.000	0.000
27	A	34	ILE	0	-0.009	0.009	28.551	0.000	0.000	0.000	0.000	0.000	0.000
28	A	35	TRP	0	0.066	0.039	31.872	0.002	0.002	0.000	0.000	0.000	0.000
29	A	36	SER	0	-0.026	-0.023	33.649	0.003	0.003	0.000	0.000	0.000	0.000
30	A	37	SER	0	-0.087	-0.050	34.422	0.000	0.000	0.000	0.000	0.000	0.000
31	A	38	GLU	-1	-0.885	-0.950	34.969	-0.029	-0.029	0.000	0.000	0.000	0.000
32	A	39	LEU	0	0.027	0.018	37.802	0.002	0.002	0.000	0.000	0.000	0.000
33	A	40	ASN	0	-0.026	-0.005	38.870	0.005	0.005	0.000	0.000	0.000	0.000
34	A	41	GLN	0	-0.036	-0.021	39.959	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	42	ALA	0	0.033	0.038	42.447	0.000	0.000	0.000	0.000	0.000	0.000
36	A	43	LEU	0	-0.009	-0.022	42.545	0.001	0.001	0.000	0.000	0.000	0.000
37	A	44	ALA	0	-0.047	-0.023	45.488	0.001	0.001	0.000	0.000	0.000	0.000
38	A	45	SER	0	-0.030	-0.012	47.421	0.000	0.000	0.000	0.000	0.000	0.000
39	A	46	GLU	-1	-0.823	-0.909	48.975	0.002	0.002	0.000	0.000	0.000	0.000
40	A	47	LYS	1	0.886	0.953	49.334	0.006	0.006	0.000	0.000	0.000	0.000
41	A	48	LEU	0	0.005	0.019	47.563	0.001	0.001	0.000	0.000	0.000	0.000
42	A	49	PRO	0	0.006	-0.009	45.640	0.000	0.000	0.000	0.000	0.000	0.000
43	A	50	THR	0	0.081	0.012	39.019	0.003	0.003	0.000	0.000	0.000	0.000
44	A	51	PRO	0	-0.007	-0.020	42.125	0.003	0.003	0.000	0.000	0.000	0.000
45	A	52	LYS	1	0.835	0.890	43.521	0.000	0.000	0.000	0.000	0.000	0.000
46	A	53	LEU	0	0.024	0.030	41.754	0.002	0.002	0.000	0.000	0.000	0.000
47	A	54	ARG	1	0.881	0.936	36.066	-0.005	-0.005	0.000	0.000	0.000	0.000
48	A	55	LEU	0	-0.004	0.010	41.673	0.004	0.004	0.000	0.000	0.000	0.000
49	A	56	LEU	0	0.020	0.008	44.397	0.002	0.002	0.000	0.000	0.000	0.000
50	A	57	SER	0	0.038	0.010	41.950	0.002	0.002	0.000	0.000	0.000	0.000
51	A	58	SER	0	-0.031	-0.022	41.150	0.004	0.004	0.000	0.000	0.000	0.000
52	A	59	LEU	0	-0.016	-0.022	42.701	0.002	0.002	0.000	0.000	0.000	0.000
53	A	60	SER	0	-0.066	-0.041	45.517	0.001	0.001	0.000	0.000	0.000	0.000
54	A	61	ALA	0	-0.025	0.005	41.386	0.001	0.001	0.000	0.000	0.000	0.000
55	A	62	TYR	0	-0.002	-0.006	37.603	0.004	0.004	0.000	0.000	0.000	0.000
56	A	63	GLY	0	-0.012	0.012	44.527	0.001	0.001	0.000	0.000	0.000	0.000
57	A	64	GLU	-1	-0.805	-0.860	47.904	0.025	0.025	0.000	0.000	0.000	0.000
58	A	65	LEU	0	-0.043	-0.010	43.301	0.002	0.002	0.000	0.000	0.000	0.000
59	A	66	THR	0	0.007	-0.030	45.026	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	67	VAL	0	0.034	-0.001	45.144	0.000	0.000	0.000	0.000	0.000	0.000
61	A	68	GLY	0	0.037	0.025	42.578	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	69	GLN	0	0.070	0.061	40.726	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	70	LEU	0	0.025	0.014	40.520	0.001	0.001	0.000	0.000	0.000	0.000
64	A	71	ALA	0	-0.025	0.003	40.317	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	72	THR	0	-0.033	-0.024	35.561	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	73	LEU	0	-0.021	-0.012	36.127	0.000	0.000	0.000	0.000	0.000	0.000
67	A	74	GLY	0	0.027	0.022	37.340	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	75	VAL	0	-0.010	0.005	33.024	-0.005	-0.005	0.000	0.000	0.000	0.000
69	A	76	MET	0	-0.041	-0.011	36.240	-0.006	-0.006	0.000	0.000	0.000	0.000
70	A	77	GLU	-1	-0.694	-0.783	38.854	0.008	0.008	0.000	0.000	0.000	0.000
71	A	78	GLN	0	0.073	0.026	40.225	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	79	SER	0	-0.033	-0.038	42.958	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	80	THR	0	-0.014	-0.043	42.798	-0.002	-0.002	0.000	0.000	0.000	0.000
74	A	81	THR	0	-0.006	0.001	42.352	0.000	0.000	0.000	0.000	0.000	0.000
75	A	82	SER	0	-0.019	-0.020	44.848	0.001	0.001	0.000	0.000	0.000	0.000
76	A	83	ARG	1	0.898	0.946	45.329	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	84	THR	0	-0.039	-0.020	46.239	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	85	VAL	0	0.012	-0.006	47.350	0.000	0.000	0.000	0.000	0.000	0.000
79	A	86	ASP	-1	-0.778	-0.883	49.922	0.012	0.012	0.000	0.000	0.000	0.000
80	A	87	GLN	0	0.029	0.030	49.816	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	88	LEU	0	0.008	0.008	48.309	0.000	0.000	0.000	0.000	0.000	0.000
82	A	89	VAL	0	-0.060	-0.013	52.875	0.001	0.001	0.000	0.000	0.000	0.000
83	A	90	ASP	-1	-0.863	-0.916	55.700	0.006	0.006	0.000	0.000	0.000	0.000
84	A	91	GLU	-1	-0.839	-0.904	53.210	0.003	0.003	0.000	0.000	0.000	0.000
85	A	92	GLY	0	0.047	0.032	57.186	0.000	0.000	0.000	0.000	0.000	0.000
86	A	93	LEU	0	-0.093	-0.033	52.442	0.001	0.001	0.000	0.000	0.000	0.000
87	A	94	ALA	0	0.015	-0.003	51.384	0.002	0.002	0.000	0.000	0.000	0.000
88	A	95	ALA	0	-0.003	-0.009	53.435	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	96	ARG	1	0.786	0.866	51.507	-0.014	-0.014	0.000	0.000	0.000	0.000
90	A	97	SER	0	-0.030	-0.043	53.281	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	98	ILE	0	-0.064	-0.024	54.250	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	99	SER	0	-0.002	-0.023	53.387	0.001	0.001	0.000	0.000	0.000	0.000
93	A	100	ASP	-1	-0.964	-0.996	55.704	0.024	0.024	0.000	0.000	0.000	0.000
94	A	101	ALA	0	0.011	0.001	57.538	0.000	0.000	0.000	0.000	0.000	0.000
95	A	102	ASP	-1	-0.890	-0.878	52.471	0.035	0.035	0.000	0.000	0.000	0.000
96	A	103	GLN	0	-0.005	-0.015	48.868	0.001	0.001	0.000	0.000	0.000	0.000
97	A	104	ARG	1	0.978	0.988	53.724	-0.024	-0.024	0.000	0.000	0.000	0.000
98	A	105	LYS	1	0.880	0.938	47.963	-0.036	-0.036	0.000	0.000	0.000	0.000
99	A	106	ARG	1	0.908	0.944	51.210	-0.015	-0.015	0.000	0.000	0.000	0.000
100	A	107	THR	0	-0.028	-0.030	49.133	0.000	0.000	0.000	0.000	0.000	0.000
101	A	108	VAL	0	-0.017	-0.015	49.047	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	109	VAL	0	0.064	0.039	50.024	0.002	0.002	0.000	0.000	0.000	0.000
103	A	110	LEU	0	0.024	0.015	49.061	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	111	THR	0	-0.012	-0.008	51.984	0.001	0.001	0.000	0.000	0.000	0.000
105	A	112	ARG	1	0.973	0.961	54.486	-0.017	-0.017	0.000	0.000	0.000	0.000
106	A	113	LYS	1	0.849	0.916	56.194	-0.009	-0.009	0.000	0.000	0.000	0.000
107	A	114	GLY	0	0.083	0.042	52.662	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	115	LYS	1	0.948	0.970	51.305	-0.023	-0.023	0.000	0.000	0.000	0.000
109	A	116	LYS	1	0.866	0.934	52.010	-0.008	-0.008	0.000	0.000	0.000	0.000
110	A	117	LYS	1	0.802	0.893	51.082	-0.004	-0.004	0.000	0.000	0.000	0.000
111	A	118	LEU	0	0.012	-0.002	46.137	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	119	ALA	0	0.000	-0.004	48.423	0.000	0.000	0.000	0.000	0.000	0.000
113	A	120	GLU	-1	-0.831	-0.895	50.156	0.006	0.006	0.000	0.000	0.000	0.000
114	A	121	ILE	0	0.019	0.014	45.442	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	122	SER	0	-0.059	-0.041	45.381	0.000	0.000	0.000	0.000	0.000	0.000
116	A	123	PRO	0	0.014	0.016	44.710	0.001	0.001	0.000	0.000	0.000	0.000
117	A	124	LEU	0	0.056	0.041	43.741	0.000	0.000	0.000	0.000	0.000	0.000
118	A	125	ILE	0	-0.033	-0.019	40.134	-0.001	-0.001	0.000	0.000	0.000	0.000
119	A	126	ASN	0	-0.043	-0.038	39.930	0.003	0.003	0.000	0.000	0.000	0.000
120	A	127	ASP	-1	-0.884	-0.933	39.954	0.005	0.005	0.000	0.000	0.000	0.000
121	A	128	PHE	0	-0.013	-0.016	38.356	-0.002	-0.002	0.000	0.000	0.000	0.000
122	A	129	HIS	0	-0.019	-0.010	33.369	-0.004	-0.004	0.000	0.000	0.000	0.000
123	A	130	ALA	0	-0.012	-0.005	35.198	0.001	0.001	0.000	0.000	0.000	0.000
124	A	131	GLU	-1	-0.919	-0.959	35.650	-0.012	-0.012	0.000	0.000	0.000	0.000
125	A	132	LEU	0	-0.091	-0.041	30.717	-0.004	-0.004	0.000	0.000	0.000	0.000
126	A	133	VAL	0	-0.046	-0.021	31.044	0.000	0.000	0.000	0.000	0.000	0.000
127	A	134	GLY	0	0.044	0.022	31.095	-0.001	-0.001	0.000	0.000	0.000	0.000
128	A	135	ASN	0	-0.078	-0.047	31.529	0.007	0.007	0.000	0.000	0.000	0.000
129	A	136	VAL	0	-0.044	-0.012	26.818	0.002	0.002	0.000	0.000	0.000	0.000
130	A	137	ASP	-1	-0.820	-0.894	27.086	0.071	0.071	0.000	0.000	0.000	0.000
131	A	138	PRO	0	0.071	0.021	28.767	0.006	0.006	0.000	0.000	0.000	0.000
132	A	139	ASP	-1	-0.830	-0.902	29.142	0.083	0.083	0.000	0.000	0.000	0.000
133	A	140	LYS	1	0.803	0.882	22.803	-0.059	-0.059	0.000	0.000	0.000	0.000
134	A	141	LEU	0	-0.004	0.005	25.595	0.007	0.007	0.000	0.000	0.000	0.000
135	A	142	GLN	0	-0.031	-0.028	28.053	-0.005	-0.005	0.000	0.000	0.000	0.000
136	A	143	THR	0	-0.002	-0.019	23.250	0.011	0.011	0.000	0.000	0.000	0.000
137	A	144	CYS	0	-0.057	-0.027	23.947	0.010	0.010	0.000	0.000	0.000	0.000
138	A	145	ILE	0	-0.021	-0.017	24.957	0.002	0.002	0.000	0.000	0.000	0.000
139	A	146	GLU	-1	-0.871	-0.906	27.205	0.123	0.123	0.000	0.000	0.000	0.000
140	A	147	VAL	0	0.022	0.014	20.950	0.005	0.005	0.000	0.000	0.000	0.000
141	A	148	LEU	0	-0.028	-0.023	23.415	0.002	0.002	0.000	0.000	0.000	0.000
142	A	149	GLY	0	0.022	0.015	25.475	-0.006	-0.006	0.000	0.000	0.000	0.000
143	A	150	GLU	-1	-0.972	-0.983	23.694	0.219	0.219	0.000	0.000	0.000	0.000
144	A	151	ILE	0	-0.016	-0.015	20.480	0.002	0.002	0.000	0.000	0.000	0.000
145	A	152	LEU	0	-0.008	-0.002	24.168	-0.005	-0.005	0.000	0.000	0.000	0.000
146	A	153	LYS	1	0.951	0.983	27.605	-0.126	-0.126	0.000	0.000	0.000	0.000
147	A	154	GLY	0	-0.004	0.006	24.669	-0.003	-0.003	0.000	0.000	0.000	0.000
148	A	155	LYS	1	0.861	0.927	22.388	-0.115	-0.115	0.000	0.000	0.000	0.000
149	A	156	THR	0	-0.076	-0.034	26.314	-0.016	-0.016	0.000	0.000	0.000	0.000

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