FMO DATABASE

FMODB ID: LZ3J9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-801558.072361
FMO2-HF: Nuclear repulsion	760917.552709
FMO2-HF: Total energy	-40640.519652
FMO2-MP2: Total energy	-40760.82115

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.
-5.992	-1.459	1.809	-2.757	-3.585	-0.001

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 : 0.017 / q_NPA : -0.005

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	0.028	-0.017	2.942	2.604	4.826	0.071	-1.038	-1.255	0.002
4	A	4	LEU	0	0.063	0.040	5.240	-0.038	0.030	-0.001	-0.011	-0.055	0.000
5	A	5	ARG	1	0.797	0.907	2.701	-5.696	-4.861	1.204	-0.737	-1.302	0.007
6	A	6	GLY	0	-0.005	-0.013	2.745	-3.091	-1.720	0.536	-0.969	-0.939	-0.010
7	A	7	GLU	-1	-0.902	-0.961	5.103	-0.100	-0.063	-0.001	-0.002	-0.034	0.000
8	A	8	PRO	0	-0.006	0.041	8.685	0.125	0.125	0.000	0.000	0.000	0.000
9	A	9	TRP	0	0.155	0.075	11.314	0.096	0.096	0.000	0.000	0.000	0.000
10	A	10	PHE	0	-0.046	-0.010	7.506	0.182	0.182	0.000	0.000	0.000	0.000
11	A	11	HIS	0	-0.073	-0.060	9.533	0.051	0.051	0.000	0.000	0.000	0.000
12	A	12	GLY	0	0.007	-0.018	9.319	-0.008	-0.008	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.892	0.942	10.090	-0.680	-0.680	0.000	0.000	0.000	0.000
14	A	14	LEU	0	0.034	0.037	12.898	-0.057	-0.057	0.000	0.000	0.000	0.000
15	A	15	SER	0	0.016	-0.001	15.852	-0.003	-0.003	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.936	0.960	19.291	-0.154	-0.154	0.000	0.000	0.000	0.000
17	A	17	ARG	1	0.966	0.969	21.726	-0.121	-0.121	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.846	-0.926	19.486	0.188	0.188	0.000	0.000	0.000	0.000
19	A	19	ALA	0	0.045	0.020	19.052	-0.011	-0.011	0.000	0.000	0.000	0.000
20	A	20	GLU	-1	-0.853	-0.932	20.522	0.121	0.121	0.000	0.000	0.000	0.000
21	A	21	ALA	0	-0.087	-0.031	23.730	-0.013	-0.013	0.000	0.000	0.000	0.000
22	A	22	LEU	0	-0.051	-0.033	18.216	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	23	LEU	0	-0.068	-0.008	21.848	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	24	GLN	0	-0.084	-0.041	24.256	-0.011	-0.011	0.000	0.000	0.000	0.000
25	A	25	LEU	0	-0.004	-0.001	26.574	-0.006	-0.006	0.000	0.000	0.000	0.000
26	A	26	ASN	0	-0.002	-0.021	26.644	0.011	0.011	0.000	0.000	0.000	0.000
27	A	27	GLY	0	0.069	0.035	25.767	-0.005	-0.005	0.000	0.000	0.000	0.000
28	A	28	ASP	-1	-0.758	-0.872	22.811	0.087	0.087	0.000	0.000	0.000	0.000
29	A	29	PHE	0	-0.028	-0.032	16.970	0.014	0.014	0.000	0.000	0.000	0.000
30	A	30	LEU	0	0.011	0.024	15.935	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	31	VAL	0	-0.022	-0.006	12.740	0.007	0.007	0.000	0.000	0.000	0.000
32	A	32	ARG	1	0.876	0.959	12.763	-0.239	-0.239	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.861	-0.939	9.980	0.901	0.901	0.000	0.000	0.000	0.000
34	A	34	SER	0	-0.052	-0.020	13.134	-0.062	-0.062	0.000	0.000	0.000	0.000
35	A	35	THR	0	0.018	-0.010	15.981	0.006	0.006	0.000	0.000	0.000	0.000
36	A	36	THR	0	-0.042	0.002	18.158	-0.009	-0.009	0.000	0.000	0.000	0.000
37	A	37	THR	0	0.025	-0.027	19.742	-0.010	-0.010	0.000	0.000	0.000	0.000
38	A	38	PRO	0	-0.157	-0.058	14.373	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	39	GLY	0	0.113	0.051	15.260	-0.033	-0.033	0.000	0.000	0.000	0.000
40	A	40	GLN	0	0.033	0.034	13.551	0.053	0.053	0.000	0.000	0.000	0.000
41	A	41	TYR	0	0.022	-0.008	8.891	0.097	0.097	0.000	0.000	0.000	0.000
42	A	42	VAL	0	-0.017	-0.017	14.701	-0.057	-0.057	0.000	0.000	0.000	0.000
43	A	43	LEU	0	0.044	0.032	16.390	0.040	0.040	0.000	0.000	0.000	0.000
44	A	44	THR	0	-0.024	-0.031	18.670	-0.011	-0.011	0.000	0.000	0.000	0.000
45	A	45	GLY	0	0.083	0.032	20.467	0.003	0.003	0.000	0.000	0.000	0.000
46	A	46	LEU	0	-0.031	0.012	23.135	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	47	GLN	0	0.024	0.010	26.543	-0.006	-0.006	0.000	0.000	0.000	0.000
48	A	48	SER	0	0.004	-0.008	29.606	0.000	0.000	0.000	0.000	0.000	0.000
49	A	49	GLY	0	-0.009	0.004	31.364	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	50	GLN	0	-0.064	-0.034	30.509	0.002	0.002	0.000	0.000	0.000	0.000
51	A	51	PRO	0	0.037	0.006	25.187	0.000	0.000	0.000	0.000	0.000	0.000
52	A	52	LYS	1	0.904	0.982	25.534	-0.091	-0.091	0.000	0.000	0.000	0.000
53	A	53	HIS	0	-0.057	-0.053	22.373	0.026	0.026	0.000	0.000	0.000	0.000
54	A	54	LEU	0	0.013	0.018	21.567	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	55	LEU	0	0.013	0.017	19.460	0.026	0.026	0.000	0.000	0.000	0.000
56	A	56	LEU	0	-0.009	0.002	15.254	-0.015	-0.015	0.000	0.000	0.000	0.000
57	A	57	VAL	0	-0.003	-0.015	16.360	0.046	0.046	0.000	0.000	0.000	0.000
58	A	58	ASP	-1	-0.884	-0.929	14.929	0.199	0.199	0.000	0.000	0.000	0.000
59	A	59	PRO	0	-0.134	-0.020	16.919	-0.017	-0.017	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.729	-0.879	18.856	0.053	0.053	0.000	0.000	0.000	0.000
61	A	61	GLY	0	-0.014	-0.002	15.307	-0.018	-0.018	0.000	0.000	0.000	0.000
62	A	62	VAL	0	-0.032	-0.021	13.995	0.020	0.020	0.000	0.000	0.000	0.000
63	A	63	VAL	0	0.039	-0.008	13.580	0.056	0.056	0.000	0.000	0.000	0.000
64	A	64	ARG	1	0.860	0.961	16.659	-0.132	-0.132	0.000	0.000	0.000	0.000
65	A	65	THR	0	-0.008	-0.006	20.372	0.013	0.013	0.000	0.000	0.000	0.000
66	A	66	LYN	0	-0.016	-0.002	23.275	-0.002	-0.002	0.000	0.000	0.000	0.000
67	A	67	ASP	-1	-0.903	-0.944	26.173	0.063	0.063	0.000	0.000	0.000	0.000
68	A	68	HIS	0	0.033	0.029	22.951	-0.013	-0.013	0.000	0.000	0.000	0.000
69	A	69	ARG	1	0.748	0.830	20.899	-0.051	-0.051	0.000	0.000	0.000	0.000
70	A	70	PHE	0	0.008	0.011	17.315	-0.013	-0.013	0.000	0.000	0.000	0.000
71	A	71	GLU	-1	-0.838	-0.948	14.399	0.002	0.002	0.000	0.000	0.000	0.000
72	A	72	SER	0	-0.009	0.001	10.048	0.061	0.061	0.000	0.000	0.000	0.000
73	A	73	VAL	0	0.006	-0.004	11.310	-0.044	-0.044	0.000	0.000	0.000	0.000
74	A	74	SER	0	0.020	-0.002	10.246	0.019	0.019	0.000	0.000	0.000	0.000
75	A	75	HIS	0	-0.019	-0.004	12.850	-0.044	-0.044	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.023	0.013	15.756	-0.017	-0.017	0.000	0.000	0.000	0.000
77	A	77	ILE	0	-0.007	-0.020	14.617	-0.018	-0.018	0.000	0.000	0.000	0.000
78	A	78	SER	0	0.030	0.023	17.238	-0.005	-0.005	0.000	0.000	0.000	0.000
79	A	79	TYR	0	0.021	0.020	18.999	-0.009	-0.009	0.000	0.000	0.000	0.000
80	A	80	HIS	0	-0.045	-0.036	21.162	-0.008	-0.008	0.000	0.000	0.000	0.000
81	A	81	MET	0	-0.013	0.005	19.647	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	82	ASP	-1	-0.890	-0.937	20.522	-0.011	-0.011	0.000	0.000	0.000	0.000
83	A	83	ASN	0	-0.067	-0.050	23.139	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	84	HIS	0	-0.063	-0.018	25.183	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	85	LEU	0	-0.025	0.001	26.235	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	86	PRO	0	-0.010	-0.004	26.070	0.009	0.009	0.000	0.000	0.000	0.000
87	A	87	ILE	0	0.052	0.022	21.523	0.001	0.001	0.000	0.000	0.000	0.000
88	A	88	ILE	0	0.018	0.007	26.038	0.000	0.000	0.000	0.000	0.000	0.000
89	A	89	SER	0	-0.042	-0.039	26.003	0.002	0.002	0.000	0.000	0.000	0.000
90	A	90	ALA	0	-0.018	-0.023	29.089	0.000	0.000	0.000	0.000	0.000	0.000
91	A	91	GLY	0	-0.029	-0.003	32.486	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	92	SER	0	-0.024	0.000	30.611	-0.004	-0.004	0.000	0.000	0.000	0.000
93	A	93	GLU	-1	-0.919	-0.969	29.370	0.060	0.060	0.000	0.000	0.000	0.000
94	A	94	LEU	0	-0.061	-0.037	23.160	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	95	CYS	0	0.000	-0.009	25.648	0.003	0.003	0.000	0.000	0.000	0.000
96	A	96	LEU	0	-0.009	0.011	19.471	0.005	0.005	0.000	0.000	0.000	0.000
97	A	97	GLN	0	-0.006	-0.016	23.022	-0.010	-0.010	0.000	0.000	0.000	0.000
98	A	98	GLN	0	-0.012	-0.006	21.839	-0.010	-0.010	0.000	0.000	0.000	0.000
99	A	99	PRO	0	0.019	0.019	16.561	0.016	0.016	0.000	0.000	0.000	0.000
100	A	100	VAL	0	0.011	0.014	18.241	-0.015	-0.015	0.000	0.000	0.000	0.000
101	A	101	GLU	-1	-0.893	-0.963	14.930	0.083	0.083	0.000	0.000	0.000	0.000
102	A	102	ARG	1	0.841	0.935	6.913	-0.245	-0.245	0.000	0.000	0.000	0.000
103	A	103	LYS	1	0.960	0.958	13.984	-0.104	-0.104	0.000	0.000	0.000	0.000
104	A	104	LEU	0	-0.014	0.015	11.109	0.001	0.001	0.000	0.000	0.000	0.000

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