FMO DATABASE

FMODB ID: J35J9

Calculation Name: 4C9Y-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4C9Y

Chain ID: A

ChEMBL ID:

UniProt ID: Q96BD8

Base Structure: X-ray

Registration Date: 2023-06-20

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	123
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1107670.867111
FMO2-HF: Nuclear repulsion	1056899.54008
FMO2-HF: Total energy	-50771.327031
FMO2-MP2: Total energy	-50919.213321

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.
-3.399	-2.071	-0.011	-0.537	-0.779	0.002

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 : -0.011 / q_NPA : -0.012

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	A	4	LYS	1	0.909	0.969	3.814	-0.958	0.195	-0.009	-0.486	-0.657	0.002
4	A	5	GLU	-1	-0.906	-0.955	6.388	1.638	1.638	0.000	0.000	0.000	0.000
5	A	6	MET	0	-0.058	-0.020	8.702	-0.246	-0.246	0.000	0.000	0.000	0.000
6	A	7	PRO	0	0.044	0.024	11.860	0.085	0.085	0.000	0.000	0.000	0.000
7	A	8	PHE	0	0.037	0.016	13.699	0.021	0.021	0.000	0.000	0.000	0.000
8	A	9	ILE	0	-0.010	0.009	17.013	-0.044	-0.044	0.000	0.000	0.000	0.000
9	A	10	THR	0	0.044	0.023	20.231	0.027	0.027	0.000	0.000	0.000	0.000
10	A	11	CYS	0	0.021	-0.004	22.227	0.009	0.009	0.000	0.000	0.000	0.000
11	A	12	ASP	-1	-0.843	-0.924	25.463	-0.080	-0.080	0.000	0.000	0.000	0.000
12	A	13	GLU	-1	-0.790	-0.872	20.544	-0.137	-0.137	0.000	0.000	0.000	0.000
13	A	14	PHE	0	0.023	0.000	24.876	0.009	0.009	0.000	0.000	0.000	0.000
14	A	15	ASN	0	-0.015	-0.012	26.410	0.014	0.014	0.000	0.000	0.000	0.000
15	A	16	GLY	0	0.029	0.030	28.305	0.002	0.002	0.000	0.000	0.000	0.000
16	A	17	VAL	0	-0.056	0.001	26.012	-0.003	-0.003	0.000	0.000	0.000	0.000
17	A	18	PRO	0	0.034	0.001	29.030	0.009	0.009	0.000	0.000	0.000	0.000
18	A	19	SER	0	0.060	0.013	32.088	0.005	0.005	0.000	0.000	0.000	0.000
19	A	20	TYR	0	0.028	0.006	32.682	0.009	0.009	0.000	0.000	0.000	0.000
20	A	21	MET	0	-0.072	-0.024	27.829	0.004	0.004	0.000	0.000	0.000	0.000
21	A	22	LYS	1	0.838	0.926	29.476	0.027	0.027	0.000	0.000	0.000	0.000
22	A	23	SER	0	-0.002	0.016	31.178	0.014	0.014	0.000	0.000	0.000	0.000
23	A	24	ARG	1	0.947	0.945	32.845	-0.051	-0.051	0.000	0.000	0.000	0.000
24	A	25	LEU	0	-0.071	-0.019	27.283	0.008	0.008	0.000	0.000	0.000	0.000
25	A	26	THR	0	0.087	0.036	28.939	-0.007	-0.007	0.000	0.000	0.000	0.000
26	A	27	TYR	0	-0.007	-0.016	22.502	0.012	0.012	0.000	0.000	0.000	0.000
27	A	28	ASN	0	0.048	0.014	24.277	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	29	GLN	0	0.035	0.027	23.785	0.010	0.010	0.000	0.000	0.000	0.000
29	A	30	ILE	0	0.005	0.002	21.478	0.018	0.018	0.000	0.000	0.000	0.000
30	A	31	ASN	0	0.047	0.023	19.680	0.012	0.012	0.000	0.000	0.000	0.000
31	A	32	ASP	-1	-0.884	-0.941	19.001	0.215	0.215	0.000	0.000	0.000	0.000
32	A	33	VAL	0	-0.033	-0.024	19.705	0.041	0.041	0.000	0.000	0.000	0.000
33	A	34	ILE	0	-0.019	-0.010	15.253	0.040	0.040	0.000	0.000	0.000	0.000
34	A	35	LYS	1	0.948	0.982	15.164	-0.189	-0.189	0.000	0.000	0.000	0.000
35	A	36	GLU	-1	-0.904	-0.952	15.218	0.514	0.514	0.000	0.000	0.000	0.000
36	A	37	ILE	0	-0.032	-0.023	14.718	0.063	0.063	0.000	0.000	0.000	0.000
37	A	38	ASN	0	0.038	0.013	11.242	0.028	0.028	0.000	0.000	0.000	0.000
38	A	39	LYS	1	0.958	1.000	11.401	-0.303	-0.303	0.000	0.000	0.000	0.000
39	A	40	ALA	0	-0.007	-0.001	12.952	0.153	0.153	0.000	0.000	0.000	0.000
40	A	41	VAL	0	-0.015	-0.005	8.859	0.076	0.076	0.000	0.000	0.000	0.000
41	A	42	ILE	0	0.012	-0.001	7.422	0.343	0.343	0.000	0.000	0.000	0.000
42	A	43	SER	0	-0.046	-0.021	9.145	0.304	0.304	0.000	0.000	0.000	0.000
43	A	44	LYS	1	0.910	0.981	11.940	-0.477	-0.477	0.000	0.000	0.000	0.000
44	A	45	TYR	0	0.010	-0.012	6.878	-0.134	-0.134	0.000	0.000	0.000	0.000
45	A	46	LYS	1	0.928	0.966	6.616	-3.285	-3.285	0.000	0.000	0.000	0.000
46	A	47	ILE	0	0.001	0.017	8.752	-0.173	-0.173	0.000	0.000	0.000	0.000
47	A	48	LEU	0	-0.034	-0.022	9.850	-0.125	-0.125	0.000	0.000	0.000	0.000
48	A	49	HIS	0	-0.028	-0.007	4.588	-0.806	-0.701	-0.001	-0.010	-0.094	0.000
49	A	50	GLN	0	-0.007	0.019	8.778	-0.022	-0.022	0.000	0.000	0.000	0.000
50	A	51	PRO	0	0.027	0.009	11.670	-0.154	-0.154	0.000	0.000	0.000	0.000
51	A	52	LYS	1	1.037	0.981	14.384	-0.368	-0.368	0.000	0.000	0.000	0.000
52	A	53	LYS	1	0.947	0.979	17.273	-0.346	-0.346	0.000	0.000	0.000	0.000
53	A	54	SER	0	-0.008	-0.002	16.146	-0.026	-0.026	0.000	0.000	0.000	0.000
54	A	55	MET	0	-0.081	0.003	14.702	-0.011	-0.011	0.000	0.000	0.000	0.000
55	A	56	ASN	0	0.066	0.044	18.765	-0.044	-0.044	0.000	0.000	0.000	0.000
56	A	57	SER	0	0.032	-0.010	21.416	0.022	0.022	0.000	0.000	0.000	0.000
57	A	58	VAL	0	0.064	0.029	20.870	-0.005	-0.005	0.000	0.000	0.000	0.000
58	A	59	THR	0	0.010	-0.003	16.259	0.030	0.030	0.000	0.000	0.000	0.000
59	A	60	ARG	1	0.900	0.959	18.254	-0.325	-0.325	0.000	0.000	0.000	0.000
60	A	61	ASN	0	0.017	0.007	20.220	-0.021	-0.021	0.000	0.000	0.000	0.000
61	A	62	LEU	0	-0.009	0.015	17.511	-0.014	-0.014	0.000	0.000	0.000	0.000
62	A	63	TYR	0	0.007	-0.009	14.169	-0.035	-0.035	0.000	0.000	0.000	0.000
63	A	64	HIS	0	0.026	-0.007	17.207	-0.005	-0.005	0.000	0.000	0.000	0.000
64	A	65	ARG	1	0.910	0.974	18.841	-0.405	-0.405	0.000	0.000	0.000	0.000
65	A	66	PHE	0	-0.038	-0.038	14.624	0.005	0.005	0.000	0.000	0.000	0.000
66	A	67	ILE	0	-0.049	-0.026	15.616	-0.035	-0.035	0.000	0.000	0.000	0.000
67	A	68	ASP	-1	-0.904	-0.943	18.194	0.159	0.159	0.000	0.000	0.000	0.000
68	A	69	GLU	-1	-0.923	-0.970	18.667	0.256	0.256	0.000	0.000	0.000	0.000
69	A	70	GLU	-1	-0.937	-0.940	14.094	0.168	0.168	0.000	0.000	0.000	0.000
70	A	71	THR	0	-0.012	-0.009	17.910	-0.030	-0.030	0.000	0.000	0.000	0.000
71	A	72	LYS	1	0.956	0.951	17.814	0.033	0.033	0.000	0.000	0.000	0.000
72	A	73	ASP	-1	-0.884	-0.925	17.998	-0.153	-0.153	0.000	0.000	0.000	0.000
73	A	74	THR	0	-0.088	-0.058	15.266	-0.038	-0.038	0.000	0.000	0.000	0.000
74	A	75	LYS	1	0.995	1.006	12.517	0.259	0.259	0.000	0.000	0.000	0.000
75	A	76	GLY	0	-0.023	-0.012	9.494	-0.083	-0.083	0.000	0.000	0.000	0.000
76	A	77	ARG	1	0.885	0.954	9.253	0.111	0.111	0.000	0.000	0.000	0.000
77	A	78	TYR	0	0.048	0.021	4.217	0.631	0.701	-0.001	-0.041	-0.028	0.000
78	A	79	PHE	0	0.003	-0.011	10.845	-0.093	-0.093	0.000	0.000	0.000	0.000
79	A	80	ILE	0	0.032	0.031	13.864	0.114	0.114	0.000	0.000	0.000	0.000
80	A	81	VAL	0	0.008	0.003	16.210	-0.083	-0.083	0.000	0.000	0.000	0.000
81	A	82	GLU	-1	-0.829	-0.936	19.875	0.178	0.178	0.000	0.000	0.000	0.000
82	A	83	ALA	0	0.000	-0.005	21.849	0.012	0.012	0.000	0.000	0.000	0.000
83	A	84	ASP	-1	-0.697	-0.850	16.851	0.469	0.469	0.000	0.000	0.000	0.000
84	A	85	ILE	0	-0.038	-0.009	18.341	0.037	0.037	0.000	0.000	0.000	0.000
85	A	86	LYS	1	0.887	0.945	20.297	-0.207	-0.207	0.000	0.000	0.000	0.000
86	A	87	GLU	-1	-0.925	-0.943	19.177	0.421	0.421	0.000	0.000	0.000	0.000
87	A	88	PHE	0	0.018	0.006	15.915	0.041	0.041	0.000	0.000	0.000	0.000
88	A	89	THR	0	-0.062	-0.036	18.090	0.013	0.013	0.000	0.000	0.000	0.000
89	A	90	THR	0	0.043	0.017	20.620	-0.015	-0.015	0.000	0.000	0.000	0.000
90	A	91	LEU	0	-0.031	-0.010	20.711	-0.039	-0.039	0.000	0.000	0.000	0.000
91	A	92	LYS	1	0.968	0.977	24.279	-0.177	-0.177	0.000	0.000	0.000	0.000
92	A	93	ALA	0	-0.002	0.009	25.348	-0.008	-0.008	0.000	0.000	0.000	0.000
93	A	94	ASP	-1	-0.836	-0.930	26.929	0.114	0.114	0.000	0.000	0.000	0.000
94	A	95	LYS	1	0.956	0.960	29.322	-0.069	-0.069	0.000	0.000	0.000	0.000
95	A	96	LYS	1	0.969	0.982	28.805	-0.110	-0.110	0.000	0.000	0.000	0.000
96	A	97	PHE	0	0.087	0.057	21.454	-0.010	-0.010	0.000	0.000	0.000	0.000
97	A	98	HIS	1	0.873	0.919	25.477	-0.111	-0.111	0.000	0.000	0.000	0.000
98	A	99	VAL	0	-0.037	-0.009	27.243	-0.013	-0.013	0.000	0.000	0.000	0.000
99	A	100	LEU	0	0.018	0.003	22.960	-0.013	-0.013	0.000	0.000	0.000	0.000
100	A	101	LEU	0	0.016	0.006	21.451	-0.013	-0.013	0.000	0.000	0.000	0.000
101	A	102	ASN	0	-0.015	-0.001	23.289	-0.025	-0.025	0.000	0.000	0.000	0.000
102	A	103	ILE	0	0.012	0.011	23.592	-0.018	-0.018	0.000	0.000	0.000	0.000
103	A	104	LEU	0	0.030	0.013	18.692	-0.020	-0.020	0.000	0.000	0.000	0.000
104	A	105	ARG	1	0.940	0.992	20.551	0.025	0.025	0.000	0.000	0.000	0.000
105	A	106	HIS	0	-0.019	-0.008	22.359	-0.028	-0.028	0.000	0.000	0.000	0.000
106	A	107	CYS	0	-0.032	-0.007	21.119	-0.014	-0.014	0.000	0.000	0.000	0.000
107	A	108	ARG	1	0.925	0.960	19.092	0.213	0.213	0.000	0.000	0.000	0.000
108	A	109	ARG	1	0.745	0.829	15.744	0.085	0.085	0.000	0.000	0.000	0.000
109	A	110	LEU	0	0.011	0.009	15.498	-0.004	-0.004	0.000	0.000	0.000	0.000
110	A	111	SER	0	-0.067	-0.040	17.490	-0.018	-0.018	0.000	0.000	0.000	0.000
111	A	112	GLU	-1	-0.905	-0.977	19.262	0.039	0.039	0.000	0.000	0.000	0.000
112	A	113	VAL	0	0.022	0.027	18.900	-0.021	-0.021	0.000	0.000	0.000	0.000
113	A	114	ARG	1	0.917	0.970	21.669	0.005	0.005	0.000	0.000	0.000	0.000
114	A	115	GLY	0	0.074	0.039	24.508	-0.012	-0.012	0.000	0.000	0.000	0.000
115	A	116	GLY	0	0.045	0.011	25.406	0.013	0.013	0.000	0.000	0.000	0.000
116	A	117	GLY	0	-0.020	-0.003	27.585	0.010	0.010	0.000	0.000	0.000	0.000
117	A	118	LEU	0	0.018	0.022	21.766	0.007	0.007	0.000	0.000	0.000	0.000
118	A	119	THR	0	-0.039	-0.049	23.115	-0.020	-0.020	0.000	0.000	0.000	0.000
119	A	120	ARG	1	0.832	0.928	18.629	-0.058	-0.058	0.000	0.000	0.000	0.000
120	A	121	TYR	0	-0.013	-0.012	18.012	-0.050	-0.050	0.000	0.000	0.000	0.000
121	A	122	VAL	0	-0.022	-0.016	14.081	0.043	0.043	0.000	0.000	0.000	0.000
122	A	123	ILE	0	0.025	0.009	10.781	-0.051	-0.051	0.000	0.000	0.000	0.000
123	A	124	THR	0	-0.024	-0.029	11.764	-0.182	-0.182	0.000	0.000	0.000	0.000

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