FMO DATABASE

FMODB ID: 85ZMY

Calculation Name: 3MEX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3MEX

Chain ID: A

ChEMBL ID:

UniProt ID: P52003

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	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	142
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1221956.094407
FMO2-HF: Nuclear repulsion	1163861.248956
FMO2-HF: Total energy	-58094.845451
FMO2-MP2: Total energy	-58261.827824

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.
-5.438	-0.588	2.178	-2.523	-4.505	-0.007

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 : 0.007 / q_NPA : 0.012

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	TYR	0	0.027	0.009	2.786	-3.528	1.322	2.178	-2.523	-4.505	-0.007
4	A	4	PRO	0	-0.013	-0.001	5.574	0.000	0.000	0.000	0.000	0.000	0.000
5	A	5	VAL	0	0.011	-0.004	9.294	-0.194	-0.194	0.000	0.000	0.000	0.000
6	A	6	ASN	0	0.025	0.009	11.437	0.186	0.186	0.000	0.000	0.000	0.000
7	A	7	PRO	0	0.017	0.003	14.186	-0.032	-0.032	0.000	0.000	0.000	0.000
8	A	8	ASP	-1	-0.875	-0.935	17.591	-0.281	-0.281	0.000	0.000	0.000	0.000
9	A	9	LEU	0	-0.027	-0.012	13.605	0.006	0.006	0.000	0.000	0.000	0.000
10	A	10	MET	0	0.017	0.005	17.448	0.011	0.011	0.000	0.000	0.000	0.000
11	A	11	PRO	0	0.010	-0.006	19.427	0.017	0.017	0.000	0.000	0.000	0.000
12	A	12	ALA	0	0.026	0.024	20.137	0.022	0.022	0.000	0.000	0.000	0.000
13	A	13	LEU	0	0.018	0.011	17.458	0.019	0.019	0.000	0.000	0.000	0.000
14	A	14	MET	0	-0.006	-0.016	21.161	0.021	0.021	0.000	0.000	0.000	0.000
15	A	15	ALA	0	0.006	0.012	23.810	0.027	0.027	0.000	0.000	0.000	0.000
16	A	16	VAL	0	0.033	0.021	23.762	0.022	0.022	0.000	0.000	0.000	0.000
17	A	17	PHE	0	-0.009	-0.005	23.695	0.022	0.022	0.000	0.000	0.000	0.000
18	A	18	GLN	0	-0.009	-0.018	25.671	0.016	0.016	0.000	0.000	0.000	0.000
19	A	19	HIS	0	0.027	0.035	28.856	0.023	0.023	0.000	0.000	0.000	0.000
20	A	20	VAL	0	0.067	0.034	26.960	0.015	0.015	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.875	0.934	29.417	0.170	0.170	0.000	0.000	0.000	0.000
22	A	22	THR	0	-0.043	-0.044	31.047	0.016	0.016	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.740	0.840	33.122	0.157	0.157	0.000	0.000	0.000	0.000
24	A	24	ILE	0	0.031	0.017	30.628	0.010	0.010	0.000	0.000	0.000	0.000
25	A	25	GLN	0	-0.004	-0.010	34.693	0.002	0.002	0.000	0.000	0.000	0.000
26	A	26	SER	0	-0.009	0.011	36.857	0.007	0.007	0.000	0.000	0.000	0.000
27	A	27	GLU	-1	-0.716	-0.826	37.139	-0.115	-0.115	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.033	-0.021	35.894	0.005	0.005	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.919	-0.948	40.018	-0.083	-0.083	0.000	0.000	0.000	0.000
30	A	30	CYS	0	-0.018	-0.014	42.782	0.005	0.005	0.000	0.000	0.000	0.000
31	A	31	GLN	0	-0.081	-0.033	40.534	0.007	0.007	0.000	0.000	0.000	0.000
32	A	32	ARG	1	0.888	0.941	44.535	0.073	0.073	0.000	0.000	0.000	0.000
33	A	33	LEU	0	0.010	0.008	39.925	0.002	0.002	0.000	0.000	0.000	0.000
34	A	34	ASP	-1	-0.925	-0.951	43.401	-0.075	-0.075	0.000	0.000	0.000	0.000
35	A	35	LEU	0	-0.009	0.015	38.298	0.001	0.001	0.000	0.000	0.000	0.000
36	A	36	THR	0	-0.037	-0.055	36.771	-0.005	-0.005	0.000	0.000	0.000	0.000
37	A	37	PRO	0	0.049	0.001	32.301	0.000	0.000	0.000	0.000	0.000	0.000
38	A	38	PRO	0	0.008	-0.001	32.014	-0.005	-0.005	0.000	0.000	0.000	0.000
39	A	39	ASP	-1	-0.756	-0.826	33.039	-0.096	-0.096	0.000	0.000	0.000	0.000
40	A	40	VAL	0	0.028	0.008	32.342	0.001	0.001	0.000	0.000	0.000	0.000
41	A	41	HIS	0	-0.034	-0.021	28.923	0.003	0.003	0.000	0.000	0.000	0.000
42	A	42	VAL	0	-0.030	-0.016	30.708	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	43	LEU	0	0.004	0.005	32.892	0.003	0.003	0.000	0.000	0.000	0.000
44	A	44	LYS	1	0.845	0.924	27.315	0.189	0.189	0.000	0.000	0.000	0.000
45	A	45	LEU	0	-0.028	-0.012	26.591	0.000	0.000	0.000	0.000	0.000	0.000
46	A	46	ILE	0	-0.051	-0.035	30.193	0.005	0.005	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.828	-0.901	33.081	-0.105	-0.105	0.000	0.000	0.000	0.000
48	A	48	GLU	-1	-0.883	-0.934	26.738	-0.187	-0.187	0.000	0.000	0.000	0.000
49	A	49	GLN	0	-0.083	-0.033	26.880	0.008	0.008	0.000	0.000	0.000	0.000
50	A	50	ARG	1	0.869	0.912	30.541	0.105	0.105	0.000	0.000	0.000	0.000
51	A	51	GLY	0	0.035	0.021	34.131	0.004	0.004	0.000	0.000	0.000	0.000
52	A	52	LEU	0	-0.035	0.007	30.418	0.006	0.006	0.000	0.000	0.000	0.000
53	A	53	ASN	0	0.015	-0.007	32.785	0.008	0.008	0.000	0.000	0.000	0.000
54	A	54	LEU	0	-0.004	-0.003	33.352	-0.005	-0.005	0.000	0.000	0.000	0.000
55	A	55	GLN	0	-0.019	-0.034	32.398	-0.009	-0.009	0.000	0.000	0.000	0.000
56	A	56	ASP	-1	-0.879	-0.936	29.228	-0.077	-0.077	0.000	0.000	0.000	0.000
57	A	57	LEU	0	0.023	0.025	28.405	-0.014	-0.014	0.000	0.000	0.000	0.000
58	A	58	GLY	0	0.017	-0.015	26.328	0.006	0.006	0.000	0.000	0.000	0.000
59	A	59	ARG	1	0.955	0.973	22.339	0.125	0.125	0.000	0.000	0.000	0.000
60	A	60	GLN	0	-0.006	0.006	19.507	0.016	0.016	0.000	0.000	0.000	0.000
61	A	61	MET	0	-0.014	0.002	21.345	-0.021	-0.021	0.000	0.000	0.000	0.000
62	A	62	CYS	0	0.014	0.017	23.670	0.018	0.018	0.000	0.000	0.000	0.000
63	A	63	ARG	1	0.964	0.960	26.054	0.100	0.100	0.000	0.000	0.000	0.000
64	A	64	ASP	-1	-0.801	-0.898	29.275	-0.056	-0.056	0.000	0.000	0.000	0.000
65	A	65	LYS	1	0.906	0.936	28.780	0.083	0.083	0.000	0.000	0.000	0.000
66	A	66	ALA	0	0.004	0.011	34.206	0.001	0.001	0.000	0.000	0.000	0.000
67	A	67	LEU	0	-0.003	0.000	34.188	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	68	ILE	0	0.007	0.008	30.998	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	69	THR	0	-0.006	-0.005	35.125	0.000	0.000	0.000	0.000	0.000	0.000
70	A	70	ARG	1	0.911	0.955	38.367	0.056	0.056	0.000	0.000	0.000	0.000
71	A	71	LYS	1	0.804	0.876	35.882	0.091	0.091	0.000	0.000	0.000	0.000
72	A	72	ILE	0	0.046	0.025	35.747	0.000	0.000	0.000	0.000	0.000	0.000
73	A	73	ARG	1	0.927	0.972	39.240	0.051	0.051	0.000	0.000	0.000	0.000
74	A	74	GLU	-1	-0.861	-0.903	41.331	-0.077	-0.077	0.000	0.000	0.000	0.000
75	A	75	LEU	0	0.033	0.002	37.366	0.001	0.001	0.000	0.000	0.000	0.000
76	A	76	GLU	-1	-0.804	-0.874	41.911	-0.055	-0.055	0.000	0.000	0.000	0.000
77	A	77	GLY	0	-0.063	-0.023	44.126	0.002	0.002	0.000	0.000	0.000	0.000
78	A	78	ARG	1	0.809	0.896	42.046	0.079	0.079	0.000	0.000	0.000	0.000
79	A	79	ASN	0	-0.006	0.007	46.405	0.000	0.000	0.000	0.000	0.000	0.000
80	A	80	LEU	0	0.028	0.053	41.270	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	81	VAL	0	-0.001	-0.007	38.687	-0.003	-0.003	0.000	0.000	0.000	0.000
82	A	82	ARG	1	0.910	0.942	41.527	0.063	0.063	0.000	0.000	0.000	0.000
83	A	83	ARG	1	0.764	0.837	41.433	0.050	0.050	0.000	0.000	0.000	0.000
84	A	84	GLU	-1	-0.834	-0.894	41.728	-0.046	-0.046	0.000	0.000	0.000	0.000
85	A	85	ARG	1	0.842	0.916	41.791	0.030	0.030	0.000	0.000	0.000	0.000
86	A	86	ASN	0	0.033	0.016	36.891	0.003	0.003	0.000	0.000	0.000	0.000
87	A	87	PRO	0	0.025	0.011	40.964	0.003	0.003	0.000	0.000	0.000	0.000
88	A	88	SER	0	-0.077	-0.044	38.409	0.003	0.003	0.000	0.000	0.000	0.000
89	A	89	ASP	-1	-0.809	-0.888	37.872	-0.026	-0.026	0.000	0.000	0.000	0.000
90	A	90	GLN	0	0.075	0.036	40.326	-0.005	-0.005	0.000	0.000	0.000	0.000
91	A	91	ARG	1	0.883	0.951	38.879	0.020	0.020	0.000	0.000	0.000	0.000
92	A	92	SER	0	-0.036	-0.034	37.355	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	93	PHE	0	-0.039	-0.025	38.691	0.002	0.002	0.000	0.000	0.000	0.000
94	A	94	GLN	0	-0.008	-0.006	36.806	0.000	0.000	0.000	0.000	0.000	0.000
95	A	95	LEU	0	-0.007	0.009	35.216	0.003	0.003	0.000	0.000	0.000	0.000
96	A	96	PHE	0	0.002	-0.014	37.287	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	97	LEU	0	0.031	0.028	36.682	0.002	0.002	0.000	0.000	0.000	0.000
98	A	98	THR	0	-0.077	-0.063	39.932	0.002	0.002	0.000	0.000	0.000	0.000
99	A	99	ASP	-1	-0.862	-0.942	42.592	-0.066	-0.066	0.000	0.000	0.000	0.000
100	A	100	GLU	-1	-0.886	-0.934	44.100	-0.069	-0.069	0.000	0.000	0.000	0.000
101	A	101	GLY	0	0.019	0.000	41.363	-0.004	-0.004	0.000	0.000	0.000	0.000
102	A	102	LEU	0	-0.031	-0.008	38.179	-0.006	-0.006	0.000	0.000	0.000	0.000
103	A	103	ALA	0	-0.009	0.000	39.529	-0.006	-0.006	0.000	0.000	0.000	0.000
104	A	104	ILE	0	0.032	0.007	39.666	-0.005	-0.005	0.000	0.000	0.000	0.000
105	A	105	HIS	0	-0.025	-0.006	32.859	-0.013	-0.013	0.000	0.000	0.000	0.000
106	A	106	GLN	0	0.009	-0.002	36.081	-0.007	-0.007	0.000	0.000	0.000	0.000
107	A	107	HIS	0	-0.035	-0.015	37.397	-0.003	-0.003	0.000	0.000	0.000	0.000
108	A	108	ALA	0	-0.008	-0.015	35.357	-0.005	-0.005	0.000	0.000	0.000	0.000
109	A	109	GLU	-1	-0.817	-0.915	30.815	-0.181	-0.181	0.000	0.000	0.000	0.000
110	A	110	ALA	0	-0.016	0.000	33.265	-0.009	-0.009	0.000	0.000	0.000	0.000
111	A	111	ILE	0	-0.031	-0.017	35.023	-0.005	-0.005	0.000	0.000	0.000	0.000
112	A	112	MET	0	-0.011	-0.003	29.279	-0.010	-0.010	0.000	0.000	0.000	0.000
113	A	113	SER	0	0.035	0.015	30.853	-0.014	-0.014	0.000	0.000	0.000	0.000
114	A	114	ARG	1	0.839	0.909	31.914	0.125	0.125	0.000	0.000	0.000	0.000
115	A	115	VAL	0	-0.035	-0.014	30.568	-0.003	-0.003	0.000	0.000	0.000	0.000
116	A	116	HIS	0	-0.070	-0.047	26.010	-0.025	-0.025	0.000	0.000	0.000	0.000
117	A	117	ASP	-1	-0.881	-0.933	29.173	-0.194	-0.194	0.000	0.000	0.000	0.000
118	A	118	GLU	-1	-0.892	-0.936	31.426	-0.153	-0.153	0.000	0.000	0.000	0.000
119	A	119	LEU	0	-0.061	-0.027	26.306	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	120	PHE	0	-0.001	-0.014	23.705	-0.014	-0.014	0.000	0.000	0.000	0.000
121	A	121	ALA	0	-0.001	0.015	28.060	-0.003	-0.003	0.000	0.000	0.000	0.000
122	A	122	PRO	0	-0.059	-0.034	30.392	0.005	0.005	0.000	0.000	0.000	0.000
123	A	123	LEU	0	-0.023	0.017	24.127	-0.002	-0.002	0.000	0.000	0.000	0.000
124	A	124	THR	0	-0.009	-0.034	26.760	0.005	0.005	0.000	0.000	0.000	0.000
125	A	125	PRO	0	0.048	0.000	26.223	-0.019	-0.019	0.000	0.000	0.000	0.000
126	A	126	VAL	0	0.006	0.008	22.688	-0.018	-0.018	0.000	0.000	0.000	0.000
127	A	127	GLU	-1	-0.823	-0.867	22.066	-0.304	-0.304	0.000	0.000	0.000	0.000
128	A	128	GLN	0	-0.033	-0.029	21.547	-0.044	-0.044	0.000	0.000	0.000	0.000
129	A	129	ALA	0	0.013	0.004	21.179	-0.027	-0.027	0.000	0.000	0.000	0.000
130	A	130	THR	0	-0.049	-0.032	16.926	-0.048	-0.048	0.000	0.000	0.000	0.000
131	A	131	LEU	0	-0.011	-0.015	16.789	-0.084	-0.084	0.000	0.000	0.000	0.000
132	A	132	VAL	0	0.025	0.011	17.266	-0.058	-0.058	0.000	0.000	0.000	0.000
133	A	133	HIS	0	0.038	0.031	11.404	0.009	0.009	0.000	0.000	0.000	0.000
134	A	134	LEU	0	-0.055	-0.031	12.269	-0.142	-0.142	0.000	0.000	0.000	0.000
135	A	135	LEU	0	0.000	0.001	12.472	-0.146	-0.146	0.000	0.000	0.000	0.000
136	A	136	ASP	-1	-0.842	-0.911	13.283	-0.633	-0.633	0.000	0.000	0.000	0.000
137	A	137	GLN	0	-0.076	-0.038	7.761	0.046	0.046	0.000	0.000	0.000	0.000
138	A	138	SER	0	-0.108	-0.052	8.317	-0.266	-0.266	0.000	0.000	0.000	0.000
139	A	139	LEU	0	-0.001	-0.010	9.805	-0.027	-0.027	0.000	0.000	0.000	0.000
140	A	140	ALA	0	-0.025	-0.012	9.502	0.094	0.094	0.000	0.000	0.000	0.000
141	A	141	ALA	0	-0.045	-0.011	5.446	0.102	0.102	0.000	0.000	0.000	0.000
142	A	142	GLN	0	-0.083	-0.030	7.378	-0.102	-0.102	0.000	0.000	0.000	0.000

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