FMO DATABASE

FMODB ID: 7GK2K

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	OptH
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	-1015120.975335
FMO2-HF: Nuclear repulsion	965130.876691
FMO2-HF: Total energy	-49990.098644
FMO2-MP2: Total energy	-50135.546513

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.
-26.256	-23.331	0.05	-1.123	-1.851	-0.001

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 : 0.961 / q_NPA : 0.966

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	0.956	0.990	3.829	30.041	31.824	-0.016	-0.827	-0.940	-0.001
4	A	5	HIS	0	0.074	0.044	5.776	-0.330	-0.330	0.000	0.000	0.000	0.000
5	A	6	GLU	-1	-0.841	-0.937	8.632	-22.288	-22.288	0.000	0.000	0.000	0.000
6	A	7	HIS	0	-0.017	-0.037	8.184	-0.903	-0.903	0.000	0.000	0.000	0.000
7	A	8	ILE	0	0.008	0.003	7.007	0.535	0.535	0.000	0.000	0.000	0.000
8	A	9	ARG	1	0.866	0.936	10.245	18.469	18.469	0.000	0.000	0.000	0.000
9	A	10	MET	0	-0.050	-0.008	12.963	0.752	0.752	0.000	0.000	0.000	0.000
10	A	11	ALA	0	0.006	0.009	11.901	1.005	1.005	0.000	0.000	0.000	0.000
11	A	12	MET	0	0.007	0.004	13.225	0.788	0.788	0.000	0.000	0.000	0.000
12	A	13	ASN	0	0.021	-0.001	15.414	1.057	1.057	0.000	0.000	0.000	0.000
13	A	14	ALA	0	-0.046	-0.014	16.779	0.737	0.737	0.000	0.000	0.000	0.000
14	A	15	TRP	0	-0.013	-0.017	15.487	0.260	0.260	0.000	0.000	0.000	0.000
15	A	16	ALA	0	0.021	0.009	18.733	0.469	0.469	0.000	0.000	0.000	0.000
16	A	17	HIS	0	-0.058	-0.022	21.389	0.735	0.735	0.000	0.000	0.000	0.000
17	A	18	PRO	0	-0.081	-0.034	22.400	0.419	0.419	0.000	0.000	0.000	0.000
18	A	19	ASP	-1	-0.854	-0.913	25.025	-10.311	-10.311	0.000	0.000	0.000	0.000
19	A	20	GLY	0	-0.027	-0.016	25.531	0.253	0.253	0.000	0.000	0.000	0.000
20	A	21	GLU	-1	-0.895	-0.981	22.147	-12.497	-12.497	0.000	0.000	0.000	0.000
21	A	22	LYS	1	0.937	0.961	22.790	9.722	9.722	0.000	0.000	0.000	0.000
22	A	23	VAL	0	0.044	0.040	22.544	-0.044	-0.044	0.000	0.000	0.000	0.000
23	A	24	PRO	0	0.029	0.017	18.238	-0.235	-0.235	0.000	0.000	0.000	0.000
24	A	25	ALA	0	0.057	0.041	19.576	-0.420	-0.420	0.000	0.000	0.000	0.000
25	A	26	ALA	0	0.003	0.049	21.182	-0.064	-0.064	0.000	0.000	0.000	0.000
26	A	27	GLU	-1	-0.920	-0.957	19.594	-13.035	-13.035	0.000	0.000	0.000	0.000
27	A	28	ILE	0	-0.038	-0.023	15.753	-0.408	-0.408	0.000	0.000	0.000	0.000
28	A	29	THR	0	-0.052	-0.087	18.109	-0.261	-0.261	0.000	0.000	0.000	0.000
29	A	30	ARG	1	0.912	0.953	20.809	12.595	12.595	0.000	0.000	0.000	0.000
30	A	31	ALA	0	0.011	0.013	16.771	0.044	0.044	0.000	0.000	0.000	0.000
31	A	32	TYR	0	-0.028	-0.039	16.968	-0.300	-0.300	0.000	0.000	0.000	0.000
32	A	33	PHE	0	0.013	-0.005	18.397	-0.113	-0.113	0.000	0.000	0.000	0.000
33	A	34	GLU	-1	-0.931	-0.943	19.840	-13.649	-13.649	0.000	0.000	0.000	0.000
34	A	35	LEU	0	-0.077	-0.049	14.387	-0.043	-0.043	0.000	0.000	0.000	0.000
35	A	36	GLY	0	-0.010	0.017	18.313	-0.182	-0.182	0.000	0.000	0.000	0.000
36	A	37	MET	0	-0.070	-0.024	13.478	-0.415	-0.415	0.000	0.000	0.000	0.000
37	A	38	THR	0	0.005	-0.004	18.363	0.407	0.407	0.000	0.000	0.000	0.000
38	A	39	PHE	0	-0.010	0.016	14.397	0.643	0.643	0.000	0.000	0.000	0.000
39	A	40	PRO	0	-0.006	-0.016	15.021	-0.783	-0.783	0.000	0.000	0.000	0.000
40	A	41	GLU	-1	-0.909	-0.957	17.942	-12.088	-12.088	0.000	0.000	0.000	0.000
41	A	42	LEU	0	-0.038	-0.015	18.814	-0.084	-0.084	0.000	0.000	0.000	0.000
42	A	43	TYR	0	-0.034	-0.021	22.336	0.256	0.256	0.000	0.000	0.000	0.000
43	A	44	ASP	-1	-0.770	-0.879	25.867	-10.316	-10.316	0.000	0.000	0.000	0.000
44	A	45	ASP	-1	-0.865	-0.951	27.192	-10.248	-10.248	0.000	0.000	0.000	0.000
45	A	46	SER	0	-0.127	-0.026	30.023	0.422	0.422	0.000	0.000	0.000	0.000
46	A	47	HIS	0	-0.072	-0.064	29.507	0.294	0.294	0.000	0.000	0.000	0.000
47	A	48	PRO	0	-0.017	-0.009	32.142	-0.076	-0.076	0.000	0.000	0.000	0.000
48	A	49	GLU	-1	-0.893	-0.955	31.248	-8.986	-8.986	0.000	0.000	0.000	0.000
49	A	50	ALA	0	0.003	0.003	27.881	-0.260	-0.260	0.000	0.000	0.000	0.000
50	A	51	LEU	0	0.064	0.040	25.420	-0.274	-0.274	0.000	0.000	0.000	0.000
51	A	52	ALA	0	0.047	0.016	26.244	-0.360	-0.360	0.000	0.000	0.000	0.000
52	A	53	ARG	1	0.893	0.951	27.291	9.497	9.497	0.000	0.000	0.000	0.000
53	A	54	ASN	0	0.013	-0.003	22.541	-0.289	-0.289	0.000	0.000	0.000	0.000
54	A	55	THR	0	0.005	-0.004	22.103	-0.618	-0.618	0.000	0.000	0.000	0.000
55	A	56	GLN	0	-0.005	0.005	22.720	-0.263	-0.263	0.000	0.000	0.000	0.000
56	A	57	LYS	1	0.842	0.919	21.236	12.300	12.300	0.000	0.000	0.000	0.000
57	A	58	ILE	0	0.042	0.017	16.981	-0.418	-0.418	0.000	0.000	0.000	0.000
58	A	59	PHE	0	0.064	0.014	17.996	-0.874	-0.874	0.000	0.000	0.000	0.000
59	A	60	ARG	1	0.978	1.019	19.710	11.729	11.729	0.000	0.000	0.000	0.000
60	A	61	TRP	0	-0.042	-0.034	15.318	-0.017	-0.017	0.000	0.000	0.000	0.000
61	A	62	VAL	0	0.008	0.013	14.791	-0.697	-0.697	0.000	0.000	0.000	0.000
62	A	63	GLU	-1	-0.932	-0.960	15.546	-12.936	-12.936	0.000	0.000	0.000	0.000
63	A	64	LYS	1	0.874	0.950	17.060	12.670	12.670	0.000	0.000	0.000	0.000
64	A	65	ASP	-1	-0.798	-0.922	13.066	-18.314	-18.314	0.000	0.000	0.000	0.000
65	A	66	THR	0	-0.047	-0.014	13.935	-0.374	-0.374	0.000	0.000	0.000	0.000
66	A	67	PRO	0	0.051	0.003	12.668	-0.549	-0.549	0.000	0.000	0.000	0.000
67	A	68	ASP	-1	-0.802	-0.883	13.013	-15.143	-15.143	0.000	0.000	0.000	0.000
68	A	69	ALA	0	-0.004	0.002	14.701	-0.322	-0.322	0.000	0.000	0.000	0.000
69	A	70	VAL	0	0.002	-0.002	8.499	-0.767	-0.767	0.000	0.000	0.000	0.000
70	A	71	GLU	-1	-0.939	-0.978	9.913	-19.212	-19.212	0.000	0.000	0.000	0.000
71	A	72	LYS	1	0.853	0.924	11.169	14.092	14.092	0.000	0.000	0.000	0.000
72	A	73	ILE	0	-0.021	-0.004	10.200	-0.094	-0.094	0.000	0.000	0.000	0.000
73	A	74	GLN	0	-0.055	-0.028	5.406	-2.661	-2.590	-0.001	-0.001	-0.068	0.000
74	A	75	ALA	0	-0.010	0.001	8.727	-1.203	-1.203	0.000	0.000	0.000	0.000
75	A	76	LEU	0	0.054	0.015	11.208	0.277	0.277	0.000	0.000	0.000	0.000
76	A	77	LEU	0	-0.023	-0.007	5.110	0.154	0.154	0.000	0.000	0.000	0.000
77	A	78	PRO	0	0.000	0.007	9.050	0.015	0.015	0.000	0.000	0.000	0.000
78	A	79	ALA	0	0.062	0.025	10.774	0.730	0.730	0.000	0.000	0.000	0.000
79	A	80	ILE	0	-0.052	-0.013	10.968	1.004	1.004	0.000	0.000	0.000	0.000
80	A	81	GLU	-1	-0.990	-1.014	6.677	-34.643	-34.643	0.000	0.000	0.000	0.000
81	A	82	LYS	1	0.843	0.931	11.199	16.134	16.134	0.000	0.000	0.000	0.000
82	A	83	SER	0	-0.011	-0.022	14.263	0.984	0.984	0.000	0.000	0.000	0.000
83	A	84	MET	0	-0.018	0.018	12.367	0.322	0.322	0.000	0.000	0.000	0.000
84	A	85	PRO	0	0.007	0.004	15.306	-0.278	-0.278	0.000	0.000	0.000	0.000
85	A	86	PRO	0	0.101	0.038	13.854	-0.906	-0.906	0.000	0.000	0.000	0.000
86	A	87	LEU	0	-0.011	-0.005	13.293	-1.121	-1.121	0.000	0.000	0.000	0.000
87	A	88	LEU	0	-0.021	-0.012	14.054	-0.590	-0.590	0.000	0.000	0.000	0.000
88	A	89	VAL	0	0.060	0.035	8.946	-1.519	-1.519	0.000	0.000	0.000	0.000
89	A	90	ALA	0	-0.040	-0.026	9.071	-2.736	-2.736	0.000	0.000	0.000	0.000
90	A	91	ARG	1	0.910	0.935	9.956	14.912	14.912	0.000	0.000	0.000	0.000
91	A	92	MET	0	0.020	0.051	7.211	-0.569	-0.569	0.000	0.000	0.000	0.000
92	A	93	ARG	1	0.877	0.943	2.915	40.661	41.121	0.025	-0.104	-0.381	0.000
93	A	94	SER	0	-0.031	-0.034	6.126	-2.633	-2.633	0.000	0.000	0.000	0.000
94	A	95	HIS	0	-0.012	-0.011	7.881	1.603	1.603	0.000	0.000	0.000	0.000
95	A	96	SER	0	-0.051	-0.018	3.075	0.681	1.292	0.042	-0.191	-0.462	0.000
96	A	97	SER	0	-0.024	-0.013	4.804	-3.117	-3.117	0.000	0.000	0.000	0.000
97	A	98	ALA	0	0.047	0.020	6.594	2.885	2.885	0.000	0.000	0.000	0.000
98	A	99	TYR	0	0.057	0.039	8.520	2.091	2.091	0.000	0.000	0.000	0.000
99	A	100	PHE	0	0.019	-0.006	5.284	1.189	1.189	0.000	0.000	0.000	0.000
100	A	101	ARG	1	0.933	0.973	9.733	22.558	22.558	0.000	0.000	0.000	0.000
101	A	102	GLU	-1	-0.949	-0.978	12.210	-18.451	-18.451	0.000	0.000	0.000	0.000
102	A	103	LEU	0	-0.009	0.014	11.878	1.462	1.462	0.000	0.000	0.000	0.000
103	A	104	VAL	0	-0.011	-0.003	12.909	1.293	1.293	0.000	0.000	0.000	0.000
104	A	105	GLU	-1	-0.853	-0.934	15.480	-16.871	-16.871	0.000	0.000	0.000	0.000
105	A	106	THR	0	-0.066	-0.047	17.672	1.179	1.179	0.000	0.000	0.000	0.000
106	A	107	ARG	1	0.979	0.986	18.018	14.534	14.534	0.000	0.000	0.000	0.000
107	A	108	GLU	-1	-0.887	-0.944	19.212	-13.901	-13.901	0.000	0.000	0.000	0.000
108	A	109	ARG	1	0.894	0.951	21.571	13.700	13.700	0.000	0.000	0.000	0.000
109	A	110	LEU	0	0.033	0.020	22.834	0.419	0.419	0.000	0.000	0.000	0.000
110	A	111	VAL	0	-0.025	-0.013	23.431	0.326	0.326	0.000	0.000	0.000	0.000
111	A	112	ARG	1	0.956	0.995	23.836	12.147	12.147	0.000	0.000	0.000	0.000
112	A	113	ASP	-1	-0.850	-0.935	27.814	-10.341	-10.341	0.000	0.000	0.000	0.000
113	A	114	ALA	0	-0.060	-0.022	28.869	0.364	0.364	0.000	0.000	0.000	0.000
114	A	115	ASP	-1	-0.915	-0.975	29.037	-9.913	-9.913	0.000	0.000	0.000	0.000
115	A	116	ASP	-1	-0.950	-0.969	31.716	-9.050	-9.050	0.000	0.000	0.000	0.000
116	A	117	PHE	0	-0.045	-0.020	33.440	0.383	0.383	0.000	0.000	0.000	0.000
117	A	118	VAL	0	-0.021	-0.001	34.082	0.323	0.323	0.000	0.000	0.000	0.000
118	A	119	ALA	0	0.006	0.007	36.092	0.279	0.279	0.000	0.000	0.000	0.000
119	A	120	VAL	0	-0.020	-0.013	37.825	0.286	0.286	0.000	0.000	0.000	0.000
120	A	121	ALA	0	-0.015	-0.022	39.204	0.230	0.230	0.000	0.000	0.000	0.000
121	A	122	ILE	0	-0.051	-0.021	39.447	0.206	0.206	0.000	0.000	0.000	0.000
122	A	123	ALA	0	-0.065	-0.034	42.182	0.191	0.191	0.000	0.000	0.000	0.000
123	A	124	GLY	0	-0.038	0.002	43.852	0.170	0.170	0.000	0.000	0.000	0.000
124	A	125	PHE	0	-0.042	-0.016	45.293	0.224	0.224	0.000	0.000	0.000	0.000

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