FMO DATABASE

FMODB ID: LL2Z9

Calculation Name: 3C1D-A-Xray308

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	146
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1283964.709847
FMO2-HF: Nuclear repulsion	1225823.557918
FMO2-HF: Total energy	-58141.151929
FMO2-MP2: Total energy	-58313.110872

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.
0.952	4.468	2.165	-2.412	-3.27	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 : 0.097 / q_NPA : 0.045

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	0.005	0.003	3.826	0.100	1.438	0.000	-0.679	-0.660	0.002
4	A	11	TYR	0	0.032	0.023	2.260	0.216	0.789	1.993	-0.973	-1.593	0.004
5	A	12	ALA	0	0.042	0.023	3.782	1.697	1.990	0.001	-0.091	-0.203	0.000
6	A	13	ARG	1	0.912	0.963	5.419	3.367	3.367	0.000	0.000	0.000	0.000
7	A	14	LEU	0	-0.015	-0.010	7.498	0.577	0.577	0.000	0.000	0.000	0.000
8	A	15	LEU	0	0.027	0.021	7.418	0.380	0.380	0.000	0.000	0.000	0.000
9	A	16	ASP	-1	-0.844	-0.909	9.242	-0.614	-0.614	0.000	0.000	0.000	0.000
10	A	17	ARG	1	0.900	0.948	11.494	1.045	1.045	0.000	0.000	0.000	0.000
11	A	18	ALA	0	0.004	0.005	12.389	0.152	0.152	0.000	0.000	0.000	0.000
12	A	19	VAL	0	0.043	0.018	12.642	0.130	0.130	0.000	0.000	0.000	0.000
13	A	20	ARG	1	0.850	0.916	14.544	0.845	0.845	0.000	0.000	0.000	0.000
14	A	21	ILE	0	-0.072	-0.025	16.562	0.074	0.074	0.000	0.000	0.000	0.000
15	A	22	LEU	0	-0.021	-0.029	16.242	0.053	0.053	0.000	0.000	0.000	0.000
16	A	23	ALA	0	-0.013	0.003	19.060	0.042	0.042	0.000	0.000	0.000	0.000
17	A	24	VAL	0	-0.054	-0.005	20.708	0.036	0.036	0.000	0.000	0.000	0.000
18	A	25	ARG	1	0.924	0.952	23.232	0.231	0.231	0.000	0.000	0.000	0.000
19	A	26	ASP	-1	-0.838	-0.906	23.315	-0.190	-0.190	0.000	0.000	0.000	0.000
20	A	27	HIS	0	-0.025	-0.004	21.323	-0.011	-0.011	0.000	0.000	0.000	0.000
21	A	28	SER	0	0.015	-0.003	22.672	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	29	GLU	-1	-0.729	-0.867	17.825	-0.212	-0.212	0.000	0.000	0.000	0.000
23	A	30	GLN	0	-0.022	-0.016	19.324	-0.039	-0.039	0.000	0.000	0.000	0.000
24	A	31	GLU	-1	-0.871	-0.922	21.264	-0.215	-0.215	0.000	0.000	0.000	0.000
25	A	32	LEU	0	0.004	0.012	14.897	-0.028	-0.028	0.000	0.000	0.000	0.000
26	A	33	ARG	1	0.809	0.877	15.306	0.187	0.187	0.000	0.000	0.000	0.000
27	A	34	ARG	1	0.882	0.938	17.761	0.169	0.169	0.000	0.000	0.000	0.000
28	A	35	LYS	1	0.848	0.918	19.362	0.313	0.313	0.000	0.000	0.000	0.000
29	A	36	LEU	0	-0.030	-0.016	12.311	-0.044	-0.044	0.000	0.000	0.000	0.000
30	A	37	ALA	0	-0.030	-0.011	15.388	-0.064	-0.064	0.000	0.000	0.000	0.000
31	A	38	ALA	0	-0.029	0.001	17.508	0.027	0.027	0.000	0.000	0.000	0.000
32	A	39	PRO	0	-0.007	-0.008	18.410	-0.053	-0.053	0.000	0.000	0.000	0.000
33	A	40	NME	0	-0.013	0.005	18.919	-0.048	-0.048	0.000	0.000	0.000	0.000
34	A	50	ACE	0	0.033	0.005	10.234	0.052	0.052	0.000	0.000	0.000	0.000
35	A	51	ALA	0	-0.030	-0.031	7.699	-0.494	-0.494	0.000	0.000	0.000	0.000
36	A	52	THR	0	0.009	0.016	6.801	0.424	0.424	0.000	0.000	0.000	0.000
37	A	53	ALA	0	0.046	0.003	9.068	-0.143	-0.143	0.000	0.000	0.000	0.000
38	A	54	GLU	-1	-0.881	-0.946	7.388	1.157	1.157	0.000	0.000	0.000	0.000
39	A	55	ASP	-1	-0.846	-0.919	4.098	-2.561	-2.409	0.000	-0.056	-0.096	0.000
40	A	56	TYR	0	0.007	-0.016	6.427	-0.159	-0.159	0.000	0.000	0.000	0.000
41	A	57	GLU	-1	-0.801	-0.880	9.851	-0.202	-0.202	0.000	0.000	0.000	0.000
42	A	58	ARG	1	0.952	0.984	2.743	-6.106	-4.946	0.171	-0.613	-0.718	0.004
43	A	59	VAL	0	-0.029	-0.012	7.238	-0.005	-0.005	0.000	0.000	0.000	0.000
44	A	60	ILE	0	-0.014	-0.001	9.482	0.092	0.092	0.000	0.000	0.000	0.000
45	A	61	ALA	0	0.037	0.012	11.476	0.042	0.042	0.000	0.000	0.000	0.000
46	A	62	TRP	0	0.026	0.019	9.878	-0.004	-0.004	0.000	0.000	0.000	0.000
47	A	63	CYS	0	-0.057	-0.047	12.022	0.019	0.019	0.000	0.000	0.000	0.000
48	A	64	HIS	0	-0.039	-0.031	14.711	0.039	0.039	0.000	0.000	0.000	0.000
49	A	65	GLU	-1	-0.964	-0.965	14.079	0.089	0.089	0.000	0.000	0.000	0.000
50	A	66	HIS	1	0.833	0.914	13.192	0.153	0.153	0.000	0.000	0.000	0.000
51	A	67	GLY	0	0.052	0.047	17.106	-0.011	-0.011	0.000	0.000	0.000	0.000
52	A	68	TYR	0	-0.002	-0.015	16.532	-0.009	-0.009	0.000	0.000	0.000	0.000
53	A	69	LEU	0	-0.053	-0.019	16.588	-0.019	-0.019	0.000	0.000	0.000	0.000
54	A	70	ASP	-1	-0.748	-0.874	19.837	-0.071	-0.071	0.000	0.000	0.000	0.000
55	A	71	ASP	-1	-0.822	-0.923	22.876	-0.152	-0.152	0.000	0.000	0.000	0.000
56	A	72	SER	0	-0.064	-0.030	24.975	0.008	0.008	0.000	0.000	0.000	0.000
57	A	73	ARG	1	0.912	0.952	22.239	0.160	0.160	0.000	0.000	0.000	0.000
58	A	74	PHE	0	-0.040	-0.023	25.786	0.002	0.002	0.000	0.000	0.000	0.000
59	A	75	VAL	0	-0.002	-0.016	27.828	0.002	0.002	0.000	0.000	0.000	0.000
60	A	76	ALA	0	0.059	0.041	30.593	0.004	0.004	0.000	0.000	0.000	0.000
61	A	77	ARG	1	0.876	0.932	27.696	0.125	0.125	0.000	0.000	0.000	0.000
62	A	78	PHE	0	-0.041	-0.017	31.331	0.000	0.000	0.000	0.000	0.000	0.000
63	A	79	ILE	0	0.041	0.013	33.277	0.002	0.002	0.000	0.000	0.000	0.000
64	A	80	ALA	0	0.064	0.037	36.139	0.003	0.003	0.000	0.000	0.000	0.000
65	A	81	SER	0	-0.090	-0.046	35.423	0.003	0.003	0.000	0.000	0.000	0.000
66	A	82	ARG	1	0.783	0.857	35.764	0.097	0.097	0.000	0.000	0.000	0.000
67	A	83	SER	0	0.026	0.020	38.681	0.004	0.004	0.000	0.000	0.000	0.000
68	A	84	ARG	1	0.975	0.990	37.105	0.081	0.081	0.000	0.000	0.000	0.000
69	A	85	LYS	1	0.865	0.937	37.154	0.102	0.102	0.000	0.000	0.000	0.000
70	A	86	GLY	0	0.014	0.021	42.834	0.000	0.000	0.000	0.000	0.000	0.000
71	A	87	TYR	0	-0.076	-0.027	41.046	0.000	0.000	0.000	0.000	0.000	0.000
72	A	88	GLY	0	0.077	0.031	42.976	0.001	0.001	0.000	0.000	0.000	0.000
73	A	89	PRO	0	0.056	0.016	40.813	-0.005	-0.005	0.000	0.000	0.000	0.000
74	A	90	ALA	0	-0.004	0.008	40.058	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	91	ARG	1	0.905	0.953	40.124	0.073	0.073	0.000	0.000	0.000	0.000
76	A	92	ILE	0	0.004	0.007	36.239	-0.006	-0.006	0.000	0.000	0.000	0.000
77	A	93	ARG	1	0.871	0.910	35.564	0.040	0.040	0.000	0.000	0.000	0.000
78	A	94	GLN	0	-0.006	0.010	34.832	-0.002	-0.002	0.000	0.000	0.000	0.000
79	A	95	GLU	-1	-0.813	-0.890	34.067	-0.100	-0.100	0.000	0.000	0.000	0.000
80	A	96	LEU	0	0.001	-0.010	30.956	-0.011	-0.011	0.000	0.000	0.000	0.000
81	A	97	ASN	0	0.023	0.022	29.981	-0.004	-0.004	0.000	0.000	0.000	0.000
82	A	98	GLN	0	-0.004	-0.001	29.577	-0.011	-0.011	0.000	0.000	0.000	0.000
83	A	99	LYS	1	0.795	0.884	27.407	0.144	0.144	0.000	0.000	0.000	0.000
84	A	100	GLY	0	-0.009	0.009	25.406	-0.016	-0.016	0.000	0.000	0.000	0.000
85	A	101	ILE	0	-0.007	0.016	25.426	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	102	SER	0	0.066	0.036	26.999	0.006	0.006	0.000	0.000	0.000	0.000
87	A	103	ARG	1	1.021	0.985	28.639	0.039	0.039	0.000	0.000	0.000	0.000
88	A	104	GLU	-1	-0.912	-0.957	29.482	-0.016	-0.016	0.000	0.000	0.000	0.000
89	A	105	ALA	0	0.016	0.013	28.342	0.003	0.003	0.000	0.000	0.000	0.000
90	A	106	THR	0	-0.015	-0.013	30.521	-0.003	-0.003	0.000	0.000	0.000	0.000
91	A	107	GLU	-1	-0.851	-0.925	33.210	-0.042	-0.042	0.000	0.000	0.000	0.000
92	A	108	LYS	1	0.890	0.950	31.435	0.030	0.030	0.000	0.000	0.000	0.000
93	A	109	ALA	0	0.026	0.012	32.959	0.001	0.001	0.000	0.000	0.000	0.000
94	A	110	MET	0	-0.053	-0.033	35.003	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	111	ARG	1	0.905	0.955	38.228	0.025	0.025	0.000	0.000	0.000	0.000
96	A	112	GLU	-1	-0.867	-0.928	35.130	-0.031	-0.031	0.000	0.000	0.000	0.000
97	A	113	ALA	0	-0.078	-0.024	38.270	0.000	0.000	0.000	0.000	0.000	0.000
98	A	114	ASP	-1	-0.930	-0.958	39.817	-0.029	-0.029	0.000	0.000	0.000	0.000
99	A	115	ILE	0	-0.033	-0.015	40.462	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	116	ASP	-1	-0.827	-0.911	44.402	-0.032	-0.032	0.000	0.000	0.000	0.000
101	A	117	TRP	0	-0.001	-0.036	40.709	-0.005	-0.005	0.000	0.000	0.000	0.000
102	A	118	ALA	0	0.058	0.034	47.477	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	119	ALA	0	0.017	0.021	50.751	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	120	LEU	0	-0.046	-0.024	45.062	-0.002	-0.002	0.000	0.000	0.000	0.000
105	A	121	ALA	0	-0.004	-0.007	49.186	-0.002	-0.002	0.000	0.000	0.000	0.000
106	A	122	ARG	1	0.910	0.959	50.589	0.032	0.032	0.000	0.000	0.000	0.000
107	A	123	ASP	-1	-0.876	-0.936	50.916	-0.048	-0.048	0.000	0.000	0.000	0.000
108	A	124	GLN	0	-0.015	-0.018	48.035	-0.003	-0.003	0.000	0.000	0.000	0.000
109	A	125	ALA	0	-0.031	-0.016	51.469	0.000	0.000	0.000	0.000	0.000	0.000
110	A	126	THR	0	0.014	0.008	54.730	0.000	0.000	0.000	0.000	0.000	0.000
111	A	127	ARG	1	0.873	0.961	48.201	0.052	0.052	0.000	0.000	0.000	0.000
112	A	128	LYS	1	0.850	0.946	52.633	0.051	0.051	0.000	0.000	0.000	0.000
113	A	129	TYR	0	-0.057	-0.055	54.810	0.000	0.000	0.000	0.000	0.000	0.000
114	A	130	GLY	0	0.044	0.040	58.725	0.002	0.002	0.000	0.000	0.000	0.000
115	A	131	GLU	-1	-0.869	-0.942	59.920	-0.034	-0.034	0.000	0.000	0.000	0.000
116	A	132	PRO	0	0.015	-0.017	62.064	0.000	0.000	0.000	0.000	0.000	0.000
117	A	133	LEU	0	-0.027	0.002	57.905	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	134	PRO	0	0.019	0.022	61.087	0.001	0.001	0.000	0.000	0.000	0.000
119	A	135	THR	0	-0.005	-0.013	63.133	0.000	0.000	0.000	0.000	0.000	0.000
120	A	136	VAL	0	0.014	0.033	65.594	0.001	0.001	0.000	0.000	0.000	0.000
121	A	137	PHE	0	0.054	0.015	64.280	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	138	SER	0	0.016	-0.006	63.743	-0.001	-0.001	0.000	0.000	0.000	0.000
123	A	139	GLU	-1	-0.894	-0.960	62.355	-0.034	-0.034	0.000	0.000	0.000	0.000
124	A	140	LYS	1	0.970	1.002	60.542	0.026	0.026	0.000	0.000	0.000	0.000
125	A	141	VAL	0	0.042	0.026	58.923	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	142	LYS	1	0.920	0.960	57.571	0.037	0.037	0.000	0.000	0.000	0.000
127	A	143	ILE	0	0.019	0.011	55.970	-0.003	-0.003	0.000	0.000	0.000	0.000
128	A	144	GLN	0	0.032	0.004	54.593	-0.002	-0.002	0.000	0.000	0.000	0.000
129	A	145	ARG	1	0.963	1.000	51.413	0.047	0.047	0.000	0.000	0.000	0.000
130	A	146	PHE	0	-0.056	-0.038	50.178	-0.003	-0.003	0.000	0.000	0.000	0.000
131	A	147	LEU	0	0.028	0.022	49.846	-0.003	-0.003	0.000	0.000	0.000	0.000
132	A	148	LEU	0	0.040	0.015	48.562	-0.002	-0.002	0.000	0.000	0.000	0.000
133	A	149	TYR	0	-0.055	-0.029	47.280	-0.003	-0.003	0.000	0.000	0.000	0.000
134	A	150	ARG	1	0.815	0.913	45.360	0.058	0.058	0.000	0.000	0.000	0.000
135	A	151	GLY	0	0.013	0.007	43.619	-0.004	-0.004	0.000	0.000	0.000	0.000
136	A	152	TYR	0	-0.011	-0.002	44.639	0.000	0.000	0.000	0.000	0.000	0.000
137	A	153	LEU	0	-0.017	-0.009	44.580	0.000	0.000	0.000	0.000	0.000	0.000
138	A	154	MET	0	0.033	0.010	48.455	0.000	0.000	0.000	0.000	0.000	0.000
139	A	155	GLU	-1	-0.885	-0.948	50.307	-0.029	-0.029	0.000	0.000	0.000	0.000
140	A	156	ASP	-1	-0.819	-0.911	47.386	-0.039	-0.039	0.000	0.000	0.000	0.000
141	A	157	ILE	0	-0.068	-0.052	50.803	0.000	0.000	0.000	0.000	0.000	0.000
142	A	158	GLN	0	-0.065	-0.034	53.658	0.000	0.000	0.000	0.000	0.000	0.000
143	A	159	ASP	-1	-0.825	-0.912	55.795	-0.023	-0.023	0.000	0.000	0.000	0.000
144	A	160	ILE	0	-0.093	-0.032	54.212	0.000	0.000	0.000	0.000	0.000	0.000
145	A	161	TRP	0	-0.076	-0.070	57.149	-0.001	-0.001	0.000	0.000	0.000	0.000
146	A	1	NME	0	0.007	0.025	59.979	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 )