FMO DATABASE

FMODB ID: 8276Y

Calculation Name: 2D1H-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2D1H

Chain ID: A

ChEMBL ID:

UniProt ID: F9VNN8

Base Structure: X-ray

Registration Date: 2023-03-13

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	101
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-788871.263735
FMO2-HF: Nuclear repulsion	746698.454058
FMO2-HF: Total energy	-42172.809677
FMO2-MP2: Total energy	-42292.243238

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.
-30.327	-41.479	44.984	-15.295	-18.535	0.049

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 : 0.065 / q_NPA : 0.088

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	LYS	1	0.895	0.939	3.873	0.596	3.696	-0.019	-1.744	-1.337	0.004
4	A	4	GLU	-1	-0.819	-0.903	6.670	-0.261	-0.261	0.000	0.000	0.000	0.000
5	A	5	LYS	1	0.874	0.939	4.306	-0.041	0.121	-0.001	-0.011	-0.149	0.000
6	A	6	LEU	0	-0.015	-0.001	2.568	0.500	1.122	0.360	-0.152	-0.831	-0.002
7	A	7	GLU	-1	-0.771	-0.867	5.972	0.840	0.840	0.000	0.000	0.000	0.000
8	A	8	SER	0	-0.085	-0.056	7.616	0.160	0.160	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.869	0.900	2.033	-20.054	-38.848	34.446	-10.590	-5.063	0.092
10	A	10	LYS	1	0.844	0.907	7.738	-0.707	-0.707	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.792	-0.878	9.656	0.789	0.789	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.847	-0.934	7.618	3.100	3.100	0.000	0.000	0.000	0.000
13	A	13	ILE	0	-0.025	-0.021	4.563	-0.412	-0.349	-0.001	-0.003	-0.058	0.000
14	A	14	ARG	1	0.802	0.892	8.004	-0.944	-0.944	0.000	0.000	0.000	0.000
15	A	15	CYS	0	-0.007	-0.006	11.674	-0.157	-0.157	0.000	0.000	0.000	0.000
16	A	16	CYS	0	-0.160	-0.076	9.249	-0.260	-0.260	0.000	0.000	0.000	0.000
17	A	17	TYR	0	-0.094	-0.081	6.766	-0.188	-0.188	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.897	0.961	11.946	-0.553	-0.553	0.000	0.000	0.000	0.000
19	A	19	ILE	0	-0.051	-0.014	11.074	-0.093	-0.093	0.000	0.000	0.000	0.000
20	A	20	THR	0	-0.006	-0.038	15.283	0.060	0.060	0.000	0.000	0.000	0.000
21	A	21	ASP	-1	-0.798	-0.918	15.528	0.435	0.435	0.000	0.000	0.000	0.000
22	A	22	THR	0	-0.012	0.001	16.382	-0.015	-0.015	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.776	-0.850	14.860	0.008	0.008	0.000	0.000	0.000	0.000
24	A	24	VAL	0	0.017	0.003	10.504	-0.087	-0.087	0.000	0.000	0.000	0.000
25	A	25	ALA	0	0.010	0.013	12.400	-0.065	-0.065	0.000	0.000	0.000	0.000
26	A	26	VAL	0	0.000	0.000	14.947	-0.081	-0.081	0.000	0.000	0.000	0.000
27	A	27	LEU	0	0.017	0.005	8.002	-0.100	-0.100	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.017	-0.022	8.266	-0.180	-0.180	0.000	0.000	0.000	0.000
29	A	29	LYS	1	0.830	0.917	11.384	0.180	0.180	0.000	0.000	0.000	0.000
30	A	30	MET	0	-0.038	-0.029	13.569	-0.034	-0.034	0.000	0.000	0.000	0.000
31	A	31	VAL	0	-0.025	-0.012	7.906	-0.136	-0.136	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.881	-0.929	11.135	-0.459	-0.459	0.000	0.000	0.000	0.000
33	A	33	ILE	0	0.009	0.004	13.266	-0.025	-0.025	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.900	-0.923	12.471	-1.304	-1.304	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.888	0.947	15.311	0.435	0.435	0.000	0.000	0.000	0.000
36	A	36	PRO	0	-0.010	-0.005	18.006	0.014	0.014	0.000	0.000	0.000	0.000
37	A	37	ILE	0	-0.020	-0.003	18.542	0.038	0.038	0.000	0.000	0.000	0.000
38	A	38	THR	0	-0.008	-0.036	21.215	0.002	0.002	0.000	0.000	0.000	0.000
39	A	39	SER	0	-0.020	-0.027	22.827	0.009	0.009	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.824	-0.934	23.850	-0.192	-0.192	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.773	-0.864	23.702	-0.306	-0.306	0.000	0.000	0.000	0.000
42	A	42	LEU	0	0.016	-0.002	18.365	0.015	0.015	0.000	0.000	0.000	0.000
43	A	43	ALA	0	-0.026	-0.010	22.397	0.026	0.026	0.000	0.000	0.000	0.000
44	A	44	ASP	-1	-0.830	-0.893	25.243	-0.089	-0.089	0.000	0.000	0.000	0.000
45	A	45	ILE	0	-0.034	-0.010	20.519	0.014	0.014	0.000	0.000	0.000	0.000
46	A	46	PHE	0	-0.044	-0.031	17.495	0.019	0.019	0.000	0.000	0.000	0.000
47	A	47	LYS	1	0.822	0.907	23.547	0.102	0.102	0.000	0.000	0.000	0.000
48	A	48	LEU	0	-0.001	0.015	22.321	0.017	0.017	0.000	0.000	0.000	0.000
49	A	49	SER	0	0.033	0.017	26.401	-0.017	-0.017	0.000	0.000	0.000	0.000
50	A	50	LYS	1	0.910	0.920	26.181	0.144	0.144	0.000	0.000	0.000	0.000
51	A	51	THR	0	0.017	0.010	25.762	-0.011	-0.011	0.000	0.000	0.000	0.000
52	A	52	THR	0	-0.011	-0.005	23.160	0.004	0.004	0.000	0.000	0.000	0.000
53	A	53	VAL	0	0.054	0.030	21.000	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.830	-0.918	20.929	-0.174	-0.174	0.000	0.000	0.000	0.000
55	A	55	ASN	0	-0.050	-0.023	21.836	-0.030	-0.030	0.000	0.000	0.000	0.000
56	A	56	SER	0	0.044	0.017	17.528	0.006	0.006	0.000	0.000	0.000	0.000
57	A	57	LEU	0	-0.042	-0.030	17.206	-0.028	-0.028	0.000	0.000	0.000	0.000
58	A	58	LYS	1	0.859	0.924	17.624	0.069	0.069	0.000	0.000	0.000	0.000
59	A	59	LYS	1	0.886	0.950	15.542	-0.049	-0.049	0.000	0.000	0.000	0.000
60	A	60	LEU	0	0.045	0.006	11.699	-0.021	-0.021	0.000	0.000	0.000	0.000
61	A	61	ILE	0	-0.055	-0.018	13.544	-0.096	-0.096	0.000	0.000	0.000	0.000
62	A	62	GLU	-1	-0.876	-0.917	15.859	-0.074	-0.074	0.000	0.000	0.000	0.000
63	A	63	LEU	0	-0.017	0.002	11.342	0.027	0.027	0.000	0.000	0.000	0.000
64	A	64	GLY	0	-0.015	-0.012	11.647	-0.074	-0.074	0.000	0.000	0.000	0.000
65	A	65	LEU	0	-0.045	-0.006	7.477	-0.238	-0.238	0.000	0.000	0.000	0.000
66	A	66	VAL	0	-0.015	-0.009	10.852	-0.135	-0.135	0.000	0.000	0.000	0.000
67	A	67	VAL	0	0.032	0.014	14.110	0.065	0.065	0.000	0.000	0.000	0.000
68	A	68	ARG	1	0.922	0.971	17.182	0.265	0.265	0.000	0.000	0.000	0.000
69	A	69	THR	0	0.023	0.000	20.805	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	70	LYS	1	0.929	0.973	23.372	0.245	0.245	0.000	0.000	0.000	0.000
71	A	71	THR	0	0.020	0.006	25.991	0.002	0.002	0.000	0.000	0.000	0.000
72	A	79	PRO	0	0.014	-0.016	33.015	-0.005	-0.005	0.000	0.000	0.000	0.000
73	A	80	LYS	1	0.920	0.994	27.939	0.253	0.253	0.000	0.000	0.000	0.000
74	A	81	TYR	0	0.003	-0.008	25.186	-0.006	-0.006	0.000	0.000	0.000	0.000
75	A	82	TYR	0	-0.024	0.001	22.234	0.022	0.022	0.000	0.000	0.000	0.000
76	A	83	TYR	0	0.012	-0.001	18.384	0.007	0.007	0.000	0.000	0.000	0.000
77	A	84	SER	0	0.058	0.019	16.361	0.035	0.035	0.000	0.000	0.000	0.000
78	A	85	ILE	0	0.020	0.017	9.790	0.039	0.039	0.000	0.000	0.000	0.000
79	A	86	SER	0	-0.027	-0.023	10.413	0.046	0.046	0.000	0.000	0.000	0.000
80	A	87	SER	0	0.039	0.010	10.550	-0.194	-0.194	0.000	0.000	0.000	0.000
81	A	88	ASN	0	-0.017	-0.006	8.801	-0.270	-0.270	0.000	0.000	0.000	0.000
82	A	89	ILE	0	0.068	0.033	6.113	-0.278	-0.278	0.000	0.000	0.000	0.000
83	A	90	LEU	0	0.001	-0.004	2.850	-1.424	0.024	0.270	-0.354	-1.363	-0.001
84	A	91	GLU	-1	-0.848	-0.937	2.343	-8.882	-7.381	2.091	-1.497	-2.096	-0.024
85	A	92	LYS	1	0.816	0.926	4.878	1.723	1.852	-0.001	-0.007	-0.121	0.000
86	A	93	ILE	0	0.061	0.022	2.221	-0.324	-0.031	1.731	-0.373	-1.651	-0.005
87	A	94	ARG	1	0.939	0.973	2.226	-2.682	-0.908	5.902	-2.801	-4.875	-0.011
88	A	95	ASN	0	-0.025	-0.037	3.119	3.493	1.481	0.157	2.372	-0.516	-0.003
89	A	96	ASP	-1	-0.767	-0.828	6.308	-0.077	-0.077	0.000	0.000	0.000	0.000
90	A	97	LEU	0	-0.009	-0.009	3.381	-0.260	0.302	0.049	-0.135	-0.475	-0.001
91	A	98	LEU	0	0.012	0.019	6.519	-0.172	-0.172	0.000	0.000	0.000	0.000
92	A	99	ASN	0	-0.025	-0.026	8.690	-0.380	-0.380	0.000	0.000	0.000	0.000
93	A	101	ALA	0	0.040	0.011	10.295	-0.158	-0.158	0.000	0.000	0.000	0.000
94	A	102	LYS	1	0.806	0.890	12.108	-1.024	-1.024	0.000	0.000	0.000	0.000
95	A	103	ARG	1	0.943	0.964	12.025	-0.843	-0.843	0.000	0.000	0.000	0.000
96	A	104	MET	0	-0.003	0.002	14.184	-0.061	-0.061	0.000	0.000	0.000	0.000
97	A	105	GLU	-1	-0.801	-0.878	16.262	0.828	0.828	0.000	0.000	0.000	0.000
98	A	106	LEU	0	-0.010	-0.021	17.995	-0.085	-0.085	0.000	0.000	0.000	0.000
99	A	107	ALA	0	-0.047	-0.004	19.816	-0.074	-0.074	0.000	0.000	0.000	0.000
100	A	108	ALA	0	-0.041	-0.011	20.951	-0.036	-0.036	0.000	0.000	0.000	0.000
101	A	109	THR	0	-0.055	-0.019	22.712	-0.032	-0.032	0.000	0.000	0.000	0.000

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