FMO DATABASE

FMODB ID: ZV8LN

Calculation Name: 3M9Q-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3M9Q

Chain ID: A

ChEMBL ID:

UniProt ID: P50536

Base Structure: X-ray

Registration Date: 2023-09-23

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	89
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-650397.983488
FMO2-HF: Nuclear repulsion	613631.054509
FMO2-HF: Total energy	-36766.928978
FMO2-MP2: Total energy	-36876.583086

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:4:LEU)

Summations of interaction energy for fragment #1(A:4:LEU)

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.
-6.322	-0.591	2.132	-3.015	-4.846	-0.015

Interaction energy analysis for fragmet #1(A:4:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.010 / q_NPA : 0.007

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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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	6	ASP	-1	-0.767	-0.873	2.901	-3.920	-0.663	0.280	-1.754	-1.782	-0.009
4	A	7	GLU	-1	-0.785	-0.868	5.440	-0.349	-0.349	0.000	0.000	0.000	0.000
5	A	8	THR	0	-0.008	-0.017	7.120	0.061	0.061	0.000	0.000	0.000	0.000
6	A	9	PRO	0	-0.006	0.004	10.884	-0.004	-0.004	0.000	0.000	0.000	0.000
7	A	10	LEU	0	0.024	0.016	11.208	0.032	0.032	0.000	0.000	0.000	0.000
8	A	11	PHE	0	-0.023	-0.013	14.473	0.023	0.023	0.000	0.000	0.000	0.000
9	A	12	HIS	0	0.025	0.008	17.660	-0.014	-0.014	0.000	0.000	0.000	0.000
10	A	13	LYS	1	0.903	0.928	20.452	0.103	0.103	0.000	0.000	0.000	0.000
11	A	14	GLY	0	-0.030	-0.018	22.864	0.008	0.008	0.000	0.000	0.000	0.000
12	A	15	GLU	-1	-0.745	-0.853	20.649	-0.062	-0.062	0.000	0.000	0.000	0.000
13	A	16	ILE	0	0.008	-0.001	24.162	-0.007	-0.007	0.000	0.000	0.000	0.000
14	A	17	VAL	0	-0.005	-0.002	19.972	0.002	0.002	0.000	0.000	0.000	0.000
15	A	18	LEU	0	0.009	0.004	21.736	-0.002	-0.002	0.000	0.000	0.000	0.000
16	A	19	CYS	0	-0.028	-0.013	19.674	-0.008	-0.008	0.000	0.000	0.000	0.000
17	A	20	TYR	0	0.019	-0.001	17.599	0.007	0.007	0.000	0.000	0.000	0.000
18	A	21	GLU	-1	-0.802	-0.873	20.440	-0.080	-0.080	0.000	0.000	0.000	0.000
19	A	22	PRO	0	-0.074	-0.030	18.642	-0.003	-0.003	0.000	0.000	0.000	0.000
20	A	23	ASP	-1	-0.781	-0.855	19.785	-0.071	-0.071	0.000	0.000	0.000	0.000
21	A	24	LYS	1	0.890	0.924	16.508	0.119	0.119	0.000	0.000	0.000	0.000
22	A	25	SER	0	-0.042	-0.031	22.129	0.008	0.008	0.000	0.000	0.000	0.000
23	A	26	LYS	1	0.831	0.901	25.227	0.057	0.057	0.000	0.000	0.000	0.000
24	A	27	ALA	0	0.054	0.032	25.468	0.001	0.001	0.000	0.000	0.000	0.000
25	A	28	ARG	1	0.916	0.961	17.943	0.038	0.038	0.000	0.000	0.000	0.000
26	A	29	VAL	0	0.080	0.048	24.205	0.005	0.005	0.000	0.000	0.000	0.000
27	A	30	LEU	0	0.001	-0.002	20.991	-0.007	-0.007	0.000	0.000	0.000	0.000
28	A	31	TYR	0	-0.024	-0.026	23.882	0.006	0.006	0.000	0.000	0.000	0.000
29	A	32	THR	0	0.077	0.053	24.480	-0.006	-0.006	0.000	0.000	0.000	0.000
30	A	33	SER	0	-0.060	-0.037	23.231	-0.004	-0.004	0.000	0.000	0.000	0.000
31	A	34	LYS	1	0.932	0.980	25.015	0.066	0.066	0.000	0.000	0.000	0.000
32	A	35	VAL	0	0.017	0.021	19.855	-0.007	-0.007	0.000	0.000	0.000	0.000
33	A	36	LEU	0	-0.032	-0.019	22.311	0.007	0.007	0.000	0.000	0.000	0.000
34	A	37	ASN	0	-0.059	-0.051	19.243	-0.004	-0.004	0.000	0.000	0.000	0.000
35	A	38	VAL	0	0.018	0.022	15.471	0.000	0.000	0.000	0.000	0.000	0.000
36	A	39	PHE	0	-0.014	0.001	15.296	0.007	0.007	0.000	0.000	0.000	0.000
37	A	40	GLU	-1	-0.775	-0.851	11.744	-0.366	-0.366	0.000	0.000	0.000	0.000
38	A	41	ARG	1	0.838	0.917	10.367	0.398	0.398	0.000	0.000	0.000	0.000
39	A	42	ARG	1	0.920	0.939	8.146	0.537	0.537	0.000	0.000	0.000	0.000
40	A	43	ASN	0	0.015	0.013	2.131	-0.132	-0.178	1.368	-0.395	-0.927	0.001
41	A	44	GLU	-1	-0.827	-0.920	5.225	-1.089	-1.089	0.000	0.000	0.000	0.000
42	A	45	HIS	0	-0.066	-0.023	3.502	-1.886	-0.486	0.078	-0.536	-0.942	-0.005
43	A	46	GLY	0	-0.006	0.006	5.666	0.003	0.003	0.000	0.000	0.000	0.000
44	A	47	LEU	0	-0.036	-0.010	2.600	-1.085	-0.016	0.407	-0.329	-1.146	-0.002
45	A	48	ARG	1	0.788	0.865	5.941	0.555	0.555	0.000	0.000	0.000	0.000
46	A	49	PHE	0	-0.067	-0.036	5.555	-0.159	-0.159	0.000	0.000	0.000	0.000
47	A	50	TYR	0	-0.028	-0.036	7.450	0.079	0.079	0.000	0.000	0.000	0.000
48	A	51	GLU	-1	-0.864	-0.918	10.873	-0.326	-0.326	0.000	0.000	0.000	0.000
49	A	52	TYR	0	0.014	-0.001	11.951	0.038	0.038	0.000	0.000	0.000	0.000
50	A	53	LYS	1	0.871	0.933	16.251	0.122	0.122	0.000	0.000	0.000	0.000
51	A	54	ILE	0	0.004	-0.006	19.119	0.010	0.010	0.000	0.000	0.000	0.000
52	A	55	HIS	1	0.825	0.905	21.627	0.072	0.072	0.000	0.000	0.000	0.000
53	A	56	PHE	0	0.064	0.031	21.600	0.003	0.003	0.000	0.000	0.000	0.000
54	A	57	GLN	0	0.016	-0.008	26.751	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	58	GLY	0	0.008	0.008	29.949	0.002	0.002	0.000	0.000	0.000	0.000
56	A	59	TRP	0	0.002	0.018	29.624	0.000	0.000	0.000	0.000	0.000	0.000
57	A	60	ARG	1	0.963	0.967	31.583	0.059	0.059	0.000	0.000	0.000	0.000
58	A	61	PRO	0	0.053	-0.007	29.289	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	62	SER	0	-0.018	0.007	28.232	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	63	TYR	0	0.013	0.010	26.947	0.000	0.000	0.000	0.000	0.000	0.000
61	A	64	ASP	-1	-0.796	-0.874	24.187	-0.097	-0.097	0.000	0.000	0.000	0.000
62	A	65	ARG	1	0.925	0.971	18.126	0.120	0.120	0.000	0.000	0.000	0.000
63	A	66	ALA	0	0.012	0.013	16.299	0.003	0.003	0.000	0.000	0.000	0.000
64	A	67	VAL	0	-0.023	-0.005	14.526	0.000	0.000	0.000	0.000	0.000	0.000
65	A	68	ARG	1	0.920	0.947	4.476	0.651	0.702	-0.001	-0.001	-0.049	0.000
66	A	69	ALA	0	0.057	0.011	10.543	0.035	0.035	0.000	0.000	0.000	0.000
67	A	70	THR	0	0.003	-0.001	8.548	0.029	0.029	0.000	0.000	0.000	0.000
68	A	71	VAL	0	-0.034	-0.009	11.613	0.026	0.026	0.000	0.000	0.000	0.000
69	A	72	LEU	0	-0.027	-0.001	15.066	0.008	0.008	0.000	0.000	0.000	0.000
70	A	73	LEU	0	0.018	0.022	16.398	0.007	0.007	0.000	0.000	0.000	0.000
71	A	74	LYS	1	0.819	0.882	18.096	0.050	0.050	0.000	0.000	0.000	0.000
72	A	75	ASP	-1	-0.820	-0.875	21.254	-0.022	-0.022	0.000	0.000	0.000	0.000
73	A	76	THR	0	-0.038	-0.035	23.487	0.000	0.000	0.000	0.000	0.000	0.000
74	A	77	GLU	-1	-0.795	-0.893	26.077	-0.007	-0.007	0.000	0.000	0.000	0.000
75	A	78	GLU	-1	-0.825	-0.906	25.395	0.010	0.010	0.000	0.000	0.000	0.000
76	A	79	ASN	0	-0.014	-0.015	21.573	0.004	0.004	0.000	0.000	0.000	0.000
77	A	80	ARG	1	0.814	0.880	24.885	0.013	0.013	0.000	0.000	0.000	0.000
78	A	81	GLN	0	-0.027	-0.016	28.115	-0.002	-0.002	0.000	0.000	0.000	0.000
79	A	82	LEU	0	0.068	0.047	22.669	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	83	GLN	0	-0.077	-0.071	26.088	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	84	ARG	1	0.849	0.910	27.274	0.006	0.006	0.000	0.000	0.000	0.000
82	A	85	GLU	-1	-0.894	-0.934	28.932	0.009	0.009	0.000	0.000	0.000	0.000
83	A	86	LEU	0	-0.013	-0.014	24.047	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	87	ALA	0	-0.036	-0.019	28.589	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	88	GLU	-1	-0.975	-0.970	30.881	-0.006	-0.006	0.000	0.000	0.000	0.000
86	A	89	ALA	0	0.048	0.018	30.271	0.000	0.000	0.000	0.000	0.000	0.000
87	A	90	ALA	0	-0.073	-0.044	29.661	0.000	0.000	0.000	0.000	0.000	0.000
88	A	91	LYS	1	0.813	0.900	31.590	0.017	0.017	0.000	0.000	0.000	0.000
89	A	92	LEU	0	-0.012	0.015	34.746	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:4:LEU)