FMO DATABASE

FMODB ID: 1N54Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1489763.045633
FMO2-HF: Nuclear repulsion	1431285.623389
FMO2-HF: Total energy	-58477.422244
FMO2-MP2: Total energy	-58650.42153

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.
-0.762	1.07	0.014	-0.729	-1.117	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 : -0.030 / q_NPA : -0.031

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	-0.033	0.000	3.740	-1.484	-0.334	0.002	-0.477	-0.675	0.001
4	A	3	ASN	0	0.016	-0.008	4.445	1.066	1.160	-0.001	-0.002	-0.090	0.000
5	A	4	VAL	0	0.014	0.007	7.779	0.037	0.037	0.000	0.000	0.000	0.000
6	A	5	GLY	0	-0.019	-0.002	11.589	0.023	0.023	0.000	0.000	0.000	0.000
7	A	6	ALA	0	-0.012	0.003	9.589	0.035	0.035	0.000	0.000	0.000	0.000
8	A	7	THR	0	-0.032	-0.027	11.709	0.144	0.144	0.000	0.000	0.000	0.000
9	A	8	ALA	0	0.018	0.015	12.369	-0.172	-0.172	0.000	0.000	0.000	0.000
10	A	9	PRO	0	-0.018	-0.007	9.870	0.119	0.119	0.000	0.000	0.000	0.000
11	A	10	ASP	-1	-0.768	-0.863	13.071	-0.277	-0.277	0.000	0.000	0.000	0.000
12	A	11	PHE	0	0.006	0.005	15.014	-0.012	-0.012	0.000	0.000	0.000	0.000
13	A	12	THR	0	0.014	0.004	17.451	0.016	0.016	0.000	0.000	0.000	0.000
14	A	13	LEU	0	-0.005	0.017	16.815	0.003	0.003	0.000	0.000	0.000	0.000
15	A	14	ARG	1	0.897	0.941	21.181	0.084	0.084	0.000	0.000	0.000	0.000
16	A	15	ASP	-1	-0.717	-0.849	23.276	-0.055	-0.055	0.000	0.000	0.000	0.000
17	A	16	GLN	0	0.085	0.038	25.432	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	17	ASN	0	-0.071	-0.037	27.649	0.014	0.014	0.000	0.000	0.000	0.000
19	A	18	GLN	0	-0.047	-0.018	28.044	0.000	0.000	0.000	0.000	0.000	0.000
20	A	19	GLN	0	-0.020	-0.007	29.072	-0.010	-0.010	0.000	0.000	0.000	0.000
21	A	20	LEU	0	-0.040	-0.020	25.089	-0.001	-0.001	0.000	0.000	0.000	0.000
22	A	21	VAL	0	0.022	0.017	22.753	0.001	0.001	0.000	0.000	0.000	0.000
23	A	22	THR	0	-0.006	-0.027	21.500	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	23	LEU	0	0.000	0.021	16.285	0.015	0.015	0.000	0.000	0.000	0.000
25	A	24	ARG	1	0.838	0.875	20.033	0.357	0.357	0.000	0.000	0.000	0.000
26	A	25	GLY	0	-0.028	-0.010	22.287	0.010	0.010	0.000	0.000	0.000	0.000
27	A	26	TYR	0	0.031	0.016	22.682	0.024	0.024	0.000	0.000	0.000	0.000
28	A	27	ARG	1	0.904	0.968	17.929	0.422	0.422	0.000	0.000	0.000	0.000
29	A	28	GLY	0	-0.052	-0.023	24.627	0.017	0.017	0.000	0.000	0.000	0.000
30	A	29	ALA	0	-0.039	-0.022	27.568	0.012	0.012	0.000	0.000	0.000	0.000
31	A	30	LYS	1	0.798	0.880	25.994	0.126	0.126	0.000	0.000	0.000	0.000
32	A	31	ASN	0	-0.013	-0.005	22.162	-0.044	-0.044	0.000	0.000	0.000	0.000
33	A	32	VAL	0	-0.020	-0.025	19.408	0.023	0.023	0.000	0.000	0.000	0.000
34	A	33	LEU	0	0.032	0.031	17.585	-0.044	-0.044	0.000	0.000	0.000	0.000
35	A	34	LEU	0	-0.049	-0.023	14.266	0.012	0.012	0.000	0.000	0.000	0.000
36	A	35	VAL	0	0.034	0.001	15.161	-0.011	-0.011	0.000	0.000	0.000	0.000
37	A	36	PHE	0	0.032	0.020	12.113	0.016	0.016	0.000	0.000	0.000	0.000
38	A	37	HIS	0	0.000	-0.063	14.293	0.015	0.015	0.000	0.000	0.000	0.000
39	A	38	PRO	0	-0.015	0.009	14.753	-0.017	-0.017	0.000	0.000	0.000	0.000
40	A	39	LEU	0	0.048	-0.008	16.491	-0.014	-0.014	0.000	0.000	0.000	0.000
41	A	40	ALA	0	0.051	0.025	20.176	-0.005	-0.005	0.000	0.000	0.000	0.000
42	A	41	PHE	0	-0.026	-0.022	23.411	0.007	0.007	0.000	0.000	0.000	0.000
43	A	42	THR	0	-0.025	0.002	21.703	0.010	0.010	0.000	0.000	0.000	0.000
44	A	43	GLY	0	0.029	0.003	24.085	-0.006	-0.006	0.000	0.000	0.000	0.000
45	A	44	ILE	0	0.005	0.006	19.627	-0.012	-0.012	0.000	0.000	0.000	0.000
46	A	45	CYM	-1	-0.840	-0.736	19.389	0.182	0.182	0.000	0.000	0.000	0.000
47	A	46	GLN	0	-0.056	-0.021	21.251	-0.015	-0.015	0.000	0.000	0.000	0.000
48	A	47	GLY	0	0.033	0.018	24.654	-0.012	-0.012	0.000	0.000	0.000	0.000
49	A	48	GLU	-1	-0.752	-0.845	17.865	0.152	0.152	0.000	0.000	0.000	0.000
50	A	49	LEU	0	0.007	0.006	20.623	-0.021	-0.021	0.000	0.000	0.000	0.000
51	A	50	ASP	-1	-0.803	-0.879	23.819	0.036	0.036	0.000	0.000	0.000	0.000
52	A	51	GLN	0	-0.007	0.009	24.429	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	52	LEU	0	-0.019	-0.006	21.471	-0.010	-0.010	0.000	0.000	0.000	0.000
54	A	53	ARG	1	0.702	0.791	25.160	-0.037	-0.037	0.000	0.000	0.000	0.000
55	A	54	ASP	-1	-0.865	-0.899	28.515	0.017	0.017	0.000	0.000	0.000	0.000
56	A	55	HIS	0	-0.040	-0.016	27.585	0.002	0.002	0.000	0.000	0.000	0.000
57	A	56	LEU	0	-0.012	0.014	27.081	-0.008	-0.008	0.000	0.000	0.000	0.000
58	A	57	PRO	0	0.013	-0.006	28.441	-0.010	-0.010	0.000	0.000	0.000	0.000
59	A	58	GLU	-1	-0.915	-0.954	27.414	-0.028	-0.028	0.000	0.000	0.000	0.000
60	A	59	PHE	0	-0.050	-0.038	22.847	-0.012	-0.012	0.000	0.000	0.000	0.000
61	A	60	GLU	-1	-0.978	-0.991	25.475	-0.085	-0.085	0.000	0.000	0.000	0.000
62	A	61	ASN	0	0.005	-0.006	28.053	0.001	0.001	0.000	0.000	0.000	0.000
63	A	62	ASP	-1	-0.880	-0.945	30.217	-0.084	-0.084	0.000	0.000	0.000	0.000
64	A	63	ASP	-1	-0.809	-0.845	27.821	-0.135	-0.135	0.000	0.000	0.000	0.000
65	A	64	SER	0	-0.008	-0.002	24.786	-0.024	-0.024	0.000	0.000	0.000	0.000
66	A	65	ALA	0	0.016	0.008	24.297	0.014	0.014	0.000	0.000	0.000	0.000
67	A	66	ALA	0	0.038	0.022	21.720	-0.018	-0.018	0.000	0.000	0.000	0.000
68	A	67	LEU	0	-0.042	-0.018	19.327	0.007	0.007	0.000	0.000	0.000	0.000
69	A	68	ALA	0	0.046	0.037	18.803	-0.010	-0.010	0.000	0.000	0.000	0.000
70	A	69	ILE	0	-0.051	-0.025	15.259	-0.015	-0.015	0.000	0.000	0.000	0.000
71	A	70	SER	0	0.016	-0.001	16.642	0.040	0.040	0.000	0.000	0.000	0.000
72	A	71	VAL	0	0.008	0.005	15.534	-0.033	-0.033	0.000	0.000	0.000	0.000
73	A	72	GLY	0	0.031	0.028	18.202	-0.005	-0.005	0.000	0.000	0.000	0.000
74	A	73	PRO	0	-0.013	0.005	22.031	-0.019	-0.019	0.000	0.000	0.000	0.000
75	A	74	PRO	0	0.050	0.014	24.465	0.006	0.006	0.000	0.000	0.000	0.000
76	A	75	PRO	0	0.019	-0.002	26.615	0.003	0.003	0.000	0.000	0.000	0.000
77	A	76	THR	0	0.018	0.011	25.512	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	77	HIS	0	0.008	0.002	20.901	0.025	0.025	0.000	0.000	0.000	0.000
79	A	78	LYS	1	0.871	0.953	26.452	0.017	0.017	0.000	0.000	0.000	0.000
80	A	79	ILE	0	0.003	0.009	30.089	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	80	TRP	0	0.025	0.010	22.621	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	81	ALA	0	0.019	0.020	27.945	0.001	0.001	0.000	0.000	0.000	0.000
83	A	82	THR	0	-0.090	-0.065	29.434	-0.004	-0.004	0.000	0.000	0.000	0.000
84	A	83	GLN	0	-0.051	-0.040	32.326	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	84	SER	0	-0.004	0.009	29.298	0.006	0.006	0.000	0.000	0.000	0.000
86	A	85	GLY	0	0.003	0.019	31.257	0.000	0.000	0.000	0.000	0.000	0.000
87	A	86	PHE	0	-0.018	-0.020	25.880	-0.006	-0.006	0.000	0.000	0.000	0.000
88	A	87	THR	0	0.009	-0.010	29.466	0.000	0.000	0.000	0.000	0.000	0.000
89	A	88	PHE	0	0.039	0.040	23.723	-0.006	-0.006	0.000	0.000	0.000	0.000
90	A	89	PRO	0	-0.013	-0.009	23.760	0.009	0.009	0.000	0.000	0.000	0.000
91	A	90	LEU	0	0.015	0.004	22.492	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	91	LEU	0	-0.023	-0.016	19.356	0.003	0.003	0.000	0.000	0.000	0.000
93	A	92	SER	0	-0.010	-0.032	19.780	0.014	0.014	0.000	0.000	0.000	0.000
94	A	93	ASP	-1	-0.772	-0.854	13.752	-0.064	-0.064	0.000	0.000	0.000	0.000
95	A	94	PHE	0	-0.023	-0.017	16.943	0.029	0.029	0.000	0.000	0.000	0.000
96	A	95	TRP	0	0.000	-0.006	19.411	0.016	0.016	0.000	0.000	0.000	0.000
97	A	96	PRO	0	-0.026	-0.020	16.284	-0.017	-0.017	0.000	0.000	0.000	0.000
98	A	97	HIS	0	-0.041	-0.037	15.369	-0.043	-0.043	0.000	0.000	0.000	0.000
99	A	98	GLY	0	0.028	0.022	13.229	0.034	0.034	0.000	0.000	0.000	0.000
100	A	99	ALA	0	0.023	0.024	11.504	0.031	0.031	0.000	0.000	0.000	0.000
101	A	100	VAL	0	-0.028	-0.023	10.966	-0.121	-0.121	0.000	0.000	0.000	0.000
102	A	101	SER	0	-0.007	-0.041	10.295	-0.138	-0.138	0.000	0.000	0.000	0.000
103	A	102	GLN	0	-0.101	-0.065	7.091	0.000	0.000	0.000	0.000	0.000	0.000
104	A	103	ALA	0	-0.036	-0.008	6.048	-0.254	-0.254	0.000	0.000	0.000	0.000
105	A	104	TYR	0	-0.016	-0.040	7.348	-0.487	-0.487	0.000	0.000	0.000	0.000
106	A	105	GLY	0	0.006	0.011	3.845	-1.293	-1.007	0.009	-0.141	-0.155	0.000
107	A	106	VAL	0	-0.027	-0.034	4.105	1.017	1.319	0.004	-0.109	-0.197	0.000
108	A	107	PHE	0	0.008	0.015	6.862	-0.177	-0.177	0.000	0.000	0.000	0.000
109	A	108	ASN	0	-0.056	-0.036	7.599	0.551	0.551	0.000	0.000	0.000	0.000
110	A	109	GLU	-1	-0.797	-0.903	8.106	0.484	0.484	0.000	0.000	0.000	0.000
111	A	110	GLN	0	-0.057	-0.027	9.813	-0.099	-0.099	0.000	0.000	0.000	0.000
112	A	111	ALA	0	-0.020	-0.008	13.357	-0.086	-0.086	0.000	0.000	0.000	0.000
113	A	112	GLY	0	0.012	0.023	14.073	-0.066	-0.066	0.000	0.000	0.000	0.000
114	A	113	ILE	0	-0.024	-0.003	13.722	-0.086	-0.086	0.000	0.000	0.000	0.000
115	A	114	ALA	0	0.040	0.021	11.593	0.131	0.131	0.000	0.000	0.000	0.000
116	A	115	ASN	0	0.007	-0.006	7.951	-0.141	-0.141	0.000	0.000	0.000	0.000
117	A	116	ARG	1	0.774	0.780	11.168	-0.364	-0.364	0.000	0.000	0.000	0.000
118	A	117	GLY	0	-0.019	-0.003	10.030	0.014	0.014	0.000	0.000	0.000	0.000
119	A	118	THR	0	-0.042	-0.046	10.696	0.004	0.004	0.000	0.000	0.000	0.000
120	A	119	PHE	0	-0.035	-0.016	7.791	-0.068	-0.068	0.000	0.000	0.000	0.000
121	A	120	VAL	0	0.034	0.029	13.631	0.071	0.071	0.000	0.000	0.000	0.000
122	A	121	VAL	0	-0.025	-0.003	15.337	-0.072	-0.072	0.000	0.000	0.000	0.000
123	A	122	ASP	-1	-0.676	-0.793	17.627	-0.299	-0.299	0.000	0.000	0.000	0.000
124	A	123	ARG	1	0.906	0.940	20.617	0.142	0.142	0.000	0.000	0.000	0.000
125	A	124	SER	0	-0.104	-0.062	20.785	0.001	0.001	0.000	0.000	0.000	0.000
126	A	125	GLY	0	0.003	-0.010	19.039	-0.008	-0.008	0.000	0.000	0.000	0.000
127	A	126	ILE	0	-0.065	-0.025	15.323	-0.084	-0.084	0.000	0.000	0.000	0.000
128	A	127	ILE	0	0.010	0.010	10.451	0.073	0.073	0.000	0.000	0.000	0.000
129	A	128	ARG	1	0.839	0.891	14.120	0.342	0.342	0.000	0.000	0.000	0.000
130	A	129	PHE	0	0.046	0.019	14.177	0.034	0.034	0.000	0.000	0.000	0.000
131	A	130	ALA	0	0.002	-0.005	9.134	-0.081	-0.081	0.000	0.000	0.000	0.000
132	A	131	GLU	-1	-0.777	-0.858	9.960	0.159	0.159	0.000	0.000	0.000	0.000
133	A	132	MET	0	-0.008	-0.003	6.167	-0.041	-0.041	0.000	0.000	0.000	0.000
134	A	133	LYS	1	0.851	0.938	9.045	-0.186	-0.186	0.000	0.000	0.000	0.000
135	A	134	GLN	0	0.030	-0.006	8.977	0.051	0.051	0.000	0.000	0.000	0.000
136	A	135	PRO	0	0.032	-0.003	12.177	-0.103	-0.103	0.000	0.000	0.000	0.000
137	A	136	GLY	0	-0.021	-0.003	15.143	-0.061	-0.061	0.000	0.000	0.000	0.000
138	A	137	GLU	-1	-0.877	-0.921	13.317	0.488	0.488	0.000	0.000	0.000	0.000
139	A	138	VAL	0	0.004	-0.022	17.150	-0.018	-0.018	0.000	0.000	0.000	0.000
140	A	139	ARG	1	0.709	0.830	14.057	-0.090	-0.090	0.000	0.000	0.000	0.000
141	A	140	ASP	-1	-0.802	-0.871	17.851	0.050	0.050	0.000	0.000	0.000	0.000
142	A	141	GLN	0	0.011	-0.019	19.815	-0.030	-0.030	0.000	0.000	0.000	0.000
143	A	142	ARG	1	0.868	0.906	21.206	-0.073	-0.073	0.000	0.000	0.000	0.000
144	A	143	LEU	0	-0.020	-0.005	16.783	-0.013	-0.013	0.000	0.000	0.000	0.000
145	A	144	TRP	0	-0.026	-0.021	16.490	-0.033	-0.033	0.000	0.000	0.000	0.000
146	A	145	THR	0	0.036	0.018	20.035	-0.019	-0.019	0.000	0.000	0.000	0.000
147	A	146	ASP	-1	-0.935	-0.959	21.841	-0.072	-0.072	0.000	0.000	0.000	0.000
148	A	147	ALA	0	-0.002	-0.010	18.524	-0.015	-0.015	0.000	0.000	0.000	0.000
149	A	148	LEU	0	-0.029	-0.020	20.451	-0.026	-0.026	0.000	0.000	0.000	0.000
150	A	149	ALA	0	0.011	0.008	22.956	-0.004	-0.004	0.000	0.000	0.000	0.000
151	A	150	ALA	0	-0.043	-0.017	22.018	0.000	0.000	0.000	0.000	0.000	0.000
152	A	151	LEU	0	-0.082	-0.036	19.826	-0.021	-0.021	0.000	0.000	0.000	0.000
153	A	152	THR	0	-0.090	-0.060	24.453	-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)