FMO DATABASE

FMODB ID: 98RM2

Calculation Name: 2II7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2II7

Chain ID: A

ChEMBL ID:

UniProt ID: Q8YSC3

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:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	112
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-848998.551532
FMO2-HF: Nuclear repulsion	805440.040169
FMO2-HF: Total energy	-43558.511362
FMO2-MP2: Total energy	-43687.062872

3D Structure Molmil

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:SER)

Summations of interaction energy for fragment #1(A:1: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.
-22.837	-30.21	21.415	-8.798	-5.243	-0.066

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.057 / q_NPA : -0.053

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	SER	0	0.015	0.018	3.789	-1.480	0.070	-0.018	-0.616	-0.915	0.003
4	A	4	ILE	0	-0.028	-0.023	5.881	-0.125	-0.125	0.000	0.000	0.000	0.000
5	A	5	GLY	0	0.023	0.018	8.761	-0.024	-0.024	0.000	0.000	0.000	0.000
6	A	6	ARG	1	0.906	0.958	12.280	-0.203	-0.203	0.000	0.000	0.000	0.000
7	A	7	THR	0	0.040	0.021	13.043	-0.001	-0.001	0.000	0.000	0.000	0.000
8	A	8	CYS	0	-0.011	-0.001	15.179	-0.034	-0.034	0.000	0.000	0.000	0.000
9	A	9	TRP	0	-0.063	-0.033	14.925	0.017	0.017	0.000	0.000	0.000	0.000
10	A	10	ALA	0	0.044	0.016	20.670	-0.012	-0.012	0.000	0.000	0.000	0.000
11	A	11	ILE	0	-0.057	-0.013	23.102	0.009	0.009	0.000	0.000	0.000	0.000
12	A	12	ALA	0	0.006	-0.010	26.408	-0.007	-0.007	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.872	-0.935	29.485	0.062	0.062	0.000	0.000	0.000	0.000
14	A	14	GLY	0	0.027	0.005	29.595	0.005	0.005	0.000	0.000	0.000	0.000
15	A	15	TYR	0	-0.020	-0.020	31.571	-0.003	-0.003	0.000	0.000	0.000	0.000
16	A	16	ILE	0	-0.040	-0.024	31.973	0.002	0.002	0.000	0.000	0.000	0.000
17	A	17	PRO	0	0.043	0.028	35.008	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	25	PRO	0	-0.018	-0.024	36.844	0.000	0.000	0.000	0.000	0.000	0.000
19	A	26	GLN	0	-0.006	-0.002	31.371	0.000	0.000	0.000	0.000	0.000	0.000
20	A	27	PHE	0	-0.012	-0.009	31.616	0.003	0.003	0.000	0.000	0.000	0.000
21	A	28	ILE	0	0.028	0.035	32.579	0.003	0.003	0.000	0.000	0.000	0.000
22	A	29	SER	0	0.020	0.022	28.317	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	30	HIS	0	0.027	-0.028	28.988	-0.007	-0.007	0.000	0.000	0.000	0.000
24	A	31	GLU	-1	-0.742	-0.838	28.248	0.080	0.080	0.000	0.000	0.000	0.000
25	A	32	THR	0	-0.055	-0.027	23.135	-0.008	-0.008	0.000	0.000	0.000	0.000
26	A	33	VAL	0	0.018	0.018	20.371	0.010	0.010	0.000	0.000	0.000	0.000
27	A	34	CYS	0	-0.057	-0.024	18.694	-0.014	-0.014	0.000	0.000	0.000	0.000
28	A	35	ILE	0	0.033	0.015	14.288	0.018	0.018	0.000	0.000	0.000	0.000
29	A	36	LEU	0	-0.021	-0.013	10.250	-0.016	-0.016	0.000	0.000	0.000	0.000
30	A	37	ASN	0	0.023	0.006	8.286	0.085	0.085	0.000	0.000	0.000	0.000
31	A	38	ALA	0	-0.053	-0.026	6.040	-0.122	-0.122	0.000	0.000	0.000	0.000
32	A	39	GLY	0	0.092	0.055	4.097	-0.053	0.167	0.001	-0.060	-0.161	0.000
33	A	40	ASP	-1	-0.799	-0.890	1.595	-24.248	-33.474	21.433	-8.101	-4.106	-0.069
34	A	41	GLU	-1	-0.927	-0.963	4.276	0.451	0.534	-0.001	-0.021	-0.061	0.000
35	A	42	ASP	-1	-0.873	-0.935	7.413	-0.243	-0.243	0.000	0.000	0.000	0.000
36	A	43	ALA	0	0.002	-0.004	10.728	0.068	0.068	0.000	0.000	0.000	0.000
37	A	44	HIS	0	-0.052	-0.035	12.475	-0.025	-0.025	0.000	0.000	0.000	0.000
38	A	45	VAL	0	-0.018	-0.015	15.906	0.023	0.023	0.000	0.000	0.000	0.000
39	A	46	GLU	-1	-0.841	-0.907	17.861	0.013	0.013	0.000	0.000	0.000	0.000
40	A	47	ILE	0	-0.020	-0.017	21.378	0.014	0.014	0.000	0.000	0.000	0.000
41	A	48	THR	0	0.004	0.023	23.843	-0.009	-0.009	0.000	0.000	0.000	0.000
42	A	49	ILE	0	-0.016	-0.006	27.122	0.007	0.007	0.000	0.000	0.000	0.000
43	A	50	TYR	0	0.006	-0.015	27.850	-0.004	-0.004	0.000	0.000	0.000	0.000
44	A	51	TYR	0	0.047	0.003	32.600	0.001	0.001	0.000	0.000	0.000	0.000
45	A	52	SER	0	0.046	0.021	36.164	0.001	0.001	0.000	0.000	0.000	0.000
46	A	53	ASP	-1	-0.871	-0.914	39.018	0.031	0.031	0.000	0.000	0.000	0.000
47	A	54	LYS	1	0.808	0.897	38.246	-0.033	-0.033	0.000	0.000	0.000	0.000
48	A	55	GLU	-1	-0.898	-0.960	36.676	0.036	0.036	0.000	0.000	0.000	0.000
49	A	56	PRO	0	-0.024	-0.014	31.645	0.000	0.000	0.000	0.000	0.000	0.000
50	A	57	VAL	0	-0.042	-0.013	31.862	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	58	GLY	0	-0.002	-0.017	30.326	0.002	0.002	0.000	0.000	0.000	0.000
52	A	59	PRO	0	-0.004	-0.003	25.094	0.002	0.002	0.000	0.000	0.000	0.000
53	A	60	TYR	0	0.007	-0.002	25.609	-0.005	-0.005	0.000	0.000	0.000	0.000
54	A	61	ARG	1	0.841	0.903	22.199	-0.006	-0.006	0.000	0.000	0.000	0.000
55	A	62	LEU	0	0.005	0.007	18.264	-0.004	-0.004	0.000	0.000	0.000	0.000
56	A	63	THR	0	0.021	0.004	15.067	0.011	0.011	0.000	0.000	0.000	0.000
57	A	64	VAL	0	-0.027	-0.011	12.800	0.002	0.002	0.000	0.000	0.000	0.000
58	A	65	PRO	0	0.028	0.013	12.331	-0.006	-0.006	0.000	0.000	0.000	0.000
59	A	66	ALA	0	0.025	0.019	6.935	0.069	0.069	0.000	0.000	0.000	0.000
60	A	67	ARG	1	0.778	0.879	5.040	2.484	2.484	0.000	0.000	0.000	0.000
61	A	68	ARG	1	0.900	0.959	7.771	0.303	0.303	0.000	0.000	0.000	0.000
62	A	69	THR	0	-0.002	-0.006	11.378	0.048	0.048	0.000	0.000	0.000	0.000
63	A	70	LYS	1	0.890	0.928	13.944	-0.027	-0.027	0.000	0.000	0.000	0.000
64	A	71	HIS	0	-0.006	0.013	17.361	0.016	0.016	0.000	0.000	0.000	0.000
65	A	72	VAL	0	0.017	0.008	20.284	-0.016	-0.016	0.000	0.000	0.000	0.000
66	A	73	ARG	1	0.918	0.977	22.954	-0.036	-0.036	0.000	0.000	0.000	0.000
67	A	74	PHE	0	0.080	0.015	26.026	-0.006	-0.006	0.000	0.000	0.000	0.000
68	A	75	ASN	0	-0.066	-0.037	28.346	-0.005	-0.005	0.000	0.000	0.000	0.000
69	A	76	ASP	-1	-0.863	-0.943	27.649	0.026	0.026	0.000	0.000	0.000	0.000
70	A	77	LEU	0	-0.052	-0.002	25.305	-0.005	-0.005	0.000	0.000	0.000	0.000
71	A	78	ASN	0	-0.083	-0.070	29.077	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	79	ASP	-1	-0.890	-0.890	28.756	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	80	PRO	0	-0.003	-0.019	28.652	0.002	0.002	0.000	0.000	0.000	0.000
74	A	81	ALA	0	0.023	-0.008	31.854	-0.002	-0.002	0.000	0.000	0.000	0.000
75	A	82	PRO	0	-0.001	0.009	32.605	0.003	0.003	0.000	0.000	0.000	0.000
76	A	83	ILE	0	-0.002	0.017	30.197	0.000	0.000	0.000	0.000	0.000	0.000
77	A	84	PRO	0	-0.031	-0.004	34.390	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	85	HIS	1	0.822	0.894	35.131	-0.028	-0.028	0.000	0.000	0.000	0.000
79	A	86	ASP	-1	-0.877	-0.909	38.244	0.033	0.033	0.000	0.000	0.000	0.000
80	A	87	THR	0	-0.042	-0.026	37.690	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	88	ASP	-1	-0.895	-0.939	36.171	0.048	0.048	0.000	0.000	0.000	0.000
82	A	89	PHE	0	-0.099	-0.046	29.453	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	90	ALA	0	0.019	0.027	30.366	0.004	0.004	0.000	0.000	0.000	0.000
84	A	91	SER	0	-0.016	-0.019	26.213	-0.003	-0.003	0.000	0.000	0.000	0.000
85	A	92	VAL	0	0.014	0.010	23.448	0.009	0.009	0.000	0.000	0.000	0.000
86	A	93	ILE	0	-0.019	-0.002	18.725	-0.007	-0.007	0.000	0.000	0.000	0.000
87	A	94	GLN	0	0.003	-0.003	18.692	0.015	0.015	0.000	0.000	0.000	0.000
88	A	95	SER	0	-0.012	-0.022	12.949	-0.034	-0.034	0.000	0.000	0.000	0.000
89	A	96	ASN	0	0.049	0.045	11.929	0.022	0.022	0.000	0.000	0.000	0.000
90	A	97	VAL	0	0.001	0.005	8.790	0.066	0.066	0.000	0.000	0.000	0.000
91	A	98	PRO	0	-0.043	-0.021	8.524	-0.071	-0.071	0.000	0.000	0.000	0.000
92	A	99	ILE	0	0.022	0.029	9.760	0.004	0.004	0.000	0.000	0.000	0.000
93	A	100	VAL	0	-0.015	-0.026	11.251	0.012	0.012	0.000	0.000	0.000	0.000
94	A	101	VAL	0	-0.009	-0.007	13.773	-0.025	-0.025	0.000	0.000	0.000	0.000
95	A	102	GLN	0	-0.010	-0.002	17.399	0.025	0.025	0.000	0.000	0.000	0.000
96	A	103	HIS	0	-0.020	-0.028	20.058	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	104	THR	0	-0.024	0.001	23.760	0.009	0.009	0.000	0.000	0.000	0.000
98	A	105	ARG	1	0.847	0.904	26.635	-0.094	-0.094	0.000	0.000	0.000	0.000
99	A	106	LEU	0	0.117	0.065	29.555	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	107	ASP	-1	-0.782	-0.862	32.286	0.078	0.078	0.000	0.000	0.000	0.000
101	A	108	SER	0	-0.051	-0.045	30.395	0.001	0.001	0.000	0.000	0.000	0.000
102	A	109	ARG	1	0.913	0.958	29.199	-0.071	-0.071	0.000	0.000	0.000	0.000
103	A	110	GLN	0	-0.051	-0.032	31.900	-0.004	-0.004	0.000	0.000	0.000	0.000
104	A	111	ALA	0	0.014	0.004	35.320	-0.003	-0.003	0.000	0.000	0.000	0.000
105	A	112	GLU	-1	-0.909	-0.952	29.757	0.096	0.096	0.000	0.000	0.000	0.000
106	A	113	ASN	0	0.016	-0.007	32.914	-0.001	-0.001	0.000	0.000	0.000	0.000
107	A	114	ALA	0	-0.006	0.029	35.579	-0.004	-0.004	0.000	0.000	0.000	0.000
108	A	115	LEU	0	-0.015	-0.010	36.443	-0.003	-0.003	0.000	0.000	0.000	0.000
109	A	116	LEU	0	-0.033	-0.017	32.555	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	117	SER	0	-0.076	-0.054	37.178	-0.003	-0.003	0.000	0.000	0.000	0.000
111	A	118	THR	0	-0.080	-0.053	39.812	-0.003	-0.003	0.000	0.000	0.000	0.000
112	A	119	ILE	0	-0.025	0.017	41.387	0.001	0.001	0.000	0.000	0.000	0.000

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