FMO DATABASE

FMODB ID: KQ943

Calculation Name: 7RGO-A-Xray547

Preferred Name:

Target Type:

Ligand Name: nadp nicotinamide-adenine-dinucleotide phosphate | 4'-chloro-3'-[(2s)-4-(2,4-diamino-6-ethylpyrimidin-5-yl)but-3-yn-2-yl][1,1'-biphenyl]-4-carboxamide

Ligand 3-letter code: NAP | 4SI

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 7RGO

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2025-10-06

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	157
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1526186.976665
FMO2-HF: Nuclear repulsion	1464317.572704
FMO2-HF: Total energy	-61869.403961
FMO2-MP2: Total energy	-62048.397272

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:1:MET)

Summations of interaction energy for fragment #1(A:1: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.
-180.046	-171.84	23.397	-9.127	-22.476	-0.112

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.809 / q_NPA : 0.918

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	3	VAL	0	0.080	0.038	2.967	-0.096	2.675	0.335	-1.243	-1.863	-0.008
4	A	4	SER	0	-0.010	-0.018	4.890	2.605	2.677	-0.001	-0.008	-0.063	0.000
40	A	40	TRP	0	0.069	0.032	4.355	2.102	2.248	-0.001	-0.004	-0.141	0.000
84	A	84	MET	0	-0.053	-0.037	4.127	-4.155	-3.534	0.032	-0.135	-0.518	0.000
85	A	85	TYR	0	-0.031	-0.004	3.980	-6.049	-4.857	0.097	-0.498	-0.791	-0.005
86	A	86	GLY	0	0.054	0.017	6.169	-1.703	-1.606	-0.001	-0.006	-0.090	0.000
87	A	87	LEU	0	-0.048	-0.032	2.144	-0.954	-1.505	4.021	-0.900	-2.570	-0.005
88	A	88	ALA	0	-0.012	-0.014	2.687	-5.559	-4.023	3.680	-1.845	-3.371	-0.011
89	A	89	GLU	-1	-0.928	-0.951	3.498	-26.971	-29.120	0.130	2.381	-0.363	-0.002
90	A	90	LEU	0	-0.073	-0.037	5.861	3.073	3.118	-0.001	-0.006	-0.038	0.000
91	A	91	THR	0	-0.077	-0.046	2.092	2.427	2.393	2.130	-0.559	-1.537	-0.006
92	A	92	ASP	-1	-0.870	-0.922	2.630	-59.459	-56.334	1.538	-1.850	-2.813	-0.024
93	A	93	HIS	0	-0.019	0.005	2.345	-17.698	-14.917	4.920	-3.526	-4.175	-0.042
94	A	94	VAL	0	0.031	0.022	2.152	2.856	1.608	6.499	-1.218	-4.032	-0.009
95	A	95	ILE	0	0.006	0.010	3.488	0.580	0.382	0.019	0.290	-0.111	0.000
5	A	5	LEU	0	-0.018	0.004	7.416	0.043	0.043	0.000	0.000	0.000	0.000
6	A	6	MET	0	-0.025	0.004	10.214	0.354	0.354	0.000	0.000	0.000	0.000
7	A	7	ALA	0	0.011	0.017	13.050	0.163	0.163	0.000	0.000	0.000	0.000
8	A	8	ALA	0	0.015	0.031	16.465	0.183	0.183	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.909	0.942	20.112	12.580	12.580	0.000	0.000	0.000	0.000
10	A	10	ALA	0	0.023	0.031	22.729	0.129	0.129	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.885	0.929	26.090	8.969	8.969	0.000	0.000	0.000	0.000
12	A	12	ASN	0	0.015	0.003	28.562	-0.386	-0.386	0.000	0.000	0.000	0.000
13	A	13	GLY	0	0.002	0.002	24.892	0.000	0.000	0.000	0.000	0.000	0.000
14	A	14	VAL	0	-0.025	0.008	24.145	-0.522	-0.522	0.000	0.000	0.000	0.000
15	A	15	ILE	0	-0.035	-0.050	19.235	-0.301	-0.301	0.000	0.000	0.000	0.000
16	A	16	GLY	0	-0.024	-0.013	22.919	-0.158	-0.158	0.000	0.000	0.000	0.000
17	A	17	CYS	0	0.003	0.002	24.455	0.277	0.277	0.000	0.000	0.000	0.000
18	A	18	GLY	0	0.028	0.010	26.939	0.192	0.192	0.000	0.000	0.000	0.000
19	A	19	PRO	0	-0.078	-0.043	23.845	-0.351	-0.351	0.000	0.000	0.000	0.000
20	A	20	HIS	0	0.000	0.013	23.970	-0.359	-0.359	0.000	0.000	0.000	0.000
21	A	21	ILE	0	0.058	0.029	20.444	-0.089	-0.089	0.000	0.000	0.000	0.000
22	A	22	PRO	0	-0.041	0.002	24.817	0.252	0.252	0.000	0.000	0.000	0.000
23	A	23	TRP	0	0.002	-0.016	22.668	0.309	0.309	0.000	0.000	0.000	0.000
24	A	24	SER	0	-0.013	-0.004	27.697	-0.259	-0.259	0.000	0.000	0.000	0.000
25	A	25	ALA	0	0.045	0.037	26.514	0.313	0.313	0.000	0.000	0.000	0.000
26	A	26	LYS	1	0.948	0.968	26.818	8.272	8.272	0.000	0.000	0.000	0.000
27	A	27	GLY	0	0.047	0.035	26.579	0.107	0.107	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.830	-0.886	20.484	-13.579	-13.579	0.000	0.000	0.000	0.000
29	A	29	GLN	0	0.055	0.010	21.106	-0.513	-0.513	0.000	0.000	0.000	0.000
30	A	30	LEU	0	-0.048	-0.024	20.595	-0.402	-0.402	0.000	0.000	0.000	0.000
31	A	31	LEU	0	0.019	0.024	18.880	-0.461	-0.461	0.000	0.000	0.000	0.000
32	A	32	PHE	0	0.065	0.024	13.920	-0.717	-0.717	0.000	0.000	0.000	0.000
33	A	33	LYS	1	0.924	0.975	15.645	12.194	12.194	0.000	0.000	0.000	0.000
34	A	34	ALA	0	-0.004	-0.001	16.819	-0.319	-0.319	0.000	0.000	0.000	0.000
35	A	35	LEU	0	0.010	0.000	13.003	-0.701	-0.701	0.000	0.000	0.000	0.000
36	A	36	THR	0	0.006	-0.018	11.505	-1.194	-1.194	0.000	0.000	0.000	0.000
37	A	37	TYR	0	-0.036	-0.014	12.116	0.040	0.040	0.000	0.000	0.000	0.000
38	A	38	ASN	0	-0.028	-0.029	12.105	-0.456	-0.456	0.000	0.000	0.000	0.000
39	A	39	GLN	0	-0.020	0.013	7.790	-3.712	-3.712	0.000	0.000	0.000	0.000
41	A	41	LEU	0	-0.054	-0.029	6.220	-1.418	-1.418	0.000	0.000	0.000	0.000
42	A	42	LEU	0	0.016	0.017	5.668	0.129	0.129	0.000	0.000	0.000	0.000
43	A	43	VAL	0	-0.012	-0.010	7.501	0.867	0.867	0.000	0.000	0.000	0.000
44	A	44	GLY	0	0.083	0.034	11.289	-0.119	-0.119	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.853	0.918	14.138	12.364	12.364	0.000	0.000	0.000	0.000
46	A	46	LYS	1	0.890	0.932	16.597	12.237	12.237	0.000	0.000	0.000	0.000
47	A	47	THR	0	0.009	-0.003	15.220	0.725	0.725	0.000	0.000	0.000	0.000
48	A	48	PHE	0	0.019	0.006	14.112	0.167	0.167	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.811	-0.892	16.288	-11.417	-11.417	0.000	0.000	0.000	0.000
50	A	50	SER	0	-0.042	-0.015	19.837	0.558	0.558	0.000	0.000	0.000	0.000
51	A	51	MET	0	-0.077	-0.017	13.480	0.083	0.083	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.042	0.020	18.900	0.264	0.264	0.000	0.000	0.000	0.000
53	A	53	ALA	0	-0.002	-0.006	15.801	-0.660	-0.660	0.000	0.000	0.000	0.000
54	A	54	LEU	0	-0.036	-0.008	16.610	0.356	0.356	0.000	0.000	0.000	0.000
55	A	55	PRO	0	0.061	0.031	16.040	-0.769	-0.769	0.000	0.000	0.000	0.000
56	A	56	ASN	0	-0.029	-0.017	15.658	-0.168	-0.168	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.860	0.947	11.717	16.027	16.027	0.000	0.000	0.000	0.000
58	A	58	LYS	1	0.906	0.970	8.818	19.758	19.758	0.000	0.000	0.000	0.000
59	A	59	TYR	0	-0.015	-0.026	8.951	-1.165	-1.165	0.000	0.000	0.000	0.000
60	A	60	ALA	0	0.066	0.044	6.314	0.244	0.244	0.000	0.000	0.000	0.000
61	A	61	VAL	0	-0.015	-0.011	8.244	0.311	0.311	0.000	0.000	0.000	0.000
62	A	62	VAL	0	0.011	0.016	10.021	0.087	0.087	0.000	0.000	0.000	0.000
63	A	63	THR	0	-0.029	-0.030	12.627	1.039	1.039	0.000	0.000	0.000	0.000
64	A	64	ARG	1	0.898	0.941	16.364	14.249	14.249	0.000	0.000	0.000	0.000
65	A	65	SER	0	-0.031	-0.011	19.130	0.373	0.373	0.000	0.000	0.000	0.000
66	A	66	ALA	0	0.030	0.005	19.821	-0.468	-0.468	0.000	0.000	0.000	0.000
67	A	67	TRP	0	-0.060	-0.030	15.573	0.008	0.008	0.000	0.000	0.000	0.000
68	A	68	THR	0	0.029	-0.014	18.071	-0.729	-0.729	0.000	0.000	0.000	0.000
69	A	69	ALA	0	-0.012	0.007	16.473	0.356	0.356	0.000	0.000	0.000	0.000
70	A	70	ASP	-1	-0.910	-0.956	18.360	-11.835	-11.835	0.000	0.000	0.000	0.000
71	A	71	ASN	0	0.007	-0.002	17.521	-0.178	-0.178	0.000	0.000	0.000	0.000
72	A	72	ASP	-1	-0.843	-0.919	16.377	-13.899	-13.899	0.000	0.000	0.000	0.000
73	A	73	ASN	0	-0.118	-0.055	14.075	-1.285	-1.285	0.000	0.000	0.000	0.000
74	A	74	VAL	0	-0.057	-0.041	12.037	-1.041	-1.041	0.000	0.000	0.000	0.000
75	A	75	ILE	0	0.027	0.028	9.016	0.471	0.471	0.000	0.000	0.000	0.000
76	A	76	VAL	0	-0.032	-0.014	10.954	-0.409	-0.409	0.000	0.000	0.000	0.000
77	A	77	PHE	0	0.037	0.022	7.935	-0.170	-0.170	0.000	0.000	0.000	0.000
78	A	78	PRO	0	0.014	0.009	12.277	0.429	0.429	0.000	0.000	0.000	0.000
79	A	79	SER	0	0.010	-0.001	12.747	0.175	0.175	0.000	0.000	0.000	0.000
80	A	80	ILE	0	0.042	0.003	8.621	-0.796	-0.796	0.000	0.000	0.000	0.000
81	A	81	GLU	-1	-0.953	-0.961	8.264	-23.753	-23.753	0.000	0.000	0.000	0.000
82	A	82	GLU	-1	-0.893	-0.959	8.595	-22.544	-22.544	0.000	0.000	0.000	0.000
83	A	83	ALA	0	-0.026	-0.015	6.851	-1.066	-1.066	0.000	0.000	0.000	0.000
96	A	96	VAL	0	-0.001	-0.010	6.996	1.675	1.675	0.000	0.000	0.000	0.000
97	A	97	SER	0	-0.001	-0.018	8.660	1.250	1.250	0.000	0.000	0.000	0.000
98	A	98	GLY	0	0.056	0.035	11.516	1.144	1.144	0.000	0.000	0.000	0.000
99	A	99	GLY	0	0.027	0.028	13.581	0.139	0.139	0.000	0.000	0.000	0.000
100	A	100	GLY	0	0.031	-0.007	15.915	-0.571	-0.571	0.000	0.000	0.000	0.000
101	A	101	GLU	-1	-0.972	-0.974	17.247	-13.150	-13.150	0.000	0.000	0.000	0.000
102	A	102	ILE	0	0.101	0.046	10.866	-0.209	-0.209	0.000	0.000	0.000	0.000
103	A	103	TYR	0	-0.003	-0.002	13.107	-0.612	-0.612	0.000	0.000	0.000	0.000
104	A	104	ARG	1	0.948	0.973	14.714	12.905	12.905	0.000	0.000	0.000	0.000
105	A	105	GLU	-1	-0.877	-0.930	13.717	-16.564	-16.564	0.000	0.000	0.000	0.000
106	A	106	THR	0	-0.013	-0.036	9.332	-1.102	-1.102	0.000	0.000	0.000	0.000
107	A	107	LEU	0	-0.006	0.012	10.818	-1.753	-1.753	0.000	0.000	0.000	0.000
108	A	108	PRO	0	0.010	-0.006	13.124	-0.616	-0.616	0.000	0.000	0.000	0.000
109	A	109	MET	0	-0.021	-0.005	8.311	-1.484	-1.484	0.000	0.000	0.000	0.000
110	A	110	ALA	0	-0.024	0.001	8.361	-3.159	-3.159	0.000	0.000	0.000	0.000
111	A	111	SER	0	-0.006	-0.011	7.714	1.056	1.056	0.000	0.000	0.000	0.000
112	A	112	THR	0	-0.033	-0.021	9.935	1.103	1.103	0.000	0.000	0.000	0.000
113	A	113	LEU	0	-0.015	-0.003	10.897	-1.013	-1.013	0.000	0.000	0.000	0.000
114	A	114	HIS	0	0.045	0.038	11.901	2.019	2.019	0.000	0.000	0.000	0.000
115	A	115	ILE	0	0.007	-0.009	15.094	0.137	0.137	0.000	0.000	0.000	0.000
116	A	116	SER	0	-0.009	-0.027	18.231	0.411	0.411	0.000	0.000	0.000	0.000
117	A	117	THR	0	-0.020	-0.011	21.097	0.063	0.063	0.000	0.000	0.000	0.000
118	A	118	ILE	0	-0.010	-0.013	23.337	0.277	0.277	0.000	0.000	0.000	0.000
119	A	119	ASP	-1	-0.871	-0.922	26.664	-8.918	-8.918	0.000	0.000	0.000	0.000
120	A	120	ILE	0	-0.006	-0.019	28.957	0.316	0.316	0.000	0.000	0.000	0.000
121	A	121	GLU	-1	-0.932	-0.970	30.046	-9.214	-9.214	0.000	0.000	0.000	0.000
122	A	122	PRO	0	-0.041	-0.004	29.199	0.286	0.286	0.000	0.000	0.000	0.000
123	A	123	GLU	-1	-0.862	-0.936	31.362	-8.405	-8.405	0.000	0.000	0.000	0.000
124	A	124	GLY	0	-0.035	-0.047	28.593	-0.179	-0.179	0.000	0.000	0.000	0.000
125	A	125	ASP	-1	-0.840	-0.904	27.255	-9.974	-9.974	0.000	0.000	0.000	0.000
126	A	126	VAL	0	-0.064	-0.018	21.237	-0.358	-0.358	0.000	0.000	0.000	0.000
127	A	127	PHE	0	0.039	0.013	23.561	0.003	0.003	0.000	0.000	0.000	0.000
128	A	128	PHE	0	-0.029	-0.016	15.902	-0.535	-0.535	0.000	0.000	0.000	0.000
129	A	129	PRO	0	-0.032	-0.019	17.276	0.498	0.498	0.000	0.000	0.000	0.000
130	A	130	ASN	0	-0.006	-0.002	20.417	-0.051	-0.051	0.000	0.000	0.000	0.000
131	A	131	ILE	0	0.007	0.007	18.163	-0.487	-0.487	0.000	0.000	0.000	0.000
132	A	132	PRO	0	-0.013	0.006	17.999	0.623	0.623	0.000	0.000	0.000	0.000
133	A	133	ASN	0	0.020	-0.008	19.946	-0.892	-0.892	0.000	0.000	0.000	0.000
134	A	134	THR	0	0.043	0.026	16.912	0.256	0.256	0.000	0.000	0.000	0.000
135	A	135	PHE	0	-0.057	-0.036	12.826	-1.064	-1.064	0.000	0.000	0.000	0.000
136	A	136	GLU	-1	-0.899	-0.945	18.086	-13.144	-13.144	0.000	0.000	0.000	0.000
137	A	137	VAL	0	-0.044	-0.019	18.918	-0.951	-0.951	0.000	0.000	0.000	0.000
138	A	138	VAL	0	-0.001	-0.009	17.528	0.268	0.268	0.000	0.000	0.000	0.000
139	A	139	PHE	0	-0.038	-0.019	20.079	0.347	0.347	0.000	0.000	0.000	0.000
140	A	140	GLU	-1	-0.821	-0.896	21.375	-12.011	-12.011	0.000	0.000	0.000	0.000
141	A	141	GLN	0	-0.026	-0.002	23.877	0.118	0.118	0.000	0.000	0.000	0.000
142	A	142	HIS	0	-0.036	-0.030	25.410	-0.043	-0.043	0.000	0.000	0.000	0.000
143	A	143	PHE	0	-0.019	-0.012	24.149	0.137	0.137	0.000	0.000	0.000	0.000
144	A	144	SER	0	0.020	0.008	29.045	0.058	0.058	0.000	0.000	0.000	0.000
145	A	145	SER	0	-0.056	-0.049	29.939	0.050	0.050	0.000	0.000	0.000	0.000
146	A	146	ASN	0	-0.061	-0.041	31.703	0.006	0.006	0.000	0.000	0.000	0.000
147	A	147	ILE	0	0.015	0.011	30.112	0.171	0.171	0.000	0.000	0.000	0.000
148	A	148	ASN	0	-0.002	-0.001	29.973	-0.232	-0.232	0.000	0.000	0.000	0.000
149	A	149	TYR	0	0.012	0.000	24.163	-0.013	-0.013	0.000	0.000	0.000	0.000
150	A	150	CYS	0	0.000	0.019	25.671	-0.016	-0.016	0.000	0.000	0.000	0.000
151	A	151	TYR	0	-0.032	-0.029	16.304	-0.107	-0.107	0.000	0.000	0.000	0.000
152	A	152	GLN	0	0.023	-0.007	20.469	-0.159	-0.159	0.000	0.000	0.000	0.000
153	A	153	ILE	0	-0.040	-0.010	15.202	-0.698	-0.698	0.000	0.000	0.000	0.000
154	A	154	TRP	0	0.015	-0.009	16.159	0.422	0.422	0.000	0.000	0.000	0.000
155	A	155	GLN	0	-0.007	-0.019	13.052	-2.987	-2.987	0.000	0.000	0.000	0.000
156	A	156	LYS	1	0.819	0.913	10.577	27.848	27.848	0.000	0.000	0.000	0.000
157	A	157	GLY	-1	-0.907	-0.934	14.243	-21.246	-21.246	0.000	0.000	0.000	0.000

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