FMO DATABASE

FMODB ID: 1727Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-827919.600892
FMO2-HF: Nuclear repulsion	784227.932767
FMO2-HF: Total energy	-43691.668125
FMO2-MP2: Total energy	-43815.880627

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.
-1.264	-0.0010000000000001	-0.01	-0.472	-0.78	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 : -0.005 / q_NPA : -0.014

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	0.044	3.831	-0.816	0.447	-0.010	-0.472	-0.780	0.002
4	A	143	MET	0	0.011	0.001	6.225	0.037	0.037	0.000	0.000	0.000	0.000
5	A	144	ARG	1	0.952	0.969	9.001	-0.402	-0.402	0.000	0.000	0.000	0.000
6	A	145	THR	0	0.016	0.006	7.662	-0.010	-0.010	0.000	0.000	0.000	0.000
7	A	146	ARG	1	0.943	0.983	5.420	-0.337	-0.337	0.000	0.000	0.000	0.000
8	A	147	VAL	0	0.013	0.013	9.178	-0.001	-0.001	0.000	0.000	0.000	0.000
9	A	148	CYS	0	-0.007	-0.009	12.786	-0.022	-0.022	0.000	0.000	0.000	0.000
10	A	149	THR	0	-0.036	-0.024	10.758	-0.002	-0.002	0.000	0.000	0.000	0.000
11	A	150	VAL	0	-0.013	0.008	12.774	-0.021	-0.021	0.000	0.000	0.000	0.000
12	A	151	ILE	0	-0.006	-0.014	14.941	-0.029	-0.029	0.000	0.000	0.000	0.000
13	A	152	ASN	0	-0.021	-0.025	16.126	-0.042	-0.042	0.000	0.000	0.000	0.000
14	A	153	ASN	0	0.044	0.035	15.196	-0.020	-0.020	0.000	0.000	0.000	0.000
15	A	154	ASN	0	-0.040	-0.020	18.786	-0.023	-0.023	0.000	0.000	0.000	0.000
16	A	155	ILE	0	0.019	0.025	21.077	0.003	0.003	0.000	0.000	0.000	0.000
17	A	156	ALA	0	0.028	0.003	22.853	0.003	0.003	0.000	0.000	0.000	0.000
18	A	157	HIS	0	0.006	0.019	22.267	-0.011	-0.011	0.000	0.000	0.000	0.000
19	A	158	GLU	-1	-0.848	-0.925	24.748	0.113	0.113	0.000	0.000	0.000	0.000
20	A	159	TRP	0	-0.039	-0.013	19.046	0.003	0.003	0.000	0.000	0.000	0.000
21	A	160	THR	0	0.008	-0.014	22.396	0.000	0.000	0.000	0.000	0.000	0.000
22	A	161	LEU	0	0.004	-0.004	18.607	0.007	0.007	0.000	0.000	0.000	0.000
23	A	162	ALA	0	0.019	-0.012	19.241	0.010	0.010	0.000	0.000	0.000	0.000
24	A	163	ARG	1	0.903	0.968	20.379	-0.109	-0.109	0.000	0.000	0.000	0.000
25	A	164	ILE	0	0.055	0.032	15.147	0.003	0.003	0.000	0.000	0.000	0.000
26	A	165	ALA	0	-0.014	-0.016	15.677	0.015	0.015	0.000	0.000	0.000	0.000
27	A	166	SER	0	-0.011	-0.008	16.108	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	167	GLU	-1	-0.883	-0.948	15.537	0.179	0.179	0.000	0.000	0.000	0.000
29	A	168	LEU	0	-0.079	-0.028	10.330	0.031	0.031	0.000	0.000	0.000	0.000
30	A	169	LEU	0	-0.011	0.004	12.315	0.002	0.002	0.000	0.000	0.000	0.000
31	A	170	MET	0	-0.046	-0.019	11.672	0.002	0.002	0.000	0.000	0.000	0.000
32	A	171	SER	0	0.049	0.020	15.275	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	172	PRO	0	0.076	0.021	17.533	0.019	0.019	0.000	0.000	0.000	0.000
34	A	173	SER	0	-0.015	-0.015	18.996	0.014	0.014	0.000	0.000	0.000	0.000
35	A	174	LEU	0	0.017	0.022	13.312	0.018	0.018	0.000	0.000	0.000	0.000
36	A	175	LEU	0	0.031	0.017	13.223	0.032	0.032	0.000	0.000	0.000	0.000
37	A	176	LYS	1	0.948	0.966	15.441	-0.161	-0.161	0.000	0.000	0.000	0.000
38	A	177	LYS	1	0.941	0.978	16.602	-0.259	-0.259	0.000	0.000	0.000	0.000
39	A	178	LYS	1	0.840	0.893	11.138	-0.507	-0.507	0.000	0.000	0.000	0.000
40	A	179	LEU	0	0.001	0.007	13.065	0.050	0.050	0.000	0.000	0.000	0.000
41	A	180	ARG	1	0.826	0.880	14.965	-0.295	-0.295	0.000	0.000	0.000	0.000
42	A	181	GLU	-1	-0.831	-0.914	13.068	0.534	0.534	0.000	0.000	0.000	0.000
43	A	182	GLU	-1	-0.840	-0.915	9.569	0.662	0.662	0.000	0.000	0.000	0.000
44	A	183	GLU	-1	-0.825	-0.875	14.188	0.315	0.315	0.000	0.000	0.000	0.000
45	A	184	THR	0	-0.007	0.000	15.483	-0.033	-0.033	0.000	0.000	0.000	0.000
46	A	185	SER	0	-0.019	-0.026	18.324	-0.009	-0.009	0.000	0.000	0.000	0.000
47	A	186	TYR	0	0.062	0.008	17.943	0.003	0.003	0.000	0.000	0.000	0.000
48	A	187	SER	0	-0.004	0.006	18.924	0.001	0.001	0.000	0.000	0.000	0.000
49	A	188	GLN	0	0.026	0.033	20.499	0.000	0.000	0.000	0.000	0.000	0.000
50	A	189	LEU	0	0.045	0.027	14.611	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	190	LEU	0	0.004	0.005	18.648	-0.007	-0.007	0.000	0.000	0.000	0.000
52	A	191	THR	0	-0.023	-0.015	20.951	-0.013	-0.013	0.000	0.000	0.000	0.000
53	A	192	GLU	-1	-0.869	-0.940	18.557	0.245	0.245	0.000	0.000	0.000	0.000
54	A	193	CYS	0	-0.025	-0.009	17.923	-0.004	-0.004	0.000	0.000	0.000	0.000
55	A	194	ARG	1	0.844	0.936	20.369	-0.139	-0.139	0.000	0.000	0.000	0.000
56	A	195	MET	0	-0.014	0.006	24.041	-0.015	-0.015	0.000	0.000	0.000	0.000
57	A	196	GLN	0	0.004	0.027	18.096	-0.009	-0.009	0.000	0.000	0.000	0.000
58	A	197	ARG	1	0.828	0.916	20.171	-0.143	-0.143	0.000	0.000	0.000	0.000
59	A	198	ALA	0	0.023	-0.010	24.384	-0.010	-0.010	0.000	0.000	0.000	0.000
60	A	199	LEU	0	-0.009	-0.001	25.997	-0.008	-0.008	0.000	0.000	0.000	0.000
61	A	200	GLN	0	-0.006	-0.001	21.769	-0.004	-0.004	0.000	0.000	0.000	0.000
62	A	201	LEU	0	-0.032	-0.018	27.243	-0.007	-0.007	0.000	0.000	0.000	0.000
63	A	202	ILE	0	-0.040	-0.008	30.178	-0.005	-0.005	0.000	0.000	0.000	0.000
64	A	203	VAL	0	0.046	0.030	31.167	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	204	ILE	0	-0.033	0.003	31.625	-0.005	-0.005	0.000	0.000	0.000	0.000
66	A	205	HIS	0	0.080	0.026	34.463	0.003	0.003	0.000	0.000	0.000	0.000
67	A	206	GLY	0	0.004	0.006	38.250	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	207	PHE	0	-0.020	-0.016	32.900	0.001	0.001	0.000	0.000	0.000	0.000
69	A	208	SER	0	0.041	0.023	37.147	0.003	0.003	0.000	0.000	0.000	0.000
70	A	209	ILE	0	0.086	0.029	35.975	0.003	0.003	0.000	0.000	0.000	0.000
71	A	210	LYS	1	0.945	0.966	35.656	-0.050	-0.050	0.000	0.000	0.000	0.000
72	A	211	ARG	1	0.933	0.991	34.417	-0.050	-0.050	0.000	0.000	0.000	0.000
73	A	212	VAL	0	0.053	0.041	30.731	0.003	0.003	0.000	0.000	0.000	0.000
74	A	213	ALA	0	0.008	0.012	31.195	0.005	0.005	0.000	0.000	0.000	0.000
75	A	214	VAL	0	0.011	0.002	31.239	0.004	0.004	0.000	0.000	0.000	0.000
76	A	215	SER	0	-0.050	-0.035	29.764	0.001	0.001	0.000	0.000	0.000	0.000
77	A	216	CYS	0	-0.068	-0.032	26.947	0.005	0.005	0.000	0.000	0.000	0.000
78	A	217	GLY	0	0.031	0.018	26.877	0.008	0.008	0.000	0.000	0.000	0.000
79	A	218	TYR	0	-0.064	-0.024	27.126	0.002	0.002	0.000	0.000	0.000	0.000
80	A	219	HIS	0	0.028	0.009	31.245	-0.009	-0.009	0.000	0.000	0.000	0.000
81	A	220	SER	0	-0.014	-0.008	34.458	-0.005	-0.005	0.000	0.000	0.000	0.000
82	A	221	VAL	0	0.049	0.006	35.193	0.004	0.004	0.000	0.000	0.000	0.000
83	A	222	SER	0	0.043	0.027	36.754	0.002	0.002	0.000	0.000	0.000	0.000
84	A	223	TYR	0	0.018	0.012	29.945	0.003	0.003	0.000	0.000	0.000	0.000
85	A	224	PHE	0	0.029	0.007	29.756	0.004	0.004	0.000	0.000	0.000	0.000
86	A	225	ILE	0	-0.007	-0.016	32.708	0.004	0.004	0.000	0.000	0.000	0.000
87	A	226	TYR	0	-0.046	-0.015	32.705	0.002	0.002	0.000	0.000	0.000	0.000
88	A	227	VAL	0	0.006	0.000	28.294	0.004	0.004	0.000	0.000	0.000	0.000
89	A	228	PHE	0	0.028	0.001	29.780	0.008	0.008	0.000	0.000	0.000	0.000
90	A	229	ARG	1	0.957	0.980	31.105	-0.083	-0.083	0.000	0.000	0.000	0.000
91	A	230	ASN	0	-0.065	-0.030	30.599	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	231	TYR	0	-0.019	-0.006	21.596	0.005	0.005	0.000	0.000	0.000	0.000
93	A	232	TYR	0	-0.033	-0.047	25.658	0.007	0.007	0.000	0.000	0.000	0.000
94	A	233	GLY	0	0.003	0.024	30.060	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	234	MET	0	-0.037	-0.009	33.064	-0.007	-0.007	0.000	0.000	0.000	0.000
96	A	235	THR	0	-0.068	-0.090	34.356	0.003	0.003	0.000	0.000	0.000	0.000
97	A	236	PRO	0	-0.025	-0.022	33.682	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	237	THR	0	0.039	0.008	35.329	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	238	GLU	-1	-0.792	-0.858	37.661	0.072	0.072	0.000	0.000	0.000	0.000
100	A	239	TYR	0	0.039	-0.008	29.481	-0.003	-0.003	0.000	0.000	0.000	0.000
101	A	240	GLN	0	-0.077	-0.045	35.408	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	241	GLU	-1	-0.846	-0.911	36.701	0.051	0.051	0.000	0.000	0.000	0.000
103	A	242	ARG	1	0.746	0.889	36.119	-0.062	-0.062	0.000	0.000	0.000	0.000
104	A	243	SER	0	0.001	0.013	34.071	-0.003	-0.003	0.000	0.000	0.000	0.000

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