FMO DATABASE

FMODB ID: 6Y27Z

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	OptHSide
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	-651047.143917
FMO2-HF: Nuclear repulsion	614280.406543
FMO2-HF: Total energy	-36766.737374
FMO2-MP2: Total energy	-36876.381649

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.
-6.219	-0.116	0.932	-2.383	-4.652	-0.011

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 : 0.002 / q_NPA : -0.004

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	-0.782	-0.863	3.277	-3.542	-0.027	0.029	-1.767	-1.777	-0.006
4	A	7	GLU	-1	-0.791	-0.884	5.654	-0.345	-0.345	0.000	0.000	0.000	0.000
5	A	8	THR	0	-0.011	-0.009	7.172	0.036	0.036	0.000	0.000	0.000	0.000
6	A	9	PRO	0	-0.013	0.004	10.873	-0.014	-0.014	0.000	0.000	0.000	0.000
7	A	10	LEU	0	0.024	0.003	11.325	0.027	0.027	0.000	0.000	0.000	0.000
8	A	11	PHE	0	-0.019	-0.009	14.614	0.018	0.018	0.000	0.000	0.000	0.000
9	A	12	HIS	0	0.016	0.008	18.005	-0.009	-0.009	0.000	0.000	0.000	0.000
10	A	13	LYS	1	0.952	0.961	20.744	0.093	0.093	0.000	0.000	0.000	0.000
11	A	14	GLY	0	-0.048	-0.027	22.985	0.007	0.007	0.000	0.000	0.000	0.000
12	A	15	GLU	-1	-0.772	-0.861	20.887	-0.068	-0.068	0.000	0.000	0.000	0.000
13	A	16	ILE	0	0.002	-0.008	24.048	-0.007	-0.007	0.000	0.000	0.000	0.000
14	A	17	VAL	0	0.005	0.004	19.982	0.002	0.002	0.000	0.000	0.000	0.000
15	A	18	LEU	0	0.007	0.008	21.647	0.000	0.000	0.000	0.000	0.000	0.000
16	A	19	CYS	0	-0.018	-0.017	19.400	-0.012	-0.012	0.000	0.000	0.000	0.000
17	A	20	TYR	0	0.002	-0.003	17.608	0.007	0.007	0.000	0.000	0.000	0.000
18	A	21	GLU	-1	-0.801	-0.879	19.740	-0.103	-0.103	0.000	0.000	0.000	0.000
19	A	22	PRO	0	-0.070	-0.031	18.585	-0.007	-0.007	0.000	0.000	0.000	0.000
20	A	23	ASP	-1	-0.785	-0.856	19.460	-0.100	-0.100	0.000	0.000	0.000	0.000
21	A	24	LYS	1	0.915	0.941	15.871	0.165	0.165	0.000	0.000	0.000	0.000
22	A	25	SER	0	-0.054	-0.042	21.476	0.008	0.008	0.000	0.000	0.000	0.000
23	A	26	LYS	1	0.819	0.901	24.489	0.081	0.081	0.000	0.000	0.000	0.000
24	A	27	ALA	0	0.060	0.037	24.791	-0.002	-0.002	0.000	0.000	0.000	0.000
25	A	28	ARG	1	0.913	0.958	17.852	0.084	0.084	0.000	0.000	0.000	0.000
26	A	29	VAL	0	0.091	0.047	23.945	0.006	0.006	0.000	0.000	0.000	0.000
27	A	30	LEU	0	0.004	0.002	20.993	-0.009	-0.009	0.000	0.000	0.000	0.000
28	A	31	TYR	0	-0.035	-0.033	23.485	0.008	0.008	0.000	0.000	0.000	0.000
29	A	32	THR	0	0.081	0.049	24.172	-0.005	-0.005	0.000	0.000	0.000	0.000
30	A	33	SER	0	-0.051	-0.033	22.732	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	34	LYS	1	0.958	0.992	24.841	0.069	0.069	0.000	0.000	0.000	0.000
32	A	35	VAL	0	0.014	0.020	19.698	-0.007	-0.007	0.000	0.000	0.000	0.000
33	A	36	LEU	0	-0.053	-0.035	22.072	0.008	0.008	0.000	0.000	0.000	0.000
34	A	37	ASN	0	-0.067	-0.062	19.582	-0.004	-0.004	0.000	0.000	0.000	0.000
35	A	38	VAL	0	0.015	0.019	15.585	-0.005	-0.005	0.000	0.000	0.000	0.000
36	A	39	PHE	0	-0.013	0.009	15.830	0.005	0.005	0.000	0.000	0.000	0.000
37	A	40	GLU	-1	-0.784	-0.852	11.783	-0.278	-0.278	0.000	0.000	0.000	0.000
38	A	41	ARG	1	0.840	0.915	10.623	0.370	0.370	0.000	0.000	0.000	0.000
39	A	42	ARG	1	0.960	0.972	8.412	0.416	0.416	0.000	0.000	0.000	0.000
40	A	43	ASN	0	0.010	0.007	2.397	-0.468	-0.033	0.588	-0.242	-0.781	0.001
41	A	44	GLU	-1	-0.829	-0.920	5.553	-1.185	-1.185	0.000	0.000	0.000	0.000
42	A	45	HIS	0	-0.079	-0.031	3.415	-1.482	-0.377	0.042	-0.329	-0.818	-0.002
43	A	46	GLY	0	-0.019	-0.002	5.487	0.049	0.049	0.000	0.000	0.000	0.000
44	A	47	LEU	0	-0.054	-0.025	2.625	-1.157	-0.149	0.274	-0.045	-1.237	-0.004
45	A	48	ARG	1	0.830	0.891	5.869	0.401	0.401	0.000	0.000	0.000	0.000
46	A	49	PHE	0	-0.071	-0.037	5.996	-0.039	-0.039	0.000	0.000	0.000	0.000
47	A	50	TYR	0	-0.046	-0.057	7.970	0.049	0.049	0.000	0.000	0.000	0.000
48	A	51	GLU	-1	-0.874	-0.923	11.067	-0.326	-0.326	0.000	0.000	0.000	0.000
49	A	52	TYR	0	0.033	0.013	11.998	0.039	0.039	0.000	0.000	0.000	0.000
50	A	53	LYS	1	0.877	0.941	16.246	0.117	0.117	0.000	0.000	0.000	0.000
51	A	54	ILE	0	-0.006	-0.007	19.022	0.011	0.011	0.000	0.000	0.000	0.000
52	A	55	HIS	1	0.812	0.903	21.589	0.077	0.077	0.000	0.000	0.000	0.000
53	A	56	PHE	0	0.055	0.026	21.305	0.001	0.001	0.000	0.000	0.000	0.000
54	A	57	GLN	0	0.021	-0.009	26.564	0.000	0.000	0.000	0.000	0.000	0.000
55	A	58	GLY	0	0.018	0.013	29.557	0.001	0.001	0.000	0.000	0.000	0.000
56	A	59	TRP	0	-0.002	0.018	29.384	0.001	0.001	0.000	0.000	0.000	0.000
57	A	60	ARG	1	0.959	0.965	31.279	0.066	0.066	0.000	0.000	0.000	0.000
58	A	61	PRO	0	0.072	0.001	29.054	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	62	SER	0	-0.003	0.019	27.936	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	63	TYR	0	-0.023	-0.014	26.863	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	64	ASP	-1	-0.769	-0.858	24.022	-0.100	-0.100	0.000	0.000	0.000	0.000
62	A	65	ARG	1	0.945	0.972	18.190	0.135	0.135	0.000	0.000	0.000	0.000
63	A	66	ALA	0	-0.001	0.012	16.286	0.005	0.005	0.000	0.000	0.000	0.000
64	A	67	VAL	0	-0.022	-0.009	14.621	-0.008	-0.008	0.000	0.000	0.000	0.000
65	A	68	ARG	1	0.926	0.948	4.701	0.573	0.613	-0.001	0.000	-0.039	0.000
66	A	69	ALA	0	0.069	0.019	10.597	0.029	0.029	0.000	0.000	0.000	0.000
67	A	70	THR	0	0.003	0.003	8.940	0.030	0.030	0.000	0.000	0.000	0.000
68	A	71	VAL	0	-0.042	-0.015	11.837	0.025	0.025	0.000	0.000	0.000	0.000
69	A	72	LEU	0	-0.037	-0.007	14.993	0.016	0.016	0.000	0.000	0.000	0.000
70	A	73	LEU	0	0.011	0.015	16.289	0.003	0.003	0.000	0.000	0.000	0.000
71	A	74	LYS	1	0.824	0.881	18.139	0.065	0.065	0.000	0.000	0.000	0.000
72	A	75	ASP	-1	-0.813	-0.862	21.011	-0.040	-0.040	0.000	0.000	0.000	0.000
73	A	76	THR	0	-0.031	-0.032	23.140	0.001	0.001	0.000	0.000	0.000	0.000
74	A	77	GLU	-1	-0.817	-0.902	25.913	-0.022	-0.022	0.000	0.000	0.000	0.000
75	A	78	GLU	-1	-0.834	-0.912	25.302	-0.012	-0.012	0.000	0.000	0.000	0.000
76	A	79	ASN	0	-0.030	-0.031	21.204	0.000	0.000	0.000	0.000	0.000	0.000
77	A	80	ARG	1	0.833	0.884	24.886	0.029	0.029	0.000	0.000	0.000	0.000
78	A	81	GLN	0	-0.040	-0.036	28.092	-0.002	-0.002	0.000	0.000	0.000	0.000
79	A	82	LEU	0	0.047	0.039	22.506	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	83	GLN	0	-0.084	-0.064	26.257	0.000	0.000	0.000	0.000	0.000	0.000
81	A	84	ARG	1	0.887	0.939	27.364	0.023	0.023	0.000	0.000	0.000	0.000
82	A	85	GLU	-1	-0.904	-0.937	28.613	-0.018	-0.018	0.000	0.000	0.000	0.000
83	A	86	LEU	0	-0.017	-0.023	23.888	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	87	ALA	0	-0.059	-0.028	28.517	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	88	GLU	-1	-0.966	-0.982	30.957	-0.021	-0.021	0.000	0.000	0.000	0.000
86	A	89	ALA	0	0.035	0.019	30.147	0.001	0.001	0.000	0.000	0.000	0.000
87	A	90	ALA	0	-0.081	-0.043	29.712	0.000	0.000	0.000	0.000	0.000	0.000
88	A	91	LYS	1	0.862	0.933	31.546	0.035	0.035	0.000	0.000	0.000	0.000
89	A	92	LEU	0	-0.003	0.022	34.775	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:4:LEU)