FMO DATABASE

FMODB ID: GNVJ1

Calculation Name: 3MQK-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3MQK

Chain ID: C

ChEMBL ID:

UniProt ID: Q8U1R4

Base Structure: X-ray

Registration Date: 2023-03-14

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	75
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-502471.21379
FMO2-HF: Nuclear repulsion	472667.959399
FMO2-HF: Total energy	-29803.254391
FMO2-MP2: Total energy	-29891.626534

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(C:1:MET)

Summations of interaction energy for fragment #1(C: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.
-20.956	-16.448	18.936	-9.039	-14.406	-0.057

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.024 / q_NPA : 0.024

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

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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	C	3	ARG	1	0.988	0.984	3.767	-0.876	1.888	-0.037	-1.353	-1.373	0.010
4	C	4	LEU	0	0.006	0.025	5.886	-0.201	-0.201	0.000	0.000	0.000	0.000
5	C	5	GLY	0	0.007	0.000	8.792	-0.109	-0.109	0.000	0.000	0.000	0.000
6	C	6	LYS	1	0.928	0.964	10.168	0.076	0.076	0.000	0.000	0.000	0.000
7	C	7	VAL	0	-0.004	0.012	11.742	-0.021	-0.021	0.000	0.000	0.000	0.000
8	C	8	LEU	0	-0.046	-0.018	14.069	-0.012	-0.012	0.000	0.000	0.000	0.000
9	C	9	HIS	0	0.033	0.005	17.728	-0.003	-0.003	0.000	0.000	0.000	0.000
10	C	10	TYR	0	0.055	0.021	18.139	0.021	0.021	0.000	0.000	0.000	0.000
11	C	11	ALA	0	-0.013	-0.011	19.750	-0.014	-0.014	0.000	0.000	0.000	0.000
12	C	12	LYS	1	1.034	0.994	22.338	-0.054	-0.054	0.000	0.000	0.000	0.000
13	C	13	GLN	0	-0.012	0.004	24.282	0.010	0.010	0.000	0.000	0.000	0.000
14	C	14	GLY	0	-0.021	0.002	21.733	0.005	0.005	0.000	0.000	0.000	0.000
15	C	15	PHE	0	-0.018	-0.031	18.071	0.016	0.016	0.000	0.000	0.000	0.000
16	C	16	LEU	0	0.014	0.023	12.966	-0.021	-0.021	0.000	0.000	0.000	0.000
17	C	17	ILE	0	0.003	0.008	15.855	-0.004	-0.004	0.000	0.000	0.000	0.000
18	C	18	VAL	0	0.011	0.016	11.527	0.002	0.002	0.000	0.000	0.000	0.000
19	C	19	ARG	1	0.888	0.942	14.774	0.088	0.088	0.000	0.000	0.000	0.000
20	C	20	THR	0	-0.046	-0.038	11.223	-0.035	-0.035	0.000	0.000	0.000	0.000
21	C	21	ASN	0	0.010	-0.009	12.287	0.003	0.003	0.000	0.000	0.000	0.000
22	C	22	TRP	0	0.015	-0.003	6.740	-0.148	-0.148	0.000	0.000	0.000	0.000
23	C	23	VAL	0	0.014	0.006	13.302	0.077	0.077	0.000	0.000	0.000	0.000
24	C	24	PRO	0	-0.036	-0.002	10.394	-0.066	-0.066	0.000	0.000	0.000	0.000
25	C	25	SER	0	0.044	0.021	11.006	0.038	0.038	0.000	0.000	0.000	0.000
26	C	26	LEU	0	-0.017	-0.014	12.830	0.068	0.068	0.000	0.000	0.000	0.000
27	C	27	ASN	0	-0.035	-0.039	14.255	0.026	0.026	0.000	0.000	0.000	0.000
28	C	28	ASP	-1	-0.812	-0.880	8.689	-0.217	-0.217	0.000	0.000	0.000	0.000
29	C	29	ARG	1	0.868	0.938	7.354	-1.842	-1.842	0.000	0.000	0.000	0.000
30	C	30	VAL	0	0.004	-0.010	6.894	0.206	0.206	0.000	0.000	0.000	0.000
31	C	31	VAL	0	0.027	0.013	2.345	-0.785	-0.607	1.428	-0.296	-1.310	-0.002
32	C	32	ASP	-1	-0.779	-0.896	4.850	0.389	0.462	-0.001	-0.009	-0.063	0.000
33	C	33	LYS	1	0.926	0.947	3.873	-0.534	-0.259	0.002	-0.063	-0.215	0.000
34	C	34	ARG	1	0.888	0.942	5.035	-0.436	-0.389	-0.001	-0.001	-0.044	0.000
35	C	35	LEU	0	0.047	0.036	2.297	-0.272	-1.063	3.545	-0.559	-2.195	-0.003
36	C	36	GLN	0	-0.033	-0.010	4.825	0.321	0.382	-0.001	-0.002	-0.059	0.000
37	C	37	PHE	0	-0.024	-0.024	7.172	0.074	0.074	0.000	0.000	0.000	0.000
38	C	38	VAL	0	0.024	0.029	7.756	-0.158	-0.158	0.000	0.000	0.000	0.000
39	C	39	GLY	0	0.008	-0.014	10.245	-0.139	-0.139	0.000	0.000	0.000	0.000
40	C	40	ILE	0	-0.071	-0.021	10.981	0.120	0.120	0.000	0.000	0.000	0.000
41	C	41	VAL	0	0.036	0.031	11.037	-0.041	-0.041	0.000	0.000	0.000	0.000
42	C	42	LYS	1	0.853	0.912	13.773	-0.158	-0.158	0.000	0.000	0.000	0.000
43	C	43	ASP	-1	-0.846	-0.924	17.059	-0.025	-0.025	0.000	0.000	0.000	0.000
44	C	44	VAL	0	-0.037	-0.003	14.996	0.008	0.008	0.000	0.000	0.000	0.000
45	C	45	PHE	0	0.035	0.024	17.705	-0.003	-0.003	0.000	0.000	0.000	0.000
46	C	46	GLY	0	0.039	0.025	19.902	-0.005	-0.005	0.000	0.000	0.000	0.000
47	C	47	PRO	0	-0.022	-0.022	21.714	-0.008	-0.008	0.000	0.000	0.000	0.000
48	C	48	VAL	0	0.089	0.044	19.918	-0.011	-0.011	0.000	0.000	0.000	0.000
49	C	49	LYS	1	0.953	0.962	18.504	0.181	0.181	0.000	0.000	0.000	0.000
50	C	50	MET	0	-0.079	-0.026	17.568	-0.030	-0.030	0.000	0.000	0.000	0.000
51	C	51	PRO	0	0.041	0.048	15.660	0.041	0.041	0.000	0.000	0.000	0.000
52	C	52	TYR	0	-0.018	-0.017	16.602	-0.004	-0.004	0.000	0.000	0.000	0.000
53	C	53	VAL	0	-0.006	-0.009	12.618	-0.012	-0.012	0.000	0.000	0.000	0.000
54	C	54	ALA	0	0.024	0.021	15.708	0.027	0.027	0.000	0.000	0.000	0.000
55	C	55	ILE	0	0.010	0.004	10.841	0.009	0.009	0.000	0.000	0.000	0.000
56	C	56	LYS	1	0.929	0.966	14.792	-0.171	-0.171	0.000	0.000	0.000	0.000
57	C	57	PRO	0	0.029	0.021	14.357	0.058	0.058	0.000	0.000	0.000	0.000
58	C	58	LYS	1	0.883	0.929	14.161	-0.345	-0.345	0.000	0.000	0.000	0.000
59	C	59	VAL	0	0.051	0.022	13.814	0.027	0.027	0.000	0.000	0.000	0.000
60	C	60	SER	0	-0.007	0.001	15.915	-0.024	-0.024	0.000	0.000	0.000	0.000
61	C	61	ASN	0	0.055	0.016	18.327	-0.022	-0.022	0.000	0.000	0.000	0.000
62	C	62	PRO	0	0.025	0.016	15.922	0.018	0.018	0.000	0.000	0.000	0.000
63	C	63	GLU	-1	-0.946	-0.972	16.389	0.124	0.124	0.000	0.000	0.000	0.000
64	C	64	ILE	0	-0.009	-0.001	15.204	-0.018	-0.018	0.000	0.000	0.000	0.000
65	C	65	TYR	0	-0.021	-0.017	10.079	0.006	0.006	0.000	0.000	0.000	0.000
66	C	66	VAL	0	-0.005	0.009	13.515	-0.004	-0.004	0.000	0.000	0.000	0.000
67	C	67	GLY	0	-0.045	-0.012	15.499	-0.002	-0.002	0.000	0.000	0.000	0.000
68	C	68	GLU	-1	-0.879	-0.956	10.079	0.174	0.174	0.000	0.000	0.000	0.000
69	C	69	VAL	0	-0.085	-0.042	6.685	-0.023	-0.023	0.000	0.000	0.000	0.000
70	C	70	LEU	0	-0.002	0.007	6.330	0.061	0.061	0.000	0.000	0.000	0.000
71	C	71	TYR	0	-0.012	-0.017	2.695	-2.988	-1.101	1.801	-0.709	-2.980	-0.002
72	C	72	VAL	0	0.013	0.001	4.505	-0.145	0.166	-0.001	-0.046	-0.264	0.000
73	C	73	ASP	-1	-0.831	-0.901	2.681	2.239	5.069	0.814	-1.406	-2.238	-0.013
74	C	74	GLU	-1	-0.854	-0.925	1.849	-15.065	-18.320	11.388	-4.589	-3.544	-0.047
75	C	75	ARG	1	0.912	0.939	4.452	-0.418	-0.290	-0.001	-0.006	-0.121	0.000

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