FMO DATABASE

FMODB ID: 5352Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1281749.061105
FMO2-HF: Nuclear repulsion	1223796.993396
FMO2-HF: Total energy	-57952.067708
FMO2-MP2: Total energy	-58123.330064

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.
-6.269	-9.106	17.067	-7.768	-6.463	0.004

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 : 0.097 / q_NPA : 0.062

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	-0.046	0.005	3.738	1.181	2.546	0.000	-0.694	-0.671	0.002
4	A	11	TYR	0	0.039	0.018	1.853	1.209	0.756	4.221	-1.688	-2.080	0.001
5	A	12	ALA	0	0.015	0.015	3.500	1.982	2.307	0.001	-0.109	-0.217	0.000
6	A	13	ARG	1	0.929	0.948	5.345	3.886	3.991	-0.001	-0.008	-0.096	0.000
7	A	14	LEU	0	-0.013	-0.005	7.103	0.586	0.586	0.000	0.000	0.000	0.000
8	A	15	LEU	0	0.035	0.023	7.232	0.406	0.406	0.000	0.000	0.000	0.000
9	A	16	ASP	-1	-0.810	-0.864	8.959	-0.665	-0.665	0.000	0.000	0.000	0.000
10	A	17	ARG	1	0.853	0.917	11.410	1.078	1.078	0.000	0.000	0.000	0.000
11	A	18	ALA	0	0.022	0.011	11.879	0.147	0.147	0.000	0.000	0.000	0.000
12	A	19	VAL	0	0.028	0.010	12.449	0.124	0.124	0.000	0.000	0.000	0.000
13	A	20	ARG	1	0.804	0.857	14.556	0.827	0.827	0.000	0.000	0.000	0.000
14	A	21	ILE	0	-0.062	-0.019	15.733	0.061	0.061	0.000	0.000	0.000	0.000
15	A	22	LEU	0	-0.029	-0.028	15.656	0.050	0.050	0.000	0.000	0.000	0.000
16	A	23	ALA	0	-0.008	-0.001	18.730	0.042	0.042	0.000	0.000	0.000	0.000
17	A	24	VAL	0	-0.035	0.001	20.501	0.028	0.028	0.000	0.000	0.000	0.000
18	A	25	ARG	1	0.889	0.939	22.726	0.203	0.203	0.000	0.000	0.000	0.000
19	A	26	ASP	-1	-0.753	-0.840	22.658	-0.130	-0.130	0.000	0.000	0.000	0.000
20	A	27	HIS	0	-0.026	-0.013	20.859	-0.023	-0.023	0.000	0.000	0.000	0.000
21	A	28	SER	0	0.023	0.009	22.340	0.003	0.003	0.000	0.000	0.000	0.000
22	A	29	GLU	-1	-0.707	-0.850	17.284	-0.126	-0.126	0.000	0.000	0.000	0.000
23	A	30	GLN	0	-0.001	-0.001	18.701	-0.065	-0.065	0.000	0.000	0.000	0.000
24	A	31	GLU	-1	-0.867	-0.925	21.018	-0.195	-0.195	0.000	0.000	0.000	0.000
25	A	32	LEU	0	0.005	0.012	14.303	-0.034	-0.034	0.000	0.000	0.000	0.000
26	A	33	ARG	1	0.754	0.812	14.637	0.105	0.105	0.000	0.000	0.000	0.000
27	A	34	ARG	1	0.863	0.926	17.237	0.139	0.139	0.000	0.000	0.000	0.000
28	A	35	LYS	1	0.852	0.910	18.817	0.281	0.281	0.000	0.000	0.000	0.000
29	A	36	LEU	0	-0.031	-0.004	11.908	-0.055	-0.055	0.000	0.000	0.000	0.000
30	A	37	ALA	0	0.003	0.012	15.152	-0.081	-0.081	0.000	0.000	0.000	0.000
31	A	38	ALA	0	-0.004	0.014	17.007	0.014	0.014	0.000	0.000	0.000	0.000
32	A	39	PRO	0	-0.031	-0.010	17.832	-0.105	-0.105	0.000	0.000	0.000	0.000
33	A	51	ALA	0	-0.007	-0.010	6.799	-0.199	-0.199	0.000	0.000	0.000	0.000
34	A	52	THR	0	-0.034	-0.042	5.779	0.664	0.664	0.000	0.000	0.000	0.000
35	A	53	ALA	0	0.062	0.007	8.169	-0.166	-0.166	0.000	0.000	0.000	0.000
36	A	54	GLU	-1	-0.832	-0.903	5.874	2.524	2.524	0.000	0.000	0.000	0.000
37	A	55	ASP	-1	-0.809	-0.889	2.864	-7.581	-6.211	0.151	-0.801	-0.721	-0.009
38	A	56	TYR	0	0.032	0.002	5.526	-0.089	-0.089	0.000	0.000	0.000	0.000
39	A	57	GLU	-1	-0.765	-0.844	9.164	-0.089	-0.089	0.000	0.000	0.000	0.000
40	A	58	ARG	1	0.849	0.907	1.943	-12.685	-18.234	12.695	-4.468	-2.678	0.010
41	A	59	VAL	0	-0.024	-0.006	6.938	0.015	0.015	0.000	0.000	0.000	0.000
42	A	60	ILE	0	-0.008	0.003	9.127	0.071	0.071	0.000	0.000	0.000	0.000
43	A	61	ALA	0	0.012	0.006	11.133	0.024	0.024	0.000	0.000	0.000	0.000
44	A	62	TRP	0	0.040	0.017	9.698	-0.086	-0.086	0.000	0.000	0.000	0.000
45	A	63	CYS	0	-0.059	-0.047	11.793	-0.043	-0.043	0.000	0.000	0.000	0.000
46	A	64	HIS	0	-0.043	-0.030	14.308	0.006	0.006	0.000	0.000	0.000	0.000
47	A	65	GLU	-1	-0.889	-0.924	13.140	0.296	0.296	0.000	0.000	0.000	0.000
48	A	66	HIS	1	0.774	0.877	13.323	-0.100	-0.100	0.000	0.000	0.000	0.000
49	A	67	GLY	0	0.030	0.034	17.189	-0.029	-0.029	0.000	0.000	0.000	0.000
50	A	68	TYR	0	0.016	-0.002	16.156	-0.020	-0.020	0.000	0.000	0.000	0.000
51	A	69	LEU	0	-0.043	-0.018	16.013	-0.031	-0.031	0.000	0.000	0.000	0.000
52	A	70	ASP	-1	-0.694	-0.853	19.168	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	71	ASP	-1	-0.814	-0.914	21.714	-0.109	-0.109	0.000	0.000	0.000	0.000
54	A	72	SER	0	-0.065	-0.039	24.257	0.004	0.004	0.000	0.000	0.000	0.000
55	A	73	ARG	1	0.811	0.895	22.123	0.088	0.088	0.000	0.000	0.000	0.000
56	A	74	PHE	0	-0.044	-0.012	25.167	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	75	VAL	0	-0.007	-0.008	27.263	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	76	ALA	0	0.060	0.037	30.005	0.000	0.000	0.000	0.000	0.000	0.000
59	A	77	ARG	1	0.870	0.913	27.460	0.080	0.080	0.000	0.000	0.000	0.000
60	A	78	PHE	0	-0.031	-0.019	30.672	-0.004	-0.004	0.000	0.000	0.000	0.000
61	A	79	ILE	0	0.053	0.024	32.602	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	80	ALA	0	0.067	0.057	35.267	0.001	0.001	0.000	0.000	0.000	0.000
63	A	81	SER	0	-0.092	-0.029	34.568	0.000	0.000	0.000	0.000	0.000	0.000
64	A	82	ARG	1	0.742	0.844	35.129	0.075	0.075	0.000	0.000	0.000	0.000
65	A	83	SER	0	0.043	0.012	38.110	0.001	0.001	0.000	0.000	0.000	0.000
66	A	84	ARG	1	0.918	0.942	36.850	0.057	0.057	0.000	0.000	0.000	0.000
67	A	85	LYS	1	0.891	0.956	36.531	0.085	0.085	0.000	0.000	0.000	0.000
68	A	86	GLY	0	0.019	0.018	42.070	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	87	TYR	0	-0.011	-0.006	40.741	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	88	GLY	0	0.078	0.032	42.701	0.002	0.002	0.000	0.000	0.000	0.000
71	A	89	PRO	0	0.021	0.004	40.597	-0.004	-0.004	0.000	0.000	0.000	0.000
72	A	90	ALA	0	-0.002	0.010	39.763	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	91	ARG	1	0.858	0.923	39.093	0.065	0.065	0.000	0.000	0.000	0.000
74	A	92	ILE	0	0.004	0.011	35.856	-0.006	-0.006	0.000	0.000	0.000	0.000
75	A	93	ARG	1	0.876	0.903	35.077	0.022	0.022	0.000	0.000	0.000	0.000
76	A	94	GLN	0	-0.011	0.004	34.362	-0.003	-0.003	0.000	0.000	0.000	0.000
77	A	95	GLU	-1	-0.775	-0.867	33.674	-0.085	-0.085	0.000	0.000	0.000	0.000
78	A	96	LEU	0	0.004	0.003	30.457	-0.011	-0.011	0.000	0.000	0.000	0.000
79	A	97	ASN	0	0.025	0.018	29.506	0.001	0.001	0.000	0.000	0.000	0.000
80	A	98	GLN	0	-0.024	-0.008	29.404	-0.011	-0.011	0.000	0.000	0.000	0.000
81	A	99	LYS	1	0.820	0.904	26.989	0.124	0.124	0.000	0.000	0.000	0.000
82	A	100	GLY	0	-0.001	0.017	25.317	-0.012	-0.012	0.000	0.000	0.000	0.000
83	A	101	ILE	0	-0.040	-0.009	25.338	0.004	0.004	0.000	0.000	0.000	0.000
84	A	102	SER	0	0.005	-0.016	26.393	0.003	0.003	0.000	0.000	0.000	0.000
85	A	103	ARG	1	0.924	0.936	28.122	0.014	0.014	0.000	0.000	0.000	0.000
86	A	104	GLU	-1	-0.811	-0.879	29.050	0.006	0.006	0.000	0.000	0.000	0.000
87	A	105	ALA	0	0.022	0.009	28.022	0.002	0.002	0.000	0.000	0.000	0.000
88	A	106	THR	0	-0.024	-0.023	30.175	-0.005	-0.005	0.000	0.000	0.000	0.000
89	A	107	GLU	-1	-0.778	-0.855	32.782	-0.019	-0.019	0.000	0.000	0.000	0.000
90	A	108	LYS	1	0.807	0.898	30.626	-0.009	-0.009	0.000	0.000	0.000	0.000
91	A	109	ALA	0	0.031	0.015	32.425	0.000	0.000	0.000	0.000	0.000	0.000
92	A	110	MET	0	-0.063	-0.041	34.512	-0.004	-0.004	0.000	0.000	0.000	0.000
93	A	111	ARG	1	0.900	0.966	37.624	0.003	0.003	0.000	0.000	0.000	0.000
94	A	112	GLU	-1	-0.788	-0.884	34.125	0.007	0.007	0.000	0.000	0.000	0.000
95	A	113	ALA	0	-0.066	-0.031	37.464	0.000	0.000	0.000	0.000	0.000	0.000
96	A	114	ASP	-1	-0.937	-0.961	39.130	-0.010	-0.010	0.000	0.000	0.000	0.000
97	A	115	ILE	0	-0.037	-0.013	39.666	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	116	ASP	-1	-0.788	-0.885	43.669	-0.019	-0.019	0.000	0.000	0.000	0.000
99	A	117	TRP	0	-0.004	-0.037	39.705	-0.006	-0.006	0.000	0.000	0.000	0.000
100	A	118	ALA	0	0.074	0.046	46.609	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	119	ALA	0	-0.008	0.005	49.844	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	120	LEU	0	-0.061	-0.031	44.137	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	121	ALA	0	0.006	0.002	48.352	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	122	ARG	1	0.805	0.854	49.991	0.022	0.022	0.000	0.000	0.000	0.000
105	A	123	ASP	-1	-0.798	-0.864	49.355	-0.039	-0.039	0.000	0.000	0.000	0.000
106	A	124	GLN	0	-0.040	-0.022	47.341	-0.005	-0.005	0.000	0.000	0.000	0.000
107	A	125	ALA	0	-0.011	0.002	50.693	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	126	THR	0	0.036	0.009	54.069	-0.001	-0.001	0.000	0.000	0.000	0.000
109	A	127	ARG	1	0.798	0.882	48.070	0.041	0.041	0.000	0.000	0.000	0.000
110	A	128	LYS	1	0.865	0.956	52.212	0.042	0.042	0.000	0.000	0.000	0.000
111	A	129	TYR	0	-0.099	-0.072	54.259	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	130	GLY	0	0.030	0.030	58.189	0.001	0.001	0.000	0.000	0.000	0.000
113	A	131	GLU	-1	-0.742	-0.858	59.364	-0.024	-0.024	0.000	0.000	0.000	0.000
114	A	132	PRO	0	0.009	-0.007	61.525	0.000	0.000	0.000	0.000	0.000	0.000
115	A	133	LEU	0	-0.024	0.011	57.191	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	134	PRO	0	-0.021	-0.007	60.517	0.001	0.001	0.000	0.000	0.000	0.000
117	A	135	THR	0	0.020	0.013	62.382	0.000	0.000	0.000	0.000	0.000	0.000
118	A	136	VAL	0	0.016	0.026	64.973	0.001	0.001	0.000	0.000	0.000	0.000
119	A	137	PHE	0	0.066	0.018	63.379	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	138	SER	0	0.014	-0.020	63.032	0.000	0.000	0.000	0.000	0.000	0.000
121	A	139	GLU	-1	-0.826	-0.877	61.574	-0.030	-0.030	0.000	0.000	0.000	0.000
122	A	140	LYS	1	0.917	0.988	59.369	0.020	0.020	0.000	0.000	0.000	0.000
123	A	141	VAL	0	0.054	0.023	58.394	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	142	LYS	1	0.817	0.890	56.882	0.030	0.030	0.000	0.000	0.000	0.000
125	A	143	ILE	0	0.006	0.018	55.330	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	144	GLN	0	0.033	0.002	53.875	-0.001	-0.001	0.000	0.000	0.000	0.000
127	A	145	ARG	1	0.955	0.982	51.549	0.042	0.042	0.000	0.000	0.000	0.000
128	A	146	PHE	0	-0.034	-0.023	49.269	-0.003	-0.003	0.000	0.000	0.000	0.000
129	A	147	LEU	0	0.027	0.023	49.066	-0.003	-0.003	0.000	0.000	0.000	0.000
130	A	148	LEU	0	0.045	0.022	47.735	-0.001	-0.001	0.000	0.000	0.000	0.000
131	A	149	TYR	0	-0.038	-0.017	46.445	-0.002	-0.002	0.000	0.000	0.000	0.000
132	A	150	ARG	1	0.803	0.893	44.520	0.049	0.049	0.000	0.000	0.000	0.000
133	A	151	GLY	0	-0.001	-0.014	43.038	-0.002	-0.002	0.000	0.000	0.000	0.000
134	A	152	TYR	0	-0.029	-0.008	44.050	0.001	0.001	0.000	0.000	0.000	0.000
135	A	153	LEU	0	-0.012	-0.012	44.304	-0.001	-0.001	0.000	0.000	0.000	0.000
136	A	154	MET	0	0.009	-0.010	47.930	-0.001	-0.001	0.000	0.000	0.000	0.000
137	A	155	GLU	-1	-0.854	-0.936	49.295	-0.019	-0.019	0.000	0.000	0.000	0.000
138	A	156	ASP	-1	-0.811	-0.906	46.790	-0.026	-0.026	0.000	0.000	0.000	0.000
139	A	157	ILE	0	-0.058	-0.039	49.964	0.000	0.000	0.000	0.000	0.000	0.000
140	A	158	GLN	0	-0.091	-0.055	53.043	0.000	0.000	0.000	0.000	0.000	0.000
141	A	159	ASP	-1	-0.792	-0.888	55.553	-0.014	-0.014	0.000	0.000	0.000	0.000
142	A	160	ILE	0	-0.060	-0.007	53.566	0.000	0.000	0.000	0.000	0.000	0.000
143	A	161	TRP	0	-0.057	-0.054	56.673	0.000	0.000	0.000	0.000	0.000	0.000

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