FMO DATABASE

FMODB ID: 2N77R

Calculation Name: 1SMT-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1SMT

Chain ID: A

ChEMBL ID:

UniProt ID: P30340

Base Structure: X-ray

Registration Date: 2023-09-20

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	98
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-668019.129422
FMO2-HF: Nuclear repulsion	629646.546411
FMO2-HF: Total energy	-38372.58301
FMO2-MP2: Total energy	-38485.717443

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:24:GLU)

Summations of interaction energy for fragment #1(A:24:GLU)

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.
6.853	8.322	-0.011	-0.653	-0.805	0.002

Interaction energy analysis for fragmet #1(A:24:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.907 / q_NPA : -0.968

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	26	GLN	0	-0.018	-0.011	3.852	-5.463	-3.994	-0.011	-0.653	-0.805	0.002
4	A	27	ALA	0	-0.010	0.005	6.658	-1.243	-1.243	0.000	0.000	0.000	0.000
5	A	28	ILE	0	-0.004	-0.004	10.402	0.283	0.283	0.000	0.000	0.000	0.000
6	A	29	ALA	0	0.044	0.029	13.112	-0.175	-0.175	0.000	0.000	0.000	0.000
7	A	30	PRO	0	0.016	0.006	15.046	-0.614	-0.614	0.000	0.000	0.000	0.000
8	A	31	GLU	-1	-0.824	-0.929	18.068	15.123	15.123	0.000	0.000	0.000	0.000
9	A	32	VAL	0	-0.011	0.007	17.070	-0.642	-0.642	0.000	0.000	0.000	0.000
10	A	33	ALA	0	-0.002	-0.006	17.489	-0.432	-0.432	0.000	0.000	0.000	0.000
11	A	34	GLN	0	-0.046	-0.033	19.338	-0.257	-0.257	0.000	0.000	0.000	0.000
12	A	35	SER	0	-0.015	-0.026	22.460	-0.638	-0.638	0.000	0.000	0.000	0.000
13	A	36	LEU	0	-0.039	-0.013	19.492	-0.450	-0.450	0.000	0.000	0.000	0.000
14	A	37	ALA	0	0.011	0.007	22.951	-0.381	-0.381	0.000	0.000	0.000	0.000
15	A	38	GLU	-1	-0.873	-0.925	24.777	10.073	10.073	0.000	0.000	0.000	0.000
16	A	39	PHE	0	-0.025	-0.008	25.730	-0.461	-0.461	0.000	0.000	0.000	0.000
17	A	40	PHE	0	0.025	-0.007	22.345	-0.343	-0.343	0.000	0.000	0.000	0.000
18	A	41	ALA	0	-0.008	0.000	27.853	-0.350	-0.350	0.000	0.000	0.000	0.000
19	A	42	VAL	0	-0.052	-0.027	30.643	-0.424	-0.424	0.000	0.000	0.000	0.000
20	A	43	LEU	0	-0.006	-0.005	28.296	-0.380	-0.380	0.000	0.000	0.000	0.000
21	A	44	ALA	0	-0.010	0.020	31.891	-0.165	-0.165	0.000	0.000	0.000	0.000
22	A	45	ASP	-1	-0.866	-0.946	33.529	7.506	7.506	0.000	0.000	0.000	0.000
23	A	46	PRO	0	0.049	0.005	37.143	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	47	ASN	0	-0.036	-0.007	39.121	-0.178	-0.178	0.000	0.000	0.000	0.000
25	A	48	ARG	1	0.894	0.948	35.775	-8.290	-8.290	0.000	0.000	0.000	0.000
26	A	49	LEU	0	0.042	0.029	33.159	-0.015	-0.015	0.000	0.000	0.000	0.000
27	A	50	ARG	1	0.908	0.966	37.115	-6.803	-6.803	0.000	0.000	0.000	0.000
28	A	51	LEU	0	-0.010	0.005	40.093	-0.084	-0.084	0.000	0.000	0.000	0.000
29	A	52	LEU	0	0.001	-0.015	33.565	-0.027	-0.027	0.000	0.000	0.000	0.000
30	A	53	SER	0	-0.039	-0.019	37.189	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	54	LEU	0	-0.032	-0.016	38.418	-0.087	-0.087	0.000	0.000	0.000	0.000
32	A	55	LEU	0	-0.005	-0.017	38.260	-0.024	-0.024	0.000	0.000	0.000	0.000
33	A	56	ALA	0	-0.008	0.006	35.228	0.094	0.094	0.000	0.000	0.000	0.000
34	A	57	ARG	1	0.873	0.942	36.661	-7.267	-7.267	0.000	0.000	0.000	0.000
35	A	58	SER	0	-0.017	-0.018	39.730	-0.129	-0.129	0.000	0.000	0.000	0.000
36	A	59	GLU	-1	-0.808	-0.850	41.200	7.264	7.264	0.000	0.000	0.000	0.000
37	A	60	LEU	0	-0.028	-0.013	42.343	-0.174	-0.174	0.000	0.000	0.000	0.000
38	A	61	CYS	0	-0.035	-0.011	45.410	0.058	0.058	0.000	0.000	0.000	0.000
39	A	62	VAL	0	-0.001	-0.014	47.571	0.036	0.036	0.000	0.000	0.000	0.000
40	A	63	GLY	0	0.105	0.047	48.870	0.014	0.014	0.000	0.000	0.000	0.000
41	A	64	ASP	-1	-0.853	-0.905	48.117	6.175	6.175	0.000	0.000	0.000	0.000
42	A	65	LEU	0	0.002	-0.002	43.601	0.016	0.016	0.000	0.000	0.000	0.000
43	A	66	ALA	0	-0.030	-0.015	47.357	0.019	0.019	0.000	0.000	0.000	0.000
44	A	67	GLN	0	-0.038	-0.031	50.324	-0.104	-0.104	0.000	0.000	0.000	0.000
45	A	68	ALA	0	-0.002	0.010	47.015	-0.026	-0.026	0.000	0.000	0.000	0.000
46	A	69	ILE	0	-0.058	-0.028	43.797	0.070	0.070	0.000	0.000	0.000	0.000
47	A	70	GLY	0	0.022	0.022	47.815	0.004	0.004	0.000	0.000	0.000	0.000
48	A	71	VAL	0	-0.044	-0.022	48.698	-0.061	-0.061	0.000	0.000	0.000	0.000
49	A	72	SER	0	0.057	0.016	51.935	0.001	0.001	0.000	0.000	0.000	0.000
50	A	73	GLU	-1	-0.810	-0.934	51.071	5.932	5.932	0.000	0.000	0.000	0.000
51	A	74	SER	0	-0.043	-0.003	50.502	0.155	0.155	0.000	0.000	0.000	0.000
52	A	75	ALA	0	0.044	0.014	49.407	0.107	0.107	0.000	0.000	0.000	0.000
53	A	76	VAL	0	0.028	0.036	45.805	0.163	0.163	0.000	0.000	0.000	0.000
54	A	77	SER	0	-0.008	-0.021	45.681	0.165	0.165	0.000	0.000	0.000	0.000
55	A	78	HIS	0	0.000	0.008	45.972	0.217	0.217	0.000	0.000	0.000	0.000
56	A	79	GLN	0	0.006	0.001	42.420	0.246	0.246	0.000	0.000	0.000	0.000
57	A	80	LEU	0	0.026	0.014	41.337	0.204	0.204	0.000	0.000	0.000	0.000
58	A	81	ARG	1	0.851	0.919	41.229	-6.463	-6.463	0.000	0.000	0.000	0.000
59	A	82	SER	0	-0.018	-0.003	39.289	0.161	0.161	0.000	0.000	0.000	0.000
60	A	83	LEU	0	0.074	0.015	36.999	0.178	0.178	0.000	0.000	0.000	0.000
61	A	84	ARG	1	0.890	0.953	36.386	-7.204	-7.204	0.000	0.000	0.000	0.000
62	A	85	ASN	0	-0.049	-0.027	36.643	0.132	0.132	0.000	0.000	0.000	0.000
63	A	86	LEU	0	-0.021	-0.005	33.679	0.157	0.157	0.000	0.000	0.000	0.000
64	A	87	ARG	1	0.932	0.974	30.237	-9.248	-9.248	0.000	0.000	0.000	0.000
65	A	88	LEU	0	0.066	0.040	31.476	0.196	0.196	0.000	0.000	0.000	0.000
66	A	89	VAL	0	-0.056	-0.025	33.725	-0.046	-0.046	0.000	0.000	0.000	0.000
67	A	90	SER	0	-0.020	-0.017	36.622	0.109	0.109	0.000	0.000	0.000	0.000
68	A	91	TYR	0	-0.001	-0.010	38.378	-0.147	-0.147	0.000	0.000	0.000	0.000
69	A	92	ARG	1	0.807	0.881	41.603	-6.879	-6.879	0.000	0.000	0.000	0.000
70	A	93	LYS	1	0.958	0.970	43.849	-6.528	-6.528	0.000	0.000	0.000	0.000
71	A	94	GLN	0	0.068	0.037	47.190	0.179	0.179	0.000	0.000	0.000	0.000
72	A	95	GLY	0	0.027	0.017	49.725	-0.097	-0.097	0.000	0.000	0.000	0.000
73	A	96	ARG	1	0.914	0.948	53.289	-5.361	-5.361	0.000	0.000	0.000	0.000
74	A	97	HIS	0	0.030	0.040	50.721	-0.027	-0.027	0.000	0.000	0.000	0.000
75	A	98	VAL	0	-0.044	-0.044	46.219	0.062	0.062	0.000	0.000	0.000	0.000
76	A	99	TYR	0	0.049	0.033	44.614	-0.081	-0.081	0.000	0.000	0.000	0.000
77	A	100	TYR	0	0.029	-0.001	41.437	0.124	0.124	0.000	0.000	0.000	0.000
78	A	101	GLN	0	0.041	0.018	37.849	-0.023	-0.023	0.000	0.000	0.000	0.000
79	A	102	LEU	0	0.042	0.023	33.414	0.019	0.019	0.000	0.000	0.000	0.000
80	A	103	GLN	0	-0.081	-0.035	31.340	-0.080	-0.080	0.000	0.000	0.000	0.000
81	A	104	ASP	-1	-0.806	-0.907	28.490	10.508	10.508	0.000	0.000	0.000	0.000
82	A	105	HIS	0	0.046	0.005	27.826	-0.291	-0.291	0.000	0.000	0.000	0.000
83	A	106	HIS	0	0.007	0.012	24.195	0.214	0.214	0.000	0.000	0.000	0.000
84	A	107	ILE	0	-0.019	-0.008	26.822	0.062	0.062	0.000	0.000	0.000	0.000
85	A	108	VAL	0	-0.010	-0.002	29.548	-0.128	-0.128	0.000	0.000	0.000	0.000
86	A	109	ALA	0	-0.012	-0.003	25.844	-0.064	-0.064	0.000	0.000	0.000	0.000
87	A	110	LEU	0	0.006	0.005	25.384	0.050	0.050	0.000	0.000	0.000	0.000
88	A	111	TYR	0	-0.020	-0.006	26.735	-0.130	-0.130	0.000	0.000	0.000	0.000
89	A	112	GLN	0	-0.005	-0.008	29.810	-0.170	-0.170	0.000	0.000	0.000	0.000
90	A	113	ASN	0	0.006	-0.002	24.880	0.194	0.194	0.000	0.000	0.000	0.000
91	A	114	ALA	0	-0.019	-0.001	27.392	0.106	0.106	0.000	0.000	0.000	0.000
92	A	115	LEU	0	-0.037	-0.019	28.515	-0.171	-0.171	0.000	0.000	0.000	0.000
93	A	116	ASP	-1	-0.867	-0.944	28.673	9.570	9.570	0.000	0.000	0.000	0.000
94	A	117	HIS	0	0.010	0.005	25.158	0.053	0.053	0.000	0.000	0.000	0.000
95	A	118	LEU	0	-0.068	-0.045	28.375	-0.104	-0.104	0.000	0.000	0.000	0.000
96	A	119	GLN	0	-0.088	-0.038	31.509	-0.266	-0.266	0.000	0.000	0.000	0.000
97	A	120	GLU	-1	-0.963	-0.968	28.219	10.017	10.017	0.000	0.000	0.000	0.000
98	A	121	CYS	0	-0.110	-0.039	28.125	0.040	0.040	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:24:GLU)