FMO DATABASE

FMODB ID: 43Y9N

Calculation Name: 3C1D-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3C1D

Chain ID: A

ChEMBL ID:

UniProt ID: P66000

Base Structure: X-ray

Registration Date: 2023-03-14

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	143
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1277173.917749
FMO2-HF: Nuclear repulsion	1219222.269597
FMO2-HF: Total energy	-57951.648153
FMO2-MP2: Total energy	-58122.972405

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:8:GLY)

Summations of interaction energy for fragment #1(A:8:GLY)

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.
-0.038999999999999	3.229	3.793	-3.124	-3.938	0.01

Interaction energy analysis for fragmet #1(A:8:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.099 / q_NPA : 0.049

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	10	ALA	0	-0.029	-0.010	3.818	0.200	1.555	-0.002	-0.683	-0.670	0.002
4	A	11	TYR	0	0.055	0.032	2.092	0.336	0.757	2.454	-1.144	-1.730	0.004
5	A	12	ALA	0	0.040	0.026	3.900	1.707	2.008	0.000	-0.095	-0.206	0.000
6	A	13	ARG	1	0.960	0.977	5.511	3.237	3.237	0.000	0.000	0.000	0.000
7	A	14	LEU	0	-0.006	-0.004	7.567	0.563	0.563	0.000	0.000	0.000	0.000
8	A	15	LEU	0	0.042	0.025	7.554	0.375	0.375	0.000	0.000	0.000	0.000
9	A	16	ASP	-1	-0.823	-0.878	9.346	-0.665	-0.665	0.000	0.000	0.000	0.000
10	A	17	ARG	1	0.866	0.930	11.587	1.028	1.028	0.000	0.000	0.000	0.000
11	A	18	ALA	0	0.001	0.002	12.461	0.152	0.152	0.000	0.000	0.000	0.000
12	A	19	VAL	0	0.044	0.022	12.819	0.128	0.128	0.000	0.000	0.000	0.000
13	A	20	ARG	1	0.812	0.872	14.553	0.874	0.874	0.000	0.000	0.000	0.000
14	A	21	ILE	0	-0.055	-0.016	16.367	0.072	0.072	0.000	0.000	0.000	0.000
15	A	22	LEU	0	-0.027	-0.031	16.237	0.054	0.054	0.000	0.000	0.000	0.000
16	A	23	ALA	0	-0.023	-0.004	19.159	0.042	0.042	0.000	0.000	0.000	0.000
17	A	24	VAL	0	-0.048	0.001	20.791	0.035	0.035	0.000	0.000	0.000	0.000
18	A	25	ARG	1	0.928	0.953	23.335	0.229	0.229	0.000	0.000	0.000	0.000
19	A	26	ASP	-1	-0.796	-0.870	23.414	-0.186	-0.186	0.000	0.000	0.000	0.000
20	A	27	HIS	0	-0.024	-0.005	21.240	-0.006	-0.006	0.000	0.000	0.000	0.000
21	A	28	SER	0	0.026	0.010	22.589	-0.004	-0.004	0.000	0.000	0.000	0.000
22	A	29	GLU	-1	-0.713	-0.846	17.717	-0.190	-0.190	0.000	0.000	0.000	0.000
23	A	30	GLN	0	-0.003	-0.003	19.262	-0.043	-0.043	0.000	0.000	0.000	0.000
24	A	31	GLU	-1	-0.869	-0.933	21.202	-0.204	-0.204	0.000	0.000	0.000	0.000
25	A	32	LEU	0	-0.001	0.009	14.774	-0.027	-0.027	0.000	0.000	0.000	0.000
26	A	33	ARG	1	0.761	0.817	14.925	0.151	0.151	0.000	0.000	0.000	0.000
27	A	34	ARG	1	0.865	0.922	17.698	0.153	0.153	0.000	0.000	0.000	0.000
28	A	35	LYS	1	0.845	0.919	19.191	0.300	0.300	0.000	0.000	0.000	0.000
29	A	36	LEU	0	-0.024	-0.009	12.276	-0.044	-0.044	0.000	0.000	0.000	0.000
30	A	37	ALA	0	-0.016	0.001	15.311	-0.068	-0.068	0.000	0.000	0.000	0.000
31	A	38	ALA	0	-0.023	0.009	17.444	0.025	0.025	0.000	0.000	0.000	0.000
32	A	39	PRO	0	-0.013	-0.005	18.326	-0.080	-0.080	0.000	0.000	0.000	0.000
33	A	51	ALA	0	-0.018	-0.009	7.683	-0.154	-0.154	0.000	0.000	0.000	0.000
34	A	52	THR	0	-0.045	-0.050	6.941	0.398	0.398	0.000	0.000	0.000	0.000
35	A	53	ALA	0	0.052	0.005	9.081	-0.143	-0.143	0.000	0.000	0.000	0.000
36	A	54	GLU	-1	-0.823	-0.909	6.575	1.694	1.694	0.000	0.000	0.000	0.000
37	A	55	ASP	-1	-0.828	-0.897	3.830	-2.827	-2.631	0.000	-0.101	-0.096	-0.001
38	A	56	TYR	0	0.020	-0.009	6.424	-0.220	-0.220	0.000	0.000	0.000	0.000
39	A	57	GLU	-1	-0.772	-0.842	9.818	-0.185	-0.185	0.000	0.000	0.000	0.000
40	A	58	ARG	1	0.872	0.938	2.383	-7.418	-6.423	1.341	-1.101	-1.236	0.005
41	A	59	VAL	0	-0.033	-0.014	7.186	-0.031	-0.031	0.000	0.000	0.000	0.000
42	A	60	ILE	0	0.001	0.008	9.411	0.073	0.073	0.000	0.000	0.000	0.000
43	A	61	ALA	0	0.026	0.010	11.469	0.031	0.031	0.000	0.000	0.000	0.000
44	A	62	TRP	0	0.027	0.017	9.777	-0.024	-0.024	0.000	0.000	0.000	0.000
45	A	63	CYS	0	-0.066	-0.049	12.072	0.004	0.004	0.000	0.000	0.000	0.000
46	A	64	HIS	0	-0.039	-0.036	14.781	0.027	0.027	0.000	0.000	0.000	0.000
47	A	65	GLU	-1	-0.893	-0.927	13.501	0.024	0.024	0.000	0.000	0.000	0.000
48	A	66	HIS	1	0.769	0.874	13.338	0.141	0.141	0.000	0.000	0.000	0.000
49	A	67	GLY	0	0.052	0.047	17.141	-0.012	-0.012	0.000	0.000	0.000	0.000
50	A	68	TYR	0	-0.014	-0.020	16.578	-0.010	-0.010	0.000	0.000	0.000	0.000
51	A	69	LEU	0	-0.039	-0.014	16.503	-0.018	-0.018	0.000	0.000	0.000	0.000
52	A	70	ASP	-1	-0.724	-0.860	19.893	-0.068	-0.068	0.000	0.000	0.000	0.000
53	A	71	ASP	-1	-0.812	-0.916	22.892	-0.144	-0.144	0.000	0.000	0.000	0.000
54	A	72	SER	0	-0.069	-0.039	24.916	0.007	0.007	0.000	0.000	0.000	0.000
55	A	73	ARG	1	0.855	0.919	22.549	0.162	0.162	0.000	0.000	0.000	0.000
56	A	74	PHE	0	-0.050	-0.025	25.638	0.002	0.002	0.000	0.000	0.000	0.000
57	A	75	VAL	0	-0.006	-0.017	27.780	0.001	0.001	0.000	0.000	0.000	0.000
58	A	76	ALA	0	0.056	0.037	30.527	0.003	0.003	0.000	0.000	0.000	0.000
59	A	77	ARG	1	0.872	0.921	27.622	0.127	0.127	0.000	0.000	0.000	0.000
60	A	78	PHE	0	-0.026	-0.017	31.219	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	79	ILE	0	0.056	0.021	33.197	0.002	0.002	0.000	0.000	0.000	0.000
62	A	80	ALA	0	0.081	0.060	36.098	0.002	0.002	0.000	0.000	0.000	0.000
63	A	81	SER	0	-0.092	-0.043	35.505	0.003	0.003	0.000	0.000	0.000	0.000
64	A	82	ARG	1	0.752	0.850	35.540	0.090	0.090	0.000	0.000	0.000	0.000
65	A	83	SER	0	0.046	0.017	38.598	0.003	0.003	0.000	0.000	0.000	0.000
66	A	84	ARG	1	0.916	0.960	37.103	0.081	0.081	0.000	0.000	0.000	0.000
67	A	85	LYS	1	0.874	0.940	37.272	0.100	0.100	0.000	0.000	0.000	0.000
68	A	86	GLY	0	0.024	0.026	42.743	0.000	0.000	0.000	0.000	0.000	0.000
69	A	87	TYR	0	-0.024	-0.014	41.022	0.000	0.000	0.000	0.000	0.000	0.000
70	A	88	GLY	0	0.087	0.038	42.903	0.001	0.001	0.000	0.000	0.000	0.000
71	A	89	PRO	0	0.051	0.012	40.755	-0.004	-0.004	0.000	0.000	0.000	0.000
72	A	90	ALA	0	-0.011	0.006	40.005	-0.003	-0.003	0.000	0.000	0.000	0.000
73	A	91	ARG	1	0.869	0.936	39.403	0.072	0.072	0.000	0.000	0.000	0.000
74	A	92	ILE	0	0.008	0.007	36.201	-0.006	-0.006	0.000	0.000	0.000	0.000
75	A	93	ARG	1	0.883	0.899	35.504	0.035	0.035	0.000	0.000	0.000	0.000
76	A	94	GLN	0	-0.012	0.007	34.784	-0.003	-0.003	0.000	0.000	0.000	0.000
77	A	95	GLU	-1	-0.795	-0.880	33.986	-0.094	-0.094	0.000	0.000	0.000	0.000
78	A	96	LEU	0	0.006	-0.004	30.959	-0.011	-0.011	0.000	0.000	0.000	0.000
79	A	97	ASN	0	0.023	0.019	29.929	-0.002	-0.002	0.000	0.000	0.000	0.000
80	A	98	GLN	0	-0.011	0.001	29.534	-0.010	-0.010	0.000	0.000	0.000	0.000
81	A	99	LYS	1	0.811	0.903	27.347	0.137	0.137	0.000	0.000	0.000	0.000
82	A	100	GLY	0	-0.011	0.007	25.365	-0.015	-0.015	0.000	0.000	0.000	0.000
83	A	101	ILE	0	-0.016	0.009	25.386	0.000	0.000	0.000	0.000	0.000	0.000
84	A	102	SER	0	0.009	-0.010	26.881	0.004	0.004	0.000	0.000	0.000	0.000
85	A	103	ARG	1	0.932	0.934	28.611	0.030	0.030	0.000	0.000	0.000	0.000
86	A	104	GLU	-1	-0.841	-0.905	28.736	-0.015	-0.015	0.000	0.000	0.000	0.000
87	A	105	ALA	0	0.023	0.014	28.327	0.002	0.002	0.000	0.000	0.000	0.000
88	A	106	THR	0	-0.020	-0.013	30.486	-0.004	-0.004	0.000	0.000	0.000	0.000
89	A	107	GLU	-1	-0.785	-0.864	33.168	-0.036	-0.036	0.000	0.000	0.000	0.000
90	A	108	LYS	1	0.827	0.909	31.351	0.028	0.028	0.000	0.000	0.000	0.000
91	A	109	ALA	0	0.030	0.013	32.880	0.001	0.001	0.000	0.000	0.000	0.000
92	A	110	MET	0	-0.059	-0.035	34.953	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	111	ARG	1	0.898	0.954	38.179	0.021	0.021	0.000	0.000	0.000	0.000
94	A	112	GLU	-1	-0.799	-0.889	34.813	-0.027	-0.027	0.000	0.000	0.000	0.000
95	A	113	ALA	0	-0.076	-0.021	38.172	0.000	0.000	0.000	0.000	0.000	0.000
96	A	114	ASP	-1	-0.924	-0.954	39.776	-0.027	-0.027	0.000	0.000	0.000	0.000
97	A	115	ILE	0	-0.041	-0.019	40.340	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	116	ASP	-1	-0.808	-0.898	44.337	-0.031	-0.031	0.000	0.000	0.000	0.000
99	A	117	TRP	0	-0.002	-0.041	40.417	-0.005	-0.005	0.000	0.000	0.000	0.000
100	A	118	ALA	0	0.065	0.040	47.412	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	119	ALA	0	0.007	0.012	50.599	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	120	LEU	0	-0.057	-0.027	44.916	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	121	ALA	0	-0.007	-0.006	49.110	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	122	ARG	1	0.842	0.882	50.517	0.031	0.031	0.000	0.000	0.000	0.000
105	A	123	ASP	-1	-0.792	-0.870	50.272	-0.049	-0.049	0.000	0.000	0.000	0.000
106	A	124	GLN	0	-0.033	-0.015	48.084	-0.004	-0.004	0.000	0.000	0.000	0.000
107	A	125	ALA	0	-0.025	-0.010	51.386	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	126	THR	0	0.033	0.012	54.650	-0.001	-0.001	0.000	0.000	0.000	0.000
109	A	127	ARG	1	0.803	0.904	48.415	0.052	0.052	0.000	0.000	0.000	0.000
110	A	128	LYS	1	0.850	0.947	52.805	0.048	0.048	0.000	0.000	0.000	0.000
111	A	129	TYR	0	-0.065	-0.059	54.829	0.000	0.000	0.000	0.000	0.000	0.000
112	A	130	GLY	0	0.039	0.039	58.635	0.001	0.001	0.000	0.000	0.000	0.000
113	A	131	GLU	-1	-0.775	-0.864	59.734	-0.032	-0.032	0.000	0.000	0.000	0.000
114	A	132	PRO	0	0.024	-0.009	61.978	0.000	0.000	0.000	0.000	0.000	0.000
115	A	133	LEU	0	-0.032	0.002	57.776	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	134	PRO	0	0.009	0.012	61.072	0.001	0.001	0.000	0.000	0.000	0.000
117	A	135	THR	0	-0.004	-0.010	63.060	0.000	0.000	0.000	0.000	0.000	0.000
118	A	136	VAL	0	0.019	0.032	65.523	0.001	0.001	0.000	0.000	0.000	0.000
119	A	137	PHE	0	0.055	0.018	64.106	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	138	SER	0	0.021	-0.004	63.679	-0.001	-0.001	0.000	0.000	0.000	0.000
121	A	139	GLU	-1	-0.910	-0.969	62.280	-0.032	-0.032	0.000	0.000	0.000	0.000
122	A	140	LYS	1	0.962	1.005	60.097	0.025	0.025	0.000	0.000	0.000	0.000
123	A	141	VAL	0	0.046	0.020	58.975	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	142	LYS	1	0.932	0.969	57.508	0.034	0.034	0.000	0.000	0.000	0.000
125	A	143	ILE	0	0.004	0.006	55.900	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	144	GLN	0	0.028	0.003	54.524	-0.001	-0.001	0.000	0.000	0.000	0.000
127	A	145	ARG	1	0.949	0.993	51.745	0.044	0.044	0.000	0.000	0.000	0.000
128	A	146	PHE	0	-0.048	-0.036	50.026	-0.003	-0.003	0.000	0.000	0.000	0.000
129	A	147	LEU	0	0.036	0.027	49.775	-0.003	-0.003	0.000	0.000	0.000	0.000
130	A	148	LEU	0	0.028	0.009	48.496	-0.002	-0.002	0.000	0.000	0.000	0.000
131	A	149	TYR	0	-0.055	-0.033	47.220	-0.002	-0.002	0.000	0.000	0.000	0.000
132	A	150	ARG	1	0.800	0.894	45.295	0.057	0.057	0.000	0.000	0.000	0.000
133	A	151	GLY	0	-0.002	0.001	43.557	-0.004	-0.004	0.000	0.000	0.000	0.000
134	A	152	TYR	0	-0.026	-0.009	44.577	0.000	0.000	0.000	0.000	0.000	0.000
135	A	153	LEU	0	-0.015	-0.012	44.575	0.000	0.000	0.000	0.000	0.000	0.000
136	A	154	MET	0	0.018	0.001	48.404	0.000	0.000	0.000	0.000	0.000	0.000
137	A	155	GLU	-1	-0.863	-0.939	50.259	-0.027	-0.027	0.000	0.000	0.000	0.000
138	A	156	ASP	-1	-0.819	-0.906	47.430	-0.037	-0.037	0.000	0.000	0.000	0.000
139	A	157	ILE	0	-0.075	-0.052	50.475	0.000	0.000	0.000	0.000	0.000	0.000
140	A	158	GLN	0	-0.077	-0.039	53.599	0.000	0.000	0.000	0.000	0.000	0.000
141	A	159	ASP	-1	-0.821	-0.908	55.737	-0.022	-0.022	0.000	0.000	0.000	0.000
142	A	160	ILE	0	-0.072	-0.019	54.053	0.000	0.000	0.000	0.000	0.000	0.000
143	A	161	TRP	0	-0.070	-0.049	57.083	0.001	0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:8:GLY)