FMO DATABASE

FMODB ID: 664NZ

Calculation Name: 3C4R-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3C4R

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H2

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	124
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1018574.392159
FMO2-HF: Nuclear repulsion	968583.140479
FMO2-HF: Total energy	-49991.25168
FMO2-MP2: Total energy	-50136.645602

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:2:LYS)

Summations of interaction energy for fragment #1(A:2:LYS)

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.
-39.697	-37.027	0.004	-1.209	-1.462	0.002

Interaction energy analysis for fragmet #1(A:2:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.004 / q_NPA : 0.998

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

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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	4	LYS	1	0.909	0.958	3.877	26.803	28.362	-0.013	-0.724	-0.821	0.001
4	A	5	HIS	0	0.042	0.025	5.813	-0.513	-0.513	0.000	0.000	0.000	0.000
5	A	6	GLU	-1	-0.752	-0.879	8.400	-22.655	-22.655	0.000	0.000	0.000	0.000
6	A	7	HIS	0	0.002	-0.020	8.686	-0.541	-0.541	0.000	0.000	0.000	0.000
7	A	8	ILE	0	0.010	0.002	6.339	0.983	0.983	0.000	0.000	0.000	0.000
8	A	9	ARG	1	0.805	0.874	10.545	18.630	18.630	0.000	0.000	0.000	0.000
9	A	10	MET	0	-0.050	-0.014	13.573	0.856	0.856	0.000	0.000	0.000	0.000
10	A	11	ALA	0	-0.007	-0.001	12.357	1.058	1.058	0.000	0.000	0.000	0.000
11	A	12	MET	0	0.008	-0.002	13.477	0.811	0.811	0.000	0.000	0.000	0.000
12	A	13	ASN	0	0.016	-0.002	15.939	0.594	0.594	0.000	0.000	0.000	0.000
13	A	14	ALA	0	-0.023	-0.009	17.430	0.769	0.769	0.000	0.000	0.000	0.000
14	A	15	TRP	0	-0.005	-0.009	16.084	0.297	0.297	0.000	0.000	0.000	0.000
15	A	16	ALA	0	0.027	0.007	19.513	0.510	0.510	0.000	0.000	0.000	0.000
16	A	17	HIS	0	-0.079	-0.030	21.974	0.615	0.615	0.000	0.000	0.000	0.000
17	A	18	PRO	0	-0.077	-0.025	23.258	0.449	0.449	0.000	0.000	0.000	0.000
18	A	19	ASP	-1	-0.854	-0.924	25.876	-10.475	-10.475	0.000	0.000	0.000	0.000
19	A	20	GLY	0	-0.025	-0.007	25.940	0.293	0.293	0.000	0.000	0.000	0.000
20	A	21	GLU	-1	-0.925	-0.989	22.241	-12.330	-12.330	0.000	0.000	0.000	0.000
21	A	22	LYS	1	0.952	0.970	22.477	9.808	9.808	0.000	0.000	0.000	0.000
22	A	23	VAL	0	0.055	0.044	22.912	-0.090	-0.090	0.000	0.000	0.000	0.000
23	A	24	PRO	0	0.012	-0.001	18.617	-0.238	-0.238	0.000	0.000	0.000	0.000
24	A	25	ALA	0	0.007	0.009	19.768	-0.426	-0.426	0.000	0.000	0.000	0.000
25	A	26	ALA	0	0.009	0.022	21.203	-0.102	-0.102	0.000	0.000	0.000	0.000
26	A	27	GLU	-1	-0.819	-0.874	20.270	-12.793	-12.793	0.000	0.000	0.000	0.000
27	A	28	ILE	0	-0.003	-0.004	15.864	-0.459	-0.459	0.000	0.000	0.000	0.000
28	A	29	THR	0	-0.005	-0.024	18.371	-0.230	-0.230	0.000	0.000	0.000	0.000
29	A	30	ARG	1	0.790	0.871	21.179	12.660	12.660	0.000	0.000	0.000	0.000
30	A	31	ALA	0	0.017	0.011	16.802	-0.039	-0.039	0.000	0.000	0.000	0.000
31	A	32	TYR	0	-0.008	-0.043	16.588	-0.471	-0.471	0.000	0.000	0.000	0.000
32	A	33	PHE	0	-0.014	-0.005	18.435	-0.106	-0.106	0.000	0.000	0.000	0.000
33	A	34	GLU	-1	-0.856	-0.918	20.217	-13.799	-13.799	0.000	0.000	0.000	0.000
34	A	35	LEU	0	-0.071	-0.031	14.456	-0.119	-0.119	0.000	0.000	0.000	0.000
35	A	36	GLY	0	-0.027	-0.001	18.517	-0.346	-0.346	0.000	0.000	0.000	0.000
36	A	37	MET	0	-0.078	-0.019	13.310	-0.236	-0.236	0.000	0.000	0.000	0.000
37	A	38	THR	0	0.001	-0.003	17.842	0.496	0.496	0.000	0.000	0.000	0.000
38	A	39	PHE	0	-0.029	-0.001	13.405	0.604	0.604	0.000	0.000	0.000	0.000
39	A	40	PRO	0	0.032	0.012	13.710	-0.829	-0.829	0.000	0.000	0.000	0.000
40	A	41	GLU	-1	-0.841	-0.904	16.593	-11.778	-11.778	0.000	0.000	0.000	0.000
41	A	42	LEU	0	-0.017	0.007	18.666	-0.065	-0.065	0.000	0.000	0.000	0.000
42	A	43	TYR	0	0.032	0.018	21.592	0.262	0.262	0.000	0.000	0.000	0.000
43	A	44	ASP	-1	-0.707	-0.816	25.004	-10.520	-10.520	0.000	0.000	0.000	0.000
44	A	45	ASP	-1	-0.911	-0.971	26.895	-10.450	-10.450	0.000	0.000	0.000	0.000
45	A	46	SER	0	-0.113	-0.067	29.877	0.408	0.408	0.000	0.000	0.000	0.000
46	A	47	HIS	0	-0.072	-0.047	29.052	0.427	0.427	0.000	0.000	0.000	0.000
47	A	48	PRO	0	-0.011	-0.019	31.583	-0.112	-0.112	0.000	0.000	0.000	0.000
48	A	49	GLU	-1	-0.898	-0.961	30.728	-9.182	-9.182	0.000	0.000	0.000	0.000
49	A	50	ALA	0	-0.004	0.011	27.302	-0.263	-0.263	0.000	0.000	0.000	0.000
50	A	51	LEU	0	0.059	0.036	25.053	-0.347	-0.347	0.000	0.000	0.000	0.000
51	A	52	ALA	0	0.042	0.040	25.779	-0.419	-0.419	0.000	0.000	0.000	0.000
52	A	53	ARG	1	0.850	0.928	26.221	9.710	9.710	0.000	0.000	0.000	0.000
53	A	54	ASN	0	0.026	-0.007	22.209	-0.220	-0.220	0.000	0.000	0.000	0.000
54	A	55	THR	0	-0.012	-0.028	21.393	-0.606	-0.606	0.000	0.000	0.000	0.000
55	A	56	GLN	0	0.016	0.010	21.800	-0.468	-0.468	0.000	0.000	0.000	0.000
56	A	57	LYS	1	0.724	0.846	19.987	12.352	12.352	0.000	0.000	0.000	0.000
57	A	58	ILE	0	0.034	0.021	16.176	-0.447	-0.447	0.000	0.000	0.000	0.000
58	A	59	PHE	0	0.072	0.018	17.071	-0.779	-0.779	0.000	0.000	0.000	0.000
59	A	60	ARG	1	0.906	0.964	18.792	11.639	11.639	0.000	0.000	0.000	0.000
60	A	61	TRP	0	-0.010	-0.010	14.712	-0.061	-0.061	0.000	0.000	0.000	0.000
61	A	62	VAL	0	0.026	0.012	14.160	-0.842	-0.842	0.000	0.000	0.000	0.000
62	A	63	GLU	-1	-0.859	-0.940	15.294	-12.698	-12.698	0.000	0.000	0.000	0.000
63	A	64	LYS	1	0.774	0.909	16.408	12.910	12.910	0.000	0.000	0.000	0.000
64	A	65	ASP	-1	-0.781	-0.865	13.194	-18.469	-18.469	0.000	0.000	0.000	0.000
65	A	66	THR	0	-0.008	-0.003	13.627	-0.416	-0.416	0.000	0.000	0.000	0.000
66	A	67	PRO	0	0.039	-0.001	12.486	-0.458	-0.458	0.000	0.000	0.000	0.000
67	A	68	ASP	-1	-0.805	-0.878	12.880	-15.263	-15.263	0.000	0.000	0.000	0.000
68	A	69	ALA	0	0.014	0.009	14.477	-0.137	-0.137	0.000	0.000	0.000	0.000
69	A	70	VAL	0	-0.005	-0.002	8.306	-0.859	-0.859	0.000	0.000	0.000	0.000
70	A	71	GLU	-1	-0.934	-0.980	9.391	-19.507	-19.507	0.000	0.000	0.000	0.000
71	A	72	LYS	1	0.821	0.910	10.277	14.213	14.213	0.000	0.000	0.000	0.000
72	A	73	ILE	0	0.002	-0.001	9.217	-0.070	-0.070	0.000	0.000	0.000	0.000
73	A	74	GLN	0	-0.070	-0.051	3.929	-5.250	-5.080	0.000	-0.067	-0.102	0.000
74	A	75	ALA	0	-0.014	-0.006	7.389	-1.443	-1.443	0.000	0.000	0.000	0.000
75	A	76	LEU	0	0.030	0.019	10.068	0.436	0.436	0.000	0.000	0.000	0.000
76	A	77	LEU	0	-0.006	-0.004	5.367	0.397	0.397	0.000	0.000	0.000	0.000
77	A	78	PRO	0	-0.029	-0.009	9.245	0.212	0.212	0.000	0.000	0.000	0.000
78	A	79	ALA	0	0.076	0.034	11.116	0.915	0.915	0.000	0.000	0.000	0.000
79	A	80	ILE	0	-0.016	0.011	10.734	0.873	0.873	0.000	0.000	0.000	0.000
80	A	81	GLU	-1	-0.838	-0.923	7.452	-34.147	-34.147	0.000	0.000	0.000	0.000
81	A	82	LYS	1	0.790	0.905	11.582	15.845	15.845	0.000	0.000	0.000	0.000
82	A	83	SER	0	-0.052	-0.051	14.759	1.287	1.287	0.000	0.000	0.000	0.000
83	A	84	MET	0	-0.013	0.008	13.173	0.422	0.422	0.000	0.000	0.000	0.000
84	A	85	PRO	0	0.024	0.007	15.775	-0.384	-0.384	0.000	0.000	0.000	0.000
85	A	86	PRO	0	0.066	0.018	14.450	-0.781	-0.781	0.000	0.000	0.000	0.000
86	A	87	LEU	0	-0.011	0.003	13.842	-1.124	-1.124	0.000	0.000	0.000	0.000
87	A	88	LEU	0	0.006	-0.001	14.291	-0.660	-0.660	0.000	0.000	0.000	0.000
88	A	89	VAL	0	0.026	0.028	9.721	-1.318	-1.318	0.000	0.000	0.000	0.000
89	A	90	ALA	0	-0.026	-0.017	9.467	-2.527	-2.527	0.000	0.000	0.000	0.000
90	A	91	ARG	1	0.884	0.913	10.013	14.756	14.756	0.000	0.000	0.000	0.000
91	A	92	MET	0	0.014	0.036	7.979	-0.343	-0.343	0.000	0.000	0.000	0.000
92	A	93	ARG	1	0.809	0.896	4.793	34.899	34.986	-0.001	-0.006	-0.080	0.000
93	A	94	SER	0	-0.044	-0.025	6.013	-2.169	-2.169	0.000	0.000	0.000	0.000
94	A	95	HIS	0	-0.053	-0.039	7.876	1.615	1.615	0.000	0.000	0.000	0.000
95	A	96	SER	0	-0.065	-0.032	3.169	1.097	1.951	0.018	-0.412	-0.459	0.001
96	A	97	SER	0	-0.058	-0.030	4.801	-4.015	-4.015	0.000	0.000	0.000	0.000
97	A	98	ALA	0	0.038	0.027	6.737	2.293	2.293	0.000	0.000	0.000	0.000
98	A	99	TYR	0	0.082	0.044	8.779	1.672	1.672	0.000	0.000	0.000	0.000
99	A	100	PHE	0	0.040	0.007	6.262	1.243	1.243	0.000	0.000	0.000	0.000
100	A	101	ARG	1	0.823	0.896	10.163	20.912	20.912	0.000	0.000	0.000	0.000
101	A	102	GLU	-1	-0.825	-0.906	12.367	-19.898	-19.898	0.000	0.000	0.000	0.000
102	A	103	LEU	0	-0.017	0.000	12.321	1.449	1.449	0.000	0.000	0.000	0.000
103	A	104	VAL	0	0.003	0.005	13.227	1.269	1.269	0.000	0.000	0.000	0.000
104	A	105	GLU	-1	-0.820	-0.909	15.798	-16.009	-16.009	0.000	0.000	0.000	0.000
105	A	106	THR	0	-0.068	-0.049	17.965	1.247	1.247	0.000	0.000	0.000	0.000
106	A	107	ARG	1	0.858	0.912	18.243	14.392	14.392	0.000	0.000	0.000	0.000
107	A	108	GLU	-1	-0.786	-0.872	18.958	-13.975	-13.975	0.000	0.000	0.000	0.000
108	A	109	ARG	1	0.858	0.936	21.200	13.615	13.615	0.000	0.000	0.000	0.000
109	A	110	LEU	0	0.048	0.032	23.571	0.381	0.381	0.000	0.000	0.000	0.000
110	A	111	VAL	0	0.003	0.000	24.144	0.340	0.340	0.000	0.000	0.000	0.000
111	A	112	ARG	1	0.958	0.995	23.387	12.163	12.163	0.000	0.000	0.000	0.000
112	A	113	ASP	-1	-0.904	-0.958	27.465	-10.589	-10.589	0.000	0.000	0.000	0.000
113	A	114	ALA	0	-0.046	-0.017	29.311	0.355	0.355	0.000	0.000	0.000	0.000
114	A	115	ASP	-1	-0.902	-0.965	29.404	-9.777	-9.777	0.000	0.000	0.000	0.000
115	A	116	ASP	-1	-0.966	-0.976	32.124	-8.492	-8.492	0.000	0.000	0.000	0.000
116	A	117	PHE	0	-0.001	0.000	33.900	0.350	0.350	0.000	0.000	0.000	0.000
117	A	118	VAL	0	-0.011	-0.008	34.545	0.293	0.293	0.000	0.000	0.000	0.000
118	A	119	ALA	0	-0.006	-0.002	36.319	0.271	0.271	0.000	0.000	0.000	0.000
119	A	120	VAL	0	-0.006	-0.010	38.149	0.276	0.276	0.000	0.000	0.000	0.000
120	A	121	ALA	0	-0.023	-0.012	39.592	0.227	0.227	0.000	0.000	0.000	0.000
121	A	122	ILE	0	-0.054	-0.031	39.258	0.215	0.215	0.000	0.000	0.000	0.000
122	A	123	ALA	0	-0.049	-0.020	42.321	0.184	0.184	0.000	0.000	0.000	0.000
123	A	124	GLY	0	-0.030	0.006	44.241	0.152	0.152	0.000	0.000	0.000	0.000
124	A	125	PHE	0	-0.062	-0.029	45.564	0.227	0.227	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:LYS)