FMO DATABASE

FMODB ID: MV13Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-802265.374881
FMO2-HF: Nuclear repulsion	761622.911953
FMO2-HF: Total energy	-40642.462928
FMO2-MP2: Total energy	-40762.563281

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.
-10.274	-4.057	5.406	-5.563	-6.061	-0.033

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 : 0.029 / q_NPA : 0.019

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	0.060	0.004	2.255	-4.674	-1.307	2.331	-2.817	-2.881	-0.017
4	A	4	LEU	0	0.045	0.032	4.566	-0.472	-0.361	-0.001	-0.022	-0.087	0.000
5	A	5	ARG	1	0.779	0.877	2.103	-2.003	-1.216	1.828	-1.055	-1.560	0.003
6	A	6	GLY	0	0.043	0.009	2.531	-3.122	-1.231	1.249	-1.663	-1.479	-0.019
7	A	7	GLU	-1	-0.772	-0.845	4.799	-0.653	-0.592	-0.001	-0.006	-0.054	0.000
8	A	8	PRO	0	-0.024	0.022	8.335	0.212	0.212	0.000	0.000	0.000	0.000
9	A	9	TRP	0	0.104	0.053	10.748	0.175	0.175	0.000	0.000	0.000	0.000
10	A	10	PHE	0	-0.017	0.005	6.696	0.209	0.209	0.000	0.000	0.000	0.000
11	A	11	HIS	0	-0.026	-0.031	9.624	0.081	0.081	0.000	0.000	0.000	0.000
12	A	12	GLY	0	-0.008	-0.011	8.570	0.132	0.132	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.829	0.900	9.544	-1.012	-1.012	0.000	0.000	0.000	0.000
14	A	14	LEU	0	0.025	0.042	12.854	-0.023	-0.023	0.000	0.000	0.000	0.000
15	A	15	SER	0	0.039	0.010	15.483	-0.020	-0.020	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.856	0.918	19.009	-0.087	-0.087	0.000	0.000	0.000	0.000
17	A	17	ARG	1	0.990	0.978	21.208	-0.111	-0.111	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.875	-0.926	18.858	0.200	0.200	0.000	0.000	0.000	0.000
19	A	19	ALA	0	0.023	-0.005	18.171	-0.021	-0.021	0.000	0.000	0.000	0.000
20	A	20	GLU	-1	-0.802	-0.891	19.775	0.023	0.023	0.000	0.000	0.000	0.000
21	A	21	ALA	0	-0.041	-0.018	23.517	-0.013	-0.013	0.000	0.000	0.000	0.000
22	A	22	LEU	0	-0.039	-0.014	17.661	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	23	LEU	0	-0.068	-0.008	21.344	-0.023	-0.023	0.000	0.000	0.000	0.000
24	A	24	GLN	0	-0.075	-0.043	24.022	0.008	0.008	0.000	0.000	0.000	0.000
25	A	25	LEU	0	-0.019	-0.011	26.238	0.007	0.007	0.000	0.000	0.000	0.000
26	A	26	ASN	0	0.012	-0.004	26.425	0.002	0.002	0.000	0.000	0.000	0.000
27	A	27	GLY	0	0.073	0.042	25.139	-0.005	-0.005	0.000	0.000	0.000	0.000
28	A	28	ASP	-1	-0.740	-0.840	22.389	-0.139	-0.139	0.000	0.000	0.000	0.000
29	A	29	PHE	0	-0.014	-0.026	15.973	0.019	0.019	0.000	0.000	0.000	0.000
30	A	30	LEU	0	-0.001	0.018	15.223	-0.023	-0.023	0.000	0.000	0.000	0.000
31	A	31	VAL	0	0.000	0.000	11.363	0.033	0.033	0.000	0.000	0.000	0.000
32	A	32	ARG	1	0.807	0.907	11.660	-0.109	-0.109	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.759	-0.877	9.733	1.131	1.131	0.000	0.000	0.000	0.000
34	A	34	SER	0	-0.045	-0.016	12.097	-0.021	-0.021	0.000	0.000	0.000	0.000
35	A	35	THR	0	0.031	0.002	15.368	0.051	0.051	0.000	0.000	0.000	0.000
36	A	36	THR	0	-0.036	-0.023	17.753	0.024	0.024	0.000	0.000	0.000	0.000
37	A	37	THR	0	0.019	-0.001	19.743	-0.006	-0.006	0.000	0.000	0.000	0.000
38	A	38	PRO	0	-0.057	-0.019	14.190	-0.020	-0.020	0.000	0.000	0.000	0.000
39	A	39	GLY	0	0.035	0.021	14.227	-0.005	-0.005	0.000	0.000	0.000	0.000
40	A	40	GLN	0	0.020	0.027	12.748	0.077	0.077	0.000	0.000	0.000	0.000
41	A	41	TYR	0	0.020	0.005	7.489	0.163	0.163	0.000	0.000	0.000	0.000
42	A	42	VAL	0	-0.021	-0.013	13.079	-0.015	-0.015	0.000	0.000	0.000	0.000
43	A	43	LEU	0	0.033	0.033	15.053	-0.015	-0.015	0.000	0.000	0.000	0.000
44	A	44	THR	0	-0.007	-0.016	16.969	0.041	0.041	0.000	0.000	0.000	0.000
45	A	45	GLY	0	0.078	0.030	19.317	-0.030	-0.030	0.000	0.000	0.000	0.000
46	A	46	LEU	0	-0.042	-0.005	22.060	0.023	0.023	0.000	0.000	0.000	0.000
47	A	47	GLN	0	0.031	-0.004	25.819	-0.008	-0.008	0.000	0.000	0.000	0.000
48	A	48	SER	0	-0.045	-0.031	28.767	0.010	0.010	0.000	0.000	0.000	0.000
49	A	49	GLY	0	-0.001	0.001	31.057	0.007	0.007	0.000	0.000	0.000	0.000
50	A	50	GLN	0	-0.038	-0.009	30.035	0.008	0.008	0.000	0.000	0.000	0.000
51	A	51	PRO	0	0.029	0.004	24.763	-0.009	-0.009	0.000	0.000	0.000	0.000
52	A	52	LYS	1	0.855	0.949	24.169	0.052	0.052	0.000	0.000	0.000	0.000
53	A	53	HIS	0	-0.037	-0.035	21.082	0.000	0.000	0.000	0.000	0.000	0.000
54	A	54	LEU	0	0.023	0.025	20.161	0.016	0.016	0.000	0.000	0.000	0.000
55	A	55	LEU	0	-0.022	-0.010	17.640	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	56	LEU	0	-0.010	-0.001	13.456	-0.033	-0.033	0.000	0.000	0.000	0.000
57	A	57	VAL	0	-0.002	-0.020	15.032	0.046	0.046	0.000	0.000	0.000	0.000
58	A	58	ASP	-1	-0.879	-0.929	14.256	-0.044	-0.044	0.000	0.000	0.000	0.000
59	A	59	PRO	0	-0.118	-0.037	16.183	0.030	0.030	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.748	-0.867	18.318	-0.084	-0.084	0.000	0.000	0.000	0.000
61	A	61	GLY	0	-0.021	0.001	14.376	-0.027	-0.027	0.000	0.000	0.000	0.000
62	A	62	VAL	0	-0.048	-0.015	13.665	-0.065	-0.065	0.000	0.000	0.000	0.000
63	A	63	VAL	0	-0.034	-0.033	13.358	0.022	0.022	0.000	0.000	0.000	0.000
64	A	64	ARG	1	0.911	0.967	15.425	0.072	0.072	0.000	0.000	0.000	0.000
65	A	65	THR	0	0.015	-0.012	19.037	0.007	0.007	0.000	0.000	0.000	0.000
66	A	66	LYN	0	-0.026	-0.016	21.808	0.014	0.014	0.000	0.000	0.000	0.000
67	A	67	ASP	-1	-0.866	-0.912	24.826	-0.136	-0.136	0.000	0.000	0.000	0.000
68	A	68	HIS	0	0.010	0.032	21.375	0.010	0.010	0.000	0.000	0.000	0.000
69	A	69	ARG	1	0.775	0.840	19.698	0.168	0.168	0.000	0.000	0.000	0.000
70	A	70	PHE	0	0.028	0.015	16.277	-0.004	-0.004	0.000	0.000	0.000	0.000
71	A	71	GLU	-1	-0.875	-0.946	13.572	-0.598	-0.598	0.000	0.000	0.000	0.000
72	A	72	SER	0	0.011	-0.007	9.597	-0.076	-0.076	0.000	0.000	0.000	0.000
73	A	73	VAL	0	-0.012	-0.008	10.186	0.042	0.042	0.000	0.000	0.000	0.000
74	A	74	SER	0	-0.007	-0.038	9.619	0.026	0.026	0.000	0.000	0.000	0.000
75	A	75	HIS	0	-0.025	-0.003	11.804	0.102	0.102	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.024	0.004	14.606	0.066	0.066	0.000	0.000	0.000	0.000
77	A	77	ILE	0	0.008	0.004	13.937	0.061	0.061	0.000	0.000	0.000	0.000
78	A	78	SER	0	0.047	0.031	16.135	0.053	0.053	0.000	0.000	0.000	0.000
79	A	79	TYR	0	-0.022	-0.028	18.051	0.045	0.045	0.000	0.000	0.000	0.000
80	A	80	HIS	0	-0.071	-0.046	19.593	0.061	0.061	0.000	0.000	0.000	0.000
81	A	81	MET	0	-0.031	-0.008	19.597	0.010	0.010	0.000	0.000	0.000	0.000
82	A	82	ASP	-1	-0.856	-0.930	19.690	-0.415	-0.415	0.000	0.000	0.000	0.000
83	A	83	ASN	0	-0.091	-0.047	22.443	0.008	0.008	0.000	0.000	0.000	0.000
84	A	84	HIS	0	-0.075	-0.037	24.495	0.033	0.033	0.000	0.000	0.000	0.000
85	A	85	LEU	0	-0.008	0.020	24.749	0.024	0.024	0.000	0.000	0.000	0.000
86	A	86	PRO	0	0.004	-0.006	24.492	-0.013	-0.013	0.000	0.000	0.000	0.000
87	A	87	ILE	0	0.027	0.004	19.857	0.006	0.006	0.000	0.000	0.000	0.000
88	A	88	ILE	0	-0.007	0.001	24.419	0.017	0.017	0.000	0.000	0.000	0.000
89	A	89	SER	0	-0.058	-0.056	25.675	0.000	0.000	0.000	0.000	0.000	0.000
90	A	90	ALA	0	-0.030	-0.019	27.933	0.005	0.005	0.000	0.000	0.000	0.000
91	A	91	GLY	0	-0.011	0.003	31.089	0.006	0.006	0.000	0.000	0.000	0.000
92	A	92	SER	0	-0.016	0.001	29.065	0.001	0.001	0.000	0.000	0.000	0.000
93	A	93	GLU	-1	-0.809	-0.900	28.020	-0.113	-0.113	0.000	0.000	0.000	0.000
94	A	94	LEU	0	-0.008	-0.012	22.102	0.013	0.013	0.000	0.000	0.000	0.000
95	A	95	CYS	0	-0.014	0.000	24.369	-0.018	-0.018	0.000	0.000	0.000	0.000
96	A	96	LEU	0	-0.038	-0.006	18.572	0.007	0.007	0.000	0.000	0.000	0.000
97	A	97	GLN	0	-0.032	-0.020	22.490	0.002	0.002	0.000	0.000	0.000	0.000
98	A	98	GLN	0	-0.014	-0.031	21.598	-0.021	-0.021	0.000	0.000	0.000	0.000
99	A	99	PRO	0	0.002	0.020	16.358	0.022	0.022	0.000	0.000	0.000	0.000
100	A	100	VAL	0	-0.009	-0.012	18.142	0.013	0.013	0.000	0.000	0.000	0.000
101	A	101	GLU	-1	-0.862	-0.949	14.641	-0.487	-0.487	0.000	0.000	0.000	0.000
102	A	102	ARG	1	0.763	0.858	8.036	0.758	0.758	0.000	0.000	0.000	0.000
103	A	103	LYS	1	0.953	0.961	13.794	0.007	0.007	0.000	0.000	0.000	0.000
104	A	104	LEU	0	-0.009	0.015	10.870	0.043	0.043	0.000	0.000	0.000	0.000

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