FMO DATABASE

FMODB ID: 2MMYR

Calculation Name: 2RC3-A-Xray547

Preferred Name:

Target Type:

Ligand Name: nicotinamide-adenine-dinucleotide | bromide ion

Ligand 3-letter code: NAD | BR

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2RC3

Chain ID: A

ChEMBL ID:

UniProt ID: Q82SE2

Base Structure: X-ray

Registration Date: 2025-10-05

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	127
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1055136.641059
FMO2-HF: Nuclear repulsion	1004523.302623
FMO2-HF: Total energy	-50613.338436
FMO2-MP2: Total energy	-50756.868878

3D Structure Molmil

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:23:MET)

Summations of interaction energy for fragment #1(A:23:MET)

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.
-126.36	-119.624	5.649	-4.761	-7.624	-0.039

Interaction energy analysis for fragmet #1(A:23:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.833 / q_NPA : 0.921

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	25	THR	0	0.065	0.031	3.400	-1.138	0.730	0.053	-0.765	-1.155	-0.001
4	A	26	VAL	0	0.059	0.022	5.233	0.856	0.883	-0.001	-0.002	-0.024	0.000
88	A	110	THR	0	0.012	-0.013	2.435	-4.100	-4.264	3.643	-0.849	-2.630	-0.003
89	A	111	ASN	0	0.050	0.004	2.544	-10.178	-7.388	1.278	-1.969	-2.100	-0.022
90	A	112	GLU	-1	-0.923	-0.951	2.748	-49.340	-47.125	0.676	-1.176	-1.715	-0.013
5	A	27	LYS	1	0.950	0.985	8.686	21.836	21.836	0.000	0.000	0.000	0.000
6	A	28	HIS	0	-0.015	-0.015	6.861	2.990	2.990	0.000	0.000	0.000	0.000
7	A	29	LEU	0	0.001	0.008	7.232	0.977	0.977	0.000	0.000	0.000	0.000
8	A	30	LEU	0	0.003	-0.004	10.319	1.965	1.965	0.000	0.000	0.000	0.000
9	A	31	GLN	0	-0.049	-0.021	12.018	2.108	2.108	0.000	0.000	0.000	0.000
10	A	32	GLU	0	-0.089	-0.070	9.374	0.169	0.169	0.000	0.000	0.000	0.000
11	A	33	LYS	1	0.774	0.898	14.051	18.564	18.564	0.000	0.000	0.000	0.000
12	A	34	GLY	0	0.010	0.013	16.094	1.172	1.172	0.000	0.000	0.000	0.000
13	A	35	HIS	0	-0.034	-0.037	15.403	-0.725	-0.725	0.000	0.000	0.000	0.000
14	A	36	THR	0	-0.008	-0.003	19.332	0.512	0.512	0.000	0.000	0.000	0.000
15	A	37	VAL	0	-0.003	0.009	21.118	-0.449	-0.449	0.000	0.000	0.000	0.000
16	A	38	VAL	0	0.013	0.014	23.262	0.536	0.536	0.000	0.000	0.000	0.000
17	A	39	ALA	0	0.019	0.016	26.037	-0.085	-0.085	0.000	0.000	0.000	0.000
18	A	40	ILE	0	-0.023	-0.007	28.038	0.298	0.298	0.000	0.000	0.000	0.000
19	A	41	GLY	0	0.083	0.051	31.057	-0.124	-0.124	0.000	0.000	0.000	0.000
20	A	42	PRO	0	0.002	-0.020	32.776	0.018	0.018	0.000	0.000	0.000	0.000
21	A	43	ASP	-1	-0.861	-0.929	34.257	-7.932	-7.932	0.000	0.000	0.000	0.000
22	A	44	ASP	-1	-0.800	-0.865	35.808	-8.126	-8.126	0.000	0.000	0.000	0.000
23	A	45	SER	0	-0.008	-0.004	37.348	-0.087	-0.087	0.000	0.000	0.000	0.000
24	A	46	VAL	0	0.020	-0.011	34.920	-0.246	-0.246	0.000	0.000	0.000	0.000
25	A	47	PHE	0	-0.005	-0.007	35.864	-0.160	-0.160	0.000	0.000	0.000	0.000
26	A	48	ASN	0	-0.002	-0.016	37.090	-0.056	-0.056	0.000	0.000	0.000	0.000
27	A	49	ALA	0	0.009	0.008	32.206	-0.207	-0.207	0.000	0.000	0.000	0.000
28	A	50	MET	0	-0.016	-0.011	30.804	-0.354	-0.354	0.000	0.000	0.000	0.000
29	A	51	GLN	0	-0.016	-0.009	33.324	-0.184	-0.184	0.000	0.000	0.000	0.000
30	A	52	LYS	1	0.894	0.952	30.176	9.999	9.999	0.000	0.000	0.000	0.000
31	A	53	MET	0	-0.041	-0.014	27.995	-0.259	-0.259	0.000	0.000	0.000	0.000
32	A	54	ALA	0	0.011	0.008	29.347	-0.292	-0.292	0.000	0.000	0.000	0.000
33	A	55	ALA	0	-0.059	-0.021	31.824	-0.036	-0.036	0.000	0.000	0.000	0.000
34	A	56	ASP	-1	-0.894	-0.960	27.391	-10.779	-10.779	0.000	0.000	0.000	0.000
35	A	57	ASN	0	-0.071	-0.026	26.278	-0.255	-0.255	0.000	0.000	0.000	0.000
36	A	58	ILE	0	-0.029	-0.005	23.787	-0.649	-0.649	0.000	0.000	0.000	0.000
37	A	59	GLY	0	0.066	0.023	23.814	0.402	0.402	0.000	0.000	0.000	0.000
38	A	60	ALA	0	-0.059	-0.060	22.783	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	61	LEU	0	-0.001	0.016	24.927	0.075	0.075	0.000	0.000	0.000	0.000
40	A	62	LEU	0	0.007	0.007	21.401	-0.028	-0.028	0.000	0.000	0.000	0.000
41	A	63	VAL	0	-0.020	-0.010	25.514	0.425	0.425	0.000	0.000	0.000	0.000
42	A	64	MET	0	0.016	0.023	26.545	-0.225	-0.225	0.000	0.000	0.000	0.000
43	A	65	LYS	1	0.928	0.947	29.720	8.763	8.763	0.000	0.000	0.000	0.000
44	A	66	ASP	-1	-0.820	-0.909	32.213	-8.603	-8.603	0.000	0.000	0.000	0.000
45	A	67	GLU	-1	-0.898	-0.951	28.507	-10.311	-10.311	0.000	0.000	0.000	0.000
46	A	68	LYS	1	0.795	0.906	27.857	8.599	8.599	0.000	0.000	0.000	0.000
47	A	69	LEU	0	0.039	0.011	22.539	0.153	0.153	0.000	0.000	0.000	0.000
48	A	70	VAL	0	-0.057	-0.039	26.651	0.050	0.050	0.000	0.000	0.000	0.000
49	A	71	GLY	0	0.021	-0.003	26.630	0.228	0.228	0.000	0.000	0.000	0.000
50	A	72	ILE	0	-0.035	0.000	21.429	-0.191	-0.191	0.000	0.000	0.000	0.000
51	A	73	LEU	0	0.007	0.008	25.469	0.311	0.311	0.000	0.000	0.000	0.000
52	A	74	THR	0	0.007	-0.025	23.699	-0.356	-0.356	0.000	0.000	0.000	0.000
53	A	75	GLU	-1	-0.844	-0.931	25.917	-11.450	-11.450	0.000	0.000	0.000	0.000
54	A	76	ARG	1	0.900	0.972	24.436	12.521	12.521	0.000	0.000	0.000	0.000
55	A	77	ASP	-1	-0.716	-0.812	27.561	-10.799	-10.799	0.000	0.000	0.000	0.000
56	A	78	PHE	0	0.055	0.019	29.958	0.353	0.353	0.000	0.000	0.000	0.000
57	A	79	SER	0	-0.049	-0.040	30.341	0.287	0.287	0.000	0.000	0.000	0.000
58	A	80	ARG	1	0.879	0.942	29.609	10.286	10.286	0.000	0.000	0.000	0.000
59	A	81	LYS	1	0.863	0.928	29.615	10.275	10.275	0.000	0.000	0.000	0.000
60	A	82	SER	0	-0.039	-0.025	35.305	0.294	0.294	0.000	0.000	0.000	0.000
61	A	83	TYR	0	-0.004	-0.009	36.112	0.110	0.110	0.000	0.000	0.000	0.000
62	A	84	LEU	0	-0.028	-0.002	37.175	0.169	0.169	0.000	0.000	0.000	0.000
63	A	85	LEU	0	-0.035	-0.010	38.708	0.109	0.109	0.000	0.000	0.000	0.000
64	A	86	ASP	-1	-0.918	-0.943	42.280	-6.524	-6.524	0.000	0.000	0.000	0.000
65	A	87	LYS	1	0.828	0.884	41.955	7.490	7.490	0.000	0.000	0.000	0.000
66	A	88	PRO	0	0.022	0.033	43.267	-0.196	-0.196	0.000	0.000	0.000	0.000
67	A	89	VAL	0	0.026	-0.008	38.764	-0.053	-0.053	0.000	0.000	0.000	0.000
68	A	90	LYS	1	0.893	0.944	40.111	6.989	6.989	0.000	0.000	0.000	0.000
69	A	91	ASP	-1	-0.850	-0.912	42.692	-6.830	-6.830	0.000	0.000	0.000	0.000
70	A	92	THR	0	-0.051	-0.026	38.314	0.038	0.038	0.000	0.000	0.000	0.000
71	A	93	GLN	0	-0.015	-0.024	38.348	-0.077	-0.077	0.000	0.000	0.000	0.000
72	A	94	VAL	0	0.022	0.010	31.764	-0.115	-0.115	0.000	0.000	0.000	0.000
73	A	95	LYS	1	0.832	0.882	33.545	7.620	7.620	0.000	0.000	0.000	0.000
74	A	96	GLU	-1	-0.844	-0.889	34.621	-7.707	-7.707	0.000	0.000	0.000	0.000
75	A	97	ILE	0	-0.006	-0.009	33.080	-0.021	-0.021	0.000	0.000	0.000	0.000
76	A	98	MET	0	-0.052	-0.004	29.213	-0.264	-0.264	0.000	0.000	0.000	0.000
77	A	99	THR	0	-0.028	-0.029	24.334	0.204	0.204	0.000	0.000	0.000	0.000
78	A	100	ARG	1	0.922	0.950	26.524	8.966	8.966	0.000	0.000	0.000	0.000
79	A	101	GLN	0	0.003	0.014	22.228	0.288	0.288	0.000	0.000	0.000	0.000
80	A	102	VAL	0	-0.014	-0.011	20.330	-0.315	-0.315	0.000	0.000	0.000	0.000
81	A	103	ALA	0	0.018	0.019	16.957	-0.058	-0.058	0.000	0.000	0.000	0.000
82	A	104	TYR	0	-0.042	-0.032	16.360	0.286	0.286	0.000	0.000	0.000	0.000
83	A	105	VAL	0	0.008	0.013	10.862	-0.519	-0.519	0.000	0.000	0.000	0.000
84	A	106	ASP	-1	-0.786	-0.890	11.344	-20.154	-20.154	0.000	0.000	0.000	0.000
85	A	107	LEU	0	-0.006	-0.030	10.841	-1.894	-1.894	0.000	0.000	0.000	0.000
86	A	108	ASN	0	-0.050	-0.032	8.147	-2.600	-2.600	0.000	0.000	0.000	0.000
87	A	109	ASN	0	0.002	0.019	6.943	-0.378	-0.378	0.000	0.000	0.000	0.000
91	A	113	ASP	-1	-0.764	-0.868	4.953	-27.406	-27.406	0.000	0.000	0.000	0.000
92	A	114	CYS	0	-0.065	-0.033	6.957	3.974	3.974	0.000	0.000	0.000	0.000
93	A	115	MET	0	0.005	-0.001	6.286	3.441	3.441	0.000	0.000	0.000	0.000
94	A	116	ALA	0	0.046	0.042	8.791	2.561	2.561	0.000	0.000	0.000	0.000
95	A	117	LEU	0	0.011	-0.002	10.497	2.263	2.263	0.000	0.000	0.000	0.000
96	A	118	ILE	0	-0.043	-0.028	12.482	1.611	1.611	0.000	0.000	0.000	0.000
97	A	119	THR	0	-0.059	-0.037	13.153	1.569	1.569	0.000	0.000	0.000	0.000
98	A	120	GLU	-1	-0.931	-0.975	13.505	-17.179	-17.179	0.000	0.000	0.000	0.000
99	A	121	MET	0	-0.063	-0.034	15.947	0.976	0.976	0.000	0.000	0.000	0.000
100	A	122	ARG	1	0.894	0.965	17.683	14.991	14.991	0.000	0.000	0.000	0.000
101	A	123	VAL	0	-0.033	0.000	16.859	0.962	0.962	0.000	0.000	0.000	0.000
102	A	124	ARG	1	0.962	0.962	17.621	12.640	12.640	0.000	0.000	0.000	0.000
103	A	125	HIS	0	-0.014	-0.013	17.473	-1.086	-1.086	0.000	0.000	0.000	0.000
104	A	126	LEU	0	0.019	0.027	12.350	0.312	0.312	0.000	0.000	0.000	0.000
105	A	127	PRO	0	-0.010	-0.008	15.668	-0.495	-0.495	0.000	0.000	0.000	0.000
106	A	128	VAL	0	0.009	0.007	13.564	-0.629	-0.629	0.000	0.000	0.000	0.000
107	A	129	LEU	0	-0.041	-0.028	15.908	1.008	1.008	0.000	0.000	0.000	0.000
108	A	130	ASP	-1	-0.923	-0.981	15.904	-17.112	-17.112	0.000	0.000	0.000	0.000
109	A	131	ASP	-1	-0.917	-0.954	17.694	-12.026	-12.026	0.000	0.000	0.000	0.000
110	A	132	GLY	0	-0.002	0.012	20.507	0.577	0.577	0.000	0.000	0.000	0.000
111	A	133	LYS	1	0.934	0.978	21.649	12.686	12.686	0.000	0.000	0.000	0.000
112	A	134	VAL	0	0.002	-0.006	20.278	-0.658	-0.658	0.000	0.000	0.000	0.000
113	A	135	ILE	0	-0.021	-0.022	15.526	0.544	0.544	0.000	0.000	0.000	0.000
114	A	136	GLY	0	0.050	0.011	17.304	-0.452	-0.452	0.000	0.000	0.000	0.000
115	A	137	LEU	0	-0.030	-0.003	17.102	0.331	0.331	0.000	0.000	0.000	0.000
116	A	138	LEU	0	0.025	0.032	10.702	-0.260	-0.260	0.000	0.000	0.000	0.000
117	A	139	SER	0	0.001	-0.030	14.807	1.032	1.032	0.000	0.000	0.000	0.000
118	A	140	ILE	0	0.024	0.003	14.105	-1.150	-1.150	0.000	0.000	0.000	0.000
119	A	141	GLY	0	0.015	0.010	14.684	-0.664	-0.664	0.000	0.000	0.000	0.000
120	A	142	ASP	-1	-0.811	-0.882	13.559	-19.033	-19.033	0.000	0.000	0.000	0.000
121	A	143	LEU	0	-0.003	-0.010	8.181	-1.608	-1.608	0.000	0.000	0.000	0.000
122	A	144	VAL	0	-0.006	0.000	10.473	-1.729	-1.729	0.000	0.000	0.000	0.000
123	A	145	LYS	1	0.973	0.988	12.999	18.714	18.714	0.000	0.000	0.000	0.000
124	A	146	ASP	-1	-0.804	-0.872	7.089	-40.650	-40.650	0.000	0.000	0.000	0.000
125	A	147	ALA	0	-0.032	-0.017	8.281	-2.416	-2.416	0.000	0.000	0.000	0.000
126	A	148	ILE	0	-0.083	-0.035	9.340	0.241	0.241	0.000	0.000	0.000	0.000
127	A	149	SER	-1	-0.972	-0.972	10.420	-24.100	-24.100	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:23:MET)