FMO DATABASE

FMODB ID: N8RJQ

Calculation Name: 1DF7-A-Xray547

Preferred Name: Dihydrofolate reductase

Target Type: SINGLE PROTEIN

Ligand Name: nadph dihydro-nicotinamide-adenine-dinucleotide phosphate | methotrexate | sulfate ion | glycerol

Ligand 3-letter code: NDP | MTX | SO4 | GOL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1DF7

Chain ID: A

ChEMBL ID: CHEMBL6065

UniProt ID: P9WNX1

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	159
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1542513.301876
FMO2-HF: Nuclear repulsion	1480676.570892
FMO2-HF: Total energy	-61836.730984
FMO2-MP2: Total energy	-62017.405842

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.
-102.613	-95.384	20.831	-10.694	-17.367	-0.116

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 : 0.773 / q_NPA : 0.885

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	GLY	0	0.062	0.036	2.826	5.873	6.419	2.911	-0.333	-3.125	-0.008
4	A	4	LEU	0	-0.028	-0.011	3.455	1.373	1.163	0.042	0.374	-0.206	0.000
89	A	89	PRO	0	0.035	0.015	3.017	-9.061	-8.409	0.040	-0.307	-0.385	-0.002
90	A	90	GLU	-1	-0.841	-0.922	1.772	-95.410	-95.011	14.063	-7.831	-6.631	-0.092
91	A	91	THR	0	0.003	-0.001	2.807	16.171	17.086	0.112	-0.170	-0.858	-0.002
92	A	92	TRP	0	-0.040	-0.028	2.837	-5.320	-3.354	1.715	-0.929	-2.752	-0.009
93	A	93	VAL	0	-0.002	-0.005	5.023	3.629	3.678	-0.001	-0.003	-0.045	0.000
108	A	108	THR	0	0.028	0.005	3.256	-4.426	-2.595	0.117	-0.897	-1.050	-0.007
109	A	109	ARG	1	0.865	0.909	3.072	33.302	34.359	1.833	-0.595	-2.295	0.004
110	A	110	CYS	0	-0.029	-0.003	5.096	-1.152	-1.128	-0.001	-0.003	-0.020	0.000
5	A	5	ILE	0	0.002	0.000	6.937	0.260	0.260	0.000	0.000	0.000	0.000
6	A	6	TRP	0	-0.033	-0.022	8.659	0.188	0.188	0.000	0.000	0.000	0.000
7	A	7	ALA	0	0.057	0.047	12.495	0.134	0.134	0.000	0.000	0.000	0.000
8	A	8	GLN	0	0.001	-0.013	15.827	-0.538	-0.538	0.000	0.000	0.000	0.000
9	A	9	ALA	0	0.034	0.036	18.614	0.215	0.215	0.000	0.000	0.000	0.000
10	A	10	THR	0	0.003	-0.023	21.358	-0.324	-0.324	0.000	0.000	0.000	0.000
11	A	11	SER	0	-0.051	-0.037	23.083	-0.215	-0.215	0.000	0.000	0.000	0.000
12	A	12	GLY	0	0.036	0.018	20.526	0.121	0.121	0.000	0.000	0.000	0.000
13	A	13	VAL	0	-0.034	-0.007	20.723	-0.451	-0.451	0.000	0.000	0.000	0.000
14	A	14	ILE	0	-0.002	-0.021	16.560	-0.228	-0.228	0.000	0.000	0.000	0.000
15	A	15	GLY	0	-0.009	-0.011	19.755	-0.155	-0.155	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.762	0.832	22.081	10.059	10.059	0.000	0.000	0.000	0.000
17	A	17	GLY	0	0.007	0.003	25.828	0.068	0.068	0.000	0.000	0.000	0.000
18	A	18	GLY	0	-0.043	-0.012	24.417	0.167	0.167	0.000	0.000	0.000	0.000
19	A	19	ASP	-1	-0.892	-0.929	23.289	-11.180	-11.180	0.000	0.000	0.000	0.000
20	A	20	ILE	0	0.013	-0.006	17.878	-0.154	-0.154	0.000	0.000	0.000	0.000
21	A	21	PRO	0	-0.054	-0.005	22.169	0.304	0.304	0.000	0.000	0.000	0.000
22	A	22	TRP	0	0.018	-0.001	19.041	0.501	0.501	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.946	0.978	23.485	9.810	9.810	0.000	0.000	0.000	0.000
24	A	24	LEU	0	0.029	0.014	19.530	0.280	0.280	0.000	0.000	0.000	0.000
25	A	25	PRO	0	-0.032	-0.023	20.186	-0.467	-0.467	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.779	-0.905	19.882	-11.542	-11.542	0.000	0.000	0.000	0.000
27	A	27	ASP	-1	-0.811	-0.882	15.233	-16.318	-16.318	0.000	0.000	0.000	0.000
28	A	28	GLN	0	-0.028	-0.014	15.204	-0.626	-0.626	0.000	0.000	0.000	0.000
29	A	29	ALA	0	-0.053	-0.012	15.797	-0.488	-0.488	0.000	0.000	0.000	0.000
30	A	30	HIS	0	0.112	0.056	11.183	-0.355	-0.355	0.000	0.000	0.000	0.000
31	A	31	PHE	0	0.036	0.011	10.789	-1.296	-1.296	0.000	0.000	0.000	0.000
32	A	32	ARG	1	0.898	0.960	10.795	14.012	14.012	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.967	-0.990	11.792	-17.090	-17.090	0.000	0.000	0.000	0.000
34	A	34	ILE	0	-0.011	0.008	6.009	-1.170	-1.170	0.000	0.000	0.000	0.000
35	A	35	THR	0	-0.019	-0.023	6.715	-2.431	-2.431	0.000	0.000	0.000	0.000
36	A	36	MET	0	-0.061	-0.017	8.095	-0.360	-0.360	0.000	0.000	0.000	0.000
37	A	37	GLY	0	0.023	0.019	9.432	-1.142	-1.142	0.000	0.000	0.000	0.000
38	A	38	HIS	1	0.814	0.919	5.006	33.717	33.717	0.000	0.000	0.000	0.000
39	A	39	THR	0	0.026	0.001	6.875	4.243	4.243	0.000	0.000	0.000	0.000
40	A	40	ILE	0	-0.041	-0.012	7.020	-2.816	-2.816	0.000	0.000	0.000	0.000
41	A	41	VAL	0	0.039	0.021	9.002	1.611	1.611	0.000	0.000	0.000	0.000
42	A	42	MET	0	-0.022	0.009	10.728	0.581	0.581	0.000	0.000	0.000	0.000
43	A	43	GLY	0	0.025	0.012	13.647	0.262	0.262	0.000	0.000	0.000	0.000
44	A	44	ARG	1	0.842	0.916	17.011	12.660	12.660	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.926	0.951	20.182	12.562	12.562	0.000	0.000	0.000	0.000
46	A	46	THR	0	0.017	0.021	15.252	0.430	0.430	0.000	0.000	0.000	0.000
47	A	47	TRP	0	0.050	0.019	17.672	-0.165	-0.165	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.849	-0.937	19.030	-12.178	-12.178	0.000	0.000	0.000	0.000
49	A	49	SER	0	-0.061	-0.029	19.622	0.291	0.291	0.000	0.000	0.000	0.000
50	A	50	LEU	0	0.007	0.020	16.210	0.160	0.160	0.000	0.000	0.000	0.000
51	A	51	PRO	0	0.005	-0.010	20.361	0.477	0.477	0.000	0.000	0.000	0.000
52	A	52	ALA	0	0.050	0.015	22.563	-0.301	-0.301	0.000	0.000	0.000	0.000
53	A	53	LYS	1	0.932	0.967	23.174	11.452	11.452	0.000	0.000	0.000	0.000
54	A	54	VAL	0	-0.092	-0.051	18.934	-0.067	-0.067	0.000	0.000	0.000	0.000
55	A	55	ARG	1	0.935	1.001	18.929	11.583	11.583	0.000	0.000	0.000	0.000
56	A	56	PRO	0	0.029	0.017	17.818	0.531	0.531	0.000	0.000	0.000	0.000
57	A	57	LEU	0	0.006	0.003	13.497	0.479	0.479	0.000	0.000	0.000	0.000
58	A	58	PRO	0	-0.029	-0.007	15.540	-0.843	-0.843	0.000	0.000	0.000	0.000
59	A	59	GLY	0	0.044	0.005	15.386	-0.445	-0.445	0.000	0.000	0.000	0.000
60	A	60	ARG	1	0.855	0.926	10.190	19.009	19.009	0.000	0.000	0.000	0.000
61	A	61	ARG	1	0.854	0.927	11.207	25.884	25.884	0.000	0.000	0.000	0.000
62	A	62	ASN	0	-0.002	-0.012	11.684	-0.946	-0.946	0.000	0.000	0.000	0.000
63	A	63	VAL	0	0.057	0.034	11.933	0.772	0.772	0.000	0.000	0.000	0.000
64	A	64	VAL	0	-0.021	-0.014	13.991	-0.358	-0.358	0.000	0.000	0.000	0.000
65	A	65	LEU	0	0.023	0.018	13.869	0.471	0.471	0.000	0.000	0.000	0.000
66	A	66	SER	0	-0.010	-0.026	17.582	1.010	1.010	0.000	0.000	0.000	0.000
67	A	67	ARG	1	0.985	0.991	21.411	13.835	13.835	0.000	0.000	0.000	0.000
68	A	68	GLN	0	-0.052	-0.023	23.850	0.262	0.262	0.000	0.000	0.000	0.000
69	A	69	ALA	0	0.023	0.004	25.503	-0.311	-0.311	0.000	0.000	0.000	0.000
70	A	70	ASP	-1	-0.855	-0.919	26.221	-11.556	-11.556	0.000	0.000	0.000	0.000
71	A	71	PHE	0	-0.055	-0.026	22.039	0.346	0.346	0.000	0.000	0.000	0.000
72	A	72	MET	0	0.034	0.014	24.381	-0.367	-0.367	0.000	0.000	0.000	0.000
73	A	73	ALA	0	-0.001	0.007	20.548	0.175	0.175	0.000	0.000	0.000	0.000
74	A	74	SER	0	0.007	-0.005	21.948	-0.232	-0.232	0.000	0.000	0.000	0.000
75	A	75	GLY	0	0.007	-0.009	21.465	0.006	0.006	0.000	0.000	0.000	0.000
76	A	76	ALA	0	-0.059	-0.033	17.531	-0.770	-0.770	0.000	0.000	0.000	0.000
77	A	77	GLU	-1	-0.823	-0.878	14.231	-21.100	-21.100	0.000	0.000	0.000	0.000
78	A	78	VAL	0	-0.037	-0.027	17.282	-0.571	-0.571	0.000	0.000	0.000	0.000
79	A	79	VAL	0	0.021	0.017	14.804	0.084	0.084	0.000	0.000	0.000	0.000
80	A	80	GLY	0	0.015	0.009	18.077	0.304	0.304	0.000	0.000	0.000	0.000
81	A	81	SER	0	-0.083	-0.079	16.023	-0.035	-0.035	0.000	0.000	0.000	0.000
82	A	82	LEU	0	0.025	-0.022	11.575	-0.643	-0.643	0.000	0.000	0.000	0.000
83	A	83	GLU	-1	-0.950	-0.957	11.020	-21.805	-21.805	0.000	0.000	0.000	0.000
84	A	84	GLU	-1	-0.781	-0.859	11.394	-19.288	-19.288	0.000	0.000	0.000	0.000
85	A	85	ALA	0	-0.019	-0.009	11.699	-1.261	-1.261	0.000	0.000	0.000	0.000
86	A	86	LEU	0	-0.066	-0.038	6.680	-1.760	-1.760	0.000	0.000	0.000	0.000
87	A	87	THR	0	0.016	0.017	6.230	-6.097	-6.097	0.000	0.000	0.000	0.000
88	A	88	SER	0	-0.030	0.004	6.395	0.795	0.795	0.000	0.000	0.000	0.000
94	A	94	ILE	0	0.002	-0.017	8.076	0.748	0.748	0.000	0.000	0.000	0.000
95	A	95	GLY	0	0.048	0.043	10.583	1.557	1.557	0.000	0.000	0.000	0.000
96	A	96	GLY	0	0.029	0.001	13.375	-0.134	-0.134	0.000	0.000	0.000	0.000
97	A	97	GLY	0	0.068	0.017	15.526	-0.732	-0.732	0.000	0.000	0.000	0.000
98	A	98	GLN	0	-0.030	-0.019	16.941	-0.009	-0.009	0.000	0.000	0.000	0.000
99	A	99	VAL	0	0.028	0.014	12.428	-0.095	-0.095	0.000	0.000	0.000	0.000
100	A	100	TYR	0	-0.021	-0.010	10.472	-0.603	-0.603	0.000	0.000	0.000	0.000
101	A	101	ALA	0	0.013	0.006	13.139	-0.840	-0.840	0.000	0.000	0.000	0.000
102	A	102	LEU	0	-0.050	-0.026	15.180	-0.247	-0.247	0.000	0.000	0.000	0.000
103	A	103	ALA	0	0.043	0.004	10.055	-0.611	-0.611	0.000	0.000	0.000	0.000
104	A	104	LEU	0	0.013	0.021	10.151	-2.553	-2.553	0.000	0.000	0.000	0.000
105	A	105	PRO	0	-0.031	-0.023	10.671	-1.261	-1.261	0.000	0.000	0.000	0.000
106	A	106	TYR	0	0.013	0.006	7.275	-0.272	-0.272	0.000	0.000	0.000	0.000
107	A	107	ALA	0	-0.044	0.006	5.961	-6.504	-6.504	0.000	0.000	0.000	0.000
111	A	111	GLU	-1	-0.791	-0.856	6.442	-23.726	-23.726	0.000	0.000	0.000	0.000
112	A	112	VAL	0	-0.004	-0.010	8.989	0.242	0.242	0.000	0.000	0.000	0.000
113	A	113	THR	0	-0.035	-0.044	12.603	0.525	0.525	0.000	0.000	0.000	0.000
114	A	114	GLU	-1	-0.753	-0.819	15.573	-12.320	-12.320	0.000	0.000	0.000	0.000
115	A	115	VAL	0	0.001	-0.022	18.885	0.309	0.309	0.000	0.000	0.000	0.000
116	A	116	ASP	-1	-0.846	-0.905	21.819	-9.974	-9.974	0.000	0.000	0.000	0.000
117	A	117	ILE	0	-0.028	-0.016	24.404	0.372	0.372	0.000	0.000	0.000	0.000
118	A	118	GLY	0	0.016	0.009	26.962	-0.132	-0.132	0.000	0.000	0.000	0.000
119	A	119	LEU	0	-0.010	-0.001	24.904	0.227	0.227	0.000	0.000	0.000	0.000
120	A	120	PRO	0	0.023	0.017	27.266	-0.390	-0.390	0.000	0.000	0.000	0.000
121	A	121	ARG	1	0.900	0.953	24.529	10.826	10.826	0.000	0.000	0.000	0.000
122	A	122	GLU	-1	-0.870	-0.928	27.875	-8.848	-8.848	0.000	0.000	0.000	0.000
123	A	123	ALA	0	-0.024	-0.022	28.513	-0.336	-0.336	0.000	0.000	0.000	0.000
124	A	124	GLY	0	-0.001	-0.003	27.847	0.174	0.174	0.000	0.000	0.000	0.000
125	A	125	ASP	-1	-0.762	-0.833	24.472	-10.837	-10.837	0.000	0.000	0.000	0.000
126	A	126	ALA	0	-0.077	-0.029	20.034	-0.315	-0.315	0.000	0.000	0.000	0.000
127	A	127	LEU	0	0.003	-0.019	20.441	0.203	0.203	0.000	0.000	0.000	0.000
128	A	128	ALA	0	0.027	0.010	16.420	-0.621	-0.621	0.000	0.000	0.000	0.000
129	A	129	PRO	0	-0.064	-0.016	12.877	0.570	0.570	0.000	0.000	0.000	0.000
130	A	130	VAL	0	-0.002	-0.012	15.877	-0.087	-0.087	0.000	0.000	0.000	0.000
131	A	131	LEU	0	-0.025	-0.005	12.166	-0.587	-0.587	0.000	0.000	0.000	0.000
132	A	132	ASP	-1	-0.812	-0.877	15.447	-17.266	-17.266	0.000	0.000	0.000	0.000
133	A	133	GLU	-1	-0.886	-0.961	15.980	-14.681	-14.681	0.000	0.000	0.000	0.000
134	A	134	THR	0	-0.121	-0.071	13.402	-0.765	-0.765	0.000	0.000	0.000	0.000
135	A	135	TRP	0	-0.066	-0.027	7.372	-2.252	-2.252	0.000	0.000	0.000	0.000
136	A	136	ARG	1	0.939	0.969	11.264	21.591	21.591	0.000	0.000	0.000	0.000
137	A	137	GLY	0	0.039	0.003	12.331	-1.229	-1.229	0.000	0.000	0.000	0.000
138	A	138	GLU	-1	-0.941	-0.955	12.009	-19.195	-19.195	0.000	0.000	0.000	0.000
139	A	139	THR	0	-0.031	-0.025	15.121	-0.203	-0.203	0.000	0.000	0.000	0.000
140	A	140	GLY	0	0.005	0.006	17.262	0.309	0.309	0.000	0.000	0.000	0.000
141	A	141	GLU	-1	-0.898	-0.971	18.500	-11.008	-11.008	0.000	0.000	0.000	0.000
142	A	142	TRP	0	-0.069	-0.031	21.254	-0.305	-0.305	0.000	0.000	0.000	0.000
143	A	143	ARG	1	0.934	0.981	17.418	13.933	13.933	0.000	0.000	0.000	0.000
144	A	144	PHE	0	0.046	0.014	24.047	0.034	0.034	0.000	0.000	0.000	0.000
145	A	145	SER	0	-0.049	-0.007	23.713	-0.163	-0.163	0.000	0.000	0.000	0.000
146	A	146	ARG	1	0.888	0.913	23.881	11.000	11.000	0.000	0.000	0.000	0.000
147	A	147	SER	0	-0.073	-0.035	26.057	0.294	0.294	0.000	0.000	0.000	0.000
148	A	148	GLY	0	0.017	0.016	28.447	0.209	0.209	0.000	0.000	0.000	0.000
149	A	149	LEU	0	-0.001	0.008	25.225	0.056	0.056	0.000	0.000	0.000	0.000
150	A	150	ARG	1	0.869	0.929	25.584	9.997	9.997	0.000	0.000	0.000	0.000
151	A	151	TYR	0	0.007	-0.017	18.655	-0.283	-0.283	0.000	0.000	0.000	0.000
152	A	152	ARG	1	0.883	0.935	19.236	12.690	12.690	0.000	0.000	0.000	0.000
153	A	153	LEU	0	-0.031	-0.013	14.196	-0.110	-0.110	0.000	0.000	0.000	0.000
154	A	154	TYR	0	-0.011	-0.020	13.971	0.639	0.639	0.000	0.000	0.000	0.000
155	A	155	SER	0	-0.016	-0.020	9.912	-0.448	-0.448	0.000	0.000	0.000	0.000
156	A	156	TYR	0	0.017	0.016	9.790	1.079	1.079	0.000	0.000	0.000	0.000
157	A	157	HIS	0	-0.058	-0.032	7.316	-2.081	-2.081	0.000	0.000	0.000	0.000
158	A	158	ARG	1	0.856	0.918	7.253	28.391	28.391	0.000	0.000	0.000	0.000
159	A	159	SER	-1	-0.935	-0.957	6.837	-31.210	-31.210	0.000	0.000	0.000	0.000

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