FMO DATABASE

FMODB ID: YV9Y2

Calculation Name: 5C04-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5C04

Chain ID: A

ChEMBL ID:

UniProt ID: P9WIE3

Base Structure: X-ray

Registration Date: 2023-09-22

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	153
LigandResidueName
LigandFragmentNumber	0
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1485527.086767
FMO2-HF: Nuclear repulsion	1427049.863094
FMO2-HF: Total energy	-58477.223673
FMO2-MP2: Total energy	-58650.205506

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:0:SER)

Summations of interaction energy for fragment #1(A:0: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.
-0.623	1.42	0.042	-0.863	-1.223	-0.001

Interaction energy analysis for fragmet #1(A:0:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.026 / q_NPA : -0.036

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	2	LEU	0	-0.043	-0.003	3.356	-2.363	-0.897	0.036	-0.661	-0.841	-0.001
4	A	3	ASN	0	0.024	-0.001	4.373	1.010	1.104	-0.001	-0.004	-0.089	0.000
5	A	4	VAL	0	0.030	0.007	7.326	0.180	0.180	0.000	0.000	0.000	0.000
6	A	5	GLY	0	-0.037	-0.011	11.055	-0.076	-0.076	0.000	0.000	0.000	0.000
7	A	6	ALA	0	-0.020	0.001	9.417	0.081	0.081	0.000	0.000	0.000	0.000
8	A	7	THR	0	-0.035	-0.026	11.511	0.194	0.194	0.000	0.000	0.000	0.000
9	A	8	ALA	0	0.017	0.007	12.215	-0.151	-0.151	0.000	0.000	0.000	0.000
10	A	9	PRO	0	-0.029	-0.004	9.746	0.126	0.126	0.000	0.000	0.000	0.000
11	A	10	ASP	-1	-0.818	-0.919	12.965	-0.193	-0.193	0.000	0.000	0.000	0.000
12	A	11	PHE	0	-0.021	-0.016	14.997	0.023	0.023	0.000	0.000	0.000	0.000
13	A	12	THR	0	0.007	-0.007	17.405	-0.009	-0.009	0.000	0.000	0.000	0.000
14	A	13	LEU	0	-0.019	-0.002	16.819	0.023	0.023	0.000	0.000	0.000	0.000
15	A	14	ARG	1	0.901	0.945	21.303	-0.039	-0.039	0.000	0.000	0.000	0.000
16	A	15	ASP	-1	-0.742	-0.863	23.646	0.022	0.022	0.000	0.000	0.000	0.000
17	A	16	GLN	0	0.052	0.012	25.744	0.009	0.009	0.000	0.000	0.000	0.000
18	A	17	ASN	0	-0.026	-0.011	28.082	0.011	0.011	0.000	0.000	0.000	0.000
19	A	18	GLN	0	-0.064	-0.038	28.343	0.003	0.003	0.000	0.000	0.000	0.000
20	A	19	GLN	0	0.010	0.016	29.108	-0.010	-0.010	0.000	0.000	0.000	0.000
21	A	20	LEU	0	-0.056	-0.026	24.960	0.007	0.007	0.000	0.000	0.000	0.000
22	A	21	VAL	0	0.054	0.033	22.327	-0.011	-0.011	0.000	0.000	0.000	0.000
23	A	22	THR	0	-0.024	-0.014	21.127	0.005	0.005	0.000	0.000	0.000	0.000
24	A	23	LEU	0	0.006	0.025	16.111	0.006	0.006	0.000	0.000	0.000	0.000
25	A	24	ARG	1	0.937	0.953	19.274	0.305	0.305	0.000	0.000	0.000	0.000
26	A	25	GLY	0	-0.021	-0.010	21.986	0.001	0.001	0.000	0.000	0.000	0.000
27	A	26	TYR	0	0.051	0.028	22.566	0.015	0.015	0.000	0.000	0.000	0.000
28	A	27	ARG	1	0.934	0.971	18.513	0.387	0.387	0.000	0.000	0.000	0.000
29	A	28	GLY	0	-0.058	-0.025	24.566	0.019	0.019	0.000	0.000	0.000	0.000
30	A	29	ALA	0	-0.053	-0.019	26.793	0.012	0.012	0.000	0.000	0.000	0.000
31	A	30	LYS	1	0.853	0.925	25.611	0.125	0.125	0.000	0.000	0.000	0.000
32	A	31	ASN	0	-0.028	-0.007	21.470	-0.050	-0.050	0.000	0.000	0.000	0.000
33	A	32	VAL	0	-0.021	-0.015	19.287	0.035	0.035	0.000	0.000	0.000	0.000
34	A	33	LEU	0	0.038	0.033	17.591	-0.056	-0.056	0.000	0.000	0.000	0.000
35	A	34	LEU	0	-0.048	-0.026	14.047	0.037	0.037	0.000	0.000	0.000	0.000
36	A	35	VAL	0	0.043	0.011	15.126	-0.021	-0.021	0.000	0.000	0.000	0.000
37	A	36	PHE	0	0.011	0.008	12.205	0.024	0.024	0.000	0.000	0.000	0.000
38	A	37	HIS	0	-0.020	-0.046	14.289	-0.005	-0.005	0.000	0.000	0.000	0.000
39	A	38	PRO	0	-0.015	0.003	14.665	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	39	LEU	0	0.027	-0.010	16.452	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	40	ALA	0	0.036	0.029	20.134	-0.020	-0.020	0.000	0.000	0.000	0.000
42	A	41	PHE	0	-0.023	-0.013	23.463	0.011	0.011	0.000	0.000	0.000	0.000
43	A	42	THR	0	-0.014	-0.007	21.784	0.014	0.014	0.000	0.000	0.000	0.000
44	A	43	GLY	0	0.013	0.003	24.196	-0.013	-0.013	0.000	0.000	0.000	0.000
45	A	44	ILE	0	0.028	0.009	19.346	-0.021	-0.021	0.000	0.000	0.000	0.000
46	A	45	CYM	-1	-0.793	-0.818	19.300	0.299	0.299	0.000	0.000	0.000	0.000
47	A	46	GLN	0	-0.062	-0.017	21.225	-0.014	-0.014	0.000	0.000	0.000	0.000
48	A	47	GLY	0	0.035	0.025	24.504	-0.020	-0.020	0.000	0.000	0.000	0.000
49	A	48	GLU	-1	-0.768	-0.868	18.075	0.196	0.196	0.000	0.000	0.000	0.000
50	A	49	LEU	0	-0.001	-0.011	20.706	-0.029	-0.029	0.000	0.000	0.000	0.000
51	A	50	ASP	-1	-0.841	-0.911	23.815	0.079	0.079	0.000	0.000	0.000	0.000
52	A	51	GLN	0	0.014	0.017	24.495	-0.005	-0.005	0.000	0.000	0.000	0.000
53	A	52	LEU	0	-0.022	-0.013	21.612	-0.015	-0.015	0.000	0.000	0.000	0.000
54	A	53	ARG	1	0.790	0.873	25.293	-0.072	-0.072	0.000	0.000	0.000	0.000
55	A	54	ASP	-1	-0.898	-0.940	28.479	0.035	0.035	0.000	0.000	0.000	0.000
56	A	55	HIS	0	-0.066	-0.027	27.709	-0.007	-0.007	0.000	0.000	0.000	0.000
57	A	56	LEU	0	0.010	0.022	27.080	-0.012	-0.012	0.000	0.000	0.000	0.000
58	A	57	PRO	0	0.005	-0.001	28.669	-0.012	-0.012	0.000	0.000	0.000	0.000
59	A	58	GLU	-1	-0.935	-0.973	27.701	-0.056	-0.056	0.000	0.000	0.000	0.000
60	A	59	PHE	0	-0.048	-0.041	22.868	-0.018	-0.018	0.000	0.000	0.000	0.000
61	A	60	GLU	-1	-0.983	-0.993	25.508	-0.057	-0.057	0.000	0.000	0.000	0.000
62	A	61	ASN	0	0.001	-0.003	27.989	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	62	ASP	-1	-0.905	-0.963	29.952	-0.091	-0.091	0.000	0.000	0.000	0.000
64	A	63	ASP	-1	-0.925	-0.956	27.729	-0.143	-0.143	0.000	0.000	0.000	0.000
65	A	64	SER	0	-0.075	-0.035	24.423	-0.032	-0.032	0.000	0.000	0.000	0.000
66	A	65	ALA	0	0.008	0.004	23.960	0.020	0.020	0.000	0.000	0.000	0.000
67	A	66	ALA	0	0.040	0.021	21.755	-0.022	-0.022	0.000	0.000	0.000	0.000
68	A	67	LEU	0	-0.048	-0.021	19.519	0.015	0.015	0.000	0.000	0.000	0.000
69	A	68	ALA	0	0.035	0.033	18.931	-0.009	-0.009	0.000	0.000	0.000	0.000
70	A	69	ILE	0	-0.030	-0.014	15.440	-0.008	-0.008	0.000	0.000	0.000	0.000
71	A	70	SER	0	0.026	0.001	16.325	0.048	0.048	0.000	0.000	0.000	0.000
72	A	71	VAL	0	0.016	0.018	15.623	-0.039	-0.039	0.000	0.000	0.000	0.000
73	A	72	GLY	0	0.021	0.022	18.294	-0.012	-0.012	0.000	0.000	0.000	0.000
74	A	73	PRO	0	0.003	0.009	22.025	-0.022	-0.022	0.000	0.000	0.000	0.000
75	A	74	PRO	0	0.041	0.008	24.589	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	75	PRO	0	0.035	0.010	26.963	-0.003	-0.003	0.000	0.000	0.000	0.000
77	A	76	THR	0	-0.004	-0.001	24.998	0.003	0.003	0.000	0.000	0.000	0.000
78	A	77	HIS	0	0.038	0.017	21.214	0.017	0.017	0.000	0.000	0.000	0.000
79	A	78	LYS	1	0.881	0.961	26.626	-0.052	-0.052	0.000	0.000	0.000	0.000
80	A	79	ILE	0	0.007	0.001	30.195	-0.008	-0.008	0.000	0.000	0.000	0.000
81	A	80	TRP	0	0.005	-0.012	22.554	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	81	ALA	0	0.016	0.017	28.207	-0.004	-0.004	0.000	0.000	0.000	0.000
83	A	82	THR	0	-0.067	-0.040	29.609	-0.011	-0.011	0.000	0.000	0.000	0.000
84	A	83	GLN	0	-0.064	-0.044	32.432	-0.007	-0.007	0.000	0.000	0.000	0.000
85	A	84	SER	0	0.002	0.015	29.492	0.003	0.003	0.000	0.000	0.000	0.000
86	A	85	GLY	0	-0.003	0.021	31.444	-0.005	-0.005	0.000	0.000	0.000	0.000
87	A	86	PHE	0	-0.022	-0.015	25.959	-0.009	-0.009	0.000	0.000	0.000	0.000
88	A	87	THR	0	-0.001	-0.021	29.617	0.003	0.003	0.000	0.000	0.000	0.000
89	A	88	PHE	0	0.039	0.046	23.602	-0.006	-0.006	0.000	0.000	0.000	0.000
90	A	89	PRO	0	-0.025	-0.017	24.040	0.017	0.017	0.000	0.000	0.000	0.000
91	A	90	LEU	0	0.002	0.004	22.513	0.000	0.000	0.000	0.000	0.000	0.000
92	A	91	LEU	0	-0.028	-0.030	19.429	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	92	SER	0	-0.056	-0.048	20.243	0.021	0.021	0.000	0.000	0.000	0.000
94	A	93	ASP	-1	-0.777	-0.880	13.995	0.277	0.277	0.000	0.000	0.000	0.000
95	A	94	PHE	0	-0.008	-0.005	17.241	0.056	0.056	0.000	0.000	0.000	0.000
96	A	95	TRP	0	-0.010	0.002	19.787	0.037	0.037	0.000	0.000	0.000	0.000
97	A	96	PRO	0	-0.006	-0.027	16.289	-0.039	-0.039	0.000	0.000	0.000	0.000
98	A	97	HIS	0	-0.048	-0.038	15.537	-0.054	-0.054	0.000	0.000	0.000	0.000
99	A	98	GLY	0	0.028	0.018	13.406	0.082	0.082	0.000	0.000	0.000	0.000
100	A	99	ALA	0	0.007	0.021	11.695	0.097	0.097	0.000	0.000	0.000	0.000
101	A	100	VAL	0	-0.007	-0.016	11.133	-0.052	-0.052	0.000	0.000	0.000	0.000
102	A	101	SER	0	-0.016	-0.044	10.447	-0.148	-0.148	0.000	0.000	0.000	0.000
103	A	102	GLN	0	-0.094	-0.062	7.363	-0.119	-0.119	0.000	0.000	0.000	0.000
104	A	103	ALA	0	-0.029	0.002	6.231	-0.039	-0.039	0.000	0.000	0.000	0.000
105	A	104	TYR	0	-0.016	-0.041	7.328	-0.552	-0.552	0.000	0.000	0.000	0.000
106	A	105	GLY	0	0.014	0.013	3.937	-1.240	-1.033	0.002	-0.100	-0.110	0.000
107	A	106	VAL	0	-0.042	-0.042	3.990	0.925	1.201	0.005	-0.098	-0.183	0.000
108	A	107	PHE	0	0.002	0.009	6.663	-0.327	-0.327	0.000	0.000	0.000	0.000
109	A	108	ASN	0	-0.062	-0.030	7.565	0.781	0.781	0.000	0.000	0.000	0.000
110	A	109	GLU	-1	-0.814	-0.922	8.675	1.291	1.291	0.000	0.000	0.000	0.000
111	A	110	GLN	0	-0.061	-0.019	10.423	-0.148	-0.148	0.000	0.000	0.000	0.000
112	A	111	ALA	0	-0.005	-0.005	13.536	-0.155	-0.155	0.000	0.000	0.000	0.000
113	A	112	GLY	0	0.017	0.029	14.039	-0.124	-0.124	0.000	0.000	0.000	0.000
114	A	113	ILE	0	-0.014	0.005	13.669	-0.141	-0.141	0.000	0.000	0.000	0.000
115	A	114	ALA	0	0.043	0.025	11.228	0.215	0.215	0.000	0.000	0.000	0.000
116	A	115	ASN	0	0.024	-0.005	7.443	-0.276	-0.276	0.000	0.000	0.000	0.000
117	A	116	ARG	1	0.783	0.848	10.923	-0.509	-0.509	0.000	0.000	0.000	0.000
118	A	117	GLY	0	-0.013	-0.001	9.987	-0.027	-0.027	0.000	0.000	0.000	0.000
119	A	118	THR	0	-0.043	-0.041	10.597	0.043	0.043	0.000	0.000	0.000	0.000
120	A	119	PHE	0	-0.017	-0.010	7.843	-0.093	-0.093	0.000	0.000	0.000	0.000
121	A	120	VAL	0	0.049	0.039	13.470	0.095	0.095	0.000	0.000	0.000	0.000
122	A	121	VAL	0	-0.043	-0.010	15.181	-0.108	-0.108	0.000	0.000	0.000	0.000
123	A	122	ASP	-1	-0.681	-0.814	17.198	-0.394	-0.394	0.000	0.000	0.000	0.000
124	A	123	ARG	1	0.968	0.978	20.028	0.214	0.214	0.000	0.000	0.000	0.000
125	A	124	SER	0	-0.096	-0.058	20.510	0.015	0.015	0.000	0.000	0.000	0.000
126	A	125	GLY	0	-0.052	-0.031	18.750	-0.013	-0.013	0.000	0.000	0.000	0.000
127	A	126	ILE	0	-0.044	-0.009	14.988	-0.082	-0.082	0.000	0.000	0.000	0.000
128	A	127	ILE	0	0.010	0.014	10.016	0.093	0.093	0.000	0.000	0.000	0.000
129	A	128	ARG	1	0.860	0.896	13.618	0.478	0.478	0.000	0.000	0.000	0.000
130	A	129	PHE	0	0.025	0.014	13.729	0.014	0.014	0.000	0.000	0.000	0.000
131	A	130	ALA	0	0.012	-0.003	8.618	-0.057	-0.057	0.000	0.000	0.000	0.000
132	A	131	GLU	-1	-0.797	-0.879	9.716	-0.009	-0.009	0.000	0.000	0.000	0.000
133	A	132	MET	0	0.004	-0.002	5.547	-0.025	-0.025	0.000	0.000	0.000	0.000
134	A	133	LYS	1	0.877	0.970	8.984	-0.017	-0.017	0.000	0.000	0.000	0.000
135	A	134	GLN	0	0.028	-0.008	8.557	0.074	0.074	0.000	0.000	0.000	0.000
136	A	135	PRO	0	0.038	0.008	12.013	-0.151	-0.151	0.000	0.000	0.000	0.000
137	A	136	GLY	0	-0.024	-0.006	15.005	-0.083	-0.083	0.000	0.000	0.000	0.000
138	A	137	GLU	-1	-0.893	-0.926	13.376	0.523	0.523	0.000	0.000	0.000	0.000
139	A	138	VAL	0	0.011	-0.010	17.061	0.003	0.003	0.000	0.000	0.000	0.000
140	A	139	ARG	1	0.702	0.844	14.017	-0.156	-0.156	0.000	0.000	0.000	0.000
141	A	140	ASP	-1	-0.802	-0.889	17.699	-0.006	-0.006	0.000	0.000	0.000	0.000
142	A	141	GLN	0	0.009	-0.020	19.632	-0.043	-0.043	0.000	0.000	0.000	0.000
143	A	142	ARG	1	0.897	0.940	21.382	0.004	0.004	0.000	0.000	0.000	0.000
144	A	143	LEU	0	-0.014	-0.009	16.607	-0.023	-0.023	0.000	0.000	0.000	0.000
145	A	144	TRP	0	-0.038	-0.022	16.503	-0.035	-0.035	0.000	0.000	0.000	0.000
146	A	145	THR	0	0.080	0.033	19.815	-0.019	-0.019	0.000	0.000	0.000	0.000
147	A	146	ASP	-1	-0.993	-0.988	21.347	-0.204	-0.204	0.000	0.000	0.000	0.000
148	A	147	ALA	0	0.005	0.002	18.143	-0.020	-0.020	0.000	0.000	0.000	0.000
149	A	148	LEU	0	-0.037	-0.028	20.068	-0.024	-0.024	0.000	0.000	0.000	0.000
150	A	149	ALA	0	0.013	0.010	22.438	-0.002	-0.002	0.000	0.000	0.000	0.000
151	A	150	ALA	0	-0.023	-0.002	21.789	0.002	0.002	0.000	0.000	0.000	0.000
152	A	151	LEU	0	-0.064	-0.029	19.296	-0.021	-0.021	0.000	0.000	0.000	0.000
153	A	152	THR	0	-0.023	0.005	23.893	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:SER)