FMO DATABASE

FMODB ID: G6L61

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	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	104
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-832411.808992
FMO2-HF: Nuclear repulsion	788720.023441
FMO2-HF: Total energy	-43691.785551
FMO2-MP2: Total energy	-43816.021114

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.
-0.953	0.206	-0.008	-0.43	-0.722	0.002

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 : -0.013

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	0.066	0.055	3.901	-0.824	0.335	-0.008	-0.430	-0.722	0.002
4	A	143	MET	0	0.008	0.005	6.153	0.012	0.012	0.000	0.000	0.000	0.000
5	A	144	ARG	1	0.889	0.919	9.183	-0.314	-0.314	0.000	0.000	0.000	0.000
6	A	145	THR	0	0.024	0.013	7.433	0.007	0.007	0.000	0.000	0.000	0.000
7	A	146	ARG	1	0.863	0.921	5.752	-0.051	-0.051	0.000	0.000	0.000	0.000
8	A	147	VAL	0	0.002	-0.002	9.066	0.034	0.034	0.000	0.000	0.000	0.000
9	A	148	CYS	0	-0.006	-0.010	12.549	-0.001	-0.001	0.000	0.000	0.000	0.000
10	A	149	THR	0	-0.030	-0.012	10.359	0.021	0.021	0.000	0.000	0.000	0.000
11	A	150	VAL	0	-0.008	-0.004	12.671	-0.013	-0.013	0.000	0.000	0.000	0.000
12	A	151	ILE	0	-0.017	-0.016	14.824	-0.016	-0.016	0.000	0.000	0.000	0.000
13	A	152	ASN	0	-0.012	-0.019	15.917	-0.026	-0.026	0.000	0.000	0.000	0.000
14	A	153	ASN	0	0.027	0.033	14.822	-0.009	-0.009	0.000	0.000	0.000	0.000
15	A	154	ASN	0	-0.031	-0.019	18.402	-0.016	-0.016	0.000	0.000	0.000	0.000
16	A	155	ILE	0	0.026	0.024	20.510	0.000	0.000	0.000	0.000	0.000	0.000
17	A	156	ALA	0	0.012	0.009	22.430	0.002	0.002	0.000	0.000	0.000	0.000
18	A	157	HIS	0	0.013	0.023	22.184	-0.007	-0.007	0.000	0.000	0.000	0.000
19	A	158	GLU	-1	-0.818	-0.886	24.455	0.088	0.088	0.000	0.000	0.000	0.000
20	A	159	TRP	0	-0.015	-0.015	18.990	0.002	0.002	0.000	0.000	0.000	0.000
21	A	160	THR	0	0.008	-0.017	21.900	0.000	0.000	0.000	0.000	0.000	0.000
22	A	161	LEU	0	0.001	0.002	18.569	0.002	0.002	0.000	0.000	0.000	0.000
23	A	162	ALA	0	0.012	-0.002	19.116	0.006	0.006	0.000	0.000	0.000	0.000
24	A	163	ARG	1	0.901	0.959	20.167	-0.084	-0.084	0.000	0.000	0.000	0.000
25	A	164	ILE	0	0.058	0.030	15.059	0.000	0.000	0.000	0.000	0.000	0.000
26	A	165	ALA	0	-0.021	-0.017	15.652	0.008	0.008	0.000	0.000	0.000	0.000
27	A	166	SER	0	-0.018	-0.012	16.073	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	167	GLU	-1	-0.883	-0.946	15.149	0.129	0.129	0.000	0.000	0.000	0.000
29	A	168	LEU	0	-0.070	-0.031	10.269	0.017	0.017	0.000	0.000	0.000	0.000
30	A	169	LEU	0	0.008	0.015	12.040	0.000	0.000	0.000	0.000	0.000	0.000
31	A	170	MET	0	-0.028	0.007	11.947	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	171	SER	0	0.061	0.028	15.406	-0.004	-0.004	0.000	0.000	0.000	0.000
33	A	172	PRO	0	0.063	0.005	17.666	0.017	0.017	0.000	0.000	0.000	0.000
34	A	173	SER	0	0.008	-0.004	19.271	0.011	0.011	0.000	0.000	0.000	0.000
35	A	174	LEU	0	0.014	0.022	13.743	0.022	0.022	0.000	0.000	0.000	0.000
36	A	175	LEU	0	0.045	0.024	13.237	0.038	0.038	0.000	0.000	0.000	0.000
37	A	176	LYS	1	0.949	0.970	15.554	-0.152	-0.152	0.000	0.000	0.000	0.000
38	A	177	LYS	1	0.926	0.972	16.290	-0.322	-0.322	0.000	0.000	0.000	0.000
39	A	178	LYS	1	0.829	0.887	11.414	-0.578	-0.578	0.000	0.000	0.000	0.000
40	A	179	LEU	0	0.004	0.011	12.766	0.044	0.044	0.000	0.000	0.000	0.000
41	A	180	ARG	1	0.813	0.870	14.777	-0.294	-0.294	0.000	0.000	0.000	0.000
42	A	181	GLU	-1	-0.810	-0.907	13.124	0.616	0.616	0.000	0.000	0.000	0.000
43	A	182	GLU	-1	-0.816	-0.887	8.990	0.603	0.603	0.000	0.000	0.000	0.000
44	A	183	GLU	-1	-0.800	-0.862	13.678	0.289	0.289	0.000	0.000	0.000	0.000
45	A	184	THR	0	-0.025	-0.016	15.285	-0.043	-0.043	0.000	0.000	0.000	0.000
46	A	185	SER	0	-0.019	-0.034	18.075	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	186	TYR	0	0.055	0.012	18.038	-0.005	-0.005	0.000	0.000	0.000	0.000
48	A	187	SER	0	0.013	0.018	19.031	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	188	GLN	0	0.046	0.061	20.332	-0.005	-0.005	0.000	0.000	0.000	0.000
50	A	189	LEU	0	0.040	0.025	14.494	-0.007	-0.007	0.000	0.000	0.000	0.000
51	A	190	LEU	0	-0.007	0.004	18.456	-0.008	-0.008	0.000	0.000	0.000	0.000
52	A	191	THR	0	-0.020	-0.019	20.848	-0.012	-0.012	0.000	0.000	0.000	0.000
53	A	192	GLU	-1	-0.852	-0.929	17.729	0.190	0.190	0.000	0.000	0.000	0.000
54	A	193	CYS	0	-0.027	-0.008	17.525	-0.007	-0.007	0.000	0.000	0.000	0.000
55	A	194	ARG	1	0.820	0.906	20.006	-0.100	-0.100	0.000	0.000	0.000	0.000
56	A	195	MET	0	-0.005	0.019	23.731	-0.011	-0.011	0.000	0.000	0.000	0.000
57	A	196	GLN	0	0.001	0.025	18.115	-0.010	-0.010	0.000	0.000	0.000	0.000
58	A	197	ARG	1	0.836	0.911	19.984	-0.098	-0.098	0.000	0.000	0.000	0.000
59	A	198	ALA	0	0.037	-0.003	24.129	-0.007	-0.007	0.000	0.000	0.000	0.000
60	A	199	LEU	0	-0.021	-0.006	25.779	-0.006	-0.006	0.000	0.000	0.000	0.000
61	A	200	GLN	0	-0.014	-0.007	21.335	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	201	LEU	0	-0.043	-0.024	26.794	-0.005	-0.005	0.000	0.000	0.000	0.000
63	A	202	ILE	0	-0.039	-0.009	29.829	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	203	VAL	0	0.055	0.037	30.833	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	204	ILE	0	-0.022	0.010	31.359	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	205	HIS	0	0.084	0.021	34.166	0.003	0.003	0.000	0.000	0.000	0.000
67	A	206	GLY	0	0.009	0.008	37.892	0.000	0.000	0.000	0.000	0.000	0.000
68	A	207	PHE	0	-0.017	-0.018	32.497	0.001	0.001	0.000	0.000	0.000	0.000
69	A	208	SER	0	0.046	0.029	36.456	0.003	0.003	0.000	0.000	0.000	0.000
70	A	209	ILE	0	0.080	0.029	35.656	0.002	0.002	0.000	0.000	0.000	0.000
71	A	210	LYS	1	0.958	0.978	35.456	-0.036	-0.036	0.000	0.000	0.000	0.000
72	A	211	ARG	1	0.927	0.988	34.286	-0.034	-0.034	0.000	0.000	0.000	0.000
73	A	212	VAL	0	0.031	0.032	30.724	0.002	0.002	0.000	0.000	0.000	0.000
74	A	213	ALA	0	0.020	0.012	30.945	0.004	0.004	0.000	0.000	0.000	0.000
75	A	214	VAL	0	0.009	0.007	30.948	0.003	0.003	0.000	0.000	0.000	0.000
76	A	215	SER	0	-0.053	-0.042	29.628	0.001	0.001	0.000	0.000	0.000	0.000
77	A	216	CYS	0	-0.063	-0.017	26.711	0.003	0.003	0.000	0.000	0.000	0.000
78	A	217	GLY	0	0.036	0.018	27.092	0.005	0.005	0.000	0.000	0.000	0.000
79	A	218	TYR	0	-0.047	-0.029	26.523	0.002	0.002	0.000	0.000	0.000	0.000
80	A	219	HIS	0	-0.018	-0.025	30.833	-0.007	-0.007	0.000	0.000	0.000	0.000
81	A	220	SER	0	-0.009	-0.004	34.380	-0.003	-0.003	0.000	0.000	0.000	0.000
82	A	221	VAL	0	0.045	0.013	35.111	0.003	0.003	0.000	0.000	0.000	0.000
83	A	222	SER	0	0.038	0.016	36.401	0.001	0.001	0.000	0.000	0.000	0.000
84	A	223	TYR	0	0.005	0.013	29.904	0.002	0.002	0.000	0.000	0.000	0.000
85	A	224	PHE	0	0.039	0.011	29.566	0.004	0.004	0.000	0.000	0.000	0.000
86	A	225	ILE	0	-0.002	-0.017	32.455	0.003	0.003	0.000	0.000	0.000	0.000
87	A	226	TYR	0	-0.034	-0.004	32.928	0.001	0.001	0.000	0.000	0.000	0.000
88	A	227	VAL	0	0.016	0.000	28.068	0.003	0.003	0.000	0.000	0.000	0.000
89	A	228	PHE	0	0.033	-0.001	29.499	0.005	0.005	0.000	0.000	0.000	0.000
90	A	229	ARG	1	0.947	0.979	30.744	-0.065	-0.065	0.000	0.000	0.000	0.000
91	A	230	ASN	0	-0.063	-0.037	30.189	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	231	TYR	0	-0.021	-0.007	21.055	0.005	0.005	0.000	0.000	0.000	0.000
93	A	232	TYR	0	-0.034	-0.045	25.283	0.004	0.004	0.000	0.000	0.000	0.000
94	A	233	GLY	0	0.008	0.019	29.663	-0.004	-0.004	0.000	0.000	0.000	0.000
95	A	234	MET	0	-0.026	0.002	32.795	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	235	THR	0	-0.074	-0.091	33.972	0.002	0.002	0.000	0.000	0.000	0.000
97	A	236	PRO	0	-0.024	-0.014	33.215	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	237	THR	0	0.030	0.002	34.944	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	238	GLU	-1	-0.780	-0.848	37.435	0.053	0.053	0.000	0.000	0.000	0.000
100	A	239	TYR	0	0.051	0.007	29.491	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	240	GLN	0	-0.084	-0.055	35.049	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	241	GLU	-1	-0.847	-0.907	36.398	0.036	0.036	0.000	0.000	0.000	0.000
103	A	242	ARG	1	0.764	0.885	35.738	-0.043	-0.043	0.000	0.000	0.000	0.000
104	A	243	SER	0	-0.048	-0.015	33.868	-0.003	-0.003	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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