FMO DATABASE

FMODB ID: 94VG2

Calculation Name: 1MIL-A-Xray372

Preferred Name: SHC-transforming protein 1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1MIL

Chain ID: A

ChEMBL ID: CHEMBL5626

UniProt ID: P29353

Base Structure: X-ray

Registration Date: 2023-09-19

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	104
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-801727.230645
FMO2-HF: Nuclear repulsion	761085.598847
FMO2-HF: Total energy	-40641.631798
FMO2-MP2: Total energy	-40761.834193

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:GLY)

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

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.
-6.469	-0.766	2.809	-4.182	-4.329	-0.01

Interaction energy analysis for fragmet #1(A:1:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.050 / q_NPA : 0.027

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	GLN	0	0.033	-0.016	2.987	-2.703	1.182	0.149	-2.192	-1.842	-0.001
4	A	4	LEU	0	0.055	0.038	4.766	-0.388	-0.292	-0.001	-0.017	-0.077	0.000
5	A	5	ARG	1	0.803	0.897	1.940	-0.226	-0.039	2.126	-0.937	-1.377	0.001
6	A	6	GLY	0	0.035	0.008	2.746	-2.656	-1.174	0.536	-1.034	-0.983	-0.010
7	A	7	GLU	-1	-0.808	-0.880	5.104	-0.666	-0.613	-0.001	-0.002	-0.050	0.000
8	A	8	PRO	0	-0.019	0.029	8.686	0.208	0.208	0.000	0.000	0.000	0.000
9	A	9	TRP	0	0.145	0.079	10.888	0.155	0.155	0.000	0.000	0.000	0.000
10	A	10	PHE	0	-0.041	-0.023	6.847	0.178	0.178	0.000	0.000	0.000	0.000
11	A	11	HIS	0	-0.048	-0.043	9.534	0.073	0.073	0.000	0.000	0.000	0.000
12	A	12	GLY	0	0.001	0.003	8.971	0.165	0.165	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.838	0.896	9.876	-0.982	-0.982	0.000	0.000	0.000	0.000
14	A	14	LEU	0	0.038	0.039	12.790	0.000	0.000	0.000	0.000	0.000	0.000
15	A	15	SER	0	0.041	0.012	15.598	-0.029	-0.029	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.868	0.924	19.056	-0.053	-0.053	0.000	0.000	0.000	0.000
17	A	17	ARG	1	0.984	0.974	21.253	-0.097	-0.097	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.862	-0.928	19.333	0.176	0.176	0.000	0.000	0.000	0.000
19	A	19	ALA	0	0.044	0.019	18.711	-0.018	-0.018	0.000	0.000	0.000	0.000
20	A	20	GLU	-1	-0.803	-0.899	20.352	-0.005	-0.005	0.000	0.000	0.000	0.000
21	A	21	ALA	0	-0.090	-0.032	23.713	-0.009	-0.009	0.000	0.000	0.000	0.000
22	A	22	LEU	0	-0.036	-0.024	18.249	0.006	0.006	0.000	0.000	0.000	0.000
23	A	23	LEU	0	-0.073	-0.018	21.255	-0.020	-0.020	0.000	0.000	0.000	0.000
24	A	24	GLN	0	-0.075	-0.041	24.257	0.010	0.010	0.000	0.000	0.000	0.000
25	A	25	LEU	0	-0.005	-0.008	26.567	0.009	0.009	0.000	0.000	0.000	0.000
26	A	26	ASN	0	0.009	-0.015	26.603	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	27	GLY	0	0.081	0.041	25.366	-0.003	-0.003	0.000	0.000	0.000	0.000
28	A	28	ASP	-1	-0.756	-0.845	22.764	-0.141	-0.141	0.000	0.000	0.000	0.000
29	A	29	PHE	0	-0.008	-0.020	16.165	0.016	0.016	0.000	0.000	0.000	0.000
30	A	30	LEU	0	0.019	0.029	15.769	-0.018	-0.018	0.000	0.000	0.000	0.000
31	A	31	VAL	0	-0.035	-0.012	11.818	0.030	0.030	0.000	0.000	0.000	0.000
32	A	32	ARG	1	0.826	0.924	12.081	-0.038	-0.038	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.796	-0.891	9.633	0.807	0.807	0.000	0.000	0.000	0.000
34	A	34	SER	0	-0.063	-0.029	12.599	0.052	0.052	0.000	0.000	0.000	0.000
35	A	35	THR	0	0.057	0.017	15.816	0.037	0.037	0.000	0.000	0.000	0.000
36	A	36	THR	0	-0.040	-0.012	18.003	0.020	0.020	0.000	0.000	0.000	0.000
37	A	37	THR	0	0.012	-0.016	19.921	0.005	0.005	0.000	0.000	0.000	0.000
38	A	38	PRO	0	-0.070	-0.024	14.366	-0.019	-0.019	0.000	0.000	0.000	0.000
39	A	39	GLY	0	0.058	0.029	15.072	0.006	0.006	0.000	0.000	0.000	0.000
40	A	40	GLN	0	0.021	0.028	13.189	0.050	0.050	0.000	0.000	0.000	0.000
41	A	41	TYR	0	0.024	-0.001	8.338	0.094	0.094	0.000	0.000	0.000	0.000
42	A	42	VAL	0	-0.014	-0.011	13.812	-0.010	-0.010	0.000	0.000	0.000	0.000
43	A	43	LEU	0	0.019	0.021	15.442	-0.025	-0.025	0.000	0.000	0.000	0.000
44	A	44	THR	0	-0.009	-0.012	17.693	0.037	0.037	0.000	0.000	0.000	0.000
45	A	45	GLY	0	0.095	0.033	19.895	-0.025	-0.025	0.000	0.000	0.000	0.000
46	A	46	LEU	0	-0.042	0.003	22.557	0.021	0.021	0.000	0.000	0.000	0.000
47	A	47	GLN	0	0.013	0.006	26.105	-0.008	-0.008	0.000	0.000	0.000	0.000
48	A	48	SER	0	-0.019	-0.013	29.047	0.008	0.008	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.005	0.007	30.959	0.007	0.007	0.000	0.000	0.000	0.000
50	A	50	GLN	0	-0.030	-0.016	29.992	0.007	0.007	0.000	0.000	0.000	0.000
51	A	51	PRO	0	0.039	0.007	24.552	-0.009	-0.009	0.000	0.000	0.000	0.000
52	A	52	LYS	1	0.860	0.960	24.759	0.067	0.067	0.000	0.000	0.000	0.000
53	A	53	HIS	0	-0.053	-0.052	21.517	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	54	LEU	0	0.016	0.022	20.462	0.016	0.016	0.000	0.000	0.000	0.000
55	A	55	LEU	0	-0.015	0.004	18.264	0.000	0.000	0.000	0.000	0.000	0.000
56	A	56	LEU	0	0.018	0.012	13.846	-0.031	-0.031	0.000	0.000	0.000	0.000
57	A	57	VAL	0	-0.001	-0.016	15.467	0.018	0.018	0.000	0.000	0.000	0.000
58	A	58	ASP	-1	-0.889	-0.926	14.485	-0.156	-0.156	0.000	0.000	0.000	0.000
59	A	59	PRO	0	-0.133	-0.027	16.481	0.034	0.034	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.745	-0.877	18.634	-0.127	-0.127	0.000	0.000	0.000	0.000
61	A	61	GLY	0	-0.014	0.001	15.272	-0.027	-0.027	0.000	0.000	0.000	0.000
62	A	62	VAL	0	-0.033	-0.021	13.899	-0.066	-0.066	0.000	0.000	0.000	0.000
63	A	63	VAL	0	0.024	-0.020	13.194	-0.016	-0.016	0.000	0.000	0.000	0.000
64	A	64	ARG	1	0.866	0.957	15.999	0.125	0.125	0.000	0.000	0.000	0.000
65	A	65	THR	0	0.023	0.000	19.632	0.003	0.003	0.000	0.000	0.000	0.000
66	A	66	LYN	0	-0.034	-0.012	22.373	0.014	0.014	0.000	0.000	0.000	0.000
67	A	67	ASP	-1	-0.891	-0.935	25.253	-0.162	-0.162	0.000	0.000	0.000	0.000
68	A	68	HIS	0	0.009	0.020	21.851	0.010	0.010	0.000	0.000	0.000	0.000
69	A	69	ARG	1	0.782	0.858	20.325	0.200	0.200	0.000	0.000	0.000	0.000
70	A	70	PHE	0	0.020	0.008	16.696	0.000	0.000	0.000	0.000	0.000	0.000
71	A	71	GLU	-1	-0.866	-0.943	14.072	-0.616	-0.616	0.000	0.000	0.000	0.000
72	A	72	SER	0	-0.012	-0.017	9.875	-0.111	-0.111	0.000	0.000	0.000	0.000
73	A	73	VAL	0	0.002	0.001	10.362	0.087	0.087	0.000	0.000	0.000	0.000
74	A	74	SER	0	-0.018	-0.044	9.674	0.038	0.038	0.000	0.000	0.000	0.000
75	A	75	HIS	0	-0.025	-0.007	11.925	0.108	0.108	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.015	0.008	14.872	0.070	0.070	0.000	0.000	0.000	0.000
77	A	77	ILE	0	-0.004	-0.012	14.101	0.063	0.063	0.000	0.000	0.000	0.000
78	A	78	SER	0	0.048	0.031	16.374	0.048	0.048	0.000	0.000	0.000	0.000
79	A	79	TYR	0	-0.011	-0.005	18.269	0.048	0.048	0.000	0.000	0.000	0.000
80	A	80	HIS	0	-0.072	-0.048	19.977	0.057	0.057	0.000	0.000	0.000	0.000
81	A	81	MET	0	-0.026	-0.002	19.588	0.011	0.011	0.000	0.000	0.000	0.000
82	A	82	ASP	-1	-0.880	-0.930	19.920	-0.410	-0.410	0.000	0.000	0.000	0.000
83	A	83	ASN	0	-0.063	-0.039	22.695	0.012	0.012	0.000	0.000	0.000	0.000
84	A	84	HIS	0	-0.073	-0.035	24.525	0.033	0.033	0.000	0.000	0.000	0.000
85	A	85	LEU	0	-0.026	0.001	25.384	0.023	0.023	0.000	0.000	0.000	0.000
86	A	86	PRO	0	-0.005	-0.005	25.084	-0.017	-0.017	0.000	0.000	0.000	0.000
87	A	87	ILE	0	0.050	0.024	20.417	0.006	0.006	0.000	0.000	0.000	0.000
88	A	88	ILE	0	0.022	0.013	25.026	0.017	0.017	0.000	0.000	0.000	0.000
89	A	89	SER	0	-0.077	-0.061	25.845	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	90	ALA	0	0.001	-0.014	28.089	0.006	0.006	0.000	0.000	0.000	0.000
91	A	91	GLY	0	-0.027	-0.002	31.496	0.007	0.007	0.000	0.000	0.000	0.000
92	A	92	SER	0	-0.019	0.001	29.406	0.003	0.003	0.000	0.000	0.000	0.000
93	A	93	GLU	-1	-0.863	-0.949	28.368	-0.124	-0.124	0.000	0.000	0.000	0.000
94	A	94	LEU	0	-0.037	-0.020	22.397	0.010	0.010	0.000	0.000	0.000	0.000
95	A	95	CYS	0	-0.018	-0.006	24.726	-0.018	-0.018	0.000	0.000	0.000	0.000
96	A	96	LEU	0	-0.030	-0.006	18.701	0.008	0.008	0.000	0.000	0.000	0.000
97	A	97	GLN	0	-0.001	-0.006	22.455	0.002	0.002	0.000	0.000	0.000	0.000
98	A	98	GLN	0	-0.034	-0.040	21.750	-0.020	-0.020	0.000	0.000	0.000	0.000
99	A	99	PRO	0	-0.011	0.018	16.504	0.019	0.019	0.000	0.000	0.000	0.000
100	A	100	VAL	0	0.001	-0.002	18.212	0.014	0.014	0.000	0.000	0.000	0.000
101	A	101	GLU	-1	-0.868	-0.951	14.932	-0.435	-0.435	0.000	0.000	0.000	0.000
102	A	102	ARG	1	0.775	0.876	8.104	0.637	0.637	0.000	0.000	0.000	0.000
103	A	103	LYS	1	0.954	0.958	13.985	-0.017	-0.017	0.000	0.000	0.000	0.000
104	A	104	LEU	0	-0.009	0.014	11.076	0.051	0.051	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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