FMO DATABASE

FMODB ID: NN86Q

Calculation Name: 1MKH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1MKH

Chain ID: A

ChEMBL ID:

UniProt ID: Q9V011

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	107
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-799318.542349
FMO2-HF: Nuclear repulsion	757573.151629
FMO2-HF: Total energy	-41745.39072
FMO2-MP2: Total energy	-41868.124853

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:1:MET)

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

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.
-3.351	-0.934	0.802	-1.468	-1.751	-0.01

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.020 / q_NPA : -0.020

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	3	VAL	0	0.025	0.016	2.601	-4.695	-2.358	0.803	-1.462	-1.679	-0.010
4	A	4	LYS	1	0.860	0.922	5.287	1.398	1.478	-0.001	-0.006	-0.072	0.000
5	A	5	PHE	0	0.039	0.011	8.692	-0.060	-0.060	0.000	0.000	0.000	0.000
6	A	6	ASP	-1	-0.783	-0.893	12.075	-0.690	-0.690	0.000	0.000	0.000	0.000
7	A	7	ASP	-1	-0.837	-0.913	7.261	-1.572	-1.572	0.000	0.000	0.000	0.000
8	A	8	PHE	0	-0.016	0.000	9.853	0.030	0.030	0.000	0.000	0.000	0.000
9	A	9	ALA	0	-0.031	-0.023	11.612	0.111	0.111	0.000	0.000	0.000	0.000
10	A	10	LYS	1	0.858	0.930	10.086	1.049	1.049	0.000	0.000	0.000	0.000
11	A	11	LEU	0	0.024	0.036	11.708	0.072	0.072	0.000	0.000	0.000	0.000
12	A	12	ASP	-1	-0.792	-0.880	15.307	-0.339	-0.339	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.036	-0.022	15.621	0.034	0.034	0.000	0.000	0.000	0.000
14	A	14	ARG	1	0.767	0.855	19.465	0.346	0.346	0.000	0.000	0.000	0.000
15	A	15	VAL	0	0.034	0.022	23.291	-0.012	-0.012	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.032	0.013	25.836	0.009	0.009	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.862	0.939	28.493	0.148	0.148	0.000	0.000	0.000	0.000
18	A	18	ILE	0	-0.022	0.003	28.033	0.000	0.000	0.000	0.000	0.000	0.000
19	A	19	ILE	0	0.024	0.007	31.842	0.012	0.012	0.000	0.000	0.000	0.000
20	A	20	GLU	-1	-0.872	-0.936	34.011	-0.126	-0.126	0.000	0.000	0.000	0.000
21	A	21	VAL	0	-0.005	-0.005	32.200	-0.014	-0.014	0.000	0.000	0.000	0.000
22	A	22	LYS	1	0.942	0.973	33.508	0.145	0.145	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.781	-0.875	33.258	-0.137	-0.137	0.000	0.000	0.000	0.000
24	A	24	HIS	0	0.033	0.018	28.385	0.010	0.010	0.000	0.000	0.000	0.000
25	A	25	PRO	0	0.033	0.020	32.676	0.001	0.001	0.000	0.000	0.000	0.000
26	A	26	ASN	0	-0.082	-0.060	31.369	0.001	0.001	0.000	0.000	0.000	0.000
27	A	27	ALA	0	0.000	0.006	28.701	-0.005	-0.005	0.000	0.000	0.000	0.000
28	A	28	ASP	-1	-0.796	-0.879	29.146	-0.147	-0.147	0.000	0.000	0.000	0.000
29	A	29	LYS	1	0.858	0.932	23.880	0.222	0.222	0.000	0.000	0.000	0.000
30	A	30	LEU	0	-0.038	-0.029	25.150	-0.014	-0.014	0.000	0.000	0.000	0.000
31	A	31	TYR	0	-0.029	-0.026	28.441	0.020	0.020	0.000	0.000	0.000	0.000
32	A	32	VAL	0	-0.033	-0.019	28.503	-0.018	-0.018	0.000	0.000	0.000	0.000
33	A	33	VAL	0	-0.009	-0.012	27.572	0.013	0.013	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.896	0.948	29.604	0.132	0.132	0.000	0.000	0.000	0.000
35	A	35	VAL	0	-0.010	-0.002	26.586	0.009	0.009	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.835	-0.921	29.845	-0.177	-0.177	0.000	0.000	0.000	0.000
37	A	37	LEU	0	-0.005	-0.031	25.836	-0.014	-0.014	0.000	0.000	0.000	0.000
38	A	38	GLY	0	-0.006	0.001	29.985	-0.004	-0.004	0.000	0.000	0.000	0.000
39	A	39	ASP	-1	-0.929	-0.969	30.015	-0.205	-0.205	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.841	-0.902	29.124	-0.231	-0.231	0.000	0.000	0.000	0.000
41	A	41	VAL	0	-0.018	-0.016	31.355	0.000	0.000	0.000	0.000	0.000	0.000
42	A	42	ARG	1	0.817	0.897	23.626	0.293	0.293	0.000	0.000	0.000	0.000
43	A	43	THR	0	-0.020	0.003	28.306	0.004	0.004	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.020	-0.007	23.708	-0.011	-0.011	0.000	0.000	0.000	0.000
45	A	45	VAL	0	-0.005	-0.011	25.087	0.023	0.023	0.000	0.000	0.000	0.000
46	A	46	ALA	0	0.040	0.021	23.917	-0.029	-0.029	0.000	0.000	0.000	0.000
47	A	47	GLY	0	-0.003	-0.005	23.644	0.025	0.025	0.000	0.000	0.000	0.000
48	A	48	LEU	0	0.049	0.002	23.878	0.002	0.002	0.000	0.000	0.000	0.000
49	A	49	LYS	1	0.872	0.944	26.901	0.144	0.144	0.000	0.000	0.000	0.000
50	A	50	LYS	1	0.891	0.939	27.120	0.131	0.131	0.000	0.000	0.000	0.000
51	A	51	TYR	0	-0.002	0.000	23.548	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	52	TYR	0	0.011	0.005	25.324	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	53	LYS	1	0.885	0.949	30.660	0.096	0.096	0.000	0.000	0.000	0.000
54	A	54	PRO	0	0.029	-0.009	33.627	-0.006	-0.006	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.851	-0.922	35.067	-0.104	-0.104	0.000	0.000	0.000	0.000
56	A	56	GLU	-1	-0.820	-0.901	32.408	-0.126	-0.126	0.000	0.000	0.000	0.000
57	A	57	LEU	0	-0.038	-0.023	28.542	-0.010	-0.010	0.000	0.000	0.000	0.000
58	A	58	LEU	0	0.003	0.005	31.838	-0.009	-0.009	0.000	0.000	0.000	0.000
59	A	59	ASN	0	-0.010	-0.017	34.684	0.002	0.002	0.000	0.000	0.000	0.000
60	A	60	ARG	1	0.873	0.960	27.939	0.169	0.169	0.000	0.000	0.000	0.000
61	A	61	TYR	0	-0.032	-0.056	28.586	-0.010	-0.010	0.000	0.000	0.000	0.000
62	A	62	VAL	0	-0.016	-0.013	24.924	0.001	0.001	0.000	0.000	0.000	0.000
63	A	63	VAL	0	0.003	0.008	19.748	0.000	0.000	0.000	0.000	0.000	0.000
64	A	64	VAL	0	-0.002	-0.003	21.586	-0.011	-0.011	0.000	0.000	0.000	0.000
65	A	65	VAL	0	0.020	0.002	15.896	-0.010	-0.010	0.000	0.000	0.000	0.000
66	A	66	ALA	0	0.008	0.015	19.027	0.010	0.010	0.000	0.000	0.000	0.000
67	A	67	ASN	0	0.036	0.011	17.095	0.008	0.008	0.000	0.000	0.000	0.000
68	A	68	LEU	0	0.004	0.018	15.208	-0.010	-0.010	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.808	-0.892	18.056	-0.341	-0.341	0.000	0.000	0.000	0.000
70	A	70	PRO	0	0.008	0.018	19.900	-0.007	-0.007	0.000	0.000	0.000	0.000
71	A	71	LYS	1	0.785	0.871	18.325	0.380	0.380	0.000	0.000	0.000	0.000
72	A	72	LYS	1	0.898	0.947	23.327	0.190	0.190	0.000	0.000	0.000	0.000
73	A	73	LEU	0	0.000	0.016	21.844	-0.005	-0.005	0.000	0.000	0.000	0.000
74	A	74	ARG	1	0.889	0.927	25.902	0.169	0.169	0.000	0.000	0.000	0.000
75	A	75	GLY	0	0.058	0.024	28.000	0.002	0.002	0.000	0.000	0.000	0.000
76	A	76	ILE	0	0.004	0.006	30.102	0.006	0.006	0.000	0.000	0.000	0.000
77	A	77	GLY	0	-0.018	-0.010	27.691	-0.009	-0.009	0.000	0.000	0.000	0.000
78	A	78	SER	0	0.013	0.007	23.451	0.010	0.010	0.000	0.000	0.000	0.000
79	A	79	GLN	0	0.014	0.003	22.207	0.010	0.010	0.000	0.000	0.000	0.000
80	A	80	GLY	0	0.057	0.040	20.488	0.011	0.011	0.000	0.000	0.000	0.000
81	A	81	MET	0	-0.030	-0.029	16.639	0.000	0.000	0.000	0.000	0.000	0.000
82	A	82	LEU	0	0.009	0.002	20.449	-0.022	-0.022	0.000	0.000	0.000	0.000
83	A	83	LEU	0	-0.007	-0.002	16.024	-0.030	-0.030	0.000	0.000	0.000	0.000
84	A	84	ALA	0	-0.013	-0.019	18.178	0.053	0.053	0.000	0.000	0.000	0.000
85	A	85	ALA	0	0.003	0.020	16.585	-0.056	-0.056	0.000	0.000	0.000	0.000
86	A	86	ASP	-1	-0.922	-0.981	16.356	-0.314	-0.314	0.000	0.000	0.000	0.000
87	A	87	ASP	-1	-0.810	-0.897	16.411	-0.166	-0.166	0.000	0.000	0.000	0.000
88	A	88	GLY	0	-0.016	0.010	18.179	0.031	0.031	0.000	0.000	0.000	0.000
89	A	89	GLU	-1	-0.960	-0.973	19.420	-0.057	-0.057	0.000	0.000	0.000	0.000
90	A	90	ARG	1	0.794	0.886	22.041	0.120	0.120	0.000	0.000	0.000	0.000
91	A	91	VAL	0	0.021	0.005	21.126	-0.021	-0.021	0.000	0.000	0.000	0.000
92	A	92	ALA	0	0.004	0.017	21.275	0.022	0.022	0.000	0.000	0.000	0.000
93	A	93	LEU	0	-0.025	-0.015	21.181	-0.030	-0.030	0.000	0.000	0.000	0.000
94	A	94	LEU	0	0.000	0.009	16.941	0.017	0.017	0.000	0.000	0.000	0.000
95	A	95	MET	0	-0.008	-0.012	21.678	0.001	0.001	0.000	0.000	0.000	0.000
96	A	96	PRO	0	-0.028	-0.004	24.232	-0.005	-0.005	0.000	0.000	0.000	0.000
97	A	97	ASP	-1	-0.814	-0.893	26.070	-0.154	-0.154	0.000	0.000	0.000	0.000
98	A	98	LYS	1	0.833	0.896	28.245	0.167	0.167	0.000	0.000	0.000	0.000
99	A	99	GLU	-1	-0.803	-0.863	30.159	-0.145	-0.145	0.000	0.000	0.000	0.000
100	A	100	VAL	0	-0.024	-0.019	28.403	0.001	0.001	0.000	0.000	0.000	0.000
101	A	101	LYS	1	0.833	0.918	31.015	0.199	0.199	0.000	0.000	0.000	0.000
102	A	102	LEU	0	0.018	0.010	30.594	-0.016	-0.016	0.000	0.000	0.000	0.000
103	A	103	GLY	0	0.082	0.047	27.657	0.007	0.007	0.000	0.000	0.000	0.000
104	A	104	ALA	0	-0.030	-0.005	27.298	-0.012	-0.012	0.000	0.000	0.000	0.000
105	A	105	LYS	1	0.852	0.924	18.282	0.490	0.490	0.000	0.000	0.000	0.000
106	A	106	VAL	0	0.022	0.015	19.208	0.019	0.019	0.000	0.000	0.000	0.000
107	A	107	ARG	1	0.939	0.968	18.011	0.262	0.262	0.000	0.000	0.000	0.000

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