FMO DATABASE

FMODB ID: QYNNY

Calculation Name: 3MI8-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3MI8

Chain ID: D

ChEMBL ID:

UniProt ID: O95150

Base Structure: X-ray

Registration Date: 2023-06-22

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	102
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-742889.831113
FMO2-HF: Nuclear repulsion	695956.084599
FMO2-HF: Total energy	-46933.746514
FMO2-MP2: Total energy	-47059.387477

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(D:33:THR)

Summations of interaction energy for fragment #1(D:33: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.
-6.27	-1.551	1.124	-2.108	-3.735	-0.016

Interaction energy analysis for fragmet #1(D:33:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.022 / q_NPA : -0.020

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	D	35	THR	0	-0.020	-0.023	2.601	-4.305	-1.651	0.773	-1.512	-1.915	-0.011
4	D	36	TYR	0	0.032	0.006	5.189	0.601	0.647	-0.001	-0.002	-0.042	0.000
5	D	37	PRO	0	-0.023	0.000	8.685	-0.009	-0.009	0.000	0.000	0.000	0.000
6	D	38	TRP	0	0.047	0.018	11.976	0.083	0.083	0.000	0.000	0.000	0.000
7	D	39	ARG	1	0.885	0.936	13.955	0.302	0.302	0.000	0.000	0.000	0.000
8	D	40	ASP	-1	-0.821	-0.896	16.137	-0.344	-0.344	0.000	0.000	0.000	0.000
9	D	41	ALA	0	0.008	-0.001	18.247	0.021	0.021	0.000	0.000	0.000	0.000
10	D	42	GLU	-1	-0.799	-0.851	20.404	-0.175	-0.175	0.000	0.000	0.000	0.000
11	D	43	THR	0	0.016	-0.009	21.794	0.016	0.016	0.000	0.000	0.000	0.000
12	D	44	GLY	0	0.037	0.028	20.655	-0.024	-0.024	0.000	0.000	0.000	0.000
13	D	45	GLU	-1	-0.874	-0.931	18.060	-0.389	-0.389	0.000	0.000	0.000	0.000
14	D	46	ARG	1	0.853	0.914	14.385	0.668	0.668	0.000	0.000	0.000	0.000
15	D	47	LEU	0	0.043	0.034	11.762	-0.040	-0.040	0.000	0.000	0.000	0.000
16	D	48	VAL	0	-0.043	-0.032	8.609	0.059	0.059	0.000	0.000	0.000	0.000
17	D	49	CYS	0	-0.051	-0.001	8.092	-0.010	-0.010	0.000	0.000	0.000	0.000
18	D	50	ALA	0	0.026	0.028	3.864	-0.679	-0.552	0.002	-0.030	-0.099	0.000
19	D	51	GLN	0	0.040	0.015	3.513	0.322	0.559	0.002	-0.047	-0.193	0.000
20	D	52	CYS	0	-0.045	-0.015	4.606	0.126	0.285	-0.002	-0.008	-0.149	0.000
21	D	53	PRO	0	0.035	0.017	5.449	0.016	0.016	0.000	0.000	0.000	0.000
22	D	54	PRO	0	0.000	0.008	7.034	-0.248	-0.248	0.000	0.000	0.000	0.000
23	D	55	GLY	0	-0.001	0.015	10.628	0.064	0.064	0.000	0.000	0.000	0.000
24	D	56	THR	0	-0.066	-0.047	9.505	-0.083	-0.083	0.000	0.000	0.000	0.000
25	D	57	PHE	0	0.002	0.000	11.765	-0.005	-0.005	0.000	0.000	0.000	0.000
26	D	58	VAL	0	0.059	0.023	9.889	0.017	0.017	0.000	0.000	0.000	0.000
27	D	59	GLN	0	-0.031	0.002	12.318	0.015	0.015	0.000	0.000	0.000	0.000
28	D	60	ARG	1	0.953	0.954	13.888	0.063	0.063	0.000	0.000	0.000	0.000
29	D	61	PRO	0	0.031	0.026	12.092	0.002	0.002	0.000	0.000	0.000	0.000
30	D	63	ARG	1	0.855	0.918	11.765	0.182	0.182	0.000	0.000	0.000	0.000
31	D	64	ARG	1	0.809	0.856	13.455	0.204	0.204	0.000	0.000	0.000	0.000
32	D	65	ASP	-1	-0.963	-0.966	15.501	-0.199	-0.199	0.000	0.000	0.000	0.000
33	D	66	SER	0	0.042	0.032	13.348	-0.010	-0.010	0.000	0.000	0.000	0.000
34	D	67	PRO	0	0.025	0.001	7.935	-0.077	-0.077	0.000	0.000	0.000	0.000
35	D	68	THR	0	-0.030	-0.038	7.421	0.032	0.032	0.000	0.000	0.000	0.000
36	D	69	THR	0	-0.023	0.004	9.134	0.137	0.137	0.000	0.000	0.000	0.000
37	D	71	GLY	0	0.055	0.039	10.898	0.048	0.048	0.000	0.000	0.000	0.000
38	D	72	PRO	0	0.000	-0.011	13.672	0.032	0.032	0.000	0.000	0.000	0.000
39	D	73	CYS	0	-0.073	-0.013	15.360	-0.050	-0.050	0.000	0.000	0.000	0.000
40	D	74	PRO	0	0.025	0.022	17.104	0.006	0.006	0.000	0.000	0.000	0.000
41	D	75	PRO	0	0.044	0.003	20.851	0.013	0.013	0.000	0.000	0.000	0.000
42	D	76	ARG	1	0.924	0.960	23.701	-0.157	-0.157	0.000	0.000	0.000	0.000
43	D	77	HIS	0	-0.029	-0.023	19.814	-0.031	-0.031	0.000	0.000	0.000	0.000
44	D	78	TYR	0	0.013	0.015	17.309	0.024	0.024	0.000	0.000	0.000	0.000
45	D	79	THR	0	-0.026	-0.042	12.553	-0.024	-0.024	0.000	0.000	0.000	0.000
46	D	80	GLN	0	0.008	0.008	13.705	0.013	0.013	0.000	0.000	0.000	0.000
47	D	81	PHE	0	-0.013	-0.013	10.400	0.098	0.098	0.000	0.000	0.000	0.000
48	D	82	TRP	0	0.043	0.017	3.128	-1.663	-0.167	0.350	-0.509	-1.337	-0.005
49	D	83	ASN	0	-0.070	-0.033	7.686	-0.279	-0.279	0.000	0.000	0.000	0.000
50	D	84	TYR	0	0.046	0.011	8.578	-0.094	-0.094	0.000	0.000	0.000	0.000
51	D	85	LEU	0	-0.008	0.006	10.651	-0.010	-0.010	0.000	0.000	0.000	0.000
52	D	86	GLU	-1	-0.886	-0.938	13.691	-0.119	-0.119	0.000	0.000	0.000	0.000
53	D	87	ARG	1	0.925	0.954	16.151	-0.042	-0.042	0.000	0.000	0.000	0.000
54	D	89	ARG	1	0.950	0.975	17.122	-0.200	-0.200	0.000	0.000	0.000	0.000
55	D	90	TYR	0	0.044	0.020	19.724	0.023	0.023	0.000	0.000	0.000	0.000
56	D	91	CYS	0	-0.120	-0.061	23.113	0.032	0.032	0.000	0.000	0.000	0.000
57	D	92	ASN	0	-0.014	-0.007	24.486	0.004	0.004	0.000	0.000	0.000	0.000
58	D	93	VAL	0	0.030	0.033	26.384	-0.011	-0.011	0.000	0.000	0.000	0.000
59	D	94	LEU	0	-0.011	-0.011	28.835	0.009	0.009	0.000	0.000	0.000	0.000
60	D	95	CYS	0	-0.062	-0.015	27.016	0.004	0.004	0.000	0.000	0.000	0.000
61	D	96	GLY	0	0.056	0.034	33.949	-0.005	-0.005	0.000	0.000	0.000	0.000
62	D	97	GLU	-1	-0.920	-0.974	37.405	0.085	0.085	0.000	0.000	0.000	0.000
63	D	98	ARG	1	0.804	0.897	39.883	-0.073	-0.073	0.000	0.000	0.000	0.000
64	D	99	GLU	-1	-0.820	-0.913	34.725	0.123	0.123	0.000	0.000	0.000	0.000
65	D	100	GLU	-1	-0.889	-0.929	34.557	0.126	0.126	0.000	0.000	0.000	0.000
66	D	101	GLU	-1	-0.798	-0.909	29.496	0.189	0.189	0.000	0.000	0.000	0.000
67	D	102	ALA	0	-0.076	-0.032	28.530	0.003	0.003	0.000	0.000	0.000	0.000
68	D	103	ARG	1	0.896	0.939	20.736	-0.332	-0.332	0.000	0.000	0.000	0.000
69	D	104	ALA	0	0.089	0.060	25.680	-0.010	-0.010	0.000	0.000	0.000	0.000
70	D	106	HIS	0	0.054	0.055	17.325	0.008	0.008	0.000	0.000	0.000	0.000
71	D	107	ALA	0	0.061	0.025	16.682	-0.013	-0.013	0.000	0.000	0.000	0.000
72	D	108	THR	0	-0.005	-0.032	13.857	0.016	0.016	0.000	0.000	0.000	0.000
73	D	109	HIS	0	-0.023	-0.013	16.012	0.041	0.041	0.000	0.000	0.000	0.000
74	D	110	ASN	0	0.057	0.019	18.757	-0.028	-0.028	0.000	0.000	0.000	0.000
75	D	111	ARG	1	0.805	0.898	21.934	-0.149	-0.149	0.000	0.000	0.000	0.000
76	D	112	ALA	0	-0.011	-0.010	25.134	-0.004	-0.004	0.000	0.000	0.000	0.000
77	D	114	ARG	1	0.915	0.972	30.709	-0.158	-0.158	0.000	0.000	0.000	0.000
78	D	115	CYS	0	0.032	0.022	32.844	-0.001	-0.001	0.000	0.000	0.000	0.000
79	D	116	ARG	1	0.870	0.918	36.418	-0.098	-0.098	0.000	0.000	0.000	0.000
80	D	117	THR	0	0.051	0.009	38.879	0.001	0.001	0.000	0.000	0.000	0.000
81	D	118	GLY	0	-0.016	0.005	40.736	-0.002	-0.002	0.000	0.000	0.000	0.000
82	D	119	PHE	0	-0.044	-0.036	40.615	-0.004	-0.004	0.000	0.000	0.000	0.000
83	D	120	PHE	0	0.005	0.003	38.924	0.006	0.006	0.000	0.000	0.000	0.000
84	D	121	ALA	0	0.056	0.016	35.833	-0.005	-0.005	0.000	0.000	0.000	0.000
85	D	122	HIS	0	0.012	-0.001	37.773	0.003	0.003	0.000	0.000	0.000	0.000
86	D	123	ALA	0	-0.015	-0.014	38.050	-0.003	-0.003	0.000	0.000	0.000	0.000
87	D	124	GLY	0	0.013	0.018	36.111	-0.002	-0.002	0.000	0.000	0.000	0.000
88	D	125	PHE	0	-0.042	-0.012	37.143	0.000	0.000	0.000	0.000	0.000	0.000
89	D	127	LEU	0	-0.005	-0.004	39.902	-0.004	-0.004	0.000	0.000	0.000	0.000
90	D	128	GLU	-1	-0.865	-0.929	43.057	0.073	0.073	0.000	0.000	0.000	0.000
91	D	129	HIS	0	0.003	0.020	42.205	-0.005	-0.005	0.000	0.000	0.000	0.000
92	D	130	ALA	0	-0.012	-0.002	46.278	0.000	0.000	0.000	0.000	0.000	0.000
93	D	131	SER	0	0.026	0.020	49.285	0.000	0.000	0.000	0.000	0.000	0.000
94	D	132	CYS	0	-0.003	0.011	48.065	-0.001	-0.001	0.000	0.000	0.000	0.000
95	D	142	GLY	0	0.013	0.004	42.498	0.000	0.000	0.000	0.000	0.000	0.000
96	D	143	THR	0	-0.014	0.005	36.172	0.003	0.003	0.000	0.000	0.000	0.000
97	D	144	PRO	0	0.047	0.005	34.764	-0.001	-0.001	0.000	0.000	0.000	0.000
98	D	145	SER	0	-0.060	-0.020	33.664	0.003	0.003	0.000	0.000	0.000	0.000
99	D	146	GLN	0	-0.028	-0.020	35.529	-0.008	-0.008	0.000	0.000	0.000	0.000
100	D	147	ASN	0	0.049	0.029	38.853	0.001	0.001	0.000	0.000	0.000	0.000
101	D	148	THR	0	-0.026	-0.032	42.642	0.001	0.001	0.000	0.000	0.000	0.000
102	D	149	GLN	0	-0.007	0.001	44.476	-0.005	-0.005	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:33:THR)