FMO DATABASE

FMODB ID: 431RN

Calculation Name: 3MAY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3MAY

Chain ID: A

ChEMBL ID:

UniProt ID: I6X8R5

Base Structure: X-ray

Registration Date: 2023-06-20

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	85
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-467527.984788
FMO2-HF: Nuclear repulsion	435820.018987
FMO2-HF: Total energy	-31707.965801
FMO2-MP2: Total energy	-31798.664095

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:40:CYS)

Summations of interaction energy for fragment #1(A:40:CYS)

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.
-34.771	-25.021	17.557	-11.747	-15.559	-0.083

Interaction energy analysis for fragmet #1(A:40:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.104 / q_NPA : -0.056

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	42	ALA	0	0.064	0.018	3.744	0.334	1.599	-0.008	-0.468	-0.788	0.004
4	A	43	SER	0	0.018	0.001	6.456	0.060	0.060	0.000	0.000	0.000	0.000
5	A	44	GLU	-1	-0.851	-0.937	3.586	2.735	3.449	0.045	-0.292	-0.467	0.002
6	A	45	VAL	0	-0.029	-0.001	3.450	-1.430	-1.008	0.015	-0.080	-0.357	0.000
7	A	46	ALA	0	0.039	0.007	5.655	-0.461	-0.461	0.000	0.000	0.000	0.000
8	A	47	ARG	1	0.878	0.950	8.230	-2.238	-2.238	0.000	0.000	0.000	0.000
9	A	48	THR	0	0.019	0.011	6.927	-0.300	-0.300	0.000	0.000	0.000	0.000
10	A	49	VAL	0	-0.025	0.003	9.240	-0.235	-0.235	0.000	0.000	0.000	0.000
11	A	50	GLY	0	0.032	0.020	11.365	-0.063	-0.063	0.000	0.000	0.000	0.000
12	A	51	SER	0	-0.055	-0.035	12.260	-0.055	-0.055	0.000	0.000	0.000	0.000
13	A	52	VAL	0	0.021	0.009	12.311	-0.059	-0.059	0.000	0.000	0.000	0.000
14	A	53	ALA	0	0.002	0.007	14.973	0.006	0.006	0.000	0.000	0.000	0.000
15	A	54	LYS	1	0.903	0.957	17.035	0.017	0.017	0.000	0.000	0.000	0.000
16	A	55	SER	0	-0.060	-0.016	17.697	-0.015	-0.015	0.000	0.000	0.000	0.000
17	A	56	MET	0	0.042	0.001	15.952	-0.010	-0.010	0.000	0.000	0.000	0.000
18	A	57	GLY	0	-0.006	-0.010	20.529	0.016	0.016	0.000	0.000	0.000	0.000
19	A	58	ASP	-1	-0.813	-0.904	22.844	-0.078	-0.078	0.000	0.000	0.000	0.000
20	A	59	TYR	0	-0.061	-0.048	23.334	0.011	0.011	0.000	0.000	0.000	0.000
21	A	60	LEU	0	0.002	-0.009	23.544	0.010	0.010	0.000	0.000	0.000	0.000
22	A	61	ASP	-1	-0.955	-0.955	26.554	-0.138	-0.138	0.000	0.000	0.000	0.000
23	A	62	SER	0	-0.061	-0.036	28.048	0.011	0.011	0.000	0.000	0.000	0.000
24	A	63	HIS	1	0.813	0.914	27.862	0.270	0.270	0.000	0.000	0.000	0.000
25	A	64	PRO	0	0.083	0.024	30.227	-0.028	-0.028	0.000	0.000	0.000	0.000
26	A	65	GLU	-1	-0.906	-0.942	32.712	-0.272	-0.272	0.000	0.000	0.000	0.000
27	A	66	THR	0	0.039	-0.041	26.431	-0.007	-0.007	0.000	0.000	0.000	0.000
28	A	67	ASN	0	-0.051	-0.010	28.202	-0.046	-0.046	0.000	0.000	0.000	0.000
29	A	68	GLN	0	0.023	0.025	29.272	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	69	VAL	0	-0.013	-0.005	28.775	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	70	MET	0	-0.025	-0.010	23.325	-0.038	-0.038	0.000	0.000	0.000	0.000
32	A	71	THR	0	-0.018	-0.022	27.227	-0.013	-0.013	0.000	0.000	0.000	0.000
33	A	72	ALA	0	-0.041	-0.023	29.284	-0.003	-0.003	0.000	0.000	0.000	0.000
34	A	73	VAL	0	0.037	-0.001	25.361	0.000	0.000	0.000	0.000	0.000	0.000
35	A	74	LEU	0	-0.007	0.004	23.304	-0.016	-0.016	0.000	0.000	0.000	0.000
36	A	75	GLN	0	-0.033	-0.006	27.239	0.010	0.010	0.000	0.000	0.000	0.000
37	A	76	GLN	0	-0.055	-0.033	30.497	0.002	0.002	0.000	0.000	0.000	0.000
38	A	77	GLN	0	-0.026	-0.001	27.553	-0.027	-0.027	0.000	0.000	0.000	0.000
39	A	78	VAL	0	-0.012	-0.008	23.338	-0.030	-0.030	0.000	0.000	0.000	0.000
40	A	79	GLY	0	0.037	0.030	26.607	-0.019	-0.019	0.000	0.000	0.000	0.000
41	A	80	PRO	0	-0.005	-0.030	29.681	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	81	GLY	0	0.010	0.005	31.296	-0.005	-0.005	0.000	0.000	0.000	0.000
43	A	82	SER	0	-0.001	0.013	29.517	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	83	VAL	0	0.082	0.026	25.879	-0.008	-0.008	0.000	0.000	0.000	0.000
45	A	84	ALA	0	-0.067	-0.135	28.487	-0.017	-0.017	0.000	0.000	0.000	0.000
46	A	85	SER	0	0.068	0.007	31.070	0.006	0.006	0.000	0.000	0.000	0.000
47	A	86	LEU	0	0.026	0.016	24.287	0.006	0.006	0.000	0.000	0.000	0.000
48	A	87	LYS	1	0.830	1.047	27.111	0.479	0.479	0.000	0.000	0.000	0.000
49	A	88	ALA	0	0.077	0.048	28.114	0.001	0.001	0.000	0.000	0.000	0.000
50	A	89	HIS	0	0.015	0.054	28.061	0.003	0.003	0.000	0.000	0.000	0.000
51	A	90	PHE	0	0.009	-0.008	23.168	0.007	0.007	0.000	0.000	0.000	0.000
52	A	91	GLU	-1	-0.927	-0.965	27.678	-0.451	-0.451	0.000	0.000	0.000	0.000
53	A	92	ALA	0	-0.047	-0.015	29.942	0.019	0.019	0.000	0.000	0.000	0.000
54	A	93	ASN	0	-0.055	-0.030	29.347	0.043	0.043	0.000	0.000	0.000	0.000
55	A	94	PRO	0	0.085	0.040	27.035	-0.027	-0.027	0.000	0.000	0.000	0.000
56	A	95	LYS	1	0.894	0.964	25.652	0.245	0.245	0.000	0.000	0.000	0.000
57	A	96	VAL	0	0.028	0.026	25.083	-0.025	-0.025	0.000	0.000	0.000	0.000
58	A	97	ALA	0	0.009	0.013	23.204	-0.040	-0.040	0.000	0.000	0.000	0.000
59	A	98	SER	0	-0.026	-0.035	21.071	-0.064	-0.064	0.000	0.000	0.000	0.000
60	A	99	ASP	-1	-0.791	-0.889	20.229	-0.405	-0.405	0.000	0.000	0.000	0.000
61	A	100	LEU	0	-0.027	-0.021	20.069	-0.025	-0.025	0.000	0.000	0.000	0.000
62	A	101	HIS	0	-0.004	0.007	14.925	-0.024	-0.024	0.000	0.000	0.000	0.000
63	A	102	ALA	0	0.011	-0.005	15.778	-0.146	-0.146	0.000	0.000	0.000	0.000
64	A	103	LEU	0	-0.039	-0.017	15.507	-0.036	-0.036	0.000	0.000	0.000	0.000
65	A	104	SER	0	-0.037	-0.026	13.793	-0.064	-0.064	0.000	0.000	0.000	0.000
66	A	105	GLN	0	0.025	0.006	10.843	-0.174	-0.174	0.000	0.000	0.000	0.000
67	A	106	PRO	0	0.042	0.041	9.362	-0.589	-0.589	0.000	0.000	0.000	0.000
68	A	107	LEU	0	-0.011	-0.008	7.697	-0.678	-0.678	0.000	0.000	0.000	0.000
69	A	108	THR	0	-0.021	-0.023	7.090	-0.940	-0.940	0.000	0.000	0.000	0.000
70	A	109	ASP	-1	-0.917	-0.958	5.695	-3.887	-3.887	0.000	0.000	0.000	0.000
71	A	110	LEU	0	0.015	-0.004	3.275	-7.569	-5.011	0.828	-1.111	-2.276	-0.005
72	A	111	SER	0	0.003	0.001	1.827	-17.672	-19.825	10.030	-4.196	-3.681	-0.062
73	A	112	THR	0	-0.066	-0.017	2.362	-2.811	3.470	0.537	-3.428	-3.389	-0.018
76	A	116	LEU	0	0.031	0.021	2.099	1.305	1.829	6.112	-2.168	-4.468	-0.004
77	A	117	PRO	0	-0.038	0.008	5.210	1.200	1.339	-0.002	-0.004	-0.133	0.000
78	A	118	ILE	0	0.052	0.023	7.387	-0.492	-0.492	0.000	0.000	0.000	0.000
79	A	119	SER	0	0.023	0.005	7.991	-0.356	-0.356	0.000	0.000	0.000	0.000
80	A	120	GLY	0	0.008	-0.010	9.019	0.385	0.385	0.000	0.000	0.000	0.000
81	A	121	LEU	0	0.091	0.043	12.009	0.095	0.095	0.000	0.000	0.000	0.000
82	A	122	GLN	0	-0.001	-0.008	7.879	-0.340	-0.340	0.000	0.000	0.000	0.000
83	A	123	ALA	0	-0.057	-0.031	10.613	0.208	0.208	0.000	0.000	0.000	0.000
84	A	124	ILE	0	-0.077	-0.019	13.104	0.112	0.112	0.000	0.000	0.000	0.000
85	A	125	GLY	0	-0.019	-0.002	13.545	0.072	0.072	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:40:CYS)