FMO DATABASE

FMODB ID: 22MMR

Calculation Name: 3EMF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EMF

Chain ID: A

ChEMBL ID:

UniProt ID: Q48152

Base Structure: X-ray

Registration Date: 2023-03-14

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	113
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-729117.868562
FMO2-HF: Nuclear repulsion	686720.345853
FMO2-HF: Total energy	-42397.522709
FMO2-MP2: Total energy	-42523.82769

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:53:THR)

Summations of interaction energy for fragment #1(A:53:THR)

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.
2.148	4.763	0.159	-1.031	-1.744	0.003

Interaction energy analysis for fragmet #1(A:53:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.031 / q_NPA : 0.013

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	55	VAL	0	0.030	0.028	3.016	-0.429	2.121	0.159	-1.014	-1.696	0.003
4	A	56	THR	0	-0.066	-0.034	4.242	0.341	0.406	0.000	-0.017	-0.048	0.000
5	A	57	ASN	0	0.010	-0.021	7.729	0.181	0.181	0.000	0.000	0.000	0.000
6	A	58	LYS	1	0.973	0.971	10.872	0.212	0.212	0.000	0.000	0.000	0.000
7	A	59	LEU	0	-0.006	0.022	14.376	0.046	0.046	0.000	0.000	0.000	0.000
8	A	60	LYS	1	0.948	0.991	16.409	0.257	0.257	0.000	0.000	0.000	0.000
9	A	61	ALA	0	-0.026	-0.009	19.192	-0.009	-0.009	0.000	0.000	0.000	0.000
10	A	62	TYR	0	0.043	0.011	21.609	0.020	0.020	0.000	0.000	0.000	0.000
11	A	63	GLY	0	0.012	-0.002	25.280	-0.018	-0.018	0.000	0.000	0.000	0.000
12	A	64	ASP	-1	-0.958	-0.969	21.451	-0.338	-0.338	0.000	0.000	0.000	0.000
13	A	65	ALA	0	0.040	0.019	24.767	0.021	0.021	0.000	0.000	0.000	0.000
14	A	66	ASN	0	-0.060	-0.033	22.446	0.008	0.008	0.000	0.000	0.000	0.000
15	A	67	PHE	0	0.029	0.036	25.348	0.007	0.007	0.000	0.000	0.000	0.000
16	A	68	ASN	0	-0.005	-0.004	26.222	0.017	0.017	0.000	0.000	0.000	0.000
17	A	69	PHE	0	0.040	-0.010	28.652	0.002	0.002	0.000	0.000	0.000	0.000
18	A	70	THR	0	-0.036	0.002	31.720	0.007	0.007	0.000	0.000	0.000	0.000
19	A	71	ASN	0	-0.027	-0.022	27.309	0.015	0.015	0.000	0.000	0.000	0.000
20	A	72	ASN	0	-0.003	0.012	26.520	-0.007	-0.007	0.000	0.000	0.000	0.000
21	A	73	SER	0	0.011	-0.011	30.032	0.008	0.008	0.000	0.000	0.000	0.000
22	A	74	ILE	0	0.068	0.009	32.527	-0.008	-0.008	0.000	0.000	0.000	0.000
23	A	75	ALA	0	0.028	0.022	32.449	-0.005	-0.005	0.000	0.000	0.000	0.000
24	A	76	ASP	-1	-0.839	-0.902	28.271	-0.177	-0.177	0.000	0.000	0.000	0.000
25	A	77	ALA	0	-0.002	-0.007	30.176	-0.013	-0.013	0.000	0.000	0.000	0.000
26	A	78	GLU	-1	-0.910	-0.964	32.189	-0.129	-0.129	0.000	0.000	0.000	0.000
27	A	79	LYS	1	0.912	0.980	28.925	0.186	0.186	0.000	0.000	0.000	0.000
28	A	80	GLN	0	-0.031	-0.017	27.095	-0.024	-0.024	0.000	0.000	0.000	0.000
29	A	81	VAL	0	-0.031	-0.015	29.611	-0.009	-0.009	0.000	0.000	0.000	0.000
30	A	82	GLN	0	-0.054	-0.031	32.192	0.007	0.007	0.000	0.000	0.000	0.000
31	A	83	GLU	-1	-0.887	-0.954	31.370	-0.227	-0.227	0.000	0.000	0.000	0.000
32	A	84	ALA	0	-0.033	-0.017	31.056	-0.015	-0.015	0.000	0.000	0.000	0.000
33	A	85	TYR	0	0.051	0.020	28.149	-0.014	-0.014	0.000	0.000	0.000	0.000
34	A	86	LYS	1	0.982	1.015	26.806	0.250	0.250	0.000	0.000	0.000	0.000
35	A	87	GLY	0	-0.048	-0.016	23.363	-0.009	-0.009	0.000	0.000	0.000	0.000
36	A	88	LEU	0	-0.044	-0.019	22.352	-0.045	-0.045	0.000	0.000	0.000	0.000
37	A	89	LEU	0	-0.068	-0.040	16.741	-0.010	-0.010	0.000	0.000	0.000	0.000
38	A	90	ASN	0	0.003	0.001	20.638	0.042	0.042	0.000	0.000	0.000	0.000
39	A	91	LEU	0	-0.018	-0.029	18.332	-0.015	-0.015	0.000	0.000	0.000	0.000
40	A	92	ASN	0	-0.009	-0.004	21.156	0.014	0.014	0.000	0.000	0.000	0.000
41	A	93	GLU	-1	-0.894	-0.934	21.727	-0.247	-0.247	0.000	0.000	0.000	0.000
42	A	94	LYS	1	0.920	0.974	22.667	0.131	0.131	0.000	0.000	0.000	0.000
43	A	95	ASN	0	0.023	-0.008	22.847	0.001	0.001	0.000	0.000	0.000	0.000
44	A	96	ALA	0	0.029	-0.003	25.548	0.004	0.004	0.000	0.000	0.000	0.000
45	A	97	SER	0	-0.098	-0.048	26.953	0.006	0.006	0.000	0.000	0.000	0.000
46	A	98	ASP	-1	-0.859	-0.920	28.531	-0.085	-0.085	0.000	0.000	0.000	0.000
47	A	99	LYS	1	0.913	0.970	23.192	0.041	0.041	0.000	0.000	0.000	0.000
48	A	100	LEU	0	0.000	-0.008	21.003	-0.004	-0.004	0.000	0.000	0.000	0.000
49	A	101	LEU	0	-0.058	-0.028	19.148	0.013	0.013	0.000	0.000	0.000	0.000
50	A	102	VAL	0	-0.048	-0.027	14.499	-0.012	-0.012	0.000	0.000	0.000	0.000
51	A	103	GLU	-1	-0.900	-0.949	16.586	-0.118	-0.118	0.000	0.000	0.000	0.000
52	A	104	ASP	-1	-0.852	-0.914	16.173	-0.181	-0.181	0.000	0.000	0.000	0.000
53	A	105	ASN	0	-0.095	-0.030	14.830	-0.048	-0.048	0.000	0.000	0.000	0.000
54	A	106	THR	0	-0.045	-0.039	11.176	0.050	0.050	0.000	0.000	0.000	0.000
55	A	107	ALA	0	-0.013	-0.006	7.921	-0.023	-0.023	0.000	0.000	0.000	0.000
56	A	108	ALA	0	0.066	0.039	9.793	-0.071	-0.071	0.000	0.000	0.000	0.000
57	A	109	THR	0	-0.007	-0.011	8.227	-0.204	-0.204	0.000	0.000	0.000	0.000
58	A	110	VAL	0	0.065	0.008	9.619	0.216	0.216	0.000	0.000	0.000	0.000
59	A	111	GLY	0	-0.018	-0.015	11.657	0.179	0.179	0.000	0.000	0.000	0.000
60	A	112	ASN	0	0.036	0.025	12.824	0.109	0.109	0.000	0.000	0.000	0.000
61	A	113	LEU	0	0.091	0.043	13.936	0.089	0.089	0.000	0.000	0.000	0.000
62	A	114	ARG	1	0.925	0.977	12.588	1.167	1.167	0.000	0.000	0.000	0.000
63	A	115	LYS	1	0.918	0.965	16.345	0.747	0.747	0.000	0.000	0.000	0.000
64	A	116	LEU	0	0.022	0.031	18.555	0.044	0.044	0.000	0.000	0.000	0.000
65	A	117	GLY	0	0.046	0.013	21.496	-0.006	-0.006	0.000	0.000	0.000	0.000
66	A	118	TRP	0	-0.028	0.005	25.243	0.015	0.015	0.000	0.000	0.000	0.000
67	A	119	VAL	0	0.011	0.002	28.660	-0.007	-0.007	0.000	0.000	0.000	0.000
68	A	120	LEU	0	0.008	0.023	31.614	0.013	0.013	0.000	0.000	0.000	0.000
69	A	121	SER	0	0.069	0.023	34.712	-0.006	-0.006	0.000	0.000	0.000	0.000
70	A	122	SER	0	-0.037	0.005	37.973	0.007	0.007	0.000	0.000	0.000	0.000
71	A	123	LYS	1	0.975	0.972	41.629	0.099	0.099	0.000	0.000	0.000	0.000
72	A	124	ASN	0	0.019	0.016	44.565	0.005	0.005	0.000	0.000	0.000	0.000
73	A	125	GLY	0	0.010	-0.008	48.119	0.001	0.001	0.000	0.000	0.000	0.000
74	A	126	THR	0	0.032	-0.002	49.424	-0.002	-0.002	0.000	0.000	0.000	0.000
75	A	127	ARG	1	0.901	0.968	47.655	0.088	0.088	0.000	0.000	0.000	0.000
76	A	128	ASN	0	0.036	0.007	43.477	0.004	0.004	0.000	0.000	0.000	0.000
77	A	129	GLU	-1	-0.934	-0.957	39.201	-0.133	-0.133	0.000	0.000	0.000	0.000
78	A	130	LYS	1	0.894	0.971	36.720	0.172	0.172	0.000	0.000	0.000	0.000
79	A	131	SER	0	0.002	-0.023	34.824	0.002	0.002	0.000	0.000	0.000	0.000
80	A	132	GLN	0	-0.038	-0.033	33.114	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	133	GLN	0	-0.067	-0.053	26.917	-0.014	-0.014	0.000	0.000	0.000	0.000
82	A	134	VAL	0	0.024	0.030	28.666	-0.004	-0.004	0.000	0.000	0.000	0.000
83	A	135	LYS	1	0.868	0.915	21.757	0.441	0.441	0.000	0.000	0.000	0.000
84	A	136	HIS	0	0.006	-0.012	20.965	0.026	0.026	0.000	0.000	0.000	0.000
85	A	137	ALA	0	-0.083	-0.044	23.409	-0.017	-0.017	0.000	0.000	0.000	0.000
86	A	138	ASP	-1	-0.818	-0.884	25.199	-0.307	-0.307	0.000	0.000	0.000	0.000
87	A	139	GLU	-1	-0.967	-0.986	28.098	-0.183	-0.183	0.000	0.000	0.000	0.000
88	A	140	VAL	0	-0.061	-0.031	31.634	0.002	0.002	0.000	0.000	0.000	0.000
89	A	141	LEU	0	0.013	0.018	34.615	0.006	0.006	0.000	0.000	0.000	0.000
90	A	142	PHE	0	-0.042	-0.031	37.072	0.002	0.002	0.000	0.000	0.000	0.000
91	A	143	GLU	-1	-0.886	-0.948	41.083	-0.110	-0.110	0.000	0.000	0.000	0.000
92	A	144	GLY	0	-0.037	-0.011	44.020	0.002	0.002	0.000	0.000	0.000	0.000
93	A	145	LYS	1	0.995	0.983	47.314	0.107	0.107	0.000	0.000	0.000	0.000
94	A	146	GLY	0	-0.038	-0.025	50.381	0.001	0.001	0.000	0.000	0.000	0.000
95	A	147	GLY	0	0.000	-0.001	53.677	0.001	0.001	0.000	0.000	0.000	0.000
96	A	148	VAL	0	-0.021	0.002	49.487	0.002	0.002	0.000	0.000	0.000	0.000
97	A	149	GLN	0	-0.030	-0.018	50.300	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	150	VAL	0	0.030	0.011	43.799	0.001	0.001	0.000	0.000	0.000	0.000
99	A	151	THR	0	-0.005	0.004	45.496	0.000	0.000	0.000	0.000	0.000	0.000
100	A	152	SER	0	-0.001	-0.012	40.775	-0.003	-0.003	0.000	0.000	0.000	0.000
101	A	153	THR	0	-0.004	0.011	42.035	0.002	0.002	0.000	0.000	0.000	0.000
102	A	154	SER	0	0.015	-0.008	37.297	-0.009	-0.009	0.000	0.000	0.000	0.000
103	A	155	GLU	-1	-0.899	-0.955	38.518	-0.076	-0.076	0.000	0.000	0.000	0.000
104	A	156	ASN	0	0.026	0.033	35.500	-0.005	-0.005	0.000	0.000	0.000	0.000
105	A	157	GLY	0	-0.022	-0.004	33.224	0.001	0.001	0.000	0.000	0.000	0.000
106	A	158	LYS	1	0.936	0.982	33.886	0.086	0.086	0.000	0.000	0.000	0.000
107	A	159	HIS	0	-0.026	-0.033	33.590	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	160	THR	0	-0.028	-0.017	37.961	0.002	0.002	0.000	0.000	0.000	0.000
109	A	161	ILE	0	0.004	0.004	39.165	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	162	THR	0	-0.014	-0.007	42.595	0.004	0.004	0.000	0.000	0.000	0.000
111	A	163	PHE	0	-0.012	-0.010	43.158	-0.002	-0.002	0.000	0.000	0.000	0.000
112	A	164	ALA	0	0.015	0.013	48.644	0.004	0.004	0.000	0.000	0.000	0.000
113	A	165	LEU	0	0.024	0.020	52.323	-0.002	-0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:53:THR)