FMO DATABASE

FMODB ID: V5851

Calculation Name: 3MKL-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3MKL

Chain ID: A

ChEMBL ID:

UniProt ID: P37639

Base Structure: X-ray

Registration Date: 2023-06-21

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. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-827060.932341
FMO2-HF: Nuclear repulsion	783369.675276
FMO2-HF: Total energy	-43691.257065
FMO2-MP2: Total energy	-43815.468011

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:140:GLN)

Summations of interaction energy for fragment #1(A:140:GLN)

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.
-0.879	0.39	-0.01	-0.47	-0.789	0.003

Interaction energy analysis for fragmet #1(A:140:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / q_NPA : -0.009

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	142	ASN	0	0.058	0.036	3.831	-0.853	0.416	-0.010	-0.470	-0.789	0.003
4	A	143	MET	0	0.008	-0.002	6.136	0.111	0.111	0.000	0.000	0.000	0.000
5	A	144	ARG	1	0.985	0.988	8.998	-0.341	-0.341	0.000	0.000	0.000	0.000
6	A	145	THR	0	0.013	0.011	7.674	0.016	0.016	0.000	0.000	0.000	0.000
7	A	146	ARG	1	0.945	0.977	5.250	-0.198	-0.198	0.000	0.000	0.000	0.000
8	A	147	VAL	0	0.020	0.018	9.215	0.014	0.014	0.000	0.000	0.000	0.000
9	A	148	CYS	0	-0.002	-0.007	12.817	-0.011	-0.011	0.000	0.000	0.000	0.000
10	A	149	THR	0	-0.046	-0.027	10.834	0.011	0.011	0.000	0.000	0.000	0.000
11	A	150	VAL	0	-0.015	0.008	12.775	-0.017	-0.017	0.000	0.000	0.000	0.000
12	A	151	ILE	0	-0.009	-0.013	14.989	-0.025	-0.025	0.000	0.000	0.000	0.000
13	A	152	ASN	0	-0.011	-0.030	15.806	-0.034	-0.034	0.000	0.000	0.000	0.000
14	A	153	ASN	0	0.011	0.017	15.618	-0.011	-0.011	0.000	0.000	0.000	0.000
15	A	154	ASN	0	-0.036	-0.016	18.826	-0.021	-0.021	0.000	0.000	0.000	0.000
16	A	155	ILE	0	0.021	0.033	20.820	0.000	0.000	0.000	0.000	0.000	0.000
17	A	156	ALA	0	0.013	-0.005	22.901	0.000	0.000	0.000	0.000	0.000	0.000
18	A	157	HIS	0	-0.004	0.014	22.968	-0.008	-0.008	0.000	0.000	0.000	0.000
19	A	158	GLU	-1	-0.900	-0.951	24.787	0.100	0.100	0.000	0.000	0.000	0.000
20	A	159	TRP	0	-0.032	-0.030	19.323	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	160	THR	0	0.027	0.006	22.386	0.000	0.000	0.000	0.000	0.000	0.000
22	A	161	LEU	0	-0.008	-0.012	18.545	0.006	0.006	0.000	0.000	0.000	0.000
23	A	162	ALA	0	0.012	-0.013	19.257	0.005	0.005	0.000	0.000	0.000	0.000
24	A	163	ARG	1	0.913	0.973	20.400	-0.090	-0.090	0.000	0.000	0.000	0.000
25	A	164	ILE	0	0.060	0.037	15.187	0.003	0.003	0.000	0.000	0.000	0.000
26	A	165	ALA	0	-0.013	-0.016	15.697	0.012	0.012	0.000	0.000	0.000	0.000
27	A	166	SER	0	-0.009	-0.011	16.127	-0.003	-0.003	0.000	0.000	0.000	0.000
28	A	167	GLU	-1	-0.900	-0.951	15.449	0.167	0.167	0.000	0.000	0.000	0.000
29	A	168	LEU	0	-0.073	-0.024	10.571	0.029	0.029	0.000	0.000	0.000	0.000
30	A	169	LEU	0	-0.020	0.001	12.334	-0.010	-0.010	0.000	0.000	0.000	0.000
31	A	170	MET	0	-0.049	-0.017	11.819	-0.014	-0.014	0.000	0.000	0.000	0.000
32	A	171	SER	0	0.046	0.019	15.283	0.002	0.002	0.000	0.000	0.000	0.000
33	A	172	PRO	0	0.076	0.019	17.530	0.013	0.013	0.000	0.000	0.000	0.000
34	A	173	SER	0	-0.009	-0.012	18.990	0.012	0.012	0.000	0.000	0.000	0.000
35	A	174	LEU	0	0.011	0.018	13.282	0.014	0.014	0.000	0.000	0.000	0.000
36	A	175	LEU	0	0.040	0.016	13.177	0.020	0.020	0.000	0.000	0.000	0.000
37	A	176	LYS	1	0.944	0.964	15.434	-0.117	-0.117	0.000	0.000	0.000	0.000
38	A	177	LYS	1	0.947	0.976	16.682	-0.139	-0.139	0.000	0.000	0.000	0.000
39	A	178	LYS	1	0.973	0.977	10.267	-0.241	-0.241	0.000	0.000	0.000	0.000
40	A	179	LEU	0	-0.008	0.003	13.039	0.041	0.041	0.000	0.000	0.000	0.000
41	A	180	ARG	1	0.908	0.961	14.925	-0.224	-0.224	0.000	0.000	0.000	0.000
42	A	181	GLU	-1	-0.939	-0.981	13.362	0.340	0.340	0.000	0.000	0.000	0.000
43	A	182	GLU	-1	-0.870	-0.935	9.579	0.502	0.502	0.000	0.000	0.000	0.000
44	A	183	GLU	-1	-0.909	-0.958	14.096	0.282	0.282	0.000	0.000	0.000	0.000
45	A	184	THR	0	0.024	0.021	15.416	-0.022	-0.022	0.000	0.000	0.000	0.000
46	A	185	SER	0	-0.029	-0.025	18.235	-0.015	-0.015	0.000	0.000	0.000	0.000
47	A	186	TYR	0	0.064	0.009	17.955	0.004	0.004	0.000	0.000	0.000	0.000
48	A	187	SER	0	0.004	0.009	18.936	0.000	0.000	0.000	0.000	0.000	0.000
49	A	188	GLN	0	-0.032	-0.012	20.586	0.006	0.006	0.000	0.000	0.000	0.000
50	A	189	LEU	0	0.050	0.032	14.624	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	190	LEU	0	-0.002	0.002	18.666	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	191	THR	0	-0.019	-0.008	20.978	-0.009	-0.009	0.000	0.000	0.000	0.000
53	A	192	GLU	-1	-0.873	-0.944	19.092	0.218	0.218	0.000	0.000	0.000	0.000
54	A	193	CYS	0	-0.020	-0.003	17.946	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	194	ARG	1	0.860	0.940	20.369	-0.127	-0.127	0.000	0.000	0.000	0.000
56	A	195	MET	0	-0.010	0.007	24.041	-0.013	-0.013	0.000	0.000	0.000	0.000
57	A	196	GLN	0	-0.004	0.022	17.991	-0.005	-0.005	0.000	0.000	0.000	0.000
58	A	197	ARG	1	0.897	0.961	20.207	-0.141	-0.141	0.000	0.000	0.000	0.000
59	A	198	ALA	0	0.035	-0.006	24.337	-0.009	-0.009	0.000	0.000	0.000	0.000
60	A	199	LEU	0	-0.004	0.001	25.650	-0.007	-0.007	0.000	0.000	0.000	0.000
61	A	200	GLN	0	-0.026	-0.008	21.912	-0.006	-0.006	0.000	0.000	0.000	0.000
62	A	201	LEU	0	-0.038	-0.023	27.196	-0.007	-0.007	0.000	0.000	0.000	0.000
63	A	202	ILE	0	-0.046	-0.010	30.130	-0.006	-0.006	0.000	0.000	0.000	0.000
64	A	203	VAL	0	0.060	0.028	31.313	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	204	ILE	0	-0.042	-0.002	31.541	-0.005	-0.005	0.000	0.000	0.000	0.000
66	A	205	HIS	0	0.084	0.025	34.417	0.002	0.002	0.000	0.000	0.000	0.000
67	A	206	GLY	0	0.007	0.007	38.204	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	207	PHE	0	-0.029	-0.018	32.764	0.000	0.000	0.000	0.000	0.000	0.000
69	A	208	SER	0	0.035	0.017	37.100	0.003	0.003	0.000	0.000	0.000	0.000
70	A	209	ILE	0	0.088	0.032	36.099	0.002	0.002	0.000	0.000	0.000	0.000
71	A	210	LYS	1	0.943	0.963	35.656	-0.049	-0.049	0.000	0.000	0.000	0.000
72	A	211	ARG	1	0.936	0.991	33.974	-0.054	-0.054	0.000	0.000	0.000	0.000
73	A	212	VAL	0	0.039	0.034	30.735	0.003	0.003	0.000	0.000	0.000	0.000
74	A	213	ALA	0	0.010	0.015	31.195	0.005	0.005	0.000	0.000	0.000	0.000
75	A	214	VAL	0	0.015	0.005	31.281	0.004	0.004	0.000	0.000	0.000	0.000
76	A	215	SER	0	-0.045	-0.038	29.815	0.000	0.000	0.000	0.000	0.000	0.000
77	A	216	CYS	0	-0.066	-0.031	26.993	0.006	0.006	0.000	0.000	0.000	0.000
78	A	217	GLY	0	0.023	0.014	26.918	0.007	0.007	0.000	0.000	0.000	0.000
79	A	218	TYR	0	-0.049	-0.014	27.369	0.001	0.001	0.000	0.000	0.000	0.000
80	A	219	HIS	0	0.053	0.025	31.503	-0.007	-0.007	0.000	0.000	0.000	0.000
81	A	220	SER	0	-0.018	-0.011	34.493	-0.004	-0.004	0.000	0.000	0.000	0.000
82	A	221	VAL	0	0.057	0.012	35.226	0.004	0.004	0.000	0.000	0.000	0.000
83	A	222	SER	0	0.037	0.024	36.754	0.002	0.002	0.000	0.000	0.000	0.000
84	A	223	TYR	0	0.023	0.014	29.843	0.003	0.003	0.000	0.000	0.000	0.000
85	A	224	PHE	0	0.033	0.008	29.917	0.004	0.004	0.000	0.000	0.000	0.000
86	A	225	ILE	0	-0.014	-0.017	32.708	0.004	0.004	0.000	0.000	0.000	0.000
87	A	226	TYR	0	-0.041	-0.017	32.211	0.003	0.003	0.000	0.000	0.000	0.000
88	A	227	VAL	0	0.001	-0.003	28.281	0.004	0.004	0.000	0.000	0.000	0.000
89	A	228	PHE	0	0.031	0.005	29.896	0.008	0.008	0.000	0.000	0.000	0.000
90	A	229	ARG	1	0.932	0.968	31.016	-0.080	-0.080	0.000	0.000	0.000	0.000
91	A	230	ASN	0	-0.049	-0.021	30.302	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	231	TYR	0	-0.029	-0.008	21.724	0.009	0.009	0.000	0.000	0.000	0.000
93	A	232	TYR	0	-0.036	-0.050	25.395	0.009	0.009	0.000	0.000	0.000	0.000
94	A	233	GLY	0	0.005	0.026	29.929	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	234	MET	0	-0.034	-0.008	33.054	-0.007	-0.007	0.000	0.000	0.000	0.000
96	A	235	THR	0	-0.045	-0.048	34.235	0.003	0.003	0.000	0.000	0.000	0.000
97	A	236	PRO	0	-0.016	-0.017	33.680	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	237	THR	0	0.044	0.018	35.284	0.000	0.000	0.000	0.000	0.000	0.000
99	A	238	GLU	-1	-0.816	-0.904	37.486	0.074	0.074	0.000	0.000	0.000	0.000
100	A	239	TYR	0	0.018	-0.013	29.499	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	240	GLN	0	-0.056	-0.031	35.354	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	241	GLU	-1	-0.933	-0.959	36.656	0.054	0.054	0.000	0.000	0.000	0.000
103	A	242	ARG	1	0.835	0.940	35.984	-0.070	-0.070	0.000	0.000	0.000	0.000
104	A	243	SER	0	0.000	0.012	34.022	-0.002	-0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:140:GLN)