FMO DATABASE

FMODB ID: GNMV1

Calculation Name: 1YQH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YQH

Chain ID: A

ChEMBL ID:

UniProt ID: Q81IG4

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	-735073.265978
FMO2-HF: Nuclear repulsion	694239.250954
FMO2-HF: Total energy	-40834.015024
FMO2-MP2: Total energy	-40951.924816

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:-2:SER)

Summations of interaction energy for fragment #1(A:-2:SER)

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.
-43.624	-35.602	22.138	-14.822	-15.339	-0.055

Interaction energy analysis for fragmet #1(A:-2:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.030 / 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	0	ALA	0	0.066	0.024	3.377	-1.093	2.429	0.021	-2.033	-1.511	0.005
4	A	1	MET	0	-0.063	-0.019	5.788	0.994	0.994	0.000	0.000	0.000	0.000
5	A	2	SER	0	-0.051	-0.020	2.433	-1.378	0.147	1.896	-1.549	-1.873	-0.011
6	A	3	GLN	0	-0.012	-0.001	4.268	-0.090	-0.067	-0.001	-0.046	0.024	0.000
7	A	4	GLN	0	-0.031	-0.018	5.502	0.579	0.579	0.000	0.000	0.000	0.000
8	A	5	VAL	0	-0.024	-0.012	6.016	0.128	0.128	0.000	0.000	0.000	0.000
9	A	6	THR	0	-0.003	-0.004	8.692	-0.331	-0.331	0.000	0.000	0.000	0.000
10	A	7	MET	0	-0.069	-0.031	8.410	0.082	0.082	0.000	0.000	0.000	0.000
11	A	8	SER	0	-0.061	-0.041	12.586	-0.116	-0.116	0.000	0.000	0.000	0.000
12	A	9	PHE	0	0.048	0.010	14.746	0.084	0.084	0.000	0.000	0.000	0.000
13	A	10	SER	0	0.010	-0.003	16.829	-0.058	-0.058	0.000	0.000	0.000	0.000
14	A	11	VAL	0	0.006	-0.003	19.157	0.021	0.021	0.000	0.000	0.000	0.000
15	A	12	VAL	0	0.000	-0.001	21.672	-0.019	-0.019	0.000	0.000	0.000	0.000
16	A	13	PRO	0	-0.006	-0.001	25.293	0.005	0.005	0.000	0.000	0.000	0.000
17	A	14	GLN	0	-0.005	0.012	26.768	-0.008	-0.008	0.000	0.000	0.000	0.000
18	A	15	ALA	0	0.049	0.010	29.840	-0.008	-0.008	0.000	0.000	0.000	0.000
19	A	16	LYS	1	0.800	0.888	31.784	-0.014	-0.014	0.000	0.000	0.000	0.000
20	A	17	THR	0	-0.062	-0.035	34.579	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	18	LYS	1	0.892	0.960	31.244	0.019	0.019	0.000	0.000	0.000	0.000
22	A	19	ASP	-1	-0.866	-0.919	33.639	0.014	0.014	0.000	0.000	0.000	0.000
23	A	20	VAL	0	0.035	0.000	28.754	-0.005	-0.005	0.000	0.000	0.000	0.000
24	A	21	TYR	0	0.012	-0.007	28.781	-0.002	-0.002	0.000	0.000	0.000	0.000
25	A	22	SER	0	0.015	0.011	28.651	-0.005	-0.005	0.000	0.000	0.000	0.000
26	A	23	VAL	0	-0.014	0.011	25.673	-0.011	-0.011	0.000	0.000	0.000	0.000
27	A	24	VAL	0	-0.002	-0.017	23.774	-0.007	-0.007	0.000	0.000	0.000	0.000
28	A	25	ASP	-1	-0.927	-0.958	23.638	-0.047	-0.047	0.000	0.000	0.000	0.000
29	A	26	LYS	1	0.855	0.923	23.766	0.091	0.091	0.000	0.000	0.000	0.000
30	A	27	ALA	0	0.009	0.008	20.059	-0.023	-0.023	0.000	0.000	0.000	0.000
31	A	28	ILE	0	-0.025	-0.022	19.083	-0.006	-0.006	0.000	0.000	0.000	0.000
32	A	29	GLU	-1	-0.831	-0.895	19.814	-0.163	-0.163	0.000	0.000	0.000	0.000
33	A	30	VAL	0	-0.009	-0.005	15.172	-0.047	-0.047	0.000	0.000	0.000	0.000
34	A	31	VAL	0	-0.026	-0.018	15.357	-0.043	-0.043	0.000	0.000	0.000	0.000
35	A	32	GLN	0	-0.046	-0.011	16.214	-0.054	-0.054	0.000	0.000	0.000	0.000
36	A	33	GLN	0	-0.041	-0.021	18.005	-0.049	-0.049	0.000	0.000	0.000	0.000
37	A	34	SER	0	-0.080	-0.043	12.344	-0.068	-0.068	0.000	0.000	0.000	0.000
38	A	35	GLY	0	0.002	0.006	12.933	-0.137	-0.137	0.000	0.000	0.000	0.000
39	A	36	VAL	0	-0.071	-0.022	9.617	-0.007	-0.007	0.000	0.000	0.000	0.000
40	A	37	ARG	1	0.837	0.880	12.720	-0.094	-0.094	0.000	0.000	0.000	0.000
41	A	38	TYR	0	-0.004	-0.019	14.285	0.094	0.094	0.000	0.000	0.000	0.000
42	A	39	GLU	-1	-0.843	-0.889	16.759	0.119	0.119	0.000	0.000	0.000	0.000
43	A	40	VAL	0	-0.007	0.005	19.769	0.039	0.039	0.000	0.000	0.000	0.000
44	A	41	GLY	0	0.044	0.026	21.871	-0.009	-0.009	0.000	0.000	0.000	0.000
45	A	42	ALA	0	-0.047	-0.034	23.851	-0.005	-0.005	0.000	0.000	0.000	0.000
46	A	43	MET	0	-0.025	-0.014	24.932	-0.012	-0.012	0.000	0.000	0.000	0.000
47	A	44	GLU	-1	-0.815	-0.871	18.992	0.387	0.387	0.000	0.000	0.000	0.000
48	A	45	THR	0	-0.003	0.006	17.109	-0.043	-0.043	0.000	0.000	0.000	0.000
49	A	46	THR	0	-0.018	-0.017	15.751	0.081	0.081	0.000	0.000	0.000	0.000
50	A	47	LEU	0	-0.007	-0.007	11.754	-0.079	-0.079	0.000	0.000	0.000	0.000
51	A	48	GLU	-1	-0.783	-0.898	11.242	0.374	0.374	0.000	0.000	0.000	0.000
52	A	49	GLY	0	0.022	0.005	8.453	-0.293	-0.293	0.000	0.000	0.000	0.000
53	A	50	GLU	-1	-0.796	-0.904	2.125	-21.990	-19.570	6.574	-4.671	-4.323	-0.043
54	A	51	LEU	0	0.002	-0.008	2.866	-1.808	-0.252	0.377	-0.720	-1.213	0.005
55	A	52	ASP	-1	-0.812	-0.919	1.947	-14.343	-15.730	13.246	-5.750	-6.109	-0.012
56	A	53	VAL	0	-0.028	-0.004	3.621	-1.471	-1.108	0.025	-0.053	-0.334	0.001
57	A	54	LEU	0	-0.004	-0.013	5.658	-0.030	-0.030	0.000	0.000	0.000	0.000
58	A	55	LEU	0	0.012	0.001	6.130	-0.361	-0.361	0.000	0.000	0.000	0.000
59	A	56	ASP	-1	-0.821	-0.878	7.643	-0.992	-0.992	0.000	0.000	0.000	0.000
60	A	57	VAL	0	0.004	0.005	9.488	-0.023	-0.023	0.000	0.000	0.000	0.000
61	A	58	VAL	0	0.017	0.013	11.399	-0.010	-0.010	0.000	0.000	0.000	0.000
62	A	59	LYS	1	0.821	0.897	9.560	0.410	0.410	0.000	0.000	0.000	0.000
63	A	60	ARG	1	0.887	0.921	10.884	0.619	0.619	0.000	0.000	0.000	0.000
64	A	61	ALA	0	0.026	0.034	15.394	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	62	GLN	0	0.045	0.020	16.483	0.037	0.037	0.000	0.000	0.000	0.000
66	A	63	GLN	0	-0.086	-0.053	18.129	0.015	0.015	0.000	0.000	0.000	0.000
67	A	64	ALA	0	0.053	0.029	19.475	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	65	CYS	0	-0.069	-0.026	21.408	0.014	0.014	0.000	0.000	0.000	0.000
69	A	66	VAL	0	0.015	0.002	23.134	0.001	0.001	0.000	0.000	0.000	0.000
70	A	67	ASP	-1	-0.874	-0.919	22.253	-0.143	-0.143	0.000	0.000	0.000	0.000
71	A	68	ALA	0	-0.057	-0.023	25.469	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	69	GLY	0	-0.073	-0.053	27.426	0.007	0.007	0.000	0.000	0.000	0.000
73	A	70	ALA	0	-0.049	-0.020	26.163	0.009	0.009	0.000	0.000	0.000	0.000
74	A	71	GLU	-1	-0.772	-0.882	27.745	0.004	0.004	0.000	0.000	0.000	0.000
75	A	72	GLU	-1	-0.965	-0.979	25.952	0.099	0.099	0.000	0.000	0.000	0.000
76	A	73	VAL	0	-0.005	-0.019	21.769	-0.007	-0.007	0.000	0.000	0.000	0.000
77	A	74	ILE	0	-0.020	0.011	23.089	0.018	0.018	0.000	0.000	0.000	0.000
78	A	75	THR	0	0.013	-0.026	16.949	-0.020	-0.020	0.000	0.000	0.000	0.000
79	A	76	SER	0	-0.029	0.003	19.028	0.037	0.037	0.000	0.000	0.000	0.000
80	A	77	ILE	0	0.027	0.003	12.341	0.004	0.004	0.000	0.000	0.000	0.000
81	A	78	LYS	1	0.896	0.958	15.254	-0.522	-0.522	0.000	0.000	0.000	0.000
82	A	79	ILE	0	0.038	0.015	8.969	0.008	0.008	0.000	0.000	0.000	0.000
83	A	80	HIS	0	0.023	0.032	12.105	-0.132	-0.132	0.000	0.000	0.000	0.000
84	A	81	TYR	0	0.047	0.009	5.298	-0.296	-0.296	0.000	0.000	0.000	0.000
85	A	82	ARG	1	0.801	0.854	9.483	-0.778	-0.778	0.000	0.000	0.000	0.000
86	A	83	PRO	0	0.034	0.020	6.761	-0.152	-0.152	0.000	0.000	0.000	0.000
87	A	84	SER	0	-0.018	-0.001	8.299	-0.142	-0.142	0.000	0.000	0.000	0.000
88	A	85	THR	0	0.008	-0.016	11.407	-0.097	-0.097	0.000	0.000	0.000	0.000
89	A	86	GLY	0	0.041	0.049	9.683	-0.106	-0.106	0.000	0.000	0.000	0.000
90	A	87	VAL	0	-0.083	-0.034	10.527	-0.095	-0.095	0.000	0.000	0.000	0.000
91	A	88	THR	0	-0.005	0.009	11.805	0.042	0.042	0.000	0.000	0.000	0.000
92	A	89	ILE	0	0.068	0.009	14.358	0.017	0.017	0.000	0.000	0.000	0.000
93	A	90	ASP	-1	-0.769	-0.822	17.054	0.117	0.117	0.000	0.000	0.000	0.000
94	A	91	GLU	-1	-0.809	-0.883	15.790	0.468	0.468	0.000	0.000	0.000	0.000
95	A	92	LYS	1	0.812	0.888	16.532	-0.558	-0.558	0.000	0.000	0.000	0.000
96	A	93	VAL	0	-0.006	-0.012	20.411	-0.007	-0.007	0.000	0.000	0.000	0.000
97	A	94	TRP	0	0.038	0.034	22.465	-0.026	-0.026	0.000	0.000	0.000	0.000
98	A	95	LYS	1	0.837	0.922	24.027	-0.246	-0.246	0.000	0.000	0.000	0.000
99	A	96	TYR	0	-0.073	-0.041	24.787	0.002	0.002	0.000	0.000	0.000	0.000
100	A	97	ARG	1	0.781	0.877	23.442	-0.141	-0.141	0.000	0.000	0.000	0.000
101	A	98	ASP	-1	-0.870	-0.933	28.633	0.080	0.080	0.000	0.000	0.000	0.000
102	A	99	GLU	-1	-0.898	-0.948	26.242	0.086	0.086	0.000	0.000	0.000	0.000
103	A	100	TYR	0	-0.101	-0.068	21.572	-0.005	-0.005	0.000	0.000	0.000	0.000
104	A	101	ALA	0	-0.006	0.000	28.119	0.005	0.005	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-2:SER)