FMO DATABASE

FMODB ID: LJK89

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	OptAll
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	-1109065.730841
FMO2-HF: Nuclear repulsion	1058293.594099
FMO2-HF: Total energy	-50772.136743
FMO2-MP2: Total energy	-50920.02482

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.
-1.545	-0.071	-0.003	-0.638	-0.832	0.003

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 : 0.023 / q_NPA : 0.002

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	4	LYS	1	0.913	0.956	3.856	-0.026	1.001	-0.003	-0.419	-0.605	0.002
4	A	5	GLU	-1	-0.856	-0.924	5.997	1.563	1.563	0.000	0.000	0.000	0.000
5	A	6	MET	0	-0.060	-0.017	8.381	-0.286	-0.286	0.000	0.000	0.000	0.000
6	A	7	PRO	0	0.014	0.018	11.467	0.098	0.098	0.000	0.000	0.000	0.000
7	A	8	PHE	0	0.043	0.009	13.268	-0.021	-0.021	0.000	0.000	0.000	0.000
8	A	9	ILE	0	-0.031	0.006	16.712	-0.046	-0.046	0.000	0.000	0.000	0.000
9	A	10	THR	0	0.052	0.012	19.922	0.024	0.024	0.000	0.000	0.000	0.000
10	A	11	CYS	0	0.031	0.000	21.973	0.003	0.003	0.000	0.000	0.000	0.000
11	A	12	ASP	-1	-0.864	-0.924	25.406	-0.016	-0.016	0.000	0.000	0.000	0.000
12	A	13	GLU	-1	-0.769	-0.829	20.421	-0.058	-0.058	0.000	0.000	0.000	0.000
13	A	14	PHE	0	0.005	-0.006	24.801	0.003	0.003	0.000	0.000	0.000	0.000
14	A	15	ASN	0	0.011	-0.002	26.281	0.007	0.007	0.000	0.000	0.000	0.000
15	A	16	GLY	0	0.010	0.017	28.194	0.000	0.000	0.000	0.000	0.000	0.000
16	A	17	VAL	0	-0.033	0.001	25.591	-0.003	-0.003	0.000	0.000	0.000	0.000
17	A	18	PRO	0	0.045	0.021	28.664	0.007	0.007	0.000	0.000	0.000	0.000
18	A	19	SER	0	0.056	0.017	31.822	0.006	0.006	0.000	0.000	0.000	0.000
19	A	20	TYR	0	0.016	0.006	32.900	0.008	0.008	0.000	0.000	0.000	0.000
20	A	21	MET	0	-0.064	-0.023	27.280	0.003	0.003	0.000	0.000	0.000	0.000
21	A	22	LYS	1	0.833	0.907	29.506	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	23	SER	0	-0.036	-0.012	31.045	0.013	0.013	0.000	0.000	0.000	0.000
23	A	24	ARG	1	0.952	0.968	32.598	-0.057	-0.057	0.000	0.000	0.000	0.000
24	A	25	LEU	0	-0.075	-0.034	27.617	0.013	0.013	0.000	0.000	0.000	0.000
25	A	26	THR	0	0.058	-0.005	28.913	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	27	TYR	0	-0.012	-0.034	21.981	0.010	0.010	0.000	0.000	0.000	0.000
27	A	28	ASN	0	0.040	0.025	24.085	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	29	GLN	0	0.051	0.054	23.611	0.012	0.012	0.000	0.000	0.000	0.000
29	A	30	ILE	0	0.003	0.001	21.487	0.017	0.017	0.000	0.000	0.000	0.000
30	A	31	ASN	0	0.043	0.020	19.535	0.014	0.014	0.000	0.000	0.000	0.000
31	A	32	ASP	-1	-0.829	-0.909	18.901	0.292	0.292	0.000	0.000	0.000	0.000
32	A	33	VAL	0	-0.041	-0.027	19.836	0.039	0.039	0.000	0.000	0.000	0.000
33	A	34	ILE	0	-0.011	-0.001	14.914	0.028	0.028	0.000	0.000	0.000	0.000
34	A	35	LYS	1	0.886	0.946	15.272	-0.258	-0.258	0.000	0.000	0.000	0.000
35	A	36	GLU	-1	-0.769	-0.885	15.360	0.547	0.547	0.000	0.000	0.000	0.000
36	A	37	ILE	0	-0.016	-0.009	14.350	0.037	0.037	0.000	0.000	0.000	0.000
37	A	38	ASN	0	0.008	-0.008	11.164	-0.053	-0.053	0.000	0.000	0.000	0.000
38	A	39	LYS	1	0.842	0.922	11.464	-0.290	-0.290	0.000	0.000	0.000	0.000
39	A	40	ALA	0	0.007	0.015	13.158	0.107	0.107	0.000	0.000	0.000	0.000
40	A	41	VAL	0	-0.012	-0.007	8.827	0.034	0.034	0.000	0.000	0.000	0.000
41	A	42	ILE	0	0.000	-0.010	7.592	0.251	0.251	0.000	0.000	0.000	0.000
42	A	43	SER	0	-0.057	-0.036	9.310	0.220	0.220	0.000	0.000	0.000	0.000
43	A	44	LYS	1	0.785	0.897	12.004	-0.295	-0.295	0.000	0.000	0.000	0.000
44	A	45	TYR	0	0.018	-0.010	7.204	-0.089	-0.089	0.000	0.000	0.000	0.000
45	A	46	LYS	1	0.919	0.965	7.631	-2.474	-2.474	0.000	0.000	0.000	0.000
46	A	47	ILE	0	0.016	0.019	8.831	-0.139	-0.139	0.000	0.000	0.000	0.000
47	A	48	LEU	0	-0.043	-0.022	9.968	-0.114	-0.114	0.000	0.000	0.000	0.000
48	A	49	HIS	0	0.005	0.000	5.108	-0.566	-0.489	-0.001	-0.009	-0.066	0.000
49	A	50	GLN	0	-0.008	0.018	9.159	-0.005	-0.005	0.000	0.000	0.000	0.000
50	A	51	PRO	0	0.016	0.000	11.875	-0.147	-0.147	0.000	0.000	0.000	0.000
51	A	52	LYS	1	0.990	0.967	14.568	-0.255	-0.255	0.000	0.000	0.000	0.000
52	A	53	LYS	1	0.950	0.984	17.561	-0.247	-0.247	0.000	0.000	0.000	0.000
53	A	54	SER	0	0.006	0.002	16.511	-0.019	-0.019	0.000	0.000	0.000	0.000
54	A	55	MET	0	-0.052	0.019	14.958	0.020	0.020	0.000	0.000	0.000	0.000
55	A	56	ASN	0	0.077	0.058	18.694	-0.054	-0.054	0.000	0.000	0.000	0.000
56	A	57	SER	0	0.050	0.010	21.548	0.013	0.013	0.000	0.000	0.000	0.000
57	A	58	VAL	0	0.057	0.025	21.396	-0.004	-0.004	0.000	0.000	0.000	0.000
58	A	59	THR	0	-0.003	-0.022	16.472	0.020	0.020	0.000	0.000	0.000	0.000
59	A	60	ARG	1	0.868	0.929	18.303	-0.250	-0.250	0.000	0.000	0.000	0.000
60	A	61	ASN	0	-0.001	0.002	20.213	-0.025	-0.025	0.000	0.000	0.000	0.000
61	A	62	LEU	0	-0.009	0.010	17.905	-0.015	-0.015	0.000	0.000	0.000	0.000
62	A	63	TYR	0	-0.003	-0.003	13.762	-0.034	-0.034	0.000	0.000	0.000	0.000
63	A	64	HIS	0	0.010	-0.005	17.375	-0.022	-0.022	0.000	0.000	0.000	0.000
64	A	65	ARG	1	0.820	0.879	18.889	-0.313	-0.313	0.000	0.000	0.000	0.000
65	A	66	PHE	0	-0.020	-0.033	14.812	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	67	ILE	0	-0.039	-0.015	15.240	-0.040	-0.040	0.000	0.000	0.000	0.000
67	A	68	ASP	-1	-0.898	-0.947	18.350	0.071	0.071	0.000	0.000	0.000	0.000
68	A	69	GLU	-1	-0.828	-0.905	18.502	0.190	0.190	0.000	0.000	0.000	0.000
69	A	70	GLU	-1	-0.865	-0.895	13.852	-0.122	-0.122	0.000	0.000	0.000	0.000
70	A	71	THR	0	-0.047	-0.036	17.674	-0.008	-0.008	0.000	0.000	0.000	0.000
71	A	72	LYS	1	0.925	0.954	18.078	0.129	0.129	0.000	0.000	0.000	0.000
72	A	73	ASP	-1	-0.844	-0.918	17.480	-0.230	-0.230	0.000	0.000	0.000	0.000
73	A	74	THR	0	-0.061	-0.048	14.903	-0.040	-0.040	0.000	0.000	0.000	0.000
74	A	75	LYS	1	0.969	0.993	12.452	0.424	0.424	0.000	0.000	0.000	0.000
75	A	76	GLY	0	0.000	-0.001	9.368	-0.065	-0.065	0.000	0.000	0.000	0.000
76	A	77	ARG	1	0.849	0.932	8.997	0.127	0.127	0.000	0.000	0.000	0.000
77	A	78	TYR	0	0.028	0.011	3.683	0.552	0.922	0.001	-0.210	-0.161	0.001
78	A	79	PHE	0	-0.012	-0.012	10.334	-0.018	-0.018	0.000	0.000	0.000	0.000
79	A	80	ILE	0	0.016	0.013	13.824	0.092	0.092	0.000	0.000	0.000	0.000
80	A	81	VAL	0	0.008	0.007	16.167	-0.066	-0.066	0.000	0.000	0.000	0.000
81	A	82	GLU	-1	-0.834	-0.943	19.958	0.153	0.153	0.000	0.000	0.000	0.000
82	A	83	ALA	0	0.008	0.012	21.678	0.010	0.010	0.000	0.000	0.000	0.000
83	A	84	ASP	-1	-0.659	-0.817	16.896	0.347	0.347	0.000	0.000	0.000	0.000
84	A	85	ILE	0	-0.048	-0.014	18.813	0.038	0.038	0.000	0.000	0.000	0.000
85	A	86	LYS	1	0.876	0.956	20.697	-0.159	-0.159	0.000	0.000	0.000	0.000
86	A	87	GLU	-1	-0.840	-0.883	18.771	0.329	0.329	0.000	0.000	0.000	0.000
87	A	88	PHE	0	0.012	0.000	15.613	0.045	0.045	0.000	0.000	0.000	0.000
88	A	89	THR	0	-0.065	-0.046	18.292	0.025	0.025	0.000	0.000	0.000	0.000
89	A	90	THR	0	0.031	0.020	20.672	-0.016	-0.016	0.000	0.000	0.000	0.000
90	A	91	LEU	0	-0.042	-0.010	21.497	-0.036	-0.036	0.000	0.000	0.000	0.000
91	A	92	LYS	1	0.979	0.976	24.511	-0.178	-0.178	0.000	0.000	0.000	0.000
92	A	93	ALA	0	0.043	0.034	25.129	-0.007	-0.007	0.000	0.000	0.000	0.000
93	A	94	ASP	-1	-0.797	-0.913	26.677	0.101	0.101	0.000	0.000	0.000	0.000
94	A	95	LYS	1	0.981	0.988	29.161	-0.059	-0.059	0.000	0.000	0.000	0.000
95	A	96	LYS	1	0.892	0.941	28.896	-0.126	-0.126	0.000	0.000	0.000	0.000
96	A	97	PHE	0	0.089	0.053	21.456	-0.009	-0.009	0.000	0.000	0.000	0.000
97	A	98	HIS	1	0.832	0.891	25.221	-0.099	-0.099	0.000	0.000	0.000	0.000
98	A	99	VAL	0	-0.017	0.000	26.777	-0.012	-0.012	0.000	0.000	0.000	0.000
99	A	100	LEU	0	0.017	0.014	22.150	-0.012	-0.012	0.000	0.000	0.000	0.000
100	A	101	LEU	0	0.034	0.009	21.064	-0.009	-0.009	0.000	0.000	0.000	0.000
101	A	102	ASN	0	-0.012	0.001	22.714	-0.028	-0.028	0.000	0.000	0.000	0.000
102	A	103	ILE	0	0.020	0.011	23.515	-0.017	-0.017	0.000	0.000	0.000	0.000
103	A	104	LEU	0	0.038	0.017	18.405	-0.017	-0.017	0.000	0.000	0.000	0.000
104	A	105	ARG	1	0.876	0.933	20.063	0.027	0.027	0.000	0.000	0.000	0.000
105	A	106	HIS	0	-0.015	-0.006	21.900	-0.023	-0.023	0.000	0.000	0.000	0.000
106	A	107	CYS	0	-0.032	-0.013	20.601	-0.012	-0.012	0.000	0.000	0.000	0.000
107	A	108	ARG	1	0.933	0.967	19.026	0.187	0.187	0.000	0.000	0.000	0.000
108	A	109	ARG	1	0.775	0.840	15.506	0.005	0.005	0.000	0.000	0.000	0.000
109	A	110	LEU	0	-0.028	-0.004	15.129	0.001	0.001	0.000	0.000	0.000	0.000
110	A	111	SER	0	-0.023	-0.011	16.919	-0.024	-0.024	0.000	0.000	0.000	0.000
111	A	112	GLU	-1	-0.805	-0.875	19.000	0.012	0.012	0.000	0.000	0.000	0.000
112	A	113	VAL	0	0.018	0.021	18.285	-0.023	-0.023	0.000	0.000	0.000	0.000
113	A	114	ARG	1	0.835	0.879	21.058	0.036	0.036	0.000	0.000	0.000	0.000
114	A	115	GLY	0	0.072	0.034	24.428	-0.016	-0.016	0.000	0.000	0.000	0.000
115	A	116	GLY	0	0.028	0.019	25.523	0.012	0.012	0.000	0.000	0.000	0.000
116	A	117	GLY	0	0.006	0.011	27.672	0.010	0.010	0.000	0.000	0.000	0.000
117	A	118	LEU	0	-0.005	0.011	22.534	0.009	0.009	0.000	0.000	0.000	0.000
118	A	119	THR	0	-0.029	-0.030	22.816	-0.024	-0.024	0.000	0.000	0.000	0.000
119	A	120	ARG	1	0.841	0.922	18.291	0.027	0.027	0.000	0.000	0.000	0.000
120	A	121	TYR	0	-0.004	-0.012	18.022	-0.043	-0.043	0.000	0.000	0.000	0.000
121	A	122	VAL	0	-0.009	-0.011	13.787	0.037	0.037	0.000	0.000	0.000	0.000
122	A	123	ILE	0	0.034	0.014	10.568	-0.030	-0.030	0.000	0.000	0.000	0.000
123	A	124	THR	0	-0.051	-0.017	11.824	-0.192	-0.192	0.000	0.000	0.000	0.000

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