FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: 1V2JZ

Calculation Name: 6NJU-D-Xray547

Preferred Name:

Target Type:

Ligand Name: 2-amino-2-hydroxymethyl-propane-1,3-diol

Ligand 3-letter code: TRS

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6NJU

Chain ID: D

ChEMBL ID:

UniProt ID: O08600

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 229
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2831768.824357
FMO2-HF: Nuclear repulsion 2742209.150653
FMO2-HF: Total energy -89559.673704
FMO2-MP2: Total energy -89824.822442


3D Structure Molmil
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
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/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:19:GLU)


Summations of interaction energy for fragment #1(A:19:GLU)
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.
4.1157.7310.496-1.507-2.6050
Interaction energy analysis for fragmet #1(A:19:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.076 / q_NPA : -0.052
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   
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].
3A21ALA00.0590.0323.4883.3345.428-0.005-0.931-1.1580.000
4A22LYS10.9150.9682.667-4.924-3.6170.500-0.541-1.2660.000
5A23TYR0-0.001-0.0104.2582.3572.5720.001-0.035-0.1810.000
6A24GLY00.0420.0407.5621.2451.2450.0000.0000.0000.000
7A25LEU0-0.013-0.0228.380-0.683-0.6830.0000.0000.0000.000
8A26PRO00.0060.00311.5610.4220.4220.0000.0000.0000.000
9A27GLY00.0070.00014.9900.4350.4350.0000.0000.0000.000
10A28VAL0-0.0230.00315.267-0.266-0.2660.0000.0000.0000.000
11A29ALA00.0360.00817.0590.3020.3020.0000.0000.0000.000
12A30GLN00.0030.01520.0260.0140.0140.0000.0000.0000.000
13A31LEU00.0270.01522.3480.1670.1670.0000.0000.0000.000
14A32ARG10.7990.87823.6391.4891.4890.0000.0000.0000.000
15A33SER00.0130.01627.6780.0530.0530.0000.0000.0000.000
16A34ARG10.7910.90329.8740.9900.9900.0000.0000.0000.000
17A35GLU-1-0.861-0.92833.488-0.749-0.7490.0000.0000.0000.000
18A36SER0-0.081-0.05636.8070.0060.0060.0000.0000.0000.000
19A37TYR0-0.036-0.04432.8780.0040.0040.0000.0000.0000.000
20A38VAL0-0.0010.00928.466-0.043-0.0430.0000.0000.0000.000
21A39LEU0-0.0190.00428.4300.0440.0440.0000.0000.0000.000
22A40SER00.0080.00724.853-0.135-0.1350.0000.0000.0000.000
23A41TYR0-0.023-0.03326.0300.1080.1080.0000.0000.0000.000
24A42ASP-1-0.735-0.84224.986-1.349-1.3490.0000.0000.0000.000
25A43PRO0-0.027-0.01722.6340.0950.0950.0000.0000.0000.000
26A44ARG10.9250.96125.5080.9170.9170.0000.0000.0000.000
27A45THR0-0.040-0.05327.1560.1000.1000.0000.0000.0000.000
28A46ARG10.7440.88127.5690.9490.9490.0000.0000.0000.000
29A47GLY00.0840.03630.1820.0670.0670.0000.0000.0000.000
30A48ALA0-0.019-0.00229.724-0.086-0.0860.0000.0000.0000.000
31A49LEU0-0.023-0.00925.5640.0580.0580.0000.0000.0000.000
32A50TRP00.003-0.01726.5560.0610.0610.0000.0000.0000.000
33A51VAL0-0.010-0.00630.952-0.069-0.0690.0000.0000.0000.000
34A52LEU0-0.020-0.00532.0480.0460.0460.0000.0000.0000.000
35A53GLU-1-0.743-0.86534.379-0.701-0.7010.0000.0000.0000.000
36A54GLN0-0.005-0.01337.486-0.034-0.0340.0000.0000.0000.000
37A55LEU0-0.062-0.02539.3620.0170.0170.0000.0000.0000.000
38A56ARG10.8860.91442.7120.5930.5930.0000.0000.0000.000
39A57PRO00.0360.01945.3890.0030.0030.0000.0000.0000.000
40A58GLU-1-0.872-0.93445.854-0.548-0.5480.0000.0000.0000.000
41A59ARG10.9010.95140.1730.6830.6830.0000.0000.0000.000
42A60LEU0-0.021-0.01046.385-0.001-0.0010.0000.0000.0000.000
43A61ARG10.8000.89048.6710.4040.4040.0000.0000.0000.000
44A62GLY00.0470.00650.303-0.013-0.0130.0000.0000.0000.000
45A63ASP-1-0.872-0.91151.316-0.379-0.3790.0000.0000.0000.000
46A64GLY00.0010.02748.3060.0040.0040.0000.0000.0000.000
47A65ASP-1-0.805-0.92549.291-0.415-0.4150.0000.0000.0000.000
48A66ARG10.8010.89043.4620.5200.5200.0000.0000.0000.000
49A67SER00.0310.02248.4870.0060.0060.0000.0000.0000.000
50A68ALA00.0480.01847.822-0.018-0.0180.0000.0000.0000.000
51A69CYS0-0.033-0.02247.164-0.002-0.0020.0000.0000.0000.000
52A70ASP-1-0.884-0.93645.058-0.493-0.4930.0000.0000.0000.000
53A71PHE00.0360.02840.471-0.018-0.0180.0000.0000.0000.000
54A72ARG10.9330.98737.9640.6860.6860.0000.0000.0000.000
55A73GLU-1-0.832-0.91534.831-0.680-0.6800.0000.0000.0000.000
56A74ASP-1-0.763-0.84031.112-1.041-1.0410.0000.0000.0000.000
57A75ASP-1-0.831-0.92130.767-0.818-0.8180.0000.0000.0000.000
58A76SER0-0.096-0.05727.285-0.075-0.0750.0000.0000.0000.000
59A77VAL0-0.0230.00626.095-0.143-0.1430.0000.0000.0000.000
60A78HIS00.0440.02223.0040.1020.1020.0000.0000.0000.000
61A79ALA00.0710.02426.1350.0140.0140.0000.0000.0000.000
62A80TYR0-0.012-0.01223.9450.0340.0340.0000.0000.0000.000
63A81HIS00.004-0.00122.7900.0690.0690.0000.0000.0000.000
64A82ARG10.8160.92627.9590.8230.8230.0000.0000.0000.000
65A83ALA00.0400.03430.8600.0570.0570.0000.0000.0000.000
66A84THR0-0.003-0.02934.3410.0120.0120.0000.0000.0000.000
67A85ASN00.041-0.01836.8650.0240.0240.0000.0000.0000.000
68A86ALA0-0.089-0.05239.7410.0290.0290.0000.0000.0000.000
69A87ASP-1-0.768-0.85336.369-0.558-0.5580.0000.0000.0000.000
70A88TYR00.1280.04837.2520.0190.0190.0000.0000.0000.000
71A89ARG10.9250.98542.1810.4250.4250.0000.0000.0000.000
72A90GLY00.0140.00445.1710.0080.0080.0000.0000.0000.000
73A91SER0-0.050-0.03343.4240.0080.0080.0000.0000.0000.000
74A92GLY00.0110.01045.3880.0010.0010.0000.0000.0000.000
75A93PHE0-0.047-0.02543.6380.0020.0020.0000.0000.0000.000
76A94ASP-1-0.744-0.84645.496-0.419-0.4190.0000.0000.0000.000
77A95ARG10.8050.90041.3140.4710.4710.0000.0000.0000.000
78A96GLY00.0420.02742.3780.0020.0020.0000.0000.0000.000
79A97ALA0-0.017-0.01439.804-0.033-0.0330.0000.0000.0000.000
80A98LEU0-0.015-0.00335.0460.0110.0110.0000.0000.0000.000
81A99ALA0-0.011-0.00737.4470.0110.0110.0000.0000.0000.000
82A100ALA00.0460.03039.1790.0100.0100.0000.0000.0000.000
83A101ALA00.0460.01642.8710.0010.0010.0000.0000.0000.000
84A102ALA0-0.046-0.03644.4940.0060.0060.0000.0000.0000.000
85A103ASN0-0.048-0.04542.2650.0480.0480.0000.0000.0000.000
86A104HIS0-0.042-0.03340.113-0.011-0.0110.0000.0000.0000.000
87A105ARG10.8770.90444.4290.4410.4410.0000.0000.0000.000
88A106TRP0-0.0290.00541.1170.0210.0210.0000.0000.0000.000
89A107SER00.0190.02042.2740.0120.0120.0000.0000.0000.000
90A108GLN00.010-0.01244.3130.0000.0000.0000.0000.0000.000
91A109ARG10.8770.93334.2130.8040.8040.0000.0000.0000.000
92A110ALA00.0310.01339.915-0.033-0.0330.0000.0000.0000.000
93A111MET0-0.0040.03740.681-0.017-0.0170.0000.0000.0000.000
94A112ASP-1-0.812-0.89041.171-0.572-0.5720.0000.0000.0000.000
95A113ASP-1-0.790-0.89136.321-0.847-0.8470.0000.0000.0000.000
96A114THR0-0.087-0.03337.229-0.029-0.0290.0000.0000.0000.000
97A115PHE00.0330.01839.4490.0020.0020.0000.0000.0000.000
98A116TYR0-0.022-0.00234.6410.0090.0090.0000.0000.0000.000
99A117LEU0-0.019-0.02535.839-0.014-0.0140.0000.0000.0000.000
100A118SER0-0.050-0.04531.0250.0130.0130.0000.0000.0000.000
101A119ASN0-0.033-0.03232.883-0.059-0.0590.0000.0000.0000.000
102A120VAL0-0.046-0.01035.3190.0410.0410.0000.0000.0000.000
103A121ALA00.0150.01435.954-0.036-0.0360.0000.0000.0000.000
104A122PRO0-0.044-0.01737.6460.0300.0300.0000.0000.0000.000
105A123GLN00.0510.03440.7940.0020.0020.0000.0000.0000.000
106A124VAL00.0210.00843.5340.0190.0190.0000.0000.0000.000
107A125PRO00.005-0.00147.041-0.004-0.0040.0000.0000.0000.000
108A126HIS0-0.047-0.01949.492-0.013-0.0130.0000.0000.0000.000
109A127LEU00.0330.02944.834-0.001-0.0010.0000.0000.0000.000
110A128ASN0-0.071-0.06246.245-0.018-0.0180.0000.0000.0000.000
111A129GLN0-0.069-0.05747.6150.0080.0080.0000.0000.0000.000
112A130ASN0-0.036-0.00651.0640.0160.0160.0000.0000.0000.000
113A131ALA00.0420.02550.407-0.009-0.0090.0000.0000.0000.000
114A132TRP00.0310.00841.178-0.010-0.0100.0000.0000.0000.000
115A133ASN00.0450.03247.618-0.001-0.0010.0000.0000.0000.000
116A134ASN00.004-0.01149.478-0.004-0.0040.0000.0000.0000.000
117A135LEU00.0470.03744.7110.0000.0000.0000.0000.0000.000
118A136GLU-1-0.893-0.95044.017-0.561-0.5610.0000.0000.0000.000
119A137ARG10.8630.92547.0190.3900.3900.0000.0000.0000.000
120A138TYR00.0230.02248.548-0.001-0.0010.0000.0000.0000.000
121A139SER00.004-0.00344.879-0.008-0.0080.0000.0000.0000.000
122A140ARG10.9420.96046.9800.4830.4830.0000.0000.0000.000
123A141SER0-0.114-0.05548.5630.0130.0130.0000.0000.0000.000
124A142LEU00.0460.02146.9910.0080.0080.0000.0000.0000.000
125A143THR0-0.050-0.03746.4620.0020.0020.0000.0000.0000.000
126A144ARG10.9010.95048.8300.4200.4200.0000.0000.0000.000
127A145THR0-0.029-0.01651.0600.0090.0090.0000.0000.0000.000
128A146TYR0-0.018-0.01246.6040.0090.0090.0000.0000.0000.000
129A147GLN00.0280.02746.0350.0040.0040.0000.0000.0000.000
130A148ASN0-0.041-0.03441.632-0.020-0.0200.0000.0000.0000.000
131A149VAL00.0140.02543.2640.0070.0070.0000.0000.0000.000
132A150TYR00.0080.00836.618-0.008-0.0080.0000.0000.0000.000
133A151VAL0-0.012-0.00838.7710.0260.0260.0000.0000.0000.000
134A152CYS0-0.0460.00233.291-0.048-0.0480.0000.0000.0000.000
135A153THR00.0220.01835.8090.0630.0630.0000.0000.0000.000
136A154GLY00.0520.01934.546-0.060-0.0600.0000.0000.0000.000
137A155PRO0-0.0090.02033.3560.0580.0580.0000.0000.0000.000
138A156LEU0-0.003-0.00534.841-0.035-0.0350.0000.0000.0000.000
139A157PHE00.023-0.00632.6570.0350.0350.0000.0000.0000.000
140A158LEU00.0150.01135.452-0.016-0.0160.0000.0000.0000.000
141A159PRO0-0.028-0.01436.4020.0220.0220.0000.0000.0000.000
142A160ARG10.8310.89138.7560.3650.3650.0000.0000.0000.000
143A161THR0-0.006-0.01141.992-0.003-0.0030.0000.0000.0000.000
144A162GLU-1-0.841-0.89843.403-0.322-0.3220.0000.0000.0000.000
145A163ALA00.020-0.00546.0540.0060.0060.0000.0000.0000.000
146A164ASP-1-0.801-0.87543.513-0.252-0.2520.0000.0000.0000.000
147A165GLY0-0.0060.00245.8220.0070.0070.0000.0000.0000.000
148A166LYS10.8930.95939.5220.2270.2270.0000.0000.0000.000
149A167SER00.009-0.00339.3680.0000.0000.0000.0000.0000.000
150A168TYR0-0.065-0.05037.858-0.023-0.0230.0000.0000.0000.000
151A169VAL00.0080.01034.3450.0030.0030.0000.0000.0000.000
152A170LYS10.9330.96936.9000.3610.3610.0000.0000.0000.000
153A171TYR00.0230.02231.7170.0110.0110.0000.0000.0000.000
154A172GLN0-0.009-0.00538.4850.0110.0110.0000.0000.0000.000
155A173VAL0-0.005-0.00134.735-0.037-0.0370.0000.0000.0000.000
156A174ILE00.0060.00637.8220.0390.0390.0000.0000.0000.000
157A175GLY00.0130.00437.575-0.034-0.0340.0000.0000.0000.000
158A176LYS10.8540.92236.5250.5130.5130.0000.0000.0000.000
159A177ASN0-0.010-0.01232.5600.0030.0030.0000.0000.0000.000
160A178HIS0-0.031-0.00832.609-0.081-0.0810.0000.0000.0000.000
161A179VAL00.0300.02433.641-0.038-0.0380.0000.0000.0000.000
162A180ALA0-0.007-0.00133.5320.0500.0500.0000.0000.0000.000
163A181VAL0-0.024-0.01035.413-0.015-0.0150.0000.0000.0000.000
164A182PRO0-0.030-0.00436.7200.0040.0040.0000.0000.0000.000
165A183THR00.015-0.00538.3770.0240.0240.0000.0000.0000.000
166A184HIS00.0080.02939.6180.0170.0170.0000.0000.0000.000
167A185PHE00.0180.00938.959-0.034-0.0340.0000.0000.0000.000
168A186PHE00.0260.01033.3680.0310.0310.0000.0000.0000.000
169A187LYS10.8780.93038.9200.6130.6130.0000.0000.0000.000
170A188VAL0-0.003-0.00337.0980.0330.0330.0000.0000.0000.000
171A189LEU0-0.0070.00039.382-0.025-0.0250.0000.0000.0000.000
172A190ILE0-0.001-0.00435.8620.0060.0060.0000.0000.0000.000
173A191LEU0-0.033-0.00640.388-0.006-0.0060.0000.0000.0000.000
174A192GLU-1-0.852-0.91241.299-0.655-0.6550.0000.0000.0000.000
175A193ALA00.018-0.00444.0730.0250.0250.0000.0000.0000.000
176A194ALA0-0.034-0.02746.826-0.011-0.0110.0000.0000.0000.000
177A195GLY0-0.0180.00948.0170.0030.0030.0000.0000.0000.000
178A196GLY00.0360.00443.949-0.017-0.0170.0000.0000.0000.000
179A197GLN0-0.0090.00142.993-0.029-0.0290.0000.0000.0000.000
180A198ILE00.0200.01639.3610.0000.0000.0000.0000.0000.000
181A199GLU-1-0.791-0.85442.632-0.472-0.4720.0000.0000.0000.000
182A200LEU0-0.021-0.00638.212-0.025-0.0250.0000.0000.0000.000
183A201ARG10.8510.90742.2700.4990.4990.0000.0000.0000.000
184A202SER0-0.003-0.00540.583-0.026-0.0260.0000.0000.0000.000
185A203TYR00.0410.01842.2530.0190.0190.0000.0000.0000.000
186A204VAL0-0.008-0.01240.393-0.037-0.0370.0000.0000.0000.000
187A205MET0-0.0260.01043.0870.0260.0260.0000.0000.0000.000
188A206PRO00.0200.00243.495-0.028-0.0280.0000.0000.0000.000
189A207ASN0-0.041-0.03641.5720.0210.0210.0000.0000.0000.000
190A208ALA0-0.016-0.01644.5850.0120.0120.0000.0000.0000.000
191A209PRO00.005-0.01048.315-0.009-0.0090.0000.0000.0000.000
192A210VAL0-0.039-0.01548.7970.0010.0010.0000.0000.0000.000
193A211ASP-1-0.837-0.89052.122-0.300-0.3000.0000.0000.0000.000
194A212GLU-1-0.843-0.93554.979-0.328-0.3280.0000.0000.0000.000
195A213THR0-0.102-0.06756.053-0.001-0.0010.0000.0000.0000.000
196A214ILE0-0.036-0.00953.7240.0040.0040.0000.0000.0000.000
197A215PRO0-0.019-0.00354.681-0.013-0.0130.0000.0000.0000.000
198A216LEU00.0410.00849.920-0.008-0.0080.0000.0000.0000.000
199A217GLU-1-0.874-0.94950.136-0.379-0.3790.0000.0000.0000.000
200A218ARG10.9220.95550.7890.3120.3120.0000.0000.0000.000
201A219PHE0-0.0080.00147.261-0.001-0.0010.0000.0000.0000.000
202A220LEU0-0.031-0.00146.106-0.029-0.0290.0000.0000.0000.000
203A221VAL0-0.003-0.00241.6290.0150.0150.0000.0000.0000.000
204A222PRO00.0590.02341.810-0.022-0.0220.0000.0000.0000.000
205A223ILE00.0040.02436.682-0.009-0.0090.0000.0000.0000.000
206A224GLU-1-0.761-0.86036.472-0.630-0.6300.0000.0000.0000.000
207A225SER0-0.069-0.05136.386-0.021-0.0210.0000.0000.0000.000
208A226ILE00.0500.02135.143-0.009-0.0090.0000.0000.0000.000
209A227GLU-1-0.817-0.88432.735-0.880-0.8800.0000.0000.0000.000
210A228ARG10.8200.88431.9590.5990.5990.0000.0000.0000.000
211A229ALA0-0.026-0.00732.897-0.004-0.0040.0000.0000.0000.000
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