FMO DATABASE

FMODB ID: 22MJR

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1014973.433692
FMO2-HF: Nuclear repulsion	964982.616059
FMO2-HF: Total energy	-49990.817632
FMO2-MP2: Total energy	-50136.259274

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.
-35.853	-32.85	-0.007	-1.362	-1.633	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 : 0.991 / q_NPA : 0.997

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	0.903	0.959	3.829	26.319	28.434	-0.021	-1.064	-1.030	0.001
4	A	5	HIS	0	0.054	0.035	5.912	-0.385	-0.385	0.000	0.000	0.000	0.000
5	A	6	GLU	-1	-0.772	-0.898	8.749	-22.814	-22.814	0.000	0.000	0.000	0.000
6	A	7	HIS	0	-0.023	-0.035	8.463	-0.765	-0.765	0.000	0.000	0.000	0.000
7	A	8	ILE	0	0.005	0.003	6.418	0.748	0.748	0.000	0.000	0.000	0.000
8	A	9	ARG	1	0.834	0.892	10.590	18.961	18.961	0.000	0.000	0.000	0.000
9	A	10	MET	0	-0.040	-0.002	13.281	0.827	0.827	0.000	0.000	0.000	0.000
10	A	11	ALA	0	0.002	0.007	12.268	1.065	1.065	0.000	0.000	0.000	0.000
11	A	12	MET	0	0.010	0.005	13.590	0.824	0.824	0.000	0.000	0.000	0.000
12	A	13	ASN	0	0.013	-0.006	15.878	0.773	0.773	0.000	0.000	0.000	0.000
13	A	14	ALA	0	-0.042	-0.012	17.122	0.762	0.762	0.000	0.000	0.000	0.000
14	A	15	TRP	0	-0.007	-0.016	15.918	0.294	0.294	0.000	0.000	0.000	0.000
15	A	16	ALA	0	0.026	0.012	19.164	0.467	0.467	0.000	0.000	0.000	0.000
16	A	17	HIS	0	-0.059	-0.023	21.845	0.665	0.665	0.000	0.000	0.000	0.000
17	A	18	PRO	0	-0.083	-0.032	22.867	0.436	0.436	0.000	0.000	0.000	0.000
18	A	19	ASP	-1	-0.866	-0.929	25.474	-10.411	-10.411	0.000	0.000	0.000	0.000
19	A	20	GLY	0	-0.021	-0.007	25.989	0.247	0.247	0.000	0.000	0.000	0.000
20	A	21	GLU	-1	-0.903	-0.980	22.499	-12.552	-12.552	0.000	0.000	0.000	0.000
21	A	22	LYS	1	0.934	0.955	22.937	9.809	9.809	0.000	0.000	0.000	0.000
22	A	23	VAL	0	0.053	0.042	22.509	-0.070	-0.070	0.000	0.000	0.000	0.000
23	A	24	PRO	0	0.041	0.023	18.488	-0.223	-0.223	0.000	0.000	0.000	0.000
24	A	25	ALA	0	0.033	0.028	19.689	-0.442	-0.442	0.000	0.000	0.000	0.000
25	A	26	ALA	0	0.012	0.021	21.189	-0.080	-0.080	0.000	0.000	0.000	0.000
26	A	27	GLU	-1	-0.863	-0.930	20.068	-12.905	-12.905	0.000	0.000	0.000	0.000
27	A	28	ILE	0	-0.049	-0.030	15.706	-0.428	-0.428	0.000	0.000	0.000	0.000
28	A	29	THR	0	-0.030	-0.050	18.109	-0.276	-0.276	0.000	0.000	0.000	0.000
29	A	30	ARG	1	0.850	0.926	20.827	12.793	12.793	0.000	0.000	0.000	0.000
30	A	31	ALA	0	0.005	0.010	16.971	0.040	0.040	0.000	0.000	0.000	0.000
31	A	32	TYR	0	-0.019	-0.042	16.857	-0.307	-0.307	0.000	0.000	0.000	0.000
32	A	33	PHE	0	0.010	-0.006	18.422	-0.124	-0.124	0.000	0.000	0.000	0.000
33	A	34	GLU	-1	-0.895	-0.906	20.129	-13.886	-13.886	0.000	0.000	0.000	0.000
34	A	35	LEU	0	-0.076	-0.047	14.436	-0.042	-0.042	0.000	0.000	0.000	0.000
35	A	36	GLY	0	-0.010	0.016	18.499	-0.187	-0.187	0.000	0.000	0.000	0.000
36	A	37	MET	0	-0.072	-0.022	13.575	-0.431	-0.431	0.000	0.000	0.000	0.000
37	A	38	THR	0	0.001	-0.008	18.387	0.468	0.468	0.000	0.000	0.000	0.000
38	A	39	PHE	0	-0.023	0.009	13.707	0.667	0.667	0.000	0.000	0.000	0.000
39	A	40	PRO	0	0.015	-0.008	14.447	-0.847	-0.847	0.000	0.000	0.000	0.000
40	A	41	GLU	-1	-0.916	-0.946	17.327	-12.033	-12.033	0.000	0.000	0.000	0.000
41	A	42	LEU	0	-0.010	0.016	19.082	-0.035	-0.035	0.000	0.000	0.000	0.000
42	A	43	TYR	0	0.026	0.006	22.151	0.221	0.221	0.000	0.000	0.000	0.000
43	A	44	ASP	-1	-0.718	-0.829	25.908	-10.465	-10.465	0.000	0.000	0.000	0.000
44	A	45	ASP	-1	-0.871	-0.953	27.237	-10.416	-10.416	0.000	0.000	0.000	0.000
45	A	46	SER	0	-0.153	-0.062	30.056	0.410	0.410	0.000	0.000	0.000	0.000
46	A	47	HIS	0	-0.066	-0.067	29.502	0.293	0.293	0.000	0.000	0.000	0.000
47	A	48	PRO	0	-0.003	-0.008	32.131	-0.070	-0.070	0.000	0.000	0.000	0.000
48	A	49	GLU	-1	-0.910	-0.962	31.001	-9.182	-9.182	0.000	0.000	0.000	0.000
49	A	50	ALA	0	0.004	0.009	27.962	-0.269	-0.269	0.000	0.000	0.000	0.000
50	A	51	LEU	0	0.074	0.047	25.280	-0.275	-0.275	0.000	0.000	0.000	0.000
51	A	52	ALA	0	0.037	0.032	26.210	-0.404	-0.404	0.000	0.000	0.000	0.000
52	A	53	ARG	1	0.857	0.929	26.890	9.771	9.771	0.000	0.000	0.000	0.000
53	A	54	ASN	0	-0.007	-0.018	22.515	-0.246	-0.246	0.000	0.000	0.000	0.000
54	A	55	THR	0	-0.006	-0.021	21.817	-0.619	-0.619	0.000	0.000	0.000	0.000
55	A	56	GLN	0	0.017	0.022	22.319	-0.413	-0.413	0.000	0.000	0.000	0.000
56	A	57	LYS	1	0.804	0.890	20.572	12.304	12.304	0.000	0.000	0.000	0.000
57	A	58	ILE	0	0.041	0.018	16.688	-0.439	-0.439	0.000	0.000	0.000	0.000
58	A	59	PHE	0	0.060	0.013	17.376	-0.867	-0.867	0.000	0.000	0.000	0.000
59	A	60	ARG	1	0.935	0.986	19.341	11.866	11.866	0.000	0.000	0.000	0.000
60	A	61	TRP	0	-0.032	-0.031	14.840	-0.081	-0.081	0.000	0.000	0.000	0.000
61	A	62	VAL	0	0.008	0.012	14.470	-0.729	-0.729	0.000	0.000	0.000	0.000
62	A	63	GLU	-1	-0.851	-0.905	15.465	-12.917	-12.917	0.000	0.000	0.000	0.000
63	A	64	LYS	1	0.785	0.889	17.138	12.839	12.839	0.000	0.000	0.000	0.000
64	A	65	ASP	-1	-0.768	-0.872	13.548	-18.527	-18.527	0.000	0.000	0.000	0.000
65	A	66	THR	0	-0.022	-0.005	14.045	-0.400	-0.400	0.000	0.000	0.000	0.000
66	A	67	PRO	0	0.050	0.003	12.764	-0.619	-0.619	0.000	0.000	0.000	0.000
67	A	68	ASP	-1	-0.790	-0.867	12.827	-15.479	-15.479	0.000	0.000	0.000	0.000
68	A	69	ALA	0	0.006	0.003	14.245	-0.374	-0.374	0.000	0.000	0.000	0.000
69	A	70	VAL	0	-0.007	-0.008	8.433	-0.878	-0.878	0.000	0.000	0.000	0.000
70	A	71	GLU	-1	-0.943	-0.978	9.390	-19.894	-19.894	0.000	0.000	0.000	0.000
71	A	72	LYS	1	0.823	0.903	10.590	14.397	14.397	0.000	0.000	0.000	0.000
72	A	73	ILE	0	-0.006	0.001	9.350	-0.114	-0.114	0.000	0.000	0.000	0.000
73	A	74	GLN	0	-0.065	-0.041	4.252	-4.579	-4.477	-0.001	-0.029	-0.072	0.000
74	A	75	ALA	0	-0.012	0.003	7.945	-1.232	-1.232	0.000	0.000	0.000	0.000
75	A	76	LEU	0	0.040	0.018	10.785	0.355	0.355	0.000	0.000	0.000	0.000
76	A	77	LEU	0	-0.011	-0.007	5.113	0.156	0.156	0.000	0.000	0.000	0.000
77	A	78	PRO	0	-0.010	0.002	9.037	0.159	0.159	0.000	0.000	0.000	0.000
78	A	79	ALA	0	0.062	0.027	10.805	0.837	0.837	0.000	0.000	0.000	0.000
79	A	80	ILE	0	-0.040	-0.012	11.006	1.087	1.087	0.000	0.000	0.000	0.000
80	A	81	GLU	-1	-0.876	-0.939	7.212	-34.680	-34.680	0.000	0.000	0.000	0.000
81	A	82	LYS	1	0.814	0.902	11.641	16.247	16.247	0.000	0.000	0.000	0.000
82	A	83	SER	0	-0.012	-0.022	14.533	1.080	1.080	0.000	0.000	0.000	0.000
83	A	84	MET	0	-0.007	0.027	12.901	0.414	0.414	0.000	0.000	0.000	0.000
84	A	85	PRO	0	0.010	0.002	15.632	-0.292	-0.292	0.000	0.000	0.000	0.000
85	A	86	PRO	0	0.089	0.035	14.325	-0.865	-0.865	0.000	0.000	0.000	0.000
86	A	87	LEU	0	-0.007	-0.001	13.743	-1.133	-1.133	0.000	0.000	0.000	0.000
87	A	88	LEU	0	-0.010	-0.009	14.287	-0.567	-0.567	0.000	0.000	0.000	0.000
88	A	89	VAL	0	0.042	0.027	9.421	-1.371	-1.371	0.000	0.000	0.000	0.000
89	A	90	ALA	0	-0.042	-0.025	9.342	-2.562	-2.562	0.000	0.000	0.000	0.000
90	A	91	ARG	1	0.878	0.907	10.076	14.864	14.864	0.000	0.000	0.000	0.000
91	A	92	MET	0	0.024	0.045	7.610	-0.433	-0.433	0.000	0.000	0.000	0.000
92	A	93	ARG	1	0.774	0.881	4.298	37.097	37.249	-0.001	-0.017	-0.134	0.000
93	A	94	SER	0	-0.039	-0.028	6.180	-2.229	-2.229	0.000	0.000	0.000	0.000
94	A	95	HIS	0	-0.026	-0.024	7.855	1.876	1.876	0.000	0.000	0.000	0.000
95	A	96	SER	0	-0.046	-0.024	3.313	0.782	1.416	0.016	-0.252	-0.397	0.000
96	A	97	SER	0	-0.044	-0.017	5.068	-2.653	-2.653	0.000	0.000	0.000	0.000
97	A	98	ALA	0	0.052	0.026	6.986	2.380	2.380	0.000	0.000	0.000	0.000
98	A	99	TYR	0	0.053	0.035	8.581	1.983	1.983	0.000	0.000	0.000	0.000
99	A	100	PHE	0	0.038	0.000	5.902	1.116	1.116	0.000	0.000	0.000	0.000
100	A	101	ARG	1	0.825	0.911	9.928	21.482	21.482	0.000	0.000	0.000	0.000
101	A	102	GLU	-1	-0.869	-0.944	12.313	-18.788	-18.788	0.000	0.000	0.000	0.000
102	A	103	LEU	0	-0.015	0.000	12.152	1.441	1.441	0.000	0.000	0.000	0.000
103	A	104	VAL	0	-0.003	0.000	13.121	1.276	1.276	0.000	0.000	0.000	0.000
104	A	105	GLU	-1	-0.821	-0.906	15.718	-16.334	-16.334	0.000	0.000	0.000	0.000
105	A	106	THR	0	-0.057	-0.038	17.864	1.220	1.220	0.000	0.000	0.000	0.000
106	A	107	ARG	1	0.878	0.931	18.306	14.423	14.423	0.000	0.000	0.000	0.000
107	A	108	GLU	-1	-0.780	-0.870	18.942	-14.005	-14.005	0.000	0.000	0.000	0.000
108	A	109	ARG	1	0.891	0.954	21.485	13.601	13.601	0.000	0.000	0.000	0.000
109	A	110	LEU	0	0.040	0.025	23.121	0.415	0.415	0.000	0.000	0.000	0.000
110	A	111	VAL	0	-0.008	-0.006	24.027	0.338	0.338	0.000	0.000	0.000	0.000
111	A	112	ARG	1	0.959	0.993	23.502	12.167	12.167	0.000	0.000	0.000	0.000
112	A	113	ASP	-1	-0.880	-0.945	28.035	-10.416	-10.416	0.000	0.000	0.000	0.000
113	A	114	ALA	0	-0.056	-0.017	29.161	0.353	0.353	0.000	0.000	0.000	0.000
114	A	115	ASP	-1	-0.918	-0.973	29.442	-9.778	-9.778	0.000	0.000	0.000	0.000
115	A	116	ASP	-1	-0.961	-0.984	31.929	-8.701	-8.701	0.000	0.000	0.000	0.000
116	A	117	PHE	0	-0.028	-0.010	33.731	0.371	0.371	0.000	0.000	0.000	0.000
117	A	118	VAL	0	-0.021	-0.004	34.489	0.313	0.313	0.000	0.000	0.000	0.000
118	A	119	ALA	0	0.015	0.011	36.245	0.276	0.276	0.000	0.000	0.000	0.000
119	A	120	VAL	0	-0.012	-0.009	38.037	0.286	0.286	0.000	0.000	0.000	0.000
120	A	121	ALA	0	-0.023	-0.024	39.510	0.230	0.230	0.000	0.000	0.000	0.000
121	A	122	ILE	0	-0.056	-0.027	39.350	0.205	0.205	0.000	0.000	0.000	0.000
122	A	123	ALA	0	-0.061	-0.030	42.324	0.189	0.189	0.000	0.000	0.000	0.000
123	A	124	GLY	0	-0.036	0.003	44.097	0.169	0.169	0.000	0.000	0.000	0.000
124	A	125	PHE	0	-0.042	-0.016	45.586	0.231	0.231	0.000	0.000	0.000	0.000

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