FMO DATABASE

FMODB ID: N9L3Q

Calculation Name: 4DS1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4DS1

Chain ID: A

ChEMBL ID:

UniProt ID: Q02647

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	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	86
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-604574.173168
FMO2-HF: Nuclear repulsion	571456.209364
FMO2-HF: Total energy	-33117.963805
FMO2-MP2: Total energy	-33218.008851

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:7:SER)

Summations of interaction energy for fragment #1(A:7:SER)

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.
-4.96	-2.202	0.149	-1.167	-1.741	0

Interaction energy analysis for fragmet #1(A:7:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.006 / q_NPA : -0.017

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

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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	9	PRO	0	0.001	0.001	3.765	-3.270	-1.772	-0.006	-0.632	-0.859	0.002
4	A	10	ILE	0	-0.010	0.005	5.319	0.390	0.390	0.000	0.000	0.000	0.000
5	A	11	VAL	0	0.001	-0.011	7.724	-0.102	-0.102	0.000	0.000	0.000	0.000
6	A	12	LYS	1	0.893	0.956	9.848	0.134	0.134	0.000	0.000	0.000	0.000
7	A	13	ALA	0	0.027	0.011	13.394	0.013	0.013	0.000	0.000	0.000	0.000
8	A	14	SER	0	-0.042	-0.031	16.279	0.004	0.004	0.000	0.000	0.000	0.000
9	A	15	ASP	-1	-0.816	-0.899	18.420	0.055	0.055	0.000	0.000	0.000	0.000
10	A	16	ILE	0	-0.051	-0.019	17.673	-0.008	-0.008	0.000	0.000	0.000	0.000
11	A	17	THR	0	0.036	0.020	21.085	0.012	0.012	0.000	0.000	0.000	0.000
12	A	18	ASP	-1	-0.803	-0.921	18.335	0.217	0.217	0.000	0.000	0.000	0.000
13	A	19	LYS	1	0.957	0.976	17.493	-0.098	-0.098	0.000	0.000	0.000	0.000
14	A	20	LEU	0	-0.009	0.006	18.210	0.009	0.009	0.000	0.000	0.000	0.000
15	A	21	LYS	1	0.934	0.973	13.608	-0.319	-0.319	0.000	0.000	0.000	0.000
16	A	22	GLU	-1	-0.864	-0.943	12.516	0.508	0.508	0.000	0.000	0.000	0.000
17	A	23	ASP	-1	-0.773	-0.815	13.326	0.179	0.179	0.000	0.000	0.000	0.000
18	A	24	ILE	0	0.003	0.002	13.438	-0.007	-0.007	0.000	0.000	0.000	0.000
19	A	25	LEU	0	-0.043	-0.011	9.564	-0.034	-0.034	0.000	0.000	0.000	0.000
20	A	26	THR	0	-0.024	-0.011	10.002	0.077	0.077	0.000	0.000	0.000	0.000
21	A	27	ILE	0	-0.016	-0.014	11.465	-0.018	-0.018	0.000	0.000	0.000	0.000
22	A	28	SER	0	-0.023	-0.024	10.158	-0.062	-0.062	0.000	0.000	0.000	0.000
23	A	29	LYS	1	0.942	0.960	4.629	-2.064	-1.962	-0.001	-0.014	-0.088	0.000
24	A	30	ASP	-1	-0.821	-0.886	8.453	-0.068	-0.068	0.000	0.000	0.000	0.000
25	A	31	ALA	0	-0.020	-0.010	11.251	-0.070	-0.070	0.000	0.000	0.000	0.000
26	A	32	LEU	0	-0.046	-0.041	6.006	-0.063	-0.063	0.000	0.000	0.000	0.000
27	A	33	ASP	-1	-0.913	-0.928	8.642	-0.271	-0.271	0.000	0.000	0.000	0.000
28	A	34	LYS	1	0.772	0.872	10.605	0.021	0.021	0.000	0.000	0.000	0.000
29	A	35	TYR	0	-0.042	-0.019	13.288	0.022	0.022	0.000	0.000	0.000	0.000
30	A	36	GLN	0	0.048	0.019	12.850	-0.058	-0.058	0.000	0.000	0.000	0.000
31	A	37	LEU	0	-0.039	-0.009	14.824	-0.019	-0.019	0.000	0.000	0.000	0.000
32	A	38	GLU	-1	-0.851	-0.941	13.276	-0.273	-0.273	0.000	0.000	0.000	0.000
33	A	39	ARG	1	0.887	0.934	15.198	0.132	0.132	0.000	0.000	0.000	0.000
34	A	40	ASP	-1	-0.834	-0.911	17.532	-0.111	-0.111	0.000	0.000	0.000	0.000
35	A	41	ILE	0	0.024	0.024	11.303	0.022	0.022	0.000	0.000	0.000	0.000
36	A	42	ALA	0	0.009	-0.008	14.849	0.028	0.028	0.000	0.000	0.000	0.000
37	A	43	GLY	0	-0.022	-0.016	16.629	0.023	0.023	0.000	0.000	0.000	0.000
38	A	44	THR	0	0.000	0.000	15.950	0.023	0.023	0.000	0.000	0.000	0.000
39	A	45	VAL	0	0.047	0.030	13.758	0.018	0.018	0.000	0.000	0.000	0.000
40	A	46	LYS	1	0.785	0.864	17.024	0.037	0.037	0.000	0.000	0.000	0.000
41	A	47	LYS	1	0.934	0.953	20.224	0.058	0.058	0.000	0.000	0.000	0.000
42	A	48	GLN	0	0.016	0.008	16.864	0.022	0.022	0.000	0.000	0.000	0.000
43	A	49	LEU	0	-0.013	-0.003	17.471	0.010	0.010	0.000	0.000	0.000	0.000
44	A	50	ASP	-1	-0.737	-0.861	21.428	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	51	VAL	0	-0.048	-0.010	24.490	0.003	0.003	0.000	0.000	0.000	0.000
46	A	52	LYS	1	0.826	0.909	19.483	-0.103	-0.103	0.000	0.000	0.000	0.000
47	A	53	TYR	0	-0.115	-0.126	19.872	0.008	0.008	0.000	0.000	0.000	0.000
48	A	54	GLY	0	0.032	0.039	25.438	0.000	0.000	0.000	0.000	0.000	0.000
49	A	55	ASN	0	-0.031	0.002	26.369	0.001	0.001	0.000	0.000	0.000	0.000
50	A	56	THR	0	-0.021	-0.046	26.815	0.005	0.005	0.000	0.000	0.000	0.000
51	A	57	TRP	0	-0.005	-0.007	20.003	0.004	0.004	0.000	0.000	0.000	0.000
52	A	58	HIS	0	-0.018	-0.004	21.879	-0.011	-0.011	0.000	0.000	0.000	0.000
53	A	59	VAL	0	-0.009	-0.004	15.827	0.005	0.005	0.000	0.000	0.000	0.000
54	A	60	ILE	0	-0.019	0.002	17.143	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	61	VAL	0	0.013	0.007	11.616	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	62	GLY	0	0.044	0.027	13.084	0.012	0.012	0.000	0.000	0.000	0.000
57	A	63	LYS	1	0.971	0.973	11.233	0.402	0.402	0.000	0.000	0.000	0.000
58	A	64	ASN	0	-0.052	-0.028	13.653	0.021	0.021	0.000	0.000	0.000	0.000
59	A	65	PHE	0	0.013	0.017	14.741	0.016	0.016	0.000	0.000	0.000	0.000
60	A	66	GLY	0	0.037	0.035	18.600	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	67	SER	0	-0.036	-0.036	20.798	0.003	0.003	0.000	0.000	0.000	0.000
62	A	68	TYR	0	0.037	0.023	22.560	0.005	0.005	0.000	0.000	0.000	0.000
63	A	69	VAL	0	-0.014	0.007	22.428	0.000	0.000	0.000	0.000	0.000	0.000
64	A	70	THR	0	0.015	0.004	25.475	0.006	0.006	0.000	0.000	0.000	0.000
65	A	71	HIS	1	0.809	0.896	23.903	-0.023	-0.023	0.000	0.000	0.000	0.000
66	A	72	GLU	-1	-0.834	-0.914	26.034	0.031	0.031	0.000	0.000	0.000	0.000
67	A	73	LYS	1	1.005	1.010	25.791	-0.047	-0.047	0.000	0.000	0.000	0.000
68	A	74	GLY	0	-0.017	-0.001	24.261	0.001	0.001	0.000	0.000	0.000	0.000
69	A	75	HIS	1	0.825	0.905	22.135	-0.038	-0.038	0.000	0.000	0.000	0.000
70	A	76	PHE	0	0.030	0.004	19.089	-0.013	-0.013	0.000	0.000	0.000	0.000
71	A	77	VAL	0	0.022	0.008	14.086	0.019	0.019	0.000	0.000	0.000	0.000
72	A	78	TYR	0	0.026	0.020	14.236	-0.020	-0.020	0.000	0.000	0.000	0.000
73	A	79	PHE	0	0.005	-0.004	8.436	0.051	0.051	0.000	0.000	0.000	0.000
74	A	80	TYR	0	0.013	0.015	6.623	0.034	0.034	0.000	0.000	0.000	0.000
75	A	81	ILE	0	0.018	0.017	3.174	-0.406	-0.060	0.085	-0.152	-0.279	-0.001
76	A	82	GLY	0	0.017	0.012	3.237	-0.481	0.289	0.067	-0.321	-0.517	-0.001
77	A	83	PRO	0	-0.017	-0.017	4.050	0.271	0.313	0.004	-0.048	0.002	0.000
78	A	84	LEU	0	-0.013	-0.002	6.803	0.190	0.190	0.000	0.000	0.000	0.000
79	A	85	ALA	0	0.005	0.010	8.197	-0.057	-0.057	0.000	0.000	0.000	0.000
80	A	86	PHE	0	0.053	0.011	7.845	0.044	0.044	0.000	0.000	0.000	0.000
81	A	87	LEU	0	-0.031	-0.011	12.322	0.029	0.029	0.000	0.000	0.000	0.000
82	A	88	VAL	0	0.011	0.006	14.615	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	89	PHE	0	0.004	-0.015	17.350	0.016	0.016	0.000	0.000	0.000	0.000
84	A	90	LYS	1	0.867	0.950	20.942	-0.026	-0.026	0.000	0.000	0.000	0.000
85	A	91	THR	0	0.038	0.023	24.225	0.000	0.000	0.000	0.000	0.000	0.000
86	A	92	ALA	0	0.025	0.023	27.816	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:SER)