FMO DATABASE

FMODB ID: G5R71

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

Total energy (hartree)

FMO2-HF: Electronic energy	-800430.666124
FMO2-HF: Nuclear repulsion	758686.81644
FMO2-HF: Total energy	-41743.849685
FMO2-MP2: Total energy	-41866.717362

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.
-2.181	-0.166	0.224	-0.975	-1.264	-0.001

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 : -0.010 / q_NPA : -0.015

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	0.032	0.029	3.011	-3.445	-1.512	0.225	-0.969	-1.190	-0.001
4	A	4	LYS	1	0.915	0.959	5.334	1.320	1.402	-0.001	-0.006	-0.074	0.000
5	A	5	PHE	0	0.063	0.013	8.522	-0.074	-0.074	0.000	0.000	0.000	0.000
6	A	6	ASP	-1	-0.815	-0.918	11.798	-0.583	-0.583	0.000	0.000	0.000	0.000
7	A	7	ASP	-1	-0.913	-0.961	7.685	-1.483	-1.483	0.000	0.000	0.000	0.000
8	A	8	PHE	0	-0.065	-0.025	10.224	-0.043	-0.043	0.000	0.000	0.000	0.000
9	A	9	ALA	0	-0.035	-0.028	11.954	0.098	0.098	0.000	0.000	0.000	0.000
10	A	10	LYS	1	0.927	0.974	11.057	0.939	0.939	0.000	0.000	0.000	0.000
11	A	11	LEU	0	-0.011	0.018	12.235	0.064	0.064	0.000	0.000	0.000	0.000
12	A	12	ASP	-1	-0.823	-0.924	16.099	-0.332	-0.332	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.014	-0.002	15.380	0.018	0.018	0.000	0.000	0.000	0.000
14	A	14	ARG	1	0.890	0.946	19.801	0.347	0.347	0.000	0.000	0.000	0.000
15	A	15	VAL	0	0.038	0.028	23.399	-0.011	-0.011	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.028	0.012	25.553	0.008	0.008	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.932	0.982	28.060	0.146	0.146	0.000	0.000	0.000	0.000
18	A	18	ILE	0	-0.012	0.011	27.779	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	19	ILE	0	-0.002	-0.004	31.427	0.012	0.012	0.000	0.000	0.000	0.000
20	A	20	GLU	-1	-0.930	-0.975	33.833	-0.133	-0.133	0.000	0.000	0.000	0.000
21	A	21	VAL	0	0.021	0.027	31.979	-0.015	-0.015	0.000	0.000	0.000	0.000
22	A	22	LYS	1	0.961	0.993	33.950	0.156	0.156	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.797	-0.893	33.730	-0.151	-0.151	0.000	0.000	0.000	0.000
24	A	24	HIS	0	-0.015	-0.020	29.859	0.009	0.009	0.000	0.000	0.000	0.000
25	A	25	PRO	0	0.015	0.007	33.295	0.000	0.000	0.000	0.000	0.000	0.000
26	A	26	ASN	0	-0.007	-0.014	32.334	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	27	ALA	0	-0.012	-0.006	29.158	-0.009	-0.009	0.000	0.000	0.000	0.000
28	A	28	ASP	-1	-0.824	-0.889	29.654	-0.175	-0.175	0.000	0.000	0.000	0.000
29	A	29	LYS	1	0.885	0.954	23.861	0.259	0.259	0.000	0.000	0.000	0.000
30	A	30	LEU	0	-0.043	-0.025	25.069	-0.011	-0.011	0.000	0.000	0.000	0.000
31	A	31	TYR	0	-0.028	-0.025	28.660	0.020	0.020	0.000	0.000	0.000	0.000
32	A	32	VAL	0	-0.041	-0.035	29.121	-0.019	-0.019	0.000	0.000	0.000	0.000
33	A	33	VAL	0	0.011	0.008	27.986	0.014	0.014	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.926	0.980	30.085	0.146	0.146	0.000	0.000	0.000	0.000
35	A	35	VAL	0	-0.048	-0.037	26.974	0.007	0.007	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.879	-0.947	30.213	-0.172	-0.172	0.000	0.000	0.000	0.000
37	A	37	LEU	0	-0.027	-0.048	26.192	-0.007	-0.007	0.000	0.000	0.000	0.000
38	A	38	GLY	0	-0.029	-0.007	30.126	-0.004	-0.004	0.000	0.000	0.000	0.000
39	A	39	ASP	-1	-0.950	-0.972	31.237	-0.201	-0.201	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.849	-0.901	29.257	-0.235	-0.235	0.000	0.000	0.000	0.000
41	A	41	VAL	0	-0.038	-0.040	32.033	0.001	0.001	0.000	0.000	0.000	0.000
42	A	42	ARG	1	0.863	0.943	24.158	0.301	0.301	0.000	0.000	0.000	0.000
43	A	43	THR	0	0.023	0.015	28.947	0.008	0.008	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.040	-0.012	24.018	-0.010	-0.010	0.000	0.000	0.000	0.000
45	A	45	VAL	0	-0.003	-0.014	25.572	0.020	0.020	0.000	0.000	0.000	0.000
46	A	46	ALA	0	0.035	0.020	24.412	-0.030	-0.030	0.000	0.000	0.000	0.000
47	A	47	GLY	0	0.012	-0.021	24.037	0.026	0.026	0.000	0.000	0.000	0.000
48	A	48	LEU	0	0.037	0.008	23.765	-0.006	-0.006	0.000	0.000	0.000	0.000
49	A	49	LYS	1	0.881	0.964	26.920	0.162	0.162	0.000	0.000	0.000	0.000
50	A	50	LYS	1	0.879	0.925	27.261	0.150	0.150	0.000	0.000	0.000	0.000
51	A	51	TYR	0	-0.005	-0.006	23.511	0.001	0.001	0.000	0.000	0.000	0.000
52	A	52	TYR	0	0.026	0.026	25.306	0.004	0.004	0.000	0.000	0.000	0.000
53	A	53	LYS	1	0.875	0.936	30.393	0.102	0.102	0.000	0.000	0.000	0.000
54	A	54	PRO	0	0.028	-0.004	33.805	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.863	-0.927	34.894	-0.106	-0.106	0.000	0.000	0.000	0.000
56	A	56	GLU	-1	-0.856	-0.918	32.145	-0.130	-0.130	0.000	0.000	0.000	0.000
57	A	57	LEU	0	-0.046	-0.026	28.327	-0.007	-0.007	0.000	0.000	0.000	0.000
58	A	58	LEU	0	0.019	0.016	31.598	-0.009	-0.009	0.000	0.000	0.000	0.000
59	A	59	ASN	0	-0.029	-0.020	34.276	0.002	0.002	0.000	0.000	0.000	0.000
60	A	60	ARG	1	0.955	0.994	27.567	0.168	0.168	0.000	0.000	0.000	0.000
61	A	61	TYR	0	0.027	0.006	28.194	-0.007	-0.007	0.000	0.000	0.000	0.000
62	A	62	VAL	0	0.003	0.004	24.655	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	63	VAL	0	0.032	0.010	19.606	0.002	0.002	0.000	0.000	0.000	0.000
64	A	64	VAL	0	0.001	-0.001	21.293	-0.015	-0.015	0.000	0.000	0.000	0.000
65	A	65	VAL	0	-0.013	-0.003	16.382	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	66	ALA	0	0.004	-0.005	19.527	0.010	0.010	0.000	0.000	0.000	0.000
67	A	67	ASN	0	0.008	-0.011	17.620	0.004	0.004	0.000	0.000	0.000	0.000
68	A	68	LEU	0	0.002	0.019	15.459	-0.020	-0.020	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.939	-0.972	18.204	-0.361	-0.361	0.000	0.000	0.000	0.000
70	A	70	PRO	0	-0.013	-0.001	20.051	-0.008	-0.008	0.000	0.000	0.000	0.000
71	A	71	LYS	1	0.972	0.979	18.577	0.421	0.421	0.000	0.000	0.000	0.000
72	A	72	LYS	1	0.920	0.976	23.554	0.215	0.215	0.000	0.000	0.000	0.000
73	A	73	LEU	0	0.104	0.041	22.635	-0.004	-0.004	0.000	0.000	0.000	0.000
74	A	74	ARG	1	0.835	0.919	26.406	0.206	0.206	0.000	0.000	0.000	0.000
75	A	75	GLY	0	0.019	-0.028	28.047	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	76	ILE	0	-0.007	0.010	29.546	0.012	0.012	0.000	0.000	0.000	0.000
77	A	77	GLY	0	-0.040	-0.013	28.188	-0.015	-0.015	0.000	0.000	0.000	0.000
78	A	78	SER	0	0.029	0.021	23.833	0.012	0.012	0.000	0.000	0.000	0.000
79	A	79	GLN	0	0.043	0.022	22.412	0.010	0.010	0.000	0.000	0.000	0.000
80	A	80	GLY	0	0.040	0.027	20.689	0.013	0.013	0.000	0.000	0.000	0.000
81	A	81	MET	0	-0.042	-0.032	17.037	-0.007	-0.007	0.000	0.000	0.000	0.000
82	A	82	LEU	0	0.020	0.008	20.512	-0.018	-0.018	0.000	0.000	0.000	0.000
83	A	83	LEU	0	-0.007	-0.002	15.909	-0.027	-0.027	0.000	0.000	0.000	0.000
84	A	84	ALA	0	-0.016	-0.023	18.035	0.053	0.053	0.000	0.000	0.000	0.000
85	A	85	ALA	0	-0.014	0.011	16.631	-0.050	-0.050	0.000	0.000	0.000	0.000
86	A	86	ASP	-1	-0.913	-0.993	16.258	-0.337	-0.337	0.000	0.000	0.000	0.000
87	A	87	ASP	-1	-0.788	-0.867	16.632	-0.158	-0.158	0.000	0.000	0.000	0.000
88	A	88	GLY	0	-0.023	0.002	18.223	0.030	0.030	0.000	0.000	0.000	0.000
89	A	89	GLU	-1	-0.989	-0.989	19.550	-0.062	-0.062	0.000	0.000	0.000	0.000
90	A	90	ARG	1	0.813	0.893	22.654	0.113	0.113	0.000	0.000	0.000	0.000
91	A	91	VAL	0	0.035	0.017	20.937	-0.018	-0.018	0.000	0.000	0.000	0.000
92	A	92	ALA	0	-0.040	-0.025	21.269	0.019	0.019	0.000	0.000	0.000	0.000
93	A	93	LEU	0	-0.041	-0.023	21.076	-0.025	-0.025	0.000	0.000	0.000	0.000
94	A	94	LEU	0	-0.003	0.013	16.916	0.016	0.016	0.000	0.000	0.000	0.000
95	A	95	MET	0	-0.024	-0.021	21.570	0.001	0.001	0.000	0.000	0.000	0.000
96	A	96	PRO	0	-0.047	-0.017	23.953	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	97	ASP	-1	-0.869	-0.942	25.624	-0.136	-0.136	0.000	0.000	0.000	0.000
98	A	98	LYS	1	0.923	0.970	27.524	0.133	0.133	0.000	0.000	0.000	0.000
99	A	99	GLU	-1	-0.923	-0.958	29.484	-0.138	-0.138	0.000	0.000	0.000	0.000
100	A	100	VAL	0	-0.029	-0.023	27.634	0.002	0.002	0.000	0.000	0.000	0.000
101	A	101	LYS	1	0.948	0.979	31.056	0.164	0.164	0.000	0.000	0.000	0.000
102	A	102	LEU	0	0.021	0.005	30.182	-0.013	-0.013	0.000	0.000	0.000	0.000
103	A	103	GLY	0	0.071	0.027	27.907	0.006	0.006	0.000	0.000	0.000	0.000
104	A	104	ALA	0	-0.074	-0.025	27.047	-0.011	-0.011	0.000	0.000	0.000	0.000
105	A	105	LYS	1	0.791	0.891	19.133	0.454	0.454	0.000	0.000	0.000	0.000
106	A	106	VAL	0	0.022	0.022	18.651	0.021	0.021	0.000	0.000	0.000	0.000
107	A	107	ARG	1	0.970	0.979	17.768	0.242	0.242	0.000	0.000	0.000	0.000

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