FMO DATABASE

FMODB ID: VQVR1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1486620.375922
FMO2-HF: Nuclear repulsion	1428142.978606
FMO2-HF: Total energy	-58477.397316
FMO2-MP2: Total energy	-58650.425057

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.
-1.028	0.943	0.017	-0.772	-1.216	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 : -0.036 / q_NPA : -0.034

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	-0.036	0.000	3.580	-1.713	-0.366	0.010	-0.576	-0.780	0.001
4	A	3	ASN	0	0.021	-0.004	4.275	0.973	1.082	-0.001	-0.004	-0.104	0.000
5	A	4	VAL	0	0.031	0.009	7.552	0.064	0.064	0.000	0.000	0.000	0.000
6	A	5	GLY	0	-0.031	-0.009	11.262	-0.002	-0.002	0.000	0.000	0.000	0.000
7	A	6	ALA	0	-0.022	0.000	9.242	0.044	0.044	0.000	0.000	0.000	0.000
8	A	7	THR	0	-0.023	-0.021	11.378	0.168	0.168	0.000	0.000	0.000	0.000
9	A	8	ALA	0	0.012	0.006	12.264	-0.168	-0.168	0.000	0.000	0.000	0.000
10	A	9	PRO	0	-0.011	0.004	9.895	0.123	0.123	0.000	0.000	0.000	0.000
11	A	10	ASP	-1	-0.770	-0.875	13.038	-0.277	-0.277	0.000	0.000	0.000	0.000
12	A	11	PHE	0	-0.005	0.000	15.114	-0.002	-0.002	0.000	0.000	0.000	0.000
13	A	12	THR	0	0.019	0.005	17.496	0.008	0.008	0.000	0.000	0.000	0.000
14	A	13	LEU	0	-0.006	0.016	17.020	0.010	0.010	0.000	0.000	0.000	0.000
15	A	14	ARG	1	0.893	0.938	21.406	0.068	0.068	0.000	0.000	0.000	0.000
16	A	15	ASP	-1	-0.707	-0.847	23.755	-0.051	-0.051	0.000	0.000	0.000	0.000
17	A	16	GLN	0	0.055	0.023	25.853	0.002	0.002	0.000	0.000	0.000	0.000
18	A	17	ASN	0	-0.056	-0.027	28.100	0.015	0.015	0.000	0.000	0.000	0.000
19	A	18	GLN	0	-0.057	-0.034	28.442	0.002	0.002	0.000	0.000	0.000	0.000
20	A	19	GLN	0	-0.006	0.007	29.222	-0.009	-0.009	0.000	0.000	0.000	0.000
21	A	20	LEU	0	-0.055	-0.026	25.133	0.000	0.000	0.000	0.000	0.000	0.000
22	A	21	VAL	0	0.041	0.027	22.735	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	22	THR	0	-0.032	-0.032	21.455	0.000	0.000	0.000	0.000	0.000	0.000
24	A	23	LEU	0	0.006	0.020	16.256	0.014	0.014	0.000	0.000	0.000	0.000
25	A	24	ARG	1	0.862	0.891	19.663	0.356	0.356	0.000	0.000	0.000	0.000
26	A	25	GLY	0	-0.024	-0.009	22.064	0.009	0.009	0.000	0.000	0.000	0.000
27	A	26	TYR	0	0.041	0.024	22.585	0.021	0.021	0.000	0.000	0.000	0.000
28	A	27	ARG	1	0.924	0.974	18.347	0.409	0.409	0.000	0.000	0.000	0.000
29	A	28	GLY	0	-0.049	-0.021	24.637	0.016	0.016	0.000	0.000	0.000	0.000
30	A	29	ALA	0	-0.048	-0.020	26.959	0.015	0.015	0.000	0.000	0.000	0.000
31	A	30	LYS	1	0.804	0.888	25.746	0.131	0.131	0.000	0.000	0.000	0.000
32	A	31	ASN	0	-0.025	-0.006	21.739	-0.046	-0.046	0.000	0.000	0.000	0.000
33	A	32	VAL	0	-0.012	-0.014	19.366	0.027	0.027	0.000	0.000	0.000	0.000
34	A	33	LEU	0	0.029	0.029	17.648	-0.048	-0.048	0.000	0.000	0.000	0.000
35	A	34	LEU	0	-0.043	-0.023	14.176	0.023	0.023	0.000	0.000	0.000	0.000
36	A	35	VAL	0	0.044	0.011	15.152	-0.019	-0.019	0.000	0.000	0.000	0.000
37	A	36	PHE	0	0.012	0.011	12.212	0.013	0.013	0.000	0.000	0.000	0.000
38	A	37	HIS	0	-0.005	-0.060	14.310	0.012	0.012	0.000	0.000	0.000	0.000
39	A	38	PRO	0	0.010	0.008	14.807	-0.010	-0.010	0.000	0.000	0.000	0.000
40	A	39	LEU	0	0.035	-0.005	16.465	-0.010	-0.010	0.000	0.000	0.000	0.000
41	A	40	ALA	0	0.019	0.014	20.147	-0.006	-0.006	0.000	0.000	0.000	0.000
42	A	41	PHE	0	-0.018	-0.011	23.478	0.008	0.008	0.000	0.000	0.000	0.000
43	A	42	THR	0	-0.013	0.000	21.719	0.014	0.014	0.000	0.000	0.000	0.000
44	A	43	GLY	0	0.019	0.006	24.209	-0.009	-0.009	0.000	0.000	0.000	0.000
45	A	44	ILE	0	0.025	0.006	19.384	-0.014	-0.014	0.000	0.000	0.000	0.000
46	A	45	CYM	-1	-0.812	-0.754	19.292	0.161	0.161	0.000	0.000	0.000	0.000
47	A	46	GLN	0	-0.047	-0.014	21.243	-0.013	-0.013	0.000	0.000	0.000	0.000
48	A	47	GLY	0	0.033	0.023	24.517	-0.013	-0.013	0.000	0.000	0.000	0.000
49	A	48	GLU	-1	-0.758	-0.850	18.010	0.117	0.117	0.000	0.000	0.000	0.000
50	A	49	LEU	0	-0.001	-0.010	20.599	-0.021	-0.021	0.000	0.000	0.000	0.000
51	A	50	ASP	-1	-0.793	-0.871	23.838	0.031	0.031	0.000	0.000	0.000	0.000
52	A	51	GLN	0	0.004	0.017	24.700	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	52	LEU	0	-0.022	-0.010	21.588	-0.010	-0.010	0.000	0.000	0.000	0.000
54	A	53	ARG	1	0.714	0.818	25.318	-0.032	-0.032	0.000	0.000	0.000	0.000
55	A	54	ASP	-1	-0.882	-0.919	28.503	0.014	0.014	0.000	0.000	0.000	0.000
56	A	55	HIS	0	-0.076	-0.037	27.720	0.001	0.001	0.000	0.000	0.000	0.000
57	A	56	LEU	0	0.012	0.026	27.128	-0.009	-0.009	0.000	0.000	0.000	0.000
58	A	57	PRO	0	0.014	0.002	28.696	-0.010	-0.010	0.000	0.000	0.000	0.000
59	A	58	GLU	-1	-0.916	-0.959	27.634	-0.037	-0.037	0.000	0.000	0.000	0.000
60	A	59	PHE	0	-0.049	-0.044	22.806	-0.013	-0.013	0.000	0.000	0.000	0.000
61	A	60	GLU	-1	-0.972	-0.985	25.534	-0.089	-0.089	0.000	0.000	0.000	0.000
62	A	61	ASN	0	-0.008	-0.015	28.016	0.001	0.001	0.000	0.000	0.000	0.000
63	A	62	ASP	-1	-0.871	-0.946	30.034	-0.090	-0.090	0.000	0.000	0.000	0.000
64	A	63	ASP	-1	-0.865	-0.936	27.708	-0.139	-0.139	0.000	0.000	0.000	0.000
65	A	64	SER	0	-0.055	-0.014	24.573	-0.025	-0.025	0.000	0.000	0.000	0.000
66	A	65	ALA	0	0.003	0.003	24.014	0.016	0.016	0.000	0.000	0.000	0.000
67	A	66	ALA	0	0.040	0.021	21.776	-0.019	-0.019	0.000	0.000	0.000	0.000
68	A	67	LEU	0	-0.040	-0.016	19.552	0.010	0.010	0.000	0.000	0.000	0.000
69	A	68	ALA	0	0.037	0.033	18.955	-0.013	-0.013	0.000	0.000	0.000	0.000
70	A	69	ILE	0	-0.036	-0.021	15.442	-0.007	-0.007	0.000	0.000	0.000	0.000
71	A	70	SER	0	0.035	0.017	16.344	0.032	0.032	0.000	0.000	0.000	0.000
72	A	71	VAL	0	0.015	0.017	15.654	-0.029	-0.029	0.000	0.000	0.000	0.000
73	A	72	GLY	0	0.015	0.021	18.305	-0.005	-0.005	0.000	0.000	0.000	0.000
74	A	73	PRO	0	-0.003	0.014	22.037	-0.020	-0.020	0.000	0.000	0.000	0.000
75	A	74	PRO	0	0.044	0.009	24.630	0.005	0.005	0.000	0.000	0.000	0.000
76	A	75	PRO	0	0.021	0.004	27.055	0.002	0.002	0.000	0.000	0.000	0.000
77	A	76	THR	0	0.026	0.010	25.295	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	77	HIS	0	0.037	0.016	21.245	0.020	0.020	0.000	0.000	0.000	0.000
79	A	78	LYS	1	0.888	0.958	26.642	0.013	0.013	0.000	0.000	0.000	0.000
80	A	79	ILE	0	0.006	0.009	30.212	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	80	TRP	0	0.011	-0.002	22.509	0.000	0.000	0.000	0.000	0.000	0.000
82	A	81	ALA	0	0.014	0.020	28.180	0.001	0.001	0.000	0.000	0.000	0.000
83	A	82	THR	0	-0.069	-0.055	29.628	-0.004	-0.004	0.000	0.000	0.000	0.000
84	A	83	GLN	0	-0.056	-0.039	32.410	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	84	SER	0	-0.008	0.003	29.485	0.006	0.006	0.000	0.000	0.000	0.000
86	A	85	GLY	0	0.001	0.018	31.465	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	86	PHE	0	-0.026	-0.021	25.906	-0.006	-0.006	0.000	0.000	0.000	0.000
88	A	87	THR	0	0.004	-0.015	29.640	0.001	0.001	0.000	0.000	0.000	0.000
89	A	88	PHE	0	0.039	0.042	23.626	-0.005	-0.005	0.000	0.000	0.000	0.000
90	A	89	PRO	0	-0.024	-0.015	24.099	0.010	0.010	0.000	0.000	0.000	0.000
91	A	90	LEU	0	0.003	0.007	22.532	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	91	LEU	0	-0.035	-0.033	19.776	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	92	SER	0	-0.053	-0.051	20.260	0.014	0.014	0.000	0.000	0.000	0.000
94	A	93	ASP	-1	-0.777	-0.872	14.096	-0.033	-0.033	0.000	0.000	0.000	0.000
95	A	94	PHE	0	-0.009	-0.006	17.336	0.033	0.033	0.000	0.000	0.000	0.000
96	A	95	TRP	0	0.007	0.012	19.877	0.023	0.023	0.000	0.000	0.000	0.000
97	A	96	PRO	0	-0.020	-0.036	16.440	-0.020	-0.020	0.000	0.000	0.000	0.000
98	A	97	HIS	0	-0.043	-0.028	15.606	-0.041	-0.041	0.000	0.000	0.000	0.000
99	A	98	GLY	0	0.033	0.022	13.418	0.044	0.044	0.000	0.000	0.000	0.000
100	A	99	ALA	0	0.003	0.018	11.794	0.037	0.037	0.000	0.000	0.000	0.000
101	A	100	VAL	0	-0.010	-0.018	11.227	-0.085	-0.085	0.000	0.000	0.000	0.000
102	A	101	SER	0	-0.013	-0.051	10.552	-0.143	-0.143	0.000	0.000	0.000	0.000
103	A	102	GLN	0	-0.105	-0.069	7.458	-0.128	-0.128	0.000	0.000	0.000	0.000
104	A	103	ALA	0	-0.037	-0.002	6.327	-0.119	-0.119	0.000	0.000	0.000	0.000
105	A	104	TYR	0	-0.017	-0.043	7.412	-0.485	-0.485	0.000	0.000	0.000	0.000
106	A	105	GLY	0	0.011	0.013	3.984	-1.150	-0.931	0.003	-0.099	-0.123	0.000
107	A	106	VAL	0	-0.044	-0.041	4.008	0.597	0.893	0.005	-0.093	-0.209	0.000
108	A	107	PHE	0	-0.001	0.011	6.680	-0.187	-0.187	0.000	0.000	0.000	0.000
109	A	108	ASN	0	-0.070	-0.039	7.566	0.515	0.515	0.000	0.000	0.000	0.000
110	A	109	GLU	-1	-0.798	-0.910	8.422	0.682	0.682	0.000	0.000	0.000	0.000
111	A	110	GLN	0	-0.063	-0.023	10.247	-0.105	-0.105	0.000	0.000	0.000	0.000
112	A	111	ALA	0	-0.010	-0.004	13.531	-0.096	-0.096	0.000	0.000	0.000	0.000
113	A	112	GLY	0	0.022	0.028	14.037	-0.077	-0.077	0.000	0.000	0.000	0.000
114	A	113	ILE	0	-0.020	-0.003	13.772	-0.091	-0.091	0.000	0.000	0.000	0.000
115	A	114	ALA	0	0.045	0.025	11.239	0.135	0.135	0.000	0.000	0.000	0.000
116	A	115	ASN	0	0.024	-0.003	7.435	-0.128	-0.128	0.000	0.000	0.000	0.000
117	A	116	ARG	1	0.770	0.798	10.938	-0.336	-0.336	0.000	0.000	0.000	0.000
118	A	117	GLY	0	-0.013	0.002	10.006	-0.004	-0.004	0.000	0.000	0.000	0.000
119	A	118	THR	0	-0.048	-0.046	10.621	0.035	0.035	0.000	0.000	0.000	0.000
120	A	119	PHE	0	-0.015	-0.009	7.752	-0.058	-0.058	0.000	0.000	0.000	0.000
121	A	120	VAL	0	0.043	0.038	13.581	0.077	0.077	0.000	0.000	0.000	0.000
122	A	121	VAL	0	-0.042	-0.014	15.241	-0.082	-0.082	0.000	0.000	0.000	0.000
123	A	122	ASP	-1	-0.666	-0.791	17.414	-0.319	-0.319	0.000	0.000	0.000	0.000
124	A	123	ARG	1	0.904	0.949	20.259	0.162	0.162	0.000	0.000	0.000	0.000
125	A	124	SER	0	-0.098	-0.070	20.695	0.012	0.012	0.000	0.000	0.000	0.000
126	A	125	GLY	0	-0.042	-0.034	18.794	-0.018	-0.018	0.000	0.000	0.000	0.000
127	A	126	ILE	0	-0.054	-0.018	15.117	-0.088	-0.088	0.000	0.000	0.000	0.000
128	A	127	ILE	0	0.010	0.013	10.274	0.081	0.081	0.000	0.000	0.000	0.000
129	A	128	ARG	1	0.848	0.892	13.858	0.378	0.378	0.000	0.000	0.000	0.000
130	A	129	PHE	0	0.032	0.014	13.821	0.044	0.044	0.000	0.000	0.000	0.000
131	A	130	ALA	0	0.010	-0.003	8.711	-0.086	-0.086	0.000	0.000	0.000	0.000
132	A	131	GLU	-1	-0.788	-0.862	9.652	0.118	0.118	0.000	0.000	0.000	0.000
133	A	132	MET	0	0.007	-0.006	6.015	-0.106	-0.106	0.000	0.000	0.000	0.000
134	A	133	LYS	1	0.843	0.947	9.007	-0.029	-0.029	0.000	0.000	0.000	0.000
135	A	134	GLN	0	0.023	-0.014	8.506	0.017	0.017	0.000	0.000	0.000	0.000
136	A	135	PRO	0	0.035	0.003	12.063	-0.101	-0.101	0.000	0.000	0.000	0.000
137	A	136	GLY	0	-0.030	-0.015	15.016	-0.058	-0.058	0.000	0.000	0.000	0.000
138	A	137	GLU	-1	-0.876	-0.917	13.285	0.475	0.475	0.000	0.000	0.000	0.000
139	A	138	VAL	0	0.002	-0.019	17.075	-0.015	-0.015	0.000	0.000	0.000	0.000
140	A	139	ARG	1	0.716	0.838	14.068	-0.040	-0.040	0.000	0.000	0.000	0.000
141	A	140	ASP	-1	-0.811	-0.884	17.722	0.045	0.045	0.000	0.000	0.000	0.000
142	A	141	GLN	0	0.004	-0.022	19.572	-0.030	-0.030	0.000	0.000	0.000	0.000
143	A	142	ARG	1	0.885	0.922	21.408	-0.061	-0.061	0.000	0.000	0.000	0.000
144	A	143	LEU	0	-0.011	0.000	16.408	-0.013	-0.013	0.000	0.000	0.000	0.000
145	A	144	TRP	0	-0.040	-0.027	16.565	-0.032	-0.032	0.000	0.000	0.000	0.000
146	A	145	THR	0	0.053	0.024	19.828	-0.020	-0.020	0.000	0.000	0.000	0.000
147	A	146	ASP	-1	-0.951	-0.967	21.360	-0.089	-0.089	0.000	0.000	0.000	0.000
148	A	147	ALA	0	-0.004	-0.007	18.213	-0.016	-0.016	0.000	0.000	0.000	0.000
149	A	148	LEU	0	-0.036	-0.029	20.143	-0.022	-0.022	0.000	0.000	0.000	0.000
150	A	149	ALA	0	0.010	0.011	22.545	-0.003	-0.003	0.000	0.000	0.000	0.000
151	A	150	ALA	0	-0.027	-0.005	21.898	0.002	0.002	0.000	0.000	0.000	0.000
152	A	151	LEU	0	-0.070	-0.031	19.409	-0.017	-0.017	0.000	0.000	0.000	0.000
153	A	152	THR	0	-0.027	0.019	24.059	-0.004	-0.004	0.000	0.000	0.000	0.000

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